diff --git a/CHANGELOG b/CHANGELOG
index 20e7a36a38c83e77511d058c8e9f459732964672..879c3a6ca5fe7c62c2a0760b5352336420d6fea9 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -5,6 +5,26 @@
Changelog
================================================================================
+Release 1.3.0
+--------------------------------------------------------------------------------
+
+* Apply Apache Version 2.0 License to the project
+* 2010 Dunbrack rotamer library has been replaced by an own backbone dependent
+ rotamer library. All scripts required to reproduce the data are in
+ extras/data_generation/rotamer_library
+* Penultimate rotamer library has been replaced by an own backbone independent
+ rotamer library. All scripts required to reproduce the data are in
+ extras/data_generation/rotamer_library
+* SampleMonteCarlo function moved to Python. This makes it possible to provide
+ sampler/closer/scorer/cooler objects implemented in both, Python and C++
+* Action script for sidechain modelling
+* Allow sequence profiles as input for build-model action script.
+* Recipe for Docker / Singularity container
+* Check peptide bonds when building a RawModel. Treat as gap if bond is
+ stereochemically problematic despite being in sequence.
+* Several minor bug fixes, improvements, and speed-ups
+
+
Release 1.2.0
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f8f1e39cc62f23c259804f99dcfe3d8e91afaa36..6b0cd5ce9587fc7fc40ec58d40b2ad68155077b7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -16,7 +16,7 @@ include(PROMOD3)
# versioning info
set(PROMOD3_VERSION_MAJOR 1)
-set(PROMOD3_VERSION_MINOR 2)
+set(PROMOD3_VERSION_MINOR 3)
set(PROMOD3_VERSION_PATCH 0)
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
@@ -86,7 +86,7 @@ if(NOT DISABLE_DOCUMENTATION)
# set this to the URL corresponding to the version of OST you are using
set(OST_DOC_URL "https://www.openstructure.org/docs/dev")
endif()
-find_package(OPENSTRUCTURE 1.8 REQUIRED
+find_package(OPENSTRUCTURE 1.8 REQUIRED
COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)
if(CMAKE_COMPILER_IS_GNUCXX)
@@ -135,6 +135,7 @@ add_subdirectory(extras)
add_subdirectory(cmake_support)
if(NOT DISABLE_DOCUMENTATION)
add_changelog_to_doc(FILE "${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG")
+ add_license_to_doc(FILE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
add_subdirectory(doc)
endif()
diff --git a/COPYING.BSD b/COPYING.BSD
deleted file mode 100644
index 655966c9db44962696bd54dc2766a3f3626010e9..0000000000000000000000000000000000000000
--- a/COPYING.BSD
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- Copyright (c) 2011, Intel Corporation. All rights reserved.
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
-
- * Redistributions of source code must retain the above copyright notice, this
- list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
- * Neither the name of Intel Corporation nor the names of its contributors may
- be used to endorse or promote products derived from this software without
- specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-*/
diff --git a/COPYING.README b/COPYING.README
deleted file mode 100644
index 74e3823187fd997f265bf17dfd0105ff0f9a548f..0000000000000000000000000000000000000000
--- a/COPYING.README
+++ /dev/null
@@ -1,2 +0,0 @@
-Some files contain third-party code under BSD licenses, whence the other
-COPYING.* files here.
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..c90fd010a07f1e1e6de3e5c1004a1bc2ffba9edf
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,210 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
+
+ "Licensor" shall mean the copyright owner or entity authorized by
+ the copyright owner that is granting the License.
+
+ "Legal Entity" shall mean the union of the acting entity and all
+ other entities that control, are controlled by, or are under common
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+ direction or management of such entity, whether by contract or
+ otherwise, or (ii) ownership of fifty percent (50%) or more of the
+ outstanding shares, or (iii) beneficial ownership of such entity.
+
+ "You" (or "Your") shall mean an individual or Legal Entity
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+ (an example is provided in the Appendix below).
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+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
+ separable from, or merely link (or bind by name) to the interfaces of,
+ the Work and Derivative Works thereof.
+
+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
+ submitted to Licensor for inclusion in the Work by the copyright owner
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+ communication on electronic mailing lists, source code control systems,
+ and issue tracking systems that are managed by, or on behalf of, the
+ Licensor for the purpose of discussing and improving the Work, but
+ excluding communication that is conspicuously marked or otherwise
+ designated in writing by the copyright owner as "Not a Contribution."
+
+ "Contributor" shall mean Licensor and any individual or Legal Entity
+ on behalf of whom a Contribution has been received by Licensor and
+ subsequently incorporated within the Work.
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+ 2. Grant of Copyright License. Subject to the terms and conditions of
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+ or a Contribution incorporated within the Work constitutes direct
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+ granted to You under this License for that Work shall terminate
+ as of the date such litigation is filed.
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+ 4. Redistribution. You may reproduce and distribute copies of the
+ Work or Derivative Works thereof in any medium, with or without
+ modifications, and in Source or Object form, provided that You
+ meet the following conditions:
+
+ (a) You must give any other recipients of the Work or
+ Derivative Works a copy of this License; and
+
+ (b) You must cause any modified files to carry prominent notices
+ stating that You changed the files; and
+
+ (c) You must retain, in the Source form of any Derivative Works
+ that You distribute, all copyright, patent, trademark, and
+ attribution notices from the Source form of the Work,
+ excluding those notices that do not pertain to any part of
+ the Derivative Works; and
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+ (d) If the Work includes a "NOTICE" text file as part of its
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+ pertain to any part of the Derivative Works, in at least one
+ of the following places: within a NOTICE text file distributed
+ as part of the Derivative Works; within the Source form or
+ documentation, if provided along with the Derivative Works; or,
+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
+ or as an addendum to the NOTICE text from the Work, provided
+ that such additional attribution notices cannot be construed
+ as modifying the License.
+
+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
+ identification within third-party archives.
+
+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+
+ProMod3 bundles the file "FindEigen3.cmake", which is availabe under a
+"2-clause BSD" license. For details, see cmake_support/FindEigen3.cmake.
+
+ProMod3 bundles the file "cmake.py", which is available under a
+"3-clause BSD" license. For details, see doc/cmake.py and
+doc/Copyright_cmake.py.txt
diff --git a/NOTICE b/NOTICE
new file mode 100644
index 0000000000000000000000000000000000000000..87ee5943e15a61d9b43b602ad07e169f97f3762a
--- /dev/null
+++ b/NOTICE
@@ -0,0 +1,11 @@
+ProMod3 - A Versatile Homology Modelling Toolbox
+Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+ Biozentrum - University of Basel
+
+ProMod3 is developed in the Schwede lab at the Biozentrum - University of Basel.
+The main authors are: Gabriel Studer, Gerardo Tauriello, Stefan Bienert,
+Marco Biasini, Niklaus Johner
+
+If you find this software useful, please cite:
+TO BE PUBLISHED
+
diff --git a/README b/README
index 225a68587660452c2e5006b3d7e1b4a1dcd70a4e..29003a0217e5bb4a96d18823be72d6817dabf46f 100644
--- a/README
+++ b/README
@@ -1,6 +1,20 @@
-=============== ProMod3 -- Homology Modelling Engine ==============
+ _____ __ __ _ ____
+ | __ \ | \/ | | |___ \
+ | |__) | __ ___ | \ / | ___ __| | __) |
+ | ___/ '__/ _ \| |\/| |/ _ \ / _` ||__ <
+ | | | | | (_) | | | | (_) | (_| |___) |
+ |_| |_| \___/|_| |_|\___/ \__,_|____/
+
-Information on ProMod3 may be found at doc/html/index.html.
+ProMod3 is a modelling engine based on the OpenStructure computational
+structural biology framework (www.openstructure.org)
+that can perform all steps required to generate a protein model by
+homology. Its modular design aims at implementing flexible modelling
+pipelines and fast prototyping of novel algorithms.
+Get started with the docs: www.openstructure.org/promod3
+
+Please do not hesitate to contact us for feedback or troubleshooting:
+
+ost-users@maillist.unibas.ch
-=============== The ProMod3 Team ==================================
diff --git a/actions/CMakeLists.txt b/actions/CMakeLists.txt
index fe50a9c8053e4bb8ad55d8e98937412a4253dd1a..7a5c3f164fad0733fae888cae9049d60171c95d6 100644
--- a/actions/CMakeLists.txt
+++ b/actions/CMakeLists.txt
@@ -6,3 +6,4 @@ pm_action_init()
pm_action(pm-build-model actions)
pm_action(pm-build-rawmodel actions)
pm_action(pm-help actions)
+pm_action(pm-build-sidechains actions)
diff --git a/actions/doc/index.rst b/actions/doc/index.rst
index 4820610c7519c44d285f2b8e76ce9fb87c6f667a..450ffa57d28ef1f491876e3f468880a55741713d 100644
--- a/actions/doc/index.rst
+++ b/actions/doc/index.rst
@@ -20,7 +20,7 @@ with
.. code-block:: console
$ pm build-model [-h] (-f <FILE> | -c <FILE> | -j <OBJECT>|<FILE>)
- (-p <FILE> | -e <FILE>) [-o <FILENAME>]
+ (-p <FILE> | -e <FILE>) [-s <FILE>] [-o <FILENAME>]
Example usage:
@@ -105,6 +105,30 @@ sequence names are:
Example: ``... -p data/2jlp.pdb.gz``, where the pdb file has chains ``A``,
``B``, ``C`` and the template sequence is named ``2jlp.A|55``.
+
+You can optionally specify sequence profiles to be added (``-s``) and linked
+to the corresponding target sequences. This has an impact on loop scoring with
+the database approach.
+The profiles can be provided as plain files or gzipped. Following file
+extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
+Consider to use :meth:`ost.bindings.hhblits.HHblits.A3MToProfile` if you have a
+file in a3m format at hand.
+
+* The profiles are mapped based on exact matches towards the gapless
+ target sequences from the provided alignment files,
+ i.e. one profile is mapped to several chains in case of homo-oligomers
+
+* Every profile must have a unique sequence to avoid ambiguities
+
+* All or nothing - You cannot provide profiles for only a subset of
+ target sequences
+
+Example usage:
+
+.. code-block:: console
+
+ $ pm build-model -f aln.fasta -p tpl.pdb -s prof.hhm
+
Possible exit codes of the action:
- 0: all went well
@@ -113,4 +137,56 @@ Possible exit codes of the action:
- 3: failed to perform modelling (internal error)
- 4: failed to write results to file
- other non-zero: failure in argument checking
- (see :class:`promod3.core.pm3argparse.PM3ArgumentParser`)
\ No newline at end of file
+ (see :class:`promod3.core.pm3argparse.PM3ArgumentParser`)
+
+
+Sidechain Modelling
+--------------------------------------------------------------------------------
+
+You can (re-)construct the sidechains in a model from the command line.
+
+.. code-block:: console
+
+ $ usage: build-sidechains [-h] (-p <FILE> | -e <FILE>) [-o <FILENAME>] [-k] [-n]
+ [-r] [-i] [-s]
+
+Example usage:
+
+.. code-block:: console
+
+ $ pm build-sidechains -p input.pdb
+
+This reads a structure stored in in.pdb, strips all sidechains,
+detects and models disulfid bonds and reconstructs all sidechains with the
+flexible rotamer model. The result is stored as :file:`out.pdb`.
+The output filename can be controlled with the ``-o`` flag.
+
+A structure can be provided in PDB (``-p``) or in any format readable by the
+:func:`ost.io.LoadEntity` method (``-e``). In the latter case, the format is
+chosen by file ending. Recognized File Extensions: ``.ent``, ``.pdb``,
+``.ent.gz``, ``.pdb.gz``, ``.cif``, ``.cif.gz``.
+
+Several flags control the modelling behaviour:
+
+.. option:: -k, --keep-sidechains
+
+ Keep existing sidechains.
+
+.. option:: -n, --no-disulfids
+
+ Do not build disulfid bonds before sidechain optimization
+
+.. option:: -r, --rigid-rotamers
+
+ Do not use rotamers with subrotamers
+
+.. option:: -i, --backbone-independent
+
+ Use backbone independent rotamer library
+ (from :meth:`promod3.sidechain.LoadLib`) instead of the default backbone
+ dependent one (from :meth:`promod3.sidechain.LoadBBDepLib`)
+
+.. option:: -s, --no-subrotamer-optimization
+
+ Dont do subrotamer optimization if flexible rotamer model is used
+
diff --git a/actions/pm-build-model b/actions/pm-build-model
index 1dcd882c96ebdf1a5a71af4a4d4126771d8237f0..4170252f5270c4a539423499dd9b8abc8756cbd6 100755
--- a/actions/pm-build-model
+++ b/actions/pm-build-model
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''
Automatically build a model from alignments and template structures.
@@ -23,6 +39,7 @@ ost.PushVerbosityLevel(2)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=True)
parser.AddAlignment()
parser.AddStructure(attach_views=True)
+parser.AddProfile()
parser.AssembleParser()
parser.add_argument('-o', '--model-file', metavar='<FILENAME>', type=str,
default='model.pdb', help='File to store model coordinates'+
@@ -43,11 +60,16 @@ for aln in opts.alignments:
for i in range(1, aln.GetCount()):
ost.mol.alg.AssignSecStruct(aln.GetSequence(i).GetAttachedView())
-
# model it
try:
# get raw model
mhandle = modelling.BuildRawModel(opts.alignments)
+ # add profiles if any
+ # no psipred predictions are added, as the default modelling pipeline
+ # we're using here never looks at them. If we need psipred predictions,
+ # pssm files would not be sufficient and we would be restricted to hhm.
+ if len(opts.profiles) > 0:
+ modelling.SetSequenceProfiles(mhandle, opts.profiles)
# build final model
final_model = modelling.BuildFromRawModel(mhandle)
except Exception as ex:
diff --git a/actions/pm-build-rawmodel b/actions/pm-build-rawmodel
index 7b5260e39c6554e1765ac928033982afa375ac89..c86000142fc3983cf6ba665ff87e8ddf7231164b 100755
--- a/actions/pm-build-rawmodel
+++ b/actions/pm-build-rawmodel
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''
Create a very basic raw model from alignments and template structures.
Conserved parts are copied from the template and an incomplete pdb file is
diff --git a/actions/pm-build-sidechains b/actions/pm-build-sidechains
new file mode 100644
index 0000000000000000000000000000000000000000..72a0ddfc6a57d9bdca6fd07d70269d47f570abce
--- /dev/null
+++ b/actions/pm-build-sidechains
@@ -0,0 +1,90 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+'''
+Automatically (re-)construct sidechains in a protein model.
+
+Example usage:
+ pm build-sidechains in.pdb
+ This reads a structure stored in in.pdb, strips all sidechains,
+ detects and models disulfid bonds and reconstructs all sidechains with the
+ flexible rotamer model. The result is stored as out.pdb
+'''
+
+import os
+import ost
+from ost import io, settings
+from promod3 import modelling, sidechain
+from promod3.core import pm3argparse, helper
+
+# make sure we see output when passing '-h'
+ost.PushVerbosityLevel(2)
+
+# parse command line
+parser = pm3argparse.PM3ArgumentParser(__doc__, action=True)
+
+parser.AddStructure()
+parser.AssembleParser()
+parser.add_argument('-o', '--out-file', metavar='<FILENAME>', type=str,
+ default='out.pdb', help='File to store coordinates ' +
+ '(default: %(default)s)')
+parser.add_argument('-k', '--keep-sidechains', action='store_true',
+ help='Keep existing sidechains')
+parser.add_argument('-n', '--no-disulfids', action='store_true',
+ help='Do not build disulfid bonds before sidechain ' +
+ 'optimization')
+parser.add_argument('-r', '--rigid-rotamers', action='store_true',
+ help='Do not use rotamers with subrotamers')
+parser.add_argument('-i', '--backbone-independent', action='store_true',
+ help='Use backbone independent rotamer library instead ' +
+ 'of the default backbone dependent one')
+parser.add_argument('-s', '--no-subrotamer-optimization', action='store_true',
+ help='Dont do subrotamer optimization if flexible ' +
+ 'rotamer model is used.')
+
+opts = parser.Parse()
+
+ost.PushVerbosityLevel(3)
+
+if len(opts.structures) != 1:
+ helper.MsgErrorAndExit("Expect exactly one input structure", 4)
+
+prot = opts.structures[0]
+rotamer_model = "frm"
+if opts.rigid_rotamers:
+ rotamer_model = "rrm"
+
+lib = None
+if opts.backbone_independent:
+ lib = sidechain.LoadLib()
+
+opt_subrot = True
+if opts.no_subrotamer_optimization:
+ opt_subrot = False
+
+# do sidechain modelling
+modelling.ReconstructSidechains(prot, keep_sidechains=opts.keep_sidechains,
+ build_disulfids=opts.no_disulfids==False,
+ rotamer_model=rotamer_model,
+ rotamer_library=lib,
+ optimize_subrotamers=opt_subrot)
+
+# output
+ost.PopVerbosityLevel()
+io.SavePDB(prot, opts.out_file)
+if not os.path.isfile(opts.out_file):
+ helper.MsgErrorAndExit("Failed to write model file '%s'." % opts.model_file, 4)
+
diff --git a/actions/pm-help b/actions/pm-help
index 274026ad1e9c616a8bee12fbbd03688f8b560c99..5c44cc63b796ff0e300f87f6e8468ac6f093b4cc 100755
--- a/actions/pm-help
+++ b/actions/pm-help
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''
Just list all actions (pm-.* files) available.
'''
diff --git a/actions/tests/test_action_build-model.py b/actions/tests/test_action_build-model.py
index a0889fd0c048c720c04d8ec7d4c07fba01f22047..a4b33c83f6a12a40c3432e34f50fc0db9835b46c 100644
--- a/actions/tests/test_action_build-model.py
+++ b/actions/tests/test_action_build-model.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for the 'build-model' action.
"""
diff --git a/actions/tests/test_action_build-rawmodel.py b/actions/tests/test_action_build-rawmodel.py
index 3f222c62a0644597920c1d7654764deb2e94a818..3f9af6d9762e9c893c5de5565ba0493be52c4b9c 100644
--- a/actions/tests/test_action_build-rawmodel.py
+++ b/actions/tests/test_action_build-rawmodel.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for the 'build-rawmodel' action.
"""
diff --git a/actions/tests/test_action_help.py b/actions/tests/test_action_help.py
index 74f24159ca4209d9211f6762a4c9279f9e9ce3cd..98309e33ea01711751e865279383e43146e2c3c9 100644
--- a/actions/tests/test_action_help.py
+++ b/actions/tests/test_action_help.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for the 'help' action.
diff --git a/actions/tests/test_actions.py b/actions/tests/test_actions.py
index 243d47b0d969ce518b7f7a552a8c62aa511ea9a2..f84622aae3cf8653e77d9db65ef24f93ee6e54ba 100644
--- a/actions/tests/test_actions.py
+++ b/actions/tests/test_actions.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
unittest.TestCase class providing common functionality for testing actions.
"""
diff --git a/cmake_support/FindBoost.cmake b/cmake_support/FindBoost.cmake
deleted file mode 100644
index e784de62ff5b451435a10116c3b8ea2c196a4191..0000000000000000000000000000000000000000
--- a/cmake_support/FindBoost.cmake
+++ /dev/null
@@ -1,881 +0,0 @@
-# - Try to find Boost include dirs and libraries
-# Usage of this module as follows:
-#
-# == Using Header-Only libraries from within Boost: ==
-#
-# find_package( Boost 1.36.0 )
-# if(Boost_FOUND)
-# include_directories(${Boost_INCLUDE_DIRS})
-# add_executable(foo foo.cc)
-# endif()
-#
-#
-# == Using actual libraries from within Boost: ==
-#
-# set(Boost_USE_STATIC_LIBS ON)
-# set(Boost_USE_MULTITHREADED ON)
-# find_package( Boost 1.36.0 COMPONENTS date_time filesystem system ... )
-#
-# if(Boost_FOUND)
-# include_directories(${Boost_INCLUDE_DIRS})
-# add_executable(foo foo.cc)
-# target_link_libraries(foo ${Boost_LIBRARIES})
-# endif()
-#
-#
-# The components list needs to contain actual names of boost libraries only,
-# such as "date_time" for "libboost_date_time". If you're using parts of
-# Boost that contain header files only (e.g. foreach) you do not need to
-# specify COMPONENTS.
-#
-# You should provide a minimum version number that should be used. If you provide this
-# version number and specify the REQUIRED attribute, this module will fail if it
-# can't find the specified or a later version. If you specify a version number this is
-# automatically put into the considered list of version numbers and thus doesn't need
-# to be specified in the Boost_ADDITIONAL_VERSIONS variable (see below).
-#
-# NOTE for Visual Studio Users:
-# Automatic linking is used on MSVC & Borland compilers by default when
-# #including things in Boost. It's important to note that setting
-# Boost_USE_STATIC_LIBS to OFF is NOT enough to get you dynamic linking,
-# should you need this feature. Automatic linking typically uses static
-# libraries with a few exceptions (Boost.Python is one).
-#
-# Please see the section below near Boost_LIB_DIAGNOSTIC_DEFINITIONS for
-# more details. Adding a TARGET_LINK_LIBRARIES() as shown in the example
-# above appears to cause VS to link dynamically if Boost_USE_STATIC_LIBS
-# gets set to OFF. It is suggested you avoid automatic linking since it
-# will make your application less portable.
-#
-# =========== The mess that is Boost_ADDITIONAL_VERSIONS (sorry?) ============
-#
-# OK, so the Boost_ADDITIONAL_VERSIONS variable can be used to specify a list of
-# boost version numbers that should be taken into account when searching
-# for Boost. Unfortunately boost puts the version number into the
-# actual filename for the libraries, so this variable will certainly be needed
-# in the future when new Boost versions are released.
-#
-# Currently this module searches for the following version numbers:
-# 1.33, 1.33.0, 1.33.1, 1.34, 1.34.0, 1.34.1, 1.35, 1.35.0, 1.35.1,
-# 1.36, 1.36.0, 1.36.1, 1.37, 1.37.0, 1.38, 1.38.0
-#
-# NOTE: If you add a new major 1.x version in Boost_ADDITIONAL_VERSIONS you should
-# add both 1.x and 1.x.0 as shown above. Official Boost include directories
-# omit the 3rd version number from include paths if it is 0 although not all
-# binary Boost releases do so.
-#
-# SET(Boost_ADDITIONAL_VERSIONS "0.99" "0.99.0" "1.78" "1.78.0")
-#
-# ============================================================================
-#
-# Variables used by this module, they can change the default behaviour and
-# need to be set before calling find_package:
-#
-# Boost_USE_MULTITHREADED Can be set to OFF to use the non-multithreaded
-# boost libraries. If not specified, defaults
-# to ON.
-#
-# Boost_USE_STATIC_LIBS Can be set to ON to force the use of the static
-# boost libraries. Defaults to OFF.
-#
-# Other Variables used by this module which you may want to set.
-#
-# Boost_ADDITIONAL_VERSIONS A list of version numbers to use for searching
-# the boost include directory. Please see
-# the documentation above regarding this
-# annoying, but necessary variable :(
-#
-# Boost_DEBUG Set this to TRUE to enable debugging output
-# of FindBoost.cmake if you are having problems.
-# Please enable this before filing any bug
-# reports.
-#
-# Boost_COMPILER Set this to the compiler suffix used by Boost
-# (e.g. "-gcc43") if FindBoost has problems finding
-# the proper Boost installation
-#
-# These last three variables are available also as environment variables:
-#
-# BOOST_ROOT or BOOSTROOT The preferred installation prefix for searching for
-# Boost. Set this if the module has problems finding
-# the proper Boost installation.
-#
-# BOOST_INCLUDEDIR Set this to the include directory of Boost, if the
-# module has problems finding the proper Boost installation
-#
-# BOOST_LIBRARYDIR Set this to the lib directory of Boost, if the
-# module has problems finding the proper Boost installation
-#
-# Variables defined by this module:
-#
-# Boost_FOUND System has Boost, this means the include dir was
-# found, as well as all the libraries specified in
-# the COMPONENTS list.
-#
-# Boost_INCLUDE_DIRS Boost include directories: not cached
-#
-# Boost_INCLUDE_DIR This is almost the same as above, but this one is
-# cached and may be modified by advanced users
-#
-# Boost_LIBRARIES Link to these to use the Boost libraries that you
-# specified: not cached
-#
-# Boost_LIBRARY_DIRS The path to where the Boost library files are.
-#
-# Boost_VERSION The version number of the boost libraries that
-# have been found, same as in version.hpp from Boost
-#
-# Boost_LIB_VERSION The version number in filename form as
-# it's appended to the library filenames
-#
-# Boost_MAJOR_VERSION major version number of boost
-# Boost_MINOR_VERSION minor version number of boost
-# Boost_SUBMINOR_VERSION subminor version number of boost
-#
-# Boost_LIB_DIAGNOSTIC_DEFINITIONS [WIN32 Only] You can call
-# add_definitions(${Boost_LIB_DIAGNOSTIC_DEFINTIIONS})
-# to have diagnostic information about Boost's
-# automatic linking outputted during compilation time.
-#
-# For each component you specify in find_package(), the following (UPPER-CASE)
-# variables are set. You can use these variables if you would like to pick and
-# choose components for your targets instead of just using Boost_LIBRARIES.
-#
-# Boost_${COMPONENT}_FOUND True IF the Boost library "component" was found.
-#
-# Boost_${COMPONENT}_LIBRARY Contains the libraries for the specified Boost
-# "component" (includes debug and optimized keywords
-# when needed).
-#
-# =====================================================================
-#
-#
-# Copyright (c) 2006-2008 Andreas Schneider <mail@cynapses.org>
-# Copyright (c) 2007 Wengo
-# Copyright (c) 2007 Mike Jackson
-# Copyright (c) 2008 Andreas Pakulat <apaku@gmx.de>
-#
-# Redistribution AND use is allowed according to the terms of the New
-# BSD license.
-# For details see the accompanying COPYING-CMAKE-SCRIPTS file.
-#
-
-
-
-#-------------------------------------------------------------------------------
-# FindBoost functions & macros
-#
-############################################
-#
-# Check the existence of the libraries.
-#
-############################################
-# This macro was taken directly from the FindQt4.cmake file that is included
-# with the CMake distribution. This is NOT my work. All work was done by the
-# original authors of the FindQt4.cmake file. Only minor modifications were
-# made to remove references to Qt and make this file more generally applicable
-# And ELSE/ENDIF pairs were removed for readability.
-#########################################################################
-
-MACRO (_Boost_ADJUST_LIB_VARS basename)
- IF (Boost_INCLUDE_DIR )
- IF (Boost_${basename}_LIBRARY_DEBUG AND Boost_${basename}_LIBRARY_RELEASE)
- # if the generator supports configuration types then set
- # optimized and debug libraries, or if the CMAKE_BUILD_TYPE has a value
- IF (CMAKE_CONFIGURATION_TYPES OR CMAKE_BUILD_TYPE)
- SET(Boost_${basename}_LIBRARY optimized ${Boost_${basename}_LIBRARY_RELEASE} debug ${Boost_${basename}_LIBRARY_DEBUG})
- ELSE()
- # if there are no configuration types and CMAKE_BUILD_TYPE has no value
- # then just use the release libraries
- SET(Boost_${basename}_LIBRARY ${Boost_${basename}_LIBRARY_RELEASE} )
- ENDIF()
- # FIXME: This probably should be set for both cases
- SET(Boost_${basename}_LIBRARIES optimized ${Boost_${basename}_LIBRARY_RELEASE} debug ${Boost_${basename}_LIBRARY_DEBUG})
- ENDIF()
-
- # if only the release version was found, set the debug variable also to the release version
- IF (Boost_${basename}_LIBRARY_RELEASE AND NOT Boost_${basename}_LIBRARY_DEBUG)
- SET(Boost_${basename}_LIBRARY_DEBUG ${Boost_${basename}_LIBRARY_RELEASE})
- SET(Boost_${basename}_LIBRARY ${Boost_${basename}_LIBRARY_RELEASE})
- SET(Boost_${basename}_LIBRARIES ${Boost_${basename}_LIBRARY_RELEASE})
- ENDIF()
-
- # if only the debug version was found, set the release variable also to the debug version
- IF (Boost_${basename}_LIBRARY_DEBUG AND NOT Boost_${basename}_LIBRARY_RELEASE)
- SET(Boost_${basename}_LIBRARY_RELEASE ${Boost_${basename}_LIBRARY_DEBUG})
- SET(Boost_${basename}_LIBRARY ${Boost_${basename}_LIBRARY_DEBUG})
- SET(Boost_${basename}_LIBRARIES ${Boost_${basename}_LIBRARY_DEBUG})
- ENDIF()
-
- IF (Boost_${basename}_LIBRARY)
- set(Boost_${basename}_LIBRARY ${Boost_${basename}_LIBRARY} CACHE FILEPATH "The Boost ${basename} library")
-
- # Remove superfluous "debug" / "optimized" keywords from
- # Boost_LIBRARY_DIRS
- FOREACH(_boost_my_lib ${Boost_${basename}_LIBRARY})
- GET_FILENAME_COMPONENT(_boost_my_lib_path "${_boost_my_lib}" PATH)
- LIST(APPEND Boost_LIBRARY_DIRS ${_boost_my_lib_path})
- ENDFOREACH()
- LIST(REMOVE_DUPLICATES Boost_LIBRARY_DIRS)
-
- set(Boost_LIBRARY_DIRS ${Boost_LIBRARY_DIRS} CACHE FILEPATH "Boost library directory")
- SET(Boost_${basename}_FOUND ON CACHE INTERNAL "Whether the Boost ${basename} library found")
- ENDIF(Boost_${basename}_LIBRARY)
-
- ENDIF (Boost_INCLUDE_DIR )
- # Make variables changeble to the advanced user
- MARK_AS_ADVANCED(
- Boost_${basename}_LIBRARY
- Boost_${basename}_LIBRARY_RELEASE
- Boost_${basename}_LIBRARY_DEBUG
- )
-ENDMACRO (_Boost_ADJUST_LIB_VARS)
-
-#-------------------------------------------------------------------------------
-
-#
-# Runs compiler with "-dumpversion" and parses major/minor
-# version with a regex.
-#
-FUNCTION(_Boost_COMPILER_DUMPVERSION _OUTPUT_VERSION)
-
- EXEC_PROGRAM(${CMAKE_CXX_COMPILER}
- ARGS ${CMAKE_CXX_COMPILER_ARG1} -dumpversion
- OUTPUT_VARIABLE _boost_COMPILER_VERSION
- )
- STRING(REGEX REPLACE "([0-9])\\.([0-9])(\\.[0-9])?" "\\1\\2"
- _boost_COMPILER_VERSION ${_boost_COMPILER_VERSION})
-
- SET(${_OUTPUT_VERSION} ${_boost_COMPILER_VERSION} PARENT_SCOPE)
-ENDFUNCTION()
-
-#
-# End functions/macros
-#
-#-------------------------------------------------------------------------------
-
-
-
-
-IF(NOT DEFINED Boost_USE_MULTITHREADED)
- SET(Boost_USE_MULTITHREADED TRUE)
-ENDIF()
-
-if(Boost_FIND_VERSION_EXACT)
- # The version may appear in a directory with or without the patch
- # level, even when the patch level is non-zero.
- set(_boost_TEST_VERSIONS
- "${Boost_FIND_VERSION_MAJOR}.${Boost_FIND_VERSION_MINOR}.${Boost_FIND_VERSION_PATCH}"
- "${Boost_FIND_VERSION_MAJOR}.${Boost_FIND_VERSION_MINOR}")
-else(Boost_FIND_VERSION_EXACT)
- # The user has not requested an exact version. Among known
- # versions, find those that are acceptable to the user request.
- set(_Boost_KNOWN_VERSIONS ${Boost_ADDITIONAL_VERSIONS}
- "1.46" "1.45" "1.44" "1.43" "1.42" "1.41.0" "1.41" "1.40.0" "1.40" "1.39.0"
- "1.39" "1.38.0" "1.38" "1.37.0" "1.37" "1.36.1" "1.36.0" "1.36" "1.35.1"
- "1.35.0" "1.35" "1.34.1" "1.34.0" "1.34" "1.33.1" "1.33.0" "1.33")
- set(_boost_TEST_VERSIONS)
- if(Boost_FIND_VERSION)
- set(_Boost_FIND_VERSION_SHORT "${Boost_FIND_VERSION_MAJOR}.${Boost_FIND_VERSION_MINOR}")
- # Select acceptable versions.
- foreach(version ${_Boost_KNOWN_VERSIONS})
- if(NOT "${version}" VERSION_LESS "${Boost_FIND_VERSION}")
- # This version is high enough.
- list(APPEND _boost_TEST_VERSIONS "${version}")
- elseif("${version}.99" VERSION_EQUAL "${_Boost_FIND_VERSION_SHORT}.99")
- # This version is a short-form for the requested version with
- # the patch level dropped.
- list(APPEND _boost_TEST_VERSIONS "${version}")
- endif()
- endforeach(version)
- else(Boost_FIND_VERSION)
- # Any version is acceptable.
- set(_boost_TEST_VERSIONS "${_Boost_KNOWN_VERSIONS}")
- endif(Boost_FIND_VERSION)
-endif(Boost_FIND_VERSION_EXACT)
-
-# The reason that we failed to find Boost. This will be set to a
-# user-friendly message when we fail to find some necessary piece of
-# Boost.
-set(Boost_ERROR_REASON)
-
-SET( _boost_IN_CACHE TRUE)
-IF(Boost_INCLUDE_DIR)
-
- # On versions < 1.35, remove the System library from the considered list
- # since it wasn't added until 1.35.
- if(Boost_FIND_VERSION AND Boost_FIND_COMPONENTS)
- math(EXPR _boost_maj "${Boost_VERSION} / 100000")
- math(EXPR _boost_min "${Boost_VERSION} / 100 % 1000")
- if(${_boost_maj}.${_boost_min} VERSION_LESS 1.35)
- list(REMOVE_ITEM Boost_FIND_COMPONENTS system)
- endif()
- endif()
-
- FOREACH(COMPONENT ${Boost_FIND_COMPONENTS})
- STRING(TOUPPER ${COMPONENT} COMPONENT)
- IF(NOT Boost_${COMPONENT}_FOUND)
- SET( _boost_IN_CACHE FALSE)
- ENDIF(NOT Boost_${COMPONENT}_FOUND)
- ENDFOREACH(COMPONENT)
-ELSE(Boost_INCLUDE_DIR)
- SET( _boost_IN_CACHE FALSE)
-ENDIF(Boost_INCLUDE_DIR)
-
-IF (_boost_IN_CACHE)
- # in cache already
- SET(Boost_FOUND TRUE)
- FOREACH(COMPONENT ${Boost_FIND_COMPONENTS})
- STRING(TOUPPER ${COMPONENT} COMPONENT)
- _Boost_ADJUST_LIB_VARS( ${COMPONENT} )
- SET(Boost_LIBRARIES ${Boost_LIBRARIES} ${Boost_${COMPONENT}_LIBRARY})
- ENDFOREACH(COMPONENT)
- SET(Boost_INCLUDE_DIRS ${Boost_INCLUDE_DIR})
- IF(Boost_VERSION AND NOT "${Boost_VERSION}" STREQUAL "0")
- MATH(EXPR Boost_MAJOR_VERSION "${Boost_VERSION} / 100000")
- MATH(EXPR Boost_MINOR_VERSION "${Boost_VERSION} / 100 % 1000")
- MATH(EXPR Boost_SUBMINOR_VERSION "${Boost_VERSION} % 100")
- ENDIF(Boost_VERSION AND NOT "${Boost_VERSION}" STREQUAL "0")
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "boost ${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION} "
- "is already in the cache. For debugging messages, please clear the cache.")
- endif()
-ELSE (_boost_IN_CACHE)
- # Need to search for boost
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "Boost not in cache")
- # Output some of their choices
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "_boost_TEST_VERSIONS = ${_boost_TEST_VERSIONS}")
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "Boost_USE_MULTITHREADED = ${Boost_USE_MULTITHREADED}")
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "Boost_USE_STATIC_LIBS = ${Boost_USE_STATIC_LIBS}")
- endif()
-
- IF(WIN32)
- # In windows, automatic linking is performed, so you do not have
- # to specify the libraries. If you are linking to a dynamic
- # runtime, then you can choose to link to either a static or a
- # dynamic Boost library, the default is to do a static link. You
- # can alter this for a specific library "whatever" by defining
- # BOOST_WHATEVER_DYN_LINK to force Boost library "whatever" to be
- # linked dynamically. Alternatively you can force all Boost
- # libraries to dynamic link by defining BOOST_ALL_DYN_LINK.
-
- # This feature can be disabled for Boost library "whatever" by
- # defining BOOST_WHATEVER_NO_LIB, or for all of Boost by defining
- # BOOST_ALL_NO_LIB.
-
- # If you want to observe which libraries are being linked against
- # then defining BOOST_LIB_DIAGNOSTIC will cause the auto-linking
- # code to emit a #pragma message each time a library is selected
- # for linking.
- SET(Boost_LIB_DIAGNOSTIC_DEFINITIONS
- "-DBOOST_LIB_DIAGNOSTIC" CACHE STRING "Boost diagnostic define")
- ENDIF(WIN32)
-
- SET(_boost_INCLUDE_SEARCH_DIRS
- C:/boost/include
- C:/boost
- "$ENV{ProgramFiles}/boost"
- /sw/local/include
- )
-
- # If BOOST_ROOT was defined in the environment, use it.
- if (NOT BOOST_ROOT AND NOT $ENV{BOOST_ROOT} STREQUAL "")
- set(BOOST_ROOT $ENV{BOOST_ROOT})
- endif(NOT BOOST_ROOT AND NOT $ENV{BOOST_ROOT} STREQUAL "")
-
- # If BOOSTROOT was defined in the environment, use it.
- if (NOT BOOST_ROOT AND NOT $ENV{BOOSTROOT} STREQUAL "")
- set(BOOST_ROOT $ENV{BOOSTROOT})
- endif(NOT BOOST_ROOT AND NOT $ENV{BOOSTROOT} STREQUAL "")
-
- # If BOOST_INCLUDEDIR was defined in the environment, use it.
- IF( NOT $ENV{BOOST_INCLUDEDIR} STREQUAL "" )
- set(BOOST_INCLUDEDIR $ENV{BOOST_INCLUDEDIR})
- ENDIF( NOT $ENV{BOOST_INCLUDEDIR} STREQUAL "" )
-
- # If BOOST_LIBRARYDIR was defined in the environment, use it.
- IF( NOT $ENV{BOOST_LIBRARYDIR} STREQUAL "" )
- set(BOOST_LIBRARYDIR $ENV{BOOST_LIBRARYDIR})
- ENDIF( NOT $ENV{BOOST_LIBRARYDIR} STREQUAL "" )
-
- IF( BOOST_ROOT )
- file(TO_CMAKE_PATH ${BOOST_ROOT} BOOST_ROOT)
- ENDIF( BOOST_ROOT )
-
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "Declared as CMake or Environmental Variables:")
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- " BOOST_ROOT = ${BOOST_ROOT}")
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- " BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- " BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "_boost_TEST_VERSIONS = ${_boost_TEST_VERSIONS}")
- endif()
-
- IF( BOOST_ROOT )
- SET(_boost_INCLUDE_SEARCH_DIRS
- ${BOOST_ROOT}/include
- ${BOOST_ROOT}
- ${_boost_INCLUDE_SEARCH_DIRS})
- ENDIF( BOOST_ROOT )
-
- IF( BOOST_INCLUDEDIR )
- file(TO_CMAKE_PATH ${BOOST_INCLUDEDIR} BOOST_INCLUDEDIR)
- SET(_boost_INCLUDE_SEARCH_DIRS
- ${BOOST_INCLUDEDIR} ${_boost_INCLUDE_SEARCH_DIRS})
- ENDIF( BOOST_INCLUDEDIR )
-
- # ------------------------------------------------------------------------
- # Search for Boost include DIR
- # ------------------------------------------------------------------------
- # Try to find Boost by stepping backwards through the Boost versions
- # we know about.
- IF( NOT Boost_INCLUDE_DIR )
- # Build a list of path suffixes for each version.
- SET(_boost_PATH_SUFFIXES)
- FOREACH(_boost_VER ${_boost_TEST_VERSIONS})
- # Add in a path suffix, based on the required version, ideally
- # we could read this from version.hpp, but for that to work we'd
- # need to know the include dir already
- set(_boost_BOOSTIFIED_VERSION)
-
- # Transform 1.35 => 1_35 and 1.36.0 => 1_36_0
- IF(_boost_VER MATCHES "[0-9]+\\.[0-9]+\\.[0-9]+")
- STRING(REGEX REPLACE "([0-9]+)\\.([0-9]+)\\.([0-9]+)" "\\1_\\2_\\3"
- _boost_BOOSTIFIED_VERSION ${_boost_VER})
- ELSEIF(_boost_VER MATCHES "[0-9]+\\.[0-9]+")
- STRING(REGEX REPLACE "([0-9]+)\\.([0-9]+)" "\\1_\\2"
- _boost_BOOSTIFIED_VERSION ${_boost_VER})
- ENDIF()
-
- list(APPEND _boost_PATH_SUFFIXES "boost-${_boost_BOOSTIFIED_VERSION}")
- list(APPEND _boost_PATH_SUFFIXES "boost-${_boost_VER}")
- if(WIN32)
- # For BoostPro's underscores (and others?)
- list(APPEND _boost_PATH_SUFFIXES "boost_${_boost_BOOSTIFIED_VERSION}")
- endif()
-
- ENDFOREACH(_boost_VER)
-
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "Include debugging info:")
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- " _boost_INCLUDE_SEARCH_DIRS = ${_boost_INCLUDE_SEARCH_DIRS}")
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- " _boost_PATH_SUFFIXES = ${_boost_PATH_SUFFIXES}")
- endif()
-
- # Look for a standard boost header file.
- FIND_PATH(Boost_INCLUDE_DIR
- NAMES boost/config.hpp
- HINTS ${_boost_INCLUDE_SEARCH_DIRS}
- PATH_SUFFIXES ${_boost_PATH_SUFFIXES}
- )
- ENDIF( NOT Boost_INCLUDE_DIR )
-
- # ------------------------------------------------------------------------
- # Extract version information from version.hpp
- # ------------------------------------------------------------------------
-
- IF(Boost_INCLUDE_DIR)
- # Extract Boost_VERSION and Boost_LIB_VERSION from version.hpp
- # Read the whole file:
- #
- SET(BOOST_VERSION 0)
- SET(BOOST_LIB_VERSION "")
- FILE(READ "${Boost_INCLUDE_DIR}/boost/version.hpp" _boost_VERSION_HPP_CONTENTS)
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "location of version.hpp: ${Boost_INCLUDE_DIR}/boost/version.hpp")
- endif()
-
- STRING(REGEX REPLACE ".*#define BOOST_VERSION ([0-9]+).*" "\\1" Boost_VERSION "${_boost_VERSION_HPP_CONTENTS}")
- STRING(REGEX REPLACE ".*#define BOOST_LIB_VERSION \"([0-9_]+)\".*" "\\1" Boost_LIB_VERSION "${_boost_VERSION_HPP_CONTENTS}")
-
- SET(Boost_LIB_VERSION ${Boost_LIB_VERSION} CACHE INTERNAL "The library version string for boost libraries")
- SET(Boost_VERSION ${Boost_VERSION} CACHE INTERNAL "The version number for boost libraries")
-
- IF(NOT "${Boost_VERSION}" STREQUAL "0")
- MATH(EXPR Boost_MAJOR_VERSION "${Boost_VERSION} / 100000")
- MATH(EXPR Boost_MINOR_VERSION "${Boost_VERSION} / 100 % 1000")
- MATH(EXPR Boost_SUBMINOR_VERSION "${Boost_VERSION} % 100")
-
- set(Boost_ERROR_REASON
- "${Boost_ERROR_REASON}Boost version: ${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION}\nBoost include path: ${Boost_INCLUDE_DIR}")
- ENDIF(NOT "${Boost_VERSION}" STREQUAL "0")
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "version.hpp reveals boost "
- "${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION}")
- endif()
- ELSE(Boost_INCLUDE_DIR)
- set(Boost_ERROR_REASON
- "${Boost_ERROR_REASON}Unable to find the Boost header files. Please set BOOST_ROOT to the root directory containing Boost or BOOST_INCLUDEDIR to the directory containing Boost's headers.")
- ENDIF(Boost_INCLUDE_DIR)
-
- # ------------------------------------------------------------------------
- # Suffix initialization and compiler suffix detection.
- # ------------------------------------------------------------------------
-
- # Setting some more suffixes for the library
- SET (Boost_LIB_PREFIX "")
- if ( WIN32 AND Boost_USE_STATIC_LIBS )
- SET (Boost_LIB_PREFIX "lib")
- endif()
-
- if (Boost_COMPILER)
- set(_boost_COMPILER ${Boost_COMPILER})
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "using user-specified Boost_COMPILER = ${_boost_COMPILER}")
- endif()
- else(Boost_COMPILER)
- # Attempt to guess the compiler suffix
- # NOTE: this is not perfect yet, if you experience any issues
- # please report them and use the Boost_COMPILER variable
- # to work around the problems.
- if (MSVC90)
- SET (_boost_COMPILER "-vc90")
- elseif (MSVC80)
- SET (_boost_COMPILER "-vc80")
- elseif (MSVC71)
- SET (_boost_COMPILER "-vc71")
- elseif (MSVC70) # Good luck!
- SET (_boost_COMPILER "-vc7") # yes, this is correct
- elseif (MSVC60) # Good luck!
- SET (_boost_COMPILER "-vc6") # yes, this is correct
- elseif (BORLAND)
- SET (_boost_COMPILER "-bcb")
- elseif("${CMAKE_CXX_COMPILER}" MATCHES "icl"
- OR "${CMAKE_CXX_COMPILER}" MATCHES "icpc")
- if(WIN32)
- set (_boost_COMPILER "-iw")
- else()
- set (_boost_COMPILER "-il")
- endif()
- elseif (MINGW)
- if(${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION} VERSION_LESS 1.34)
- SET(_boost_COMPILER "-mgw") # no GCC version encoding prior to 1.34
- else()
- _Boost_COMPILER_DUMPVERSION(_boost_COMPILER_VERSION)
- SET (_boost_COMPILER "-mgw${_boost_COMPILER_VERSION}")
- endif()
- elseif (UNIX)
- if (CMAKE_COMPILER_IS_GNUCXX)
- if(${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION} VERSION_LESS 1.34)
- SET(_boost_COMPILER "-gcc") # no GCC version encoding prior to 1.34
- else()
- _Boost_COMPILER_DUMPVERSION(_boost_COMPILER_VERSION)
- # Determine which version of GCC we have.
- IF(APPLE)
- IF(Boost_MINOR_VERSION)
- IF(${Boost_MINOR_VERSION} GREATER 35)
- # In Boost 1.36.0 and newer, the mangled compiler name used
- # on Mac OS X/Darwin is "xgcc".
- SET(_boost_COMPILER "-xgcc${_boost_COMPILER_VERSION}")
- ELSE(${Boost_MINOR_VERSION} GREATER 35)
- # In Boost <= 1.35.0, there is no mangled compiler name for
- # the Mac OS X/Darwin version of GCC.
- SET(_boost_COMPILER "")
- ENDIF(${Boost_MINOR_VERSION} GREATER 35)
- ELSE(Boost_MINOR_VERSION)
- # We don't know the Boost version, so assume it's
- # pre-1.36.0.
- SET(_boost_COMPILER "")
- ENDIF(Boost_MINOR_VERSION)
- ELSE()
- SET (_boost_COMPILER "-gcc${_boost_COMPILER_VERSION}")
- ENDIF()
- endif()
- endif (CMAKE_COMPILER_IS_GNUCXX)
- endif()
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "guessed _boost_COMPILER = ${_boost_COMPILER}")
- endif()
- endif(Boost_COMPILER)
-
- SET (_boost_MULTITHREADED "-mt")
- if( NOT Boost_USE_MULTITHREADED )
- set (_boost_MULTITHREADED "")
- endif()
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "_boost_MULTITHREADED = ${_boost_MULTITHREADED}")
- endif()
-
- SET( _boost_STATIC_TAG "")
- set( _boost_ABI_TAG "")
- IF (WIN32)
- IF(MSVC)
- SET (_boost_ABI_TAG "g")
- ENDIF(MSVC)
- IF( Boost_USE_STATIC_LIBS )
- SET( _boost_STATIC_TAG "-s")
- ENDIF( Boost_USE_STATIC_LIBS )
- ENDIF(WIN32)
- SET (_boost_ABI_TAG "${_boost_ABI_TAG}d")
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "_boost_STATIC_TAG = ${_boost_STATIC_TAG}")
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "_boost_ABI_TAG = ${_boost_ABI_TAG}")
- endif()
-
- # ------------------------------------------------------------------------
- # Begin finding boost libraries
- # ------------------------------------------------------------------------
-
- SET(_boost_LIBRARIES_SEARCH_DIRS
- C:/boost/lib
- C:/boost
- "$ENV{ProgramFiles}/boost/boost_${Boost_MAJOR_VERSION}_${Boost_MINOR_VERSION}_${Boost_SUBMINOR_VERSION}/lib"
- "$ENV{ProgramFiles}/boost"
- /sw/local/lib
- )
- IF( BOOST_ROOT )
- SET(_boost_LIBRARIES_SEARCH_DIRS
-${BOOST_ROOT}/lib
-${BOOST_ROOT}/lib/boost-${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION}
- ${BOOST_ROOT}/stage/lib
- ${_boost_LIBRARIES_SEARCH_DIRS})
-message("boost searchdirs:${_boost_LIBRARIES_SEARCH_DIRS}")
- ENDIF( BOOST_ROOT )
-
- IF( BOOST_LIBRARYDIR )
- file(TO_CMAKE_PATH ${BOOST_LIBRARYDIR} BOOST_LIBRARYDIR)
- SET(_boost_LIBRARIES_SEARCH_DIRS
- ${BOOST_LIBRARYDIR} ${_boost_LIBRARIES_SEARCH_DIRS})
- ENDIF( BOOST_LIBRARYDIR )
-
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] "
- "_boost_LIBRARIES_SEARCH_DIRS = ${_boost_LIBRARIES_SEARCH_DIRS}")
- endif()
-
- FOREACH(COMPONENT ${Boost_FIND_COMPONENTS})
- STRING(TOUPPER ${COMPONENT} UPPERCOMPONENT)
- SET( Boost_${UPPERCOMPONENT}_LIBRARY "Boost_${UPPERCOMPONENT}_LIBRARY-NOTFOUND" )
- SET( Boost_${UPPERCOMPONENT}_LIBRARY_RELEASE "Boost_${UPPERCOMPONENT}_LIBRARY_RELEASE-NOTFOUND" )
- SET( Boost_${UPPERCOMPONENT}_LIBRARY_DEBUG "Boost_${UPPERCOMPONENT}_LIBRARY_DEBUG-NOTFOUND")
-
- # Support preference of static libs by adjusting CMAKE_FIND_LIBRARY_SUFFIXES
- IF( Boost_USE_STATIC_LIBS )
- SET( _boost_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES})
- IF(WIN32)
- SET(CMAKE_FIND_LIBRARY_SUFFIXES .lib .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
- ELSE(WIN32)
- SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
- ENDIF(WIN32)
- ENDIF( Boost_USE_STATIC_LIBS )
-
- FIND_LIBRARY(Boost_${UPPERCOMPONENT}_LIBRARY_RELEASE
- NAMES ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_COMPILER}${_boost_MULTITHREADED}-${Boost_LIB_VERSION}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_COMPILER}${_boost_MULTITHREADED}${_boost_STATIC_TAG}-${Boost_LIB_VERSION}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_MULTITHREADED}-${Boost_LIB_VERSION}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_MULTITHREADED}${_boost_STATIC_TAG}-${Boost_LIB_VERSION}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_MULTITHREADED}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_MULTITHREADED}${_boost_STATIC_TAG}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}
- HINTS ${_boost_LIBRARIES_SEARCH_DIRS}
- )
-
- FIND_LIBRARY(Boost_${UPPERCOMPONENT}_LIBRARY_DEBUG
- NAMES ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_COMPILER}${_boost_MULTITHREADED}-${_boost_ABI_TAG}-${Boost_LIB_VERSION}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_COMPILER}${_boost_MULTITHREADED}${_boost_STATIC_TAG}${_boost_ABI_TAG}-${Boost_LIB_VERSION}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_MULTITHREADED}-${_boost_ABI_TAG}-${Boost_LIB_VERSION}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_MULTITHREADED}${_boost_STATIC_TAG}${_boost_ABI_TAG}-${Boost_LIB_VERSION}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_MULTITHREADED}-${_boost_ABI_TAG}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}${_boost_MULTITHREADED}${_boost_STATIC_TAG}${_boost_ABI_TAG}
- ${Boost_LIB_PREFIX}boost_${COMPONENT}-${_boost_ABI_TAG}
- HINTS ${_boost_LIBRARIES_SEARCH_DIRS}
- )
-
- _Boost_ADJUST_LIB_VARS(${UPPERCOMPONENT})
- IF( Boost_USE_STATIC_LIBS )
- SET(CMAKE_FIND_LIBRARY_SUFFIXES ${_boost_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})
- ENDIF( Boost_USE_STATIC_LIBS )
- ENDFOREACH(COMPONENT)
- # ------------------------------------------------------------------------
- # End finding boost libraries
- # ------------------------------------------------------------------------
-
- SET(Boost_INCLUDE_DIRS
- ${Boost_INCLUDE_DIR}
- )
-
- SET(Boost_FOUND FALSE)
- IF(Boost_INCLUDE_DIR)
- SET( Boost_FOUND TRUE )
-
- # Check the version of Boost against the requested version.
- if (Boost_FIND_VERSION AND NOT Boost_FIND_VERSION_MINOR)
- message(SEND_ERROR "When requesting a specific version of Boost, you must provide at least the major and minor version numbers, e.g., 1.34")
- endif (Boost_FIND_VERSION AND NOT Boost_FIND_VERSION_MINOR)
- if(Boost_MAJOR_VERSION LESS "${Boost_FIND_VERSION_MAJOR}" )
- set( Boost_FOUND FALSE )
- set(_Boost_VERSION_AGE "old")
- elseif(Boost_MAJOR_VERSION EQUAL "${Boost_FIND_VERSION_MAJOR}" )
- if(Boost_MINOR_VERSION LESS "${Boost_FIND_VERSION_MINOR}" )
- set( Boost_FOUND FALSE )
- set(_Boost_VERSION_AGE "old")
- elseif(Boost_MINOR_VERSION EQUAL "${Boost_FIND_VERSION_MINOR}" )
- if( Boost_FIND_VERSION_PATCH AND Boost_SUBMINOR_VERSION LESS "${Boost_FIND_VERSION_PATCH}" )
- set( Boost_FOUND FALSE )
- set(_Boost_VERSION_AGE "old")
- endif( Boost_FIND_VERSION_PATCH AND Boost_SUBMINOR_VERSION LESS "${Boost_FIND_VERSION_PATCH}" )
- endif( Boost_MINOR_VERSION LESS "${Boost_FIND_VERSION_MINOR}" )
- endif( Boost_MAJOR_VERSION LESS "${Boost_FIND_VERSION_MAJOR}" )
-
- if (Boost_FOUND AND Boost_FIND_VERSION_EXACT)
- # If the user requested an exact version of Boost, check
- # that. We already know that the Boost version we have is >= the
- # requested version.
- set(_Boost_VERSION_AGE "new")
-
- # If the user didn't specify a patchlevel, it's 0.
- if (NOT Boost_FIND_VERSION_PATCH)
- set(Boost_FIND_VERSION_PATCH 0)
- endif (NOT Boost_FIND_VERSION_PATCH)
-
- # We'll set Boost_FOUND true again if we have an exact version match.
- set(Boost_FOUND FALSE)
- if(Boost_MAJOR_VERSION EQUAL "${Boost_FIND_VERSION_MAJOR}" )
- if(Boost_MINOR_VERSION EQUAL "${Boost_FIND_VERSION_MINOR}" )
- if(Boost_SUBMINOR_VERSION EQUAL "${Boost_FIND_VERSION_PATCH}" )
- set( Boost_FOUND TRUE )
- endif(Boost_SUBMINOR_VERSION EQUAL "${Boost_FIND_VERSION_PATCH}" )
- endif( Boost_MINOR_VERSION EQUAL "${Boost_FIND_VERSION_MINOR}" )
- endif( Boost_MAJOR_VERSION EQUAL "${Boost_FIND_VERSION_MAJOR}" )
- endif (Boost_FOUND AND Boost_FIND_VERSION_EXACT)
-
- if(NOT Boost_FOUND)
- # State that we found a version of Boost that is too new or too old.
- set(Boost_ERROR_REASON
- "${Boost_ERROR_REASON}\nDetected version of Boost is too ${_Boost_VERSION_AGE}. Requested version was ${Boost_FIND_VERSION_MAJOR}.${Boost_FIND_VERSION_MINOR}")
- if (Boost_FIND_VERSION_PATCH)
- set(Boost_ERROR_REASON
- "${Boost_ERROR_REASON}.${Boost_FIND_VERSION_PATCH}")
- endif (Boost_FIND_VERSION_PATCH)
- if (NOT Boost_FIND_VERSION_EXACT)
- set(Boost_ERROR_REASON "${Boost_ERROR_REASON} (or newer)")
- endif (NOT Boost_FIND_VERSION_EXACT)
- set(Boost_ERROR_REASON "${Boost_ERROR_REASON}.")
- endif (NOT Boost_FOUND)
-
- if (Boost_FOUND)
- set(_boost_CHECKED_COMPONENT FALSE)
- set(_Boost_MISSING_COMPONENTS)
- foreach(COMPONENT ${Boost_FIND_COMPONENTS})
- string(TOUPPER ${COMPONENT} COMPONENT)
- set(_boost_CHECKED_COMPONENT TRUE)
- if(NOT Boost_${COMPONENT}_FOUND)
- string(TOLOWER ${COMPONENT} COMPONENT)
- list(APPEND _Boost_MISSING_COMPONENTS ${COMPONENT})
- set( Boost_FOUND FALSE)
- endif(NOT Boost_${COMPONENT}_FOUND)
- endforeach(COMPONENT)
- endif (Boost_FOUND)
-
- if(Boost_DEBUG)
- message(STATUS "[ ${CMAKE_CURRENT_LIST_FILE}:${CMAKE_CURRENT_LIST_LINE} ] Boost_FOUND = ${Boost_FOUND}")
- endif()
-
- if (_Boost_MISSING_COMPONENTS)
- # We were unable to find some libraries, so generate a sensible
- # error message that lists the libraries we were unable to find.
- set(Boost_ERROR_REASON
- "${Boost_ERROR_REASON}\nThe following Boost libraries could not be found:\n")
- foreach(COMPONENT ${_Boost_MISSING_COMPONENTS})
- set(Boost_ERROR_REASON
- "${Boost_ERROR_REASON} boost_${COMPONENT}\n")
- endforeach(COMPONENT)
-
- list(LENGTH Boost_FIND_COMPONENTS Boost_NUM_COMPONENTS_WANTED)
- list(LENGTH _Boost_MISSING_COMPONENTS Boost_NUM_MISSING_COMPONENTS)
- if (${Boost_NUM_COMPONENTS_WANTED} EQUAL ${Boost_NUM_MISSING_COMPONENTS})
- set(Boost_ERROR_REASON
- "${Boost_ERROR_REASON}No Boost libraries were found. You may need to set Boost_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT to the location of Boost.")
- else (${Boost_NUM_COMPONENTS_WANTED} EQUAL ${Boost_NUM_MISSING_COMPONENTS})
- set(Boost_ERROR_REASON
- "${Boost_ERROR_REASON}Some (but not all) of the required Boost libraries were found. You may need to install these additional Boost libraries. Alternatively, set Boost_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT to the location of Boost.")
- endif (${Boost_NUM_COMPONENTS_WANTED} EQUAL ${Boost_NUM_MISSING_COMPONENTS})
- endif (_Boost_MISSING_COMPONENTS)
-
- IF( NOT Boost_LIBRARY_DIRS AND NOT _boost_CHECKED_COMPONENT )
- # Compatibility Code for backwards compatibility with CMake
- # 2.4's FindBoost module.
-
- # Look for the boost library path.
- # Note that the user may not have installed any libraries
- # so it is quite possible the Boost_LIBRARY_PATH may not exist.
- SET(_boost_LIB_DIR ${Boost_INCLUDE_DIR})
-
- IF("${_boost_LIB_DIR}" MATCHES "boost-[0-9]+")
- GET_FILENAME_COMPONENT(_boost_LIB_DIR ${_boost_LIB_DIR} PATH)
- ENDIF ("${_boost_LIB_DIR}" MATCHES "boost-[0-9]+")
-
- IF("${_boost_LIB_DIR}" MATCHES "/include$")
- # Strip off the trailing "/include" in the path.
- GET_FILENAME_COMPONENT(_boost_LIB_DIR ${_boost_LIB_DIR} PATH)
- ENDIF("${_boost_LIB_DIR}" MATCHES "/include$")
-
- IF(EXISTS "${_boost_LIB_DIR}/lib")
- SET (_boost_LIB_DIR ${_boost_LIB_DIR}/lib)
- ELSE(EXISTS "${_boost_LIB_DIR}/lib")
- IF(EXISTS "${_boost_LIB_DIR}/stage/lib")
- SET(_boost_LIB_DIR ${_boost_LIB_DIR}/stage/lib)
- ELSE(EXISTS "${_boost_LIB_DIR}/stage/lib")
- SET(_boost_LIB_DIR "")
- ENDIF(EXISTS "${_boost_LIB_DIR}/stage/lib")
- ENDIF(EXISTS "${_boost_LIB_DIR}/lib")
-
- IF(_boost_LIB_DIR AND EXISTS "${_boost_LIB_DIR}")
- SET(Boost_LIBRARY_DIRS ${_boost_LIB_DIR} CACHE FILEPATH "Boost library directory")
- ENDIF(_boost_LIB_DIR AND EXISTS "${_boost_LIB_DIR}")
-
- ENDIF( NOT Boost_LIBRARY_DIRS AND NOT _boost_CHECKED_COMPONENT )
-
- ELSE(Boost_INCLUDE_DIR)
- SET( Boost_FOUND FALSE)
- ENDIF(Boost_INCLUDE_DIR)
-
- IF (Boost_FOUND)
- IF (NOT Boost_FIND_QUIETLY)
- MESSAGE(STATUS "Boost version: ${Boost_MAJOR_VERSION}.${Boost_MINOR_VERSION}.${Boost_SUBMINOR_VERSION}")
- ENDIF(NOT Boost_FIND_QUIETLY)
- IF (NOT Boost_FIND_QUIETLY)
- MESSAGE(STATUS "Found the following Boost libraries:")
- ENDIF(NOT Boost_FIND_QUIETLY)
- FOREACH ( COMPONENT ${Boost_FIND_COMPONENTS} )
- STRING( TOUPPER ${COMPONENT} UPPERCOMPONENT )
- IF ( Boost_${UPPERCOMPONENT}_FOUND )
- IF (NOT Boost_FIND_QUIETLY)
- MESSAGE (STATUS " ${COMPONENT}")
- ENDIF(NOT Boost_FIND_QUIETLY)
- SET(Boost_LIBRARIES ${Boost_LIBRARIES} ${Boost_${UPPERCOMPONENT}_LIBRARY})
- ENDIF ( Boost_${UPPERCOMPONENT}_FOUND )
- ENDFOREACH(COMPONENT)
- ELSE (Boost_FOUND)
- IF (Boost_FIND_REQUIRED)
- message(SEND_ERROR "Unable to find the requested Boost libraries.\n${Boost_ERROR_REASON}")
- ENDIF(Boost_FIND_REQUIRED)
- ENDIF(Boost_FOUND)
-
- # show the Boost_INCLUDE_DIRS AND Boost_LIBRARIES variables only in the advanced view
- MARK_AS_ADVANCED(Boost_INCLUDE_DIR
- Boost_INCLUDE_DIRS
- Boost_LIBRARY_DIRS
- )
-ENDIF(_boost_IN_CACHE)
-
diff --git a/cmake_support/PROMOD3.cmake b/cmake_support/PROMOD3.cmake
index db12a874b6b7060d95ae6904aea51c5bccd4f017..6c7ae410fd2d23bbb8a9200be273080d926a116e 100644
--- a/cmake_support/PROMOD3.cmake
+++ b/cmake_support/PROMOD3.cmake
@@ -1162,6 +1162,22 @@ macro(add_changelog_to_doc)
set(PM3_DOC_CHANGELOG "${_ARG_CLOG_FILE}" CACHE INTERNAL "" FORCE)
endmacro(add_changelog_to_doc)
+#-------------------------------------------------------------------------------
+# Synopsis:
+# add_license_to_doc(FILE license file)
+#
+# Description:
+# Add a LICENSE file to the documentation.
+# FILE - name of the license file
+#-------------------------------------------------------------------------------
+macro(add_license_to_doc)
+ parse_argument_list(_ARG_LICENSE "FILE" "" ${ARGN})
+ if(NOT _ARG_LICENSE_FILE)
+ message(FATAL_ERROR "invalid use of add_license_to_doc(): file missing")
+ endif()
+ set(PM3_DOC_LICENSE "${_ARG_LICENSE_FILE}" CACHE INTERNAL "" FORCE)
+endmacro(add_license_to_doc)
+
#-------------------------------------------------------------------------------
# Synopsis:
# pm_action_init()
diff --git a/config/src/config.hh.in b/config/src/config.hh.in
index d5fd0ccef3fb4510eae5051b87fa758eb9356295..b864eb0aaf25ac8b75030c3dbe9c0db27002392e 100644
--- a/config/src/config.hh.in
+++ b/config/src/config.hh.in
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/*
DO NOT EDIT the '.hh' file, it is processed from a template '.hh.in' by CMake.
*/
diff --git a/container/Dockerfile b/container/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..481b72fd03297d248d83c76c8e0b6a0ada521ceb
--- /dev/null
+++ b/container/Dockerfile
@@ -0,0 +1,141 @@
+FROM ubuntu:18.04
+
+# ARGUMENTS
+###########
+ARG OPENSTRUCTURE_VERSION="1.9.0"
+ARG PROMOD_VERSION="1.3.0"
+ARG SRC_FOLDER="/usr/local/src"
+ARG CPUS_FOR_MAKE=2
+ARG COMPLIB_DIR="/usr/local/share/ost_complib"
+ARG OPENMM_VERSION="7.1.1"
+ARG OPENMM_INCLUDE_PATH="/usr/local/openmm/include/"
+ARG OPENMM_LIB_PATH="/usr/local/openmm/lib/"
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# INSTALL SYSTEM DEPS
+#####################
+RUN apt-get update -y && apt-get install -y cmake \
+ sip-dev \
+ libtiff-dev \
+ libfftw3-dev \
+ libeigen3-dev \
+ libboost-all-dev \
+ libpng-dev \
+ python2.7 \
+ python-qt4 \
+ python-numpy \
+ python-scipy \
+ python-pandas \
+ python-matplotlib \
+ qt4-qtconfig \
+ qt4-qmake \
+ libqt4-dev \
+ libpng-dev \
+ wget \
+ gfortran \
+ python-pip \
+ python-sphinx \
+ tar \
+ libbz2-dev \
+ doxygen \
+ swig \
+ clustalw \
+ dssp \
+ locales && \
+ # CLEANUP
+ rm -rf /var/lib/apt/lists/*
+
+# SET LOCALE
+############
+# RUN echo "LC_ALL=en_US.UTF-8" >> /etc/environment
+# RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
+# RUN echo "LANG=en_US.UTF-8" > /etc/locale.conf
+# RUN locale-gen en_US.UTF-8
+
+# ENVIRONMENT
+##############################################################################
+ENV OPENSTRUCTURE_VERSION="${OPENSTRUCTURE_VERSION}"
+ENV PROMOD_VERSION="${PROMOD_VERSION}"
+ENV OST_ROOT="/usr/local"
+ENV DNG_ROOT="/usr/local"
+ENV PROMOD_ROOT="/usr/local"
+ENV PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
+ENV LD_LIBRARY_PATH="/usr/local/lib64:/usr/local/openmm/lib/$LD_LIBRARY_PATH"
+ENV QT_X11_NO_MITSHM=1
+
+# COMPILE OPENMM FROM SOURCES. INSTALL TO /usr/local
+####################################################
+RUN cd ${SRC_FOLDER} && \
+ wget -O openmm-${OPENMM_VERSION}.tar.gz -nc https://github.com/pandegroup/openmm/archive/${OPENMM_VERSION}.tar.gz && \
+ mkdir ${SRC_FOLDER}/openmm-${OPENMM_VERSION} && \
+ tar xf openmm-${OPENMM_VERSION}.tar.gz -C ${SRC_FOLDER}/openmm-${OPENMM_VERSION} --strip-components=1 && \
+ mkdir -p ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && \
+ cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && \
+ cmake .. && make -j $CPUS_FOR_MAKE && make install && \
+ cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build/python && \
+ python setup.py build && python setup.py install && \
+ cd ${SRC_FOLDER} && rm ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \
+ rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
+
+# INSTALL OST
+#############
+RUN cd ${SRC_FOLDER} && \
+ # copy ost release
+ wget -O openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/openstructure/repository/${OPENSTRUCTURE_VERSION}/archive.tar.gz && \
+ mkdir openstructure-${OPENSTRUCTURE_VERSION} && \
+ tar xf openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -C ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} --strip-components=1 && \
+ mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && \
+ cd ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && \
+ # cmake ost
+ cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
+ -DOPTIMIZE=ON \
+ -DENABLE_MM=ON \
+ -DCOMPILE_TMTOOLS=1 \
+ -DOPEN_MM_LIBRARY=$OPENMM_LIB_PATH/libOpenMM.so \
+ -DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
+ -DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
+ -DENABLE_GFX=ON \
+ -DENABLE_GUI=ON && \
+ make -j ${CPUS_FOR_MAKE} &&\
+ # get the compound library \
+ wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz &&\
+ stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb && stage/bin/chemdict_tool update modules/conop/data/charmm.cif compounds.chemlib charmm &&\
+ mkdir -p $COMPLIB_DIR && chmod a+rw -R $COMPLIB_DIR && mv compounds.chemlib $COMPLIB_DIR && \
+ # rerun cmake and specify compount lib location
+ cmake .. -DCOMPOUND_LIB=$COMPLIB_DIR/compounds.chemlib && \
+ # Build OST with compound library
+ make -j ${CPUS_FOR_MAKE} && make check && make install && \
+ # cleanup
+ cd ${SRC_FOLDER} && rm ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}.tar.gz && \
+ rm -rf ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} && \
+ # BEND AROUND COMPOUND LIB
+ # By default, the compound library is moved to
+ # /usr/local/share/openstructure/compounds.chemlib upon building
+ # We replace that file with a symbolic link to the compound.chemlib in
+ # $COMPLIB_DIR
+ # The advantage is that we can later on mount any directory containing this file
+ # in that directory and override the compound lib with updated versions.
+ rm /usr/local/share/openstructure/compounds.chemlib && \
+ ln -s $COMPLIB_DIR/compounds.chemlib /usr/local/share/openstructure/compounds.chemlib
+
+# INSTALL ProMod3
+#################
+RUN cd ${SRC_FOLDER} && \
+ # copy promod release
+ wget -O promod-${PROMOD_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/ProMod3/repository/${PROMOD_VERSION}/archive.tar.gz && \
+ mkdir promod-${PROMOD_VERSION} && \
+ tar xf promod-${PROMOD_VERSION}.tar.gz -C ${SRC_FOLDER}/promod-${PROMOD_VERSION} --strip-components=1 && \
+ mkdir -p ${SRC_FOLDER}/promod-${PROMOD_VERSION}/build && \
+ cd ${SRC_FOLDER}/promod-${PROMOD_VERSION}/build && \
+ # Build and install ProMod3
+ cmake .. -DOST_ROOT=/usr/local \
+ -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
+ -DOPTIMIZE=ON \
+ -DENABLE_SSE=1 && \
+ make && make codetest && make install && \
+ # cleanup
+ cd ${SRC_FOLDER} && rm ${SRC_FOLDER}/promod-${PROMOD_VERSION}.tar.gz && \
+ rm -rf ${SRC_FOLDER}/promod-${PROMOD_VERSION}
+
+WORKDIR /home
diff --git a/container/Singularity b/container/Singularity
new file mode 100644
index 0000000000000000000000000000000000000000..7fb04357d405209c1b3251b15542344e9ffa4ae2
--- /dev/null
+++ b/container/Singularity
@@ -0,0 +1,116 @@
+BootStrap: docker
+Registry: http://localhost:5000
+Namespace:
+From: promod:latest
+
+%post
+##############################################################################
+# POST
+##############################################################################
+
+# CHANGE DASH TO BASH
+rm /bin/sh
+ln -sf /bin/bash /bin/sh
+
+# INSTALL NGL AND JUPYTER WITH PIP
+######################################
+pip install --no-cache-dir nglview==1.1.6 \
+ jupyter==1.0.0
+
+# SETUP JUPYTER
+###############
+mkdir -p /usr/local/share/ipython
+mkdir -p /usr/local/share/jupyter
+mkdir -p /usr/local/etc/jupyter
+mkdir -p /usr/local/share/jupyter/runtime
+mkdir -p /usr/local/share/jupyter/kernels/ost-kernel
+chmod a+rw -R /usr/local/share/ipython
+chmod a+rw -R /usr/local/share/jupyter
+chmod a+rw -R /usr/local/etc/jupyter
+chmod a+rw -R /usr/local/share/jupyter/runtime
+cat > /usr/local/share/jupyter/kernels/ost-kernel/kernel.json <<EOF
+{
+ "display_name": "OST",
+ "language": "python",
+ "argv": [
+ "python",
+ "-m", "ipykernel",
+ "-f", "{connection_file}",
+ "--InteractiveShellApp.exec_PYTHONSTARTUP=False",
+ "--InteractiveShellApp.exec_files=['/usr/local/lib64/python2.7/site-packages/ost/ost_startup.py']"
+ ],
+ "env": {
+ }
+}
+EOF
+
+jupyter nbextension enable nglview --py --sys-prefix
+
+%environment
+##############################################################################
+# ENVIRONMENT
+##############################################################################
+export QT_X11_NO_MITSHM=1
+export IPYTHONDIR=/usr/local/share/ipython
+export JUPYTER_CONFIG_DIR=/usr/local/etc/jupyter
+export JUPYTER_PATH=/usr/local/share/jupyter
+export JUPYTER_RUNTIME_DIR=$JUPYTER_PATH/runtime
+
+%apprun Notebook
+##############################################################################
+# NOTEBOOK APP
+##############################################################################
+jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@"
+
+%apphelp Notebook
+A Jupyter notebook playground with OST ProMod3 and nglview.
+
+Usage:
+
+ singularity run --app Notebook <IMAGE> [options]
+
+The Jupyter notebook is run by default with `--NotebookApp.iopub_data_rate_limit=10000000`
+and `--no-browser` options.
+
+Useful options when running on remote server:
+ --ip=<Unicode> (NotebookApp.ip)
+ Default: 'localhost'
+ The IP address the notebook server will listen on.
+ --port=<Integer> (NotebookApp.port)
+ Default: 8888
+ The port the notebook server will listen on.
+
+Copy the URL to the browser and launch the notebook with OST kernel. This will
+load all necessary OST components just like in the OST shell.
+ProMod3 modules can be imported as needed. We also enabled
+the nglview widget to interactively view molecular structures and trajectories.
+For more details on how to use nglview see http://nglviewer.org/nglview/latest/.
+
+As the Singularity mounts $HOME by default, Jupyter and Ipython config files
+are moved to separate directories. Proper environmental variables are also set.
+
+To list of all available options:
+
+ singularity run --app Notebook <IMAGE> --help
+
+%runscript
+##############################################################################
+# RUNSCRIPT
+##############################################################################
+cat << EOF
+Singularity container for OST $OPENSTRUCTURE_VERSION and ProMod3 $PROMOD_VERSION
+
+This container can run the ost, pm or chemdict_tool executables.
+For convenience, a jupyter notebook playground with OST, ProMod3 and nglview is
+available.
+
+To run ost, pm or chemdict_tool executables, use the exec command.
+E.g. to run scripts with pm:
+
+singularity exec <IMAGE> pm my_script.py [options]
+
+To get more information on how to run the Notebook run:
+
+singularity help --app Notebook <IMAGE NAME>
+EOF
+
diff --git a/core/doc/geometry.rst b/core/doc/geometry.rst
index 3d36b1bd13c2506eb51fad21c9bd61712a9ad5c8..1ac82fac9c1ecc650be29cd7a099f122ed7a6a5a 100644
--- a/core/doc/geometry.rst
+++ b/core/doc/geometry.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Geometry functions
================================================================================
@@ -53,7 +69,7 @@ Geometry functions
.. function:: ConstructCBetaPos(n_pos, ca_pos, c_pos)
Constructs position of C-beta atom given the positions of the backbone nitrogen,
- C-alpha and c atoms.
+ C-alpha and C atoms.
:param n_pos: Position of nitrogen atom
:type n_pos: :class:`~ost.geom.Vec3`
diff --git a/core/doc/graph_minimizer.rst b/core/doc/graph_minimizer.rst
index a1ddb9639f2816086ee62f64861e5e2e5b9dacb2..a38bca5895963caf439339bf5e57af6459d10847 100644
--- a/core/doc/graph_minimizer.rst
+++ b/core/doc/graph_minimizer.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Graph Minimizer
================================================================================
@@ -228,8 +244,3 @@ a set :math:`X=[x_1, x_2, ..., x_n]` that minimizes:
representing the single solutions minimizing
the overall energy function.
The second element is the according energy value.
-
-
-.. [goldstein1994] Goldstein RF (1994). Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J.
-
-.. [leach1998] Leach AR, Lemon AP (1998). Explring the conformational space of prootein side chains using dead-end elimination and the A* algorithm. Proteins.
diff --git a/core/doc/helper.rst b/core/doc/helper.rst
index 03d2cef127c61cb16af4680f5580673c34dae2e7..6684d1247ae7c8a53785187b4dd24a4b38737ac0 100644
--- a/core/doc/helper.rst
+++ b/core/doc/helper.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.core.helper` - Shared Functionality For the Everything
================================================================================
diff --git a/core/doc/index.rst b/core/doc/index.rst
index 2af5fca9cace92deef375d4857a1c9b55f9ec0d5..91b0d9c39c77212b3747e804b1a12191f422a213 100644
--- a/core/doc/index.rst
+++ b/core/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.core` - ProMod3 Core Functionality
================================================================================
diff --git a/core/doc/pm3argparse.rst b/core/doc/pm3argparse.rst
index 927faf547e89cc54e508fa38abfbf18b39fb217b..f6a048252ec82ce7dabbb48da87a242e26d82aa4 100644
--- a/core/doc/pm3argparse.rst
+++ b/core/doc/pm3argparse.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.core.pm3argparse` - Parsing Command Lines
================================================================================
diff --git a/core/doc/runtime_profiling.rst b/core/doc/runtime_profiling.rst
index 07c51ad5bb447b99aaf0335a1cd5f8e48d4a5c75..44bd8621a4ad7a5b77b185f5a9be069afbc9440c 100644
--- a/core/doc/runtime_profiling.rst
+++ b/core/doc/runtime_profiling.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Runtime profiling
================================================================================
diff --git a/core/doc/setcompoundschemlib.rst b/core/doc/setcompoundschemlib.rst
index fb0223432967ffc2ed53d542191c52fce4fb770b..2c6e660ffb8e1cf6d4d3df93a7f16fda04340724 100644
--- a/core/doc/setcompoundschemlib.rst
+++ b/core/doc/setcompoundschemlib.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:func:`~promod3.SetCompoundsChemlib`
================================================================================
diff --git a/core/init/__init__.py.in b/core/init/__init__.py.in
index 13cbe40a2ada8bb58cbb9a62a540424e485baf83..3be41dac459e2ba3cbeed1f8ae70cecb281470c9 100644
--- a/core/init/__init__.py.in
+++ b/core/init/__init__.py.in
@@ -1,3 +1,18 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
# enable access to loop and modelling via "import promod3"
import promod3.core
import promod3.sidechain
diff --git a/core/pymod/__init__.py b/core/pymod/__init__.py
index 4254903896c35f8649996983219c43382bb03390..1eac336f15bb63c7f87c2b62c281dbcb444572be 100644
--- a/core/pymod/__init__.py
+++ b/core/pymod/__init__.py
@@ -1,2 +1,18 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from _core import *
from _filecache import FileCache
diff --git a/core/pymod/_filecache.py b/core/pymod/_filecache.py
index 7fb9e5e2671124b914b2cec628ac91f50d8ffbd3..26b25b2484e3d0f5c428ad8452e0ae581b420c2d 100644
--- a/core/pymod/_filecache.py
+++ b/core/pymod/_filecache.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os
import shutil
diff --git a/core/pymod/export_geom.cc b/core/pymod/export_geom.cc
index c00233c513d754f8bfc31ec0b1aa105e3350e507..b26d5dba8f0bea9980182ac7804b461994ba9c5c 100644
--- a/core/pymod/export_geom.cc
+++ b/core/pymod/export_geom.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/core/message.hh>
diff --git a/core/pymod/export_graph_minimizer.cc b/core/pymod/export_graph_minimizer.cc
index bd301c84f7a3289d6ee1f3f9e91f8975be0718f7..a652c9a9ca37786161badd2e0acd1f0e63465414 100644
--- a/core/pymod/export_graph_minimizer.cc
+++ b/core/pymod/export_graph_minimizer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/graph_minimizer.hh>
diff --git a/core/pymod/export_runtime_profiling.cc b/core/pymod/export_runtime_profiling.cc
index 7386a4af9bc0e7f9aed7c0f61ed564cf0cc39ac7..aa61d4881968cafed2fdbb676567c72e29cd831e 100644
--- a/core/pymod/export_runtime_profiling.cc
+++ b/core/pymod/export_runtime_profiling.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/shared_ptr.hpp>
diff --git a/core/pymod/helper.py b/core/pymod/helper.py
index 91e9d6a5783805caca7b10f2ffe94dbdb01ef77f..3d6d6a09b58b8428804bf6c23f0017d620431e7f 100644
--- a/core/pymod/helper.py
+++ b/core/pymod/helper.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Uncategorised functions which may come handy at several places.
"""
diff --git a/core/pymod/pm3argparse.py b/core/pymod/pm3argparse.py
index b8b6a640bf92ae736bfdfe6a3bddb827919f68ea..d4c9643f23532260f831e265e98178271792b129 100644
--- a/core/pymod/pm3argparse.py
+++ b/core/pymod/pm3argparse.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Extensions for the argparse module.
"""
@@ -232,6 +248,17 @@ def _LoadEntity(filename):
str(exc), 33)
return ent
+def _FetchProfileFromFile(filename):
+ """Load generic profile file from filename and return it."""
+ argstr = "'--seqprof " + filename + "'"
+ helper.FileExists("Profile", 51, filename)
+ try:
+ prof = io.LoadSequenceProfile(filename)
+ except Exception, exc:
+ helper.MsgErrorAndExit(argstr + ": failure to parse profile file: " +
+ str(exc), 52)
+ return prof
+
def _GetChains(structures, structure_sources):
"""Get chain id to entity view (single chain) mapping (dict)."""
# IDs: (file_base = base file name with no extensions)
@@ -398,6 +425,8 @@ class PM3ArgumentParser(argparse.ArgumentParser):
self._AssembleAlignment()
if 'STRUCTURE' in self.activate:
self._AssembleStructure()
+ if 'PROFILE' in self.activate:
+ self._AssembleProfile()
def AddAlignment(self, allow_multitemplate=False):
"""Commandline options for alignments.
@@ -474,7 +503,7 @@ class PM3ArgumentParser(argparse.ArgumentParser):
def AddStructure(self, attach_views=False):
"""Commandline options for structures.
- Activate everything needed to load alignments to the argument parser.
+ Activate everything needed to load structures to the argument parser.
Command line arguments are then added in :meth:`AssembleParser` and the
input is post processed and checked in :meth:`Parse`.
@@ -532,6 +561,48 @@ class PM3ArgumentParser(argparse.ArgumentParser):
if attach_views:
self.activate.add('ATTACH_VIEWS')
+ def AddProfile(self):
+ """Commandline options for profiles
+
+ Activate everything needed to load profiles to the argument parser.
+ Command line arguments are then added in :meth:`AssembleParser` and the
+ input is post processed and checked in :meth:`Parse`.
+
+ Options/arguments added:
+
+ * ``-s/--seqprof <FILE>`` - Sequence profile in any format readable
+ by the :meth:`ost.io.LoadSequenceProfile` method. Format is chosen by
+ file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm,
+ .pssm.gz. Consider to use
+ :meth:`ost.bindings.hhblits.HHblits.A3MToProfile` if you have a file
+ in a3m format at hand.
+
+ Notes:
+
+ * the profiles are mapped based on exact matches towards the gapless
+ target sequences, i.e. one profile is mapped to several chains in
+ case of homo-oligomers
+
+ * every profile must have a unique sequence to avoid ambiguities
+
+ * all or nothing - you cannot provide profiles for only a subset of
+ target sequences
+
+ Attributes added to the namespace returned by :meth:`Parse`:
+
+ * :attr:`profiles` - :class:`list` of :class:`ost.seq.ProfileHandle`,
+ ordered to match the target sequences.
+
+ Exit codes related to profile input:
+
+ * 51 - a given profile file does not exist
+ * 52 - failure to read a given profile file
+ * 53 - a profile cannot be mapped to any target sequence
+ * 54 - profile sequences are not unique
+ * 55 - only subset of target sequences is covered by profile
+ """
+ self.activate.add('PROFILE')
+
def _AssembleAlignment(self):
"""Actually add alignment arguments/options."""
aln_grp = self.add_mutually_exclusive_group(required=True)
@@ -571,6 +642,14 @@ class PM3ArgumentParser(argparse.ArgumentParser):
".ent.gz, .pdb.gz, .cif, .cif.gz.",
action='append', default=list())
+ def _AssembleProfile(self):
+ self.add_argument('-s', '--seqprof', metavar=('<FILE>'),
+ help="Sequence profile in any format readable by "+
+ "OST's io.LoadSequenceProfile method. Format is "+
+ "chosen by file ending. Recognized File Extensions: "+
+ ".hhm, .hhm.gz, .pssm, .pssm.gz", action='append',
+ default=list())
+
class PM3OptionsNamespace(object):
# class will grow, so for the moment pylint is ignored
#pylint: disable=too-few-public-methods
@@ -591,6 +670,8 @@ class PM3OptionsNamespace(object):
self._PostProcessStructure()
if 'ATTACH_VIEWS' in activated:
self._AttachViews()
+ if 'PROFILE' in activated:
+ self._PostProcessProfile()
def _PostProcessAlignment(self):
#pylint: disable=no-member
@@ -640,6 +721,42 @@ class PM3OptionsNamespace(object):
for aln in self.alignments:
_AttachViewsToAln(aln, chain_entities)
+ def _PostProcessProfile(self):
+ """Get Profiles from command line input."""
+ self.profiles = list()
+
+ if len(self.seqprof) == 0:
+ # no profiles provided, remember the all or nothing principle
+ # so not having any profile is fine
+ return
+
+ loaded_profiles = list()
+ for src in self.seqprof:
+ loaded_profiles.append(_FetchProfileFromFile(src))
+
+ prof_sequences = [p.sequence for p in loaded_profiles]
+
+ # check uniqueness of loaded profiles
+ if len(set(prof_sequences)) != len(prof_sequences):
+ helper.MsgErrorAndExit("All sequence profiles must have unique " +
+ "sequence.", 54)
+
+ # map onto alignment target sequences
+ trg_sequences = [aln.GetSequence(0).GetGaplessString() \
+ for aln in self.alignments]
+ for s in trg_sequences:
+ try:
+ self.profiles.append(loaded_profiles[prof_sequences.index(s)])
+ except Exception, exc:
+ helper.MsgErrorAndExit("Could not find profile with sequence " +
+ "that exactly matches trg seq: " + s, 55)
+
+ # We found a profile for every target sequence. So if the size of unique
+ # target sequences is not the same as for unique profile sequences,
+ # we know that we have additional profiles that never got mapped
+ if len(set(trg_sequences)) != len(set(prof_sequences)):
+ helper.MsgErrorAndExit("Could not map every profile to a target " +
+ "sequence", 53)
# LocalWords: param attr prog argparse ArgumentParser bool sys os init str
# LocalWords: progattr descattr argpinit argv formatter meth args namespace
diff --git a/core/pymod/wrap_core.cc b/core/pymod/wrap_core.cc
index ae1381eb24b990738ffa5c5751665f231856ff2f..8891cf7a2b2d814d96a36ce1cdce4fa0a7c852e4 100644
--- a/core/pymod/wrap_core.cc
+++ b/core/pymod/wrap_core.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
void export_geom();
diff --git a/core/src/check_io.hh b/core/src/check_io.hh
index 8ddb610ad84e8a779eedd9725a38ddb071cec7bb..e4013eca3009ec9a26f0f77d912644c13dd954fc 100644
--- a/core/src/check_io.hh
+++ b/core/src/check_io.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines procedures to check validity of binary files.
/// (see portableIO doc for details)
diff --git a/core/src/cluster.cc b/core/src/cluster.cc
index 3c579730429acd631911538e2df574101ff955cf..d9bbd65e15696fe12875208f7d4d2c078956d786 100644
--- a/core/src/cluster.cc
+++ b/core/src/cluster.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/cluster.hh>
#include <promod3/core/message.hh>
diff --git a/core/src/cluster.hh b/core/src/cluster.hh
index 5c86bf02796e6566ba7fbcdbc3fef71ec655a46d..d9d475d35e921a5dbee3af30e9af51bb4394f00f 100644
--- a/core/src/cluster.hh
+++ b/core/src/cluster.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_CLUSTER_HH
#define PROMOD_LOOP_CLUSTER_HH
diff --git a/core/src/dynamic_spatial_organizer.hh b/core/src/dynamic_spatial_organizer.hh
index 455389667c1fd725595dad3276d308a4c7a55ffb..9565e49e3f1471e3f23d95bd9d74d5da6f988cf0 100644
--- a/core/src/dynamic_spatial_organizer.hh
+++ b/core/src/dynamic_spatial_organizer.hh
@@ -1,11 +1,24 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_DYNAMIC_SPATIAL_ORGANIZER_HI
#define PROMOD3_DYNAMIC_SPATIAL_ORGANIZER_HI
#include <vector>
#include <map>
-#include <cmath>
-#include <limits>
-#include <stdint.h>
#include <ost/geom/geom.hh>
@@ -19,91 +32,43 @@ class SpatialOrganizerCell{
public:
- SpatialOrganizerCell(): num_items_(0),
- capacity_(32) {
- x_ = new Real[capacity_];
- y_ = new Real[capacity_];
- z_ = new Real[capacity_];
- pointers_ = new ITEM*[capacity_];
- distance_buffer_ = new Real[capacity_];
- }
-
- ~SpatialOrganizerCell() {
- delete [] x_;
- delete [] y_;
- delete [] z_;
- delete [] pointers_;
- delete [] distance_buffer_;
+ SpatialOrganizerCell() {
+ x_.reserve(32);
+ y_.reserve(32);
+ z_.reserve(32);
+ pointers_.reserve(32);
+ distance_buffer_.reserve(32);
}
void AddItem(ITEM* item, Real x, Real y, Real z) {
-
- int idx = this->GetIdx(item);
- if(idx != -1) {
- throw promod3::Error("Item is already in spatial organizer cell!");
- }
-
- if(num_items_ == capacity_) {
- capacity_ *= 2;
-
- Real* new_x = new Real[capacity_];
- Real* new_y = new Real[capacity_];
- Real* new_z = new Real[capacity_];
- ITEM** new_pointers = new ITEM*[capacity_];
- Real* new_distance_buffer_ = new Real[capacity_];
-
- memcpy(new_x, x_, num_items_ * sizeof(Real));
- memcpy(new_y, y_, num_items_ * sizeof(Real));
- memcpy(new_z, z_, num_items_ * sizeof(Real));
- memcpy(new_pointers, pointers_, num_items_ * sizeof(ITEM*));
-
- delete [] x_;
- delete [] y_;
- delete [] z_;
- delete [] pointers_;
- delete [] distance_buffer_;
-
- x_ = new_x;
- y_ = new_y;
- z_ = new_z;
- pointers_ = new_pointers;
- distance_buffer_ = new_distance_buffer_;
- }
-
- x_[num_items_] = x;
- y_[num_items_] = y;
- z_[num_items_] = z;
- pointers_[num_items_] = item;
- ++num_items_;
+ x_.push_back(x);
+ y_.push_back(y);
+ z_.push_back(z);
+ pointers_.push_back(item);
+ distance_buffer_.push_back(0.0);
}
void RemoveItem(ITEM* item) {
-
- if(num_items_ == 0) {
- throw promod3::Error("Cannot remove item from empty spatial organizer cell!");
- }
-
- int idx = this->GetIdx(item);
-
- if(idx == -1) {
+ typename std::vector<ITEM*>::iterator it =
+ std::find(pointers_.begin(), pointers_.end(), item);
+ if(it == pointers_.end()) {
throw promod3::Error("Cannot Remove inexistent item from spatial organizer cell!");
}
-
- if(idx < (num_items_-1)) {
- int num_bytes = (num_items_-(idx+1))*sizeof(Real);
- memmove(&x_[idx],&x_[idx+1],num_bytes);
- memmove(&y_[idx],&y_[idx+1],num_bytes);
- memmove(&z_[idx],&z_[idx+1],num_bytes);
- memmove(&pointers_[idx],&pointers_[idx+1], (num_items_-(idx+1))*sizeof(ITEM*));
- }
- --num_items_;
+ int idx = std::distance(pointers_.begin(), it);
+ x_.erase(x_.begin() + idx);
+ y_.erase(y_.begin() + idx);
+ z_.erase(z_.begin() + idx);
+ pointers_.erase(pointers_.begin() + idx);
+ distance_buffer_.pop_back();
}
void ResetPos(ITEM* item, Real x, Real y, Real z) {
- int idx = this->GetIdx(item);
- if(idx == -1) {
- throw promod3::Error("Cannot reset pos of inexistent item from spatial organizer cell!");
+ typename std::vector<ITEM*>::iterator it =
+ std::find(pointers_.begin(), pointers_.end(), item);
+ if(it == pointers_.end()) {
+ throw promod3::Error("Cannot Remove inexistent item from spatial organizer cell!");
}
+ int idx = std::distance(pointers_.begin(), it);
x_[idx] = x;
y_[idx] = y;
z_[idx] = z;
@@ -114,15 +79,16 @@ public:
Real dx, dy, dz;
Real squared_cutoff = dist*dist;
+ int num_items = x_.size();
- for(int i = 0; i < num_items_; ++i) {
+ for(int i = 0; i < num_items; ++i) {
dx = x_[i] - x;
dy = y_[i] - y;
dz = z_[i] - z;
distance_buffer_[i] = dx*dx + dy*dy + dz*dz;
}
- for(int i = 0; i < num_items_; ++i) {
+ for(int i = 0; i < num_items; ++i) {
if(distance_buffer_[i] <= squared_cutoff) {
result_vec.push_back(std::make_pair(pointers_[i],std::sqrt(distance_buffer_[i])));
}
@@ -130,22 +96,11 @@ public:
}
private:
-
-
- int GetIdx(ITEM* ptr) {
- for(int i = 0; i < num_items_; ++i) {
- if(pointers_[i] == ptr) return i;
- }
- return -1;
- }
-
- int num_items_;
- int capacity_;
- Real* x_;
- Real* y_;
- Real* z_;
- ITEM** pointers_;
- Real* distance_buffer_;
+ std::vector<Real> x_;
+ std::vector<Real> y_;
+ std::vector<Real> z_;
+ std::vector<ITEM*> pointers_;
+ mutable std::vector<Real> distance_buffer_;
};
//! spatial organizer
@@ -200,6 +155,7 @@ private:
typedef std::map<Index,SpatialOrganizerCell<ITEM>*> ItemMap;
+
public:
DynamicSpatialOrganizer(Real delta,
@@ -222,15 +178,12 @@ public:
}
void Add(ITEM* item, const geom::Vec3& pos) {
-
Index indx=gen_index(pos);
typename ItemMap::iterator it = map_.find(indx);
-
if(it == map_.end()) {
map_[indx] = new SpatialOrganizerCell<ITEM>;
it = map_.find(indx);
}
-
it->second->AddItem(item,pos[0],pos[1],pos[2]);
}
@@ -248,28 +201,20 @@ public:
void Reset(ITEM* item, const geom::Vec3& actual_pos, const geom::Vec3& new_pos) {
Index actual_indx=gen_index(actual_pos);
Index new_indx=gen_index(new_pos);
- if(actual_indx != new_indx) {
- typename ItemMap::iterator i = map_.find(actual_indx);
- if(i != map_.end()) {
- typename ItemMap::iterator j = map_.find(new_indx);
- if(j == map_.end()) {
- map_[new_indx] = new SpatialOrganizerCell<ITEM>;
- j = map_.find(new_indx);
- }
- i->second->RemoveItem(item);
- j->second->AddItem(item,new_pos[0],new_pos[1],new_pos[2]);
- return;
- }
- throw promod3::Error("Could not find specified item in dynamic spatial organizer!");
+ typename ItemMap::iterator i = map_.find(actual_indx);
+ if(i == map_.end()) {
+ throw promod3::Error("Could not find specified item in dynamic spatial organizer!");
}
- else{
- typename ItemMap::iterator i = map_.find(actual_indx);
- if(i != map_.end()) {
- i->second->ResetPos(item,new_pos[0],new_pos[1],new_pos[2]);
- }
- else{
- throw promod3::Error("Could not find specified item in dynamic spatial organizer!");
+ if(actual_indx == new_indx) {
+ i->second->ResetPos(item,new_pos[0],new_pos[1],new_pos[2]);
+ } else {
+ typename ItemMap::iterator j = map_.find(new_indx);
+ if(j == map_.end()) {
+ map_[new_indx] = new SpatialOrganizerCell<ITEM>;
+ j = map_.find(new_indx);
}
+ i->second->RemoveItem(item);
+ j->second->AddItem(item,new_pos[0],new_pos[1],new_pos[2]);
}
}
@@ -332,7 +277,6 @@ public:
return return_vec;
}
-
void Clear() {
for(typename ItemMap::iterator i = map_.begin(); i != map_.end(); ++i) {
delete i->second;
@@ -348,9 +292,8 @@ private:
mutable WithinList result_buffer_;
Index gen_index(const geom::Vec3& pos) const {
- Index nrvo(static_cast<int>(round(pos[0]/delta_)),
- static_cast<int>(round(pos[1]/delta_)),
- static_cast<int>(round(pos[2]/delta_)));
+ Index nrvo(std::floor(pos[0]/delta_), std::floor(pos[1]/delta_),
+ std::floor(pos[2]/delta_));
return nrvo;
}
};
diff --git a/core/src/eigen_types.hh b/core/src/eigen_types.hh
index 8eff20ee824802fee2c78246bcc9126a5fc48c47..773998c0c393179e37f0c9c89ce1804905217f53 100644
--- a/core/src/eigen_types.hh
+++ b/core/src/eigen_types.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_EIGEN_TYPES_HH
#define PROMOD3_EIGEN_TYPES_HH
diff --git a/core/src/enumerator.hh b/core/src/enumerator.hh
index 3fa65d54ca902e04f3ceee273fd0f98f2c4839ea..1eb1790e1e8124611c948c38757e2677b2ce9a5f 100644
--- a/core/src/enumerator.hh
+++ b/core/src/enumerator.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_CORE_ENUMERATOR_HH
#define PM3_CORE_ENUMERATOR_HH
diff --git a/core/src/export_helper.hh b/core/src/export_helper.hh
index 5f6bd0c89dd10beb34e6566d289348a19e39952d..9f86b080d6a26ed49e00f5024b41b2aa2a72c288 100644
--- a/core/src/export_helper.hh
+++ b/core/src/export_helper.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines helpers to convert STL objects to python objects
#ifndef PROMOD3_EXPORT_HELPERS_HH
diff --git a/core/src/geom_base.cc b/core/src/geom_base.cc
index 5b956ad31f6eb6513d7ccd9a9b9faeee6e2350b4..de84ef134953f7de798b4c678295cd2396479b23 100644
--- a/core/src/geom_base.cc
+++ b/core/src/geom_base.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <cmath>
#include <cassert>
#include <promod3/core/geom_base.hh>
diff --git a/core/src/geom_base.hh b/core/src/geom_base.hh
index 405907b704f2e4939db62e603d2da9421d61173e..8307a7192f797037943a9fa9d05fab5c85ba3911 100644
--- a/core/src/geom_base.hh
+++ b/core/src/geom_base.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_GEOM_BASE_HH
#define PROMOD3_GEOM_BASE_HH
diff --git a/core/src/geom_stems.cc b/core/src/geom_stems.cc
index b1bf3cf1978f6e43bab68cd05834e96e3614e9d8..2194e1a775ba7615297d9409e2320a2cb2e5544c 100644
--- a/core/src/geom_stems.cc
+++ b/core/src/geom_stems.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/geom_stems.hh>
#include <cmath>
#include <cassert>
diff --git a/core/src/geom_stems.hh b/core/src/geom_stems.hh
index 09069d8a1a3edb867fe1bf68f2aa12064071bc23..fc0128bf8d35f0a0b4cf4c318710870e0d4871b7 100644
--- a/core/src/geom_stems.hh
+++ b/core/src/geom_stems.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_GEOM_STEMS_HH
#define PROMOD3_GEOM_STEMS_HH
diff --git a/core/src/graph.cc b/core/src/graph.cc
index 995a6517eb9705e6099bce090b0636fa86dbd741..90082ccaaec1a7d08db9674088b1ef596b3d6866 100644
--- a/core/src/graph.cc
+++ b/core/src/graph.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/graph.hh>
#include <promod3/core/message.hh>
#include <algorithm>
diff --git a/core/src/graph.hh b/core/src/graph.hh
index 2638e8276cd7dc03e4352d7021b4d7047256217c..7187be85c776c451610ccab47aedbc916fbe168c 100644
--- a/core/src/graph.hh
+++ b/core/src/graph.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_GRAPH_HH
#define PROMOD3_GRAPH_HH
diff --git a/core/src/graph_minimizer.cc b/core/src/graph_minimizer.cc
index e524efc2fb53447967c9c37b2f9fc985072b1b00..0f9bd8fd05d25610376ffa6087b1418ad25fd0ee 100644
--- a/core/src/graph_minimizer.cc
+++ b/core/src/graph_minimizer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <algorithm>
#include <queue>
#include <limits>
diff --git a/core/src/graph_minimizer.hh b/core/src/graph_minimizer.hh
index 410cc21d0eb4664f1b6c8ef70e4b7caf6ec6535b..28e9df7b9324a7d81845d39e321cb843b99f30a6 100644
--- a/core/src/graph_minimizer.hh
+++ b/core/src/graph_minimizer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_GRAPH_MINIMIZER_HH
#define PROMOD3_GRAPH_MINIMIZER_HH
diff --git a/core/src/message.hh b/core/src/message.hh
index f0d4368ed6bba7588f2d1483f38e6d177207f9f6..c652f2bab02703d4edc0635aec78856b54b4bbad 100644
--- a/core/src/message.hh
+++ b/core/src/message.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_MESSAGE_HH
#define PROMOD3_MESSAGE_HH
diff --git a/core/src/portable_binary_data_sink.hh b/core/src/portable_binary_data_sink.hh
index 40e3fdab7809ffd7a6cb824ae4a4525ef4537f78..c3c8c9e93e1013747f0981862882a98ded0124e2 100644
--- a/core/src/portable_binary_data_sink.hh
+++ b/core/src/portable_binary_data_sink.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines a portable binary data sink.
/// This generates files to be read by PortableBinaryDataSink.
/// The interface is compatible with ost-like data sinks.
diff --git a/core/src/portable_binary_data_source.hh b/core/src/portable_binary_data_source.hh
index b97491520197be70645d6c2b796b9c318bd00c17..00d80a50d5c1ea69ce48f68fab080c82d0124e57 100644
--- a/core/src/portable_binary_data_source.hh
+++ b/core/src/portable_binary_data_source.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines a portable binary data source.
/// This works with files dumped by PortableBinaryDataSink.
/// The interface is compatible with ost-like data sources.
diff --git a/core/src/portable_binary_serializer.hh b/core/src/portable_binary_serializer.hh
index 8c5a570cd784c210784b6a91892c411c6157dd49..4a5b52efab05161da16c1bf30c66828e81eb4f5a 100644
--- a/core/src/portable_binary_serializer.hh
+++ b/core/src/portable_binary_serializer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Define everything needed for portable I/O.
/// Here we include any custom Serialize function.
/// Main classes are PortableBinaryDataSink and PortableBinaryDataSource.
diff --git a/core/src/runtime_profiling.hh b/core/src/runtime_profiling.hh
index 379b6e40c5febcf5c0c003d327f5c5b5b51f36ee..343666befacf48c27eb5b1b7f27e300aea93864c 100644
--- a/core/src/runtime_profiling.hh
+++ b/core/src/runtime_profiling.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines functionality for runtime profiling.
/// All profiling can be completely turned off by setting
/// PM3_RUNTIME_PROFILING_LEVEL=0
diff --git a/core/src/superpose.cc b/core/src/superpose.cc
index 717b9de6b7fb06794fa42412ce072d3d69c93a9a..0e06a6e6994588fd83c925f26cabe64b05d5dc4f 100644
--- a/core/src/superpose.cc
+++ b/core/src/superpose.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/superpose.hh>
#include <Eigen/SVD>
#include <Eigen/Geometry>
diff --git a/core/src/superpose.hh b/core/src/superpose.hh
index 8a3fdcec3b0c4d4e8e3ce13c7bdce1ef286304d1..2fd82314a9fbeb3ab2510ba478963793f4490dfd 100644
--- a/core/src/superpose.hh
+++ b/core/src/superpose.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SUPERPOSE_HH
#define PROMOD3_SUPERPOSE_HH
diff --git a/core/src/tetrahedral_polytope.cc b/core/src/tetrahedral_polytope.cc
index 576ab1fd82093f5c4c0c8cc6a18f8c987577796d..40bf460479765da8c31d5451a3b14f28fea49154 100644
--- a/core/src/tetrahedral_polytope.cc
+++ b/core/src/tetrahedral_polytope.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/tetrahedral_polytope.hh>
#include <limits>
diff --git a/core/src/tetrahedral_polytope.hh b/core/src/tetrahedral_polytope.hh
index 3a2863b2854aaca9f2eee184c5fa9a8260d3125e..31c88a77d99719ddd68e1da69d51dc0201ed9275 100644
--- a/core/src/tetrahedral_polytope.hh
+++ b/core/src/tetrahedral_polytope.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_CORE_TETRAHEDRAL_POLYTOPE_HH
#define PROMOD3_CORE_TETRAHEDRAL_POLYTOPE_HH
diff --git a/core/src/tree.cc b/core/src/tree.cc
index 4bf941d486b4583a2d6b9ea8cc8e22bbad364236..8e32afb18e0f80d14e1337b544015efe29a7b464 100644
--- a/core/src/tree.cc
+++ b/core/src/tree.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/tree.hh>
#include <promod3/core/message.hh>
#include <stack>
diff --git a/core/src/tree.hh b/core/src/tree.hh
index c8a1628c78cfeb609a7fd3063bf6ff86476fa9d9..dd45dc327e907021c6176a14e8fc09bced8fe2b2 100644
--- a/core/src/tree.hh
+++ b/core/src/tree.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_TREE_HH
#define PROMOD3_TREE_HH
diff --git a/core/tests/CMakeLists.txt b/core/tests/CMakeLists.txt
index b7eebec0e86b04939ab02ac83281e74ac17ab1ef..829a9961c6ff7488d0b5ea3761f75bbe7b40987a 100644
--- a/core/tests/CMakeLists.txt
+++ b/core/tests/CMakeLists.txt
@@ -23,6 +23,10 @@ set(CORE_TEST_DATA
data/aln_tpl/5d52-1_cut.pdb
data/aln_tpl/5d52-1_cut_A.fasta
data/aln_tpl/5d52-1_cut_B.fasta
+ data/aln_tpl/1crn.hhm
+ data/aln_tpl/1crn_corrupted.hhm
+ data/aln_tpl/5ua4_B.fasta
+ data/aln_tpl/5ua4_B.hhm
data/fasta/alignment.fas
data/fasta/1ake.fas
data/fasta/1ake_1.fas
@@ -31,6 +35,7 @@ set(CORE_TEST_DATA
data/fasta/1ake.fas.gz
data/fasta/1ake_nel.fas
data/fasta/1ake_sw.fas
+
)
promod3_unittest(MODULE core
diff --git a/core/tests/data/aln_tpl/1crn.hhm b/core/tests/data/aln_tpl/1crn.hhm
new file mode 100644
index 0000000000000000000000000000000000000000..eb35d07151bbc66ea6f979f155f3f1fef9cf2d40
--- /dev/null
+++ b/core/tests/data/aln_tpl/1crn.hhm
@@ -0,0 +1,180 @@
+HHsearch 1.5
+NAME c6a0deb50c4f69619d193f0fde0517c2
+FAM
+FILE seq01
+COM /scicore/soft/apps/HH-suite/2.0.16-goolf-1.4.10/bin/hhmake -i /scratch/14369431.1.short.q/tmpqOaEJI/seq01.a3m -o /scratch/14369431.1.short.q/tmpqOaEJI/seq01.hhm
+DATE Mon Mar 7 14:19:45 2016
+LENG 46 match states, 46 columns in multiple alignment
+FILT 55 out of 57 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCHHHHHHHHHCCCCCCCHHHHHHHCCCEEECCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9877783554421111168998455542048366208989999999
+>Consensus
+xsCCpstxaRnxYnxCrxxgxsxxxCaxxsgCkixsgxxCPxxyxx
+>c6a0deb50c4f69619d193f0fde0517c2
+TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN
+>gi|115605364|gb|ABJ15789.1| putative thionin precursor [Polygonum sibiricum]
+-SCCQTTTARNIYNSCRLAGGSRERCASLSGCKHVTGNTCSPGWEK
+>gi|4007745|emb|CAA65316.1| purothionin [Secale cereale]
+-SCCKSTLGRNCYNLCRTRGAQK-LCANFCRCKLISSTSCPKEFPK
+>gi|17381172|gb|AAL36398.1| putative thionin protein [Arabidopsis thaliana]gi|62320644|dbj|BAD95310.1| putative thionin [Arabidopsis thaliana]
+-TCCPSQSTRKGFEDCISEGNLQILCSAESGCRDTYVGYCPSGFPY
+>gi|802170|gb|AAB33011.1| crambin precursor=thionin variant Thi2Ca12 [Crambe abyssinica, seeds, Peptide Partial, 135 aa]
+-SCCPTKSARNTFDVCRLTGTSMGLCAAISECKILSVTKCPSNLPY
+>gi|21553588|gb|AAM62681.1| thionin Thi2.2 [Arabidopsis thaliana]
+-ICCPTKDDRSVYFVCMLSVSSQFYCLLKSKCKNTSQTICPPGYTN
+>gi|15218931|ref|NP_176784.1| thionin [Arabidopsis thaliana]gi|44888531|sp|Q9C8D6.1|THN24_ARATH RecName: Full=Probable thionin-2.4; Contains: RecName: Full=Probable thionin-2.4; Contains: RecName: Full=Acidic protein; Flags: Precursorgi|12322605|gb|AAG51299.1|AC026480_6 thionin, putative [Arabidopsis thaliana]gi|14190505|gb|AAK55733.1|AF380652_1 At1g66100/F15E12_20 [Arabidopsis thaliana]gi|15809774|gb|AAL06815.1| At1g66100/F15E12_20 [Arabidopsis thaliana]gi|332196341|gb|AEE34462.1| thionin [Arabidopsis thaliana]
+-ICCPSIQARTFYNACLFAVGSPSSCIRNSSCLDISESTCPRGYTN
+>gi|1729954|sp|Q05806.1|THN5_WHEAT RecName: Full=Type-5 thionin; Contains: RecName: Full=Type-5 thionin; AltName: Full=Type V thionin; Contains: RecName: Full=Acidic protein; Flags: Precursorgi|21885|emb|CAA43844.1| wheat type V thionin [Triticum aestivum]gi|21887|emb|CAA43845.1| wheat type V thionin [Triticum aestivum]
+-DCGANPFKVACFNSCLLGPSTVFQCADFCACRLPAG---------
+>gi|120564556|gb|ABM30200.1| thionin [Brassica juncea]
+-SCCPSTAARWAYYLCTNSWPLTPLCISHTGC-IESETTCPPGYPY
+>gi|545031|gb|AAB29760.1| thionin precursor {clone Thi1Va1} [Viscum album=mistletoe, Peptide, 115 aa]
+-ICCRAPAGKKCYNLCTA-lLSSE-TCANTCYCKDVSGETCPAD---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+T 1 * * * * * * * * * * * * * * * * 0 * * * 1
+ 0 * * * * * * 1000 0 0
+
+T 2 * * 4186 * * 5283 * 2677 * 5264 * * * * * 833 3153 3986 * * 2
+ 0 * * * * * * 3941 0 0
+
+C 3 * 0 * * * * * * * * * * * * * * * * * * 3
+ 0 * * * * * * 3941 0 0
+
+C 4 * 122 * * 5259 4186 * * * * * * * * * * * * * * 4
+ 0 * * * * * * 3941 0 0
+
+P 5 4186 * * * * * * * 3250 * * * 549 5753 2856 * * * * * 5
+ 0 * * * * * * 3941 0 0
+
+S 6 5271 * 4429 * * * * * * * * 2329 * * 5941 866 2612 * * * 6
+ 0 * * * * * * 3941 0 0
+
+I 7 * * 5440 4820 * * * 3810 4212 * 5935 4983 3272 3386 4684 5283 1068 5174 * * 7
+ 0 * * * * * * 3941 0 0
+
+V 8 2614 * 4805 * 4186 * * 3036 * 3320 * * * 4094 * 2750 1838 5660 5873 * 8
+ 0 * * * * * * 3941 0 0
+
+A 9 646 * 4264 * * 2749 * * 4186 * * * * * * 3803 4903 * * * 9
+ 0 * * * * * * 3941 0 0
+
+R 10 * * * * * * * 5975 4265 * * * * * 189 * * 4186 * * 10
+ 0 * * * * * * 3941 0 0
+
+S 11 4186 * * 3803 * * * 5935 3608 * * 836 * * * 2953 5214 * 4935 5259 11
+ 0 * * * * * * 3941 0 0
+
+N 12 4935 1544 * 4787 5214 3942 * 2698 5264 * 4684 3736 * 5164 5174 * 3934 3625 * * 12
+ 0 * * * * * * 3941 0 0
+
+F 13 * * * * 2199 * * * * * * * * * * * * * * 354 13
+ 0 * * * * * * 3941 0 0
+
+N 14 * * 4222 3844 4805 * * * * 5264 * 510 * * * 4983 5283 5464 * 4935 14
+ 0 * * * * * * 3941 0 0
+
+V 15 2800 * 3844 * * * * 5271 * 2403 5174 * * * * 2663 3074 1902 * * 15
+ 0 * * * * * * 3941 0 0
+
+C 16 * 0 * * * * * * * * * * * * * * * * * * 16
+ 0 * * * * * * 3941 0 0
+
+R 17 * * * * * * 6200 2932 * 3611 4805 * * * 558 * 4093 * * * 17
+ 0 * * * * * * 3941 0 0
+
+L 18 3969 * * * 2171 * * 3956 * 1318 5174 4935 * * 5264 3115 6073 4979 * * 18
+ 38 * 5271 * * * * 3941 0 0
+
+P 19 3003 * * 4863 * 3441 * * * 5901 * * 2369 4784 2418 3812 2907 3735 * 4814 19
+ 41 * 5155 0 * 0 * 3898 1025 1025
+
+G 20 * * * * 4949 454 6123 * * 4542 * * 3604 * * * * 3948 4909 * 20
+ 72 * 4354 * * * 0 3901 0 1033
+
+T 21 2209 5224 * * * 2278 * * * * * 3752 4867 * * 2344 2028 * * * 21
+ 39 5224 * 0 * 669 1430 3845 1023 1191
+
+P 22 5624 * * * * * * 5870 * 3138 * * 1935 4054 * 1200 3439 * * * 22
+ 0 * * * * 0 * 3903 0 1033
+
+E 23 5952 6850 * 3099 * * 4802 5475 3316 * 4903 * 4232 2872 1627 5880 4176 4193 * 5287 23
+ 184 * 3059 * * * * 3943 0 0
+
+A 24 4442 * 3710 2779 2989 4157 * 4702 * * * * 1565 * 5707 4382 3234 * * * 24
+ 28 5707 * 0 * 0 * 3843 1000 1329
+
+I 25 4358 * * * 6658 * 5279 3244 4611 2579 * 5958 * 4193 3566 3476 2812 2484 * 4816 25
+ 0 * * * * * * 3943 0 0
+
+C 26 * 31 * * * * * * * * * * * * * 5573 * * * * 26
+ 0 * * * * * * 3943 0 0
+
+A 27 560 6231 * * * 4233 * 3636 * 4029 4985 * * * * 3609 * * * * 27
+ 0 * * * * * * 3943 0 0
+
+T 28 2460 * 3819 * * 4273 * 5850 2738 4816 * 3203 * 4985 3239 2607 3596 * * * 28
+ 0 * * * * * * 3943 0 0
+
+Y 29 4929 * 5658 4919 2879 4802 4950 3737 4252 1699 5444 5287 5995 * 5262 * 3899 3734 * 4566 29
+ 0 * * * * * * 3943 0 0
+
+T 30 3911 1554 * * * * * * * * * * * * * 1040 3227 * * * 30
+ 0 * * * * * * 3943 0 0
+
+G 31 4193 * 3877 5850 * 811 * * 4816 * * * * * 2699 4815 4659 * * 5301 31
+ 0 * * * * * * 3943 0 0
+
+C 32 * 0 * * * * * * * * * * * * * * * * * * 32
+ 47 * 4950 * * * * 3943 0 0
+
+I 33 * * * 4672 * * * 2865 809 3414 * * * 4933 3475 * * 4789 * * 33
+ 0 * * * * 0 * 3904 0 1044
+
+I 34 * * 3573 4802 * * 3933 921 * 2779 * 3898 * * 4839 * 5475 5952 * * 34
+ 0 * * * * * * 3943 0 0
+
+I 35 * * 5287 4950 4358 * * 1603 * 3869 * * 4193 6130 * 3498 3006 2227 * * 35
+ 46 * 4985 * * * * 3943 0 0
+
+P 36 4173 * 2874 * 5250 * * 5139 * 4792 * * 4633 4645 5394 1055 4050 * * 3805 36
+ 201 * 2941 * * * 0 3881 0 1045
+
+G 37 5480 * 5485 3849 * 869 * * * * * * * 4548 5245 3819 4686 2648 * * 37
+ 22 * 6064 * * 0 * 3796 0 1453
+
+A 38 4564 * 4944 5167 * 1910 * * 4653 4470 * 3572 4946 * 5111 2927 1892 * * * 38
+ 0 * * * * 0 * 3775 0 1000
+
+T 39 * 4660 * 5366 4744 6406 * 3919 2193 * * 4099 * 5382 5207 3976 1348 * * 4782 39
+ 0 * * * * * * 3764 0 0
+
+C 40 * 58 * * * * * * 4660 * * * * * * * * * * * 40
+ 0 * * * * * * 3764 0 0
+
+P 41 * * 4306 * * * * * 3731 * * 6351 322 4587 * 5643 * * * * 41
+ 0 * * * * * * 3764 0 0
+
+G 42 4398 * 6402 * * 4592 * * 4079 * * 4374 1200 * 3395 2109 5063 * * * 42
+ 0 * * * * * * 3764 0 0
+
+D 43 * * 2024 6014 4769 1231 4660 * * * * 4386 3096 4744 * 4862 * * * * 43
+ 0 * * * * * * 3764 0 0
+
+Y 44 * * * * 2991 * 4830 * * 3705 * * * * * * * * 2806 691 44
+ 0 * * * * * * 3718 0 0
+
+A 45 4566 * 3231 5056 * * * 3467 * * * 5405 1034 * 5100 6384 2896 4532 * * 45
+ 35 5366 * 4087 87 * * 3718 1002 0
+
+N 46 * * 4370 * * * 2588 * 1723 * * 2200 * * 5953 * * * * 2008 46
+ 0 * * 0 * * * 3699 0 0
+
+//
diff --git a/core/tests/data/aln_tpl/1crn_corrupted.hhm b/core/tests/data/aln_tpl/1crn_corrupted.hhm
new file mode 100644
index 0000000000000000000000000000000000000000..01765421ff452e8094d103970ff78277a80e1a5e
--- /dev/null
+++ b/core/tests/data/aln_tpl/1crn_corrupted.hhm
@@ -0,0 +1,185 @@
+#######################################################################
+# THIS FILE IS CORRUPTED!!!!!!!!! #
+# First three amino acids do not have the right number of frequencies #
+#######################################################################
+
+HHsearch 1.5
+NAME c6a0deb50c4f69619d193f0fde0517c2
+FAM
+FILE seq01
+COM /scicore/soft/apps/HH-suite/2.0.16-goolf-1.4.10/bin/hhmake -i /scratch/14369431.1.short.q/tmpqOaEJI/seq01.a3m -o /scratch/14369431.1.short.q/tmpqOaEJI/seq01.hhm
+DATE Mon Mar 7 14:19:45 2016
+LENG 46 match states, 46 columns in multiple alignment
+FILT 55 out of 57 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCHHHHHHHHHCCCCCCCHHHHHHHCCCEEECCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9877783554421111168998455542048366208989999999
+>Consensus
+xsCCpstxaRnxYnxCrxxgxsxxxCaxxsgCkixsgxxCPxxyxx
+>c6a0deb50c4f69619d193f0fde0517c2
+TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN
+>gi|115605364|gb|ABJ15789.1| putative thionin precursor [Polygonum sibiricum]
+-SCCQTTTARNIYNSCRLAGGSRERCASLSGCKHVTGNTCSPGWEK
+>gi|4007745|emb|CAA65316.1| purothionin [Secale cereale]
+-SCCKSTLGRNCYNLCRTRGAQK-LCANFCRCKLISSTSCPKEFPK
+>gi|17381172|gb|AAL36398.1| putative thionin protein [Arabidopsis thaliana]gi|62320644|dbj|BAD95310.1| putative thionin [Arabidopsis thaliana]
+-TCCPSQSTRKGFEDCISEGNLQILCSAESGCRDTYVGYCPSGFPY
+>gi|802170|gb|AAB33011.1| crambin precursor=thionin variant Thi2Ca12 [Crambe abyssinica, seeds, Peptide Partial, 135 aa]
+-SCCPTKSARNTFDVCRLTGTSMGLCAAISECKILSVTKCPSNLPY
+>gi|21553588|gb|AAM62681.1| thionin Thi2.2 [Arabidopsis thaliana]
+-ICCPTKDDRSVYFVCMLSVSSQFYCLLKSKCKNTSQTICPPGYTN
+>gi|15218931|ref|NP_176784.1| thionin [Arabidopsis thaliana]gi|44888531|sp|Q9C8D6.1|THN24_ARATH RecName: Full=Probable thionin-2.4; Contains: RecName: Full=Probable thionin-2.4; Contains: RecName: Full=Acidic protein; Flags: Precursorgi|12322605|gb|AAG51299.1|AC026480_6 thionin, putative [Arabidopsis thaliana]gi|14190505|gb|AAK55733.1|AF380652_1 At1g66100/F15E12_20 [Arabidopsis thaliana]gi|15809774|gb|AAL06815.1| At1g66100/F15E12_20 [Arabidopsis thaliana]gi|332196341|gb|AEE34462.1| thionin [Arabidopsis thaliana]
+-ICCPSIQARTFYNACLFAVGSPSSCIRNSSCLDISESTCPRGYTN
+>gi|1729954|sp|Q05806.1|THN5_WHEAT RecName: Full=Type-5 thionin; Contains: RecName: Full=Type-5 thionin; AltName: Full=Type V thionin; Contains: RecName: Full=Acidic protein; Flags: Precursorgi|21885|emb|CAA43844.1| wheat type V thionin [Triticum aestivum]gi|21887|emb|CAA43845.1| wheat type V thionin [Triticum aestivum]
+-DCGANPFKVACFNSCLLGPSTVFQCADFCACRLPAG---------
+>gi|120564556|gb|ABM30200.1| thionin [Brassica juncea]
+-SCCPSTAARWAYYLCTNSWPLTPLCISHTGC-IESETTCPPGYPY
+>gi|545031|gb|AAB29760.1| thionin precursor {clone Thi1Va1} [Viscum album=mistletoe, Peptide, 115 aa]
+-ICCRAPAGKKCYNLCTA-lLSSE-TCANTCYCKDVSGETCPAD---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+T 1 * * * * * * * * * * * * * * * * 0 * *
+ 0 * * * * * * 1000 0 0
+
+T 2 * * 4186 * * 5283 * 2677 * 5264 * * * * * 833 3153 3986 *
+ 0 * * * * * * 3941 0 0
+
+C 3 * 0 * * * * * * * * * * * * * * * * *
+ 0 * * * * * * 3941 0 0
+
+C 4 * 122 * * 5259 4186 * * * * * * * * * * * * * * 4
+ 0 * * * * * * 3941 0 0
+
+P 5 4186 * * * * * * * 3250 * * * 549 5753 2856 * * * * * 5
+ 0 * * * * * * 3941 0 0
+
+S 6 5271 * 4429 * * * * * * * * 2329 * * 5941 866 2612 * * * 6
+ 0 * * * * * * 3941 0 0
+
+I 7 * * 5440 4820 * * * 3810 4212 * 5935 4983 3272 3386 4684 5283 1068 5174 * * 7
+ 0 * * * * * * 3941 0 0
+
+V 8 2614 * 4805 * 4186 * * 3036 * 3320 * * * 4094 * 2750 1838 5660 5873 * 8
+ 0 * * * * * * 3941 0 0
+
+A 9 646 * 4264 * * 2749 * * 4186 * * * * * * 3803 4903 * * * 9
+ 0 * * * * * * 3941 0 0
+
+R 10 * * * * * * * 5975 4265 * * * * * 189 * * 4186 * * 10
+ 0 * * * * * * 3941 0 0
+
+S 11 4186 * * 3803 * * * 5935 3608 * * 836 * * * 2953 5214 * 4935 5259 11
+ 0 * * * * * * 3941 0 0
+
+N 12 4935 1544 * 4787 5214 3942 * 2698 5264 * 4684 3736 * 5164 5174 * 3934 3625 * * 12
+ 0 * * * * * * 3941 0 0
+
+F 13 * * * * 2199 * * * * * * * * * * * * * * 354 13
+ 0 * * * * * * 3941 0 0
+
+N 14 * * 4222 3844 4805 * * * * 5264 * 510 * * * 4983 5283 5464 * 4935 14
+ 0 * * * * * * 3941 0 0
+
+V 15 2800 * 3844 * * * * 5271 * 2403 5174 * * * * 2663 3074 1902 * * 15
+ 0 * * * * * * 3941 0 0
+
+C 16 * 0 * * * * * * * * * * * * * * * * * * 16
+ 0 * * * * * * 3941 0 0
+
+R 17 * * * * * * 6200 2932 * 3611 4805 * * * 558 * 4093 * * * 17
+ 0 * * * * * * 3941 0 0
+
+L 18 3969 * * * 2171 * * 3956 * 1318 5174 4935 * * 5264 3115 6073 4979 * * 18
+ 38 * 5271 * * * * 3941 0 0
+
+P 19 3003 * * 4863 * 3441 * * * 5901 * * 2369 4784 2418 3812 2907 3735 * 4814 19
+ 41 * 5155 0 * 0 * 3898 1025 1025
+
+G 20 * * * * 4949 454 6123 * * 4542 * * 3604 * * * * 3948 4909 * 20
+ 72 * 4354 * * * 0 3901 0 1033
+
+T 21 2209 5224 * * * 2278 * * * * * 3752 4867 * * 2344 2028 * * * 21
+ 39 5224 * 0 * 669 1430 3845 1023 1191
+
+P 22 5624 * * * * * * 5870 * 3138 * * 1935 4054 * 1200 3439 * * * 22
+ 0 * * * * 0 * 3903 0 1033
+
+E 23 5952 6850 * 3099 * * 4802 5475 3316 * 4903 * 4232 2872 1627 5880 4176 4193 * 5287 23
+ 184 * 3059 * * * * 3943 0 0
+
+A 24 4442 * 3710 2779 2989 4157 * 4702 * * * * 1565 * 5707 4382 3234 * * * 24
+ 28 5707 * 0 * 0 * 3843 1000 1329
+
+I 25 4358 * * * 6658 * 5279 3244 4611 2579 * 5958 * 4193 3566 3476 2812 2484 * 4816 25
+ 0 * * * * * * 3943 0 0
+
+C 26 * 31 * * * * * * * * * * * * * 5573 * * * * 26
+ 0 * * * * * * 3943 0 0
+
+A 27 560 6231 * * * 4233 * 3636 * 4029 4985 * * * * 3609 * * * * 27
+ 0 * * * * * * 3943 0 0
+
+T 28 2460 * 3819 * * 4273 * 5850 2738 4816 * 3203 * 4985 3239 2607 3596 * * * 28
+ 0 * * * * * * 3943 0 0
+
+Y 29 4929 * 5658 4919 2879 4802 4950 3737 4252 1699 5444 5287 5995 * 5262 * 3899 3734 * 4566 29
+ 0 * * * * * * 3943 0 0
+
+T 30 3911 1554 * * * * * * * * * * * * * 1040 3227 * * * 30
+ 0 * * * * * * 3943 0 0
+
+G 31 4193 * 3877 5850 * 811 * * 4816 * * * * * 2699 4815 4659 * * 5301 31
+ 0 * * * * * * 3943 0 0
+
+C 32 * 0 * * * * * * * * * * * * * * * * * * 32
+ 47 * 4950 * * * * 3943 0 0
+
+I 33 * * * 4672 * * * 2865 809 3414 * * * 4933 3475 * * 4789 * * 33
+ 0 * * * * 0 * 3904 0 1044
+
+I 34 * * 3573 4802 * * 3933 921 * 2779 * 3898 * * 4839 * 5475 5952 * * 34
+ 0 * * * * * * 3943 0 0
+
+I 35 * * 5287 4950 4358 * * 1603 * 3869 * * 4193 6130 * 3498 3006 2227 * * 35
+ 46 * 4985 * * * * 3943 0 0
+
+P 36 4173 * 2874 * 5250 * * 5139 * 4792 * * 4633 4645 5394 1055 4050 * * 3805 36
+ 201 * 2941 * * * 0 3881 0 1045
+
+G 37 5480 * 5485 3849 * 869 * * * * * * * 4548 5245 3819 4686 2648 * * 37
+ 22 * 6064 * * 0 * 3796 0 1453
+
+A 38 4564 * 4944 5167 * 1910 * * 4653 4470 * 3572 4946 * 5111 2927 1892 * * * 38
+ 0 * * * * 0 * 3775 0 1000
+
+T 39 * 4660 * 5366 4744 6406 * 3919 2193 * * 4099 * 5382 5207 3976 1348 * * 4782 39
+ 0 * * * * * * 3764 0 0
+
+C 40 * 58 * * * * * * 4660 * * * * * * * * * * * 40
+ 0 * * * * * * 3764 0 0
+
+P 41 * * 4306 * * * * * 3731 * * 6351 322 4587 * 5643 * * * * 41
+ 0 * * * * * * 3764 0 0
+
+G 42 4398 * 6402 * * 4592 * * 4079 * * 4374 1200 * 3395 2109 5063 * * * 42
+ 0 * * * * * * 3764 0 0
+
+D 43 * * 2024 6014 4769 1231 4660 * * * * 4386 3096 4744 * 4862 * * * * 43
+ 0 * * * * * * 3764 0 0
+
+Y 44 * * * * 2991 * 4830 * * 3705 * * * * * * * * 2806 691 44
+ 0 * * * * * * 3718 0 0
+
+A 45 4566 * 3231 5056 * * * 3467 * * * 5405 1034 * 5100 6384 2896 4532 * * 45
+ 35 5366 * 4087 87 * * 3718 1002 0
+
+N 46 * * 4370 * * * 2588 * 1723 * * 2200 * * 5953 * * * * 2008 46
+ 0 * * 0 * * * 3699 0 0
+
+//
diff --git a/core/tests/data/aln_tpl/5ua4_B.fasta b/core/tests/data/aln_tpl/5ua4_B.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..92c2692ce0377b23b6f6fc861ee165c3e39eb344
--- /dev/null
+++ b/core/tests/data/aln_tpl/5ua4_B.fasta
@@ -0,0 +1,4 @@
+>target
+SESQEAVIRDIARHLARIGDRMEYGIRPGLVDSL
+>pdb_id=4bd2, chain=B, assembly_id=1, offset=0 atoms
+SESQEDIIRNIARHLAQVGDSMDRSIPPGL----
diff --git a/core/tests/data/aln_tpl/5ua4_B.hhm b/core/tests/data/aln_tpl/5ua4_B.hhm
new file mode 100644
index 0000000000000000000000000000000000000000..a038b72184271d8c02f22a4f5f40cb28efa2fbe9
--- /dev/null
+++ b/core/tests/data/aln_tpl/5ua4_B.hhm
@@ -0,0 +1,144 @@
+HHsearch 1.5
+NAME target
+FAM
+FILE query_hhblits
+COM /scicore/soft/apps/HH-suite/2.0.16-goolf-1.4.10-Boost-1.53.0/bin/hhmake -i <101 characters> -o <101 characters>
+DATE Sat Dec 31 05:49:23 2016
+LENG 34 match states, 34 columns in multiple alignment
+FILT 11 out of 13 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 2.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCC
+>ss_conf PSIPRED confidence values
+9159999999999999975443036780111159
+>Consensus
+SEsQEeiIxxiArxLAqiGDxmdxsIxPxlvxxL
+>target
+SESQEAVIRDIARHLARIGDRMEYGIRPGLVDSL
+>gi|12083631|ref|NP_073175.1| BH3-interacting domain death agonist [Rattus norvegicus]gi|88909592|sp|Q9JLT6.2|BID_RAT RecName: Full=BH3-interacting domain death agonist; AltName: Full=p22 BID; Short=BID; Contains: RecName: Full=BH3-interacting domain death agonist p15; AltName: Full=p15 BID; Contains: RecName: Full=BH3-interacting domain death agonist p13; AltName: Full=p13 BID; Contains: RecName: Full=BH3-interacting domain death agonist p11; AltName: Full=p11 BIDgi|8050830|gb|AAF71759.1|AF259503_1 BID protein [Rattus norvegicus]gi|149049571|gb|EDM02025.1| BH3 interacting domain death agonist [Rattus norvegicus]gi|157041211|dbj|BAF79674.1| desmocollin type 4 [Rattus norvegicus]
+SESQDEVIHNIARHLAQAGDELDHSIQPTLVRQL
+>gi|115495761|ref|NP_001068914.1| BH3 interacting domain death agonist [Bos taurus]gi|109658413|gb|AAI18360.1| BH3 interacting domain death agonist [Bos taurus]gi|296486995|gb|DAA29108.1| BH3 interacting domain death agonist [Bos taurus]
+SERQEEAVREVARQLAQIGDRLEGSIHPGMVAGL
+>gi|281341033|gb|EFB16617.1| hypothetical protein PANDA_016465 [Ailuropoda melanoleuca]
+SQGQEEIIQDIARQLAQIGDDMDHSIHPGLMNNL
+>gi|307335680|gb|ADN43410.1| BH3 interacting domain death agonist [Lemur catta]
+SESEEDLIQTLARQLAQIGDSMERSIPPRLVDHL
+>gi|307335678|gb|ADN43409.1| BH3 interacting domain death agonist [Felis catus]
+SESQEEIIQDIARQLAQIGDRMDHSIHPRVVNNL
+>gi|307335682|gb|ADN43411.1| BH3 interacting domain death agonist [Saimiri boliviensis]
+SESQEDIIRNIARQLAQVGDSMDRSIPPGLVNRL
+>gi|291412643|ref|XP_002722593.1| PREDICTED: BH3 interacting domain death agonist-like [Oryctolagus cuniculus]
+SESQEEVIRNIARRLAQIGDRMDHHIQPELLNNL
+>gi|296191314|ref|XP_002743575.1| PREDICTED: hypothetical protein LOC100403496 [Callithrix jacchus]
+SESQEDVIRSIARHLAHIGDSMDRSIPLDLVDRL
+>gi|334348150|ref|XP_001373913.2| PREDICTED: envelope glycoprotein-like [Monodelphis domestica]
+SESQEEIIQRIAMQLAKIGDNIENSIQPRVVDEL
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 * * * * * * * * * * * * * * * 0 * * * * 1
+ 0 * * * * * * 1973 0 0
+
+E 2 * * * 143 * * * * * * * * * 3405 * * * * * * 2
+ 0 * * * * * * 1973 0 0
+
+S 3 * * * * * 3405 * * * * * * * * 2994 358 * * * * 3
+ 0 * * * * * * 1973 0 0
+
+Q 4 * * * 3344 * * * * * * * * * 150 * * * * * * 4
+ 0 * * * * * * 1973 0 0
+
+E 5 * * 3425 141 * * * * * * * * * * * * * * * * 5
+ 0 * * * * * * 1973 0 0
+
+A 6 3391 * 1939 635 * * * * * * * * * * * * * * * * 6
+ 0 * * * * * * 1973 0 0
+
+V 7 2994 * * * * * * 1285 * 3344 * * * * * * * 1452 * * 7
+ 0 * * * * * * 1973 0 0
+
+I 8 * * * * * * * 194 * * * * * * * * * 2994 * * 8
+ 0 * * * * * * 1973 0 0
+
+R 9 * * * * * * 2586 * * * * * * 1457 1092 * * * * * 9
+ 0 * * * * * * 1973 0 0
+
+D 10 * * 1981 2994 * * * * * * * 1628 * * 3212 3454 3344 * * * 10
+ 0 * * * * * * 1973 0 0
+
+I 11 * * * * * * * 366 * 3344 * * * * * * * 2994 * * 11
+ 0 * * * * * * 1973 0 0
+
+A 12 0 * * * * * * * * * * * * * * * * * * * 12
+ 0 * * * * * * 1973 0 0
+
+R 13 * * * * * * * * * * 3212 * * * 165 * * * * * 13
+ 0 * * * * * * 1973 0 0
+
+H 14 * * * * * * 1502 * * * * * * 834 3540 * * * * * 14
+ 0 * * * * * * 1973 0 0
+
+L 15 * * * * * * * * * 0 * * * * * * * * * * 15
+ 0 * * * * * * 1973 0 0
+
+A 16 0 * * * * * * * * * * * * * * * * * * * 16
+ 0 * * * * * * 1973 0 0
+
+R 17 * * * * * * 3454 * 3212 * * * * 503 3391 * * * * * 17
+ 0 * * * * * * 1973 0 0
+
+I 18 3425 * * * * * * 259 * * * * * * * * * 3816 * * 18
+ 0 * * * * * * 1973 0 0
+
+G 19 * * * * * 0 * * * * * * * * * * * * * * 19
+ 0 * * * * * * 1973 0 0
+
+D 20 * * 0 * * * * * * * * * * * * * * * * * 20
+ 0 * * * * * * 1973 0 0
+
+R 21 * * 3405 2586 * * * * * * * 3212 * * 1433 1939 * * * * 21
+ 0 * * * * * * 1973 0 0
+
+M 22 * * * * * * * 3212 * 2194 570 * * * * * * * * * 22
+ 0 * * * * * * 1973 0 0
+
+E 23 * * 804 1227 * * * * * * * * * * * * * * * * 23
+ 0 * * * * * * 1973 0 0
+
+Y 24 * * * * * 2994 1285 * * * * 3212 * * 1939 * * * * 3391 24
+ 0 * * * * * * 1973 0 0
+
+G 25 * * * * * 3391 3540 * * * * 3766 * * * 424 * * * * 25
+ 0 * * * * * * 1973 0 0
+
+I 26 * * * * * * * 0 * * * * * * * * * * * * 26
+ 0 * * * * * * 1973 0 0
+
+R 27 * * * * * * 1819 * * * * * 1939 1472 3391 * * * * * 27
+ 0 * * * * * * 1973 0 0
+
+P 28 * * * * * * * * * 3454 * * 138 * * * * * * * 28
+ 0 * * * * * * 1973 0 0
+
+G 29 * * 3454 3540 * 1372 * * * * * * * * 1889 * 2586 * * * 29
+ 0 * * * * * * 1973 0 0
+
+L 30 * * * * * * * * * 508 2994 * * * * * * 2544 * * 30
+ 0 * * * * * * 1973 0 0
+
+V 31 * * * * * * * * * 3540 3405 * * * * * * 287 * * 31
+ 0 * * * * * * 1973 0 0
+
+D 32 2994 * 1348 * * * * * * * * 1667 * * 2586 * * * * * 32
+ 0 * * * * * * 1973 0 0
+
+S 33 * * * 3212 * 2994 3344 * * * * 2036 * 2586 2624 3391 * * * * 33
+ 0 * * * * * * 1973 0 0
+
+L 34 * * * * * * * * * 0 * * * * * * * * * * 34
+ 0 * * 0 * * * 1973 0 0
+
+//
diff --git a/core/tests/test_check_io.cc b/core/tests/test_check_io.cc
index 742694b3df2ccf4d57b840f408f3aca287d54b04..87a951d780c0ed7850e659f39ff0f9729bdc93c7 100644
--- a/core/tests/test_check_io.cc
+++ b/core/tests/test_check_io.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/check_io.hh>
#include <promod3/core/portable_binary_serializer.hh>
#define BOOST_TEST_DYN_LINK
diff --git a/core/tests/test_graph_minimizer.cc b/core/tests/test_graph_minimizer.cc
index 7a52ae53b6e1cc49eab7cab236c3a9b304c9b589..c5737eb86718c4856f35e8c3d72e870c3952c8fd 100644
--- a/core/tests/test_graph_minimizer.cc
+++ b/core/tests/test_graph_minimizer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/eigen_types.hh>
#include <promod3/core/graph_minimizer.hh>
#define BOOST_TEST_DYN_LINK
diff --git a/core/tests/test_helper.py b/core/tests/test_helper.py
index 9005334a502988f194c650fa776c416ebf2060b7..eb82be1d97daed11716f60332cf080886099a1f1 100644
--- a/core/tests/test_helper.py
+++ b/core/tests/test_helper.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import unittest
import ost
from promod3.core import helper
diff --git a/core/tests/test_pm3argparse.py b/core/tests/test_pm3argparse.py
index f7e9ff7bce47a59a17d5bd68220c4cf5e6e041c6..a9626bf498adda61f58388636cfbdbd74fd08430 100644
--- a/core/tests/test_pm3argparse.py
+++ b/core/tests/test_pm3argparse.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Testing our own little argument parser.
"""
@@ -5,10 +21,7 @@ Testing our own little argument parser.
import unittest
import tempfile
import gzip
-try:
- import ujson as json
-except ImportError:
- import json
+import json
import ost
from promod3.core import pm3argparse
@@ -1104,7 +1117,113 @@ class PM3ArgParseTests(unittest.TestCase):
self.assertEqual(len(self.log.messages['ERROR']), 1)
self.assertEqual(self.log.messages['ERROR'],
['Could not find chain with ID tpl (should be '+
- '<FILE>.<CHAIN>) to attach to sequence named tpl'])
+ '<FILE>.<CHAIN>) to attach to sequence named tpl'])
+
+ def testProfileDoesNotExist(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/IDoNotExist.hhm'])
+ self.assertEqual(ecd.exception.code, 51)
+ self.assertEqual(len(self.log.messages['ERROR']), 1)
+
+ def testProfileIsFuckedUp(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/1crn_corrupted.hhm'])
+ self.assertEqual(ecd.exception.code, 52)
+ self.assertEqual(len(self.log.messages['ERROR']), 1)
+
+ def testAdditionalProfile(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm',
+ '-s', 'data/aln_tpl/5ua4_B.hhm'])
+ self.assertEqual(ecd.exception.code, 53)
+ self.assertEqual(len(self.log.messages['ERROR']), 1)
+
+ def testUniqueProfiles(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm',
+ '-s', 'data/aln_tpl/1crn.hhm'])
+ self.assertEqual(ecd.exception.code, 54)
+ self.assertEqual(len(self.log.messages['ERROR']), 1)
+
+ def testAllCovered(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+ with self.assertRaises(SystemExit) as ecd:
+ parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-f', 'data/aln_tpl/5d52-1_cut_A.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm'])
+ self.assertEqual(ecd.exception.code, 55)
+ self.assertEqual(len(self.log.messages['ERROR']), 1)
+
+ def testAllGoodOneChain(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+
+ opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm'])
+
+ self.assertEqual(len(opts.alignments), 1)
+ self.assertEqual(len(opts.profiles), 1)
+ self.assertEqual(opts.alignments[0].GetSequence(0).GetGaplessString(),
+ opts.profiles[0].sequence)
+
+ def testAllGoodHomoOligo(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+
+ opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-f', 'data/aln_tpl/1crn.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm'])
+ self.assertEqual(len(opts.alignments), 2)
+ self.assertEqual(len(opts.profiles), 2)
+ self.assertEqual(opts.alignments[0].GetSequence(0).GetGaplessString(),
+ opts.profiles[0].sequence)
+ self.assertEqual(opts.alignments[1].GetSequence(0).GetGaplessString(),
+ opts.profiles[1].sequence)
+
+ def testAllGoodHeteroOligo(self):
+ parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+ parser.AddAlignment()
+ parser.AddProfile()
+ parser.AssembleParser()
+
+ opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+ '-f', 'data/aln_tpl/5ua4_B.fasta',
+ '-s', 'data/aln_tpl/1crn.hhm',
+ '-s', 'data/aln_tpl/5ua4_B.hhm'])
+ self.assertEqual(len(opts.alignments), 2)
+ self.assertEqual(len(opts.profiles), 2)
+ self.assertEqual(opts.alignments[0].GetSequence(0).GetGaplessString(),
+ opts.profiles[0].sequence)
+ self.assertEqual(opts.alignments[1].GetSequence(0).GetGaplessString(),
+ opts.profiles[1].sequence)
+
# test options: --disable-aln check (for amino acids)
# test options: --disable-input-checks (for all)
diff --git a/core/tests/test_portable_binary.cc b/core/tests/test_portable_binary.cc
index 31102f39f1c5401ed2d9fc3c6b65dd2b0b93ed9c..0cadce21d330ade13fe2a620915712672030a395 100644
--- a/core/tests/test_portable_binary.cc
+++ b/core/tests/test_portable_binary.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/portable_binary_serializer.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
diff --git a/core/tests/test_setcompoundschemlib.py b/core/tests/test_setcompoundschemlib.py
index 8f90d569b4e802974429034b424f675d0233aa07..2da5ead8d841146fb9bcdc57f4dfc5652dde157f 100644
--- a/core/tests/test_setcompoundschemlib.py
+++ b/core/tests/test_setcompoundschemlib.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import unittest
import os
from ost import conop
diff --git a/core/tests/tests.cc b/core/tests/tests.cc
index f3c1473f9e8e9e8e759cb7e2a590870dedbd4b69..723aa61416a8bb5d5eb9935903958c1ffba5f12f 100644
--- a/core/tests/tests.cc
+++ b/core/tests/tests.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_core
#define BOOST_AUTO_TEST_MAIN
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index c79f0aa9a66d0e7d0c7786858f0b8517a90b47c9..17d0e2b2dc485dc830a21e1ad789800b662affd7 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -14,8 +14,12 @@ buildsystem.rst
contributing.rst
gettingstarted.rst
portableIO.rst
+references.rst
+license.rst
)
+add_subdirectory(container)
+
# add documentation tests (must be done before rest below!)
add_custom_target(doctest)
add_subdirectory(tests)
@@ -78,6 +82,15 @@ if(DEFINED PM3_DOC_CHANGELOG)
set(_RST_DEPS ${_RST_DEPS} "${_RST_SOURCE_DIR}/changelog.rst")
endif()
+if(DEFINED PM3_DOC_LICENSE)
+ # copy to different file name
+ add_custom_command(OUTPUT "${_RST_SOURCE_DIR}/license.txt"
+ MAIN_DEPENDENCY "${PM3_DOC_LICENSE}"
+ COMMAND ${CMAKE_COMMAND} -E copy
+ "${PM3_DOC_LICENSE}" "${_RST_SOURCE_DIR}/license.txt")
+ set(_RST_DEPS ${_RST_DEPS} "${_RST_SOURCE_DIR}/license.txt")
+endif()
+
# iterate list of ALL modules registered by pymod()/ add_doc_source()
foreach(mod ${PM3_PY_MS})
# only modules with dedicated rst files are considered for documentation, so
diff --git a/doc/buildsystem.rst b/doc/buildsystem.rst
index a601d619b695a46a2f15352e312e4bdaf91ab90f..7f975230cc64e605d3b77f8ef48eaf322bb69459 100644
--- a/doc/buildsystem.rst
+++ b/doc/buildsystem.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
.. _building-promod:
Building |project|
@@ -7,18 +23,15 @@ Building |project|
Dependencies
--------------------------------------------------------------------------------
-|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version
-1.7. |ost_s| must be configured and compiled with ``ENABLE_MM=1`` to use |openmm|_.
-To create the build system, |cmake|_ is required in version
-2.8.7 or higher. |python|_ works well from version 2.7. For |ost_s| and the
-|C++| bit of |project|, |boost|_ is required in version 1.53.0 (the same as
-used for |ost_s|). Also |eigen3|_ is needed. To build
-documentation, |sphinx|_ 1.2b1 is required.
-
+|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version 1.8.
+|ost_s| must be configured and compiled with ``ENABLE_MM=1`` to use |openmm|_.
+To create the build system, |cmake|_ is required. The same versions of |python|_
+and |boost|_ are needed as used in |ost_s|. For |eigen3|_ we need at least
+version 3.3.0. To build the documentation, |sphinx|_ is required.
The currently preferred versions are:
-* |ost_s|_ 1.7
+* |ost_s|_ 1.9
* |openmm|_ 7.1.1
* |cmake|_ 2.8.12
* |python|_ 2.7.5
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 1219c73e05d9a4047ac23d72dcc449f8581265eb..713d4a748c49463ee41f7f27ef33e0f620478468 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -37,7 +37,7 @@ extensions = ['sphinx.ext.autodoc',
'sphinx.ext.intersphinx',
'sphinx.ext.todo',
'sphinx.ext.coverage',
- 'sphinx.ext.pngmath',
+ 'sphinx.ext.mathjax',
'sphinx.ext.ifconfig',
'sphinx.ext.viewcode',
'sphinx.ext.extlinks', 'cmake']
@@ -59,7 +59,7 @@ master_doc = 'index'
# General information about the project.
project = u'ProMod3'
-copyright = u'2018, ProMod3 authors'# pylint: disable=redefined-builtin
+copyright = u'2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# pylint: disable=redefined-builtin
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -107,6 +107,13 @@ pygments_style = 'sphinx'
# -- Options for HTML output ---------------------------------------------------
+# Since we use sphinx.ext.mathjax to render formulas on HTML pages: The
+# MathJax web-page deprecated their own CDN to serve JavaScript but it is
+# still the default for Sphinx. Here we redirect to the CDN recommended by
+# MathJax.
+mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML'
+
+
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'alabaster'
@@ -300,6 +307,6 @@ rst_epilog = """
""" % project
# increase default timeout (5s) for linkcheck
-linkcheck_timeout = 15.0
+linkcheck_timeout = 15
# LocalWords: cmake
diff --git a/doc/container/CMakeLists.txt b/doc/container/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35219690fafc72ce0d4509a035533d25a9965186
--- /dev/null
+++ b/doc/container/CMakeLists.txt
@@ -0,0 +1,7 @@
+set(CONTAINER_RST
+ index.rst
+ docker.rst
+ singularity.rst
+)
+
+add_doc_source(NAME container RST ${CONTAINER_RST})
diff --git a/doc/container/docker.rst b/doc/container/docker.rst
new file mode 100644
index 0000000000000000000000000000000000000000..cc5faaa095f903fc4f5a68ba776b5b8b144874ff
--- /dev/null
+++ b/doc/container/docker.rst
@@ -0,0 +1,116 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+Docker
+======
+
+Build Docker Image
+------------------
+
+In order to build the image:
+
+.. code-block:: bash
+
+ sudo docker build --tag <IMAGE_NAME> -f Dockerfile <PATH_TO_DOCKERFILE_DIR>
+
+You can chose any image name (tag) eg. promod.
+
+
+Run scripts and actions with OST/PM
+-----------------------------------
+
+If script or action requires some external files eg. PDBs, they have to be located in the
+path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
+path. Eg. assuming that we have a struc.pdb file in /home/<USER>/pdbs directory and
+a script.py in /home/<USER> we could mount the /home/<USER> to /home in docker as
+above by specifying -v /home/<USER>:/home. To run the script we thus need to
+provide the (relative) path to the script and (relative) path to the file eg:
+
+.. code-block:: bash
+
+ sudo docker run --rm -v /home/<USER>:/home <IMAGE_NAME> pm script.py pdbs/struct.pdb
+
+or with absolute paths:
+
+.. code-block:: bash
+
+ sudo docker run --rm -v /home/<USER>:/home <IMAGE_NAME> pm /home/script.py /home/pdbs/struct.pdb
+
+An alternative is to mount the current working directory into the docker home:
+
+.. code-block:: bash
+
+ sudo docker run --rm -v $(pwd):/home <IMAGE_NAME> pm script.py pdbs/struct.pdb
+
+
+.. _docker_compound_lib:
+
+The Compound Library
+--------------------
+
+At build time of the container, a :class:`~ost.conop.CompoundLib` is generated.
+Compound libraries contain information on chemical compounds, such as their
+connectivity, chemical class and one-letter-code. The compound library has
+several uses, but the most important one is to provide the connectivy
+information for the rule-based processor.
+
+The compound library is generated with the components.cif dictionary provided by
+the PDB. As the PDB updates regularly, the compound library shipped with the
+container is quickly outdated. For most use cases, this is not problematic.
+However, if you rely on correct connectivity information of the latest and
+greatest compounds, you have to keep the compound library up to date manually.
+
+The suggested way of doing this is to generate your own compound library and
+mount it into the container where the original compound lib resides to
+override it.
+
+The simplest way to create a compound library is to use the
+:program:`chemdict_tool` available in the container. The program allows you
+to import the chemical description of the compounds from a MMCIF dictionary,
+e.g. the components.cif dictionary provided by the PDB.
+The latest dictionary can be downloaded from the
+`wwPDB site <http://www.wwpdb.org/ccd.html>`_.
+The files are rather large, it is therefore recommended to download the
+gzipped version.
+
+After downloading the file use :program:`chemdict_tool` in the container to
+convert the MMCIF dictionary into our internal format:
+
+.. code-block:: bash
+
+ sudo docker run --rm -v $(pwd):/home <IMAGE_NAME> chemdict_tool create components.cif.gz compounds.chemlib
+
+To run a script with the upated compound library, use the -v option for mounting/overriding:
+
+.. code-block:: bash
+
+ sudo docker run --rm -v /home/<USER>:/home -v <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> <IMAGE_NAME> pm script.py pdbs/struct.pdb
+
+with COMPLIB_DIR_LOCALHOST being the directory that contains the newly generated
+compound library with name compounds.chemlib and COMPLIB_DIR_CONTAINER the
+according path in the container.
+If you didnt change anything in the Dockerfile, the latter should be
+/usr/local/share/ost_complib
+
+You can check whether the default lib is successfully overriden by looking at the
+output when running a Python script with following code in the container:
+
+.. code-block:: python
+
+ import promod3 # required to setup default lib
+ from ost import conop
+ lib = conop.GetDefaultLib()
+ print lib.GetCreationDate()
diff --git a/doc/container/index.rst b/doc/container/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..9cf79e23f891def49bfd42346f0e31c027838b79
--- /dev/null
+++ b/doc/container/index.rst
@@ -0,0 +1,36 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+ProMod3 and Containers
+======================
+
+
+ProMod3 offers build recipes for Docker and Singularity in
+<PATH_TO_PROMOD3_CHECKOUT>/container. To avoid code duplication,
+the Singularity container bootstraps from the Docker one and adds
+some sugar on top.
+
+.. toctree::
+ :maxdepth: 1
+
+ Docker <docker>
+ Singularity <singularity>
+
+
+
+
+
+
diff --git a/doc/container/singularity.rst b/doc/container/singularity.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ede88ddb3845154c24ea1534d96ebc6bb964b02a
--- /dev/null
+++ b/doc/container/singularity.rst
@@ -0,0 +1,120 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+Singularity
+===========
+
+We do not provide a "standalone" Singularity image, but rather bootstrap from a
+Docker image.
+
+Build Singularity Image
+-----------------------
+
+You can pull the Docker image to start with from two different sources.
+
+Option One:
+
+You built the Docker image locally and want to use it as a starting point. For
+this we have to fire up a local Docker registry and pull from there. Let's
+assume you built the Docker image with tag promod.
+
+Fire the local Registry and push the promod image to it:
+
+.. code-block:: bash
+
+ sudo docker run -d -p 5000:5000 --restart=always --name registry registry:2
+ sudo docker tag promod localhost:5000/promod
+ sudo docker push localhost:5000/promod
+
+Make sure, that on top of your Singularity recipe you have something like:
+
+.. code-block:: bash
+
+ BootStrap: docker
+ Registry: http://localhost:5000
+ Namespace:
+ From: promod:latest
+
+and build the image with:
+
+.. code-block:: bash
+
+ sudo SINGULARITY_NOHTTPS=1 singularity build promod.img Singularity
+
+
+Option Two:
+
+You pull a Docker image from an external Docker registry.
+Fill in a lot of words as soon as its on Dockerhub. Many words. The best words.
+
+and build the image with:
+
+.. code-block:: bash
+
+ sudo singularity build promod.img Singularity
+
+
+Run scripts and actions with OST/PM
+-----------------------------------
+
+The created container can run the ost, pm or chemdict_tool executables.
+For convenience, a jupyter notebook playground with OST, ProMod3 and nglview is
+available.
+
+To run ost, pm or chemdict_tool executables, use the exec command.
+E.g. to run scripts with pm:
+
+.. code-block:: bash
+
+ singularity exec <IMAGE> pm my_script.py [options]
+
+The jupyter notebook is setup as an app in the container.
+To get help on how to run it:
+
+.. code-block:: bash
+
+ singularity run --app Notebook <IMAGE> --help
+
+
+The Compound Library
+--------------------
+
+You'll have the exact same problem with outdated compound libraries as in the
+raw Docker image. You can find more information on that matter in the Docker
+section of the documentation: :ref:`docker_compound_lib`.
+
+The same trick of mounting an up to date compound library from the local host into
+the container applies. The two relevant commands for Singularity are building
+a new library and mount it.
+
+Build a new library:
+
+.. code-block:: bash
+
+ singularity exec <IMAGE_NAME> chemdict_tool create components.cif.gz compounds.chemlib
+
+Run some script with an updated compound library from localhost:
+
+.. code-block:: bash
+
+ singularity exec -B <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> <IMAGE_NAME> pm my_script.py
+
+Same as for the Docker, if you didn't meddle with the original Dockerfile,
+<COMPLIB_DIR_CONTAINER> should be /usr/local/share/ost_complib.
+<COMPLIB_DIR_LOCALHOST> is the directory that contains the compound lib with the
+name compounds.chemlib that you created before. Make sure that everything works
+as expected by executing the exact same lines of Python code as described
+in the Docker documentation: :ref:`docker_compound_lib`.
diff --git a/doc/contributing.rst b/doc/contributing.rst
index ae3c842c641522624e55d208c51e6a146773a033..3a261b411ab249a578a79cf8c0760ef1deb68150 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Contributing
================================================================================
@@ -475,23 +491,19 @@ Hence, the :file:`CMakeLists.txt` of the :file:`doc` directory of a module is
crucial. For documentation which does not relate to a particular module, the
repository comes with a top-level :file:`doc` directory.
-While you should not spend to much time thinking about how to format
-documentation, here is a helpful list of standard formatters:
-http://sphinx-doc.org/en/stable/markup/inline.html
-
If you write new functionality for |project|, or fix bugs, feel free to extend
the :file:`CHANGELOG` file. It will be automatically pulled into the
documentation.
It is highly recommended to add code examples with your documentation. For that
-purpose, you should write a fully runnable script, which is to be placed in the
+purpose, you should write a fully runnable script which is to be placed in the
:file:`doc/tests/scripts` directory. The script is to be runnable from within
the :file:`doc/tests` directory as ``pm SCRIPTPATH`` and may use data stored in
the :file:`doc/tests/data` directory. The script and any data needed by it, must
then be referenced in the :file:`doc/tests/CMakeLists.txt` file. Afterwards,
-they can be included in the documentation using the
-`literalinclude <http://www.sphinx-doc.org/en/stable/markup/code.html#includes>`_
-directive. For instance, if you add a new example code :file:`loop_main.py`,
+they can be included in the documentation using the literalinclude
+directive.
+For instance, if you add a new example code :file:`loop_main.py`,
you would add it in your module documentation as follows:
.. code-block:: rest
diff --git a/doc/dev_setup.rst b/doc/dev_setup.rst
index 3b450accf0a5cb18ada95e2e7b1ab6d0e35799dd..91909c30154907dcbb269a4d5cb805ef6af9d1bf 100644
--- a/doc/dev_setup.rst
+++ b/doc/dev_setup.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
|project| Setup
================================================================================
diff --git a/doc/developers.rst b/doc/developers.rst
index 3955c47c1cab44e3274e54919b0b0d949299c0f6..f15f85db820e896de015b614c871d0317030dc38 100644
--- a/doc/developers.rst
+++ b/doc/developers.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Documentation For Developers
===============================================================================
diff --git a/doc/gettingstarted.rst b/doc/gettingstarted.rst
index 9b2b8024b6cb6e7cd2e98aa10c3c86df5754f645..2bed4049fe4de07f7fafe0994c1867fd40f5be61 100644
--- a/doc/gettingstarted.rst
+++ b/doc/gettingstarted.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Getting Started
================================================================================
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 6964cf96734a79a1c9de4932da5588a9924935da..34b3643fae8b4809c9baf48948c58af7c088f0cc 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Overview: module code — ProMod3 1.2.0 documentation</title>
+ <title>Overview: module code — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -58,7 +59,9 @@
<li><a href="CBetaScorer.html">CBetaScorer</a></li>
<li><a href="CCD.html">CCD</a></li>
<li><a href="CCDCloser.html">CCDCloser</a></li>
+<li><a href="CTerminalCloser.html">CTerminalCloser</a></li>
<li><a href="ClashScorer.html">ClashScorer</a></li>
+<li><a href="DeNovoCloser.html">DeNovoCloser</a></li>
<li><a href="DirtyCCDCloser.html">DirtyCCDCloser</a></li>
<li><a href="DiscoContainer.html">DiscoContainer</a></li>
<li><a href="ExponentialCooler.html">ExponentialCooler</a></li>
@@ -76,9 +79,11 @@
<li><a href="HBondScorer.html">HBondScorer</a></li>
<li><a href="KIC.html">KIC</a></li>
<li><a href="KICCloser.html">KICCloser</a></li>
+<li><a href="LinearScorer.html">LinearScorer</a></li>
<li><a href="LoopCandidates.html">LoopCandidates</a></li>
<li><a href="MmSystemCreator.html">MmSystemCreator</a></li>
<li><a href="ModellingHandle.html">ModellingHandle</a></li>
+<li><a href="NTerminalCloser.html">NTerminalCloser</a></li>
<li><a href="PairwiseScorer.html">PairwiseScorer</a></li>
<li><a href="Particle.html">Particle</a></li>
<li><a href="PhiPsiSampler.html">PhiPsiSampler</a></li>
@@ -112,6 +117,7 @@
<li><a href="promod3/modelling/_fragger_handle.html">promod3.modelling._fragger_handle</a></li>
<li><a href="promod3/modelling/_modelling.html">promod3.modelling._modelling</a></li>
<li><a href="promod3/modelling/_molprobity.html">promod3.modelling._molprobity</a></li>
+<li><a href="promod3/modelling/_monte_carlo.html">promod3.modelling._monte_carlo</a></li>
<li><a href="promod3/modelling/_pipeline.html">promod3.modelling._pipeline</a></li>
<li><a href="promod3/modelling/_reconstruct_sidechains.html">promod3.modelling._reconstruct_sidechains</a></li>
<li><a href="promod3/modelling/_ring_punches.html">promod3.modelling._ring_punches</a></li>
@@ -146,7 +152,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3.html b/doc/html/_modules/promod3.html
index 140c70b9d3e7b6edc1001cd57344d3a21c5babd7..8a2048004ddf4859b43bd89d82e36f5dc1f6d570 100644
--- a/doc/html/_modules/promod3.html
+++ b/doc/html/_modules/promod3.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3 — ProMod3 1.2.0 documentation</title>
+ <title>promod3 — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Module code" href="index.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -40,7 +41,22 @@
<div class="body" role="main">
<h1>Source code for promod3</h1><div class="highlight"><pre>
-<span></span><span class="c1"># enable access to loop and modelling via "import promod3"</span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+<span class="c1"># enable access to loop and modelling via "import promod3"</span>
<span class="kn">import</span> <span class="nn">promod3.core</span>
<span class="kn">import</span> <span class="nn">promod3.sidechain</span>
<span class="kn">import</span> <span class="nn">promod3.loop</span>
@@ -107,8 +123,8 @@
<span class="n">SetProMod3SharedDataPath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">promod3_root</span><span class="p">,</span> <span class="s2">"share"</span><span class="p">,</span> <span class="s2">"promod3"</span><span class="p">))</span>
<span class="c1"># set version</span>
-<span class="n">__version__</span> <span class="o">=</span> <span class="s2">"1.2.0"</span>
-<span class="n">__version_extended__</span> <span class="o">=</span> <span class="s2">"1.2.0 (release-1.2.0|d086aed)"</span>
+<span class="n">__version__</span> <span class="o">=</span> <span class="s2">"1.3.0"</span>
+<span class="n">__version_extended__</span> <span class="o">=</span> <span class="s2">"1.3.0 (release-1.3.0|01e00a8)"</span>
<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s1">'SetCompoundsChemlib'</span><span class="p">,</span> <span class="s1">'GetProMod3SharedDataPath'</span><span class="p">,</span>
<span class="s1">'SetProMod3SharedDataPath'</span><span class="p">)</span>
@@ -146,7 +162,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index 2266f1a35bc7f1a3cb8be03cbadf869949896d0b..6b8aadaa06e2d54b59d72a8f13b445c9417a8dbb 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.core.helper — ProMod3 1.2.0 documentation</title>
+ <title>promod3.core.helper — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
<link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
@@ -40,7 +41,23 @@
<div class="body" role="main">
<h1>Source code for promod3.core.helper</h1><div class="highlight"><pre>
-<span></span><span class="sd">"""</span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">"""</span>
<span class="sd">Uncategorised functions which may come handy at several places.</span>
<span class="sd">"""</span>
@@ -231,7 +248,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/core/pm3argparse.html b/doc/html/_modules/promod3/core/pm3argparse.html
index e10fff03f913d8b7779021287b59d397b5f58634..8f04b46752cadb137143cf633aa80b86a878cbcc 100644
--- a/doc/html/_modules/promod3/core/pm3argparse.html
+++ b/doc/html/_modules/promod3/core/pm3argparse.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.core.pm3argparse — ProMod3 1.2.0 documentation</title>
+ <title>promod3.core.pm3argparse — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
<link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
@@ -40,7 +41,23 @@
<div class="body" role="main">
<h1>Source code for promod3.core.pm3argparse</h1><div class="highlight"><pre>
-<span></span><span class="sd">"""</span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">"""</span>
<span class="sd">Extensions for the argparse module.</span>
<span class="sd">"""</span>
@@ -274,6 +291,17 @@
<span class="nb">str</span><span class="p">(</span><span class="n">exc</span><span class="p">),</span> <span class="mi">33</span><span class="p">)</span>
<span class="k">return</span> <span class="n">ent</span>
+<span class="k">def</span> <span class="nf">_FetchProfileFromFile</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
+ <span class="sd">"""Load generic profile file from filename and return it."""</span>
+ <span class="n">argstr</span> <span class="o">=</span> <span class="s2">"'--seqprof "</span> <span class="o">+</span> <span class="n">filename</span> <span class="o">+</span> <span class="s2">"'"</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s2">"Profile"</span><span class="p">,</span> <span class="mi">51</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">prof</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadSequenceProfile</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s2">": failure to parse profile file: "</span> <span class="o">+</span>
+ <span class="nb">str</span><span class="p">(</span><span class="n">exc</span><span class="p">),</span> <span class="mi">52</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">prof</span>
+
<span class="k">def</span> <span class="nf">_GetChains</span><span class="p">(</span><span class="n">structures</span><span class="p">,</span> <span class="n">structure_sources</span><span class="p">):</span>
<span class="sd">"""Get chain id to entity view (single chain) mapping (dict)."""</span>
<span class="c1"># IDs: (file_base = base file name with no extensions)</span>
@@ -439,7 +467,9 @@
<span class="k">if</span> <span class="s1">'ALIGNMENT'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_AssembleAlignment</span><span class="p">()</span>
<span class="k">if</span> <span class="s1">'STRUCTURE'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">_AssembleStructure</span><span class="p">()</span></div>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_AssembleStructure</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s1">'PROFILE'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_AssembleProfile</span><span class="p">()</span></div>
<div class="viewcode-block" id="PM3ArgumentParser.AddAlignment"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment">[docs]</a> <span class="k">def</span> <span class="nf">AddAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">allow_multitemplate</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""Commandline options for alignments.</span>
@@ -516,7 +546,7 @@
<div class="viewcode-block" id="PM3ArgumentParser.AddStructure"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure">[docs]</a> <span class="k">def</span> <span class="nf">AddStructure</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attach_views</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""Commandline options for structures.</span>
-<span class="sd"> Activate everything needed to load alignments to the argument parser.</span>
+<span class="sd"> Activate everything needed to load structures to the argument parser.</span>
<span class="sd"> Command line arguments are then added in :meth:`AssembleParser` and the</span>
<span class="sd"> input is post processed and checked in :meth:`Parse`.</span>
@@ -574,6 +604,48 @@
<span class="k">if</span> <span class="n">attach_views</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">'ATTACH_VIEWS'</span><span class="p">)</span></div>
+<div class="viewcode-block" id="PM3ArgumentParser.AddProfile"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile">[docs]</a> <span class="k">def</span> <span class="nf">AddProfile</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Commandline options for profiles</span>
+
+<span class="sd"> Activate everything needed to load profiles to the argument parser.</span>
+<span class="sd"> Command line arguments are then added in :meth:`AssembleParser` and the</span>
+<span class="sd"> input is post processed and checked in :meth:`Parse`.</span>
+
+<span class="sd"> Options/arguments added:</span>
+
+<span class="sd"> * ``-s/--seqprof <FILE>`` - Sequence profile in any format readable</span>
+<span class="sd"> by the :meth:`ost.io.LoadSequenceProfile` method. Format is chosen by </span>
+<span class="sd"> file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm, </span>
+<span class="sd"> .pssm.gz. Consider to use </span>
+<span class="sd"> :meth:`ost.bindings.hhblits.HHblits.A3MToProfile` if you have a file </span>
+<span class="sd"> in a3m format at hand. </span>
+
+<span class="sd"> Notes:</span>
+
+<span class="sd"> * the profiles are mapped based on exact matches towards the gapless</span>
+<span class="sd"> target sequences, i.e. one profile is mapped to several chains in</span>
+<span class="sd"> case of homo-oligomers</span>
+
+<span class="sd"> * every profile must have a unique sequence to avoid ambiguities</span>
+
+<span class="sd"> * all or nothing - you cannot provide profiles for only a subset of</span>
+<span class="sd"> target sequences</span>
+
+<span class="sd"> Attributes added to the namespace returned by :meth:`Parse`:</span>
+
+<span class="sd"> * :attr:`profiles` - :class:`list` of :class:`ost.seq.ProfileHandle`, </span>
+<span class="sd"> ordered to match the target sequences.</span>
+
+<span class="sd"> Exit codes related to profile input:</span>
+
+<span class="sd"> * 51 - a given profile file does not exist</span>
+<span class="sd"> * 52 - failure to read a given profile file </span>
+<span class="sd"> * 53 - a profile cannot be mapped to any target sequence</span>
+<span class="sd"> * 54 - profile sequences are not unique</span>
+<span class="sd"> * 55 - only subset of target sequences is covered by profile</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">'PROFILE'</span><span class="p">)</span></div>
+
<span class="k">def</span> <span class="nf">_AssembleAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""Actually add alignment arguments/options."""</span>
<span class="n">aln_grp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_mutually_exclusive_group</span><span class="p">(</span><span class="n">required</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
@@ -611,7 +683,15 @@
<span class="s2">"io.LoadEntity method. Format is chosen by file "</span><span class="o">+</span>
<span class="s2">"ending. Recognized File Extensions: .ent, .pdb, "</span><span class="o">+</span>
<span class="s2">".ent.gz, .pdb.gz, .cif, .cif.gz."</span><span class="p">,</span>
- <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span></div>
+ <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
+
+ <span class="k">def</span> <span class="nf">_AssembleProfile</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-s'</span><span class="p">,</span> <span class="s1">'--seqprof'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s1">'<FILE>'</span><span class="p">),</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Sequence profile in any format readable by "</span><span class="o">+</span>
+ <span class="s2">"OST's io.LoadSequenceProfile method. Format is "</span><span class="o">+</span>
+ <span class="s2">"chosen by file ending. Recognized File Extensions: "</span><span class="o">+</span>
+ <span class="s2">".hhm, .hhm.gz, .pssm, .pssm.gz"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span></div>
<span class="k">class</span> <span class="nc">PM3OptionsNamespace</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="c1"># class will grow, so for the moment pylint is ignored</span>
@@ -633,6 +713,8 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_PostProcessStructure</span><span class="p">()</span>
<span class="k">if</span> <span class="s1">'ATTACH_VIEWS'</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_AttachViews</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s1">'PROFILE'</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_PostProcessProfile</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">_PostProcessAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="c1">#pylint: disable=no-member</span>
@@ -682,6 +764,42 @@
<span class="k">for</span> <span class="n">aln</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">alignments</span><span class="p">:</span>
<span class="n">_AttachViewsToAln</span><span class="p">(</span><span class="n">aln</span><span class="p">,</span> <span class="n">chain_entities</span><span class="p">)</span>
+ <span class="k">def</span> <span class="nf">_PostProcessProfile</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Get Profiles from command line input."""</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">profiles</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqprof</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="c1"># no profiles provided, remember the all or nothing principle</span>
+ <span class="c1"># so not having any profile is fine</span>
+ <span class="k">return</span>
+
+ <span class="n">loaded_profiles</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqprof</span><span class="p">:</span>
+ <span class="n">loaded_profiles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_FetchProfileFromFile</span><span class="p">(</span><span class="n">src</span><span class="p">))</span>
+
+ <span class="n">prof_sequences</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="o">.</span><span class="n">sequence</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">loaded_profiles</span><span class="p">]</span>
+
+ <span class="c1"># check uniqueness of loaded profiles</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">prof_sequences</span><span class="p">))</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">prof_sequences</span><span class="p">):</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"All sequence profiles must have unique "</span> <span class="o">+</span>
+ <span class="s2">"sequence."</span><span class="p">,</span> <span class="mi">54</span><span class="p">)</span>
+
+ <span class="c1"># map onto alignment target sequences</span>
+ <span class="n">trg_sequences</span> <span class="o">=</span> <span class="p">[</span><span class="n">aln</span><span class="o">.</span><span class="n">GetSequence</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">GetGaplessString</span><span class="p">()</span> \
+ <span class="k">for</span> <span class="n">aln</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">alignments</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">trg_sequences</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">profiles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">loaded_profiles</span><span class="p">[</span><span class="n">prof_sequences</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">s</span><span class="p">)])</span>
+ <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"Could not find profile with sequence "</span> <span class="o">+</span>
+ <span class="s2">"that exactly matches trg seq: "</span> <span class="o">+</span> <span class="n">s</span><span class="p">,</span> <span class="mi">55</span><span class="p">)</span>
+
+ <span class="c1"># We found a profile for every target sequence. So if the size of unique </span>
+ <span class="c1"># target sequences is not the same as for unique profile sequences, </span>
+ <span class="c1"># we know that we have additional profiles that never got mapped</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">trg_sequences</span><span class="p">))</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">prof_sequences</span><span class="p">)):</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"Could not map every profile to a target "</span> <span class="o">+</span>
+ <span class="s2">"sequence"</span><span class="p">,</span> <span class="mi">53</span><span class="p">)</span>
<span class="c1"># LocalWords: param attr prog argparse ArgumentParser bool sys os init str</span>
<span class="c1"># LocalWords: progattr descattr argpinit argv formatter meth args namespace</span>
@@ -725,7 +843,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_closegaps.html b/doc/html/_modules/promod3/modelling/_closegaps.html
index 85c8c033bdc62ac51dc8c0529b0e2ca2ad5f1f0f..f7cc176c6f7c946a20e74f7aaa7e715f825f0f34 100644
--- a/doc/html/_modules/promod3/modelling/_closegaps.html
+++ b/doc/html/_modules/promod3/modelling/_closegaps.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._closegaps — ProMod3 1.2.0 documentation</title>
+ <title>promod3.modelling._closegaps — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
<link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
@@ -40,7 +41,23 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._closegaps</h1><div class="highlight"><pre>
-<span></span><span class="sd">'''High-level functionality for modelling module to close gaps. Added in the</span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">'''High-level functionality for modelling module to close gaps. Added in the</span>
<span class="sd">__init__.py file. To be used directly by passing a ModellingHandle instance</span>
<span class="sd">as argument.</span>
<span class="sd">'''</span>
@@ -1627,7 +1644,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_denovo.html b/doc/html/_modules/promod3/modelling/_denovo.html
index b2100964e66fb6ebbc6d9f4a3a710767ffecfc50..efcbd769d745a6cc900c9a0163d0678c4737ac22 100644
--- a/doc/html/_modules/promod3/modelling/_denovo.html
+++ b/doc/html/_modules/promod3/modelling/_denovo.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._denovo — ProMod3 1.2.0 documentation</title>
+ <title>promod3.modelling._denovo — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
<link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
@@ -40,7 +41,23 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._denovo</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">loop</span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">loop</span>
<span class="kn">from</span> <span class="nn">_modelling</span> <span class="kn">import</span> <span class="o">*</span>
<div class="viewcode-block" id="GenerateDeNovoTrajectories"><a class="viewcode-back" href="../../../modelling/algorithms.html#promod3.modelling.GenerateDeNovoTrajectories">[docs]</a><span class="k">def</span> <span class="nf">GenerateDeNovoTrajectories</span><span class="p">(</span><span class="n">sequence</span><span class="p">,</span>
@@ -200,7 +217,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_fragger_handle.html b/doc/html/_modules/promod3/modelling/_fragger_handle.html
index 0ef683b33454d388f4ec6354c16ddeef42fc101d..8b753363ea873ecc3d0bc79eaabe665443b3af30 100644
--- a/doc/html/_modules/promod3/modelling/_fragger_handle.html
+++ b/doc/html/_modules/promod3/modelling/_fragger_handle.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._fragger_handle — ProMod3 1.2.0 documentation</title>
+ <title>promod3.modelling._fragger_handle — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
<link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
@@ -40,7 +41,23 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._fragger_handle</h1><div class="highlight"><pre>
-<span></span><span class="sd">'''Python functionality to generate fraggers.'''</span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">'''Python functionality to generate fraggers.'''</span>
<span class="kn">from</span> <span class="nn">promod3.loop</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">ost.conop</span> <span class="kn">import</span> <span class="n">OneLetterCodeToResidueName</span>
@@ -423,7 +440,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_molprobity.html b/doc/html/_modules/promod3/modelling/_molprobity.html
index b9441021b1cca2bd98ef90666bf96c15f20509f6..d06f4a2445ab072ee42803ebf27e02259678f97a 100644
--- a/doc/html/_modules/promod3/modelling/_molprobity.html
+++ b/doc/html/_modules/promod3/modelling/_molprobity.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._molprobity — ProMod3 1.2.0 documentation</title>
+ <title>promod3.modelling._molprobity — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
<link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
@@ -40,7 +41,23 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._molprobity</h1><div class="highlight"><pre>
-<span></span><span class="sd">'''Binding to external MolProbity tool to get scores.'''</span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">'''Binding to external MolProbity tool to get scores.'''</span>
<span class="kn">import</span> <span class="nn">ost</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">settings</span>
@@ -189,7 +206,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_monte_carlo.html b/doc/html/_modules/promod3/modelling/_monte_carlo.html
new file mode 100644
index 0000000000000000000000000000000000000000..f7f1be544569c2fa420a2a0180963f32d0449edf
--- /dev/null
+++ b/doc/html/_modules/promod3/modelling/_monte_carlo.html
@@ -0,0 +1,194 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>promod3.modelling._monte_carlo — ProMod3 1.3.0 documentation</title>
+
+ <link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../../../',
+ VERSION: '1.3.0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="../../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../../_static/doctools.js"></script>
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../../../index.html" />
+ <link rel="up" title="promod3" href="../../promod3.html" />
+
+ <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+ </head>
+ <body role="document">
+
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <h1>Source code for promod3.modelling._monte_carlo</h1><div class="highlight"><pre>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="kn">import</span> <span class="nn">random</span>
+<span class="kn">import</span> <span class="nn">math</span>
+
+
+<div class="viewcode-block" id="SampleMonteCarlo"><a class="viewcode-back" href="../../../modelling/monte_carlo.html#promod3.modelling.SampleMonteCarlo">[docs]</a><span class="k">def</span> <span class="nf">SampleMonteCarlo</span><span class="p">(</span><span class="n">sampler</span><span class="p">,</span> <span class="n">closer</span><span class="p">,</span> <span class="n">scorer</span><span class="p">,</span> <span class="n">cooler</span><span class="p">,</span> <span class="n">steps</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">,</span>
+ <span class="n">initialize</span><span class="p">,</span> <span class="n">seed</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">lowest_energy_conformation</span> <span class="o">=</span> <span class="bp">True</span><span class="p">):</span>
+ <span class="sd">''' A convenient function to perform Monte Carlo sampling using a simulated</span>
+<span class="sd"> annealing scheme. In every iteration, a new loop conformation gets proposed </span>
+<span class="sd"> by the provided *sampler* and closed by the *closer*. Upon scoring, this new</span>
+<span class="sd"> conformation gets accepted/rejected using a metropolis criterion based on </span>
+<span class="sd"> the temperature given by the *cooler* </span>
+<span class="sd"> => acceptance probability: exp(-delta_score/T).</span>
+<span class="sd"> The result is stored in *bb_list* (passed by reference, so NO return value) </span>
+<span class="sd"> and is either the lowest energy conformation ever encountered or the last </span>
+<span class="sd"> accepted proposal.</span>
+
+<span class="sd"> :param sampler: Sampler object capable of initializing and altering</span>
+<span class="sd"> conformations.</span>
+<span class="sd"> :param closer: Closer object to adapt a new conformation to</span>
+<span class="sd"> the environment.</span>
+<span class="sd"> :param scorer: Scorer object to score new loop conformations.</span>
+<span class="sd"> :param cooler: Cooler object to control the temperature of the </span>
+<span class="sd"> Monte Carlo trajectory.</span>
+<span class="sd"> :param steps: Number of Monte Carlo iterations to be performed.</span>
+<span class="sd"> :param bb_list: The chosen conformation gets stored here.</span>
+<span class="sd"> :param initialize: Whether a new bb_list should be generated as starting</span>
+<span class="sd"> point, based on the samplers Initialize function.</span>
+<span class="sd"> The input *bb_list* gets used otherwise.</span>
+<span class="sd"> :param seed: Seed for internal random number generator.</span>
+<span class="sd"> :param lowest_energy_conformation: If True, we choose the lowest scoring</span>
+<span class="sd"> conformation of the trajectory. </span>
+<span class="sd"> Otherwise, the last accepted proposal.</span>
+
+<span class="sd"> :type sampler: :ref:`mc-sampler-object`</span>
+<span class="sd"> :type closer: :ref:`mc-closer-object`</span>
+<span class="sd"> :type scorer: :ref:`mc-scorer-object`</span>
+<span class="sd"> :type cooler: :ref:`mc-cooler-object`</span>
+<span class="sd"> :type steps: :class:`int`</span>
+<span class="sd"> :type bb_list: :class:`~promod3.loop.BackboneList`</span>
+<span class="sd"> :type initialize: :class:`bool`</span>
+<span class="sd"> :type seed: :class:`int`</span>
+<span class="sd"> :type lowest_energy_conformation: :class:`bool`</span>
+<span class="sd"> '''</span>
+
+ <span class="c1"># Initialize from scratch if necessary</span>
+ <span class="k">if</span> <span class="n">initialize</span><span class="p">:</span>
+ <span class="n">initialized</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">100</span><span class="p">):</span>
+ <span class="n">sampler</span><span class="o">.</span><span class="n">Initialize</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">closer</span><span class="o">.</span><span class="n">Close</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">):</span>
+ <span class="n">initialized</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="k">break</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">initialized</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Failed to initialize monte carlo protocol!"</span><span class="p">)</span>
+
+ <span class="c1"># setup</span>
+ <span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="n">seed</span><span class="p">)</span>
+ <span class="n">score</span> <span class="o">=</span> <span class="n">scorer</span><span class="o">.</span><span class="n">GetScore</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)</span>
+ <span class="n">closed</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="n">min_score</span> <span class="o">=</span> <span class="n">score</span>
+ <span class="n">min_score_bb_list</span> <span class="o">=</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+ <span class="n">proposed_bb_list</span> <span class="o">=</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">steps</span><span class="p">):</span>
+
+ <span class="c1"># try several proposals (we might not be able to close at first attempt)</span>
+ <span class="n">closed</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span>
+ <span class="n">sampler</span><span class="o">.</span><span class="n">ProposeStep</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="n">proposed_bb_list</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">closer</span><span class="o">.</span><span class="n">Close</span><span class="p">(</span><span class="n">proposed_bb_list</span><span class="p">,</span> <span class="n">proposed_bb_list</span><span class="p">):</span>
+ <span class="n">closed</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="k">break</span>
+
+ <span class="c1"># check for success, try again in next step in case of failure</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">closed</span><span class="p">:</span>
+ <span class="k">continue</span>
+
+ <span class="c1"># accept / reject based on Metropolis criterion</span>
+ <span class="n">temperature</span> <span class="o">=</span> <span class="n">cooler</span><span class="o">.</span><span class="n">GetTemperature</span><span class="p">()</span>
+ <span class="n">new_score</span> <span class="o">=</span> <span class="n">scorer</span><span class="o">.</span><span class="n">GetScore</span><span class="p">(</span><span class="n">proposed_bb_list</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">math</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="p">(</span><span class="n">new_score</span><span class="o">-</span><span class="n">score</span><span class="p">)</span><span class="o">/</span><span class="n">temperature</span><span class="p">)</span> <span class="o">></span> <span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">():</span>
+ <span class="n">positions</span> <span class="o">=</span> <span class="n">proposed_bb_list</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+ <span class="n">score</span> <span class="o">=</span> <span class="n">new_score</span>
+ <span class="k">if</span> <span class="n">lowest_energy_conformation</span> <span class="ow">and</span> <span class="n">score</span> <span class="o"><</span> <span class="n">min_score</span><span class="p">:</span>
+ <span class="n">min_score</span> <span class="o">=</span> <span class="n">score</span>
+ <span class="n">min_score_bb_list</span> <span class="o">=</span> <span class="n">positions</span>
+
+ <span class="k">if</span> <span class="n">lowest_energy_conformation</span><span class="p">:</span>
+ <span class="n">bb_list</span> <span class="o">=</span> <span class="n">min_score_bb_list</span></div>
+</pre></div>
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../../../index.html">Documentation overview</a><ul>
+ <li><a href="../../index.html">Module code</a><ul>
+ <li><a href="../../promod3.html">promod3</a><ul>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
+ <form class="search" action="../../../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="footer">
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+
+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+
+ </div>
+
+
+
+
+ </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/_modules/promod3/modelling/_pipeline.html b/doc/html/_modules/promod3/modelling/_pipeline.html
index 3ea48e01d1e4a82180c71d72adbae5297ad85c69..fa63da280cc9574c757edda6f802723f995b494f 100644
--- a/doc/html/_modules/promod3/modelling/_pipeline.html
+++ b/doc/html/_modules/promod3/modelling/_pipeline.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._pipeline — ProMod3 1.2.0 documentation</title>
+ <title>promod3.modelling._pipeline — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
<link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
@@ -40,7 +41,23 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._pipeline</h1><div class="highlight"><pre>
-<span></span><span class="sd">'''High-level functionality for modelling module to build pipelines. Added in </span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">'''High-level functionality for modelling module to build pipelines. Added in </span>
<span class="sd">the __init__.py file. To be used directly by passing a ModellingHandle instance</span>
<span class="sd">as argument.</span>
<span class="sd">'''</span>
@@ -206,7 +223,8 @@
<div class="viewcode-block" id="BuildSidechains"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.BuildSidechains">[docs]</a><span class="k">def</span> <span class="nf">BuildSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span> <span class="n">fragment_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
- <span class="n">structure_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+ <span class="n">structure_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
+ <span class="n">rotamer_library</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">'''Build sidechains for model.</span>
<span class="sd"> This is a wrapper for :func:`promod3.modelling.ReconstructSidechains`, </span>
@@ -232,10 +250,16 @@
<span class="sd"> if ring punches are found. A default one is loaded</span>
<span class="sd"> if None.</span>
<span class="sd"> :type torsion_sampler: :class:`~promod3.loop.TorsionSampler`</span>
+<span class="sd"> :param rotamer_library: Used as parameter for </span>
+<span class="sd"> :func:`modelling.ReconstructSidechains`, a default </span>
+<span class="sd"> one is loaded if None.</span>
+<span class="sd"> :type rotamer_library: :class:`~promod3.sidechain.RotamerLib` or</span>
+<span class="sd"> :class:`~promod3.sidechain.BBDepRotamerLib` </span>
<span class="sd"> '''</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s1">'pipeline::BuildSidechains'</span><span class="p">)</span>
<span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Rebuilding sidechains."</span><span class="p">)</span>
- <span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+ <span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
+ <span class="n">rotamer_library</span><span class="o">=</span><span class="n">rotamer_library</span><span class="p">)</span>
<span class="c1"># check for ring punches</span>
<span class="n">rings</span> <span class="o">=</span> <span class="n">GetRings</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
<span class="n">ring_punches</span> <span class="o">=</span> <span class="n">GetRingPunches</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
@@ -263,7 +287,8 @@
<span class="n">FillLoopsByDatabase</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span>
<span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">ring_punch_detection</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
<span class="c1"># re-build sidechains</span>
- <span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+ <span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
+ <span class="n">rotamer_library</span><span class="o">=</span><span class="n">rotamer_library</span><span class="p">)</span>
<span class="c1"># restore gaps</span>
<span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span> <span class="o">=</span> <span class="n">StructuralGapList</span><span class="p">()</span>
<span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="n">old_gaps</span><span class="p">:</span>
@@ -501,6 +526,7 @@
<span class="n">fragment_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
<span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">()</span>
+ <span class="n">rotamer_library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadBBDepLib</span><span class="p">()</span>
<span class="n">merge_distance</span> <span class="o">=</span> <span class="mi">4</span>
<span class="c1"># remove terminal gaps</span>
@@ -513,7 +539,7 @@
<span class="c1"># build sidechains</span>
<span class="n">BuildSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span>
- <span class="n">structure_db</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">)</span>
+ <span class="n">structure_db</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">rotamer_library</span><span class="p">)</span>
<span class="c1"># minimize energy of final model using molecular mechanics</span>
<span class="n">MinimizeModelEnergy</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">use_amber_ff</span><span class="o">=</span><span class="n">use_amber_ff</span><span class="p">,</span>
@@ -560,7 +586,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html b/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
index a8840922170b8f1448c05531aba3a51c444ff34e..61d1d54bf02c0b8b81d1c3377f559d485743a4de 100644
--- a/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
+++ b/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._reconstruct_sidechains — ProMod3 1.2.0 documentation</title>
+ <title>promod3.modelling._reconstruct_sidechains — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
<link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
@@ -40,7 +41,23 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._reconstruct_sidechains</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">geom</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">conop</span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">geom</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">conop</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">core</span><span class="p">,</span> <span class="n">sidechain</span>
<span class="kn">import</span> <span class="nn">traceback</span>
@@ -438,8 +455,7 @@
<span class="sd"> :type consider_ligands: :class:`bool`</span>
<span class="sd"> :param rotamer_library: A rotamer library to extract the rotamers from. The</span>
-<span class="sd"> default is the :meth:`Dunbrack <LoadDunbrackLib>`</span>
-<span class="sd"> library.</span>
+<span class="sd"> default is to call :meth:`<LoadBBDepLib>`.</span>
<span class="sd"> :type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib`</span>
<span class="sd"> :param optimize_subrotamers: Only considered when *rotamer_model*</span>
@@ -469,7 +485,7 @@
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Only </span><span class="se">\"</span><span class="s2">rrm</span><span class="se">\"</span><span class="s2"> and </span><span class="se">\"</span><span class="s2">frm</span><span class="se">\"</span><span class="s2"> allowed for rotamer_model!"</span><span class="p">)</span>
<span class="k">if</span> <span class="n">rotamer_library</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
- <span class="n">rotamer_library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadDunbrackLib</span><span class="p">()</span>
+ <span class="n">rotamer_library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadBBDepLib</span><span class="p">()</span>
<span class="n">bbdep</span> <span class="o">=</span> <span class="bp">False</span>
<span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">rotamer_library</span><span class="p">)</span> <span class="ow">is</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">BBDepRotamerLib</span><span class="p">:</span>
<span class="n">bbdep</span> <span class="o">=</span> <span class="bp">True</span>
@@ -594,7 +610,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/promod3/modelling/_ring_punches.html b/doc/html/_modules/promod3/modelling/_ring_punches.html
index a443928984846cc8360ea5a3b7339d0c45757d85..810839fc68173993b7c1ecd858177195a2491a93 100644
--- a/doc/html/_modules/promod3/modelling/_ring_punches.html
+++ b/doc/html/_modules/promod3/modelling/_ring_punches.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._ring_punches — ProMod3 1.2.0 documentation</title>
+ <title>promod3.modelling._ring_punches — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
<link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
@@ -40,7 +41,23 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._ring_punches</h1><div class="highlight"><pre>
-<span></span><span class="sd">'''Helper functions to deal with ring punchings.'''</span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">'''Helper functions to deal with ring punchings.'''</span>
<span class="kn">import</span> <span class="nn">ost</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">geom</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">core</span>
@@ -308,7 +325,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_modules/test_actions.html b/doc/html/_modules/test_actions.html
index f9739b382679bc7bfe2aafe0e47bace71563dd75..8e193e5e386bc26b66383ccefdf133aefee3ae13 100644
--- a/doc/html/_modules/test_actions.html
+++ b/doc/html/_modules/test_actions.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>test_actions — ProMod3 1.2.0 documentation</title>
+ <title>test_actions — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Module code" href="index.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -40,7 +41,23 @@
<div class="body" role="main">
<h1>Source code for test_actions</h1><div class="highlight"><pre>
-<span></span><span class="sd">"""</span>
+<span></span><span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1"># Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the "License");</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">"""</span>
<span class="sd">unittest.TestCase class providing common functionality for testing actions.</span>
<span class="sd">"""</span>
<span class="kn">import</span> <span class="nn">unittest</span>
@@ -197,7 +214,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/_sources/actions/index.txt b/doc/html/_sources/actions/index.txt
index 4820610c7519c44d285f2b8e76ce9fb87c6f667a..450ffa57d28ef1f491876e3f468880a55741713d 100644
--- a/doc/html/_sources/actions/index.txt
+++ b/doc/html/_sources/actions/index.txt
@@ -20,7 +20,7 @@ with
.. code-block:: console
$ pm build-model [-h] (-f <FILE> | -c <FILE> | -j <OBJECT>|<FILE>)
- (-p <FILE> | -e <FILE>) [-o <FILENAME>]
+ (-p <FILE> | -e <FILE>) [-s <FILE>] [-o <FILENAME>]
Example usage:
@@ -105,6 +105,30 @@ sequence names are:
Example: ``... -p data/2jlp.pdb.gz``, where the pdb file has chains ``A``,
``B``, ``C`` and the template sequence is named ``2jlp.A|55``.
+
+You can optionally specify sequence profiles to be added (``-s``) and linked
+to the corresponding target sequences. This has an impact on loop scoring with
+the database approach.
+The profiles can be provided as plain files or gzipped. Following file
+extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
+Consider to use :meth:`ost.bindings.hhblits.HHblits.A3MToProfile` if you have a
+file in a3m format at hand.
+
+* The profiles are mapped based on exact matches towards the gapless
+ target sequences from the provided alignment files,
+ i.e. one profile is mapped to several chains in case of homo-oligomers
+
+* Every profile must have a unique sequence to avoid ambiguities
+
+* All or nothing - You cannot provide profiles for only a subset of
+ target sequences
+
+Example usage:
+
+.. code-block:: console
+
+ $ pm build-model -f aln.fasta -p tpl.pdb -s prof.hhm
+
Possible exit codes of the action:
- 0: all went well
@@ -113,4 +137,56 @@ Possible exit codes of the action:
- 3: failed to perform modelling (internal error)
- 4: failed to write results to file
- other non-zero: failure in argument checking
- (see :class:`promod3.core.pm3argparse.PM3ArgumentParser`)
\ No newline at end of file
+ (see :class:`promod3.core.pm3argparse.PM3ArgumentParser`)
+
+
+Sidechain Modelling
+--------------------------------------------------------------------------------
+
+You can (re-)construct the sidechains in a model from the command line.
+
+.. code-block:: console
+
+ $ usage: build-sidechains [-h] (-p <FILE> | -e <FILE>) [-o <FILENAME>] [-k] [-n]
+ [-r] [-i] [-s]
+
+Example usage:
+
+.. code-block:: console
+
+ $ pm build-sidechains -p input.pdb
+
+This reads a structure stored in in.pdb, strips all sidechains,
+detects and models disulfid bonds and reconstructs all sidechains with the
+flexible rotamer model. The result is stored as :file:`out.pdb`.
+The output filename can be controlled with the ``-o`` flag.
+
+A structure can be provided in PDB (``-p``) or in any format readable by the
+:func:`ost.io.LoadEntity` method (``-e``). In the latter case, the format is
+chosen by file ending. Recognized File Extensions: ``.ent``, ``.pdb``,
+``.ent.gz``, ``.pdb.gz``, ``.cif``, ``.cif.gz``.
+
+Several flags control the modelling behaviour:
+
+.. option:: -k, --keep-sidechains
+
+ Keep existing sidechains.
+
+.. option:: -n, --no-disulfids
+
+ Do not build disulfid bonds before sidechain optimization
+
+.. option:: -r, --rigid-rotamers
+
+ Do not use rotamers with subrotamers
+
+.. option:: -i, --backbone-independent
+
+ Use backbone independent rotamer library
+ (from :meth:`promod3.sidechain.LoadLib`) instead of the default backbone
+ dependent one (from :meth:`promod3.sidechain.LoadBBDepLib`)
+
+.. option:: -s, --no-subrotamer-optimization
+
+ Dont do subrotamer optimization if flexible rotamer model is used
+
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
index a601d619b695a46a2f15352e312e4bdaf91ab90f..7f975230cc64e605d3b77f8ef48eaf322bb69459 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
.. _building-promod:
Building |project|
@@ -7,18 +23,15 @@ Building |project|
Dependencies
--------------------------------------------------------------------------------
-|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version
-1.7. |ost_s| must be configured and compiled with ``ENABLE_MM=1`` to use |openmm|_.
-To create the build system, |cmake|_ is required in version
-2.8.7 or higher. |python|_ works well from version 2.7. For |ost_s| and the
-|C++| bit of |project|, |boost|_ is required in version 1.53.0 (the same as
-used for |ost_s|). Also |eigen3|_ is needed. To build
-documentation, |sphinx|_ 1.2b1 is required.
-
+|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version 1.8.
+|ost_s| must be configured and compiled with ``ENABLE_MM=1`` to use |openmm|_.
+To create the build system, |cmake|_ is required. The same versions of |python|_
+and |boost|_ are needed as used in |ost_s|. For |eigen3|_ we need at least
+version 3.3.0. To build the documentation, |sphinx|_ is required.
The currently preferred versions are:
-* |ost_s|_ 1.7
+* |ost_s|_ 1.9
* |openmm|_ 7.1.1
* |cmake|_ 2.8.12
* |python|_ 2.7.5
diff --git a/doc/html/_sources/changelog.txt b/doc/html/_sources/changelog.txt
index 20e7a36a38c83e77511d058c8e9f459732964672..879c3a6ca5fe7c62c2a0760b5352336420d6fea9 100644
--- a/doc/html/_sources/changelog.txt
+++ b/doc/html/_sources/changelog.txt
@@ -5,6 +5,26 @@
Changelog
================================================================================
+Release 1.3.0
+--------------------------------------------------------------------------------
+
+* Apply Apache Version 2.0 License to the project
+* 2010 Dunbrack rotamer library has been replaced by an own backbone dependent
+ rotamer library. All scripts required to reproduce the data are in
+ extras/data_generation/rotamer_library
+* Penultimate rotamer library has been replaced by an own backbone independent
+ rotamer library. All scripts required to reproduce the data are in
+ extras/data_generation/rotamer_library
+* SampleMonteCarlo function moved to Python. This makes it possible to provide
+ sampler/closer/scorer/cooler objects implemented in both, Python and C++
+* Action script for sidechain modelling
+* Allow sequence profiles as input for build-model action script.
+* Recipe for Docker / Singularity container
+* Check peptide bonds when building a RawModel. Treat as gap if bond is
+ stereochemically problematic despite being in sequence.
+* Several minor bug fixes, improvements, and speed-ups
+
+
Release 1.2.0
--------------------------------------------------------------------------------
diff --git a/doc/html/_sources/container/docker.txt b/doc/html/_sources/container/docker.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc5faaa095f903fc4f5a68ba776b5b8b144874ff
--- /dev/null
+++ b/doc/html/_sources/container/docker.txt
@@ -0,0 +1,116 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+Docker
+======
+
+Build Docker Image
+------------------
+
+In order to build the image:
+
+.. code-block:: bash
+
+ sudo docker build --tag <IMAGE_NAME> -f Dockerfile <PATH_TO_DOCKERFILE_DIR>
+
+You can chose any image name (tag) eg. promod.
+
+
+Run scripts and actions with OST/PM
+-----------------------------------
+
+If script or action requires some external files eg. PDBs, they have to be located in the
+path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
+path. Eg. assuming that we have a struc.pdb file in /home/<USER>/pdbs directory and
+a script.py in /home/<USER> we could mount the /home/<USER> to /home in docker as
+above by specifying -v /home/<USER>:/home. To run the script we thus need to
+provide the (relative) path to the script and (relative) path to the file eg:
+
+.. code-block:: bash
+
+ sudo docker run --rm -v /home/<USER>:/home <IMAGE_NAME> pm script.py pdbs/struct.pdb
+
+or with absolute paths:
+
+.. code-block:: bash
+
+ sudo docker run --rm -v /home/<USER>:/home <IMAGE_NAME> pm /home/script.py /home/pdbs/struct.pdb
+
+An alternative is to mount the current working directory into the docker home:
+
+.. code-block:: bash
+
+ sudo docker run --rm -v $(pwd):/home <IMAGE_NAME> pm script.py pdbs/struct.pdb
+
+
+.. _docker_compound_lib:
+
+The Compound Library
+--------------------
+
+At build time of the container, a :class:`~ost.conop.CompoundLib` is generated.
+Compound libraries contain information on chemical compounds, such as their
+connectivity, chemical class and one-letter-code. The compound library has
+several uses, but the most important one is to provide the connectivy
+information for the rule-based processor.
+
+The compound library is generated with the components.cif dictionary provided by
+the PDB. As the PDB updates regularly, the compound library shipped with the
+container is quickly outdated. For most use cases, this is not problematic.
+However, if you rely on correct connectivity information of the latest and
+greatest compounds, you have to keep the compound library up to date manually.
+
+The suggested way of doing this is to generate your own compound library and
+mount it into the container where the original compound lib resides to
+override it.
+
+The simplest way to create a compound library is to use the
+:program:`chemdict_tool` available in the container. The program allows you
+to import the chemical description of the compounds from a MMCIF dictionary,
+e.g. the components.cif dictionary provided by the PDB.
+The latest dictionary can be downloaded from the
+`wwPDB site <http://www.wwpdb.org/ccd.html>`_.
+The files are rather large, it is therefore recommended to download the
+gzipped version.
+
+After downloading the file use :program:`chemdict_tool` in the container to
+convert the MMCIF dictionary into our internal format:
+
+.. code-block:: bash
+
+ sudo docker run --rm -v $(pwd):/home <IMAGE_NAME> chemdict_tool create components.cif.gz compounds.chemlib
+
+To run a script with the upated compound library, use the -v option for mounting/overriding:
+
+.. code-block:: bash
+
+ sudo docker run --rm -v /home/<USER>:/home -v <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> <IMAGE_NAME> pm script.py pdbs/struct.pdb
+
+with COMPLIB_DIR_LOCALHOST being the directory that contains the newly generated
+compound library with name compounds.chemlib and COMPLIB_DIR_CONTAINER the
+according path in the container.
+If you didnt change anything in the Dockerfile, the latter should be
+/usr/local/share/ost_complib
+
+You can check whether the default lib is successfully overriden by looking at the
+output when running a Python script with following code in the container:
+
+.. code-block:: python
+
+ import promod3 # required to setup default lib
+ from ost import conop
+ lib = conop.GetDefaultLib()
+ print lib.GetCreationDate()
diff --git a/doc/html/_sources/container/index.txt b/doc/html/_sources/container/index.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9cf79e23f891def49bfd42346f0e31c027838b79
--- /dev/null
+++ b/doc/html/_sources/container/index.txt
@@ -0,0 +1,36 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+ProMod3 and Containers
+======================
+
+
+ProMod3 offers build recipes for Docker and Singularity in
+<PATH_TO_PROMOD3_CHECKOUT>/container. To avoid code duplication,
+the Singularity container bootstraps from the Docker one and adds
+some sugar on top.
+
+.. toctree::
+ :maxdepth: 1
+
+ Docker <docker>
+ Singularity <singularity>
+
+
+
+
+
+
diff --git a/doc/html/_sources/container/singularity.txt b/doc/html/_sources/container/singularity.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ede88ddb3845154c24ea1534d96ebc6bb964b02a
--- /dev/null
+++ b/doc/html/_sources/container/singularity.txt
@@ -0,0 +1,120 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+Singularity
+===========
+
+We do not provide a "standalone" Singularity image, but rather bootstrap from a
+Docker image.
+
+Build Singularity Image
+-----------------------
+
+You can pull the Docker image to start with from two different sources.
+
+Option One:
+
+You built the Docker image locally and want to use it as a starting point. For
+this we have to fire up a local Docker registry and pull from there. Let's
+assume you built the Docker image with tag promod.
+
+Fire the local Registry and push the promod image to it:
+
+.. code-block:: bash
+
+ sudo docker run -d -p 5000:5000 --restart=always --name registry registry:2
+ sudo docker tag promod localhost:5000/promod
+ sudo docker push localhost:5000/promod
+
+Make sure, that on top of your Singularity recipe you have something like:
+
+.. code-block:: bash
+
+ BootStrap: docker
+ Registry: http://localhost:5000
+ Namespace:
+ From: promod:latest
+
+and build the image with:
+
+.. code-block:: bash
+
+ sudo SINGULARITY_NOHTTPS=1 singularity build promod.img Singularity
+
+
+Option Two:
+
+You pull a Docker image from an external Docker registry.
+Fill in a lot of words as soon as its on Dockerhub. Many words. The best words.
+
+and build the image with:
+
+.. code-block:: bash
+
+ sudo singularity build promod.img Singularity
+
+
+Run scripts and actions with OST/PM
+-----------------------------------
+
+The created container can run the ost, pm or chemdict_tool executables.
+For convenience, a jupyter notebook playground with OST, ProMod3 and nglview is
+available.
+
+To run ost, pm or chemdict_tool executables, use the exec command.
+E.g. to run scripts with pm:
+
+.. code-block:: bash
+
+ singularity exec <IMAGE> pm my_script.py [options]
+
+The jupyter notebook is setup as an app in the container.
+To get help on how to run it:
+
+.. code-block:: bash
+
+ singularity run --app Notebook <IMAGE> --help
+
+
+The Compound Library
+--------------------
+
+You'll have the exact same problem with outdated compound libraries as in the
+raw Docker image. You can find more information on that matter in the Docker
+section of the documentation: :ref:`docker_compound_lib`.
+
+The same trick of mounting an up to date compound library from the local host into
+the container applies. The two relevant commands for Singularity are building
+a new library and mount it.
+
+Build a new library:
+
+.. code-block:: bash
+
+ singularity exec <IMAGE_NAME> chemdict_tool create components.cif.gz compounds.chemlib
+
+Run some script with an updated compound library from localhost:
+
+.. code-block:: bash
+
+ singularity exec -B <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> <IMAGE_NAME> pm my_script.py
+
+Same as for the Docker, if you didn't meddle with the original Dockerfile,
+<COMPLIB_DIR_CONTAINER> should be /usr/local/share/ost_complib.
+<COMPLIB_DIR_LOCALHOST> is the directory that contains the compound lib with the
+name compounds.chemlib that you created before. Make sure that everything works
+as expected by executing the exact same lines of Python code as described
+in the Docker documentation: :ref:`docker_compound_lib`.
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index ae3c842c641522624e55d208c51e6a146773a033..3a261b411ab249a578a79cf8c0760ef1deb68150 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Contributing
================================================================================
@@ -475,23 +491,19 @@ Hence, the :file:`CMakeLists.txt` of the :file:`doc` directory of a module is
crucial. For documentation which does not relate to a particular module, the
repository comes with a top-level :file:`doc` directory.
-While you should not spend to much time thinking about how to format
-documentation, here is a helpful list of standard formatters:
-http://sphinx-doc.org/en/stable/markup/inline.html
-
If you write new functionality for |project|, or fix bugs, feel free to extend
the :file:`CHANGELOG` file. It will be automatically pulled into the
documentation.
It is highly recommended to add code examples with your documentation. For that
-purpose, you should write a fully runnable script, which is to be placed in the
+purpose, you should write a fully runnable script which is to be placed in the
:file:`doc/tests/scripts` directory. The script is to be runnable from within
the :file:`doc/tests` directory as ``pm SCRIPTPATH`` and may use data stored in
the :file:`doc/tests/data` directory. The script and any data needed by it, must
then be referenced in the :file:`doc/tests/CMakeLists.txt` file. Afterwards,
-they can be included in the documentation using the
-`literalinclude <http://www.sphinx-doc.org/en/stable/markup/code.html#includes>`_
-directive. For instance, if you add a new example code :file:`loop_main.py`,
+they can be included in the documentation using the literalinclude
+directive.
+For instance, if you add a new example code :file:`loop_main.py`,
you would add it in your module documentation as follows:
.. code-block:: rest
diff --git a/doc/html/_sources/core/geometry.txt b/doc/html/_sources/core/geometry.txt
index 3d36b1bd13c2506eb51fad21c9bd61712a9ad5c8..1ac82fac9c1ecc650be29cd7a099f122ed7a6a5a 100644
--- a/doc/html/_sources/core/geometry.txt
+++ b/doc/html/_sources/core/geometry.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Geometry functions
================================================================================
@@ -53,7 +69,7 @@ Geometry functions
.. function:: ConstructCBetaPos(n_pos, ca_pos, c_pos)
Constructs position of C-beta atom given the positions of the backbone nitrogen,
- C-alpha and c atoms.
+ C-alpha and C atoms.
:param n_pos: Position of nitrogen atom
:type n_pos: :class:`~ost.geom.Vec3`
diff --git a/doc/html/_sources/core/graph_minimizer.txt b/doc/html/_sources/core/graph_minimizer.txt
index a1ddb9639f2816086ee62f64861e5e2e5b9dacb2..a38bca5895963caf439339bf5e57af6459d10847 100644
--- a/doc/html/_sources/core/graph_minimizer.txt
+++ b/doc/html/_sources/core/graph_minimizer.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Graph Minimizer
================================================================================
@@ -228,8 +244,3 @@ a set :math:`X=[x_1, x_2, ..., x_n]` that minimizes:
representing the single solutions minimizing
the overall energy function.
The second element is the according energy value.
-
-
-.. [goldstein1994] Goldstein RF (1994). Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J.
-
-.. [leach1998] Leach AR, Lemon AP (1998). Explring the conformational space of prootein side chains using dead-end elimination and the A* algorithm. Proteins.
diff --git a/doc/html/_sources/core/helper.txt b/doc/html/_sources/core/helper.txt
index 03d2cef127c61cb16af4680f5580673c34dae2e7..6684d1247ae7c8a53785187b4dd24a4b38737ac0 100644
--- a/doc/html/_sources/core/helper.txt
+++ b/doc/html/_sources/core/helper.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.core.helper` - Shared Functionality For the Everything
================================================================================
diff --git a/doc/html/_sources/core/index.txt b/doc/html/_sources/core/index.txt
index 2af5fca9cace92deef375d4857a1c9b55f9ec0d5..91b0d9c39c77212b3747e804b1a12191f422a213 100644
--- a/doc/html/_sources/core/index.txt
+++ b/doc/html/_sources/core/index.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.core` - ProMod3 Core Functionality
================================================================================
diff --git a/doc/html/_sources/core/pm3argparse.txt b/doc/html/_sources/core/pm3argparse.txt
index 927faf547e89cc54e508fa38abfbf18b39fb217b..f6a048252ec82ce7dabbb48da87a242e26d82aa4 100644
--- a/doc/html/_sources/core/pm3argparse.txt
+++ b/doc/html/_sources/core/pm3argparse.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.core.pm3argparse` - Parsing Command Lines
================================================================================
diff --git a/doc/html/_sources/core/runtime_profiling.txt b/doc/html/_sources/core/runtime_profiling.txt
index 07c51ad5bb447b99aaf0335a1cd5f8e48d4a5c75..44bd8621a4ad7a5b77b185f5a9be069afbc9440c 100644
--- a/doc/html/_sources/core/runtime_profiling.txt
+++ b/doc/html/_sources/core/runtime_profiling.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Runtime profiling
================================================================================
diff --git a/doc/html/_sources/core/setcompoundschemlib.txt b/doc/html/_sources/core/setcompoundschemlib.txt
index fb0223432967ffc2ed53d542191c52fce4fb770b..2c6e660ffb8e1cf6d4d3df93a7f16fda04340724 100644
--- a/doc/html/_sources/core/setcompoundschemlib.txt
+++ b/doc/html/_sources/core/setcompoundschemlib.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:func:`~promod3.SetCompoundsChemlib`
================================================================================
diff --git a/doc/html/_sources/dev_setup.txt b/doc/html/_sources/dev_setup.txt
index 3b450accf0a5cb18ada95e2e7b1ab6d0e35799dd..91909c30154907dcbb269a4d5cb805ef6af9d1bf 100644
--- a/doc/html/_sources/dev_setup.txt
+++ b/doc/html/_sources/dev_setup.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
|project| Setup
================================================================================
diff --git a/doc/html/_sources/developers.txt b/doc/html/_sources/developers.txt
index 3955c47c1cab44e3274e54919b0b0d949299c0f6..f15f85db820e896de015b614c871d0317030dc38 100644
--- a/doc/html/_sources/developers.txt
+++ b/doc/html/_sources/developers.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Documentation For Developers
===============================================================================
diff --git a/doc/html/_sources/gettingstarted.txt b/doc/html/_sources/gettingstarted.txt
index 9b2b8024b6cb6e7cd2e98aa10c3c86df5754f645..2bed4049fe4de07f7fafe0994c1867fd40f5be61 100644
--- a/doc/html/_sources/gettingstarted.txt
+++ b/doc/html/_sources/gettingstarted.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Getting Started
================================================================================
diff --git a/doc/html/_sources/index.txt b/doc/html/_sources/index.txt
index 0699c60545cfc1014f4753e6f9a6b8647e822cc7..74cb15e8f60d131996ed5d81cc1b0950b4abf718 100644
--- a/doc/html/_sources/index.txt
+++ b/doc/html/_sources/index.txt
@@ -1,28 +1,41 @@
-.. ProMod3 documentation master file, created by
- sphinx-quickstart on Thu Oct 10 23:17:00 2013.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Welcome To ProMod3's Documentation!
-===================================
-
-Contents:
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+ProMod3
+=======
+
+ProMod3 is a modelling engine based on the OpenStructure [biasini2013]_
+computational structural biology framework that can perform all steps required
+to generate a protein model by homology. Its modular design aims at
+implementing flexible modelling pipelines and fast prototyping of novel
+algorithms.
+
+
+Documentation
+=============
.. toctree::
- :maxdepth: 2
+ :maxdepth: 2
- Users <users>
- Developers <developers>
+ Users <users>
.. toctree::
- :maxdepth: 1
-
- changelog
-
-
-Indices And Tables
-==================
+ :maxdepth: 1
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+ Developers <developers>
+ License <license>
+ References <references>
+ Changelog <changelog>
diff --git a/doc/html/_sources/license.txt b/doc/html/_sources/license.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ff0971e35f8e7c9fdf99a1e6191409ae2a7e375
--- /dev/null
+++ b/doc/html/_sources/license.txt
@@ -0,0 +1,22 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+License
+=======
+
+
+
+.. literalinclude:: license.txt
diff --git a/doc/html/_sources/loop/all_atom.txt b/doc/html/_sources/loop/all_atom.txt
index b2f19a81997933e3ac1815f2a7759cb0f8b06613..eaeb294774c88c8f4c239fc493e2eb641ee7408f 100644
--- a/doc/html/_sources/loop/all_atom.txt
+++ b/doc/html/_sources/loop/all_atom.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Handling All Atom Positions
================================================================================
diff --git a/doc/html/_sources/loop/backbone.txt b/doc/html/_sources/loop/backbone.txt
index 15288fb3c55e5af3ff5a698fc8fc41a9223778a4..3acc2f8e1a2b74a97e559c050e71eb97c777802e 100644
--- a/doc/html/_sources/loop/backbone.txt
+++ b/doc/html/_sources/loop/backbone.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Representing Loops
================================================================================
@@ -143,7 +159,8 @@ The BackboneList class
:type sequence: :class:`str`
:raises: :exc:`~exceptions.RuntimeError` if *sequence* contains a one letter
- code which is not one of the 20 default amino acids.
+ code which is not one of the 20 default amino acids or size of
+ *sequence* does not match.
.. method:: Extract(from, to)
@@ -450,8 +467,8 @@ The BackboneList class
.. method:: SetBackrub(index, primary_rot_angle, flanking_rot_angle_one, flanking_rot_angle_two)
- Applies a backrub motion at residue defined by **index**. The first
- rotation axis is defined by the CA positions from residues at
+ Applies a backrub motion [davis2006]_ at residue defined by **index**.
+ The first rotation axis is defined by the CA positions from residues at
**index** -1 and **index** +1. All atoms in between get rotated around this
axis by **primary_rot_angle**. To restore the the hydrogen bond network
of the two transformed oxygens, the backrub motion gets completed by
diff --git a/doc/html/_sources/loop/index.txt b/doc/html/_sources/loop/index.txt
index f60393092beaea6d8315036c82ee7dfb02b267d7..1b4199c068f6532d019465b011fb112ef140443f 100644
--- a/doc/html/_sources/loop/index.txt
+++ b/doc/html/_sources/loop/index.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.loop` - Loop Handling
================================================================================
diff --git a/doc/html/_sources/loop/load_loop_objects.txt b/doc/html/_sources/loop/load_loop_objects.txt
index 00365ca9dcbf02c832bd8ea7c018b31f5e99a78f..a8410bea4fa9ec2f5a7ff3ac96ed26d06f707aea 100644
--- a/doc/html/_sources/loop/load_loop_objects.txt
+++ b/doc/html/_sources/loop/load_loop_objects.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Loading Precomputed Objects
================================================================================
@@ -10,7 +26,7 @@ Several data objects are used throughout the loop module.
.. method:: LoadTorsionSampler(seed=0)
Loads and returns a torsion sampler with an amino acid grouping
- as defined by Solis & Rachovsky [1] that has been trained on
+ as defined by [solis2006]_ that has been trained on
non-redundant protein structures.
:param seed: Seed for internal random number generator
@@ -24,7 +40,7 @@ Several data objects are used throughout the loop module.
.. method:: LoadTorsionSamplerCoil(seed=0)
Loads and returns a torsion sampler with an amino acid grouping
- as defined by Solis & Rachovsky [1] that has been trained on coil
+ as defined by [solis2006]_ that has been trained on coil
residues of non-redundant protein structures.
:param seed: Seed for internal random number generator
@@ -38,7 +54,7 @@ Several data objects are used throughout the loop module.
.. method:: LoadTorsionSamplerHelical(seed=0)
Loads and returns a torsion sampler with an amino acid grouping
- as defined by Solis & Rachovsky [1] that has been trained on helical
+ as defined by [solis2006]_ that has been trained on helical
residues of non-redundant protein structures.
:param seed: Seed for internal random number generator
@@ -52,7 +68,7 @@ Several data objects are used throughout the loop module.
.. method:: LoadTorsionSamplerExtended(seed=0)
Loads and returns a torsion sampler with an amino acid grouping
- as defined by Solis & Rachovsky [1] that has been trained on extended
+ as defined by [solis2006]_ that has been trained on extended
residues of non-redundant protein structures.
:param seed: Seed for internal random number generator
@@ -63,28 +79,22 @@ Several data objects are used throughout the loop module.
:rtype: :class:`TorsionSampler`
-.. method:: LoadFragDB()
-
- Loads and returns a FragDB containing fragments up to the length of 14,
- therefore capable of bridging gaps up to the length of 12.
+.. method:: LoadStructureDB()
- :returns: The Fragment database
- :rtype: :class:`FragDB`
+ Loads and returns a structure db containing roughly 21000 chains form the
+ PDB with seqid redundancy cutoff of 60%
-.. method:: LoadStructureDB(load_frequencies=True)
+ :returns: The structure db
+ :rtype: :class:`StructureDB`
- Loads and returns a structure db containing roughly 24000 chains form the
- PDB with redundancy cutoff of 90%
- :param load_frequencies: If True, the full database including profile
- information gets loaded (see
- :meth:`StructureDB.Load`).
- :type load_frequencies: :class:`bool`
+.. method:: LoadFragDB()
- :returns: The structure db
- :rtype: :class:`StructureDB`
-
+ Loads and returns a FragDB containing fragments up to the length of 14,
+ therefore capable of bridging gaps up to the length of 12. The returned
+ databases contains the location of fragments in the :class:`StructureDB`
+ returned by :meth:`LoadStructureDB`.
-[1] A. D. Solis and S. Rackovsky. Improvement of statistical potentials and
- threading score functions using information maximization.
- Proteins, 62(4):892–908, Mar 2006.
+ :returns: The Fragment database
+ :rtype: :class:`FragDB`
+
\ No newline at end of file
diff --git a/doc/html/_sources/loop/mm_system_creation.txt b/doc/html/_sources/loop/mm_system_creation.txt
index 7ad0c03a88e75d071685fbee47a3d5f88dcc6530..87b6fb05808a9d70e5e489638d087cd99d95c46c 100644
--- a/doc/html/_sources/loop/mm_system_creation.txt
+++ b/doc/html/_sources/loop/mm_system_creation.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Generate :mod:`ost.mol.mm` systems
================================================================================
diff --git a/doc/html/_sources/loop/structure_db.txt b/doc/html/_sources/loop/structure_db.txt
index a967d08a3823e6ae0eba26410ba7bdfa313ba358..b3089c7248bc40d5f4bd292125795b2edde82204 100644
--- a/doc/html/_sources/loop/structure_db.txt
+++ b/doc/html/_sources/loop/structure_db.txt
@@ -1,9 +1,25 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Structural Data
================================================================================
.. currentmodule:: promod3.loop
-The structural database serves as a container for structural backbone and
+The :class:`StructureDB` serves as a container for structural backbone and
sequence data. Custom accessor objects can be implemented that relate
arbitrary features to structural data. Examples provided by ProMod3 include
accession using matching stem geometry (see: :class:`FragDB`) or sequence
@@ -41,7 +57,7 @@ Defining Chains and Fragments
.. class:: CoordInfo()
The CoordInfo gets automatically generated when new chains are added to
- the structural database. It contains internal information of how a
+ a :class:`StructureDB`. It contains internal information of how a
connected stretch of residues is stored in the database.
.. attribute:: id
@@ -68,17 +84,17 @@ Defining Chains and Fragments
Residue number of first residue in the added stretch. The residue number
is relative to the SEQRES provided in the input profile when adding the
- stuff to the structure db.
+ stuff to the structure db. (:class:`int`)
.. attribute:: shift
Translation from original coordinates that has been applied before storing
- structural information in db.
+ structural information in db. (:class:`ost.geom.Vec3`)
.. class:: FragmentInfo(chain_index, offset, length)
- The FragmentInfo defines any fragment in the structural database. If you
+ The FragmentInfo defines any fragment in the :class:`StructureDB`. If you
implement your own accessor object, thats the information you want to store.
:param chain_index: Fills :attr:`chain_index`
@@ -89,8 +105,8 @@ Defining Chains and Fragments
.. attribute:: chain_index
- The index of the chain (defined by :class:`CoordInfo`) in the structure db
- this particle belongs to. (:class:`int`)
+ The index of the chain (defined by :class:`CoordInfo`) in the
+ :class:`StructureDB` this particle belongs to. (:class:`int`)
.. attribute:: offset
@@ -127,7 +143,7 @@ database, you might want to consider two things:
to backbone coordinates and sequence.
If you want to store all data possible, use All. If you only want a subset,
you can combine some of the datatypes with a bitwise or operation
- (see example script for StructureDB). One important note:
+ (see example script for :class:`StructureDB`). One important note:
If you enable AAFrequenciesStruct, the actual information is not automatically
assigned. Only the according memory is allocated and set to zero, the actual
information must be assigned manually (see example script again...).
@@ -138,8 +154,8 @@ database, you might want to consider two things:
.. class:: StructureDB(data_to_store)
- Generates an empty StructureDB that can be filled with content through
- :func:`AddCoordinates`. The information extracted there is defined by
+ Generates an empty :class:`StructureDB` that can be filled with content
+ through :func:`AddCoordinates`. The information extracted there is defined by
*data_to_store*. Have a look at the :class:`StructureDBDataType`
documentation and at the example script...
@@ -263,7 +279,7 @@ database, you might want to consider two things:
.. method:: GetCoordIdx(id, chain_name)
- :returns: The StructureDB indices (in [0, :meth:`GetNumCoords`-1]) of
+ :returns: The :class:`StructureDB` indices (in [0, :meth:`GetNumCoords`-1])
of all coords (connected stretches) with matching
*id* / *chain_name*.
:rtype: :class:`list` of :class:`int`
@@ -281,7 +297,7 @@ database, you might want to consider two things:
index *idx*.
:rtype: :class:`CoordInfo`
- :param idx: The StructureDB index (in [0, :meth:`GetNumCoords`-1])
+ :param idx: The :class:`StructureDB` index (in [0, :meth:`GetNumCoords`-1])
:type idx: :class:`int`
@@ -379,7 +395,8 @@ database, you might want to consider two things:
.. method:: GetSolventAccessibilitites(fragment)
:returns: Solvent accessibility for each residue of *fragment* in square A
- as calculated by dssp.
+ as calculated by :meth:`~ost.mol.alg.Accessibility` when adding
+ the structure to the database.
:rtype: :class:`list` of :class:`float`
:param fragment: Fragment definition from which to extract the solvent
@@ -472,7 +489,7 @@ database, you might want to consider two things:
to make sure that you have no close homologue in the database.
:rtype: :class:`StructureDB`
- :param indices: StructureDB indices to be added to the sub database (in [0,
+ :param indices: Indices of chains to be added to the sub database (in [0,
:meth:`GetNumCoords`-1])
:type indices: :class:`list`
@@ -532,14 +549,16 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
.. method:: GetAngularBinSize()
- The size of the bins for the 4 angles describing the stem geometry and used to organize the fragments in the database.
+ The size of the bins for the 4 angles describing the stem geometry and used
+ to organize the fragments in the database.
:return: The bin size in degrees
:rtype: :class:`int`
.. method:: GetDistBinSize()
- The size of the bins for the distance describing the stem geometry and used to organize the fragments in the database.
+ The size of the bins for the distance describing the stem geometry and used
+ to organize the fragments in the database.
:return: The bin size
:rtype: :class:`float`
@@ -547,8 +566,13 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
.. method:: AddFragments(fragment_length, rmsd_cutoff, structure_db)
- Iterates over all fragments of length **fragment_length** in the given structural database and adds them to the fragment database. Fragments will be skipped if there is already a fragment in the database that has an RMSD to the one being added smaller than **rmsd_cutoff**.
- As the fragments are added they are organized in bins described by their length and the geometry of their N and C stem.
+ Iterates over all fragments of length **fragment_length** in
+ **structure_db** and adds them to the fragment database.
+ Fragments will be skipped if there is already a fragment in the database
+ that has an RMSD smaller than **rmsd_cutoff**, where RMSD is calculated
+ upon superposing the stem residues.
+ As the fragments are added they are organized in bins described by their
+ length and the geometry of their N and C stem.
:param fragment_length: The length of the fragments that should be added to the databse
:param rmsd_cutoff: The minimal RMSD between two fragments in the fragment database
@@ -560,7 +584,7 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
.. method:: PrintStatistics()
- Prints statistics about the fragment databse, notably:
+ Prints statistics about the fragment database, notably:
1. the number of different stem groups (number of bins used to group the
fragments according to the geometry of their stem residues)
@@ -598,12 +622,12 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
:param loop_length: The length of the fragments
:type loop_length: :class:`int`
- :returns: True if fragments of given length exist. This function is quick.
+ :returns: True if fragments of given length exist.
:rtype: :class:`bool`
.. method:: MaxFragLength()
- :returns: Maximal fragment length contained in db. This function is quick.
+ :returns: Maximal fragment length contained in db.
:rtype: :class:`int`
.. method:: SearchDB(n_stem, c_stem, frag_size, extra_bins=0)
@@ -635,7 +659,7 @@ In some cases you might want to use the :class:`StructureDB` to search
for fragments that possibly represent the structural conformation of interest.
The :class:`Fragger` searches a :class:`StructureDB` for n fragments,
that maximize a certain score and gathers a set of fragments with a guaranteed
-structural diversity based on an rmsd_threshold. You can use the :class:`Fragger`
+structural diversity based on an rmsd threshold. You can use the :class:`Fragger`
wrapped in a full fletched pipeline implemented in
:class:`~promod3.modelling.FraggerHandle` or search for fragments from scratch
using an arbitrary linear combination of scores:
@@ -882,7 +906,7 @@ The PsipredPrediction class
.. class:: PsipredPrediction
- A container for the secondary structure prediction by Psipred.
+ A container for the secondary structure prediction by PSIPRED [Jones1999]_.
.. method:: PsipredPrediction()
@@ -974,11 +998,3 @@ The PsipredPrediction class
.. method:: __len__()
:returns: Number of elements in container
-
-
-
-.. [soding2005] Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.
-.. [chakravarty1999] Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.
-.. [zhou2005] Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.
-.. [Jones1999] Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.
-.. [kabsch1983] Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 2577-2637.
diff --git a/doc/html/_sources/loop/torsion_sampler.txt b/doc/html/_sources/loop/torsion_sampler.txt
index 0962c3563d62638c5948f7d6f08189b2fcf6a95b..8344079a5065f12c19e844f50be70636032ba365 100644
--- a/doc/html/_sources/loop/torsion_sampler.txt
+++ b/doc/html/_sources/loop/torsion_sampler.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Sampling Dihedral Angles
================================================================================
diff --git a/doc/html/_sources/modelling/algorithms.txt b/doc/html/_sources/modelling/algorithms.txt
index 7ff5ae3a33e08ccccdf6d98f87abe2748e1d0d19..51357bc0615a49e58f2ef12f3efad67eeb3b003d 100644
--- a/doc/html/_sources/modelling/algorithms.txt
+++ b/doc/html/_sources/modelling/algorithms.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Modelling Algorithms
================================================================================
diff --git a/doc/html/_sources/modelling/gap_handling.txt b/doc/html/_sources/modelling/gap_handling.txt
index e939f9f60fa779b43bfdb196e0649ebd28306a08..b70d39a57558559a9ee4f6240384ffdbeb4df34c 100644
--- a/doc/html/_sources/modelling/gap_handling.txt
+++ b/doc/html/_sources/modelling/gap_handling.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Handling Gaps
================================================================================
diff --git a/doc/html/_sources/modelling/index.txt b/doc/html/_sources/modelling/index.txt
index 27ed61013a17190ebef7f0afb0027241c0e19294..ce9be313f8c26c747a5e1d711c9bf44751ac8587 100644
--- a/doc/html/_sources/modelling/index.txt
+++ b/doc/html/_sources/modelling/index.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.modelling` - Protein Modelling
================================================================================
diff --git a/doc/html/_sources/modelling/loop_candidates.txt b/doc/html/_sources/modelling/loop_candidates.txt
index d0711c5a7c89292a61e3f1547ed28af62841382b..927107a0ddaa78b2bb6efe78b80c0f1dbc5aae1e 100644
--- a/doc/html/_sources/modelling/loop_candidates.txt
+++ b/doc/html/_sources/modelling/loop_candidates.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Handling Loop Candidates
================================================================================
diff --git a/doc/html/_sources/modelling/loop_closing.txt b/doc/html/_sources/modelling/loop_closing.txt
index 7ec7230b20a4e32fd9cc1f15a9e84ea7b549c113..21b842f5d1e25b00dc2f2cb863bf8124ccfb8f81 100644
--- a/doc/html/_sources/modelling/loop_closing.txt
+++ b/doc/html/_sources/modelling/loop_closing.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Fitting Loops Into Gaps
================================================================================
@@ -7,7 +23,7 @@ Loops often need to undergo conformational changes to fit into gaps defined by
stem residues. |project| implements two algorithms performing this task:
* Cyclic coordinate descent (CCD) [canutescu2003]_
- * Kinematic closure (KIC) [mandell2009]_
+ * Kinematic closure (KIC) [coutsias2005]_
In case of small gaps or small issues in the loop you might also consider the
:class:`BackboneRelaxer`.
@@ -374,8 +390,4 @@ Example usage:
:rtype: :class:`~promod3.loop.MmSystemCreator`
-.. rubric:: Citations
-
-.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003). Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12(5):963–972.
-.. [mandell2009] Mandell DJ, Coutsias EA and Kortemme T (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 6(8):551-2.
diff --git a/doc/html/_sources/modelling/model_checking.txt b/doc/html/_sources/modelling/model_checking.txt
index 97d7f69a83735d2757ede0afee224f181afdd6d5..03763e178971929ce13573f5ac8d72dc6624434d 100644
--- a/doc/html/_sources/modelling/model_checking.txt
+++ b/doc/html/_sources/modelling/model_checking.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Model Checking
================================================================================
diff --git a/doc/html/_sources/modelling/monte_carlo.txt b/doc/html/_sources/modelling/monte_carlo.txt
index 56e572a8788749bde35c415893a964126c5e67b9..1cb924b406ab017598f909d34872c0394697cb72 100644
--- a/doc/html/_sources/modelling/monte_carlo.txt
+++ b/doc/html/_sources/modelling/monte_carlo.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Generating Loops De Novo
================================================================================
@@ -21,46 +37,7 @@ Carlo sampling to the N-terminal part of crambin:
.. literalinclude:: ../../../tests/doc/scripts/modelling_monte_carlo.py
-.. method:: SampleMonteCarlo(sampler, closer, scorer, cooler, steps,\
- bb_list, initialize=True, seed=0,\
- lowest_energy_conformation=True)
-
- A convenient function to perform Monte Carlo sampling using a simulated
- annealing scheme. In every iteration, a new loop conformation gets proposed by
- the provided *sampler* and closed by the *closer*. Upon scoring, this new
- conformation gets accepted/rejected using a metropolis criterion based on the
- temperature given by the *cooler*
- => acceptance probability: exp(-delta_score/T).
- The result is stored in *bb_list* and is either the lowest energy conformation
- ever encountered or the last accepted proposal.
-
- :param sampler: Sampler object capable of initializing and altering
- conformations.
- :param closer: Closer object to adapt a new conformation to
- the environment.
- :param scorer: Scorer object to score new loop conformations.
- :param cooler: Cooler object to control the temperature of the
- Monte Carlo trajectory.
- :param steps: Number of Monte Carlo iterations to be performed.
- :param bb_list: The chosen conformation gets stored here.
- :param initialize: Whether a new bb_list should be generated as starting
- point, based on the samplers Initialize function.
- The input *bb_list* gets used otherwise.
- :param seed: Seed for internal random number generator.
- :param lowest_energy_conformation: If True, we choose the lowest scoring
- conformation of the trajectory. Otherwise,
- the last accepted proposal.
-
- :type sampler: :ref:`mc-sampler-object`
- :type closer: :ref:`mc-closer-object`
- :type scorer: :ref:`mc-scorer-object`
- :type cooler: :ref:`mc-cooler-object`
- :type steps: :class:`int`
- :type bb_list: :class:`~promod3.loop.BackboneList`
- :type initialize: :class:`bool`
- :type seed: :class:`int`
- :type lowest_energy_conformation: :class:`bool`
-
+.. autofunction:: SampleMonteCarlo
.. _mc-sampler-object:
@@ -69,7 +46,46 @@ Sampler Object
The sampler objects can be used to generate initial conformations and
propose new conformations for a sequence of interest. They build the basis
-for any Monte Carlo sampling pipeline.
+for any Monte Carlo sampling pipeline. You can either use one of the
+provided samplers or any object that implements the functionality of
+:class:`SamplerBase`.
+
+
+.. class:: SamplerBase
+
+ Abstract base class defining the functions that must be implemented by any
+ sampler.
+
+ .. method:: Initialize(bb_list)
+
+ Supposed to initialize structural information from scratch. The sequence
+ of the generated :class:`promod3.loop.BackboneList` is taken from *bb_list*.
+
+ :param bb_list: Passed by reference, so the resulting
+ :class:`promod3.loop.BackboneList` is assigned to this
+ parameter. Sequence / length stay the same.
+
+ :type bb_list: :class:`promod3.loop.BackboneList`
+
+ :returns: None
+
+ .. method:: ProposeStep(actual_positions, proposed_positions)
+
+ Takes current positions and proposes a new conformation. There is no
+ guarantee on maintining any special RT state. The :ref:`mc-closer-object`
+ is supposed to sort that out.
+
+ :param actual_positions: Starting point, must not change when calling this
+ function.
+ :param proposed_positions: Passed by reference, so the resulting
+ :class:`promod3.loop.BackboneList` is assigned to
+ this parameter.
+
+ :type actual_positions: :class:`promod3.loop.BackboneList`
+ :type proposed_positions: :class:`promod3.loop.BackboneList`
+
+ :returns: None
+
.. class:: PhiPsiSampler(sequence, torsion_sampler, n_stem_phi=-1.0472,\
c_stem_psi=-0.78540, prev_aa='A', next_aa='A', seed=0)
@@ -237,9 +253,9 @@ for any Monte Carlo sampling pipeline.
:param seed: Seed for the internal random number generators
:type sequence: :class:`str`
- :type fraggers: :class:`str`
+ :type fraggers: :class:`list`
:type init_bb_list: :class:`~promod3.loop.BackboneList`
- :type samplint_start_index: :class:`int`
+ :type sampling_start_index: :class:`int`
:type init_fragments: :class:`int`
:type seed: :class:`int`
@@ -276,7 +292,32 @@ After the proposal of new conformations by the sampler objects, the
conformations typically have to undergo some structural changes, so they
fit to a given environment. This can either be structural changes, that
the stems of the sampled conformation overlap with given stem residues or
-or simple stem superposition in case of terminal sampling.
+or simple stem superposition in case of terminal sampling. You can either
+use any of the provided closers or any object that implements the
+functionality of :class:`CloserBase`.
+
+.. class:: CloserBase
+
+ Abstract base class defining the functions that must be implemented by any
+ closer.
+
+ .. method:: Close(actual_positions, closed_positions)
+
+ Takes current positions and proposes a new conformation that fits to a
+ given environment.
+
+ :param actual_positions: Starting point, must not change when calling this
+ function.
+ :param closed_positions: Passed by reference, so the resulting
+ :class:`promod3.loop.BackboneList` is assigned to
+ this parameter.
+
+ :type actual_positions: :class:`promod3.loop.BackboneList`
+ :type closed_positions: :class:`promod3.loop.BackboneList`
+
+ :returns: Whether closing procedure was successful
+ :rtype: :class:`bool`
+
.. class:: CCDCloser(n_stem, c_stem, sequence, torsion_sampler, seed)
@@ -305,7 +346,7 @@ or simple stem superposition in case of terminal sampling.
of :class:`~promod3.loop.TorsionSampler`
:type seed: :class:`int`
- .. method:: Close(actual_positions,closed_positions)
+ .. method:: Close(actual_positions, closed_positions)
:param actual_positions: Conformation to be closed.
:param closed_positions: Closed conformation gets stored in here.
@@ -320,7 +361,8 @@ or simple stem superposition in case of terminal sampling.
The DirtyCCDCloser applies the CCD algorithm to the sampled conformation
to enforce the match between the conformations stem residue and
- the stems given by the closer.
+ the stems given by the closer. There is no check for reasonable backbone
+ dihedral angles as it is the case for the :class:`CCDCloser`.
:param n_stem: Defining stem positions the closed conformation
should adapt.
@@ -331,7 +373,7 @@ or simple stem superposition in case of terminal sampling.
:type n_stem: :class:`ost.mol.ResidueHandle`
:type c_stem: :class:`ost.mol.ResidueHandle`
- .. method:: Close(actual_positions,closed_positions)
+ .. method:: Close(actual_positions, closed_positions)
:param actual_positions: Conformation to be closed.
:param closed_positions: Closed conformation gets stored in here.
@@ -355,10 +397,10 @@ or simple stem superposition in case of terminal sampling.
:param seed: Seed for internal random generators.
:type n_stem: :class:`ost.mol.ResidueHandle`
- :type n_stem: :class:`ost.mol.ResidueHandle`
+ :type c_stem: :class:`ost.mol.ResidueHandle`
:type seed: :class:`int`
- .. method:: Close(actual_positions,closed_positions)
+ .. method:: Close(actual_positions, closed_positions)
:param actual_positions: Conformation to be closed.
:param closed_positions: Closed conformation gets stored in here.
@@ -371,26 +413,60 @@ or simple stem superposition in case of terminal sampling.
.. class:: NTerminalCloser(c_stem)
- The NTerminalCloser simply takes the conformation and closes by superposing
- the c_stem with the desired positions.
+ The :class:`NTerminalCloser` simply takes the conformation and closes by
+ superposing the c_stem with the desired positions.
:param c_stem: Defining stem positions the closed conformation should
adapt.
:type c_stem: :class:`ost.mol.ResidueHandle`
- :returns: Whether closing was successful
+
+ .. method:: Close(actual_positions, closed_positions)
+
+ :param actual_positions: Conformation to be closed (or in this case
+ transformed in space).
+ :param closed_positions: Closed (transformed) conformation gets stored in
+ here.
+
+ :type actual_positions: :class:`~promod3.loop.BackboneList`
+ :type closed_positions: :class:`~promod3.loop.BackboneList`
+
+ :returns: Whether closing was successful
.. class:: CTerminalCloser(n_stem)
- The CTerminalCloser simply takes the conformation and closes by superposing
- the n_stem with the desired positions.
+ The :class:`CTerminalCloser` simply takes the conformation and closes by
+ superposing the n_stem with the desired positions.
:param n_stem: Defining stem positions the closed conformation should
adapt.
:type n_stem: :class:`ost.mol.ResidueHandle`
- :returns: Whether closing was successful
+ .. method:: Close(actual_positions,closed_positions)
+
+ :param actual_positions: Conformation to be closed (or in this case
+ transformed in space).
+ :param closed_positions: Closed (transformed) conformation gets stored in
+ here.
+
+ :type actual_positions: :class:`~promod3.loop.BackboneList`
+ :type closed_positions: :class:`~promod3.loop.BackboneList`
+
+ :returns: Whether closing was successful
+
+
+.. class:: DeNovoCloser
+
+ In case of sampling a full stretch, you dont have external constraints. The
+ closer has a rather boring job in this case.
+
+ .. method:: Close(actual_positions,closed_positions)
+
+ Does absolutely nothing, except copying over the coordinates from
+ *actual_positions* to *closed_positions* and return true.
+
+
.. _mc-scorer-object:
@@ -399,10 +475,27 @@ Scorer Object
--------------------------------------------------------------------------------
The scorer asses a proposed conformation and are intended to return a pseudo
-energy, the lower the better.
+energy, the lower the better. You can either use the provided scorer or any
+object implementing the functionality defined in :class:`ScorerBase`.
+
+
+.. class:: ScorerBase
+ Abstract base class defining the functions that must be implemented by any
+ scorer.
+
+ .. method:: GetScore(bb_list)
-.. class:: LinearScorer(scorer, scorer_env, start_resnum, num_residues,
+ Takes coordinates and spits out a score given some internal structural
+ environment.
+
+ :param bb_list: Coordinates to be scored
+ :type bb_list: :class:`promod3.loop.BackboneList`
+
+ :returns: The score
+ :rtype: :class:`float`
+
+.. class:: LinearScorer(scorer, scorer_env, start_resnum, num_residues,\
chain_idx, linear_weights)
The LinearScorer allows to combine the scores available from
@@ -450,13 +543,31 @@ Cooler Object
The cooler objects control the temperature of the Monte Carlo trajectory.
They're intended to deliver steadily decreasing temperatures with calls
-to their GetTemperature function.
+to their GetTemperature function. You can either use the provided cooler
+or any object implementing the functionality defined in
+:class:`CoolerBase`.
+
+.. class:: CoolerBase
+
+ Abstract base class defining the functions that must be implemented by any
+ cooler.
+
+ .. method:: GetTemperature()
+
+ :returns: The Temperature
+ :rtype: :class:`float`
+
+ .. method:: Reset()
+
+ Resets to original state, so a new Monte Carlo trajectory can be generated
+
.. class:: ExponentialCooler(change_frequency, start_temperature, cooling_factor)
The exponential cooler starts with a given *start_temperature* and counts the
- calls to its GetTemperature function. According to the *change_frequency*,
- the returned temperature gets multiplied by the *cooling_factor*.
+ calls to its :meth:`GetTemperature` function. According to the
+ *change_frequency*, the returned temperature gets multiplied by the
+ *cooling_factor*.
:param change_frequency: Frequency to change temperature
:param start_temperature: temperature to start with
@@ -472,4 +583,5 @@ to their GetTemperature function.
.. method:: Reset()
- Sets current temperature back to *start_temperature*
+ Sets current temperature back to *start_temperature* and the
+ internal counter to 0
diff --git a/doc/html/_sources/modelling/pipeline.txt b/doc/html/_sources/modelling/pipeline.txt
index 175b65c5d6554d15f76076e3bd3c530595a7cf64..54d86037d316ed87434fea7ae1cca2e3a2ae11d0 100644
--- a/doc/html/_sources/modelling/pipeline.txt
+++ b/doc/html/_sources/modelling/pipeline.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Modelling Pipeline
================================================================================
diff --git a/doc/html/_sources/modelling/sidechain_reconstruction.txt b/doc/html/_sources/modelling/sidechain_reconstruction.txt
index 72e93a0a96a3f793542c32062748295655c010b7..f6a076c6b780c809d729bf52882d7e7e1fc04cb0 100644
--- a/doc/html/_sources/modelling/sidechain_reconstruction.txt
+++ b/doc/html/_sources/modelling/sidechain_reconstruction.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Sidechain Reconstruction
================================================================================
@@ -144,9 +160,9 @@ SidechainReconstructor Class
:param use_frm: If True, use flexible rotamer model, else rigid.
:type use_frm: :class:`bool`
:param use_bbdep_lib: If True, use default backbone dependent rot. library
- (:meth:`Dunbrack <LoadDunbrackLib>`), else use
+ (:meth:`LoadBBDepLib`), else use
backbone independent one
- (:meth:`Penultimate <LoadPenultimateLib>`).
+ (:meth:`LoadLib`).
:type use_bbdep_lib: :class:`bool`
:param rotamer_library: Custom rotamer library to be used.
:type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib`
diff --git a/doc/html/_sources/portableIO.txt b/doc/html/_sources/portableIO.txt
index d7122a208d30e34f4f4e47ce1e0890fe0f1454ef..a548e3c86400f7e09a9c7cc65c9c2fd7de19e8ce 100644
--- a/doc/html/_sources/portableIO.txt
+++ b/doc/html/_sources/portableIO.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
.. _portableIO:
Using Binary Files In |project|
@@ -387,9 +403,9 @@ The following binary files are currently in |project|:
- module ``sidechain``:
- - :file:`2010DunbrackLib.dat`
+ - :file:`bb_dep_lib.dat`
(:class:`~promod3.sidechain.BBDepRotamerLib`)
- - :file:`PenultimateLib.dat`
+ - :file:`lib.dat`
(:class:`~promod3.sidechain.RotamerLib`)
During the ``make`` process, portable versions of the files (stored in the
diff --git a/doc/html/_sources/references.txt b/doc/html/_sources/references.txt
new file mode 100644
index 0000000000000000000000000000000000000000..927de6ddbad6c032f0f760c17384e977d1ed31e9
--- /dev/null
+++ b/doc/html/_sources/references.txt
@@ -0,0 +1,82 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+References
+==========
+
+.. [biasini2013] Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J,
+ Johner N, Schenk AD, Philippsen A and Schwede T (2013).
+ OpenStructure: an integrated software framework for
+ computational structural biology. Acta Cryst.
+
+.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003).
+ Cyclic coordinate descent: A robotics algorithm for protein
+ loop closure. Protein Sci.
+
+.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003).
+ A graph-theory algorithm for rapid protein side-chain
+ prediction. Protein Sci.
+
+.. [coutsias2005] Coutsias EA, Seok C, Wester MJ, Dill KA (2005).
+ Resultants and loop closure. International Journal of Quantum
+ Chemistry.
+
+.. [chakravarty1999] Chakravarty S, Varadarajan R (1999).
+ Residue depth: a novel parameter for the analysis of
+ protein structure and stability. Structure.
+
+.. [davis2006] Davis IW, Arendall WB, Richardson DC, Richardson JS (2006).
+ The backrub motion: how protein backbone shrugs when a sidechain
+ dances. Structure.
+
+.. [goldstein1994] Goldstein RF (1994).
+ Efficient rotamer elimination applied to protein side-chains
+ and related spin glasses. Biophys J.
+
+.. [Jones1999] Jones DT (1999).
+ Protein secondary structure prediction based on position-specific
+ scoring matrices. J. Mol. Biol.
+
+.. [kabsch1983] Kabsch W, Sander C (1983).
+ Dictionary of protein secondary structure: pattern recognition of
+ hydrogen-bonded and geometrical features. Biopolymers.
+
+.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009).
+ Improved prediction of protein side-chain conformations with
+ SCWRL4. Proteins.
+
+.. [leach1998] Leach AR, Lemon AP (1998).
+ Exploring the conformational space of protein side chains using
+ dead-end elimination and the A* algorithm. Proteins.
+
+.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011).
+ A smoothed backbone-dependent rotamer library for proteins
+ derived from adaptive kernel density estimates and
+ regressions. Structure.
+
+.. [soding2005] Söding J (2005).
+ Protein homology detection by HMM-HMM comparison.
+ Bioinformatics.
+
+.. [solis2006] Solis AD, Rackovsky S (2006). Improvement of statistical
+ potentials and threading score functions using information
+ maximization. Proteins.
+
+.. [zhou2005] Zhou H, Zhou Y (2005).
+ Fold Recognition by Combining Sequence Profiles Derived From
+ Evolution and From Depth-Dependent Structural Alignment of
+ Fragments. Proteins.
+
diff --git a/doc/html/_sources/scoring/all_atom_scorers.txt b/doc/html/_sources/scoring/all_atom_scorers.txt
index 0a1b39b1613522dd671df0b73b32e98dcaac55eb..bcb3cdc43ed0e78becf8a07467928571d60bf604 100644
--- a/doc/html/_sources/scoring/all_atom_scorers.txt
+++ b/doc/html/_sources/scoring/all_atom_scorers.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
All Atom Scorers
================================================================================
diff --git a/doc/html/_sources/scoring/backbone_score_env.txt b/doc/html/_sources/scoring/backbone_score_env.txt
index 25980a4d34ba90890e7686c87838fa8dcd0f1679..11ea33ce9e947a60b120cc82e658231249e48082 100644
--- a/doc/html/_sources/scoring/backbone_score_env.txt
+++ b/doc/html/_sources/scoring/backbone_score_env.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Backbone Score Environment
================================================================================
@@ -187,9 +203,9 @@ Pairwise function classes
Inherits all functionality of :class:`PairwiseFunction`.
Defines a constraint function. The score for a distance between *min_dist* and
- *max_dist* is determined by liner interpolation assuming the first and last
- value exactly lying on *min_dist* ang *max_dist*. For distances outside the
- range defined by *min_dist* and *max_dist*, the score is 0.0.
+ *max_dist* is determined by linear interpolation assuming the first and last
+ value exactly lying on *min_dist* and *max_dist*. For distances outside the
+ range defined by *min_dist* and *max_dist*, the returned score is 0.0.
:param min_dist: Minimal distance to be considered
:param max_dist: Maximal distance to be considered
@@ -200,9 +216,6 @@ Pairwise function classes
:type max_dist: :class:`float`
:type values: :class:`list` of :class:`float`
-
- :returns: Index of added constraint definition
-
:raises: :exc:`~exceptions.RuntimeError` if *min_dist* >= *max_dist* or when
*min_dist* or *max_dist* are negative or when *values* contains no
elements
@@ -211,7 +224,7 @@ Pairwise function classes
Inherits all functionality of :class:`PairwiseFunction`.
Defines a simple contact function. The score value is *score* if
- distance < *max_dist* and 0 otherwise.
+ distance < *max_dist* and 0.0 otherwise.
:param max_dist: Maximal distance to be in contact
:param score: Value that gets returned if in contact
diff --git a/doc/html/_sources/scoring/backbone_scorers.txt b/doc/html/_sources/scoring/backbone_scorers.txt
index 55a07ec77cc2e0ebc0b619c90c4ebaf824e9531a..68a45cab6d736cc1963c245bb0c5cf1e0e140e08 100644
--- a/doc/html/_sources/scoring/backbone_scorers.txt
+++ b/doc/html/_sources/scoring/backbone_scorers.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Backbone Scorers
================================================================================
@@ -249,10 +265,10 @@ CBetaScorer class
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadCBetaScorer`) or by setting all energies (see :meth:`SetEnergy`).
- :param cutoff: Radius in which other cbeta atoms are counted.
+ :param cutoff: Radius in which other cbeta atoms are considered.
:type cutoff: :class:`float`
:param bins: Number of equally sized bins to discretize distances (range
- of [0,*cutoff*]).
+ of [0, *cutoff*]).
:type bins: :class:`int`
:param seq_sep: Minimal separation in sequence two cbeta atoms must have to
be considered.
diff --git a/doc/html/_sources/scoring/index.txt b/doc/html/_sources/scoring/index.txt
index 983d6b5587c5f70fc9088e6bdac386567fef16c3..d21154f06951fcdb6bbbe1c11f329f69f24bd57c 100644
--- a/doc/html/_sources/scoring/index.txt
+++ b/doc/html/_sources/scoring/index.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.scoring` - Loop Scoring
================================================================================
@@ -7,7 +23,11 @@
.. currentmodule:: promod3.scoring
Tools and algorithms to score loops. The scoring system is split between an
-environment which contains model-specific data and scorers which evaluate loops.
+environment and scorers.
+Several scorers can be attached to the same environment containing the
+actual structural data of the current modelling problem.
+The environment is updated as the modelling proceeds and manages efficient
+spatial lookups to be used by the attached scorers.
In this example, we load a structure, setup a score environment, link a few
scorers to it and finally score some loops:
diff --git a/doc/html/_sources/scoring/other_scoring_functions.txt b/doc/html/_sources/scoring/other_scoring_functions.txt
index f505232e026655cdebf83d068269e805eb99fedd..80487531f986d6004e6764b8a8575be11b8bf6de 100644
--- a/doc/html/_sources/scoring/other_scoring_functions.txt
+++ b/doc/html/_sources/scoring/other_scoring_functions.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Other Scoring Functions
================================================================================
@@ -53,4 +69,3 @@ Scoring Functions from SCWRL3
-.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
diff --git a/doc/html/_sources/sidechain/disulfid.txt b/doc/html/_sources/sidechain/disulfid.txt
index 1cee3075640728b8c205c8bf9d9ff0128d6eeb9d..d078a6c5a65e20f2b4fc682f26a1e5b7853d6a92 100644
--- a/doc/html/_sources/sidechain/disulfid.txt
+++ b/doc/html/_sources/sidechain/disulfid.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Disulfid Bond Evaluation
================================================================================
diff --git a/doc/html/_sources/sidechain/frame.txt b/doc/html/_sources/sidechain/frame.txt
index d5e355915971ca7a0cd140036d366d9812f777e3..d8365f4a5316d2efebaaaafb50a87238b1b3ac2d 100644
--- a/doc/html/_sources/sidechain/frame.txt
+++ b/doc/html/_sources/sidechain/frame.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Frame
================================================================================
diff --git a/doc/html/_sources/sidechain/graph.txt b/doc/html/_sources/sidechain/graph.txt
index 118c72eabb98ed98acdc13eafcb6f3af4bbbb867..44606b2766a57c90bfa7f74d86cfc720ddf4ed71 100644
--- a/doc/html/_sources/sidechain/graph.txt
+++ b/doc/html/_sources/sidechain/graph.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamer Graph
================================================================================
@@ -6,7 +22,7 @@ Rotamer Graph
Once having a frame representing the rigid parts, the internal energies in
rotamer groups can be calculated. To come to a final solution of the sidechain
modelling problem, the pairwise energies also have to be evaluated and an
-overall solution has to be found. PROMOD3 implements a
+overall solution has to be found. ProMod3 implements a
:class:`promod3.core.GraphMinimizer` that allows to find solutions using
tree decomposition, A* and Monte Carlo algorithms.
diff --git a/doc/html/_sources/sidechain/index.txt b/doc/html/_sources/sidechain/index.txt
index c0a24dce4ca854bcd16c85d29094dcd1ff799f71..aeac7212ce7a9232b81c95d2178cb32d07ff6595 100644
--- a/doc/html/_sources/sidechain/index.txt
+++ b/doc/html/_sources/sidechain/index.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.sidechain` - Sidechain Modelling
================================================================================
@@ -9,7 +25,7 @@
Tools and algorithms to model sidechains given backbone coordinates. The full
module is heavily based on SCWRL4 [krivov2009]_ . The according paper describes
the modelling of sidechains using two different rotamer models. A rigid model,
-as well as a flexible model. Both models are implemented in PROMOD3 and can be
+as well as a flexible model. Both models are implemented in ProMod3 and can be
applied in flexible ways.
The following code fragment shows an example of a basic sidechain reconstruction
@@ -37,4 +53,3 @@ Contents:
subrotamer_optimizer
-.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.
diff --git a/doc/html/_sources/sidechain/loading.txt b/doc/html/_sources/sidechain/loading.txt
index b795abc601ad9c617895d86a63316a14623727bf..83e9390b16d8b8726c23a58f79dfdbf0eff22790 100644
--- a/doc/html/_sources/sidechain/loading.txt
+++ b/doc/html/_sources/sidechain/loading.txt
@@ -1,32 +1,50 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Loading Rotamer Libraries
================================================================================
.. currentmodule:: promod3.sidechain
-Since the PROMOD3 sidechain modelling algorithms are mainly designed after the
-work of the Dunbrack lab [krivov2009]_ , their backbone dependent rotamer
-library is probably the way to go. There exists a binary version of their
-2010 libary [shapovalov2011]_ , that can
-directly be loaded. As an alternative, there is also a binary file containing
-the backbone independent Penultimate library [lovell2000]_ .
+There are several rotamer libraries that can be used in ProMod3. ProMod3
+is optimized for the use with backbone dependent rotamer libraries such
+as the 2010 library provided by the Dunbrack lab [shapovalov2011]_.
+You can request a licence `here <http://dunbrack.fccc.edu/bbdep2010/>`_
+and generate such a library as described in
+extras/data_generation/rotamer_library/README. Alternatively, ProMod3
+provides its own backbone dependent or backbone independent libraries
+that can be loaded with :meth:`LoadBBDepLib` / :meth:`LoadLib`.
-.. method:: LoadDunbrackLib()
+.. method:: LoadBBDepLib()
- Loads the 2010 backbone dependent rotamer library from the dunbrack lab.
- The library has been generated using the ReadDunbrackFile function
- using the file with smoothing factor 5 and nonrotameric dihedrals
- sampled in 20 degree steps.
+ A backbone dependent rotamer library shipped with ProMod3. You can find
+ details on how it is created in extras/data_generation/rotamer_library/README.
+ All scripts to build it are in the same directory as the README file and
+ build the basis for custom versions.
- :returns: The requested library
+ :returns: The requested Library
:rtype: :class:`BBDepRotamerLib`
-.. method:: LoadPenultimateLib()
+.. method:: LoadLib()
- Loads the backbone independent Penultimate library. The values for the dihedral
- angles are directly extracted from the publication without considering the
- probabilities specific for helices/sheets. Due to no assigned standard
- deviations, the flexible rotamer model won't produce meaningful results.
+ A backbone independent rotamer library shipped with ProMod3. You can find
+ details on how it is created in extras/data_generation/rotamer_library/README.
+ All scripts to build it are in the same directory as the README file and
+ build the basis for custom versions.
:returns: The requested library
:rtype: :class:`RotamerLib`
@@ -36,8 +54,9 @@ the backbone independent Penultimate library [lovell2000]_ .
Reads a file as it is provided when you get a licence for the 2010 library of
the Dunbrack lab. It can only read the classic version, where all rotamers
- are in a single file. Specific distributions of nonrotameric sidechains
- cannot be read.
+ are in a single file. Specific distributions of non-rotameric sidechains
+ cannot be read. You can find an example described in
+ extras/data_generation/rotamer_library/README
:param filename: Name of the file
:type param: :class:`str`
@@ -49,9 +68,3 @@ the backbone independent Penultimate library [lovell2000]_ .
:returns: The read library
:rtype: :class:`BBDepRotamerLib`
-
-
-.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011). A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure.
-
-.. [lovell2000] Lovell SC, Word JM, Richardson JS, Richardson DC (2000). The penultimate rotamer library. Proteins.
-
diff --git a/doc/html/_sources/sidechain/rotamer.txt b/doc/html/_sources/sidechain/rotamer.txt
index 40f882320bb51f59b604a6ea7de7106d8582ca2a..30b3c7ca3b06602a1fbade371a3abdbc5a4e9029 100644
--- a/doc/html/_sources/sidechain/rotamer.txt
+++ b/doc/html/_sources/sidechain/rotamer.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamers
================================================================================
@@ -7,7 +23,7 @@ A rotamer represents an amino acid sidechain and is basically a set of
:class:`Particle` objects. There exist two types. The :class:`RRMRotamer` and
:class:`FRMRotamer`.
To gather all possible rotamers for one particular sidechain position,
-PROMOD3 offers the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
+ProMod3 offers the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
Pairwise interactions between particles give raise to pairwise energies between
rotamers. Nevertheless, the energy calculation itself happens on the level
of RotamerGroups and is mostly hidden away in the construction of the
@@ -264,7 +280,7 @@ Rotamers
The FRMRotamer represents a rotamer of the so called flexible rotamer model,
where one rotamer gets represented by several subrotamers.
- The idea is, that all particles of all subrotamers are given at
+ The idea is that all particles of all subrotamers are given at
initialization. Subrotamers are then defined by providing lists of indices.
One particle can be part of several subrotamers.
diff --git a/doc/html/_sources/sidechain/rotamer_constructor.txt b/doc/html/_sources/sidechain/rotamer_constructor.txt
index 36c76a2c0857dc5bdbd5b3257e24e8b2bde5eaac..82f9626c2afedb57149fc5c55042ee13dcd8fcb8 100644
--- a/doc/html/_sources/sidechain/rotamer_constructor.txt
+++ b/doc/html/_sources/sidechain/rotamer_constructor.txt
@@ -1,10 +1,26 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamer Constructor
================================================================================
.. currentmodule:: promod3.sidechain
Instead of creating rotamers by yourself, you can simply use the convenient
-functionality provided by PROMOD3
+functionality provided by ProMod3
Constructing Rotamers and Frame Residues
diff --git a/doc/html/_sources/sidechain/rotamer_id.txt b/doc/html/_sources/sidechain/rotamer_id.txt
index 7eac7b85ca8de53c2ee27619089aa93a1907da66..746a51641352c7295152567a742eda8befedc803 100644
--- a/doc/html/_sources/sidechain/rotamer_id.txt
+++ b/doc/html/_sources/sidechain/rotamer_id.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
RotamerID
================================================================================
diff --git a/doc/html/_sources/sidechain/rotamer_lib.txt b/doc/html/_sources/sidechain/rotamer_lib.txt
index 21ca7e4e93a69de5fe2a556da1e1b66a128d4ab1..0069c3888b70f7ad37acbf984cd3c95470af9840 100644
--- a/doc/html/_sources/sidechain/rotamer_lib.txt
+++ b/doc/html/_sources/sidechain/rotamer_lib.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamer Library
================================================================================
@@ -9,7 +25,7 @@ sidechain can completely be described in terms of dihedral angles. Preferred
combinations of such dihedral angles are a result of steric properties and
can be gathered in rotamer libraries. Different libraries exist in the field
and their main difference is, whether the provided sidechain conformations
-are dependent on their backbone or not. PROMOD3 provides you with a
+are dependent on their backbone or not. ProMod3 provides you with a
:class:`BBDepRotamerLib` organizing rotamers for the different aminoacids
in equidistant phi/psi bins, as well as a simple :class:`RotamerLib`.
Both libraries are containers for :class:`RotamerLibEntry` and are optimized
@@ -168,10 +184,12 @@ The Backbone Dependent Rotamer Library
added to the library or can be interpolated.
In the first option, *phi* and *psi* simply get transformed to the
according bin using following formalism: bin = round((angle + pi)/bin_size).
- In case of interpolation, the chi angles and the according standard
- deviations of the rotamers get bilinearly interpolated using the
- corresponding rotamers with same configuration from the neighbouring bins.
- This behaviour can be controlled with the SetInterpolate function.
+ In case of interpolation, the chi angles of rotameric dihedral angles and the
+ according standard deviations of the rotamers get bilinearly interpolated
+ using the corresponding rotamers with same configuration from the
+ neighbouring bins. No interplation is applied to non-rotameric dihedral
+ angles (chi2 in ASP, ASN, HIS, PHE, TRP, TYR; chi3 in GLU, GLN).
+ This behaviour can be controlled with :meth:`SetInterpolate`.
The query function follows following strategies in case of
special *id* requests.
@@ -220,7 +238,8 @@ The Backbone Dependent Rotamer Library
.. method:: SetInterpolate(interpolate)
- :param interpolate: Controls behaviour when QueryLib function gets called
+ :param interpolate: Controls behaviour when :meth:`QueryLib`
+ gets called
:type interpolate: :class:`bool`
@@ -302,9 +321,9 @@ functionalities.
Creates a :class:`RotamerLibEntry` from the given *res*.
The function tries to automatically identify the :class:`RotamerID` based
- on the residue name. The probability gets set to zero and the standard
- deviations to 0. All not required chi angles with their corresponding
- standard deviations are NaN.
+ on the residue name. The probability and standard deviations are set to 0.0,
+ all not required chi angles with their corresponding standard deviations to
+ NaN.
:param res: Source of dihedral angles
@@ -418,4 +437,55 @@ functionalities.
:returns: :class:`bool` Whether both dihedrals are defined
(not NaN) and within the specified threshold
+Rotamer Configurations
+--------------------------------------------------------------------------------
+
+In rotamers, one distinguishes between rotameric and non-rotameric sidechain
+dihedral angles. The rotameric ones are around SP3-SP3 hybridized bonds and
+typically have three distinct configurations (trans, gauche-, gauche+).
+The non-rotameric ones behave differently. ProMod3 offers some functionality
+to estimate those configurations.
+
+.. class:: DihedralConfiguration
+
+ Enumerates the possible sidechain dihedral configurations
+
+ .. hlist::
+ :columns: 1
+
+ * TRANS - Trans configuration (120 < angle < -120)
+ * GAUCHE_PLUS - Gauche+ configuration (0 < angle < 120)
+ * GAUCHE_MINUS - Gauce- configuration (-120 < angle < 0)
+ * NON_ROTAMERIC - Dihedral without SP3-SP3 bond
+ * INVALID - Invalid configuration, e.g. chi3 of ALA (doesnt exist...)
+
+.. method:: GetRotamericConfiguration(angle)
+
+ Evaluates the *angle* according to the ranges specified for
+ :class:`DihedralConfiguration`.
+
+ :param angle: Angle to be evaluated
+ :type angle: :class:`float`
+
+ :returns: TRANS, GAUCHE_PLUS or GAUCHE_MINUS.
+ INVALID if *angle* is NaN.
+
+.. method:: GetDihedralConfiguration(entry, id, dihedral_idx)
+
+ Estimates configuration of a sidechain dihedral angle in a specific
+ :class:`RotamerLibEntry` with the knowledge of its identity. This allows
+ to also return NON_ROTAMERIC (e.g. chi2 for ASN).
+
+ :param entry: Sidechain dihedral angle comes from here
+ :param id: Identity of rotamer
+ :param dihedral_idx: Specifies angle (0 => chi1, ..., 3 => chi4)
+
+ :type entry: :class:`RotamerLibEntry`
+ :type id: :class:`RotamerID`
+ :type dihedral_idx: :class:`int`
+
+ :returns: Result of :meth:`GetRotamericConfiguration` if specified
+ angle is Rotameric, NON_ROTAMERIC if specified angle is
+ valid and non rotameric, INVALID otherwise.
+
diff --git a/doc/html/_sources/sidechain/subrotamer_optimizer.txt b/doc/html/_sources/sidechain/subrotamer_optimizer.txt
index e4124466394f2bdc0248aa40056a590f5b556dcb..27315888d85598b7f8830e1241b5139c65af0db5 100644
--- a/doc/html/_sources/sidechain/subrotamer_optimizer.txt
+++ b/doc/html/_sources/sidechain/subrotamer_optimizer.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Subrotamer Optimization
================================================================================
diff --git a/doc/html/_sources/users.txt b/doc/html/_sources/users.txt
index 7764b3750cebd2a03cc65dffecb0f9170092cae9..3b11ff195d4009fcf10bea662e5f54367150d90c 100644
--- a/doc/html/_sources/users.txt
+++ b/doc/html/_sources/users.txt
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Documentation For Users
=======================
@@ -12,6 +28,7 @@ Contents:
gettingstarted
actions/index
buildsystem
+ container/index
modelling/index
sidechain/index
scoring/index
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index f83632f45740b0b6ed02b2d4176abe058c068625..84c071d639ea16a4ecb45996fa791fd6451a80fe 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 Actions — ProMod3 1.2.0 documentation</title>
+ <title>ProMod3 Actions — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Building ProMod3" href="../buildsystem.html" />
<link rel="prev" title="Getting Started" href="../gettingstarted.html" />
@@ -52,7 +53,7 @@ you can type <code class="docutils literal"><span class="pre">pm</span> <span cl
<p>You can run a full protein homology modelling pipeline from the command line
with</p>
<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-f <FILE> <span class="p">|</span> -c <FILE> <span class="p">|</span> -j <OBJECT><span class="p">|</span><FILE><span class="o">)</span>
-<span class="go"> (-p <FILE> | -e <FILE>) [-o <FILENAME>]</span>
+<span class="go"> (-p <FILE> | -e <FILE>) [-s <FILE>] [-o <FILENAME>]</span>
</pre></div>
</div>
<p>Example usage:</p>
@@ -110,7 +111,7 @@ Example:</p>
</li>
</ul>
<p>Structures can be provided in PDB (<code class="docutils literal"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/dev/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.7.1)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/dev/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.8.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
chosen by file ending. Recognized File Extensions: <code class="docutils literal"><span class="pre">.ent</span></code>, <code class="docutils literal"><span class="pre">.pdb</span></code>,
<code class="docutils literal"><span class="pre">.ent.gz</span></code>, <code class="docutils literal"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal"><span class="pre">.cif</span></code>, <code class="docutils literal"><span class="pre">.cif.gz</span></code>. At least one structure must be
given and you cannot mix file formats. Multiple structures can be given and each
@@ -132,6 +133,25 @@ residue in the aligned sequence. Leading/trailing whitespaces of <CHAINID>
</ul>
<p>Example: <code class="docutils literal"><span class="pre">...</span> <span class="pre">-p</span> <span class="pre">data/2jlp.pdb.gz</span></code>, where the pdb file has chains <code class="docutils literal"><span class="pre">A</span></code>,
<code class="docutils literal"><span class="pre">B</span></code>, <code class="docutils literal"><span class="pre">C</span></code> and the template sequence is named <code class="docutils literal"><span class="pre">2jlp.A|55</span></code>.</p>
+<p>You can optionally specify sequence profiles to be added (<code class="docutils literal"><span class="pre">-s</span></code>) and linked
+to the corresponding target sequences. This has an impact on loop scoring with
+the database approach.
+The profiles can be provided as plain files or gzipped. Following file
+extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
+Consider to use <a class="reference external" href="https://www.openstructure.org/docs/dev/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
+file in a3m format at hand.</p>
+<ul class="simple">
+<li>The profiles are mapped based on exact matches towards the gapless
+target sequences from the provided alignment files,
+i.e. one profile is mapped to several chains in case of homo-oligomers</li>
+<li>Every profile must have a unique sequence to avoid ambiguities</li>
+<li>All or nothing - You cannot provide profiles for only a subset of
+target sequences</li>
+</ul>
+<p>Example usage:</p>
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb -s prof.hhm
+</pre></div>
+</div>
<p>Possible exit codes of the action:</p>
<ul class="simple">
<li>0: all went well</li>
@@ -142,6 +162,59 @@ residue in the aligned sequence. Leading/trailing whitespaces of <CHAINID>
<li>other non-zero: failure in argument checking
(see <a class="reference internal" href="../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal"><span class="pre">promod3.core.pm3argparse.PM3ArgumentParser</span></code></a>)</li>
</ul>
+</div>
+<div class="section" id="sidechain-modelling">
+<h2>Sidechain Modelling<a class="headerlink" href="#sidechain-modelling" title="Permalink to this headline">¶</a></h2>
+<p>You can (re-)construct the sidechains in a model from the command line.</p>
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> usage: build-sidechains <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-p <FILE> <span class="p">|</span> -e <FILE><span class="o">)</span> <span class="o">[</span>-o <FILENAME><span class="o">]</span> <span class="o">[</span>-k<span class="o">]</span> <span class="o">[</span>-n<span class="o">]</span>
+<span class="go"> [-r] [-i] [-s]</span>
+</pre></div>
+</div>
+<p>Example usage:</p>
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-sidechains -p input.pdb
+</pre></div>
+</div>
+<p>This reads a structure stored in in.pdb, strips all sidechains,
+detects and models disulfid bonds and reconstructs all sidechains with the
+flexible rotamer model. The result is stored as <code class="file docutils literal"><span class="pre">out.pdb</span></code>.
+The output filename can be controlled with the <code class="docutils literal"><span class="pre">-o</span></code> flag.</p>
+<p>A structure can be provided in PDB (<code class="docutils literal"><span class="pre">-p</span></code>) or in any format readable by the
+<a class="reference external" href="https://www.openstructure.org/docs/dev/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.8.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
+chosen by file ending. Recognized File Extensions: <code class="docutils literal"><span class="pre">.ent</span></code>, <code class="docutils literal"><span class="pre">.pdb</span></code>,
+<code class="docutils literal"><span class="pre">.ent.gz</span></code>, <code class="docutils literal"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal"><span class="pre">.cif</span></code>, <code class="docutils literal"><span class="pre">.cif.gz</span></code>.</p>
+<p>Several flags control the modelling behaviour:</p>
+<dl class="option">
+<dt id="cmdoption-k">
+<span id="cmdoption--keep-sidechains"></span><code class="descname">-k</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--keep-sidechains</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-k" title="Permalink to this definition">¶</a></dt>
+<dd><p>Keep existing sidechains.</p>
+</dd></dl>
+
+<dl class="option">
+<dt id="cmdoption-n">
+<span id="cmdoption--no-disulfids"></span><code class="descname">-n</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--no-disulfids</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-n" title="Permalink to this definition">¶</a></dt>
+<dd><p>Do not build disulfid bonds before sidechain optimization</p>
+</dd></dl>
+
+<dl class="option">
+<dt id="cmdoption-r">
+<span id="cmdoption--rigid-rotamers"></span><code class="descname">-r</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--rigid-rotamers</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-r" title="Permalink to this definition">¶</a></dt>
+<dd><p>Do not use rotamers with subrotamers</p>
+</dd></dl>
+
+<dl class="option">
+<dt id="cmdoption-i">
+<span id="cmdoption--backbone-independent"></span><code class="descname">-i</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--backbone-independent</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-i" title="Permalink to this definition">¶</a></dt>
+<dd><p>Use backbone independent rotamer library
+(from <a class="reference internal" href="../sidechain/loading.html#promod3.sidechain.LoadLib" title="promod3.sidechain.LoadLib"><code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.LoadLib()</span></code></a>) instead of the default backbone
+dependent one (from <a class="reference internal" href="../sidechain/loading.html#promod3.sidechain.LoadBBDepLib" title="promod3.sidechain.LoadBBDepLib"><code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.LoadBBDepLib()</span></code></a>)</p>
+</dd></dl>
+
+<dl class="option">
+<dt id="cmdoption-s">
+<span id="cmdoption--no-subrotamer-optimization"></span><code class="descname">-s</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--no-subrotamer-optimization</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-s" title="Permalink to this definition">¶</a></dt>
+<dd><p>Dont do subrotamer optimization if flexible rotamer model is used</p>
+</dd></dl>
+
</div>
</div>
@@ -155,6 +228,7 @@ residue in the aligned sequence. Leading/trailing whitespaces of <CHAINID>
<ul>
<li><a class="reference internal" href="#">ProMod3 Actions</a><ul>
<li><a class="reference internal" href="#building-models">Building models</a></li>
+<li><a class="reference internal" href="#sidechain-modelling">Sidechain Modelling</a></li>
</ul>
</li>
</ul>
@@ -191,7 +265,7 @@ residue in the aligned sequence. Leading/trailing whitespaces of <CHAINID>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 7a72c1a6616b45888b696930be029d8e2cb467f2..a0e99aa96c64327e2f9ef87b6f20d146553846cc 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>test_actions - Testing Actions — ProMod3 1.2.0 documentation</title>
+ <title>test_actions - Testing Actions — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="ProMod3‘s Share Of CMake" href="../cmake/index.html" />
<link rel="prev" title="Contributing" href="../contributing.html" />
@@ -193,7 +194,7 @@ happens if a user throws dirty input data in.</p>
</div>
<div class="section" id="making-the-script-executable">
<h3>Making the Script Executable<a class="headerlink" href="#making-the-script-executable" title="Permalink to this headline">¶</a></h3>
-<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>‘s <a class="reference external" href="https://www.openstructure.org/docs/dev/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python‘s
+<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>‘s <a class="reference external" href="https://www.openstructure.org/docs/dev/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.8.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python‘s
<a class="reference external" href="https://docs.python.org/2.7/library/unittest.html#unittest.TestCase" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed
as a script:</p>
<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
@@ -410,7 +411,7 @@ file (also complains if a directory is found instead).</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 05f730f28a2e8349dffce5b4b7a0fcbfb68a61a0..98547d3d3af494f637315ee884317ecf466bbbea 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Building ProMod3 — ProMod3 1.2.0 documentation</title>
+ <title>Building ProMod3 — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,9 +23,10 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Users" href="users.html" />
- <link rel="next" title="modelling - Protein Modelling" href="modelling/index.html" />
+ <link rel="next" title="ProMod3 and Containers" href="container/index.html" />
<link rel="prev" title="ProMod3 Actions" href="actions/index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -45,16 +46,14 @@
<span id="building-promod"></span><h1>Building ProMod3<a class="headerlink" href="#building-project" title="Permalink to this headline">¶</a></h1>
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
-<p>ProMod3 is build on top of <a class="reference external" href="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
-1.7. OST must be configured and compiled with <code class="docutils literal"><span class="pre">ENABLE_MM=1</span></code> to use <a class="reference external" href="http://openmm.org">OpenMM</a>.
-To create the build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required in version
-2.8.7 or higher. <a class="reference external" href="https://www.python.org/">Python</a> works well from version 2.7. For OST and the
-C++ bit of ProMod3, <a class="reference external" href="https://www.boost.org/">Boost</a> is required in version 1.53.0 (the same as
-used for OST). Also <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> is needed. To build
-documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.2b1 is required.</p>
+<p>ProMod3 is build on top of <a class="reference external" href="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version 1.8.
+OST must be configured and compiled with <code class="docutils literal"><span class="pre">ENABLE_MM=1</span></code> to use <a class="reference external" href="http://openmm.org">OpenMM</a>.
+To create the build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required. The same versions of <a class="reference external" href="https://www.python.org/">Python</a>
+and <a class="reference external" href="https://www.boost.org/">Boost</a> are needed as used in OST. For <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> we need at least
+version 3.3.0. To build the documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> is required.</p>
<p>The currently preferred versions are:</p>
<ul class="simple">
-<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 1.7</li>
+<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 1.9</li>
<li><a class="reference external" href="http://openmm.org">OpenMM</a> 7.1.1</li>
<li><a class="reference external" href="https://cmake.org/">CMake</a> 2.8.12</li>
<li><a class="reference external" href="https://www.python.org/">Python</a> 2.7.5</li>
@@ -177,7 +176,7 @@ safely delete the whole source folder.</p>
<li><a href="index.html">Documentation overview</a><ul>
<li><a href="users.html">Documentation For Users</a><ul>
<li>Previous: <a href="actions/index.html" title="previous chapter">ProMod3 Actions</a></li>
- <li>Next: <a href="modelling/index.html" title="next chapter"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+ <li>Next: <a href="container/index.html" title="next chapter">ProMod3 and Containers</a></li>
</ul></li>
</ul></li>
</ul>
@@ -204,7 +203,7 @@ safely delete the whole source folder.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 776b517f5d8af27418df83b927924c2b327d2a65..460b1c777626dfb68d4c125b3c815c2c07d80afa 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Changelog — ProMod3 1.2.0 documentation</title>
+ <title>Changelog — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,8 +23,9 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
- <link rel="prev" title="Using Binary Files In ProMod3" href="portableIO.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
+ <link rel="prev" title="References" href="references.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -41,6 +42,26 @@
<div class="section" id="changelog">
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="release-1-3-0">
+<h2>Release 1.3.0<a class="headerlink" href="#release-1-3-0" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li>Apply Apache Version 2.0 License to the project</li>
+<li>2010 Dunbrack rotamer library has been replaced by an own backbone dependent
+rotamer library. All scripts required to reproduce the data are in
+extras/data_generation/rotamer_library</li>
+<li>Penultimate rotamer library has been replaced by an own backbone independent
+rotamer library. All scripts required to reproduce the data are in
+extras/data_generation/rotamer_library</li>
+<li>SampleMonteCarlo function moved to Python. This makes it possible to provide
+sampler/closer/scorer/cooler objects implemented in both, Python and C++</li>
+<li>Action script for sidechain modelling</li>
+<li>Allow sequence profiles as input for build-model action script.</li>
+<li>Recipe for Docker / Singularity container</li>
+<li>Check peptide bonds when building a RawModel. Treat as gap if bond is
+stereochemically problematic despite being in sequence.</li>
+<li>Several minor bug fixes, improvements, and speed-ups</li>
+</ul>
+</div>
<div class="section" id="release-1-2-0">
<h2>Release 1.2.0<a class="headerlink" href="#release-1-2-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
@@ -111,6 +132,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Changelog</a><ul>
+<li><a class="reference internal" href="#release-1-3-0">Release 1.3.0</a></li>
<li><a class="reference internal" href="#release-1-2-0">Release 1.2.0</a></li>
<li><a class="reference internal" href="#release-1-1-0">Release 1.1.0</a></li>
<li><a class="reference internal" href="#release-1-0">Release 1.0</a></li>
@@ -121,7 +143,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
- <li>Previous: <a href="portableIO.html" title="previous chapter">Using Binary Files In ProMod3</a></li>
+ <li>Previous: <a href="references.html" title="previous chapter">References</a></li>
</ul></li>
</ul>
</div>
@@ -147,7 +169,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index f80cc16828502e7b936f090bbb38cd803d3b88ee..a53376df30cd861071eff20559be430bf5902a0d 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3‘s Share Of CMake — ProMod3 1.2.0 documentation</title>
+ <title>ProMod3‘s Share Of CMake — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="Using Binary Files In ProMod3" href="../portableIO.html" />
<link rel="prev" title="test_actions - Testing Actions" href="../actions/index_dev.html" />
@@ -372,7 +373,7 @@ target has to be created <strong>before</strong> any action may be attached to i
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
new file mode 100644
index 0000000000000000000000000000000000000000..d744acd6dcb4e38f5f3cce1f73137aac7f377f83
--- /dev/null
+++ b/doc/html/container/docker.html
@@ -0,0 +1,188 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Docker — ProMod3 1.3.0 documentation</title>
+
+ <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '1.3.0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
+ <link rel="up" title="ProMod3 and Containers" href="index.html" />
+ <link rel="next" title="Singularity" href="singularity.html" />
+ <link rel="prev" title="ProMod3 and Containers" href="index.html" />
+
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+ </head>
+ <body role="document">
+
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <div class="section" id="docker">
+<h1>Docker<a class="headerlink" href="#docker" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="build-docker-image">
+<h2>Build Docker Image<a class="headerlink" href="#build-docker-image" title="Permalink to this headline">¶</a></h2>
+<p>In order to build the image:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo docker build --tag <IMAGE_NAME> -f Dockerfile <PATH_TO_DOCKERFILE_DIR>
+</pre></div>
+</div>
+<p>You can chose any image name (tag) eg. promod.</p>
+</div>
+<div class="section" id="run-scripts-and-actions-with-ost-pm">
+<h2>Run scripts and actions with OST/PM<a class="headerlink" href="#run-scripts-and-actions-with-ost-pm" title="Permalink to this headline">¶</a></h2>
+<p>If script or action requires some external files eg. PDBs, they have to be located in the
+path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
+path. Eg. assuming that we have a struc.pdb file in /home/<USER>/pdbs directory and
+a script.py in /home/<USER> we could mount the /home/<USER> to /home in docker as
+above by specifying -v /home/<USER>:/home. To run the script we thus need to
+provide the (relative) path to the script and (relative) path to the file eg:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo docker run --rm -v /home/<USER>:/home <IMAGE_NAME> pm script.py pdbs/struct.pdb
+</pre></div>
+</div>
+<p>or with absolute paths:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo docker run --rm -v /home/<USER>:/home <IMAGE_NAME> pm /home/script.py /home/pdbs/struct.pdb
+</pre></div>
+</div>
+<p>An alternative is to mount the current working directory into the docker home:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo docker run --rm -v <span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span>:/home <IMAGE_NAME> pm script.py pdbs/struct.pdb
+</pre></div>
+</div>
+</div>
+<div class="section" id="the-compound-library">
+<span id="docker-compound-lib"></span><h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
+<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">CompoundLib</span></code></a> is generated.
+Compound libraries contain information on chemical compounds, such as their
+connectivity, chemical class and one-letter-code. The compound library has
+several uses, but the most important one is to provide the connectivy
+information for the rule-based processor.</p>
+<p>The compound library is generated with the components.cif dictionary provided by
+the PDB. As the PDB updates regularly, the compound library shipped with the
+container is quickly outdated. For most use cases, this is not problematic.
+However, if you rely on correct connectivity information of the latest and
+greatest compounds, you have to keep the compound library up to date manually.</p>
+<p>The suggested way of doing this is to generate your own compound library and
+mount it into the container where the original compound lib resides to
+override it.</p>
+<p>The simplest way to create a compound library is to use the
+<strong class="program">chemdict_tool</strong> available in the container. The program allows you
+to import the chemical description of the compounds from a MMCIF dictionary,
+e.g. the components.cif dictionary provided by the PDB.
+The latest dictionary can be downloaded from the
+<a class="reference external" href="http://www.wwpdb.org/ccd.html">wwPDB site</a>.
+The files are rather large, it is therefore recommended to download the
+gzipped version.</p>
+<p>After downloading the file use <strong class="program">chemdict_tool</strong> in the container to
+convert the MMCIF dictionary into our internal format:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo docker run --rm -v <span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span>:/home <IMAGE_NAME> chemdict_tool create components.cif.gz compounds.chemlib
+</pre></div>
+</div>
+<p>To run a script with the upated compound library, use the -v option for mounting/overriding:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo docker run --rm -v /home/<USER>:/home -v <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> <IMAGE_NAME> pm script.py pdbs/struct.pdb
+</pre></div>
+</div>
+<p>with COMPLIB_DIR_LOCALHOST being the directory that contains the newly generated
+compound library with name compounds.chemlib and COMPLIB_DIR_CONTAINER the
+according path in the container.
+If you didnt change anything in the Dockerfile, the latter should be
+/usr/local/share/ost_complib</p>
+<p>You can check whether the default lib is successfully overriden by looking at the
+output when running a Python script with following code in the container:</p>
+<div class="highlight-python"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">promod3</span> <span class="c1"># required to setup default lib</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
+<span class="n">lib</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">GetDefaultLib</span><span class="p">()</span>
+<span class="k">print</span> <span class="n">lib</span><span class="o">.</span><span class="n">GetCreationDate</span><span class="p">()</span>
+</pre></div>
+</div>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+ <h3><a href="../index.html">Table Of Contents</a></h3>
+ <ul>
+<li><a class="reference internal" href="#">Docker</a><ul>
+<li><a class="reference internal" href="#build-docker-image">Build Docker Image</a></li>
+<li><a class="reference internal" href="#run-scripts-and-actions-with-ost-pm">Run scripts and actions with OST/PM</a></li>
+<li><a class="reference internal" href="#the-compound-library">The Compound Library</a></li>
+</ul>
+</li>
+</ul>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../users.html">Documentation For Users</a><ul>
+ <li><a href="index.html">ProMod3 and Containers</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter">ProMod3 and Containers</a></li>
+ <li>Next: <a href="singularity.html" title="next chapter">Singularity</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
+ <div role="note" aria-label="source link">
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/container/docker.txt"
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diff --git a/doc/html/container/index.html b/doc/html/container/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..43bb816fec83eb168a32729db87046c27bc72834
--- /dev/null
+++ b/doc/html/container/index.html
@@ -0,0 +1,112 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>ProMod3 and Containers — ProMod3 1.3.0 documentation</title>
+
+ <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '1.3.0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
+ <link rel="up" title="Documentation For Users" href="../users.html" />
+ <link rel="next" title="Docker" href="docker.html" />
+ <link rel="prev" title="Building ProMod3" href="../buildsystem.html" />
+
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
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+ </head>
+ <body role="document">
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+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <div class="section" id="promod3-and-containers">
+<h1>ProMod3 and Containers<a class="headerlink" href="#promod3-and-containers" title="Permalink to this headline">¶</a></h1>
+<p>ProMod3 offers build recipes for Docker and Singularity in
+<PATH_TO_PROMOD3_CHECKOUT>/container. To avoid code duplication,
+the Singularity container bootstraps from the Docker one and adds
+some sugar on top.</p>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker</a></li>
+<li class="toctree-l1"><a class="reference internal" href="singularity.html">Singularity</a></li>
+</ul>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../users.html">Documentation For Users</a><ul>
+ <li>Previous: <a href="../buildsystem.html" title="previous chapter">Building ProMod3</a></li>
+ <li>Next: <a href="docker.html" title="next chapter">Docker</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
+ <div role="note" aria-label="source link">
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/container/index.txt"
+ rel="nofollow">Show Source</a></li>
+ </ul>
+ </div>
+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="footer">
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+
+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+
+ |
+ <a href="../_sources/container/index.txt"
+ rel="nofollow">Page source</a>
+ </div>
+
+
+
+
+ </body>
+</html>
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diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
new file mode 100644
index 0000000000000000000000000000000000000000..276529329e0e0a577e68aeb24cb562b08b701a6f
--- /dev/null
+++ b/doc/html/container/singularity.html
@@ -0,0 +1,187 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Singularity — ProMod3 1.3.0 documentation</title>
+
+ <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '1.3.0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
+ <link rel="up" title="ProMod3 and Containers" href="index.html" />
+ <link rel="next" title="modelling - Protein Modelling" href="../modelling/index.html" />
+ <link rel="prev" title="Docker" href="docker.html" />
+
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+ </head>
+ <body role="document">
+
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <div class="section" id="singularity">
+<h1>Singularity<a class="headerlink" href="#singularity" title="Permalink to this headline">¶</a></h1>
+<p>We do not provide a “standalone” Singularity image, but rather bootstrap from a
+Docker image.</p>
+<div class="section" id="build-singularity-image">
+<h2>Build Singularity Image<a class="headerlink" href="#build-singularity-image" title="Permalink to this headline">¶</a></h2>
+<p>You can pull the Docker image to start with from two different sources.</p>
+<p>Option One:</p>
+<p>You built the Docker image locally and want to use it as a starting point. For
+this we have to fire up a local Docker registry and pull from there. Let’s
+assume you built the Docker image with tag promod.</p>
+<p>Fire the local Registry and push the promod image to it:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo docker run -d -p 5000:5000 --restart<span class="o">=</span>always --name registry registry:2
+sudo docker tag promod localhost:5000/promod
+sudo docker push localhost:5000/promod
+</pre></div>
+</div>
+<p>Make sure, that on top of your Singularity recipe you have something like:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>BootStrap: docker
+Registry: http://localhost:5000
+Namespace:
+From: promod:latest
+</pre></div>
+</div>
+<p>and build the image with:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo <span class="nv">SINGULARITY_NOHTTPS</span><span class="o">=</span><span class="m">1</span> singularity build promod.img Singularity
+</pre></div>
+</div>
+<p>Option Two:</p>
+<p>You pull a Docker image from an external Docker registry.
+Fill in a lot of words as soon as its on Dockerhub. Many words. The best words.</p>
+<p>and build the image with:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo singularity build promod.img Singularity
+</pre></div>
+</div>
+</div>
+<div class="section" id="run-scripts-and-actions-with-ost-pm">
+<h2>Run scripts and actions with OST/PM<a class="headerlink" href="#run-scripts-and-actions-with-ost-pm" title="Permalink to this headline">¶</a></h2>
+<p>The created container can run the ost, pm or chemdict_tool executables.
+For convenience, a jupyter notebook playground with OST, ProMod3 and nglview is
+available.</p>
+<p>To run ost, pm or chemdict_tool executables, use the exec command.
+E.g. to run scripts with pm:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity <span class="nb">exec</span> <IMAGE> pm my_script.py <span class="o">[</span>options<span class="o">]</span>
+</pre></div>
+</div>
+<p>The jupyter notebook is setup as an app in the container.
+To get help on how to run it:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity run --app Notebook <IMAGE> --help
+</pre></div>
+</div>
+</div>
+<div class="section" id="the-compound-library">
+<h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
+<p>You’ll have the exact same problem with outdated compound libraries as in the
+raw Docker image. You can find more information on that matter in the Docker
+section of the documentation: <a class="reference internal" href="docker.html#docker-compound-lib"><span class="std std-ref">The Compound Library</span></a>.</p>
+<p>The same trick of mounting an up to date compound library from the local host into
+the container applies. The two relevant commands for Singularity are building
+a new library and mount it.</p>
+<p>Build a new library:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity <span class="nb">exec</span> <IMAGE_NAME> chemdict_tool create components.cif.gz compounds.chemlib
+</pre></div>
+</div>
+<p>Run some script with an updated compound library from localhost:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity <span class="nb">exec</span> -B <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> <IMAGE_NAME> pm my_script.py
+</pre></div>
+</div>
+<p>Same as for the Docker, if you didn’t meddle with the original Dockerfile,
+<COMPLIB_DIR_CONTAINER> should be /usr/local/share/ost_complib.
+<COMPLIB_DIR_LOCALHOST> is the directory that contains the compound lib with the
+name compounds.chemlib that you created before. Make sure that everything works
+as expected by executing the exact same lines of Python code as described
+in the Docker documentation: <a class="reference internal" href="docker.html#docker-compound-lib"><span class="std std-ref">The Compound Library</span></a>.</p>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+ <h3><a href="../index.html">Table Of Contents</a></h3>
+ <ul>
+<li><a class="reference internal" href="#">Singularity</a><ul>
+<li><a class="reference internal" href="#build-singularity-image">Build Singularity Image</a></li>
+<li><a class="reference internal" href="#run-scripts-and-actions-with-ost-pm">Run scripts and actions with OST/PM</a></li>
+<li><a class="reference internal" href="#the-compound-library">The Compound Library</a></li>
+</ul>
+</li>
+</ul>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../users.html">Documentation For Users</a><ul>
+ <li><a href="index.html">ProMod3 and Containers</a><ul>
+ <li>Previous: <a href="docker.html" title="previous chapter">Docker</a></li>
+ <li>Next: <a href="../modelling/index.html" title="next chapter"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
+ <div role="note" aria-label="source link">
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/container/singularity.txt"
+ rel="nofollow">Show Source</a></li>
+ </ul>
+ </div>
+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="footer">
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+
+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+
+ |
+ <a href="../_sources/container/singularity.txt"
+ rel="nofollow">Page source</a>
+ </div>
+
+
+
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+ </body>
+</html>
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diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 069ec304aa26f141410c4fe3bfd06b0b7624cbce..aeb7bd45f118da8573b28eb010866d3abb3bebb7 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Contributing — ProMod3 1.2.0 documentation</title>
+ <title>Contributing — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="test_actions - Testing Actions" href="actions/index_dev.html" />
<link rel="prev" title="ProMod3 Setup" href="dev_setup.html" />
@@ -518,21 +519,18 @@ needed to create the actual documentation is done by CMake and its makefiles.
Hence, the <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> of the <code class="file docutils literal"><span class="pre">doc</span></code> directory of a module is
crucial. For documentation which does not relate to a particular module, the
repository comes with a top-level <code class="file docutils literal"><span class="pre">doc</span></code> directory.</p>
-<p>While you should not spend to much time thinking about how to format
-documentation, here is a helpful list of standard formatters:
-<a class="reference external" href="http://sphinx-doc.org/en/stable/markup/inline.html">http://sphinx-doc.org/en/stable/markup/inline.html</a></p>
<p>If you write new functionality for ProMod3, or fix bugs, feel free to extend
the <code class="file docutils literal"><span class="pre">CHANGELOG</span></code> file. It will be automatically pulled into the
documentation.</p>
<p>It is highly recommended to add code examples with your documentation. For that
-purpose, you should write a fully runnable script, which is to be placed in the
+purpose, you should write a fully runnable script which is to be placed in the
<code class="file docutils literal"><span class="pre">doc/tests/scripts</span></code> directory. The script is to be runnable from within
the <code class="file docutils literal"><span class="pre">doc/tests</span></code> directory as <code class="docutils literal"><span class="pre">pm</span> <span class="pre">SCRIPTPATH</span></code> and may use data stored in
the <code class="file docutils literal"><span class="pre">doc/tests/data</span></code> directory. The script and any data needed by it, must
then be referenced in the <code class="file docutils literal"><span class="pre">doc/tests/CMakeLists.txt</span></code> file. Afterwards,
-they can be included in the documentation using the
-<a class="reference external" href="http://www.sphinx-doc.org/en/stable/markup/code.html#includes">literalinclude</a>
-directive. For instance, if you add a new example code <code class="file docutils literal"><span class="pre">loop_main.py</span></code>,
+they can be included in the documentation using the literalinclude
+directive.
+For instance, if you add a new example code <code class="file docutils literal"><span class="pre">loop_main.py</span></code>,
you would add it in your module documentation as follows:</p>
<div class="highlight-rest"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../../tests/doc/scripts/loop_main.py
</pre></div>
@@ -648,7 +646,7 @@ contributions to web pages using ProMod3.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index 3cdcb509f583cc24facb60b9bcd5c19e7db01f34..236cc3934d3aaa79ffb708540fc64c1382caa561 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Geometry functions — ProMod3 1.2.0 documentation</title>
+ <title>Geometry functions — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Runtime profiling" href="runtime_profiling.html" />
<link rel="prev" title="helper - Shared Functionality For the Everything" href="helper.html" />
@@ -55,14 +56,14 @@
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Gromacs rule</li>
<li><strong>number</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Desired number of positions (max. 3)</li>
-<li><strong>anchors</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
+<li><strong>anchors</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Constructed <em>number</em> positions.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -78,16 +79,16 @@
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Positions of O and OXT atoms.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -104,9 +105,9 @@ dihedral (A-B-C-D).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
-<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
-<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
+<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
+<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
+<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
<li><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Bond length (C-D)</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (B-C-D)</li>
<li><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</li>
@@ -116,7 +117,7 @@ dihedral (A-B-C-D).</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of atom D</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -127,22 +128,22 @@ dihedral (A-B-C-D).</p>
<dt id="promod3.core.ConstructCBetaPos">
<code class="descclassname">promod3.core.</code><code class="descname">ConstructCBetaPos</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>c_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructCBetaPos" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs position of C-beta atom given the positions of the backbone nitrogen,
-C-alpha and c atoms.</p>
+C-alpha and C atoms.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of C-beta atom</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -159,8 +160,8 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
-<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
</ul>
</td>
@@ -168,7 +169,7 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Transformation matrix</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
</td>
</tr>
</tbody>
@@ -185,7 +186,7 @@ going through the origin.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
</ul>
</td>
@@ -193,7 +194,7 @@ going through the origin.</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Rotation matrix</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -210,7 +211,7 @@ going through the origin.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>res</em> does not contain N, CA and C
atoms.</td>
@@ -229,7 +230,7 @@ atoms.</td>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
</tr>
</tbody>
</table>
@@ -346,7 +347,7 @@ angles and one distance and is used in the fragment database for fast lookups.</
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index b99d92a070ce4ed9faef1242be310ea4eb2a9fe7..751d2f810451874742d7d44dd31528e9d19927de 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Graph Minimizer — ProMod3 1.2.0 documentation</title>
+ <title>Graph Minimizer — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" />
<link rel="prev" title="Runtime profiling" href="runtime_profiling.html" />
@@ -44,13 +45,13 @@
<div class="section" id="graph-minimizer">
<h1>Graph Minimizer<a class="headerlink" href="#graph-minimizer" title="Permalink to this headline">¶</a></h1>
<p>The graph minimizer solves an energy minimization problem where we have n
-nodes <span class="math">N_i</span>, with each node having several possible solutions.
-Every solution has a self energy <span class="math">E_{self}</span> and pairwise energies in between nodes
+nodes <span class="math">\(N_i\)</span>, with each node having several possible solutions.
+Every solution has a self energy <span class="math">\(E_{self}\)</span> and pairwise energies in between nodes
are possible. The goal is to select exactly one solution per node to obtain
-a set <span class="math">X=[x_1, x_2, ..., x_n]</span> that minimizes:</p>
+a set <span class="math">\(X=[x_1, x_2, ..., x_n]\)</span> that minimizes:</p>
<div class="math">
-<p><span class="math">F(X)=\displaystyle\sum_iE_{self}(N_i[x_i]) +\displaystyle \sum_i \displaystyle \sum_{j>i}E_{pair}(N_i[x_i], N_j[x_j])</span></p>
-</div><dl class="class">
+\[F(X)=\displaystyle\sum_iE_{self}(N_i[x_i]) +\displaystyle \sum_i \displaystyle \sum_{j>i}E_{pair}(N_i[x_i], N_j[x_j])\]</div>
+<dl class="class">
<dt id="promod3.core.GraphMinimizer">
<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">GraphMinimizer</code><a class="headerlink" href="#promod3.core.GraphMinimizer" title="Permalink to this definition">¶</a></dt>
<dd><dl class="method">
@@ -111,7 +112,7 @@ inconsistent with the number of solutions in the specified nodes.</p>
<code class="descname">ApplyDEE</code><span class="sig-paren">(</span><em>node_idx</em><span class="optional">[</span>, <em>e_cut=0.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyDEE" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies dead end elimination on one particular node and potentially
deactivates certain solutions. The goldstein criterion is described in
-<a class="reference internal" href="#goldstein1994" id="id1">[goldstein1994]</a>.</p>
+<a class="reference internal" href="../references.html#goldstein1994" id="id1">[goldstein1994]</a>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -138,7 +139,7 @@ a solution must be dominated by at least this <strong>e_cut</strong>.</li>
<code class="descname">ApplyEdgeDecomposition</code><span class="sig-paren">(</span><em>edge_idx</em>, <em>epsilon</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyEdgeDecomposition" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies edge decomposition on one particular edge and potentially
deactivates it. The exact decomposition procedure is described in
-<a class="reference internal" href="../sidechain/index.html#krivov2009" id="id2">[krivov2009]</a>.</p>
+<a class="reference internal" href="../references.html#krivov2009" id="id2">[krivov2009]</a>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -202,7 +203,7 @@ particular connected component is is larger <strong>max_complexity</strong>,
this component is solved in a later iteration. The algorithm iterates until
all connected components are solved and steadily increases the epsilon value
resulting in a more and more agressive edge decomposition.
-Algorithm further descsribed in <a class="reference internal" href="../sidechain/index.html#krivov2009" id="id3">[krivov2009]</a>.</p>
+Algorithm further descsribed in <a class="reference internal" href="../references.html#krivov2009" id="id3">[krivov2009]</a>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -241,7 +242,7 @@ runtime or even hit the <strong>max_visited_nodes</strong> parameter that caps t
usage.
To have a valid solution you have to take care that you set the <strong>e_cut</strong>
parameter in the pruning function to <strong>e_tresh</strong>.
-Algorithm is described in <a class="reference internal" href="#leach1998" id="id4">[leach1998]</a>.</p>
+Algorithm is described in <a class="reference internal" href="../references.html#leach1998" id="id4">[leach1998]</a>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -277,7 +278,7 @@ of that random selection relative to the current configuration is
estimated. If the difference in energy is negative, the step is
accepted. If not, the step is accepted with a probability given by
the temperature dependent Metropolis criterion
-<span class="math">exp^{\left(\frac{-e_{diff}}{T}\right)}</span>.
+<span class="math">\(exp^{\left(\frac{-e_{diff}}{T}\right)}\)</span>.
The temperature for every run starts with <strong>start_temperature</strong>
and is multiplied every <strong>change_frequency</strong> steps with <strong>cooling_factor</strong>
to achieve a simulated annealing effect.
@@ -330,18 +331,6 @@ The second element is the according energy value.</td>
</dd></dl>
-<table class="docutils citation" frame="void" id="goldstein1994" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[goldstein1994]</a></td><td>Goldstein RF (1994). Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="leach1998" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id4">[leach1998]</a></td><td>Leach AR, Lemon AP (1998). Explring the conformational space of prootein side chains using dead-end elimination and the A* algorithm. Proteins.</td></tr>
-</tbody>
-</table>
</div>
@@ -384,7 +373,7 @@ The second element is the according energy value.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 2ef049d9bc9fdc579ad7b7dffa6e9227371c6429..138df0862e217d75bf7574e2c44f62590d1576d8 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>helper - Shared Functionality For the Everything — ProMod3 1.2.0 documentation</title>
+ <title>helper - Shared Functionality For the Everything — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Geometry functions" href="geometry.html" />
<link rel="prev" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
@@ -246,7 +247,7 @@ script will terminate if a gzip file is found.</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 774d53ed424cd8915182a7f8216297a4fe85bde9..d65e79fbf1e65c7e73829aef4c97f8b9b527f37c 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>core - ProMod3 Core Functionality — ProMod3 1.2.0 documentation</title>
+ <title>core - ProMod3 Core Functionality — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
<link rel="prev" title="Loading Precomputed Objects" href="../loop/load_loop_objects.html" />
@@ -104,7 +105,7 @@ modeling per se but cover standard programming issues.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index c92c89603a57ec80a32e2435a5661d076d14f31a..e527fc76ef4254701b89b5a79b35112c10300692 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>pm3argparse - Parsing Command Lines — ProMod3 1.2.0 documentation</title>
+ <title>pm3argparse - Parsing Command Lines — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
<link rel="prev" title="core - ProMod3 Core Functionality" href="index.html" />
@@ -198,11 +199,51 @@ wrong type</li>
</ul>
</dd></dl>
+<dl class="method">
+<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddProfile">
+<code class="descname">AddProfile</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.AddProfile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Commandline options for profiles</p>
+<p>Activate everything needed to load profiles to the argument parser.
+Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a> and the
+input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>.</p>
+<p>Options/arguments added:</p>
+<ul class="simple">
+<li><code class="docutils literal"><span class="pre">-s/--seqprof</span> <span class="pre"><FILE></span></code> - Sequence profile in any format readable
+by the <code class="xref py py-meth docutils literal"><span class="pre">ost.io.LoadSequenceProfile()</span></code> method. Format is chosen by
+file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm,
+.pssm.gz. Consider to use
+<a class="reference external" href="https://www.openstructure.org/docs/dev/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a file
+in a3m format at hand.</li>
+</ul>
+<p>Notes:</p>
+<ul class="simple">
+<li>the profiles are mapped based on exact matches towards the gapless
+target sequences, i.e. one profile is mapped to several chains in
+case of homo-oligomers</li>
+<li>every profile must have a unique sequence to avoid ambiguities</li>
+<li>all or nothing - you cannot provide profiles for only a subset of
+target sequences</li>
+</ul>
+<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>:</p>
+<ul class="simple">
+<li><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code> - <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
+ordered to match the target sequences.</li>
+</ul>
+<p>Exit codes related to profile input:</p>
+<ul class="simple">
+<li>51 - a given profile file does not exist</li>
+<li>52 - failure to read a given profile file</li>
+<li>53 - a profile cannot be mapped to any target sequence</li>
+<li>54 - profile sequences are not unique</li>
+<li>55 - only subset of target sequences is covered by profile</li>
+</ul>
+</dd></dl>
+
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddStructure">
<code class="descname">AddStructure</code><span class="sig-paren">(</span><em>attach_views=False</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.AddStructure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure" title="Permalink to this definition">¶</a></dt>
<dd><p>Commandline options for structures.</p>
-<p>Activate everything needed to load alignments to the argument parser.
+<p>Activate everything needed to load structures to the argument parser.
Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a> and the
input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>.</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -343,7 +384,7 @@ and with the right constraints.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index 2466ad9d3f6e6d8de264e1874c43332677a3a97a..d7218105ee41bcf6fdb9ef0e92ad11406d389553 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Runtime profiling — ProMod3 1.2.0 documentation</title>
+ <title>Runtime profiling — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Graph Minimizer" href="graph_minimizer.html" />
<link rel="prev" title="Geometry functions" href="geometry.html" />
@@ -200,7 +201,7 @@ will fail miserably if timers are currently running.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index e0e9cb4d4256b35a60b91b487c28cbea9efd04cf..724fb324faeef1dfd700327218734323f18813ac 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>SetCompoundsChemlib() — ProMod3 1.2.0 documentation</title>
+ <title>SetCompoundsChemlib() — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Documentation For Developers" href="../developers.html" />
<link rel="prev" title="Graph Minimizer" href="graph_minimizer.html" />
@@ -105,7 +106,7 @@ enabled globally.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index f58b1ee6ad20de2cf87c9fc6bf8c81d1ba15d6b5..075ba92b7bf050a989eebdc8b4c6927a62b89ef3 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 Setup — ProMod3 1.2.0 documentation</title>
+ <title>ProMod3 Setup — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="Contributing" href="contributing.html" />
<link rel="prev" title="Documentation For Developers" href="developers.html" />
@@ -292,7 +293,7 @@ modules from there, use the binaries from <code class="file docutils literal"><s
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 89882a9474b79f60d2d36dbbc47bec5394e3ccc3..e1c550bbbbdea027b691ada3779a6814064890f4 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Documentation For Developers — ProMod3 1.2.0 documentation</title>
+ <title>Documentation For Developers — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
<link rel="next" title="ProMod3 Setup" href="dev_setup.html" />
<link rel="prev" title="SetCompoundsChemlib()" href="core/setcompoundschemlib.html" />
@@ -123,7 +124,7 @@ new features.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 4e5da3b46b5ba10cbb6458cf8b9eee2e6aeedac4..97e9e9d6addfc26832a37135fd38ff0207c79073 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -7,7 +7,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Index — ProMod3 1.2.0 documentation</title>
+ <title>Index — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,8 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -43,7 +44,8 @@
<h1 id="index">Index</h1>
<div class="genindex-jumpbox">
- <a href="#_"><strong>_</strong></a>
+ <a href="#Symbols"><strong>Symbols</strong></a>
+ | <a href="#_"><strong>_</strong></a>
| <a href="#A"><strong>A</strong></a>
| <a href="#B"><strong>B</strong></a>
| <a href="#C"><strong>C</strong></a>
@@ -66,6 +68,69 @@
| <a href="#U"><strong>U</strong></a>
</div>
+<h2 id="Symbols">Symbols</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt>
+ -i, --backbone-independent
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="actions/index.html#cmdoption-i">command line option</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt>
+ -k, --keep-sidechains
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="actions/index.html#cmdoption-k">command line option</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt>
+ -n, --no-disulfids
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="actions/index.html#cmdoption-n">command line option</a>
+ </dt>
+
+ </dl></dd>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt>
+ -r, --rigid-rotamers
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="actions/index.html#cmdoption-r">command line option</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt>
+ -s, --no-subrotamer-optimization
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="actions/index.html#cmdoption-s">command line option</a>
+ </dt>
+
+ </dl></dd>
+ </dl></td>
+</tr></table>
+
<h2 id="_">_</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
@@ -282,6 +347,10 @@
</dt>
+ <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile">AddProfile() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.AddRotamer">AddRotamer() (promod3.sidechain.BBDepRotamerLib method)</a>
</dt>
@@ -737,12 +806,12 @@
</dt>
</dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="modelling/gap_handling.html#promod3.modelling.ClearGaps">ClearGaps() (in module promod3.modelling)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ClearPos">ClearPos() (promod3.loop.AllAtomPositions method)</a>
</dt>
@@ -761,6 +830,18 @@
</dt>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.CTerminalCloser.Close">(promod3.modelling.CTerminalCloser method)</a>
+ </dt>
+
+
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.CloserBase.Close">(promod3.modelling.CloserBase method)</a>
+ </dt>
+
+
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.DeNovoCloser.Close">(promod3.modelling.DeNovoCloser method)</a>
+ </dt>
+
+
<dt><a href="modelling/monte_carlo.html#promod3.modelling.DirtyCCDCloser.Close">(promod3.modelling.DirtyCCDCloser method)</a>
</dt>
@@ -772,6 +853,10 @@
<dt><a href="modelling/monte_carlo.html#promod3.modelling.KICCloser.Close">(promod3.modelling.KICCloser method)</a>
</dt>
+
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.NTerminalCloser.Close">(promod3.modelling.NTerminalCloser method)</a>
+ </dt>
+
</dl></dd>
<dt><a href="modelling/pipeline.html#promod3.modelling.CloseGaps">CloseGaps() (in module promod3.modelling)</a>
@@ -782,6 +867,10 @@
</dt>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.CloserBase">CloserBase (class in promod3.modelling)</a>
+ </dt>
+
+
<dt><a href="modelling/pipeline.html#promod3.modelling.CloseSmallDeletions">CloseSmallDeletions() (in module promod3.modelling)</a>
</dt>
@@ -821,6 +910,33 @@
</dl></dd>
+ <dt>
+ command line option
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="actions/index.html#cmdoption-i">-i, --backbone-independent</a>
+ </dt>
+
+
+ <dt><a href="actions/index.html#cmdoption-k">-k, --keep-sidechains</a>
+ </dt>
+
+
+ <dt><a href="actions/index.html#cmdoption-n">-n, --no-disulfids</a>
+ </dt>
+
+
+ <dt><a href="actions/index.html#cmdoption-r">-r, --rigid-rotamers</a>
+ </dt>
+
+
+ <dt><a href="actions/index.html#cmdoption-s">-s, --no-subrotamer-optimization</a>
+ </dt>
+
+ </dl></dd>
+
<dt><a href="scoring/backbone_score_env.html#promod3.scoring.ConstraintFunction">ConstraintFunction (class in promod3.scoring)</a>
</dt>
@@ -890,6 +1006,10 @@
</dl></dd>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase">CoolerBase (class in promod3.modelling)</a>
+ </dt>
+
+
<dt><a href="loop/structure_db.html#promod3.loop.CoordInfo">CoordInfo (class in promod3.loop)</a>
</dt>
@@ -946,6 +1066,14 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.DeNovoCloser">DeNovoCloser (class in promod3.modelling)</a>
+ </dt>
+
+
+ <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.DihedralConfiguration">DihedralConfiguration (class in promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="modelling/monte_carlo.html#promod3.modelling.DirtyCCDCloser">DirtyCCDCloser (class in promod3.modelling)</a>
</dt>
@@ -969,12 +1097,12 @@
<dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.disulfid_bridges">disulfid_bridges (promod3.modelling.SidechainReconstructionData attribute)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="sidechain/disulfid.html#promod3.sidechain.DisulfidScore">DisulfidScore() (in module promod3.sidechain)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoExternalScores">DoExternalScores() (promod3.scoring.AllAtomClashScorer method)</a>
</dt>
@@ -1542,6 +1670,10 @@
</dt>
+ <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.GetDihedralConfiguration">GetDihedralConfiguration() (in module promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="loop/structure_db.html#promod3.loop.FragDB.GetDistBinSize">GetDistBinSize() (promod3.loop.FragDB method)</a>
</dt>
@@ -1892,12 +2024,20 @@
</dt>
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.GetScore">GetScore() (in module promod3.modelling)</a>
+ <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.GetRotamericConfiguration">GetRotamericConfiguration() (in module promod3.sidechain)</a>
+ </dt>
+
+
+ <dt><a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">GetScore() (promod3.loop.Fragger method)</a>, <a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">[1]</a>
</dt>
<dd><dl>
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">(promod3.loop.Fragger method)</a>, <a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">[1]</a>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.LinearScorer.GetScore">(promod3.modelling.LinearScorer method)</a>
+ </dt>
+
+
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.ScorerBase.GetScore">(promod3.modelling.ScorerBase method)</a>
</dt>
</dl></dd>
@@ -1984,11 +2124,15 @@
</dt>
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.GetTemperature">GetTemperature() (promod3.modelling.ExponentialCooler method)</a>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase.GetTemperature">GetTemperature() (promod3.modelling.CoolerBase method)</a>
</dt>
<dd><dl>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.GetTemperature">(promod3.modelling.ExponentialCooler method)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetTemperature">(promod3.sidechain.FRMRotamer method)</a>
</dt>
@@ -2145,6 +2289,10 @@
</dt>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase.Initialize">(promod3.modelling.SamplerBase method)</a>
+ </dt>
+
+
<dt><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler.Initialize">(promod3.modelling.SoftSampler method)</a>
</dt>
@@ -2270,6 +2418,10 @@
</dt>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.LinearScorer">LinearScorer (class in promod3.modelling)</a>
+ </dt>
+
+
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.lj_pairs">lj_pairs (promod3.loop.ForcefieldConnectivity attribute)</a>
</dt>
@@ -2348,6 +2500,10 @@
</dt>
+ <dt><a href="sidechain/loading.html#promod3.sidechain.LoadBBDepLib">LoadBBDepLib() (in module promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.LoadCached">LoadCached() (promod3.modelling.FraggerHandle method)</a>
</dt>
@@ -2371,22 +2527,18 @@
<dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadDefaultBackboneOverallScorer">LoadDefaultBackboneOverallScorer() (in module promod3.scoring)</a>
</dt>
-
- <dt><a href="sidechain/loading.html#promod3.sidechain.LoadDunbrackLib">LoadDunbrackLib() (in module promod3.sidechain)</a>
- </dt>
-
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/load_loop_objects.html#promod3.loop.LoadFragDB">LoadFragDB() (in module promod3.loop)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadHBondScorer">LoadHBondScorer() (in module promod3.scoring)</a>
</dt>
- <dt><a href="sidechain/loading.html#promod3.sidechain.LoadPenultimateLib">LoadPenultimateLib() (in module promod3.sidechain)</a>
+ <dt><a href="sidechain/loading.html#promod3.sidechain.LoadLib">LoadLib() (in module promod3.sidechain)</a>
</dt>
@@ -2788,6 +2940,10 @@
</dt>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase.ProposeStep">(promod3.modelling.SamplerBase method)</a>
+ </dt>
+
+
<dt><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler.ProposeStep">(promod3.modelling.SoftSampler method)</a>
</dt>
@@ -2903,6 +3059,10 @@
<dd><dl>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase.Reset">(promod3.modelling.CoolerBase method)</a>
+ </dt>
+
+
<dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.Reset">(promod3.modelling.ExponentialCooler method)</a>
</dt>
@@ -3010,6 +3170,10 @@
</dt>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase">SamplerBase (class in promod3.modelling)</a>
+ </dt>
+
+
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.Save">Save() (promod3.loop.ForcefieldLookup method)</a>
</dt>
@@ -3146,6 +3310,10 @@
</dt>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.ScorerBase">ScorerBase (class in promod3.modelling)</a>
+ </dt>
+
+
<dt><a href="modelling/gap_handling.html#promod3.modelling.ScoringGapExtender">ScoringGapExtender (class in promod3.modelling)</a>
</dt>
@@ -3383,12 +3551,12 @@
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetOLC">SetOLC() (promod3.loop.BackboneList method)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity">SetPeptideBoundConnectivity() (promod3.loop.ForcefieldLookup method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.SetPolarDirection">SetPolarDirection() (promod3.sidechain.Particle method)</a>
</dt>
@@ -3715,7 +3883,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index f984958d7fd43ff0e604a8031e37bb8b44e74eec..f28f4800a5b0ebadeba73fabd887cbb4187419cd 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Getting Started — ProMod3 1.2.0 documentation</title>
+ <title>Getting Started — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Users" href="users.html" />
<link rel="next" title="ProMod3 Actions" href="actions/index.html" />
<link rel="prev" title="Documentation For Users" href="users.html" />
@@ -88,7 +89,7 @@ is conserved</li>
<li>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal"><span class="pre">loop</span></code></a> module)</li>
<li>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal"><span class="pre">sidechain</span></code></a> module)</li>
<li>Minimize energy of final model using molecular mechanics
-(using <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
+(using <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.8.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
</ul>
<p>Since a good amount of time is spent in OpenMM routines to minimize energy, we
try to use the fast and multi-threaded “CPU” platform of OpenMM (should be
@@ -147,7 +148,7 @@ not set, 1 thread will be used by default.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/index.html b/doc/html/index.html
index 9a9a20281972b758a64c9e1976765ce31fd410cc..01e2cbfaf22aa5dd703cdd8476e46b4176815030 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Welcome To ProMod3’s Documentation! — ProMod3 1.2.0 documentation</title>
+ <title>ProMod3 — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="#" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="#" />
<link rel="next" title="Documentation For Users" href="users.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -39,15 +40,23 @@
<div class="bodywrapper">
<div class="body" role="main">
- <div class="section" id="welcome-to-promod3-s-documentation">
-<h1>Welcome To ProMod3’s Documentation!<a class="headerlink" href="#welcome-to-promod3-s-documentation" title="Permalink to this headline">¶</a></h1>
-<p>Contents:</p>
+ <div class="section" id="promod3">
+<h1>ProMod3<a class="headerlink" href="#promod3" title="Permalink to this headline">¶</a></h1>
+<p>ProMod3 is a modelling engine based on the OpenStructure <a class="reference internal" href="references.html#biasini2013" id="id1">[biasini2013]</a>
+computational structural biology framework that can perform all steps required
+to generate a protein model by homology. Its modular design aims at
+implementing flexible modelling pipelines and fast prototyping of novel
+algorithms.</p>
+</div>
+<div class="section" id="documentation">
+<h1>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a><ul>
<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
@@ -56,29 +65,16 @@
<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="dev_setup.html">ProMod3 Setup</a></li>
-<li class="toctree-l2"><a class="reference internal" href="contributing.html">Contributing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="actions/index_dev.html"><code class="docutils literal"><span class="pre">test_actions</span></code> - Testing Actions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cmake/index.html">ProMod3‘s Share Of CMake</a></li>
-<li class="toctree-l2"><a class="reference internal" href="portableIO.html">Using Binary Files In ProMod3</a></li>
-</ul>
-</li>
</ul>
</div>
<div class="toctree-wrapper compound">
<ul>
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
</ul>
</div>
-</div>
-<div class="section" id="indices-and-tables">
-<h1>Indices And Tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
-<li><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></li>
-<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li>
-</ul>
</div>
@@ -89,10 +85,10 @@
<div class="sphinxsidebarwrapper">
<h3><a href="#">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#">Welcome To ProMod3’s Documentation!</a><ul>
+<li><a class="reference internal" href="#">ProMod3</a></li>
+<li><a class="reference internal" href="#documentation">Documentation</a><ul>
</ul>
</li>
-<li><a class="reference internal" href="#indices-and-tables">Indices And Tables</a></li>
</ul>
<div class="relations">
<h3>Related Topics</h3>
@@ -124,7 +120,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/license.html b/doc/html/license.html
new file mode 100644
index 0000000000000000000000000000000000000000..6fe3a3cad151efe00afbb56d17a09686d0a9822b
--- /dev/null
+++ b/doc/html/license.html
@@ -0,0 +1,311 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
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+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>License — ProMod3 1.3.0 documentation</title>
+
+ <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '1.3.0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
+ <link rel="next" title="References" href="references.html" />
+ <link rel="prev" title="Using Binary Files In ProMod3" href="portableIO.html" />
+
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+ </head>
+ <body role="document">
+
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <div class="section" id="license">
+<h1>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h1>
+<div class="highlight-default"><div class="highlight"><pre><span></span>
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
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+ "License" shall mean the terms and conditions for use, reproduction,
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+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
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+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
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+
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+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
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+ 9. Accepting Warranty or Additional Liability. While redistributing
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+ and charge a fee for, acceptance of support, warranty, indemnity,
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+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
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+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+
+ProMod3 bundles the file "FindEigen3.cmake", which is availabe under a
+"2-clause BSD" license. For details, see cmake_support/FindEigen3.cmake.
+
+ProMod3 bundles the file "cmake.py", which is available under a
+"3-clause BSD" license. For details, see doc/cmake.py and
+doc/Copyright_cmake.py.txt
+</pre></div>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
+ <li>Previous: <a href="portableIO.html" title="previous chapter">Using Binary Files In ProMod3</a></li>
+ <li>Next: <a href="references.html" title="next chapter">References</a></li>
+ </ul></li>
+</ul>
+</div>
+ <div role="note" aria-label="source link">
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
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+ rel="nofollow">Show Source</a></li>
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+ </div>
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+ <div class="clearer"></div>
+ </div>
+ <div class="footer">
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+
+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+
+ |
+ <a href="_sources/license.txt"
+ rel="nofollow">Page source</a>
+ </div>
+
+
+
+
+ </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index df65f9c542ab9108208ba0e8740ebb02e80413e0..0566e8bfdc93c7b7ac7921816c9ed17834a69859 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling All Atom Positions — ProMod3 1.2.0 documentation</title>
+ <title>Handling All Atom Positions — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
<link rel="prev" title="Structural Data" href="structure_db.html" />
@@ -90,8 +91,8 @@ new loop is being added.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
</tr>
</tbody>
@@ -113,7 +114,7 @@ concatenated one after each other (indexing starts at 0)</li>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</td>
</tr>
@@ -143,7 +144,7 @@ means, that positions in the env. may be reset, newly set or cleared.</p>
<li><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</li>
<li><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</li>
<li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
</ul>
</td>
@@ -220,7 +221,7 @@ a loop to reset later with <a class="reference internal" href="#promod3.loop.All
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -354,7 +355,7 @@ and if found set the corresponding position, otherwise we unset it.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
</ul>
</td>
</tr>
@@ -400,7 +401,7 @@ out of bounds or if residues in the two containers are inconsistent
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Set position at that index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
</ul>
</td>
</tr>
@@ -450,7 +451,7 @@ out of bounds or if residues in the two containers are inconsistent
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom position index.</td>
</tr>
@@ -554,7 +555,7 @@ if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of residue at index <em>res_index</em>.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</td>
</tr>
@@ -833,9 +834,9 @@ atom (N, CA, C, O).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">All residues packed in a single chain as an OST entity.
-Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -855,8 +856,8 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
</ul>
</td>
</tr>
@@ -949,7 +950,7 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
<dt id="promod3.loop.AminoAcidLookup">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
<dd><p>Collection of static methods to lookup properties of amino acid types
-(<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) and
+(<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) and
hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidHydrogen</span></code></a>).</p>
<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetOLC">
@@ -962,7 +963,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -984,7 +985,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumAtoms(aa)-1])</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
@@ -1014,7 +1015,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumHydrogens(aa)-1])</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
@@ -1043,7 +1044,7 @@ atom.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
</td>
@@ -1071,7 +1072,7 @@ and atom.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
</td>
@@ -1095,7 +1096,7 @@ hydrogens of <em>aa</em>.</p>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -1127,7 +1128,7 @@ hydrogens of <em>aa</em>.</p>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -1160,7 +1161,7 @@ hydrogens of <em>aa</em>.</p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Amino acid type of the given heavy atom type</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
@@ -1254,7 +1255,7 @@ when residue is peptide bound.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if no such atom (i.e. PRO)</td>
</tr>
@@ -1278,7 +1279,7 @@ when residue is N terminal.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if no such atom (i.e. H3 for PRO)</td>
</tr>
@@ -1342,7 +1343,7 @@ when residue is N terminal.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index 096e988e0855d432d670e2d868e5e9d6da9309ab..9d5e222b29480b28114ff9d969e7dc4c7ea390fd 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Representing Loops — ProMod3 1.2.0 documentation</title>
+ <title>Representing Loops — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
<link rel="prev" title="loop - Loop Handling" href="index.html" />
@@ -46,7 +47,7 @@
<p>The most simple representation of structural information in ProMod3 is the
<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>. It provides a way to store the backbone positions of
residues. They provide structural manipulations, they can be manipulated and
-converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
@@ -160,7 +161,7 @@ code which is not one of the 20 default amino acids or if
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</li>
-<li><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – List of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<li><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – List of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
which the backbone positions are extracted.</li>
</ul>
</td>
@@ -184,7 +185,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to a density map.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -194,7 +195,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
-<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – </li>
+<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – </li>
<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </li>
</ul>
@@ -213,7 +214,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to an OST entity.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -230,8 +231,8 @@ be replaced, otherwise they will be added to the entity.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
</ul>
</td>
</tr>
@@ -247,7 +248,7 @@ be replaced, otherwise they will be added to the entity.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
+<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </li>
</ul>
@@ -266,7 +267,7 @@ be replaced, otherwise they will be added to the entity.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </td>
</tr>
@@ -299,7 +300,8 @@ be replaced, otherwise they will be added to the entity.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Set amino acid sequence to this.</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>sequence</em> contains a one letter
-code which is not one of the 20 default amino acids.</td>
+code which is not one of the 20 default amino acids or size of
+<em>sequence</em> does not match.</td>
</tr>
</tbody>
</table>
@@ -369,7 +371,7 @@ actual fragment at specified <em>index</em></p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
atom for residue at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</td>
</tr>
@@ -394,7 +396,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
/ oxygen atom to this.</li>
</ul>
</td>
@@ -446,7 +448,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of the residue at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</td>
</tr>
@@ -463,7 +465,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
</ul>
</td>
</tr>
@@ -489,12 +491,12 @@ and set the amino acid type according to the given one letter code.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
<li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
</td>
@@ -564,12 +566,12 @@ to the given one letter code.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
<li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
</td>
@@ -633,7 +635,7 @@ reconstructed if the residue handle is valid.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
element of this backbone list)</td>
</tr>
</tbody>
@@ -650,7 +652,7 @@ element of this backbone list)</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
</td>
</tr>
@@ -670,7 +672,7 @@ element of this backbone list)</td>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Start index.</li>
<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – End index (one past last residue to transform).</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
</td>
</tr>
@@ -686,7 +688,7 @@ element of this backbone list)</td>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
</tr>
</tbody>
</table>
@@ -706,12 +708,12 @@ residue <em>other_index</em> of <em>other</em> backbone list considering the
positions of the N, CA and C atoms.</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
<li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</li>
<li><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</li>
</ul>
@@ -731,7 +733,7 @@ positions of the N, CA and C atoms.</p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Get minimum RMSD transformation of CA positions of this backbone
list onto CA positions of <em>other</em> backbone list.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
</tr>
@@ -847,8 +849,8 @@ smaller than 3.</p>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetBackrub">
<code class="descname">SetBackrub</code><span class="sig-paren">(</span><em>index</em>, <em>primary_rot_angle</em>, <em>flanking_rot_angle_one</em>, <em>flanking_rot_angle_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetBackrub" title="Permalink to this definition">¶</a></dt>
-<dd><p>Applies a backrub motion at residue defined by <strong>index</strong>. The first
-rotation axis is defined by the CA positions from residues at
+<dd><p>Applies a backrub motion <a class="reference internal" href="../references.html#davis2006" id="id1">[davis2006]</a> at residue defined by <strong>index</strong>.
+The first rotation axis is defined by the CA positions from residues at
<strong>index</strong> -1 and <strong>index</strong> +1. All atoms in between get rotated around this
axis by <strong>primary_rot_angle</strong>. To restore the the hydrogen bond network
of the two transformed oxygens, the backrub motion gets completed by
@@ -1003,7 +1005,7 @@ backbone list.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 4ceff047a047b214b7ec544b3426b6026963b818..7564641ee912944a4e121b4fae73c19bc9bcddb0 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>loop - Loop Handling — ProMod3 1.2.0 documentation</title>
+ <title>loop - Loop Handling — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Representing Loops" href="backbone.html" />
<link rel="prev" title="Other Scoring Functions" href="../scoring/other_scoring_functions.html" />
@@ -162,7 +163,7 @@ loops. The following example should give you an idea of what can be done:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index 8425953c8165937468f1c690d1e44d38250cfe99..ab7769618f810185d5317090ed4d90d69be1b015 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Loading Precomputed Objects — ProMod3 1.2.0 documentation</title>
+ <title>Loading Precomputed Objects — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="core - ProMod3 Core Functionality" href="../core/index.html" />
<link rel="prev" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
@@ -49,7 +50,7 @@ ProMod3 offers to load precomputed instances for direct usage.</p>
<dt id="promod3.loop.LoadTorsionSampler">
<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSampler</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by Solis & Rachovsky [1] that has been trained on
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id1">[solis2006]</a> that has been trained on
non-redundant protein structures.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -69,7 +70,7 @@ non-redundant protein structures.</p>
<dt id="promod3.loop.LoadTorsionSamplerCoil">
<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerCoil</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerCoil" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by Solis & Rachovsky [1] that has been trained on coil
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id2">[solis2006]</a> that has been trained on coil
residues of non-redundant protein structures.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -89,7 +90,7 @@ residues of non-redundant protein structures.</p>
<dt id="promod3.loop.LoadTorsionSamplerHelical">
<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerHelical</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerHelical" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by Solis & Rachovsky [1] that has been trained on helical
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id3">[solis2006]</a> that has been trained on helical
residues of non-redundant protein structures.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -109,7 +110,7 @@ residues of non-redundant protein structures.</p>
<dt id="promod3.loop.LoadTorsionSamplerExtended">
<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerExtended</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerExtended" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by Solis & Rachovsky [1] that has been trained on extended
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id4">[solis2006]</a> that has been trained on extended
residues of non-redundant protein structures.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -126,48 +127,41 @@ residues of non-redundant protein structures.</p>
</dd></dl>
<dl class="method">
-<dt id="promod3.loop.LoadFragDB">
-<code class="descclassname">promod3.loop.</code><code class="descname">LoadFragDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadFragDB" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads and returns a FragDB containing fragments up to the length of 14,
-therefore capable of bridging gaps up to the length of 12.</p>
+<dt id="promod3.loop.LoadStructureDB">
+<code class="descclassname">promod3.loop.</code><code class="descname">LoadStructureDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadStructureDB" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads and returns a structure db containing roughly 21000 chains form the
+PDB with seqid redundancy cutoff of 60%</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Fragment database</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The structure db</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.loop.LoadStructureDB">
-<code class="descclassname">promod3.loop.</code><code class="descname">LoadStructureDB</code><span class="sig-paren">(</span><em>load_frequencies=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadStructureDB" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads and returns a structure db containing roughly 24000 chains form the
-PDB with redundancy cutoff of 90%</p>
+<dt id="promod3.loop.LoadFragDB">
+<code class="descclassname">promod3.loop.</code><code class="descname">LoadFragDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadFragDB" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads and returns a FragDB containing fragments up to the length of 14,
+therefore capable of bridging gaps up to the length of 12. The returned
+databases contains the location of fragments in the <a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>
+returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" title="promod3.loop.LoadStructureDB"><code class="xref py py-meth docutils literal"><span class="pre">LoadStructureDB()</span></code></a>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>load_frequencies</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If True, the full database including profile
-information gets loaded (see
-<a class="reference internal" href="structure_db.html#promod3.loop.StructureDB.Load" title="promod3.loop.StructureDB.Load"><code class="xref py py-meth docutils literal"><span class="pre">StructureDB.Load()</span></code></a>).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The structure db</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Fragment database</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a></td>
</tr>
</tbody>
</table>
</dd></dl>
-<dl class="docutils">
-<dt>[1] A. D. Solis and S. Rackovsky. Improvement of statistical potentials and</dt>
-<dd>threading score functions using information maximization.
-Proteins, 62(4):892–908, Mar 2006.</dd>
-</dl>
</div>
@@ -210,7 +204,7 @@ Proteins, 62(4):892–908, Mar 2006.</dd>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 38cdf31e4748d13ed4624067799504894827ea98..d3e6544cd24bc573c0b568c01010e7905009a4e2 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Generate ost.mol.mm systems — ProMod3 1.2.0 documentation</title>
+ <title>Generate ost.mol.mm systems — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Loading Precomputed Objects" href="load_loop_objects.html" />
<link rel="prev" title="Handling All Atom Positions" href="all_atom.html" />
@@ -42,8 +43,8 @@
<div class="body" role="main">
<div class="section" id="generate-ost-mol-mm-systems">
-<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
-<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.8.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
+<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.8.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
proteins, we define a system creator for loops (<a class="reference internal" href="#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal"><span class="pre">MmSystemCreator</span></code></a>) and a
specialized forcefield lookup for amino acids (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a>).</p>
<p>The example below showcases the creation and use of an MM system:</p>
@@ -288,7 +289,7 @@ acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]<
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Simulation object setup by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>. Use this to run
MM simulations.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
</tr>
</tbody>
</table>
@@ -435,7 +436,7 @@ FF specific data for amino acids in a protein. We distinguish amino acid types
<dl class="class">
<dt id="promod3.loop.ForcefieldLookup">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
+<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
<ul class="simple">
<li>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
<em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
@@ -548,7 +549,7 @@ for details.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type for given <em>ff_aa</em></td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</td>
</tr>
@@ -664,7 +665,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for LJ 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
</tr>
@@ -680,7 +681,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for electrostatic 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
</tr>
@@ -695,7 +696,7 @@ for details.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -719,7 +720,7 @@ for details.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -744,7 +745,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Sigma in nm for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -769,7 +770,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Epsilon in kJ/mol for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -915,7 +916,7 @@ for details.</p>
<dt id="promod3.loop.ForcefieldAminoAcid">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the amino acid types for forcefields. The first 20 values
-correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
+correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
there are values for disulfid bridges (<em>FF_CYS2</em>), d-protonated histidine
(<em>FF_HISD</em>, default for <em>ost.conop.HIS</em> is <em>FF_HISE</em>) and <em>FF_XXX</em> for unknown
types. The full list of values is:</p>
@@ -932,7 +933,7 @@ types. The full list of values is:</p>
<dd><p>Contains lists of bonds, angles, dihedrals, impropers and LJ pairs (exclusions
are the combination of all bonds and 1,3 pairs of angles and are not stored
separately). Each type of connectivity has it’s own class (see below) storing
-indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Topology</span></code></a>.
+indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Topology</span></code></a>.
The indexing of atoms for internal connectivities is in [<em>0, N-1</em>], where <em>N</em>
= <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">ForcefieldLookup.GetNumAtoms()</span></code></a>. For connectivities of pairs of
residues, atoms of the first residue are in [<em>0, N1-1</em>] and atoms of the
@@ -1042,7 +1043,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldBondInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
+<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1104,7 +1105,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
+<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1181,7 +1182,7 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define Urey-Bradley angle
-(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1286,8 +1287,8 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define periodic dihedral or improper (see
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1391,7 +1392,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
+<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1481,7 +1482,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldLJPairInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
+<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1592,7 +1593,7 @@ False, False)</em>.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 9e2c5705f18ee62396096e5fb1a4622a9ff814dc..6f0cff9e04a1148be311f7ecac8b1f82cd0d264c 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Structural Data — ProMod3 1.2.0 documentation</title>
+ <title>Structural Data — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Handling All Atom Positions" href="all_atom.html" />
<link rel="prev" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
@@ -43,7 +44,7 @@
<div class="section" id="structural-data">
<h1>Structural Data<a class="headerlink" href="#structural-data" title="Permalink to this headline">¶</a></h1>
-<p>The structural database serves as a container for structural backbone and
+<p>The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> serves as a container for structural backbone and
sequence data. Custom accessor objects can be implemented that relate
arbitrary features to structural data. Examples provided by ProMod3 include
accession using matching stem geometry (see: <a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) or sequence
@@ -66,10 +67,10 @@ to the OUTER surface. To determine whether an atom is part of that outer
surface, the full structure is placed into a 3D grid and a flood fill
algorithm is used to determine the atoms of interest.
Internal cavities are excluded by using this approach. This is a simplified
-version of the residue depth as discussed in <a class="reference internal" href="#chakravarty1999" id="id1">[chakravarty1999]</a> and gets
+version of the residue depth as discussed in <a class="reference internal" href="../references.html#chakravarty1999" id="id1">[chakravarty1999]</a> and gets
directly calculated when structural information is added to the StructureDB.</li>
<li>The amino acid frequency derived from structural alignments as described
-in <a class="reference internal" href="#zhou2005" id="id2">[zhou2005]</a> - Since the calculation of such a profile already requires a
+in <a class="reference internal" href="../references.html#zhou2005" id="id2">[zhou2005]</a> - Since the calculation of such a profile already requires a
StructureDB, we end up in a hen and egg problem here... When adding
structural information to the StructureDB, the according memory gets
just allocated and set to zero. The usage of this information
@@ -83,7 +84,7 @@ and manually set them (or load the provided default database).</li>
<dt id="promod3.loop.CoordInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">CoordInfo</code><a class="headerlink" href="#promod3.loop.CoordInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>The CoordInfo gets automatically generated when new chains are added to
-the structural database. It contains internal information of how a
+a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>. It contains internal information of how a
connected stretch of residues is stored in the database.</p>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.id">
@@ -118,14 +119,14 @@ structure. (<a class="reference external" href="https://docs.python.org/2.7/libr
<code class="descname">start_resnum</code><a class="headerlink" href="#promod3.loop.CoordInfo.start_resnum" title="Permalink to this definition">¶</a></dt>
<dd><p>Residue number of first residue in the added stretch. The residue number
is relative to the SEQRES provided in the input profile when adding the
-stuff to the structure db.</p>
+stuff to the structure db. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.shift">
<code class="descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
<dd><p>Translation from original coordinates that has been applied before storing
-structural information in db.</p>
+structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
</dd></dl>
</dd></dl>
@@ -133,7 +134,7 @@ structural information in db.</p>
<dl class="class">
<dt id="promod3.loop.FragmentInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FragmentInfo</code><span class="sig-paren">(</span><em>chain_index</em>, <em>offset</em>, <em>length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragmentInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>The FragmentInfo defines any fragment in the structural database. If you
+<dd><p>The FragmentInfo defines any fragment in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>. If you
implement your own accessor object, thats the information you want to store.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -151,8 +152,8 @@ implement your own accessor object, thats the information you want to store.</p>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.chain_index">
<code class="descname">chain_index</code><a class="headerlink" href="#promod3.loop.FragmentInfo.chain_index" title="Permalink to this definition">¶</a></dt>
-<dd><p>The index of the chain (defined by <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a>) in the structure db
-this particle belongs to. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<dd><p>The index of the chain (defined by <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a>) in the
+<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> this particle belongs to. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
@@ -194,8 +195,8 @@ and fill it with content.</p>
<span class="n">prof_dir</span> <span class="o">=</span> <span class="s2">"data"</span>
<span class="c1"># The naming of the files in the directories is e.g. 1CRN.pdb for </span>
-<span class="c1"># the structure and 1CRNA.hhm for the profile. Please note, </span>
-<span class="c1"># that the structure can contain several chains, whereas the hhm </span>
+<span class="c1"># the structure and 1CRNA.hhm for the profile. </span>
+<span class="c1"># The structure possibly contain several chains, whereas the hhm </span>
<span class="c1"># file is only for that specific chain.</span>
<span class="n">structure_ids</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"1CRN"</span><span class="p">,</span> <span class="s2">"1AKI"</span><span class="p">]</span>
<span class="n">chain_names</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"A"</span><span class="p">,</span> <span class="s2">"A"</span><span class="p">]</span>
@@ -227,11 +228,14 @@ and fill it with content.</p>
<span class="c1"># We now have two structures in both databases...</span>
-
-<span class="c1"># Please note, that there is no profile derived from structures</span>
-<span class="c1"># assigned yet to structure_db_one, the memory is only allocated</span>
-<span class="c1"># and set to zero. In structure_db_two, there'll never be stored a </span>
-<span class="c1"># structure profile as we did not initialize it accordingly. </span>
+<span class="c1"># Lets get a summary of whats actually in there</span>
+<span class="n">structure_db_one</span><span class="o">.</span><span class="n">PrintStatistics</span><span class="p">()</span>
+<span class="n">structure_db_two</span><span class="o">.</span><span class="n">PrintStatistics</span><span class="p">()</span>
+
+<span class="c1"># There is no profile derived from structures assigned to </span>
+<span class="c1"># structure_db_one yet, the memory is only allocated and set to </span>
+<span class="c1"># zero. In structure_db_two, there'll never be stored a structure </span>
+<span class="c1"># profile as we did not initialize it accordingly. </span>
<span class="c1"># However, we can still use its coordinates and residue depths to</span>
<span class="c1"># generate profiles! </span>
<span class="c1"># To demonstrate, we use our structure_db_two to derive profiles </span>
@@ -271,7 +275,7 @@ database, you might want to consider two things:</p>
<ol class="arabic simple">
<li>Use a database of limited size to generate the actual profiles (something
in between 5000 and 10000 nonredundant chains is enough)</li>
-<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
running in parallel</li>
</ol>
<dl class="class">
@@ -282,7 +286,7 @@ StructureDB in order to define what data you want to store additionally
to backbone coordinates and sequence.
If you want to store all data possible, use All. If you only want a subset,
you can combine some of the datatypes with a bitwise or operation
-(see example script for StructureDB). One important note:
+(see example script for <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>). One important note:
If you enable AAFrequenciesStruct, the actual information is not automatically
assigned. Only the according memory is allocated and set to zero, the actual
information must be assigned manually (see example script again...).</p>
@@ -293,8 +297,8 @@ AAFrequenciesStruct</p>
<dl class="class">
<dt id="promod3.loop.StructureDB">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">StructureDB</code><span class="sig-paren">(</span><em>data_to_store</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB" title="Permalink to this definition">¶</a></dt>
-<dd><p>Generates an empty StructureDB that can be filled with content through
-<a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-func docutils literal"><span class="pre">AddCoordinates()</span></code></a>. The information extracted there is defined by
+<dd><p>Generates an empty <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> that can be filled with content
+through <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-func docutils literal"><span class="pre">AddCoordinates()</span></code></a>. The information extracted there is defined by
<em>data_to_store</em>. Have a look at the <a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal"><span class="pre">StructureDBDataType</span></code></a>
documentation and at the example script...</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -405,10 +409,10 @@ in the according <a class="reference internal" href="#promod3.loop.CoordInfo" ti
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – identifier of the added structure (e.g. pdb id)</li>
<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of the chain in <em>ent</em> you want to add</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
as specified by <em>chain_name</em>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
<em>chain_name</em>. The profile sequence must match <em>seqres</em>.</li>
<li><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
connected stretch of residues are all connected
@@ -460,7 +464,7 @@ accordingly!</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The StructureDB indices (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1]) of
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> indices (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])
of all coords (connected stretches) with matching
<em>id</em> / <em>chain_name</em>.</p>
</td>
@@ -490,7 +494,7 @@ index <em>idx</em>.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The StructureDB index (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> index (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</td>
</tr>
</tbody>
</table>
@@ -536,9 +540,9 @@ the database.</td>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract positions.</li>
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence to set for the returned backbone list.</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
superposed onto.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
superposed onto.</li>
</ul>
</td>
@@ -649,7 +653,8 @@ connected stretches of residues in the database.</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Solvent accessibility for each residue of <em>fragment</em> in square A
-as calculated by dssp.</td>
+as calculated by <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">Accessibility()</span></code></a> when adding
+the structure to the database.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
</tr>
@@ -675,7 +680,7 @@ connected stretches of residues in the database.</td>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The sequence profile for the residues defined by <em>fragment</em> with
the BLOSUM62 probabilities as NULL model.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence
profile</td>
@@ -699,7 +704,7 @@ connected stretches of residues in the database.</td>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The structure profile for the residues defined by <em>fragment</em> with
the BLOSUM62 probabilities as NULL model.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the structure
profile</td>
@@ -734,7 +739,7 @@ containing that data.</li>
probabilities as NULL model.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>bb_list</em> and
@@ -756,7 +761,7 @@ frequencies in entry with <em>coord_idx</em></p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
(in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</li>
</ul>
@@ -785,7 +790,7 @@ to make sure that you have no close homologue in the database.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – StructureDB indices to be added to the sub database (in [0,
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – Indices of chains to be added to the sub database (in [0,
<a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if you provide an invalid index</td>
@@ -906,7 +911,8 @@ for details.</p>
<dl class="method">
<dt id="promod3.loop.FragDB.GetAngularBinSize">
<code class="descname">GetAngularBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetAngularBinSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>The size of the bins for the 4 angles describing the stem geometry and used to organize the fragments in the database.</p>
+<dd><p>The size of the bins for the 4 angles describing the stem geometry and used
+to organize the fragments in the database.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -922,7 +928,8 @@ for details.</p>
<dl class="method">
<dt id="promod3.loop.FragDB.GetDistBinSize">
<code class="descname">GetDistBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetDistBinSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>The size of the bins for the distance describing the stem geometry and used to organize the fragments in the database.</p>
+<dd><p>The size of the bins for the distance describing the stem geometry and used
+to organize the fragments in the database.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -938,8 +945,13 @@ for details.</p>
<dl class="method">
<dt id="promod3.loop.FragDB.AddFragments">
<code class="descname">AddFragments</code><span class="sig-paren">(</span><em>fragment_length</em>, <em>rmsd_cutoff</em>, <em>structure_db</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.AddFragments" title="Permalink to this definition">¶</a></dt>
-<dd><p>Iterates over all fragments of length <strong>fragment_length</strong> in the given structural database and adds them to the fragment database. Fragments will be skipped if there is already a fragment in the database that has an RMSD to the one being added smaller than <strong>rmsd_cutoff</strong>.
-As the fragments are added they are organized in bins described by their length and the geometry of their N and C stem.</p>
+<dd><p>Iterates over all fragments of length <strong>fragment_length</strong> in
+<strong>structure_db</strong> and adds them to the fragment database.
+Fragments will be skipped if there is already a fragment in the database
+that has an RMSD smaller than <strong>rmsd_cutoff</strong>, where RMSD is calculated
+upon superposing the stem residues.
+As the fragments are added they are organized in bins described by their
+length and the geometry of their N and C stem.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -958,7 +970,7 @@ As the fragments are added they are organized in bins described by their length
<dl class="method">
<dt id="promod3.loop.FragDB.PrintStatistics">
<code class="descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
-<dd><p>Prints statistics about the fragment databse, notably:</p>
+<dd><p>Prints statistics about the fragment database, notably:</p>
<ol class="arabic simple">
<li>the number of different stem groups (number of bins used to group the
fragments according to the geometry of their stem residues)</li>
@@ -1019,7 +1031,7 @@ a given length.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The length of the fragments</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">True if fragments of given length exist. This function is quick.</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">True if fragments of given length exist.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
</tr>
@@ -1034,7 +1046,7 @@ a given length.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Maximal fragment length contained in db. This function is quick.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Maximal fragment length contained in db.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
@@ -1052,8 +1064,8 @@ and <strong>c_stem</strong> and of the same length as the <strong>frag_size</str
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
<li><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues of the fragment</li>
<li><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
<em>extra_bins</em> additional bins surrounding the bin given by
@@ -1080,7 +1092,7 @@ function.</p>
for fragments that possibly represent the structural conformation of interest.
The <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> searches a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> for n fragments,
that maximize a certain score and gathers a set of fragments with a guaranteed
-structural diversity based on an rmsd_threshold. You can use the <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a>
+structural diversity based on an rmsd threshold. You can use the <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a>
wrapped in a full fletched pipeline implemented in
<a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">FraggerHandle</span></code></a> or search for fragments from scratch
using an arbitrary linear combination of scores:</p>
@@ -1093,9 +1105,9 @@ Calculates the avg. substitution matrix based sequence similarity of amino acids
when comparing a potential fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> and the target
sequence</li>
<li><strong>SSAgree</strong>:
-Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="#jones1999" id="id3">[Jones1999]</a>
-and the dssp <a class="reference internal" href="#kabsch1983" id="id4">[kabsch1983]</a> assignment stored in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>.
-The Agreement term is based on a probabilistic approach also used in HHSearch <a class="reference internal" href="#soding2005" id="id5">[soding2005]</a>.</li>
+Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id3">[Jones1999]</a>
+and the dssp <a class="reference internal" href="../references.html#kabsch1983" id="id4">[kabsch1983]</a> assignment stored in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>.
+The Agreement term is based on a probabilistic approach also used in HHSearch <a class="reference internal" href="../references.html#soding2005" id="id5">[soding2005]</a>.</li>
<li><strong>TorsionProbability</strong>:
Calculates the avg. probability of observing the phi/psi dihedral angles of a potential
fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> given the target sequence. The probabilities are
@@ -1277,7 +1289,7 @@ linked to this object.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -1295,7 +1307,7 @@ linked to this object.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -1511,7 +1523,7 @@ coordinates. This file will hence be much larger than the one saved with
<dl class="class">
<dt id="promod3.loop.PsipredPrediction">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">PsipredPrediction</code><a class="headerlink" href="#promod3.loop.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
-<dd><p>A container for the secondary structure prediction by Psipred.</p>
+<dd><p>A container for the secondary structure prediction by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id6">[Jones1999]</a>.</p>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.PsipredPrediction">
<code class="descname">PsipredPrediction</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
@@ -1694,36 +1706,6 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
</dd></dl>
-<table class="docutils citation" frame="void" id="soding2005" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id5">[soding2005]</a></td><td>Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="chakravarty1999" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[chakravarty1999]</a></td><td>Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="zhou2005" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id2">[zhou2005]</a></td><td>Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="jones1999" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id3">[Jones1999]</a></td><td>Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="kabsch1983" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id4">[kabsch1983]</a></td><td>Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 2577-2637.</td></tr>
-</tbody>
-</table>
</div>
</div>
@@ -1779,7 +1761,7 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index c9d75287ca27196ad6349d2f16c1aeb7a3c7df34..fa5416d4e0c15c8af944940c4079c2eebe1649da 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Sampling Dihedral Angles — ProMod3 1.2.0 documentation</title>
+ <title>Sampling Dihedral Angles — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Structural Data" href="structure_db.html" />
<link rel="prev" title="Representing Loops" href="backbone.html" />
@@ -138,7 +139,7 @@ acids not matching any of the group definitions.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
</tr>
</tbody>
</table>
@@ -210,9 +211,9 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
</ul>
</td>
</tr>
@@ -252,9 +253,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
</ul>
</td>
</tr>
@@ -290,9 +291,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <em>psi</em> angle</li>
</ul>
</td>
@@ -334,9 +335,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <em>phi</em> angle</li>
</ul>
</td>
@@ -378,9 +379,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
@@ -424,9 +425,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
@@ -448,9 +449,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
@@ -589,7 +590,7 @@ standard amino acid</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 0cd8be8702bde9b8f390725a811a36e6c272ea21..bc65d5f6ae40d7d1d8b756f2addcb9a2319ac84b 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Modelling Algorithms — ProMod3 1.2.0 documentation</title>
+ <title>Modelling Algorithms — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="sidechain - Sidechain Modelling" href="../sidechain/index.html" />
<link rel="prev" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
@@ -94,7 +95,7 @@ of the solutions</li>
indices of the common subsets (rigid blocks) relative
to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>bb_list_one</strong>
onto <strong>bb_list_two</strong></p>
</td>
@@ -112,7 +113,7 @@ onto <strong>bb_list_two</strong></p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
objects from which the positions are extracted</li>
<li><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
positions will be extracted</li>
@@ -133,9 +134,9 @@ of the solutions</li>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> with the first element being a
<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <code class="xref py py-class docutils literal"><span class="pre">list</span></code> defining the
column indices of the common subsets (rigid blocks)
-relative to the input <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
+relative to the input <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions from the first
sequence onto the second sequence.</p>
</td>
@@ -172,7 +173,7 @@ of the solutions</li>
indices of the common subsets (rigid blocks) relative
to the input <code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code> objects
and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>pos_one</strong>
onto <strong>pos_two</strong></p>
</td>
@@ -235,8 +236,8 @@ Weird things are happening otherwise.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
-<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
<li><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</li>
<li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length (num. residues) of fragments to be extracted.</li>
<li><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
@@ -328,7 +329,7 @@ want to generate</li>
<li><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
the total number is:
len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></li>
-<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
fragment search performance.</li>
<li><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
increases the fragment search performance</li>
@@ -411,7 +412,7 @@ with the keys of the scores in <strong>scorer</strong></li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 032f3350c35708976935479acb04659939e587f6..d273996b81a2fd13fd7400c246e1e0a508db258b 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling Gaps — ProMod3 1.2.0 documentation</title>
+ <title>Handling Gaps — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Handling Loop Candidates" href="loop_candidates.html" />
<link rel="prev" title="Model Checking" href="model_checking.html" />
@@ -60,8 +61,8 @@ invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a></li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a></li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a></li>
<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal"><span class="pre">seq</span></code></a></li>
</ul>
</td>
@@ -116,7 +117,7 @@ are valid and:</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Chain, the gap is belonging to</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -267,13 +268,13 @@ extend the gap past another gap.</p>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.before">
<code class="descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.after">
<code class="descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
@@ -318,7 +319,7 @@ False if no new extension possible.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
</ul>
</td>
</tr>
@@ -359,7 +360,7 @@ valid termini.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <ul>
<li>If -1, all possible non-terminal gaps are returned.</li>
<li>If >= 0, this restricts the max. gap-length
@@ -412,7 +413,7 @@ score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalti
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
<li><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Penalty for length of gap.</li>
<li><strong>penalties</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Penalty for each residue added to gap.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <ul>
<li>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a>
(i.e. it stops at gaps and termini).</li>
@@ -652,7 +653,7 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index 79fbb0d1cc6ff30dd9e85dc0aebdb05f2097a5e4..a3ac0b9ca1f43d9a5f6127e1c42b354a7820dfaf 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>modelling - Protein Modelling — ProMod3 1.2.0 documentation</title>
+ <title>modelling - Protein Modelling — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,10 +23,11 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Modelling Pipeline" href="pipeline.html" />
- <link rel="prev" title="Building ProMod3" href="../buildsystem.html" />
+ <link rel="prev" title="Singularity" href="../container/singularity.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -129,7 +130,7 @@ a model fully automatically as follows:</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li>Previous: <a href="../buildsystem.html" title="previous chapter">Building ProMod3</a></li>
+ <li>Previous: <a href="../container/singularity.html" title="previous chapter">Singularity</a></li>
<li>Next: <a href="pipeline.html" title="next chapter">Modelling Pipeline</a></li>
</ul></li>
</ul></li>
@@ -157,7 +158,7 @@ a model fully automatically as follows:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index b1803ae6baaba3a96330a07192ae2987307a9f9b..de65ccf216e9c07d06b70446a5853ad3d27c6c3d 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling Loop Candidates — ProMod3 1.2.0 documentation</title>
+ <title>Handling Loop Candidates — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Fitting Loops Into Gaps" href="loop_closing.html" />
<link rel="prev" title="Handling Gaps" href="gap_handling.html" />
@@ -132,8 +133,8 @@ a fragment database.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
<em>n_stem</em> and <em>c_stem</em></li>
<li><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) – The fragment database</li>
@@ -244,9 +245,9 @@ not depending on a metropolis criterium.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A torsion sampler (used for all residues) or a list
@@ -288,9 +289,9 @@ candidate. This leads to an increase in number of loops.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match</li>
<li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – First pivot residue</li>
<li><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Second pivot residue</li>
@@ -364,7 +365,7 @@ anything is raised when calculating the scores.</p>
<code class="descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a score comparing the given profile <em>prof</em> starting at <em>offset</em>
with the sequence / structure profile of each candidate as extracted from
-<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
+<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
details, <em>prof.null_model</em> is used for weighting).</p>
<p>Note that for profile scores a higher “score” is better! So take care when
combining this to other scores, where it is commonly the other way around.</p>
@@ -380,7 +381,7 @@ with this DB).</p>
<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a></li>
<li><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal"><span class="pre">FillFromDatabase()</span></code></a></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
<li><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</li>
</ul>
</td>
@@ -412,8 +413,8 @@ positions and the corresponding atoms in <em>c_stem</em>.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a></li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
</ul>
</td>
</tr>
@@ -1139,7 +1140,7 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index d6e5827539347b83e178f2de00f6fbfc0a8fd73c..52ebde2059feba7e72d096792b30be8f0b7a702f 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Fitting Loops Into Gaps — ProMod3 1.2.0 documentation</title>
+ <title>Fitting Loops Into Gaps — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Generating Loops De Novo" href="monte_carlo.html" />
<link rel="prev" title="Handling Loop Candidates" href="loop_candidates.html" />
@@ -47,8 +48,8 @@
stem residues. ProMod3 implements two algorithms performing this task:</p>
<blockquote>
<div><ul class="simple">
-<li>Cyclic coordinate descent (CCD) <a class="reference internal" href="#canutescu2003" id="id1">[canutescu2003]</a></li>
-<li>Kinematic closure (KIC) <a class="reference internal" href="#mandell2009" id="id2">[mandell2009]</a></li>
+<li>Cyclic coordinate descent (CCD) <a class="reference internal" href="../references.html#canutescu2003" id="id1">[canutescu2003]</a></li>
+<li>Kinematic closure (KIC) <a class="reference internal" href="../references.html#coutsias2005" id="id2">[coutsias2005]</a></li>
</ul>
</div></blockquote>
<p>In case of small gaps or small issues in the loop you might also consider the
@@ -83,11 +84,11 @@ to avoid moving into unfavourable regions of the backbone dihedrals.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of the backbones to be closed</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
If the residue before <em>n_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
and phi angle (-1.0472) to evaluate the first angle.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
If the residue after <em>c_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
psi angle (-0.7854) to evaluate the last angle.</li>
@@ -124,8 +125,8 @@ This is faster but might lead to weird backbone dihedral pairs.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal number of iterations</li>
<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
be closed has RMSD below the given <em>c_stem</em></li>
@@ -326,7 +327,7 @@ size or sequence as the initial one.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -348,7 +349,7 @@ size or sequence as the initial one.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -371,7 +372,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -393,7 +394,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -415,7 +416,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -588,19 +589,6 @@ the one given in the constructor.</td>
</dd></dl>
-<p class="rubric">Citations</p>
-<table class="docutils citation" frame="void" id="canutescu2003" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[canutescu2003]</a></td><td>Canutescu AA and Dunbrack RL Jr. (2003). Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12(5):963–972.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="mandell2009" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id2">[mandell2009]</a></td><td>Mandell DJ, Coutsias EA and Kortemme T (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 6(8):551-2.</td></tr>
-</tbody>
-</table>
</div>
</div>
@@ -655,7 +643,7 @@ the one given in the constructor.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 914620c01d9b7ab91692936ea61927682e9a7a87..906b67d17afa9e1c515359689b1bd6c60e4febb2 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Model Checking — ProMod3 1.2.0 documentation</title>
+ <title>Model Checking — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Handling Gaps" href="gap_handling.html" />
<link rel="prev" title="Modelling Pipeline" href="pipeline.html" />
@@ -57,14 +58,14 @@ three of the atoms exist (center and radii are estimated then).</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of rings to perform ring checks. Each ring is a named
tuple with:
-center (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>),
-plane (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Plane</span></code></a>),
+center (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>),
+plane (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Plane</span></code></a>),
radius (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>),
-residue (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
+residue (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
</tr>
</tbody>
</table>
@@ -80,11 +81,11 @@ residue (<a class="reference external" href="https://www.openstructure.org/docs/
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of residues (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of residues (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
have a punched ring.</p>
</td>
</tr>
@@ -103,7 +104,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
</ul>
</td>
</tr>
@@ -128,7 +129,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>candidates</strong> (<code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
Offending candidates are removed from this list.</li>
-<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
+<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
<li><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</li>
<li><strong>orig_indices</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – Mapping to old indexing of candidates. If given, it
must have as many elements as <em>candidates</em>.</li>
@@ -193,7 +194,7 @@ with <code class="docutils literal"><span class="pre">MolProbity</span> <span cl
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a></p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
executable is not found.</p>
</td>
</tr>
@@ -210,7 +211,7 @@ executable is not found.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
</tr>
</tbody>
</table>
@@ -282,7 +283,7 @@ executable is not found.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index 6732e2a0fa011a0b43ada5c9968d35caabf3e393..8186f35520f454fd595ac135a1b5696efbe6f7fa 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Generating Loops De Novo — ProMod3 1.2.0 documentation</title>
+ <title>Generating Loops De Novo — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
<link rel="prev" title="Fitting Loops Into Gaps" href="loop_closing.html" />
@@ -111,17 +112,18 @@ Carlo sampling to the N-terminal part of crambin:</p>
<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">"sampled_frag.pdb"</span><span class="p">)</span>
</pre></div>
</div>
-<dl class="method">
+<dl class="function">
<dt id="promod3.modelling.SampleMonteCarlo">
-<code class="descclassname">promod3.modelling.</code><code class="descname">SampleMonteCarlo</code><span class="sig-paren">(</span><em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>steps</em>, <em>bb_list</em>, <em>initialize=True</em>, <em>seed=0</em>, <em>lowest_energy_conformation=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SampleMonteCarlo" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">SampleMonteCarlo</code><span class="sig-paren">(</span><em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>steps</em>, <em>bb_list</em>, <em>initialize</em>, <em>seed=0</em>, <em>lowest_energy_conformation=True</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_monte_carlo.html#SampleMonteCarlo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.SampleMonteCarlo" title="Permalink to this definition">¶</a></dt>
<dd><p>A convenient function to perform Monte Carlo sampling using a simulated
-annealing scheme. In every iteration, a new loop conformation gets proposed by
-the provided <em>sampler</em> and closed by the <em>closer</em>. Upon scoring, this new
-conformation gets accepted/rejected using a metropolis criterion based on the
-temperature given by the <em>cooler</em>
+annealing scheme. In every iteration, a new loop conformation gets proposed
+by the provided <em>sampler</em> and closed by the <em>closer</em>. Upon scoring, this new
+conformation gets accepted/rejected using a metropolis criterion based on
+the temperature given by the <em>cooler</em>
=> acceptance probability: exp(-delta_score/T).
-The result is stored in <em>bb_list</em> and is either the lowest energy conformation
-ever encountered or the last accepted proposal.</p>
+The result is stored in <em>bb_list</em> (passed by reference, so NO return value)
+and is either the lowest energy conformation ever encountered or the last
+accepted proposal.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -132,7 +134,7 @@ conformations.</li>
<li><strong>closer</strong> (<a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Closer object to adapt a new conformation to
the environment.</li>
<li><strong>scorer</strong> (<a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Scorer object to score new loop conformations.</li>
-<li><strong>cooler</strong> (<a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Cooler object to control the temperature of the
+<li><strong>cooler</strong> (<a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Cooler object to control the temperature of the
Monte Carlo trajectory.</li>
<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of Monte Carlo iterations to be performed.</li>
<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The chosen conformation gets stored here.</li>
@@ -141,8 +143,8 @@ point, based on the samplers Initialize function.
The input <em>bb_list</em> gets used otherwise.</li>
<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random number generator.</li>
<li><strong>lowest_energy_conformation</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If True, we choose the lowest scoring
-conformation of the trajectory. Otherwise,
-the last accepted proposal.</li>
+conformation of the trajectory.
+Otherwise, the last accepted proposal.</li>
</ul>
</td>
</tr>
@@ -154,7 +156,61 @@ the last accepted proposal.</li>
<span id="mc-sampler-object"></span><h2>Sampler Object<a class="headerlink" href="#sampler-object" title="Permalink to this headline">¶</a></h2>
<p>The sampler objects can be used to generate initial conformations and
propose new conformations for a sequence of interest. They build the basis
-for any Monte Carlo sampling pipeline.</p>
+for any Monte Carlo sampling pipeline. You can either use one of the
+provided samplers or any object that implements the functionality of
+<a class="reference internal" href="#promod3.modelling.SamplerBase" title="promod3.modelling.SamplerBase"><code class="xref py py-class docutils literal"><span class="pre">SamplerBase</span></code></a>.</p>
+<dl class="class">
+<dt id="promod3.modelling.SamplerBase">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">SamplerBase</code><a class="headerlink" href="#promod3.modelling.SamplerBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>Abstract base class defining the functions that must be implemented by any
+sampler.</p>
+<dl class="method">
+<dt id="promod3.modelling.SamplerBase.Initialize">
+<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.Initialize" title="Permalink to this definition">¶</a></dt>
+<dd><p>Supposed to initialize structural information from scratch. The sequence
+of the generated <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is taken from <em>bb_list</em>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to this
+parameter. Sequence / length stay the same.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">None</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.SamplerBase.ProposeStep">
+<code class="descname">ProposeStep</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>proposed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.ProposeStep" title="Permalink to this definition">¶</a></dt>
+<dd><p>Takes current positions and proposes a new conformation. There is no
+guarantee on maintining any special RT state. The <a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>
+is supposed to sort that out.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Starting point, must not change when calling this
+function.</li>
+<li><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to
+this parameter.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">None</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
<dl class="class">
<dt id="promod3.modelling.PhiPsiSampler">
<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">PhiPsiSampler</code><span class="sig-paren">(</span><em>sequence</em>, <em>torsion_sampler</em>, <em>n_stem_phi=-1.0472</em>, <em>c_stem_psi=-0.78540</em>, <em>prev_aa='A'</em>, <em>next_aa='A'</em>, <em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler" title="Permalink to this definition">¶</a></dt>
@@ -337,7 +393,7 @@ by any fragger remain rigid.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Overall sequence</li>
-<li><strong>fraggers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – A list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> objects. The first
+<li><strong>fraggers</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – A list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> objects. The first
fragger covers the region starting at the letter
<em>sampling_start_index</em> of the <em>sequence</em> and so on.
All fraggers must contain fragments of equal size.</li>
@@ -345,7 +401,7 @@ All fraggers must contain fragments of equal size.</li>
sampling. The default gets constructed using the default
constructor of <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> and
results in a helix.</li>
-<li><strong>sampling_start_index</strong> – Defines the beginning of the region, that actually
+<li><strong>sampling_start_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Defines the beginning of the region, that actually
gets sampled.</li>
<li><strong>init_fragments</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – When calling the Initialize function, the positions get set
to the ones of <em>init_bb_list</em>. This is the number of
@@ -400,7 +456,44 @@ fragger object to alter the conformation.</p>
conformations typically have to undergo some structural changes, so they
fit to a given environment. This can either be structural changes, that
the stems of the sampled conformation overlap with given stem residues or
-or simple stem superposition in case of terminal sampling.</p>
+or simple stem superposition in case of terminal sampling. You can either
+use any of the provided closers or any object that implements the
+functionality of <a class="reference internal" href="#promod3.modelling.CloserBase" title="promod3.modelling.CloserBase"><code class="xref py py-class docutils literal"><span class="pre">CloserBase</span></code></a>.</p>
+<dl class="class">
+<dt id="promod3.modelling.CloserBase">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CloserBase</code><a class="headerlink" href="#promod3.modelling.CloserBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>Abstract base class defining the functions that must be implemented by any
+closer.</p>
+<dl class="method">
+<dt id="promod3.modelling.CloserBase.Close">
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloserBase.Close" title="Permalink to this definition">¶</a></dt>
+<dd><p>Takes current positions and proposes a new conformation that fits to a
+given environment.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Starting point, must not change when calling this
+function.</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to
+this parameter.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Whether closing procedure was successful</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
<dl class="class">
<dt id="promod3.modelling.CCDCloser">
<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CCDCloser</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>sequence</em>, <em>torsion_sampler</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCDCloser" title="Permalink to this definition">¶</a></dt>
@@ -413,9 +506,9 @@ avoid moving into unfavourable phi/psi ranges.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of the conformation to be closed.</li>
<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
@@ -456,15 +549,16 @@ conformation to be closed.</li>
<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">DirtyCCDCloser</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DirtyCCDCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>The DirtyCCDCloser applies the CCD algorithm to the sampled conformation
to enforce the match between the conformations stem residue and
-the stems given by the closer.</p>
+the stems given by the closer. There is no check for reasonable backbone
+dihedral angles as it is the case for the <a class="reference internal" href="#promod3.modelling.CCDCloser" title="promod3.modelling.CCDCloser"><code class="xref py py-class docutils literal"><span class="pre">CCDCloser</span></code></a>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</li>
</ul>
</td>
@@ -504,9 +598,9 @@ solutions. The KICCloser simply picks the first one.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</li>
-<li><strong>c_stem</strong> – Defining stem positions the closed conformation should
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</li>
<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random generators.</li>
</ul>
@@ -539,49 +633,128 @@ adapt.</li>
<dl class="class">
<dt id="promod3.modelling.NTerminalCloser">
<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">NTerminalCloser</code><span class="sig-paren">(</span><em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser" title="Permalink to this definition">¶</a></dt>
-<dd><p>The NTerminalCloser simply takes the conformation and closes by superposing
-the c_stem with the desired positions.</p>
+<dd><p>The <a class="reference internal" href="#promod3.modelling.NTerminalCloser" title="promod3.modelling.NTerminalCloser"><code class="xref py py-class docutils literal"><span class="pre">NTerminalCloser</span></code></a> simply takes the conformation and closes by
+superposing the c_stem with the desired positions.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether closing was successful</td>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.modelling.NTerminalCloser.Close">
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed (or in this case
+transformed in space).</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Closed (transformed) conformation gets stored in
+here.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether closing was successful</p>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
+</dd></dl>
+
<dl class="class">
<dt id="promod3.modelling.CTerminalCloser">
<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CTerminalCloser</code><span class="sig-paren">(</span><em>n_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser" title="Permalink to this definition">¶</a></dt>
-<dd><p>The CTerminalCloser simply takes the conformation and closes by superposing
-the n_stem with the desired positions.</p>
+<dd><p>The <a class="reference internal" href="#promod3.modelling.CTerminalCloser" title="promod3.modelling.CTerminalCloser"><code class="xref py py-class docutils literal"><span class="pre">CTerminalCloser</span></code></a> simply takes the conformation and closes by
+superposing the n_stem with the desired positions.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether closing was successful</td>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.modelling.CTerminalCloser.Close">
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed (or in this case
+transformed in space).</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Closed (transformed) conformation gets stored in
+here.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether closing was successful</p>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.modelling.DeNovoCloser">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">DeNovoCloser</code><a class="headerlink" href="#promod3.modelling.DeNovoCloser" title="Permalink to this definition">¶</a></dt>
+<dd><p>In case of sampling a full stretch, you dont have external constraints. The
+closer has a rather boring job in this case.</p>
+<dl class="method">
+<dt id="promod3.modelling.DeNovoCloser.Close">
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DeNovoCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><p>Does absolutely nothing, except copying over the coordinates from
+<em>actual_positions</em> to <em>closed_positions</em> and return true.</p>
+</dd></dl>
+
+</dd></dl>
+
</div>
<div class="section" id="scorer-object">
<span id="mc-scorer-object"></span><h2>Scorer Object<a class="headerlink" href="#scorer-object" title="Permalink to this headline">¶</a></h2>
<p>The scorer asses a proposed conformation and are intended to return a pseudo
-energy, the lower the better.</p>
+energy, the lower the better. You can either use the provided scorer or any
+object implementing the functionality defined in <a class="reference internal" href="#promod3.modelling.ScorerBase" title="promod3.modelling.ScorerBase"><code class="xref py py-class docutils literal"><span class="pre">ScorerBase</span></code></a>.</p>
+<dl class="class">
+<dt id="promod3.modelling.ScorerBase">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ScorerBase</code><a class="headerlink" href="#promod3.modelling.ScorerBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>Abstract base class defining the functions that must be implemented by any
+scorer.</p>
+<dl class="method">
+<dt id="promod3.modelling.ScorerBase.GetScore">
+<code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScorerBase.GetScore" title="Permalink to this definition">¶</a></dt>
+<dd><p>Takes coordinates and spits out a score given some internal structural
+environment.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Coordinates to be scored</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The score</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
<dl class="class">
-<dt>
-<code class="descname">LinearScorer(scorer, scorer_env, start_resnum, num_residues,</code></dt>
-<dt>
-<code class="descname">chain_idx, linear_weights)</code></dt>
+<dt id="promod3.modelling.LinearScorer">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">LinearScorer</code><span class="sig-paren">(</span><em>scorer</em>, <em>scorer_env</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx</em>, <em>linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>The LinearScorer allows to combine the scores available from
<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a> in a linear manner. See
<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="promod3.scoring.BackboneOverallScorer.CalculateLinearCombination"><code class="xref py py-meth docutils literal"><span class="pre">CalculateLinearCombination()</span></code></a> for a
@@ -589,7 +762,7 @@ detailed description of the arguments.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The provided <em>scorer_env</em> will be altered in every
-<a class="reference internal" href="#promod3.modelling.GetScore" title="promod3.modelling.GetScore"><code class="xref py py-func docutils literal"><span class="pre">GetScore()</span></code></a> call.
+<a class="reference internal" href="#promod3.modelling.LinearScorer.GetScore" title="promod3.modelling.LinearScorer.GetScore"><code class="xref py py-func docutils literal"><span class="pre">GetScore()</span></code></a> call.
You might consider the Stash / Pop mechanism of the
<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> to restore to the
original state once the sampling is done.</p>
@@ -617,8 +790,8 @@ which no scorer exists</p>
</tbody>
</table>
<dl class="method">
-<dt id="promod3.modelling.GetScore">
-<code class="descclassname">promod3.modelling.</code><code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetScore" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.modelling.LinearScorer.GetScore">
+<code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer.GetScore" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -640,13 +813,44 @@ which no scorer exists</p>
<span id="mc-cooler-object"></span><h2>Cooler Object<a class="headerlink" href="#cooler-object" title="Permalink to this headline">¶</a></h2>
<p>The cooler objects control the temperature of the Monte Carlo trajectory.
They’re intended to deliver steadily decreasing temperatures with calls
-to their GetTemperature function.</p>
+to their GetTemperature function. You can either use the provided cooler
+or any object implementing the functionality defined in
+<a class="reference internal" href="#promod3.modelling.CoolerBase" title="promod3.modelling.CoolerBase"><code class="xref py py-class docutils literal"><span class="pre">CoolerBase</span></code></a>.</p>
+<dl class="class">
+<dt id="promod3.modelling.CoolerBase">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CoolerBase</code><a class="headerlink" href="#promod3.modelling.CoolerBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>Abstract base class defining the functions that must be implemented by any
+cooler.</p>
+<dl class="method">
+<dt id="promod3.modelling.CoolerBase.GetTemperature">
+<code class="descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.GetTemperature" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Temperature</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.CoolerBase.Reset">
+<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.Reset" title="Permalink to this definition">¶</a></dt>
+<dd><p>Resets to original state, so a new Monte Carlo trajectory can be generated</p>
+</dd></dl>
+
+</dd></dl>
+
<dl class="class">
<dt id="promod3.modelling.ExponentialCooler">
<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ExponentialCooler</code><span class="sig-paren">(</span><em>change_frequency</em>, <em>start_temperature</em>, <em>cooling_factor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler" title="Permalink to this definition">¶</a></dt>
<dd><p>The exponential cooler starts with a given <em>start_temperature</em> and counts the
-calls to its GetTemperature function. According to the <em>change_frequency</em>,
-the returned temperature gets multiplied by the <em>cooling_factor</em>.</p>
+calls to its <a class="reference internal" href="#promod3.modelling.ExponentialCooler.GetTemperature" title="promod3.modelling.ExponentialCooler.GetTemperature"><code class="xref py py-meth docutils literal"><span class="pre">GetTemperature()</span></code></a> function. According to the
+<em>change_frequency</em>, the returned temperature gets multiplied by the
+<em>cooling_factor</em>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -676,7 +880,8 @@ the returned temperature gets multiplied by the <em>cooling_factor</em>.</p>
<dl class="method">
<dt id="promod3.modelling.ExponentialCooler.Reset">
<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler.Reset" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sets current temperature back to <em>start_temperature</em></p>
+<dd><p>Sets current temperature back to <em>start_temperature</em> and the
+internal counter to 0</p>
</dd></dl>
</dd></dl>
@@ -735,7 +940,7 @@ the returned temperature gets multiplied by the <em>cooling_factor</em>.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index 9973f610b7e21bd5badbd8e66be478d0bc0272bd..7d998f48befc7775c95dbfd58b7046cf79c583d8 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Modelling Pipeline — ProMod3 1.2.0 documentation</title>
+ <title>Modelling Pipeline — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Model Checking" href="model_checking.html" />
<link rel="prev" title="modelling - Protein Modelling" href="index.html" />
@@ -117,7 +118,7 @@ chain follows afterwards.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -143,13 +144,13 @@ Gaps of different chains are appended one after another.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.seqres">
<code class="descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">SequenceHandle</span></code></a> for each chain
+<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceHandle</span></code></a> for each chain
of the target protein.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -158,7 +159,7 @@ of the target protein.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.profiles">
<code class="descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
+<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">seqres</span></code></a>). Please note, that this
attribute won’t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>. You have
to fill it manually or even better by the convenient function
@@ -167,7 +168,7 @@ to fill it manually or even better by the convenient function
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -321,7 +322,7 @@ alignment handle or an alignment handle list. Every list item is treated as a
single chain in the final raw model.</p>
<p>Each alignment handle must contain exactly two sequences and the second
sequence is considered the template sequence, which must have a
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a> attached.</p>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a> attached.</p>
<p>This is a basic protein core modelling algorithm that copies backbone
coordinates based on the sequence alignment. For matching residues, the
side chain coordinates are also copied. Gaps are ignored. Hydrogen an
@@ -349,7 +350,7 @@ as information about insertions and deletions in the gaps list.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
list of alignment handles for raw model with multiple chains.</li>
<li><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True, if we wish to include ligands in the model. This
searches for ligands in all OST handles of the views
@@ -375,7 +376,7 @@ in SMTL). All ligands are added to a new chain named
<li>the second sequence does not have an attached structure</li>
<li>the residues of the template structure do not match with the
alignment sequence (note that you can set an “offset” (see
-<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">SetSequenceOffset()</span></code></a>) for the
+<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">SetSequenceOffset()</span></code></a>) for the
template sequence (but not for the target))</li>
<li>the target sequence has a non-zero offset (cannot be honored as
the resulting model will always start its residue numbering at 1)</li>
@@ -413,12 +414,12 @@ return an incomplete model.</p>
<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
alignment.</li>
<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
-CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
-and <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
+CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.8.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
+and <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.8.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
Both do a similarly good job without ligands (CHARMM
slightly better), but you will want to be consistent
with the optional force fields in <cite>extra_force_fields</cite>.</li>
-<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
+<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
(ligand) residue cannot be parametrized with the
default force field. The force fields are tried
in the order as given and ligands without an
@@ -429,7 +430,7 @@ existing parametrization are skipped.</li>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Delivers the model as an OST entity.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
</td>
</tr>
</tbody>
@@ -604,7 +605,7 @@ environments get updated in <strong>target_mhandle</strong>.</p>
<li><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – This is the chain where the info goes to</li>
<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – First residue of the copied stretch</li>
<li><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Last residue of the copied stretch</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
they’re copied over</li>
</ul>
</td>
@@ -635,7 +636,7 @@ while ensuring consistency with the <a class="reference internal" href="#promod3
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</li>
-<li><strong>profiles</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
+<li><strong>profiles</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
</ul>
</td>
</tr>
@@ -769,7 +770,7 @@ For the scondary-structure-penalty to work,
the model-template must have the appropriate
information before <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildRawModel()</span></code></a> is
called (e.g. with
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a> instead of
of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>. Also works in combination
with <cite>use_scoring_extender</cite>. This allows the gap
@@ -1100,7 +1101,7 @@ fragger handle for each chain in <em>mhandle</em>.</li>
<dl class="function">
<dt id="promod3.modelling.BuildSidechains">
-<code class="descclassname">promod3.modelling.</code><code class="descname">BuildSidechains</code><span class="sig-paren">(</span><em>mhandle</em>, <em>merge_distance=4</em>, <em>fragment_db=None</em>, <em>structure_db=None</em>, <em>torsion_sampler=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_pipeline.html#BuildSidechains"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.BuildSidechains" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">BuildSidechains</code><span class="sig-paren">(</span><em>mhandle</em>, <em>merge_distance=4</em>, <em>fragment_db=None</em>, <em>structure_db=None</em>, <em>torsion_sampler=None</em>, <em>rotamer_library=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_pipeline.html#BuildSidechains"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.BuildSidechains" title="Permalink to this definition">¶</a></dt>
<dd><p>Build sidechains for model.</p>
<p>This is a wrapper for <a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a>,
followed by a check for ring punches. If ring punches are found it
@@ -1123,6 +1124,10 @@ if None.</li>
<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>
if ring punches are found. A default one is loaded
if None.</li>
+<li><strong>rotamer_library</strong> (<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a> or
+<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Used as parameter for
+<code class="xref py py-func docutils literal"><span class="pre">modelling.ReconstructSidechains()</span></code>, a default
+one is loaded if None.</li>
</ul>
</td>
</tr>
@@ -1134,7 +1139,7 @@ if None.</li>
<dt id="promod3.modelling.MinimizeModelEnergy">
<code class="descclassname">promod3.modelling.</code><code class="descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_iterations=12</em>, <em>max_iter_sd=20</em>, <em>max_iter_lbfgs=10</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_pipeline.html#MinimizeModelEnergy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Minimize energy of final model using molecular mechanics.</p>
-<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
+<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.8.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
It will iteratively (at most <em>max_iterations</em> times):</p>
<ul class="simple">
<li>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</li>
@@ -1158,7 +1163,7 @@ If the variable is not set, 1 thread will be used by default.</p>
<li><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max. number of iterations within LBFGS method</li>
<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
-<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
+<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
</ul>
</td>
@@ -1166,7 +1171,7 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The model including all oxygens as used in the minimizer.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
</td>
</tr>
</tbody>
@@ -1240,7 +1245,7 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index 85e5fae720597dac6cad027ccab4fa3d2bf0d636..67bb2f71a5b0c7250f34c6ed6ce9b7c40924eaf6 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Sidechain Reconstruction — ProMod3 1.2.0 documentation</title>
+ <title>Sidechain Reconstruction — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Modelling Algorithms" href="algorithms.html" />
<link rel="prev" title="Generating Loops De Novo" href="monte_carlo.html" />
@@ -46,7 +47,7 @@
<p>Two methods are provided to fully reconstruct sidechains of residues:</p>
<ul class="simple">
<li>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></li>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></li>
<li>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
and used to reconstruct sidechains of single loops</li>
</ul>
@@ -101,7 +102,7 @@ and used to reconstruct sidechains of single loops</li>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
reconstruction gets directly applied on the structure itself.</li>
<li><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in <em>ent</em> (i.e.
containing all required atoms) should be kept rigid
@@ -114,8 +115,7 @@ the frame.</li>
<li><strong>consider_ligands</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether to add ligands (anything in chain
‘_’) as static objects.</li>
<li><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code>) – A rotamer library to extract the rotamers from. The
-default is the <code class="xref py py-meth docutils literal"><span class="pre">Dunbrack</span></code>
-library.</li>
+default is to call <code class="xref py py-meth docutils literal"><span class="pre"><LoadBBDepLib>()</span></code>.</li>
<li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Only considered when <em>rotamer_model</em>
is “frm”.
If set to True, the FRM solution undergoes
@@ -212,7 +212,7 @@ environment before calling this!</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Chain the loop belongs to.</li>
<li><strong>start_resnum_list</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Starts of loops.</li>
@@ -253,9 +253,9 @@ if multiple reconstructors are used (or you must use a distinct <em>env</em>).</
<li><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>) – Link to this environment.</li>
<li><strong>use_frm</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If True, use flexible rotamer model, else rigid.</li>
<li><strong>use_bbdep_lib</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If True, use default backbone dependent rot. library
-(<code class="xref py py-meth docutils literal"><span class="pre">Dunbrack</span></code>), else use
+(<code class="xref py py-meth docutils literal"><span class="pre">LoadBBDepLib()</span></code>), else use
backbone independent one
-(<code class="xref py py-meth docutils literal"><span class="pre">Penultimate</span></code>).</li>
+(<code class="xref py py-meth docutils literal"><span class="pre">LoadLib()</span></code>).</li>
<li><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code>) – Custom rotamer library to be used.</li>
</ul>
</td>
@@ -439,7 +439,7 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index c7226c83d6d29c07ee6392a031ad29887d8c9f0f..f48241f38276d2e99ac3e7e82e959edb969244eb 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index ce9c3bed25946e90ca661dc414a86805a914c840..4fb4577a3af5b85d4e07184e241a77d59a86565c 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Using Binary Files In ProMod3 — ProMod3 1.2.0 documentation</title>
+ <title>Using Binary Files In ProMod3 — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,9 +23,10 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developers" href="developers.html" />
- <link rel="next" title="Changelog" href="changelog.html" />
+ <link rel="next" title="License" href="license.html" />
<link rel="prev" title="ProMod3‘s Share Of CMake" href="cmake/index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -408,9 +409,9 @@ and non-portable I/O:</p>
</ul>
</li>
<li>module <code class="docutils literal"><span class="pre">sidechain</span></code>:<ul>
-<li><code class="file docutils literal"><span class="pre">2010DunbrackLib.dat</span></code>
+<li><code class="file docutils literal"><span class="pre">bb_dep_lib.dat</span></code>
(<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">PenultimateLib.dat</span></code>
+<li><code class="file docutils literal"><span class="pre">lib.dat</span></code>
(<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a>)</li>
</ul>
</li>
@@ -450,7 +451,7 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
<li><a href="index.html">Documentation overview</a><ul>
<li><a href="developers.html">Documentation For Developers</a><ul>
<li>Previous: <a href="cmake/index.html" title="previous chapter">ProMod3‘s Share Of CMake</a></li>
- <li>Next: <a href="changelog.html" title="next chapter">Changelog</a></li>
+ <li>Next: <a href="license.html" title="next chapter">License</a></li>
</ul></li>
</ul></li>
</ul>
@@ -477,7 +478,7 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 94cc934014dc70ed49d89fbccbc9117b373ad337..dfe91145475f83d296f076a203068b815e156073 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Python Module Index — ProMod3 1.2.0 documentation</title>
+ <title>Python Module Index — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -131,7 +132,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/references.html b/doc/html/references.html
new file mode 100644
index 0000000000000000000000000000000000000000..c6a966468b4a871b84239adaf9a4c5424a94750e
--- /dev/null
+++ b/doc/html/references.html
@@ -0,0 +1,222 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>References — ProMod3 1.3.0 documentation</title>
+
+ <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '1.3.0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
+ <link rel="next" title="Changelog" href="changelog.html" />
+ <link rel="prev" title="License" href="license.html" />
+
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+ </head>
+ <body role="document">
+
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <div class="section" id="references">
+<h1>References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h1>
+<table class="docutils citation" frame="void" id="biasini2013" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[biasini2013]</td><td>Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J,
+Johner N, Schenk AD, Philippsen A and Schwede T (2013).
+OpenStructure: an integrated software framework for
+computational structural biology. Acta Cryst.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="canutescu2003" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[canutescu2003]</td><td>Canutescu AA and Dunbrack RL Jr. (2003).
+Cyclic coordinate descent: A robotics algorithm for protein
+loop closure. Protein Sci.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="canutescu2003b" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[canutescu2003b]</td><td>Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003).
+A graph-theory algorithm for rapid protein side-chain
+prediction. Protein Sci.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="coutsias2005" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[coutsias2005]</td><td>Coutsias EA, Seok C, Wester MJ, Dill KA (2005).
+Resultants and loop closure. International Journal of Quantum
+Chemistry.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="chakravarty1999" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[chakravarty1999]</td><td>Chakravarty S, Varadarajan R (1999).
+Residue depth: a novel parameter for the analysis of
+protein structure and stability. Structure.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="davis2006" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[davis2006]</td><td>Davis IW, Arendall WB, Richardson DC, Richardson JS (2006).
+The backrub motion: how protein backbone shrugs when a sidechain
+dances. Structure.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="goldstein1994" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[goldstein1994]</td><td>Goldstein RF (1994).
+Efficient rotamer elimination applied to protein side-chains
+and related spin glasses. Biophys J.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="jones1999" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[Jones1999]</td><td>Jones DT (1999).
+Protein secondary structure prediction based on position-specific
+scoring matrices. J. Mol. Biol.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="kabsch1983" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[kabsch1983]</td><td>Kabsch W, Sander C (1983).
+Dictionary of protein secondary structure: pattern recognition of
+hydrogen-bonded and geometrical features. Biopolymers.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="krivov2009" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[krivov2009]</td><td>Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009).
+Improved prediction of protein side-chain conformations with
+SCWRL4. Proteins.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="leach1998" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[leach1998]</td><td>Leach AR, Lemon AP (1998).
+Exploring the conformational space of protein side chains using
+dead-end elimination and the A* algorithm. Proteins.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="shapovalov2011" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[shapovalov2011]</td><td>Shapovalov MV and Dunbrack RL Jr. (2011).
+A smoothed backbone-dependent rotamer library for proteins
+derived from adaptive kernel density estimates and
+regressions. Structure.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="soding2005" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[soding2005]</td><td>Söding J (2005).
+Protein homology detection by HMM-HMM comparison.
+Bioinformatics.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="solis2006" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[solis2006]</td><td>Solis AD, Rackovsky S (2006). Improvement of statistical
+potentials and threading score functions using information
+maximization. Proteins.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="zhou2005" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[zhou2005]</td><td>Zhou H, Zhou Y (2005).
+Fold Recognition by Combining Sequence Profiles Derived From
+Evolution and From Depth-Dependent Structural Alignment of
+Fragments. Proteins.</td></tr>
+</tbody>
+</table>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
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+ <ul class="this-page-menu">
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+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+
+ |
+ <a href="_sources/references.txt"
+ rel="nofollow">Page source</a>
+ </div>
+
+
+
+
+ </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 983fd1a43688c709ba13f6608a27e1cbd61780b1..0fce2172d3357e8ab9a5bee0837e943696cc9a74 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>All Atom Scorers — ProMod3 1.2.0 documentation</title>
+ <title>All Atom Scorers — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="Other Scoring Functions" href="other_scoring_functions.html" />
<link rel="prev" title="Backbone Scorers" href="backbone_scorers.html" />
@@ -568,7 +569,7 @@ of residues in the input loop. True by default.</td>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomScorer</span></code></a>. Calculates a simple
clash score of all atoms against the environment. There is no need to define
any parameters here as all interaction energies are fixed (see Eq. (11) in
-<a class="reference internal" href="other_scoring_functions.html#canutescu2003b" id="id1">[canutescu2003b]</a>). By default, the scorer calculates the scores by
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>). By default, the scorer calculates the scores by
including everything, the stuff set in the environment and the coordinates
in the input loops. You can change this behaviour with the according
functions.</p>
@@ -671,7 +672,7 @@ of residues in the input loop. True by default.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index e1b57c32a98e58a6133441cde6027450387db6b9..a5a744a73dde97efc0b9395b123095eef4ce1fac 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Backbone Score Environment — ProMod3 1.2.0 documentation</title>
+ <title>Backbone Score Environment — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="Backbone Scorers" href="backbone_scorers.html" />
<link rel="prev" title="scoring - Loop Scoring" href="index.html" />
@@ -68,8 +69,8 @@ task.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
</tr>
</tbody>
@@ -106,7 +107,7 @@ structural data was already set, all the existing data gets cleared first.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</td>
</tr>
@@ -130,7 +131,7 @@ positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
</ul>
</td>
@@ -279,7 +280,7 @@ providing lists of integers.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -328,9 +329,9 @@ providing lists of integers.</p>
<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ConstraintFunction</code><span class="sig-paren">(</span><em>min_dist</em>, <em>max_dist</em>, <em>values</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ConstraintFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunction</span></code></a>.
Defines a constraint function. The score for a distance between <em>min_dist</em> and
-<em>max_dist</em> is determined by liner interpolation assuming the first and last
-value exactly lying on <em>min_dist</em> ang <em>max_dist</em>. For distances outside the
-range defined by <em>min_dist</em> and <em>max_dist</em>, the score is 0.0.</p>
+<em>max_dist</em> is determined by linear interpolation assuming the first and last
+value exactly lying on <em>min_dist</em> and <em>max_dist</em>. For distances outside the
+range defined by <em>min_dist</em> and <em>max_dist</em>, the returned score is 0.0.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -343,10 +344,7 @@ between <em>min_dist</em> and <em>max_dist</em></li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Index of added constraint definition</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>min_dist</em> >= <em>max_dist</em> or when
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>min_dist</em> >= <em>max_dist</em> or when
<em>min_dist</em> or <em>max_dist</em> are negative or when <em>values</em> contains no
elements</p>
</td>
@@ -360,7 +358,7 @@ elements</p>
<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ContactFunction</code><span class="sig-paren">(</span><em>max_dist</em>, <em>score</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ContactFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunction</span></code></a>.
Defines a simple contact function. The score value is <em>score</em> if
-distance < <em>max_dist</em> and 0 otherwise.</p>
+distance < <em>max_dist</em> and 0.0 otherwise.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -389,7 +387,7 @@ The constraint functions are built after the principle of QMEANDisCo.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
<li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
or CB atoms</li>
</ul>
@@ -404,7 +402,7 @@ or CB atoms</li>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
SEQRES and the second sequence the actual structural
info. The second sequence must have a view attached.</td>
</tr>
@@ -510,7 +508,7 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index 71276424ad8d5762fa2f4f87b16a5e46d6c22fa1..986fd44da79fc557f4e535321a4c4dfb06a8ad33 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Backbone Scorers — ProMod3 1.2.0 documentation</title>
+ <title>Backbone Scorers — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="All Atom Scorers" href="all_atom_scorers.html" />
<link rel="prev" title="Backbone Score Environment" href="backbone_score_env.html" />
@@ -380,7 +381,7 @@ called for every type of amino acids and for every <em>count</em> <= <em>max_
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
<li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of surrounding CB positions for which to set energy.</li>
<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
@@ -442,9 +443,9 @@ of amino acids.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Radius in which other cbeta atoms are counted.</li>
+<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Radius in which other cbeta atoms are considered.</li>
<li><strong>bins</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
-of [0,*cutoff*]).</li>
+of [0, <em>cutoff</em>]).</li>
<li><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Minimal separation in sequence two cbeta atoms must have to
be considered.</li>
</ul>
@@ -514,8 +515,8 @@ SetEnergy(aa2, aa1, bin, energy).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
<li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
@@ -694,8 +695,8 @@ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
<li><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
<li><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the alpha angle.</li>
<li><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the beta angle.</li>
@@ -780,7 +781,7 @@ of residues to be scored. True by default.</td>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Calculates a simple
clash score of a loop itself and with the set environment. There is no need to
define any parameters here as all interaction energies are fixed (see Eq. (11)
-in <a class="reference internal" href="other_scoring_functions.html#canutescu2003b" id="id1">[canutescu2003b]</a>).</p>
+in <a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>).</p>
<dl class="method">
<dt id="promod3.scoring.ClashScorer.DoInternalScores">
<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
@@ -1387,7 +1388,7 @@ of residues to be scored. True by default.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index e733603063ec5484bad703f5de8006b1f24d4029..000b9b1b51955a090a9d37b16767545126d35e66 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>scoring - Loop Scoring — ProMod3 1.2.0 documentation</title>
+ <title>scoring - Loop Scoring — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Backbone Score Environment" href="backbone_score_env.html" />
<link rel="prev" title="Subrotamer Optimization" href="../sidechain/subrotamer_optimizer.html" />
@@ -44,7 +45,11 @@
<div class="section" id="module-promod3.scoring">
<span id="scoring-loop-scoring"></span><h1><a class="reference internal" href="#module-promod3.scoring" title="promod3.scoring: Loop Scoring"><code class="xref py py-mod docutils literal"><span class="pre">scoring</span></code></a> - Loop Scoring<a class="headerlink" href="#module-promod3.scoring" title="Permalink to this headline">¶</a></h1>
<p>Tools and algorithms to score loops. The scoring system is split between an
-environment which contains model-specific data and scorers which evaluate loops.</p>
+environment and scorers.
+Several scorers can be attached to the same environment containing the
+actual structural data of the current modelling problem.
+The environment is updated as the modelling proceeds and manages efficient
+spatial lookups to be used by the attached scorers.</p>
<p>In this example, we load a structure, setup a score environment, link a few
scorers to it and finally score some loops:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
@@ -147,7 +152,7 @@ scorers to it and finally score some loops:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index 998c0c6c19f3cec55ad955d5c844295d786d62b2..808f5acc128c968b6770224ed24e8f5aa87dfa3a 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Other Scoring Functions — ProMod3 1.2.0 documentation</title>
+ <title>Other Scoring Functions — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="loop - Loop Handling" href="../loop/index.html" />
<link rel="prev" title="All Atom Scorers" href="all_atom_scorers.html" />
@@ -49,7 +50,7 @@
<dt id="promod3.scoring.SCWRL3PairwiseScore">
<code class="descclassname">promod3.scoring.</code><code class="descname">SCWRL3PairwiseScore</code><span class="sig-paren">(</span><em>d</em>, <em>Rij</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3PairwiseScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Pairwise score from the SCWRL3 sidechain construction algorithm
-<a class="reference internal" href="#canutescu2003b" id="id1">[canutescu2003b]</a>.</p>
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -82,7 +83,7 @@ Suggestions from the paper:</p>
<dt id="promod3.scoring.SCWRL3DisulfidScore">
<code class="descclassname">promod3.scoring.</code><code class="descname">SCWRL3DisulfidScore</code><span class="sig-paren">(</span><em>ca_pos_one</em>, <em>cb_pos_one</em>, <em>sg_pos_one ca_pos_two</em>, <em>cb_pos_two</em>, <em>sg_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3DisulfidScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Implements the empirically derived disulfid score from the SCWRL3 sidechain
-construction algorithm <a class="reference internal" href="#canutescu2003b" id="id2">[canutescu2003b]</a>.</p>
+construction algorithm <a class="reference internal" href="../references.html#canutescu2003b" id="id2">[canutescu2003b]</a>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -107,12 +108,6 @@ construction algorithm <a class="reference internal" href="#canutescu2003b" id="
</table>
</dd></dl>
-<table class="docutils citation" frame="void" id="canutescu2003b" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[canutescu2003b]</td><td><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id2">2</a>)</em> Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).</td></tr>
-</tbody>
-</table>
</div>
</div>
@@ -164,7 +159,7 @@ construction algorithm <a class="reference internal" href="#canutescu2003b" id="
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/search.html b/doc/html/search.html
index 175b5dbecda4fd05bc276408aaeabcf79e257d85..385d102bf319742391c5f947956f78f14f02b593 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Search — ProMod3 1.2.0 documentation</title>
+ <title>Search — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,8 +23,9 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<script type="text/javascript" src="_static/searchtools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
<script type="text/javascript">
jQuery(function() { Search.loadIndex("searchindex.js"); });
</script>
@@ -86,7 +87,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 0c62df2650b19609ccc5d2fdf8536279e9693cc2..97200f95abb98a15977970df4ef4efcfaf0cbab7 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
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Actions","<code class=\"docutils literal\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3‘s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"docutils literal\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"docutils literal\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"docutils literal\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame","Rotamer Graph","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Rotamers","Rotamer Constructor","RotamerID","Rotamer Library","Subrotamer Optimization","Documentation For Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43],acid:[21,25,27],action:[0,1,4,5,7,8],actiontestcas:1,algorithm:28,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angl:27,api:1,argument:13,atom:[21,32,39],backbon:[32,40,41,52],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,7,35,49],can:51,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:52,construct:[40,50],constructor:50,contain:6,contribut:8,conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,52],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entri:52,environ:40,evalu:44,everyth:11,exampl:[31,37],execut:1,exisit:37,extend:29,featur:[8,26],file:[11,37],find:26,fit:32,forcefield:25,fragment:26,frame:[45,50],from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,51],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,51],imag:[5,7],instal:2,integr:1,introduct:[4,11,13],issu:8,keep:31,kic:32,librari:[5,7,48,52],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,must:1,non:52,novo:[28,34],object:[24,34,45],optim:53,ost:[5,7,25],other:43,output:1,own:8,pairwis:40,pairwisescor:41,pars:13,parser:13,parti:8,particl:49,pipelin:[18,35],pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,relax:32,releas:3,repres:22,residu:50,rigid:28,ring:33,rotam:[46,48,49,50,52],rotamerid:51,run:[1,2,5,7,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43],scorer:[8,34,39,41],script:[1,5,7],scwrl3:43,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,11],sidechain:[0,36,47],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:53,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:52,unit:[1,4,8],user:54,write:8,your:8}})
\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 3724f552e9c88343293899410277feb0d2ee412e..40a2bd960a95f431a9a7aaca9ca974811a07f73c 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Disulfid Bond Evaluation — ProMod3 1.2.0 documentation</title>
+ <title>Disulfid Bond Evaluation — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Loading Rotamer Libraries" href="loading.html" />
<link rel="prev" title="Rotamer Graph" href="graph.html" />
@@ -49,7 +50,7 @@ the sulfur atoms. It is possible to improve performance in sidechain
reconstruction regarding cysteins when finding and separately handle
disulfid bonds. The scoring module implements an empirically derived disulfid
score (<a class="reference internal" href="../scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore" title="promod3.scoring.SCWRL3DisulfidScore"><code class="xref py py-func docutils literal"><span class="pre">promod3.scoring.SCWRL3DisulfidScore()</span></code></a>) as defined in
-<a class="reference internal" href="../scoring/other_scoring_functions.html#canutescu2003b" id="id1">[canutescu2003b]</a>. The paper proposes two rotamers to be in a disulfid
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>. The paper proposes two rotamers to be in a disulfid
bonded state, if the resulting disulfid score plus the self energies of the
involved rotamers is below 45. If there are several cysteines close together,
this problem gets another layer of complexity. One has to assure, that
@@ -76,10 +77,10 @@ rotamers to the result of the geometric expression.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</li>
<li><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</li>
-<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
-<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
-<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
-<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
+<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
+<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
+<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
+<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
</ul>
</td>
</tr>
@@ -112,8 +113,8 @@ possible, the one with the optimal sum of scores gets estimated.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rotamer_groups</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>) – Every group represents a cysteine</li>
-<li><strong>ca_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
-<li><strong>cb_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
+<li><strong>ca_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
+<li><strong>cb_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
<li><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
as a disulfid bond</li>
<li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
@@ -179,7 +180,7 @@ describe the optimal rotamers in the according rotamer groups.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index 9230a415148eeae3d628663743913f9c46ab6705..f43158c010feb69e7320bf4bb7e27b2e335e4b00 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Frame — ProMod3 1.2.0 documentation</title>
+ <title>Frame — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamer Library" href="rotamer_lib.html" />
<link rel="prev" title="Rotamers" href="rotamer.html" />
@@ -168,7 +169,7 @@ can be passed to rotamer groups for calculating frame energies.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index e547f6f72ad4a595a7f20713cf3469da52324898..c0032b487e3c751493d13b3d194207f752817da3 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Graph — ProMod3 1.2.0 documentation</title>
+ <title>Rotamer Graph — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Disulfid Bond Evaluation" href="disulfid.html" />
<link rel="prev" title="Rotamer Constructor" href="rotamer_constructor.html" />
@@ -46,7 +47,7 @@
<p>Once having a frame representing the rigid parts, the internal energies in
rotamer groups can be calculated. To come to a final solution of the sidechain
modelling problem, the pairwise energies also have to be evaluated and an
-overall solution has to be found. PROMOD3 implements a
+overall solution has to be found. ProMod3 implements a
<a class="reference internal" href="../core/graph_minimizer.html#promod3.core.GraphMinimizer" title="promod3.core.GraphMinimizer"><code class="xref py py-class docutils literal"><span class="pre">promod3.core.GraphMinimizer</span></code></a> that allows to find solutions using
tree decomposition, A* and Monte Carlo algorithms.</p>
<dl class="class">
@@ -119,7 +120,7 @@ conformations for every amino acid position.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index 3af49da0fb86f519b9e07bbc4fd4a050449415a8..e4fe610fd18a0d85406815cb0d8e8341bb0be7ad 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>sidechain - Sidechain Modelling — ProMod3 1.2.0 documentation</title>
+ <title>sidechain - Sidechain Modelling — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="RotamerID" href="rotamer_id.html" />
<link rel="prev" title="Modelling Algorithms" href="../modelling/algorithms.html" />
@@ -44,9 +45,9 @@
<div class="section" id="module-promod3.sidechain">
<span id="sidechain-sidechain-modelling"></span><h1><a class="reference internal" href="#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal"><span class="pre">sidechain</span></code></a> - Sidechain Modelling<a class="headerlink" href="#module-promod3.sidechain" title="Permalink to this headline">¶</a></h1>
<p>Tools and algorithms to model sidechains given backbone coordinates. The full
-module is heavily based on SCWRL4 <a class="reference internal" href="#krivov2009" id="id1">[krivov2009]</a> . The according paper describes
+module is heavily based on SCWRL4 <a class="reference internal" href="../references.html#krivov2009" id="id1">[krivov2009]</a> . The according paper describes
the modelling of sidechains using two different rotamer models. A rigid model,
-as well as a flexible model. Both models are implemented in PROMOD3 and can be
+as well as a flexible model. Both models are implemented in ProMod3 and can be
applied in flexible ways.</p>
<p>The following code fragment shows an example of a basic sidechain reconstruction
algorithm using the functionality in the module. Note, that this code will crash
@@ -59,7 +60,7 @@ pipelines available in the modelling module.</p>
<span class="c1"># load a protein</span>
<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
<span class="c1"># load rotamer library</span>
-<span class="n">library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadDunbrackLib</span><span class="p">()</span>
+<span class="n">library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadBBDepLib</span><span class="p">()</span>
<span class="c1"># we need a rotamer constructor to create any rotamers or </span>
<span class="c1"># frame residues </span>
<span class="n">rot_constructor</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">SCWRLRotamerConstructor</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
@@ -111,6 +112,9 @@ pipelines available in the modelling module.</p>
<span class="n">r</span><span class="p">,</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">i</span><span class="p">,</span> <span class="n">library</span><span class="p">,</span>
<span class="n">torsion_angles</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">torsion_angles</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span>
+ <span class="c1"># calculate pairwise energies towards the rigid frame</span>
+ <span class="c1"># the values will be stored and used by the solving algorithm</span>
+ <span class="c1"># later on when considering self energies</span>
<span class="n">rot_group</span><span class="o">.</span><span class="n">SetFrameEnergy</span><span class="p">(</span><span class="n">frame</span><span class="p">)</span>
<span class="c1"># remove super unlikely rotamer in rotamer group </span>
<span class="c1"># e.g. those who clash with the frame</span>
@@ -157,6 +161,7 @@ pipelines available in the modelling module.</p>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-non-backbone-dependent-rotamer-library">The Non Backbone Dependent Rotamer Library</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-backbone-dependent-rotamer-library">The Backbone Dependent Rotamer Library</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-library-entry-type">The Library Entry Type</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#rotamer-configurations">Rotamer Configurations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="rotamer_constructor.html">Rotamer Constructor</a><ul>
@@ -169,12 +174,6 @@ pipelines available in the modelling module.</p>
<li class="toctree-l1"><a class="reference internal" href="subrotamer_optimizer.html">Subrotamer Optimization</a></li>
</ul>
</div>
-<table class="docutils citation" frame="void" id="krivov2009" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[krivov2009]</a></td><td>Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.</td></tr>
-</tbody>
-</table>
</div>
@@ -215,7 +214,7 @@ pipelines available in the modelling module.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index cca071873f529654b50e681922af16e723f72672..e45d778f149915ce50e57f6fd4f27a19e284e22a 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Loading Rotamer Libraries — ProMod3 1.2.0 documentation</title>
+ <title>Loading Rotamer Libraries — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Subrotamer Optimization" href="subrotamer_optimizer.html" />
<link rel="prev" title="Disulfid Bond Evaluation" href="disulfid.html" />
@@ -43,24 +44,26 @@
<div class="section" id="loading-rotamer-libraries">
<h1>Loading Rotamer Libraries<a class="headerlink" href="#loading-rotamer-libraries" title="Permalink to this headline">¶</a></h1>
-<p>Since the PROMOD3 sidechain modelling algorithms are mainly designed after the
-work of the Dunbrack lab <a class="reference internal" href="index.html#krivov2009" id="id1">[krivov2009]</a> , their backbone dependent rotamer
-library is probably the way to go. There exists a binary version of their
-2010 libary <a class="reference internal" href="#shapovalov2011" id="id2">[shapovalov2011]</a> , that can
-directly be loaded. As an alternative, there is also a binary file containing
-the backbone independent Penultimate library <a class="reference internal" href="#lovell2000" id="id3">[lovell2000]</a> .</p>
+<p>There are several rotamer libraries that can be used in ProMod3. ProMod3
+is optimized for the use with backbone dependent rotamer libraries such
+as the 2010 library provided by the Dunbrack lab <a class="reference internal" href="../references.html#shapovalov2011" id="id1">[shapovalov2011]</a>.
+You can request a licence <a class="reference external" href="http://dunbrack.fccc.edu/bbdep2010/">here</a>
+and generate such a library as described in
+extras/data_generation/rotamer_library/README. Alternatively, ProMod3
+provides its own backbone dependent or backbone independent libraries
+that can be loaded with <a class="reference internal" href="#promod3.sidechain.LoadBBDepLib" title="promod3.sidechain.LoadBBDepLib"><code class="xref py py-meth docutils literal"><span class="pre">LoadBBDepLib()</span></code></a> / <a class="reference internal" href="#promod3.sidechain.LoadLib" title="promod3.sidechain.LoadLib"><code class="xref py py-meth docutils literal"><span class="pre">LoadLib()</span></code></a>.</p>
<dl class="method">
-<dt id="promod3.sidechain.LoadDunbrackLib">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadDunbrackLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadDunbrackLib" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads the 2010 backbone dependent rotamer library from the dunbrack lab.
-The library has been generated using the ReadDunbrackFile function
-using the file with smoothing factor 5 and nonrotameric dihedrals
-sampled in 20 degree steps.</p>
+<dt id="promod3.sidechain.LoadBBDepLib">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadBBDepLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadBBDepLib" title="Permalink to this definition">¶</a></dt>
+<dd><p>A backbone dependent rotamer library shipped with ProMod3. You can find
+details on how it is created in extras/data_generation/rotamer_library/README.
+All scripts to build it are in the same directory as the README file and
+build the basis for custom versions.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The requested library</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The requested Library</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a></td>
</tr>
@@ -69,12 +72,12 @@ sampled in 20 degree steps.</p>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.LoadPenultimateLib">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadPenultimateLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadPenultimateLib" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads the backbone independent Penultimate library. The values for the dihedral
-angles are directly extracted from the publication without considering the
-probabilities specific for helices/sheets. Due to no assigned standard
-deviations, the flexible rotamer model won’t produce meaningful results.</p>
+<dt id="promod3.sidechain.LoadLib">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadLib" title="Permalink to this definition">¶</a></dt>
+<dd><p>A backbone independent rotamer library shipped with ProMod3. You can find
+details on how it is created in extras/data_generation/rotamer_library/README.
+All scripts to build it are in the same directory as the README file and
+build the basis for custom versions.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -92,8 +95,9 @@ deviations, the flexible rotamer model won’t produce meaningful results.</
<code class="descclassname">promod3.sidechain.</code><code class="descname">ReadDunbrackFile</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ReadDunbrackFile" title="Permalink to this definition">¶</a></dt>
<dd><p>Reads a file as it is provided when you get a licence for the 2010 library of
the Dunbrack lab. It can only read the classic version, where all rotamers
-are in a single file. Specific distributions of nonrotameric sidechains
-cannot be read.</p>
+are in a single file. Specific distributions of non-rotameric sidechains
+cannot be read. You can find an example described in
+extras/data_generation/rotamer_library/README</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -113,18 +117,6 @@ incomplete if the last problem gets triggered.</td>
</table>
</dd></dl>
-<table class="docutils citation" frame="void" id="shapovalov2011" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id2">[shapovalov2011]</a></td><td>Shapovalov MV and Dunbrack RL Jr. (2011). A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="lovell2000" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id3">[lovell2000]</a></td><td>Lovell SC, Word JM, Richardson JS, Richardson DC (2000). The penultimate rotamer library. Proteins.</td></tr>
-</tbody>
-</table>
</div>
@@ -167,7 +159,7 @@ incomplete if the last problem gets triggered.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index 582ce7f7647665d09d4bb7ee052bdda578fd494e..05a359066a65e58535e1799f87a8219853f63f9d 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamers — ProMod3 1.2.0 documentation</title>
+ <title>Rotamers — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Frame" href="frame.html" />
<link rel="prev" title="RotamerID" href="rotamer_id.html" />
@@ -47,7 +48,7 @@
<a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects. There exist two types. The <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> and
<a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>.
To gather all possible rotamers for one particular sidechain position,
-PROMOD3 offers the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>.
+ProMod3 offers the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>.
Pairwise interactions between particles give raise to pairwise energies between
rotamers. Nevertheless, the energy calculation itself happens on the level
of RotamerGroups and is mostly hidden away in the construction of the
@@ -86,11 +87,11 @@ has to be defined at initialization.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>type</strong> (<a class="reference internal" href="#promod3.sidechain.SidechainParticle" title="promod3.sidechain.SidechainParticle"><code class="xref py py-class docutils literal"><span class="pre">SidechainParticle</span></code></a>) – Type of particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Positions of particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Positions of particle</li>
<li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Charge of particle, will be used in case H-Bonds</li>
<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of particle. This name will be given to an actual
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> if a rotamer gets applied
-to a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a></li>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> if a rotamer gets applied
+to a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a></li>
</ul>
</td>
</tr>
@@ -198,7 +199,7 @@ to a <a class="reference external" href="https://www.openstructure.org/docs/dev/
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>lone_pair</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Lone pair direction</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>lone_pair</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Lone pair direction</td>
</tr>
</tbody>
</table>
@@ -213,7 +214,7 @@ hydrogen, this would be the direction of backbone-N to backbone-H.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Polar direction of particle</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Polar direction of particle</td>
</tr>
</tbody>
</table>
@@ -290,7 +291,7 @@ in this process.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
<strong>res</strong></li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
@@ -485,7 +486,7 @@ belongs to.</p>
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">FRMRotamer</code><span class="sig-paren">(</span><em>particles</em>, <em>T</em>, <em>probability</em>, <em>internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer" title="Permalink to this definition">¶</a></dt>
<dd><p>The FRMRotamer represents a rotamer of the so called flexible rotamer model,
where one rotamer gets represented by several subrotamers.
-The idea is, that all particles of all subrotamers are given at
+The idea is that all particles of all subrotamers are given at
initialization. Subrotamers are then defined by providing lists of indices.
One particle can be part of several subrotamers.</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -566,7 +567,7 @@ No atoms are removed from <strong>res</strong> in this process.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -966,7 +967,7 @@ particles of the same residue.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1100,7 +1101,7 @@ particles of the same residue.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1224,7 +1225,7 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 0a026c732216121edf1f9e241a6df6442596da23..f787eed4d887a4e48d10d03d259d07aaeaca1667 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Constructor — ProMod3 1.2.0 documentation</title>
+ <title>Rotamer Constructor — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamer Graph" href="graph.html" />
<link rel="prev" title="Rotamer Library" href="rotamer_lib.html" />
@@ -44,7 +45,7 @@
<div class="section" id="rotamer-constructor">
<h1>Rotamer Constructor<a class="headerlink" href="#rotamer-constructor" title="Permalink to this headline">¶</a></h1>
<p>Instead of creating rotamers by yourself, you can simply use the convenient
-functionality provided by PROMOD3</p>
+functionality provided by ProMod3</p>
<div class="section" id="constructing-rotamers-and-frame-residues">
<h2>Constructing Rotamers and Frame Residues<a class="headerlink" href="#constructing-rotamers-and-frame-residues" title="Permalink to this headline">¶</a></h2>
<dl class="class">
@@ -107,7 +108,7 @@ any rotamers for ALA and GLY.</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the required backbone atoms</li>
@@ -167,7 +168,7 @@ why the phi angle of the residue is required as an input.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the backbone positions</li>
@@ -213,7 +214,7 @@ particles for all polar hydrogens.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the sidechain positions</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the sidechain positions</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the sidechain positions</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the sidechain positions</li>
@@ -237,7 +238,7 @@ atom positions are set in <strong>all_atom_pos</strong>.</p>
<dl class="method">
<dt id="promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue">
<code class="descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
This can be useful to mark a region occupied by a ligand. Note, that
there won’t be any parametrization of hbonds in this function. All atoms
of the residue will be represented as carbons and hydrogens are skipped.</p>
@@ -246,7 +247,7 @@ of the residue will be represented as carbons and hydrogens are skipped.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
</ul>
@@ -262,7 +263,7 @@ construct a <a class="reference internal" href="frame.html#promod3.sidechain.Fra
<dl class="method">
<dt id="promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidueHeuristic">
<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em>, <em>comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms based on the passed compounds library.
This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal"><span class="pre">ConstructFrameResidue()</span></code></a>,
which will be called by this function if the residue is not known by the given
@@ -280,10 +281,10 @@ as in the <a class="reference internal" href="rotamer.html#promod3.sidechain.Sid
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
-<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
+<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
</ul>
</td>
</tr>
@@ -368,7 +369,7 @@ to be assigned</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/rotamer_id.html b/doc/html/sidechain/rotamer_id.html
index e324b292b422c8a57350ef8cfba159adabf832f7..d63d36c4ee0736c3ef8d85b6be5f069cd16f711f 100644
--- a/doc/html/sidechain/rotamer_id.html
+++ b/doc/html/sidechain/rotamer_id.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>RotamerID — ProMod3 1.2.0 documentation</title>
+ <title>RotamerID — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamers" href="rotamer.html" />
<link rel="prev" title="sidechain - Sidechain Modelling" href="index.html" />
@@ -93,7 +94,7 @@ or as <code class="docutils literal"><span class="pre">promod3.sidechain.Rotamer
<div class="section" id="how-can-i-get-an-id">
<h2>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h2>
<p>The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
+functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
or from amino acid three letter codes.</p>
<dl class="method">
<dt id="promod3.sidechain.TLCToRotID">
@@ -118,12 +119,12 @@ exactly the naming convention defined above.</p>
<dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
to generate special IDs this way
(e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not
-defined in <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+defined in <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
</tr>
@@ -183,7 +184,7 @@ defined in <a class="reference external" href="https://www.openstructure.org/doc
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 7bfcf345dae719027bd12f4096db2da54f3ca84b..ef5d182244d1865d6c23c4b7b05816d4aa3b179d 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Library — ProMod3 1.2.0 documentation</title>
+ <title>Rotamer Library — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
<link rel="prev" title="Frame" href="frame.html" />
@@ -48,7 +49,7 @@ sidechain can completely be described in terms of dihedral angles. Preferred
combinations of such dihedral angles are a result of steric properties and
can be gathered in rotamer libraries. Different libraries exist in the field
and their main difference is, whether the provided sidechain conformations
-are dependent on their backbone or not. PROMOD3 provides you with a
+are dependent on their backbone or not. ProMod3 provides you with a
<a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a> organizing rotamers for the different aminoacids
in equidistant phi/psi bins, as well as a simple <a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a>.
Both libraries are containers for <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> and are optimized
@@ -262,10 +263,12 @@ is given or when the library is already static.</p>
added to the library or can be interpolated.
In the first option, <em>phi</em> and <em>psi</em> simply get transformed to the
according bin using following formalism: bin = round((angle + pi)/bin_size).
-In case of interpolation, the chi angles and the according standard
-deviations of the rotamers get bilinearly interpolated using the
-corresponding rotamers with same configuration from the neighbouring bins.
-This behaviour can be controlled with the SetInterpolate function.
+In case of interpolation, the chi angles of rotameric dihedral angles and the
+according standard deviations of the rotamers get bilinearly interpolated
+using the corresponding rotamers with same configuration from the
+neighbouring bins. No interplation is applied to non-rotameric dihedral
+angles (chi2 in ASP, ASN, HIS, PHE, TRP, TYR; chi3 in GLU, GLN).
+This behaviour can be controlled with <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.SetInterpolate" title="promod3.sidechain.BBDepRotamerLib.SetInterpolate"><code class="xref py py-meth docutils literal"><span class="pre">SetInterpolate()</span></code></a>.
The query function follows following strategies in case of
special <em>id</em> requests.</p>
<ul class="simple">
@@ -330,7 +333,8 @@ not fulfilled</td>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>interpolate</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Controls behaviour when QueryLib function gets called</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>interpolate</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Controls behaviour when <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.QueryLib" title="promod3.sidechain.BBDepRotamerLib.QueryLib"><code class="xref py py-meth docutils literal"><span class="pre">QueryLib()</span></code></a>
+gets called</td>
</tr>
</tbody>
</table>
@@ -433,14 +437,14 @@ functionalities.</p>
<em class="property">static </em><code class="descname">FromResidue</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.FromResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> from the given <em>res</em>.
The function tries to automatically identify the <a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> based
-on the residue name. The probability gets set to zero and the standard
-deviations to 0. All not required chi angles with their corresponding
-standard deviations are NaN.</p>
+on the residue name. The probability and standard deviations are set to 0.0,
+all not required chi angles with their corresponding standard deviations to
+NaN.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></td>
</tr>
@@ -464,7 +468,7 @@ are NaN.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></li>
</ul>
</td>
@@ -596,6 +600,72 @@ considered similar</li>
</dd></dl>
+</div>
+<div class="section" id="rotamer-configurations">
+<h2>Rotamer Configurations<a class="headerlink" href="#rotamer-configurations" title="Permalink to this headline">¶</a></h2>
+<p>In rotamers, one distinguishes between rotameric and non-rotameric sidechain
+dihedral angles. The rotameric ones are around SP3-SP3 hybridized bonds and
+typically have three distinct configurations (trans, gauche-, gauche+).
+The non-rotameric ones behave differently. ProMod3 offers some functionality
+to estimate those configurations.</p>
+<dl class="class">
+<dt id="promod3.sidechain.DihedralConfiguration">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">DihedralConfiguration</code><a class="headerlink" href="#promod3.sidechain.DihedralConfiguration" title="Permalink to this definition">¶</a></dt>
+<dd><p>Enumerates the possible sidechain dihedral configurations</p>
+<table class="hlist"><tr><td><ul class="simple">
+<li>TRANS - Trans configuration (120 < angle < -120)</li>
+<li>GAUCHE_PLUS - Gauche+ configuration (0 < angle < 120)</li>
+<li>GAUCHE_MINUS - Gauce- configuration (-120 < angle < 0)</li>
+<li>NON_ROTAMERIC - Dihedral without SP3-SP3 bond</li>
+<li>INVALID - Invalid configuration, e.g. chi3 of ALA (doesnt exist...)</li>
+</ul>
+</td></tr></table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.GetRotamericConfiguration">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetRotamericConfiguration</code><span class="sig-paren">(</span><em>angle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetRotamericConfiguration" title="Permalink to this definition">¶</a></dt>
+<dd><p>Evaluates the <em>angle</em> according to the ranges specified for
+<a class="reference internal" href="#promod3.sidechain.DihedralConfiguration" title="promod3.sidechain.DihedralConfiguration"><code class="xref py py-class docutils literal"><span class="pre">DihedralConfiguration</span></code></a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle to be evaluated</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">TRANS, GAUCHE_PLUS or GAUCHE_MINUS.
+INVALID if <em>angle</em> is NaN.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.GetDihedralConfiguration">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetDihedralConfiguration</code><span class="sig-paren">(</span><em>entry</em>, <em>id</em>, <em>dihedral_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetDihedralConfiguration" title="Permalink to this definition">¶</a></dt>
+<dd><p>Estimates configuration of a sidechain dihedral angle in a specific
+<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> with the knowledge of its identity. This allows
+to also return NON_ROTAMERIC (e.g. chi2 for ASN).</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>entry</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – Sidechain dihedral angle comes from here</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer</li>
+<li><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Specifies angle (0 => chi1, ..., 3 => chi4)</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Result of <a class="reference internal" href="#promod3.sidechain.GetRotamericConfiguration" title="promod3.sidechain.GetRotamericConfiguration"><code class="xref py py-meth docutils literal"><span class="pre">GetRotamericConfiguration()</span></code></a> if specified
+angle is Rotameric, NON_ROTAMERIC if specified angle is
+valid and non rotameric, INVALID otherwise.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</div>
</div>
@@ -611,6 +681,7 @@ considered similar</li>
<li><a class="reference internal" href="#the-non-backbone-dependent-rotamer-library">The Non Backbone Dependent Rotamer Library</a></li>
<li><a class="reference internal" href="#the-backbone-dependent-rotamer-library">The Backbone Dependent Rotamer Library</a></li>
<li><a class="reference internal" href="#the-library-entry-type">The Library Entry Type</a></li>
+<li><a class="reference internal" href="#rotamer-configurations">Rotamer Configurations</a></li>
</ul>
</li>
</ul>
@@ -649,7 +720,7 @@ considered similar</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index 569714780b9983a1a1ad56afc95d30978e7b9a21..9527a393dae8afd9857efbf63596c446818cc2da 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Subrotamer Optimization — ProMod3 1.2.0 documentation</title>
+ <title>Subrotamer Optimization — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,7 +23,8 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="scoring - Loop Scoring" href="../scoring/index.html" />
<link rel="prev" title="Loading Rotamer Libraries" href="loading.html" />
@@ -125,7 +126,7 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/users.html b/doc/html/users.html
index cbda6deb9b452b831f78abc83db49bf749632748..241d36312acdc11c8a1c4680094ecb4d8239e3fb 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Documentation For Users — ProMod3 1.2.0 documentation</title>
+ <title>Documentation For Users — ProMod3 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.2.0',
+ VERSION: '1.3.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,9 +23,10 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <link rel="top" title="ProMod3 1.3.0 documentation" href="index.html" />
<link rel="next" title="Getting Started" href="gettingstarted.html" />
- <link rel="prev" title="Welcome To ProMod3’s Documentation!" href="index.html" />
+ <link rel="prev" title="ProMod3" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -54,6 +55,7 @@ scripts using the functionality of this library.</p>
</li>
<li class="toctree-l1"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="actions/index.html#building-models">Building models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="actions/index.html#sidechain-modelling">Sidechain Modelling</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="buildsystem.html">Building ProMod3</a><ul>
@@ -63,6 +65,11 @@ scripts using the functionality of this library.</p>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html#installing-project">Installing ProMod3</a></li>
</ul>
</li>
+<li class="toctree-l1"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="container/docker.html">Docker</a></li>
+<li class="toctree-l2"><a class="reference internal" href="container/singularity.html">Singularity</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="modelling/index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="modelling/pipeline.html">Modelling Pipeline</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/model_checking.html">Model Checking</a></li>
@@ -124,7 +131,7 @@ scripts using the functionality of this library.</p>
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter">Welcome To ProMod3’s Documentation!</a></li>
+ <li>Previous: <a href="index.html" title="previous chapter">ProMod3</a></li>
<li>Next: <a href="gettingstarted.html" title="next chapter">Getting Started</a></li>
</ul></li>
</ul>
@@ -151,7 +158,7 @@ scripts using the functionality of this library.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2018, ProMod3 authors.
+ ©2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/index.rst b/doc/index.rst
index 0699c60545cfc1014f4753e6f9a6b8647e822cc7..74cb15e8f60d131996ed5d81cc1b0950b4abf718 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -1,28 +1,41 @@
-.. ProMod3 documentation master file, created by
- sphinx-quickstart on Thu Oct 10 23:17:00 2013.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Welcome To ProMod3's Documentation!
-===================================
-
-Contents:
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+ProMod3
+=======
+
+ProMod3 is a modelling engine based on the OpenStructure [biasini2013]_
+computational structural biology framework that can perform all steps required
+to generate a protein model by homology. Its modular design aims at
+implementing flexible modelling pipelines and fast prototyping of novel
+algorithms.
+
+
+Documentation
+=============
.. toctree::
- :maxdepth: 2
+ :maxdepth: 2
- Users <users>
- Developers <developers>
+ Users <users>
.. toctree::
- :maxdepth: 1
-
- changelog
-
-
-Indices And Tables
-==================
+ :maxdepth: 1
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+ Developers <developers>
+ License <license>
+ References <references>
+ Changelog <changelog>
diff --git a/doc/license.rst b/doc/license.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1ff0971e35f8e7c9fdf99a1e6191409ae2a7e375
--- /dev/null
+++ b/doc/license.rst
@@ -0,0 +1,22 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+License
+=======
+
+
+
+.. literalinclude:: license.txt
diff --git a/doc/portableIO.rst b/doc/portableIO.rst
index d7122a208d30e34f4f4e47ce1e0890fe0f1454ef..a548e3c86400f7e09a9c7cc65c9c2fd7de19e8ce 100644
--- a/doc/portableIO.rst
+++ b/doc/portableIO.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
.. _portableIO:
Using Binary Files In |project|
@@ -387,9 +403,9 @@ The following binary files are currently in |project|:
- module ``sidechain``:
- - :file:`2010DunbrackLib.dat`
+ - :file:`bb_dep_lib.dat`
(:class:`~promod3.sidechain.BBDepRotamerLib`)
- - :file:`PenultimateLib.dat`
+ - :file:`lib.dat`
(:class:`~promod3.sidechain.RotamerLib`)
During the ``make`` process, portable versions of the files (stored in the
diff --git a/doc/references.rst b/doc/references.rst
new file mode 100644
index 0000000000000000000000000000000000000000..927de6ddbad6c032f0f760c17384e977d1ed31e9
--- /dev/null
+++ b/doc/references.rst
@@ -0,0 +1,82 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
+References
+==========
+
+.. [biasini2013] Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J,
+ Johner N, Schenk AD, Philippsen A and Schwede T (2013).
+ OpenStructure: an integrated software framework for
+ computational structural biology. Acta Cryst.
+
+.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003).
+ Cyclic coordinate descent: A robotics algorithm for protein
+ loop closure. Protein Sci.
+
+.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003).
+ A graph-theory algorithm for rapid protein side-chain
+ prediction. Protein Sci.
+
+.. [coutsias2005] Coutsias EA, Seok C, Wester MJ, Dill KA (2005).
+ Resultants and loop closure. International Journal of Quantum
+ Chemistry.
+
+.. [chakravarty1999] Chakravarty S, Varadarajan R (1999).
+ Residue depth: a novel parameter for the analysis of
+ protein structure and stability. Structure.
+
+.. [davis2006] Davis IW, Arendall WB, Richardson DC, Richardson JS (2006).
+ The backrub motion: how protein backbone shrugs when a sidechain
+ dances. Structure.
+
+.. [goldstein1994] Goldstein RF (1994).
+ Efficient rotamer elimination applied to protein side-chains
+ and related spin glasses. Biophys J.
+
+.. [Jones1999] Jones DT (1999).
+ Protein secondary structure prediction based on position-specific
+ scoring matrices. J. Mol. Biol.
+
+.. [kabsch1983] Kabsch W, Sander C (1983).
+ Dictionary of protein secondary structure: pattern recognition of
+ hydrogen-bonded and geometrical features. Biopolymers.
+
+.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009).
+ Improved prediction of protein side-chain conformations with
+ SCWRL4. Proteins.
+
+.. [leach1998] Leach AR, Lemon AP (1998).
+ Exploring the conformational space of protein side chains using
+ dead-end elimination and the A* algorithm. Proteins.
+
+.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011).
+ A smoothed backbone-dependent rotamer library for proteins
+ derived from adaptive kernel density estimates and
+ regressions. Structure.
+
+.. [soding2005] Söding J (2005).
+ Protein homology detection by HMM-HMM comparison.
+ Bioinformatics.
+
+.. [solis2006] Solis AD, Rackovsky S (2006). Improvement of statistical
+ potentials and threading score functions using information
+ maximization. Proteins.
+
+.. [zhou2005] Zhou H, Zhou Y (2005).
+ Fold Recognition by Combining Sequence Profiles Derived From
+ Evolution and From Depth-Dependent Structural Alignment of
+ Fragments. Proteins.
+
diff --git a/doc/tests/scripts/loop_structure_db.py b/doc/tests/scripts/loop_structure_db.py
index e8aca38a2d3b101be4a486209203f62116caf01b..09258a9236b4c8dc6e27dfb866c83df17c6067e4 100644
--- a/doc/tests/scripts/loop_structure_db.py
+++ b/doc/tests/scripts/loop_structure_db.py
@@ -18,8 +18,8 @@ structure_dir = "data"
prof_dir = "data"
# The naming of the files in the directories is e.g. 1CRN.pdb for
-# the structure and 1CRNA.hhm for the profile. Please note,
-# that the structure can contain several chains, whereas the hhm
+# the structure and 1CRNA.hhm for the profile.
+# The structure possibly contain several chains, whereas the hhm
# file is only for that specific chain.
structure_ids = ["1CRN", "1AKI"]
chain_names = ["A", "A"]
@@ -51,11 +51,14 @@ for s_id, ch_name in zip(structure_ids, chain_names):
# We now have two structures in both databases...
-
-# Please note, that there is no profile derived from structures
-# assigned yet to structure_db_one, the memory is only allocated
-# and set to zero. In structure_db_two, there'll never be stored a
-# structure profile as we did not initialize it accordingly.
+# Lets get a summary of whats actually in there
+structure_db_one.PrintStatistics()
+structure_db_two.PrintStatistics()
+
+# There is no profile derived from structures assigned to
+# structure_db_one yet, the memory is only allocated and set to
+# zero. In structure_db_two, there'll never be stored a structure
+# profile as we did not initialize it accordingly.
# However, we can still use its coordinates and residue depths to
# generate profiles!
# To demonstrate, we use our structure_db_two to derive profiles
diff --git a/doc/tests/scripts/modelling_monte_carlo.py b/doc/tests/scripts/modelling_monte_carlo.py
index b3d7d07b76016f7f9f3746a5ea683a4dd9630165..97ae54c956a0f0ca9d0315ef8fc80958eeeeff32 100644
--- a/doc/tests/scripts/modelling_monte_carlo.py
+++ b/doc/tests/scripts/modelling_monte_carlo.py
@@ -48,4 +48,4 @@ modelling.SampleMonteCarlo(mc_sampler, mc_closer, mc_scorer,
mc_cooler, 10000, bb_list, False, 0)
# save down the result
-io.SavePDB(bb_list.ToEntity(), "sampled_frag.pdb")
\ No newline at end of file
+io.SavePDB(bb_list.ToEntity(), "sampled_frag.pdb")
diff --git a/doc/tests/scripts/sidechain_steps.py b/doc/tests/scripts/sidechain_steps.py
index aa903d2477f57fcdaee574060afddb3b6c4a013e..854ff709f9b88187d7db704bc681a2132740a6df 100644
--- a/doc/tests/scripts/sidechain_steps.py
+++ b/doc/tests/scripts/sidechain_steps.py
@@ -4,7 +4,7 @@ from promod3 import sidechain
# load a protein
prot = io.LoadPDB('data/1CRN.pdb')
# load rotamer library
-library = sidechain.LoadDunbrackLib()
+library = sidechain.LoadBBDepLib()
# we need a rotamer constructor to create any rotamers or
# frame residues
rot_constructor = sidechain.SCWRLRotamerConstructor(False)
@@ -56,6 +56,9 @@ for i,r in enumerate(prot.residues):
r, rotamer_ids[i], i, library,
torsion_angles[i][0], torsion_angles[i][1])
+ # calculate pairwise energies towards the rigid frame
+ # the values will be stored and used by the solving algorithm
+ # later on when considering self energies
rot_group.SetFrameEnergy(frame)
# remove super unlikely rotamer in rotamer group
# e.g. those who clash with the frame
diff --git a/doc/tests/test_doctests.py b/doc/tests/test_doctests.py
index bd9d89a001f8f883e1804a08bf7dd3d48dbbf009..42d8071136c6a94d82d91cdcaded36bdcf36d819 100644
--- a/doc/tests/test_doctests.py
+++ b/doc/tests/test_doctests.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Test example codes from documentation.
Each example code is given as a python script in scripts-folder and may use
diff --git a/doc/users.rst b/doc/users.rst
index 7764b3750cebd2a03cc65dffecb0f9170092cae9..3b11ff195d4009fcf10bea662e5f54367150d90c 100644
--- a/doc/users.rst
+++ b/doc/users.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Documentation For Users
=======================
@@ -12,6 +28,7 @@ Contents:
gettingstarted
actions/index
buildsystem
+ container/index
modelling/index
sidechain/index
scoring/index
diff --git a/extras/code_generation/amino_acid_atoms.py b/extras/code_generation/amino_acid_atoms.py
index 87e562d73a9b9cd27f82450886aae3c2eec842d6..be8d8cfce8ec1cd7fe33a4ebba96c5a0b09f4161 100644
--- a/extras/code_generation/amino_acid_atoms.py
+++ b/extras/code_generation/amino_acid_atoms.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Code generation of code snippets for heavy atom part of amino_acid_atoms."""
from ost import conop
diff --git a/extras/code_generation/amino_acid_atoms_hydrogens.py b/extras/code_generation/amino_acid_atoms_hydrogens.py
index 5150f3576e808d326656240b6072326c62179718..52c8c6cc44179b6adb4c9863d18f5b723d7918ad 100644
--- a/extras/code_generation/amino_acid_atoms_hydrogens.py
+++ b/extras/code_generation/amino_acid_atoms_hydrogens.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Code generation of code snippets for hydrogen part of amino_acid_atoms."""
import promod3
diff --git a/extras/code_generation/backbone_score_unittest.py b/extras/code_generation/backbone_score_unittest.py
index fd66538682832f42877ac54d2db4037504e9bc62..67b0af45a8ad03f558b75dd3a5859cb218d04704 100644
--- a/extras/code_generation/backbone_score_unittest.py
+++ b/extras/code_generation/backbone_score_unittest.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from qmean import *
import os
from promod3 import loop
diff --git a/extras/code_generation/hydrogen_rules.py b/extras/code_generation/hydrogen_rules.py
index 1142ebb3266ab194d57c53181fc23e7a2f929928..cdcac7e2f869b0b598c3d97d9c56b3916173349e 100644
--- a/extras/code_generation/hydrogen_rules.py
+++ b/extras/code_generation/hydrogen_rules.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Code generation of code snippets for hydrogen_constructor."""
from promod3 import loop
diff --git a/extras/code_generation/ideal_bb_param.py b/extras/code_generation/ideal_bb_param.py
index 348519eae01252878ab2e76275e4bc5042e68d03..b9ceef405a54ca9f8169e0506a4606170c8d8fd2 100644
--- a/extras/code_generation/ideal_bb_param.py
+++ b/extras/code_generation/ideal_bb_param.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import conop
import numpy as np
diff --git a/extras/code_generation/sidechain_atom_rule_lookup.py b/extras/code_generation/sidechain_atom_rule_lookup.py
index fe4ba9157cb27c4457c1890f50c23f91e78b161b..684d9682f2368be99359bd3ea5f6aec78c392dd4 100644
--- a/extras/code_generation/sidechain_atom_rule_lookup.py
+++ b/extras/code_generation/sidechain_atom_rule_lookup.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
from ost import conop
from ost.mol import mm
diff --git a/extras/data_generation/all_atom_scorer/create_default_aa_scorer.py b/extras/data_generation/all_atom_scorer/create_default_aa_scorer.py
index 9f390f8531c2dff964ec13578ae732c28c134614..92c786e6c5bfe5bab02bea88d33938afb2c7ecd4 100644
--- a/extras/data_generation/all_atom_scorer/create_default_aa_scorer.py
+++ b/extras/data_generation/all_atom_scorer/create_default_aa_scorer.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import ost
from qmean import *
from promod3 import scoring, loop
diff --git a/extras/data_generation/backbone_scorer/create_default_scorer.py b/extras/data_generation/backbone_scorer/create_default_scorer.py
index 8ffd8de2ca2fe8f24dc99d2b5a07dcb91d8a74fb..585e00c93837fd21e9d9e8b9a82c8bfdd13c6db9 100644
--- a/extras/data_generation/backbone_scorer/create_default_scorer.py
+++ b/extras/data_generation/backbone_scorer/create_default_scorer.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import ost
from qmean import *
from promod3 import scoring
diff --git a/extras/data_generation/force_field/create_charmm_force_field.py b/extras/data_generation/force_field/create_charmm_force_field.py
index 1ba4b09ca9e5ac84c8f27fe5bfc68d4be52b6eb9..8ec3d23813a77ee30603529bb08fd29d76931412 100644
--- a/extras/data_generation/force_field/create_charmm_force_field.py
+++ b/extras/data_generation/force_field/create_charmm_force_field.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
from ost import conop, io
from ost.mol import mm
diff --git a/extras/data_generation/frag_db/build_frag_db.py b/extras/data_generation/frag_db/build_frag_db.py
index 5faa5ad22d6b209846544ddbc1900aa43e5c7b36..b58530ad80e3569d08dec153693d96e84110ece9 100644
--- a/extras/data_generation/frag_db/build_frag_db.py
+++ b/extras/data_generation/frag_db/build_frag_db.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
diff --git a/extras/data_generation/portable_binaries/convert_data.cc b/extras/data_generation/portable_binaries/convert_data.cc
index 447f1b80d5081e51e3d626e8b188f13d2e49fe51..4b0e3483003b8e1187078457955f83e28e2e1795 100644
--- a/extras/data_generation/portable_binaries/convert_data.cc
+++ b/extras/data_generation/portable_binaries/convert_data.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
// Test code for promod3
#include <promod3/loop/loop_object_loader.hh>
@@ -386,8 +402,8 @@ int main() {
// convert_frag_db("frag_db.dat");
// convert_structure_db("structure_db.dat");
// convert_structure_db("structure_db_small.dat", "structure_db_new.dat");
- // convert_BBDepRotamerLib("2010DunbrackLib.dat");
- // convert_RotamerLib("PenultimateLib.dat");
+ // convert_BBDepRotamerLib("bb_dep_lib.dat");
+ // convert_RotamerLib("lib.dat");
/////////////////////////////////////////////////////////////
// MAKE PORTABLE VERSIONS
@@ -408,10 +424,10 @@ int main() {
portable_structure_db("src_data/structure_db_small.dat",
"structure_db_new.dat",
"p_data/portable_structure_db_small.dat");
- portable_BBDepRotamerLib("2010DunbrackLib.dat",
- "p_data/portable_2010DunbrackLib.dat");
- portable_RotamerLib("PenultimateLib.dat",
- "p_data/portable_PenultimateLib.dat");
+ portable_BBDepRotamerLib("bb_dep_lib.dat",
+ "p_data/portable_bb_dep_lib.dat");
+ portable_RotamerLib("lib.dat",
+ "p_data/portable_lib.dat");
return 0;
}
diff --git a/extras/data_generation/rotamer_library/CreateDunbrackLibrary.py b/extras/data_generation/rotamer_library/CreateDunbrackLibrary.py
index 7d3d65c805aa106f455412a9a61b0ccbe19eb175..7b2a53ada798b63e6f42c8cef8e67183794320b7 100644
--- a/extras/data_generation/rotamer_library/CreateDunbrackLibrary.py
+++ b/extras/data_generation/rotamer_library/CreateDunbrackLibrary.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import sidechain
# the file is available here: http://dunbrack.fccc.edu/bbdep2010/
diff --git a/extras/data_generation/rotamer_library/README b/extras/data_generation/rotamer_library/README
new file mode 100644
index 0000000000000000000000000000000000000000..a387512ede267d0ec674f34a9765e6f9b5001d4e
--- /dev/null
+++ b/extras/data_generation/rotamer_library/README
@@ -0,0 +1,233 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+You can get rotamer libraries from several sources.
+
+#############################
+# The Dunbrack 2010 Library #
+#############################
+
+You can apply for a licence here: http://dunbrack.fccc.edu/bbdep2010/
+You'll get the library in several different options. The options
+we can read in are SimpleOpt1 and SimpleOpt2.
+Adapt the according path in CreateDunbrackLibrary.py and run it to read
+the provided file and dump it as a binary that can be read by ProMod3.
+
+
+#################################
+# The ProMod3 Rotamer Libraries #
+#################################
+
+ProMod3 comes with basic functionality to generate backbone dependent
+and backbone independent rotamer libraries. Both types of rotamer libraries are
+available in default binary versions and can directly be loaded by the user.
+The following sections guide you through the process of building such libraries.
+Feel free to adapt any step to get your custom library.
+
+
+####################
+# FETCH STRUCTURES #
+####################
+
+No matter whether you want to generate a backbone dependent or independent
+library: you need data
+
+ost fetch_data.py
+
+This script uses a pisces file downloaded from
+http://dunbrack.fccc.edu/Guoli/pisces_download.php
+and stores following information for each residue in a csv file:
+
+ * residue name
+ * phi / psi backbone dihedral angles in radians
+ * sidechain dihedral angles in radians
+ * the configuration of sidechain dihedral angles,
+ one of [GAUCHE_MINUS, GAUCHE_PLUS, TRANS, NON_ROTAMERIC, INVALID]
+
+Residues from which you'll get data:
+ARG, ASN, ASP, GLN, GLU, LYS, SER, CYH, CYD, CYS, MET, TRP, TYR, THR, VAL, ILE,
+LEU, CPR, TPR, PRO, HIS, PHE
+
+Special cases:
+
+ CYH, CYD, CYS:
+
+ CYS contains the data for all cysteins. CYD only contains data from cysteins
+ that build a disulfid bond. Criteria: The SG atom from another cysteins is
+ within 2.5A of its own SG atom. Cysteins for which this criteria is not
+ fulfilled are added to CYH
+
+ CPR, TPR, PRO:
+
+ PRO contains the data for all prolines. Prolines with a trans-omega
+ backbone dihedral are added to TPR and prolines with a cis-omega
+ backbone dihedral are added to CPR.
+
+The behaviour of the script can be controlled by setting the documented
+variables on the top.
+Only data from residues will be dumped where everything is available,
+e.g. terminal residues without valid phi/psi or residues without
+all their sidechain atoms will be skipped.
+
+####################################################
+# OPTION ONE: BACKBONE INDEPENDENT ROTAMER LIBRARY #
+####################################################
+
+ost do_lib.py <data> <out_file_name>
+
+Loads csv generated by fetch_data.py, determines a set of rotamers for each
+type of amino acids and dumps a full backbone independent library to disk.
+
+The general approach for each amino acid is to look at each possible
+combination of rotameric configurations and obtain a rotamer by simply
+calculating the mean and standard deviation of all datapoints with
+this particular configuration. The probability of that rotamer is the number
+of data points with this configuration divided by the total number of
+datapoints for this amino acid.
+
+The situation becomes more difficult for the so called non rotameric dihedral
+angles.
+Non rotameric dihedral angles are: ASN(chi2), ASP(chi2), PHE(chi2), TYR(chi2),
+HIS(chi2), TRP(chi2), GLN(chi3) and GLU(chi3).
+
+The approach used here is exaclty the same as described for option two:
+backbone dependent rotamer library with the exception that there is no
+weighted mean etc, each datapoint contributes equally to the mean and
+std.
+
+##################################################
+# OPTION TWO: BACKBONE DEPENDENT ROTAMER LIBRARY #
+##################################################
+
+ost do_bb_dep_lib.py <data> <aa_name>
+
+This script uses the csv generated by fetch data (provided as data parameter)
+and the name of any amino acid (provided as aa_name parameter) to generate
+a backbone dependent rotamer library for that amino acid and dumps it as
+<aa_name>.txt.
+
+Some theory (You don't have to read this if you believe we're doing
+ awesome science...):
+
+In order to get weighted distributions etc. we rely on the Mises distribution
+that can considered to be a circular gaussian:
+p(x,y) = 1.0/(4*pi*pi*i0(kappa)*i0(kappa)) * exp(kappa*(cos(x-x0)+sin(y-y0)))
+where i0() is the modified Bessel function of first order and (x0, y0) the mean.
+kappa is a measure of concentration.
+
+This distribution is used to determine weights that are used in:
+ * calculating the probability of a rotamer configuration given the backbone
+ dihedral angles
+ * calculating sidechain dihedral angles given the backbone dihedral angles
+
+Every datapoint contributes to a final value with a weight. These weights depend
+on the distance to the query point. In case of many data close to the query point,
+only close data points should contribute. If the region around the query data
+point is only sparsely populated, data points that are a bit further away should
+also contribute. We achieve this by using position dependent kappa values for
+the underlying Mises distribution.
+
+For large kappas, the Mises distribution is basically a repetitive normal
+distribution with the relation: sigma*sigma = 1.0/kappa
+=> r = sqrt(1.0/kappa) corresponds to the radius of a circle around the mean,
+that covers approximately 67% of the density.
+kappa can be estimated such that this "circle" includes exactly N data points.
+
+We sample the backbone dihedral space with n_bins x n_bins bins, where n_bins
+can be set on top of the script. For each bin, we estimate two things:
+
+ * Estimate the probability of every possible rotamer configuration
+ * Estimate mean and standard deviation of every sidechain dihedral angle
+
+Step one: Estimation of Rotamer Probabilities
+
+For every bin, a kappa is estimated as outlined above (the whole circle
+story with N). For amino acids with many dihedral angles, N should be larger
+to guarantee enough sampling. N can be controlled on top of the script by
+adjusting the p_threshold_67 parameter.
+
+The probability for each rotamer configuration is then estimated with a
+histogram approach where every possible configuration has one bin.
+Every datapoint adds a value to its corresponding bin.
+This value is the evaluation of the Mises distribution for that data point
+with the query bin as mean and the previously determined kappa.
+Subsequent normalization leads to the final probabilities.
+
+Step two: Estimation of mean and standard deviations of sidechain dihedral
+angles for each rotamer configuration:
+
+This is a tougher business, as we have to deal with rotameric dihedral angles
+and non rotameric dihedral angles...
+Non rotameric dihedral angles are: ASN(chi2), ASP(chi2), PHE(chi2), TYR(chi2),
+HIS(chi2), TRP(chi2), GLN(chi3) and GLU(chi3) and will be discussed later.
+
+First of all, we again determine our query bin dependent kappa but this time
+N only relates to the data points with the same configuration. N can be
+controlled by adjusting the chi_threshold_67 parameter on top of the script.
+And again, we determine a weight for each datapoint with the same configuration
+based on the mises distribution. All those datapoints then contribute to a
+weighted mean and weighted standard deviation as estimated in the
+GetChiStats function of the do_bb_dep_lib.py script.
+
+As a last step we have to determine the mean and std values for non rotameric
+sidechain dihedral angles. For this we first estimate a full probability density
+function (pdf) of chi (the non-rotameric sidechain dihedral angle).
+The pdf is based on a histogram, where we simply add up the Mises based weights
+of all data points with the same rotameric configuration at the according
+histogram position.
+This histogram is then smoothed with a circular gaussian filter with std
+non_rotameric_smooth_std and finally normalized. non_rotameric_smooth_std
+can be set on top of the script.
+The full non-rotameric chi angle is then sampled in a binned manner, where the
+center of the first bin is determined by the mode of the initial pdf.
+The number of bins can be controlled by the parameter non_rotameric_sampling
+on top of the script.
+For each bin we estimate a probability, a mean and a standard deviation
+based on the underlying distribution. See the function GetNonRotChiStats
+function for more details. Given these values we can then determine all
+possible rotamers.
+E.g. ASN has one rotameric dihedral angle => 3 possible rotameric
+configurations. Lets say the trans configuration has probability p.
+We then do the described sampling of the non-rotamerich chi2 angle.
+with default parametrization, this gives a total of 12 possible chi2
+configurations. Each with a probability p_chi2_n, a mean m_chi2_n and a standard
+deviation std_chi2_n. The probability of a certain rotamer n is then p*p_chi2_n.
+
+###############################
+# DO THIS FOR ALL AMINO ACIDS #
+###############################
+
+The file rotamer_lib_creation.cmd contains all commands required to generate the
+rotamers for all amino acids. With a working ProMod3 installation and the csv
+file generated at the very beginning, you can do:
+source rotamer_lib_creation.cmd
+
+##############
+# READ IT IN #
+##############
+
+You should now have a file for every amino acid... you can concatenate them
+with the bash script: concatenate_library.sh
+The resulting file can be loaded with ProMod3 and converted to binary version:
+
+import sidechain
+lib = sidechain.ReadDunbrackFile("bb_dep_lib.txt")
+
+And then dump it in binary format:
+lib.Save("my_awesome_rotamer_library.dat")
+
+This file can be loaded again with:
+lib = sidechain.BBDepRotamerLib.Load("my_awesome_rotamer_library.dat")
diff --git a/extras/data_generation/rotamer_library/concatenate_library.sh b/extras/data_generation/rotamer_library/concatenate_library.sh
new file mode 100755
index 0000000000000000000000000000000000000000..616d6dc25fa4be1427a27cf657c31c752012117f
--- /dev/null
+++ b/extras/data_generation/rotamer_library/concatenate_library.sh
@@ -0,0 +1 @@
+cat ARG.txt <(echo) ASN.txt <(echo) ASP.txt <(echo) GLN.txt <(echo) GLU.txt <(echo) LYS.txt <(echo) SER.txt <(echo) CYH.txt <(echo) CYD.txt <(echo) CYS.txt <(echo) MET.txt <(echo) TRP.txt <(echo) TYR.txt <(echo) THR.txt <(echo) VAL.txt <(echo) ILE.txt <(echo) LEU.txt <(echo) CPR.txt <(echo) TPR.txt <(echo) PRO.txt <(echo) HIS.txt <(echo) PHE.txt > bb_dep_lib.txt
diff --git a/extras/data_generation/rotamer_library/create_penultimate.py b/extras/data_generation/rotamer_library/create_penultimate.py
deleted file mode 100644
index 0ea845b8e987a4b4ddd4d2c0c5f4da104733c602..0000000000000000000000000000000000000000
--- a/extras/data_generation/rotamer_library/create_penultimate.py
+++ /dev/null
@@ -1,1384 +0,0 @@
-from promod3 import sidechain
-import numpy as np
-import traceback
-
-def ToRadian(deg_angle):
- return float(deg_angle)/180*np.pi
-
-lib = sidechain.RotamerLib()
-lib_alpha = sidechain.RotamerLib()
-lib_beta = sidechain.RotamerLib()
-lib_other = sidechain.RotamerLib()
-
-data = open("penultimate.csv",'r').readlines()
-
-
-#handling arginine
-
-print
-print
-print "ARG"
-
-for i in range(5,41):
- temp = data[i].split(',')
-
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
- chi3 = int(temp[10])
- chi4 = int(temp[12])
-
- sig1 = int(temp[14])
- sig2 = int(temp[15])
- sig3 = int(temp[16])
- sig4 = int(temp[17])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "ARG fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
-
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- lib.AddRotamer(sidechain.ARG,entry)
- lib_alpha.AddRotamer(sidechain.ARG,entry_alpha)
- lib_beta.AddRotamer(sidechain.ARG,entry_beta)
- lib_other.AddRotamer(sidechain.ARG,entry_other)
-
-
-print
-print
-print "LYS"
-
-#handling Lysine
-for i in range(42,71):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
- chi3 = int(temp[10])
- chi4 = int(temp[12])
-
- sig1 = int(temp[14])
- sig2 = int(temp[15])
- sig3 = int(temp[16])
- sig4 = int(temp[17])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "LYS fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.LYS,entry)
- lib_alpha.AddRotamer(sidechain.LYS,entry_alpha)
- lib_beta.AddRotamer(sidechain.LYS,entry_beta)
- lib_other.AddRotamer(sidechain.LYS,entry_other)
-
-
-print
-print
-print "MET"
-
-#handling Methionine
-for i in range(72,87):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
- chi3 = int(temp[10])
-
- sig1 = int(temp[13])
- sig2 = int(temp[14])
- sig3 = int(temp[15])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "MET fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.MET,entry)
- lib_alpha.AddRotamer(sidechain.MET,entry_alpha)
- lib_beta.AddRotamer(sidechain.MET,entry_beta)
- lib_other.AddRotamer(sidechain.MET,entry_other)
-
-print
-print
-print "GLU"
-
-#handling Glutamate
-for i in range(88,98):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
- chi3 = int(temp[10])
-
- sig1 = int(temp[13])
- sig2 = int(temp[14])
- sig3 = int(temp[15])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "GLU fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.GLU,entry)
- lib_alpha.AddRotamer(sidechain.GLU,entry_alpha)
- lib_beta.AddRotamer(sidechain.GLU,entry_beta)
- lib_other.AddRotamer(sidechain.GLU,entry_other)
-
-
-print
-print
-print "GLN"
-
-#handling Glutamine
-for i in range(99,110):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
- chi3 = int(temp[10])
-
- sig1 = int(temp[13])
- sig2 = int(temp[14])
- sig3 = int(temp[15])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "GLN fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.GLN,entry)
- lib_alpha.AddRotamer(sidechain.GLN,entry_alpha)
- lib_beta.AddRotamer(sidechain.GLN,entry_beta)
- lib_other.AddRotamer(sidechain.GLN,entry_other)
-
-
-print
-print
-print "ASP"
-
-
-#handling Aspartate
-for i in range(111,118):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
-
- sig1 = int(temp[13])
- sig2 = int(temp[14])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "ASP fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.ASP,entry)
- lib_alpha.AddRotamer(sidechain.ASP,entry_alpha)
- lib_beta.AddRotamer(sidechain.ASP,entry_beta)
- lib_other.AddRotamer(sidechain.ASP,entry_other)
-
-print
-print
-print "ASN"
-
-#handling Asparagine
-for i in range(119,128):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
-
- sig1 = int(temp[13])
- sig2 = int(temp[14])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "ASN fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.ASN,entry)
- lib_alpha.AddRotamer(sidechain.ASN,entry_alpha)
- lib_beta.AddRotamer(sidechain.ASN,entry_beta)
- lib_other.AddRotamer(sidechain.ASN,entry_other)
-
-print
-print
-print "ILE"
-
-#handling IsoLeucine
-for i in range(129,138):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
-
- sig1 = int(temp[11])
- sig2 = int(temp[12])
-
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "ILE fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.ILE,entry)
- lib_alpha.AddRotamer(sidechain.ILE,entry_alpha)
- lib_beta.AddRotamer(sidechain.ILE,entry_beta)
- lib_other.AddRotamer(sidechain.ILE,entry_other)
-
-
-print
-print
-print "LEU"
-
-#handling Leucine
-for i in range(139,146):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
-
- sig1 = int(temp[11])
- sig2 = int(temp[12])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "LEU fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.LEU,entry)
- lib_alpha.AddRotamer(sidechain.LEU,entry_alpha)
- lib_beta.AddRotamer(sidechain.LEU,entry_beta)
- lib_other.AddRotamer(sidechain.LEU,entry_other)
-
-
-
-print
-print
-print "HIS"
-
-#handling Histidine
-for i in range(147,157):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
-
- sig1 = int(temp[11])
- sig2 = int(temp[12])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "HIS fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.HIS,entry)
- lib_alpha.AddRotamer(sidechain.HIS,entry_alpha)
- lib_beta.AddRotamer(sidechain.HIS,entry_beta)
- lib_other.AddRotamer(sidechain.HIS,entry_other)
-
-
-print
-print
-print "TRP"
-
-#handling Tryptophane
-for i in range(158,167):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
-
- sig1 = int(temp[11])
- sig2 = int(temp[12])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "TRP fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.TRP,entry)
- lib_alpha.AddRotamer(sidechain.TRP,entry_alpha)
- lib_beta.AddRotamer(sidechain.TRP,entry_beta)
- lib_other.AddRotamer(sidechain.TRP,entry_other)
-
-
-print
-print
-print "TYR"
-
-#handling Tyrosine
-for i in range(168,174):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
-
- sig1 = int(temp[11])
- sig2 = int(temp[12])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "TYR fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.TYR,entry)
- lib_alpha.AddRotamer(sidechain.TYR,entry_alpha)
- lib_beta.AddRotamer(sidechain.TYR,entry_beta)
- lib_other.AddRotamer(sidechain.TYR,entry_other)
-
-
-print
-print
-print "PHE"
-
-#handling Phenylalanine
-for i in range(175,181):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
- chi2 = int(temp[8])
-
- sig1 = int(temp[11])
- sig2 = int(temp[12])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "PHE fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.PHE,entry)
- lib_alpha.AddRotamer(sidechain.PHE,entry_alpha)
- lib_beta.AddRotamer(sidechain.PHE,entry_beta)
- lib_other.AddRotamer(sidechain.PHE,entry_other)
-
-print
-print
-print "PRO"
-
-#handling Proline
-for i in range(182,187):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
-
- sig1 = int(temp[11])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "PRO fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.PRO,entry)
- lib_alpha.AddRotamer(sidechain.PRO,entry_alpha)
- lib_beta.AddRotamer(sidechain.PRO,entry_beta)
- lib_other.AddRotamer(sidechain.PRO,entry_other)
-
-
-print
-print
-print "THR"
-
-#handling Threonine
-for i in range(188,193):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
-
- sig1 = int(temp[9])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "THR fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.THR,entry)
- lib_alpha.AddRotamer(sidechain.THR,entry_alpha)
- lib_beta.AddRotamer(sidechain.THR,entry_beta)
- lib_other.AddRotamer(sidechain.THR,entry_other)
-
-
-
-print
-print
-print "VAL"
-
-#handling Valine
-for i in range(194,199):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
-
- sig1 = int(temp[9])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "VAL fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.VAL,entry)
- lib_alpha.AddRotamer(sidechain.VAL,entry_alpha)
- lib_beta.AddRotamer(sidechain.VAL,entry_beta)
- lib_other.AddRotamer(sidechain.VAL,entry_other)
-
-print
-print
-print "SER"
-
-#handling Serine
-for i in range(200,205):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
-
- sig1 = int(temp[9])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "SER fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.SER,entry)
- lib_alpha.AddRotamer(sidechain.SER,entry_alpha)
- lib_beta.AddRotamer(sidechain.SER,entry_beta)
- lib_other.AddRotamer(sidechain.SER,entry_other)
-
-
-
-print
-print
-print "CYS"
-
-#handling Cysteine
-for i in range(206,len(data)):
- temp = data[i].split(',')
- chi1 = float('NaN')
- chi2 = float('NaN')
- chi3 = float('NaN')
- chi4 = float('NaN')
-
- sig1 = float('NaN')
- sig2 = float('NaN')
- sig3 = float('NaN')
- sig4 = float('NaN')
-
- try:
- chi1 = int(temp[6])
-
- sig1 = int(temp[9])
- except:
- #some rotamers have really low probability and consequently no
- #no mode values. This results in int(' ') => error => neglect the shit
- print "CYS fail..."
- continue
-
- p = 0.0
- p_alpha = 0.0
- p_beta = 0.0
- p_other = 0.0
-
- str_p = temp[2]
- if "<1%" in str_p:
- p = 0.5
- else:
- p = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[3]
- if "<1%" in str_p:
- p_alpha = 0.5
- else:
- p_alpha = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[4]
- if "<1%" in str_p:
- p_beta = 0.5
- else:
- p_beta = float(str_p.strip().strip('%').strip('<'))
-
- str_p = temp[5]
- if "<1%" in str_p:
- p_other = 0.5
- else:
- p_other = float(str_p.strip().strip('%').strip('<'))
-
- print p, p_alpha, p_beta, p_other, chi1,chi2,chi3,chi4,sig1,sig2,sig3,sig4
-
- entry = sidechain.RotamerLibEntry(p*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_alpha = sidechain.RotamerLibEntry(p_alpha*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_beta = sidechain.RotamerLibEntry(p_beta*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
- entry_other = sidechain.RotamerLibEntry(p_other*0.01,ToRadian(chi1),ToRadian(chi2),ToRadian(chi3),ToRadian(chi4),
- ToRadian(sig1),ToRadian(sig2),ToRadian(sig3),ToRadian(sig4))
-
- lib.AddRotamer(sidechain.CYS,entry)
- lib_alpha.AddRotamer(sidechain.CYS,entry_alpha)
- lib_beta.AddRotamer(sidechain.CYS,entry_beta)
- lib_other.AddRotamer(sidechain.CYS,entry_other)
-
-
-
-lib.Save("Penultimate.dat")
-lib_alpha.Save("PenultimateAlpha.dat")
-lib_beta.Save("PenultimateBeta.dat")
-lib_other.Save("PenultimateOther.dat")
-
-
-
diff --git a/extras/data_generation/rotamer_library/cullpdb_pc40_res1.6_R0.25_d180913_chains5877 b/extras/data_generation/rotamer_library/cullpdb_pc40_res1.6_R0.25_d180913_chains5877
new file mode 100644
index 0000000000000000000000000000000000000000..6b5908afece2a83b63af926d2f2b2bd3d0e28eca
--- /dev/null
+++ b/extras/data_generation/rotamer_library/cullpdb_pc40_res1.6_R0.25_d180913_chains5877
@@ -0,0 +1,5878 @@
+IDs length Exptl. resolution R-factor FreeRvalue
+1A2PC 110 XRAY 1.500 0.12 0.17
+1A62A 130 XRAY 1.550 0.22 0.25
+1A7SA 225 XRAY 1.120 0.16 0.19
+1A8DA 452 XRAY 1.570 0.19 0.26
+1ABAA 87 XRAY 1.450 0.17 1.00
+1AH7A 245 XRAY 1.501 0.20 0.23
+1AHOA 64 XRAY 0.960 0.16 1.00
+1AMTC 21 XRAY 1.500 0.15 1.00
+1AOEA 192 XRAY 1.600 0.15 1.00
+1ATGA 231 XRAY 1.200 0.16 0.18
+1B0BA 142 XRAY 1.430 0.12 0.17
+1B0UA 262 XRAY 1.500 0.18 0.21
+1B5EA 246 XRAY 1.600 0.19 0.21
+1B67B 68 XRAY 1.480 0.19 0.27
+1B6GA 310 XRAY 1.150 0.10 0.14
+1B9OA 123 XRAY 1.150 0.12 0.16
+1BGFA 124 XRAY 1.450 0.19 0.22
+1BKRA 109 XRAY 1.100 0.14 0.19
+1BRTA 277 XRAY 1.500 0.14 0.16
+1BTEA 97 XRAY 1.500 0.18 0.22
+1BTKB 169 XRAY 1.600 0.23 0.28
+1BX7A 55 XRAY 1.200 0.18 0.23
+1BYIA 224 XRAY 0.970 0.12 1.00
+1C0PA 363 XRAY 1.200 0.12 0.15
+1C1DA 355 XRAY 1.250 0.20 0.24
+1C1KA 217 XRAY 1.450 0.20 0.25
+1C4QD 69 XRAY 1.520 0.17 0.19
+1C52A 131 XRAY 1.280 0.19 0.22
+1C5EB 95 XRAY 1.100 0.10 0.13
+1C75A 71 XRAY 0.970 0.12 1.00
+1C7KA 132 XRAY 1.000 0.15 0.18
+1C9OB 66 XRAY 1.170 0.12 0.18
+1CC8A 73 XRAY 1.020 0.14 0.17
+1CCWC 137 XRAY 1.600 0.14 0.17
+1CCWD 483 XRAY 1.600 0.14 0.17
+1CG5A 141 XRAY 1.600 0.19 0.23
+1CG5B 141 XRAY 1.600 0.19 0.23
+1CRUB 454 XRAY 1.500 0.18 0.20
+1CS1B 386 XRAY 1.500 0.20 0.26
+1CSEI 70 XRAY 1.200 0.18 1.00
+1CXQA 162 XRAY 1.020 0.13 0.16
+1CY5A 97 XRAY 1.300 0.17 0.20
+1D2SA 170 XRAY 1.550 0.21 0.25
+1D4OA 184 XRAY 1.210 0.17 0.22
+1D4TA 104 XRAY 1.100 0.13 0.17
+1D5TA 433 XRAY 1.040 0.17 0.21
+1D8WD 426 XRAY 1.600 0.18 0.24
+1DBWB 126 XRAY 1.600 0.19 0.22
+1DCIA 275 XRAY 1.500 0.18 0.20
+1DCSA 311 XRAY 1.300 0.13 0.15
+1DD9A 338 XRAY 1.600 0.23 0.28
+1DFMA 223 XRAY 1.500 0.19 0.22
+1DG6A 191 XRAY 1.300 0.14 0.20
+1DI6A 195 XRAY 1.450 0.19 0.21
+1DJ0A 264 XRAY 1.500 0.16 0.22
+1DK8A 147 XRAY 1.570 0.17 0.20
+1DLWA 116 XRAY 1.540 0.13 0.18
+1DP7P 76 XRAY 1.500 0.19 0.23
+1DS1A 324 XRAY 1.080 0.14 0.17
+1DYPA 271 XRAY 1.540 0.18 0.19
+1DYQA 234 XRAY 1.500 0.19 0.24
+1DYSA 348 XRAY 1.600 0.18 0.24
+1DZKA 157 XRAY 1.480 0.23 0.24
+1E29A 135 XRAY 1.210 0.15 0.21
+1E2WA 251 XRAY 1.600 0.20 0.23
+1E4MM 501 XRAY 1.200 0.12 0.14
+1E58A 249 XRAY 1.250 0.12 0.17
+1E5KA 201 XRAY 1.350 0.18 0.21
+1E6UA 321 XRAY 1.450 0.14 0.17
+1E7LA 157 XRAY 1.320 0.14 0.19
+1E9GA 286 XRAY 1.150 0.14 1.00
+1EAJB 126 XRAY 1.350 0.14 0.15
+1EAQB 140 XRAY 1.250 0.15 0.17
+1EAZA 125 XRAY 1.400 0.17 0.23
+1EB6A 177 XRAY 1.000 0.10 0.13
+1EDGA 380 XRAY 1.600 0.19 0.22
+1EGWC 77 XRAY 1.500 0.21 0.23
+1EJ0A 180 XRAY 1.500 0.20 0.23
+1EJ8A 140 XRAY 1.550 0.20 0.26
+1EKQA 272 XRAY 1.500 0.22 0.25
+1ELKB 157 XRAY 1.500 0.20 0.22
+1ELUA 390 XRAY 1.550 0.22 0.26
+1ELWB 118 XRAY 1.600 0.18 0.21
+1EN2A 89 XRAY 1.400 0.20 0.20
+1EP0A 185 XRAY 1.500 0.18 0.21
+1ES5A 262 XRAY 1.400 0.21 0.24
+1ES9A 232 XRAY 1.300 0.19 0.22
+1ET1B 34 XRAY 0.900 0.14 0.14
+1EU1A 780 XRAY 1.300 0.12 0.14
+1EUVA 221 XRAY 1.600 0.19 0.25
+1EUWA 152 XRAY 1.050 0.14 0.16
+1EVLD 401 XRAY 1.550 0.22 0.23
+1EW0A 130 XRAY 1.400 0.20 0.27
+1EW4A 106 XRAY 1.400 0.19 0.21
+1EYVB 156 XRAY 1.600 0.19 0.23
+1EZGB 84 XRAY 1.400 0.16 0.20
+1F0LB 535 XRAY 1.550 0.19 0.24
+1F1EA 154 XRAY 1.370 0.17 0.21
+1F2TA 149 XRAY 1.600 0.19 0.23
+1F2TB 148 XRAY 1.600 0.19 0.23
+1F46B 140 XRAY 1.500 0.20 0.22
+1F74A 293 XRAY 1.600 0.17 0.20
+1F7DB 136 XRAY 1.400 0.19 0.22
+1F7LA 121 XRAY 1.500 0.19 0.20
+1F86A 115 XRAY 1.100 0.14 0.18
+1F94A 63 XRAY 0.970 0.12 0.18
+1F9VA 347 XRAY 1.300 0.22 0.24
+1F9ZB 135 XRAY 1.500 0.21 0.27
+1FCQA 350 XRAY 1.600 0.19 0.23
+1FCYA 236 XRAY 1.300 0.13 0.16
+1FG7A 356 XRAY 1.500 0.20 0.22
+1FGYA 127 XRAY 1.500 0.21 0.25
+1FIUD 286 XRAY 1.600 0.17 0.20
+1FJ2B 232 XRAY 1.500 0.18 0.24
+1FM0D 81 XRAY 1.450 0.15 0.18
+1FM0E 150 XRAY 1.450 0.15 0.18
+1FO8A 343 XRAY 1.400 0.17 0.18
+1FP2A 352 XRAY 1.400 0.23 0.23
+1FR3L 67 XRAY 1.500 0.18 0.20
+1FSGC 233 XRAY 1.050 0.12 0.15
+1FT5A 211 XRAY 1.600 0.19 0.21
+1FX2A 235 XRAY 1.460 0.18 0.20
+1FYEA 229 XRAY 1.200 0.16 0.19
+1G12A 167 XRAY 1.600 0.22 0.23
+1G2QB 187 XRAY 1.500 0.20 0.23
+1G2RA 100 XRAY 1.350 0.16 0.18
+1G2YC 32 XRAY 1.000 0.20 0.20
+1G3PA 217 XRAY 1.460 0.19 0.23
+1G4IA 123 XRAY 0.970 0.09 1.00
+1G5AA 628 XRAY 1.400 0.19 0.20
+1G61A 228 XRAY 1.300 0.13 0.18
+1G66A 207 XRAY 0.900 0.11 0.13
+1G6GA 127 XRAY 1.600 0.21 0.24
+1G6HA 257 XRAY 1.600 0.22 0.25
+1G6IA 545 XRAY 1.590 0.23 0.25
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diff --git a/extras/data_generation/rotamer_library/do_bbdep_lib.py b/extras/data_generation/rotamer_library/do_bbdep_lib.py
new file mode 100644
index 0000000000000000000000000000000000000000..9dab196e971b33a3677160cf42fbe11cd894a4c0
--- /dev/null
+++ b/extras/data_generation/rotamer_library/do_bbdep_lib.py
@@ -0,0 +1,497 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+import os, math, sys
+import numpy as np
+from scipy.ndimage import gaussian_filter
+from promod3 import sidechain
+
+if len(sys.argv) != 3:
+ print "USAGE: ost do_lib.py <path_to_data> <aa_name>"
+ sys.exit(0)
+
+# the csv file you created with fetch_data.py
+data_file_path = sys.argv[1]
+
+# the name of the amino acids for which you want to create a library
+# => can be any amino acid you have in the provided datafile
+aa_name = sys.argv[2]
+
+# The mises distribution depends on kappa to determine the smoothness.
+# When thinking of a classical gaussian, r = sqrt(1.0/kappa) corresponds to
+# the radius of a circle around the mean that covers 67% of the density.
+# In order to generate adaptive distributions with respect to phi/psi,
+# kappa is estimated such that this "circle" includes exactly N data points.
+# Be aware that N needs to be increased in case of higher dimensional
+# probability functions (e.g. more rotameric dihedral angles)
+p_threshold_67 = 30
+if aa_name in ["LYS", "ARG"]:
+ p_threshold_67 = 50
+
+# Same threshold but for the chi angles
+# In this case we're considering only data with same configuration
+chi_threshold_67 = 20
+
+# if you want to have 10 degree bins for backbone dihedral angles, use 36
+n_bins = 36
+
+# Width of bins to sample for non rotameric dihedral angles (in degrees)
+# e.g. in case of GLN you'll have 360 / 30 = 12 conformations for the
+# terminal dihedral angle if you keep the default (30).
+non_rotameric_sampling = 30
+
+# An initial pdf is generated for the non-rotameric chi angles. The pdf is
+# smoothed with a circular gaussian function with following standard
+# deviation (in degrees)
+non_rotameric_smooth_std = 10
+
+def EvalMises(phi0, psi0, kappa, phi, psi):
+ prefac = 1.0 / (4*np.pi*np.pi*math.pow(np.i0(kappa), 2))
+ exponent = kappa*(np.add(np.cos(phi-phi0), np.cos(psi-psi0)))
+ return prefac * np.exp(exponent)
+
+def EstimateKappa(n_within_one_std, phi, psi, phi_data, psi_data):
+ min_phi_diff = np.minimum(np.minimum(np.absolute(phi_data - phi),
+ np.absolute(phi_data - (phi + 2*np.pi))),
+ np.absolute(phi_data - (phi - 2*np.pi)))
+ min_psi_diff = np.minimum(np.minimum(np.absolute(psi_data - psi),
+ np.absolute(psi_data - (psi + 2*np.pi))),
+ np.absolute(psi_data - (psi - 2*np.pi)))
+ squared_radii = np.add(np.square(min_phi_diff), np.square(min_psi_diff))
+ squared_radii = np.sort(squared_radii)
+ # if theres simply not enough data, the returned kappe will be super small
+ radius_at_n = 1000.
+ if n_within_one_std < len(squared_radii):
+ radius_at_n = np.sqrt(squared_radii[n_within_one_std - 1])
+
+ return 1.0 / (radius_at_n * radius_at_n)
+
+def GetChiStats(current_phi, current_psi, phi, psi, chi, kappa):
+ weights = EvalMises(current_phi, current_psi, kappa,
+ phi, psi)
+ weights /= np.sum(weights)
+ # do the mean
+ a = np.sum(np.multiply(np.sin(chi), weights))
+ b = np.sum(np.multiply(np.cos(chi), weights))
+ mean_value = np.arctan2(a, b)
+ # do the std
+ diffs = np.minimum(np.minimum(np.absolute(chi - mean_value),
+ np.absolute(chi - (mean_value + 2*np.pi))),
+ np.absolute(chi - (mean_value - 2*np.pi)))
+ squared_std = np.sum(np.multiply(np.square(diffs), weights))
+
+ return (mean_value, np.sqrt(squared_std))
+
+def GetNonRotChiStats(current_phi, current_psi, phi, psi, chi,
+ non_rotameric_sampling, symmetric, kappa,
+ smooth_std):
+ # stupid check
+ if 180 % non_rotameric_sampling != 0:
+ raise RuntimeError("180 must be dividable by non_rotameric_sampling!")
+
+ n_sampled_rotamers = 360 / non_rotameric_sampling
+ if symmetric:
+ n_sampled_rotamers = 180 / non_rotameric_sampling
+
+ # symmetric or not, we first fill in a histogram covering a range of 2 pi
+ n_histogram_bins = 2 * 360
+ histogram = np.zeros(n_histogram_bins)
+ bin_size = 2*np.pi/n_histogram_bins
+
+ # we add up the histogram by weights as estimated with the mises distribution
+ weights = EvalMises(current_phi, current_psi, kappa,
+ phi, psi)
+ angle_bins = np.clip(np.floor((chi + np.pi) / bin_size), 0, len(histogram)-1)
+ for angle_bin, w in zip(angle_bins, weights):
+ histogram[int(angle_bin)] += w
+
+ # if we're dealing with a symmetric distribution, we simply add up the
+ # first and second half of the histogram. The histogram has then an angle
+ # range of [-pi,0.0[
+ if symmetric:
+ n_histogram_bins /= 2
+ histogram = np.add(histogram[:n_histogram_bins],
+ histogram[n_histogram_bins:])
+
+ # translate the smooth_std, which is in degree, to bins in the histogram
+ # and apply it with a simple gaussian filter
+ gaussian_std = float(smooth_std) / 180 * np.pi / bin_size
+ histogram = gaussian_filter(histogram, gaussian_std, mode="wrap")
+ histogram = histogram / sum(histogram)
+
+ # find the maximum element, as this is the center of the first "window"
+ # of width non_rotameric_sampling
+ max_idx = np.argmax(histogram)
+ current_angle = max_idx * bin_size - np.pi
+
+ # concatenate, so we dont have to care for circularity anymore
+ histogram = np.concatenate((histogram, histogram, histogram, histogram))
+
+ rad_non_rotameric_sampling = float(non_rotameric_sampling) / 180 * np.pi
+ first_start_angle = current_angle - rad_non_rotameric_sampling / 2
+
+ if first_start_angle < -np.pi:
+ # With this first angle we would get an underflow...
+ # we did so many concatenatinons, that we can add 360 degrees, even for
+ # the symmetric case
+ current_angle += 2*np.pi
+
+ probabilities = np.zeros(n_sampled_rotamers)
+ mean_values = np.zeros(n_sampled_rotamers)
+ std_values = np.zeros(n_sampled_rotamers)
+
+ for i in range(n_sampled_rotamers):
+ start_angle = current_angle - rad_non_rotameric_sampling / 2
+ end_angle = current_angle + rad_non_rotameric_sampling / 2
+
+ start_bin = int((start_angle + np.pi) / bin_size)
+ end_bin = int((end_angle + np.pi) / bin_size)
+ local_values = histogram[start_bin:end_bin+1]
+ normalized_local_values = local_values / sum(local_values)
+ angle_values = np.linspace(start_angle, end_angle, len(local_values))
+
+ probabilities[i] = np.sum(local_values)
+ mean_values[i] = np.sum(np.multiply(normalized_local_values, angle_values))
+ squared_std = np.sum(np.multiply(np.square(angle_values - mean_values[i]),
+ normalized_local_values))
+ std_values[i] = np.sqrt(squared_std)
+
+ current_angle += rad_non_rotameric_sampling
+
+ # The probabilities of all ranges should add up to one...
+ # however, depending on the rounding etc., this might not exactly be the case.
+ # All probabilities need an additional normalization in the end
+ probabilities /= np.sum(probabilities)
+
+ # due to the concatenation, we still have mean values > pi.
+ # let's enforce valid ranges...
+ for i in range(len(mean_values)):
+ while mean_values[i] > np.pi:
+ mean_values[i] -= 2*np.pi
+
+ return probabilities, mean_values, std_values
+
+def DoIt(aa_name, aa_data, n_bins, p_n_67, chi_n_67, out_path,
+ non_rotameric_sampling=30, non_rotameric_smooth_std = 10):
+
+ # output lines are added here
+ out_stuff = list()
+
+ # the configurations in aa_data are stored in four lists with keys
+ # conf1, conf2... we tranlate that to a unique string
+ configurations = list()
+ for a, b, c, d in zip(aa_data["conf1"], aa_data["conf2"],
+ aa_data["conf3"], aa_data["conf4"]):
+ configurations.append("%i%i%i%i"%(int(a), int(b), int(c), int(d)))
+ unique_configurations = list(set(configurations))
+
+ # we need configuration dependent phi, psi, chix
+ conf_phi = dict()
+ conf_psi = dict()
+ conf_chi1 = dict()
+ conf_chi2 = dict()
+ conf_chi3 = dict()
+ conf_chi4 = dict()
+
+ # the actual output is stored in following configuration dependent matrices
+ rotameric_probabilities = dict()
+ rotameric_chi1 = dict()
+ rotameric_chi2 = dict()
+ rotameric_chi3 = dict()
+ rotameric_chi4 = dict()
+ rotameric_sig1 = dict()
+ rotameric_sig2 = dict()
+ rotameric_sig3 = dict()
+ rotameric_sig4 = dict()
+
+ for uc in unique_configurations:
+ indices = [i for i, c in enumerate(configurations) if c == uc]
+ conf_phi[uc] = aa_data["phi"][indices]
+ conf_psi[uc] = aa_data["psi"][indices]
+ conf_chi1[uc] = aa_data["chi1"][indices]
+ conf_chi2[uc] = aa_data["chi2"][indices]
+ conf_chi3[uc] = aa_data["chi3"][indices]
+ conf_chi4[uc] = aa_data["chi4"][indices]
+ rotameric_probabilities[uc] = np.zeros((n_bins, n_bins))
+ rotameric_chi1[uc] = np.zeros((n_bins, n_bins))
+ rotameric_chi2[uc] = np.zeros((n_bins, n_bins))
+ rotameric_chi3[uc] = np.zeros((n_bins, n_bins))
+ rotameric_chi4[uc] = np.zeros((n_bins, n_bins))
+ rotameric_sig1[uc] = np.zeros((n_bins, n_bins))
+ rotameric_sig2[uc] = np.zeros((n_bins, n_bins))
+ rotameric_sig3[uc] = np.zeros((n_bins, n_bins))
+ rotameric_sig4[uc] = np.zeros((n_bins, n_bins))
+
+ ########################################
+ # GET PHI/PSI DEPENDENT DATA SITUATION #
+ ########################################
+ # the data in n_data_points will be used to fill the second column in the
+ # output file: number of data points for that backbone dihedral bin
+ bin_size = 2*np.pi/n_bins
+ n_data_points = np.zeros((n_bins, n_bins))
+ for phi, psi in zip(aa_data["phi"], aa_data["psi"]):
+ phi_bin = int((phi + np.pi) / bin_size)
+ psi_bin = int((psi + np.pi) / bin_size)
+ # enforce range (should be fulfilled anyway)
+ phi_bin = max(min(phi_bin, n_bins-1), 0)
+ psi_bin = max(min(psi_bin, n_bins-1), 0)
+ # the bins are now just rounded down... if they're rounded by more than
+ # half of the bin size, we count them to the bin after
+ d_phi = (phi+np.pi) - phi_bin*bin_size
+ d_psi = (psi+np.pi) - psi_bin*bin_size
+ if d_phi > bin_size/2.:
+ phi_bin += 1
+ if d_psi > bin_size/2.:
+ psi_bin += 1
+ # deal with circularity
+ if phi_bin == n_bins:
+ phi_bin = 0
+ if psi_bin == n_bins:
+ psi_bin = 0
+ n_data_points[(phi_bin, psi_bin)] += 1
+
+ # Do not allow super large kappas. This happens in high density regions of
+ # of the Ramachandran plot and given a binning of 10 degrees, only a fraction
+ # of the data is considered. This might lead to a bumpy probability landscape
+ min_kappa = 0.1
+ max_kappa = 1.0 / math.pow(bin_size / 2., 2)
+
+ for i in range(n_bins):
+ current_phi = -np.pi + i*(2*np.pi/n_bins)
+ for j in range(n_bins):
+ current_psi = -np.pi + j*(2*np.pi/n_bins)
+
+ print "processing", aa_name, "phi:",current_phi,"psi:",current_psi
+
+ ###############################################################
+ # GET THE PROBABILITIES OF ALL CONFIGURATIONS GIVEN PHI / PSI #
+ ###############################################################
+ conf_counter = dict()
+ for uc in unique_configurations:
+ conf_counter[uc] = 0.0
+
+ # bb_kappa determines the smoothness of the mises distribution that
+ # is used for the weighted counting approach to determine the
+ # probabilities of rotamer configurations
+ bb_kappa = EstimateKappa(p_n_67, current_phi, current_psi,
+ aa_data["phi"], aa_data["psi"])
+ bb_kappa = max(min(bb_kappa, max_kappa), min_kappa)
+
+ bb_weights = EvalMises(current_phi, current_psi, bb_kappa,
+ aa_data["phi"], aa_data["psi"])
+ sum_bb_weights = np.sum(bb_weights)
+ for w, c in zip(bb_weights, configurations):
+ conf_counter[c] += w
+ for uc in unique_configurations:
+ rotameric_probabilities[uc][(i,j)] = conf_counter[uc] / sum_bb_weights
+
+ #####################################################################
+ # GET THE DIHEDRAL STATISTICS OF ALL CONFIGURATIONS GIVEN PHI / PSI #
+ #####################################################################
+ # non_rotameric_configurations remains empty for rotameric-only sidechains
+ non_rotameric_configurations = dict()
+
+ for uc in unique_configurations:
+ # conf_kappa determines the smoothness of the mises distribution that
+ # is used for the weighted mean approach to determine chi angles / stds
+ conf_kappa = EstimateKappa(chi_n_67, current_phi, current_psi,
+ conf_phi[uc], conf_psi[uc])
+ conf_kappa = max(min(conf_kappa, max_kappa), min_kappa)
+ rot_confs = [int(sidechain.TRANS), int(sidechain.GAUCHE_MINUS),
+ int(sidechain.GAUCHE_PLUS)]
+ # do chi1
+ if int(uc[0]) in rot_confs:
+ mean, std = GetChiStats(current_phi, current_psi, conf_phi[uc],
+ conf_psi[uc], conf_chi1[uc], conf_kappa)
+ rotameric_chi1[uc][(i,j)] = mean
+ rotameric_sig1[uc][(i,j)] = std
+ # do chi2
+ if int(uc[1]) in rot_confs:
+ mean, std = GetChiStats(current_phi, current_psi, conf_phi[uc],
+ conf_psi[uc], conf_chi2[uc], conf_kappa)
+ rotameric_chi2[uc][(i,j)] = mean
+ rotameric_sig2[uc][(i,j)] = std
+ # do chi3
+ if int(uc[2]) in rot_confs:
+ mean, std = GetChiStats(current_phi, current_psi, conf_phi[uc],
+ conf_psi[uc], conf_chi3[uc], conf_kappa)
+ rotameric_chi3[uc][(i,j)] = mean
+ rotameric_sig3[uc][(i,j)] = std
+ # do chi4
+ if int(uc[3]) in rot_confs:
+ mean, std = GetChiStats(current_phi, current_psi, conf_phi[uc],
+ conf_psi[uc], conf_chi4[uc], conf_kappa)
+ rotameric_chi4[uc][(i,j)] = mean
+ rotameric_sig4[uc][(i,j)] = std
+
+ # so far we only treated rotameric dihedral angles.
+ # ASN(chi2), ASP(chi2), PHE(chi2), TYR(chi2), HIS(chi2), TRP(chi2),
+ # GLN(chi3) and GLU(chi3) exhibit so called non-rotameric degrees
+ # of freedom and require further sampling of their terminal
+ # dihedral angle.
+ if aa_name in ["ASN", "ASP", "PHE", "TYR", "HIS", "TRP", "GLN", "GLU"]:
+ non_rotameric_chi_idx = 1
+ if aa_name in ["GLN", "GLU"]:
+ non_rotameric_chi_idx = 2
+ symmetric = False
+ if aa_name in ["ASP", "PHE", "TYR", "GLU"]:
+ symmetric = True
+ chi_angles = None
+ if non_rotameric_chi_idx == 1:
+ chi_angles = conf_chi2[uc]
+ elif non_rotameric_chi_idx == 2:
+ chi_angles = conf_chi3[uc]
+
+ non_rot_kappa = conf_kappa
+ if symmetric:
+ non_rot_kappa = EstimateKappa(int(chi_n_67/2), current_phi,
+ current_psi, conf_phi[uc],
+ conf_psi[uc])
+ non_rot_kappa = max(min(non_rot_kappa, max_kappa), min_kappa)
+
+ probs, mean_values, std_values = GetNonRotChiStats(current_phi,
+ current_psi,
+ conf_phi[uc],
+ conf_psi[uc],
+ chi_angles,
+ non_rotameric_sampling,
+ symmetric,
+ non_rot_kappa,
+ non_rotameric_smooth_std)
+
+ non_rotameric_configurations[uc] = (non_rotameric_chi_idx,
+ probs, mean_values, std_values)
+ # generate output
+ for uc in unique_configurations:
+ if uc in non_rotameric_configurations:
+ for k in range(len(non_rotameric_configurations[uc][1])):
+ c2 = str(uc[1])
+ chi2 = rotameric_chi2[uc][(i,j)]
+ sig2 = rotameric_sig2[uc][(i,j)]
+ c3 = str(uc[2])
+ chi3 = rotameric_chi3[uc][(i,j)]
+ sig3 = rotameric_sig3[uc][(i,j)]
+ non_rot_idx = non_rotameric_configurations[uc][0]
+ if non_rot_idx == 1:
+ c2 = str(k+1)
+ chi2 = non_rotameric_configurations[uc][2][k]
+ sig2 = non_rotameric_configurations[uc][3][k]
+ elif non_rot_idx == 2:
+ c3 = str(k+1)
+ chi3 = non_rotameric_configurations[uc][2][k]
+ sig3 = non_rotameric_configurations[uc][3][k]
+ else:
+ raise RuntimeError("Invalid non rot idx!")
+
+ out = list()
+ out.append(aa_name)
+ out.append(str(-180 + i*10))
+ out.append(str(-180 + j*10))
+ out.append(str(int(n_data_points[(i,j)])))
+ out.append(' '.join([str(uc[0]), c2, c3, str(uc[3])]))
+ out.append("%.4f"%(non_rotameric_configurations[uc][1][k] * \
+ rotameric_probabilities[uc][(i,j)]))
+ out.append("%.2f"%(rotameric_chi1[uc][(i,j)] / np.pi * 180))
+ out.append("%.2f"%(chi2 / np.pi * 180))
+ out.append("%.2f"%(chi3 / np.pi * 180))
+ out.append("%.2f"%(rotameric_chi4[uc][(i,j)] / np.pi * 180))
+ out.append("%.2f"%(rotameric_sig1[uc][(i,j)] / np.pi * 180))
+ out.append("%.2f"%(sig2 / np.pi * 180))
+ out.append("%.2f"%(sig3 / np.pi * 180))
+ out.append("%.2f"%(rotameric_sig4[uc][(i,j)] / np.pi * 180))
+ outline = ' '.join(out)
+ out_stuff.append(outline)
+
+ else:
+ out = list()
+ out.append(aa_name)
+ out.append(str(-180 + i*10))
+ out.append(str(-180 + j*10))
+ out.append(str(int(n_data_points[(i,j)])))
+ out.append(' '.join([str(uc[0]), str(uc[1]), str(uc[2]), str(uc[3])]))
+ out.append("%.4f"%(rotameric_probabilities[uc][(i,j)]))
+ out.append("%.2f"%(rotameric_chi1[uc][(i,j)] / np.pi * 180))
+ out.append("%.2f"%(rotameric_chi2[uc][(i,j)] / np.pi * 180))
+ out.append("%.2f"%(rotameric_chi3[uc][(i,j)] / np.pi * 180))
+ out.append("%.2f"%(rotameric_chi4[uc][(i,j)] / np.pi * 180))
+ out.append("%.2f"%(rotameric_sig1[uc][(i,j)] / np.pi * 180))
+ out.append("%.2f"%(rotameric_sig2[uc][(i,j)] / np.pi * 180))
+ out.append("%.2f"%(rotameric_sig3[uc][(i,j)] / np.pi * 180))
+ out.append("%.2f"%(rotameric_sig4[uc][(i,j)] / np.pi * 180))
+ outline = ' '.join(out)
+ out_stuff.append(outline)
+
+ outfile = open(out_path, 'w')
+ outfile.write('\n'.join(out_stuff))
+ outfile.close()
+
+# read csv file (generated with fetch_data.py)
+data = open(data_file_path, 'r').readlines()
+
+# get data indices
+header = [item.strip() for item in data[0].split(',')]
+
+# will throw an error if not there
+rname_idx = header.index("rname")
+phi_idx = header.index("phi")
+psi_idx = header.index("psi")
+chi1_idx = header.index("chi1")
+chi2_idx = header.index("chi2")
+chi3_idx = header.index("chi3")
+chi4_idx = header.index("chi4")
+conf1_idx = header.index("conf1")
+conf2_idx = header.index("conf2")
+conf3_idx = header.index("conf3")
+conf4_idx = header.index("conf4")
+
+# helpers for parsing...
+str_c = ["GAUCHE_MINUS", "GAUCHE_PLUS", "TRANS", "NON_ROTAMERIC", "INVALID"]
+promod_c = [sidechain.GAUCHE_MINUS, sidechain.GAUCHE_PLUS, sidechain.TRANS,
+ sidechain.NON_ROTAMERIC, sidechain.INVALID]
+
+# get the data
+aa_data = {"phi" : [], "psi" : [], "chi1" : [], "chi2" : [], "chi3" : [],
+ "chi4" : [], "conf1" : [], "conf2" : [], "conf3" : [], "conf4" : []}
+
+for line in data[1:]:
+ split_line = [item.strip() for item in line.split(',')]
+ rname = split_line[rname_idx]
+ if rname == aa_name:
+ aa_data["phi"].append(float(split_line[phi_idx]))
+ aa_data["psi"].append(float(split_line[psi_idx]))
+ aa_data["chi1"].append(float(split_line[chi1_idx]))
+ aa_data["chi2"].append(float(split_line[chi2_idx]))
+ aa_data["chi3"].append(float(split_line[chi3_idx]))
+ aa_data["chi4"].append(float(split_line[chi4_idx]))
+ aa_data["conf1"].append(promod_c[str_c.index(split_line[conf1_idx])])
+ aa_data["conf2"].append(promod_c[str_c.index(split_line[conf2_idx])])
+ aa_data["conf3"].append(promod_c[str_c.index(split_line[conf3_idx])])
+ aa_data["conf4"].append(promod_c[str_c.index(split_line[conf4_idx])])
+
+# convert all dihedral angles into numpy arrays
+aa_data["phi"] = np.array(aa_data["phi"])
+aa_data["psi"] = np.array(aa_data["psi"])
+aa_data["chi1"] = np.array(aa_data["chi1"])
+aa_data["chi2"] = np.array(aa_data["chi2"])
+aa_data["chi3"] = np.array(aa_data["chi3"])
+aa_data["chi4"] = np.array(aa_data["chi4"])
+
+###############################################
+# GENERATE THE LIBRARY FOR DESIRED AMINO ACID #
+###############################################
+DoIt(aa_name, aa_data, n_bins, p_threshold_67, chi_threshold_67,
+ aa_name+".txt", non_rotameric_sampling=non_rotameric_sampling,
+ non_rotameric_smooth_std = non_rotameric_smooth_std)
diff --git a/extras/data_generation/rotamer_library/do_lib.py b/extras/data_generation/rotamer_library/do_lib.py
new file mode 100644
index 0000000000000000000000000000000000000000..abb4ce3aa993f99454f851c26366eccf72076431
--- /dev/null
+++ b/extras/data_generation/rotamer_library/do_lib.py
@@ -0,0 +1,340 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+import os, math, sys
+import numpy as np
+from scipy.ndimage import gaussian_filter
+from promod3 import sidechain
+
+if len(sys.argv) != 3:
+ print "USAGE: ost do_lib.py <path_to_data> <library_out_path>"
+ sys.exit(0)
+
+# the csv file you created with fetch_data.py
+data_file_path = sys.argv[1]
+
+# library will be dumped here using the SavePortable() method
+library_out_path = sys.argv[2]
+
+
+# default parametrization
+
+# Width of bins to sample for non rotameric dihedral angles (in degrees)
+# e.g. in case of GLN you'll have 360 / 30 = 12 conformations for the
+# terminal dihedral angle if you keep the default (30).
+non_rot_sampling = 30
+
+# An initial pdf is generated for the non-rotameric chi angles. The pdf is
+# smoothed with a circular gaussian function with following standard
+# deviation (in degrees)
+non_rot_smooth_std = 10
+
+def GetNonRotChiStats(chi, non_rot_sampling, symmetric, smooth_std):
+
+ # stupid check
+ if 180 % non_rot_sampling != 0:
+ raise RuntimeError("180 must be dividable by non_rot_sampling!")
+
+ n_sampled_rotamers = 360 / non_rot_sampling
+ if symmetric:
+ n_sampled_rotamers = 180 / non_rot_sampling
+
+ # symmetric or not, we first fill in a histogram covering a range of 2 pi
+ n_histogram_bins = 2 * 360
+ histogram = np.zeros(n_histogram_bins)
+ bin_size = 2*np.pi/n_histogram_bins
+
+ # we add up the histogram by weights as estimated with the mises distribution
+ angle_bins = np.clip(np.floor((chi + np.pi) / bin_size), 0, len(histogram)-1)
+ for angle_bin in angle_bins:
+ histogram[int(angle_bin)] += 1.0
+
+ # if we're dealing with a symmetric distribution, we simply add up the
+ # first and second half of the histogram. The histogram has then an angle
+ # range of [-pi,0.0[
+ if symmetric:
+ n_histogram_bins /= 2
+ histogram = np.add(histogram[:n_histogram_bins],
+ histogram[n_histogram_bins:])
+
+ # translate the smooth_std, which is in degree, to bins in the histogram
+ # and apply it with a simple gaussian filter
+ gaussian_std = float(smooth_std) / 180 * np.pi / bin_size
+ histogram = gaussian_filter(histogram, gaussian_std, mode="wrap")
+ histogram = histogram / sum(histogram)
+
+ # find the maximum element, as this is the center of the first "window"
+ # of width non_rot_sampling
+ max_idx = np.argmax(histogram)
+ current_angle = max_idx * bin_size - np.pi
+
+ # concatenate, so we dont have to care for circularity anymore
+ histogram = np.concatenate((histogram, histogram, histogram, histogram))
+
+ rad_non_rot_sampling = float(non_rot_sampling) / 180 * np.pi
+ first_start_angle = current_angle - rad_non_rot_sampling / 2
+
+ if first_start_angle < -np.pi:
+ # With this first angle we would get an underflow...
+ # we did so many concatenatinons, that we can add 360 degrees, even for
+ # the symmetric case
+ current_angle += 2*np.pi
+
+ probabilities = np.zeros(n_sampled_rotamers)
+ mean_values = np.zeros(n_sampled_rotamers)
+ std_values = np.zeros(n_sampled_rotamers)
+
+ for i in range(n_sampled_rotamers):
+ start_angle = current_angle - rad_non_rot_sampling / 2
+ end_angle = current_angle + rad_non_rot_sampling / 2
+
+ start_bin = int((start_angle + np.pi) / bin_size)
+ end_bin = int((end_angle + np.pi) / bin_size)
+ local_values = histogram[start_bin:end_bin+1]
+ normalized_local_values = local_values / sum(local_values)
+ angle_values = np.linspace(start_angle, end_angle, len(local_values))
+
+ probabilities[i] = np.sum(local_values)
+ mean_values[i] = np.sum(np.multiply(normalized_local_values, angle_values))
+ squared_std = np.sum(np.multiply(np.square(angle_values - mean_values[i]),
+ normalized_local_values))
+ std_values[i] = np.sqrt(squared_std)
+
+ current_angle += rad_non_rot_sampling
+
+ # The probabilities of all ranges should add up to one...
+ # however, depending on the rounding etc., this might not exactly be the case.
+ # All probabilities need an additional normalization in the end
+ probabilities /= np.sum(probabilities)
+
+ # due to the concatenation, we still have mean values > pi.
+ # let's enforce valid ranges...
+ for i in range(len(mean_values)):
+ while mean_values[i] > np.pi:
+ mean_values[i] -= 2*np.pi
+
+ return probabilities, mean_values, std_values
+
+def GetChiStats(chi):
+ # do the mean
+ a = np.sum(np.sin(chi))
+ b = np.sum(np.cos(chi))
+ mean_value = np.arctan2(a, b)
+ # do the std
+ diffs = np.minimum(np.minimum(np.absolute(chi - mean_value),
+ np.absolute(chi - (mean_value + 2*np.pi))),
+ np.absolute(chi - (mean_value - 2*np.pi)))
+ squared_std = np.sum(np.square(diffs)) / len(diffs)
+ return (mean_value, np.sqrt(squared_std))
+
+
+def DoIt(aa_name, data_file_path, library, non_rot_sampling = 30,
+ non_rot_smooth_std = 10):
+
+ print "processing", aa_name
+
+ # Parse CSV file
+ data = open(data_file_path, 'r').readlines()
+
+ # get data indices
+ header = [item.strip() for item in data[0].split(',')]
+
+ # will throw an error if not there
+ rname_idx = header.index("rname")
+ chi1_idx = header.index("chi1")
+ chi2_idx = header.index("chi2")
+ chi3_idx = header.index("chi3")
+ chi4_idx = header.index("chi4")
+ conf1_idx = header.index("conf1")
+ conf2_idx = header.index("conf2")
+ conf3_idx = header.index("conf3")
+ conf4_idx = header.index("conf4")
+ str_c = ["GAUCHE_MINUS", "GAUCHE_PLUS", "TRANS", "NON_ROTAMERIC", "INVALID"]
+ promod_c = [sidechain.GAUCHE_MINUS, sidechain.GAUCHE_PLUS, sidechain.TRANS,
+ sidechain.NON_ROTAMERIC, sidechain.INVALID]
+
+ # get the data
+ aa_data = {"chi1" : [], "chi2" : [], "chi3" : [], "chi4" : [],
+ "conf1" : [], "conf2" : [], "conf3" : [], "conf4" : []}
+
+ for line in data[1:]:
+ split_line = [item.strip() for item in line.split(',')]
+ rname = split_line[rname_idx]
+ if rname == aa_name:
+ aa_data["chi1"].append(float(split_line[chi1_idx]))
+ aa_data["chi2"].append(float(split_line[chi2_idx]))
+ aa_data["chi3"].append(float(split_line[chi3_idx]))
+ aa_data["chi4"].append(float(split_line[chi4_idx]))
+ aa_data["conf1"].append(promod_c[str_c.index(split_line[conf1_idx])])
+ aa_data["conf2"].append(promod_c[str_c.index(split_line[conf2_idx])])
+ aa_data["conf3"].append(promod_c[str_c.index(split_line[conf3_idx])])
+ aa_data["conf4"].append(promod_c[str_c.index(split_line[conf4_idx])])
+
+ # convert all dihedral angles into numpy arrays
+ aa_data["chi1"] = np.array(aa_data["chi1"])
+ aa_data["chi2"] = np.array(aa_data["chi2"])
+ aa_data["chi3"] = np.array(aa_data["chi3"])
+ aa_data["chi4"] = np.array(aa_data["chi4"])
+
+ # the configurations in aa_data are stored in four lists with keys
+ # conf1, conf2... we translate that to a unique string
+ configurations = list()
+ for a, b, c, d in zip(aa_data["conf1"], aa_data["conf2"],
+ aa_data["conf3"], aa_data["conf4"]):
+ configurations.append("%i%i%i%i"%(int(a), int(b), int(c), int(d)))
+ unique_configurations = list(set(configurations))
+
+ # we need configuration dependent chix
+ conf_chi1 = dict()
+ conf_chi2 = dict()
+ conf_chi3 = dict()
+ conf_chi4 = dict()
+ rotameric_probabilities = dict()
+
+ for uc in unique_configurations:
+ indices = [i for i, c in enumerate(configurations) if c == uc]
+ conf_chi1[uc] = aa_data["chi1"][indices]
+ conf_chi2[uc] = aa_data["chi2"][indices]
+ conf_chi3[uc] = aa_data["chi3"][indices]
+ conf_chi4[uc] = aa_data["chi4"][indices]
+ rotameric_probabilities[uc] = float(len(indices)) / len(configurations)
+
+ rot_confs = [int(sidechain.TRANS), int(sidechain.GAUCHE_MINUS),
+ int(sidechain.GAUCHE_PLUS)]
+
+ for uc in unique_configurations:
+
+ rotameric_chi1 = float("nan")
+ rotameric_sig1 = float("nan")
+ rotameric_chi2 = float("nan")
+ rotameric_sig2 = float("nan")
+ rotameric_chi3 = float("nan")
+ rotameric_sig3 = float("nan")
+ rotameric_chi4 = float("nan")
+ rotameric_sig4 = float("nan")
+
+ # do chi1
+ if int(uc[0]) in rot_confs:
+ mean, std = GetChiStats(conf_chi1[uc])
+ rotameric_chi1 = mean
+ rotameric_sig1 = std
+ # do chi2
+ if int(uc[1]) in rot_confs:
+ mean, std = GetChiStats(conf_chi2[uc])
+ rotameric_chi2 = mean
+ rotameric_sig2 = std
+ # do chi3
+ if int(uc[2]) in rot_confs:
+ mean, std = GetChiStats(conf_chi3[uc])
+ rotameric_chi3 = mean
+ rotameric_sig3 = std
+ # do chi4
+ if int(uc[3]) in rot_confs:
+ mean, std = GetChiStats(conf_chi4[uc])
+ rotameric_chi4 = mean
+ rotameric_sig4 = std
+
+ # so far we only treated rotameric dihedral angles.
+ # ASN(chi2), ASP(chi2), PHE(chi2), TYR(chi2), HIS(chi2), TRP(chi2),
+ # GLN(chi3) and GLU(chi3) exhibit so called non-rotameric degrees
+ # of freedom and require further sampling of their terminal
+ # dihedral angle.
+ if aa_name in ["ASN", "ASP", "PHE", "TYR", "HIS", "TRP", "GLN", "GLU"]:
+ non_rotameric_chi_idx = 1
+ if aa_name in ["GLN", "GLU"]:
+ non_rotameric_chi_idx = 2
+ symmetric = False
+ if aa_name in ["ASP", "PHE", "TYR", "GLU"]:
+ symmetric = True
+ chi_angles = None
+ if non_rotameric_chi_idx == 1:
+ chi_angles = conf_chi2[uc]
+ elif non_rotameric_chi_idx == 2:
+ chi_angles = conf_chi3[uc]
+ probs, mean_values, std_values = GetNonRotChiStats(chi_angles,
+ non_rot_sampling,
+ symmetric,
+ non_rot_smooth_std)
+ for p, m, s in zip(probs, mean_values, std_values):
+ rot = sidechain.RotamerLibEntry(p*rotameric_probabilities[uc],
+ rotameric_chi1, rotameric_chi2,
+ rotameric_chi3, rotameric_chi4,
+ rotameric_sig1, rotameric_sig2,
+ rotameric_sig3, rotameric_sig4)
+ if non_rotameric_chi_idx == 1:
+ rot.chi2 = m
+ rot.sig2 = s
+ elif non_rotameric_chi_idx == 2:
+ rot.chi3 = m
+ rot.sig3 = s
+ lib.AddRotamer(sidechain.TLCToRotID(aa_name), rot)
+ else:
+ rot = sidechain.RotamerLibEntry(rotameric_probabilities[uc],
+ rotameric_chi1, rotameric_chi2,
+ rotameric_chi3, rotameric_chi4,
+ rotameric_sig1, rotameric_sig2,
+ rotameric_sig3, rotameric_sig4)
+ lib.AddRotamer(sidechain.TLCToRotID(aa_name), rot)
+
+
+
+lib = sidechain.RotamerLib()
+DoIt("ARG", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("ASN", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("ASP", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("GLN", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("GLU", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("LYS", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("SER", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("CYH", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("CYD", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("CYS", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("MET", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("TRP", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("TYR", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("THR", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("VAL", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("ILE", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("LEU", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("CPR", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("TPR", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("PRO", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("HIS", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+DoIt("PHE", data_file_path, lib, non_rot_sampling = non_rot_sampling,
+ non_rot_smooth_std = non_rot_smooth_std)
+lib.MakeStatic()
+lib.SavePortable(library_out_path)
diff --git a/extras/data_generation/rotamer_library/fetch_data.py b/extras/data_generation/rotamer_library/fetch_data.py
new file mode 100644
index 0000000000000000000000000000000000000000..97ad79363270fe540dacdaab3b1f5f7ed69647ab
--- /dev/null
+++ b/extras/data_generation/rotamer_library/fetch_data.py
@@ -0,0 +1,202 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+import os
+from promod3 import sidechain
+import numpy as np
+
+# file of non redundant X-Ray structures.
+# Get one at: http://dunbrack.fccc.edu/Guoli/pisces_download.php
+pisces_filename = "cullpdb_pc40_res1.6_R0.25_d180913_chains5877"
+
+# Directory from where to load the structures.
+# Filename name of pisces entry 5XDTA in that directory should be: 5xdt.pdb.
+# Chain A gets then selected automatically at the data extraction step.
+# If you set the structure_dir to none, the file is automatically fetched from
+# rcsb but this takes much longer...
+structure_dir = None
+
+# filename for output data that will be in csv format
+out_path = "raw_data.csv"
+
+sidechain_data = dict()
+sidechain_data["ARG"] = list()
+sidechain_data["ASN"] = list()
+sidechain_data["ASP"] = list()
+sidechain_data["GLN"] = list()
+sidechain_data["GLU"] = list()
+sidechain_data["LYS"] = list()
+sidechain_data["SER"] = list()
+sidechain_data["CYH"] = list()
+sidechain_data["CYD"] = list()
+sidechain_data["CYS"] = list()
+sidechain_data["MET"] = list()
+sidechain_data["TRP"] = list()
+sidechain_data["TYR"] = list()
+sidechain_data["THR"] = list()
+sidechain_data["VAL"] = list()
+sidechain_data["ILE"] = list()
+sidechain_data["LEU"] = list()
+sidechain_data["CPR"] = list()
+sidechain_data["TPR"] = list()
+sidechain_data["PRO"] = list()
+sidechain_data["HIS"] = list()
+sidechain_data["PHE"] = list()
+
+dihedral_data = dict()
+for k in sidechain_data.keys():
+ dihedral_data[k] = list()
+
+infile = open(pisces_filename, 'r')
+data = infile.readlines()
+infile.close()
+
+for line in data[1:]:
+
+ pdb_id = line[:4]
+ chain_id = line[4]
+
+ print "processing", pdb_id
+
+ prot = None
+
+ try:
+ if structure_dir == None:
+ prot = io.LoadPDB(pdb_id.lower(), remote=True)
+ else:
+ prot = io.LoadPDB(os.path.join(structure_dir, pdb_id.lower() + ".pdb"))
+ prot = prot.Select("peptide=true and cname="+chain_id)
+ except:
+ print "Failed to get the structure! skip..."
+ continue
+
+ for r in prot.residues:
+
+ rname = r.GetName()
+ phi_handle = r.GetPhiTorsion()
+ psi_handle = r.GetPsiTorsion()
+ if not (phi_handle.IsValid() and psi_handle.IsValid()):
+ continue
+ phi = phi_handle.GetAngle()
+ psi = psi_handle.GetAngle()
+
+ # no processing of boring stuff
+ if rname == "ALA" or rname == "GLY":
+ continue
+
+ # do the special cases first
+ if rname == "CYS":
+ sg = r.FindAtom("SG")
+
+ if not sg.IsValid():
+ continue
+
+ close_atoms = prot.FindWithin(sg.GetPos(), 2.5)
+ disulfid = False
+
+ for a in close_atoms:
+ if a.name == "SG":
+ if a.GetResidue().GetHandle() != r.handle:
+ disulfid = True
+ break
+
+ if disulfid:
+ try:
+ rot_lib_entry = sidechain.RotamerLibEntry.FromResidue(r, sidechain.CYD)
+ except:
+ continue
+ sidechain_data["CYD"].append(rot_lib_entry)
+ dihedral_data["CYD"].append((phi, psi))
+ sidechain_data["CYS"].append(rot_lib_entry)
+ dihedral_data["CYS"].append((phi, psi))
+
+ else:
+ try:
+ rot_lib_entry = sidechain.RotamerLibEntry.FromResidue(r, sidechain.CYH)
+ except:
+ continue
+ sidechain_data["CYH"].append(rot_lib_entry)
+ dihedral_data["CYH"].append((phi, psi))
+ sidechain_data["CYS"].append(rot_lib_entry)
+ dihedral_data["CYS"].append((phi, psi))
+
+ elif rname == "PRO":
+ rprev = r.handle.GetPrev()
+ if not rprev.IsValid():
+ continue
+ if not mol.InSequence(rprev, r.handle):
+ continue
+
+ caprev = rprev.FindAtom("CA")
+ cprev = rprev.FindAtom("C")
+ n = r.FindAtom("N")
+ ca = r.FindAtom("CA")
+
+ if not (caprev.IsValid() and cprev.IsValid() and n.IsValid() and ca.IsValid()):
+ continue
+
+ omega = geom.DihedralAngle(caprev.GetPos(), cprev.GetPos(), n.GetPos(), ca.GetPos())
+
+ if abs(omega) > 90.0 / 180 * np.pi:
+ try:
+ rot_lib_entry = sidechain.RotamerLibEntry.FromResidue(r, sidechain.TPR)
+ except:
+ continue
+ sidechain_data["TPR"].append(rot_lib_entry)
+ dihedral_data["TPR"].append((phi, psi))
+ sidechain_data["PRO"].append(rot_lib_entry)
+ dihedral_data["PRO"].append((phi, psi))
+ else:
+ try:
+ rot_lib_entry = sidechain.RotamerLibEntry.FromResidue(r, sidechain.CPR)
+ except:
+ continue
+ sidechain_data["CPR"].append(rot_lib_entry)
+ dihedral_data["CPR"].append((phi, psi))
+ sidechain_data["PRO"].append(rot_lib_entry)
+ dihedral_data["PRO"].append((phi, psi))
+
+ else:
+ # we don't process exotic stuff...
+ if rname not in sidechain_data:
+ continue
+ rot_id = sidechain.TLCToRotID(rname)
+ try:
+ rot_lib_entry = sidechain.RotamerLibEntry.FromResidue(r, rot_id)
+ except:
+ # not all atoms present...
+ continue
+ sidechain_data[rname].append(rot_lib_entry)
+ dihedral_data[rname].append((phi, psi))
+
+# data output
+file_content = ["rname, phi, psi, chi1, chi2, chi3, chi4, conf1, conf2, conf3, conf4"]
+for rname, entry_list in sidechain_data.iteritems():
+ rot_id = sidechain.TLCToRotID(rname)
+ for e, dihedral_angles in zip(entry_list, dihedral_data[rname]):
+ temp = [rname, "%.4f"%(dihedral_angles[0]), "%.4f"%(dihedral_angles[1]),
+ "%.4f"%(e.chi1), "%.4f"%(e.chi2), "%.4f"%(e.chi3), "%.4f"%(e.chi4),
+ str(sidechain.GetDihedralConfiguration(e, rot_id, 0)),
+ str(sidechain.GetDihedralConfiguration(e, rot_id, 1)),
+ str(sidechain.GetDihedralConfiguration(e, rot_id, 2)),
+ str(sidechain.GetDihedralConfiguration(e, rot_id, 3))]
+
+ file_content.append(','.join(temp))
+
+outfile = open(out_path, 'w')
+outfile.write('\n'.join(file_content))
+outfile.close()
+
diff --git a/extras/data_generation/rotamer_library/penultimate.csv b/extras/data_generation/rotamer_library/penultimate.csv
deleted file mode 100755
index 8f4e358125c69728d11444394ebb7385d90b6da0..0000000000000000000000000000000000000000
--- a/extras/data_generation/rotamer_library/penultimate.csv
+++ /dev/null
@@ -1,211 +0,0 @@
-#This file is simply copied and pasted from the online publication...
-#Note, that it can't be changed anymore, so the according script can
-#parse it in a simple manner...
-
-Arginine, , , , , , , , , , , , , , , , ,
-ptp85°b,3,<1%c,0%,1%,<1%, ,62, ,180, ,65, ,85, , , ,
-ptp180°,11,1%,0%,2%,2%,71,62,171,180,65,65,-161,-175,14,17,10,13
-ptt85°,16,2%,1%,2%,2%,65,62,-178,180,-179,180,88,85,13,14,13,17
-ptt180°,16,2%,1%,2%,2%,59,62,176,180,-178,180,-177,180,15,13,15,19
-ptt-85°,15,2%,1%,2%,2%,66,62,-176,180,-178,180,-83,-85,15,14,12,14
-ptm180°,6,1%,0%,1%,1%, ,62, ,180, ,-65, ,175, , , ,
-ptm-85°,5,1%,0%,0%,1%, ,62, ,180, ,-65, ,-85, , , ,
-tpp85°,11,1%,3%,1%,<1%,-178,-177,57,65,57,65,85,85,13,13,12,15
-tpp180°,8,1%,1%,0%,1%, ,-177, ,65, ,65, ,-175, , , ,
-tpt85°,20,2%,3%,2%,2%,177,-177,64,65,180,180,86,85,14,13,15,14
-tpt180°,15,2%,3%,1%,1%,179,-177,60,65,178,180,163,180,13,17,14,17
-ttp85°,33,4%,5%,3%,3%,-179,-177,177,180,65,65,83,85,14,17,13,15
-ttp180°,25,3%,5%,3%,1%,-178,-177,-178,180,65,65,-162,-175,14,16,14,26
-ttp-105°,9,1%,1%,1%,1%, ,-177, ,180, ,65, ,-105, , , ,
-ttt85°,19,2%,2%,2%,2%,-175,-177,176,180,179,180,83,85,14,14,13,14
-ttt180°,33,4%,3%,7%,3%,-179,-177,177,180,-179,180,170,180,15,13,12,27
-ttt-85°,26,3%,3%,3%,2%,-179,-177,179,180,180,180,-86,-85,15,14,14,15
-ttm105°,10,1%,2%,1%,<1%,-178,-177,170,180,-66,-65,107,105,15,16,15,15
-ttm180°,13,1%,<1%,4%,1%,180,-177,-178,180,-67,-65,176,175,15,12,11,15
-ttm-85°,28,3%,3%,3%,3%,-175,-177,-178,180,-65,-65,-84,-85,14,16,15,14
-mtp85°,22,2%,2%,3%,2%,-69,-67,177,180,64,65,84,85,13,17,13,13
-mtp180°,45,5%,4%,3%,6%,-65,-67,176,180,64,65,-174,-175,12,19,13,19
-mtp-105°,7,1%,0%,2%,1%,-62,-67,179,180,67,65,-113,-105,11,15,13,15
-mtt85°,34,4%,4%,4%,3%,-67,-67,178,180,179,180,83,85,12,19,13,19
-mtt180°,89,9%,9%,5%,12%,-67,-67,-178,180,-177,180,174,180,14,13,13,21
-mtt-85°,53,6%,4%,7%,6%,-66,-67,-177,180,-179,180,-83,-85,13,13,13,13
-mtm105°,15,2%,1%,1%,2%,-68,-67,-179,180,-65,-65,103,105,12,13,13,15
-mtm180°,48,5%,1%,4%,8%,-68,-67,173,180,-64,-65,180,175,14,17,13,30
-mtm-85°,54,6%,13%,2%,3%,-69,-67,-167,-167,-63,-65,-86,-85,14,13,13,13
-mmt85°,7,1%,1%,1%,1%, ,-62, ,-68, ,180, ,85, , , ,
-mmt180°,18,2%,1%,3%,2%,-63,-62,-66,-68,-179,180,-168,180,13,13,10,29
-mmt-85°,22,2%,<1%,4%,3%,-60,-62,-72,-68,-178,180,-92,-85,14,13,15,13
-mmm180°,11,1%,<1%,2%,2%,-64,-62,-74,-68,-67,-65,172,175,14,15,10,13
-mmm-85°,22,2%,2%,3%,3%,-62,-62,-64,-68,-61,-65,-82,-85,14,13,15,13
- , ,82%,79%,81%,84%, , , , , , , , , , , ,
- ,769/938d, ,234,146,389, , , , , , , , , , , ,
-Lysine, , , , , , , , , , , , , , , , ,
-ptpt,7,1%,0%,2%,<1%, ,62, ,180, ,68, ,180, , , ,
-pttp,13,1%,0%,1%,2%,63,62,-170,180,-177,180,72,65,13,14,14,11
-pttt,29,2%,0%,4%,3%,63,62,-178,180,178,180,-179,180,13,13,13,10
-pttm,8,1%,0%,1%,1%, ,62, ,180, ,180, ,-65, , , ,
-ptmt,5,<1%,0%,1%,<1%, ,62, ,180, ,-68, ,180, , , ,
-tptp,11,1%,1%,1%,1%,179,-177,59,68,163,180,60,65,13,12,10,11
-tptt,32,3%,5%,1%,2%,179,-177,62,68,173,180,171,180,10,10,13,14
-tptm,7,1%,1%,1%,<1%, ,-177, ,68, ,180, ,-65,14,9,12,10
-ttpp,12,1%,1%,<1%,1%, ,-177, ,180, ,68, ,65, , , ,
-ttpt,25,2%,2%,5%,1%,180,-177,179,180,78,68,179,180,14,12,14,14
-tttp,49,4%,5%,5%,3%,-177,-177,180,180,171,180,63,65,14,13,12,12
-tttt,162,13%,17%,19%,10%,-177,-177,178,180,179,180,180,180,13,13,15,13
-tttm,37,3%,4%,2%,3%,-177,-177,172,180,178,180,-72,-65,12,13,15,13
-ttmt,20,2%,2%,4%,1%,-175,-177,-174,180,-69,-68,179,180,14,14,10,15
-ttmm,5,<1%,1%,0%,<1%, ,-177, ,180, ,-68, ,-65, , , ,
-mptt,4,<1%,0%,0%,1%, ,-90, ,68, ,180, ,180, , , ,
-mtpp,12,1%,1%,1%,1%,-69,-67,-179,180,70,68,67,65,10,9,10,13
-mtpt,38,3%,4%,2%,3%,-69,-67,164,180,62,68,-179,180,12,13,11,9
-mttp,42,3%,2%,4%,4%,-67,-67,-176,180,174,180,76,65,13,13,14,14
-mttt,244,20%,23%,14%,21%,-67,-67,176,180,179,180,177,180,14,13,12,14
-mttm,56,5%,3%,5%,6%,-67,-67,-179,180,-179,180,-63,-65,13,12,13,14
-mtmt,40,3%,6%,2%,3%,-70,-67,-170,180,-66,-68,-175,180,12,13,14,13
-mtmm,12,1%,0%,1%,1%,-70,-67,-179,180,-66,-68,-64,-65,12,12,12,11
-mmtp,9,1%,<1%,0%,1%, ,-62, ,-68, ,180, ,65, , , ,
-mmtt,77,6%,3%,5%,8%,-58,-62,-61,-68,-177,180,-179,180,12,13,13,13
-mmtm,18,1%,1%,1%,2%,-59,-62,-69,-68,-176,180,-70,-65,14,12,10,15
-mmmt,10,1%,<1%,1%,1%,-59,-62,-58,-68,-75,-68,-174,180,12,13,10,15
- , ,81%,82%,80%,82%, , , , , , , , , , , ,
- ,984/1209, ,261,194,529,,,,,,,,,,,,
-Methionine, , , , , , , , , , , , , , , ,,
-ptp,12,2%,1%,3%,3%,68,62,-167,180,88,75, ,11,17,12,,
-ptm,17,3%,1%,6%,4%,67,62,174,180,-78,-75, ,9,10,9,,
-tpp,30,5%,8%,2%,5%,-177,-177,66,65,75,75, ,10,15,15,,
-tpt,9,2%,1%,4%,1%,179,-177,67,65,-179,180, ,9,8,9,,
-ttp,28,5%,7%,7%,2%,176,-177,178,180,73,75, ,10,11,11,,
-ttt,17,3%,5%,2%,2%,180,-177,171,180,174,180, ,9,9,19,,
-ttm,36,7%,3%,10%,8%,-177,-177,176,180,-78,-75, ,10,10,13,,
-mtp,92,17%,22%,10%,17%,-68,-67,177,180,72,75, ,10,12,14,,
-mtt,43,8%,9%,8%,7%,-67,-67,177,180,-178,180, ,10,13,15,,
-mtm,58,11%,12%,11%,9%,-67,-67,-177,180,-76,-75, ,12,11,16,,
-mmp,15,3%,3%,1%,4%,-64,-65,-63,-65,103,103, ,9,10,10,,
-mmt,10,2%,0%,2%,3%,-63,-65,-64,-65,180,180, ,12,14,19,,
-mmm,105,19%,21%,16%,19%,-66,-65,-60,-65,-67,-70, ,11,13,16,,
- , ,86%,91%,84%,83%, , , , , , , , , , ,,
- ,472/550, ,175,112,185, , , , , , , , , , ,,
-Glutamate, , , , , , , , , , , , , , , ,,
-pt-20°,80,5%,1%,9%,7%,63,62,-175,180,-18,-20,-90 to 90,14,13,23,,
-pm0°,32,2%,0%,0%,4%,71,70,-79,-80,5,0,-50 to 50,14,13,17,,
-tp10°,91,6%,10%,2%,6%,-177,-177,65,65,13,10,-10 to 90,14,13,17,,
-tt 0°,350,24%,25%,42%,18%,-177,-177,178,180,2,0,-90 to 90,14,14,30,,
-tm-20°,17,1%,1%,1%,1%, ,-177, ,-80, ,-25,-50 to 10,13,13,15,,
-mp0°,88,6%,<1%,2%,10%,-65,-65,85,85,-3,0,-60 to 60,14,13,25,,
-mt-10°,484,33%,36%,29%,32%,-67,-67,177,180,-10,-10,-90 to 90,13,16,25,,
-mm-40°,197,13%,19%,7%,12%,-65,-65,-58,-65,-40,-40,-90 to 30,14,14,25,,
- , ,91%,92%,92%,90%, , , , , , , , , , ,,
- ,1339/1470, ,394,225,720, , , , , , , , , , ,,
-Glutamine, , , , , , , , , , , , , , , ,,
-pt 20°,37,4%,1%,5%,6%,64,62,180,180,20,20,-90 to 90,13,14,16,,
-pm0°,15,2%,0%,1%,3%, ,70, ,-75, ,0,-60 to 60, , , ,,
-tp-100°,14,2%,4%,2%,<1%, ,-177, ,65, ,-100,-150 to 0, , , ,,
-tp60°,78,9%,13%,9%,7%,-175,-177,64,65,60,60,0 to 90,14,15,24,,
-tt 0°,140,16%,16%,29%,12%,-174,-177,173,180,-5,0,-90 to 90,14,13,40,,
-mp0°,24,3%,<1%,1%,5%, ,-65, ,85, ,0,-60 to 60, , , ,,
-mt-30°,304,35%,40%,26%,36%,-67,-67,177,180,-25,-25,-90 to 90,16,15,37,,
-mm-40°,127,15%,12%,13%,17%,-66,-65,-60,-65,-40,-40,-95 to 0,16,18,26,,
-mm100°,22,3%,4%,1%,2%, ,-65, ,-65, ,100,0 to 150, , , ,,
- , ,88%,89%,86%,88%, , , , , , , , , , ,,
- ,761/863, ,229,137,395, , , , , , ,χ2, , , ,,
-Aspartate, , , , , , , , , , , ,range, , , ,,
-p-10°,203,10%,1%,2%,13%,61,62,-4,-10, , ,-90 to 0,9,19, ,,
-p30°,194,9%,1%,5%,12%,65,62,9,30, , ,0 to 90,8,14, ,,
-t0°,438,21%,8%,44%,20%,-176,-177,1,0, , ,-50 to 50,12,30, ,,
-t70°,118,6%,11%,7%,4%,-179,-177,65,65, , ,50 to 90,12,18, ,,
-m-20°,1088,51%,77%,38%,47%,-71,-70,-15,-15, , ,-90 to 20,10,16, ,,
- , ,96%,97%,95%,96%, , , , , , , , , , ,,
- ,2041/2124, ,365,232,1444, , , , , , , , , , ,,
-Asparagine, , , , , , , , , , , , , , , ,,
-p-10°,103,7%,0%,1%,10%,63,62,-13,-10, , ,-90 to 0,8,9, ,,
-p30°,132,9%,<1%,7%,12%,64,62,34,30, , ,0 to 90,6,7, ,,
-t-20°,177,12%,5%,21%,12%,-174,-174,-20,-20, , ,-120 to 0,5,21, ,,
-t30°,228,15%,13%,18%,15%,-168,-177,31,30, , ,0 to 80,14,22, ,,
-m-20°,580,39%,65%,28%,33%,-71,-65,-23,-20, , ,-60 to 10,10,20, ,,
-m-80°,118,8%,8%,9%,8%,-71,-65,-76,-75, , ,-100 to -60,9,9, ,,
-m120°,58,4%,3%,3%,4%,-64,-65,132,120, , ,60 to 160,9,18, ,,
- , ,94%,95%,88%,95%, , , , , , , , , , ,,
- ,1396/1490, ,293,179,924,,,,,,,,,,,,
-Isoleucine, , , , , , , , , , , , ,,,,,
-pp,10,1%,<1%,1%,<1%, ,62, ,100, , ,,,,,,
-pt,216,13%,4%,13%,22%,61,62,171,170, ,10,10,,,,,
-tp,36,2%,2%,1%,4%,-169,-177,66,66, ,13,11,,,,,
-tt,127,8%,1%,8%,14%,-174,-177,167,165, ,13,11,,,,,
-mp,19,1%,0%,2%,1%, ,-65, ,100, , , ,,,,,
-mt,993,60%,81%,58%,41%,-66,-65,169,170, ,10,10,,,,,
-mm,242,15%,10%,16%,17%,-57,-57,-59,-60, ,10,10,,,,,
- , ,99%,99%,98%,99%, , , , , , , ,,,,,
- ,1643/1667, ,496,629,518, , , , , , , ,,,,,
-Leucine, , , , , , , , , , , , ,,,,,
-pp,21,1%,<1%,2%,1%, ,62, ,80, , , ,,,,,
-tp,750,29%,30%,36%,23%,177,-177,63,65, ,10,10,,,,,
-tt,49,2%,1%,3%,1%,-172,-172,147,145,120 to 180,9,9,,,,,
-mp,63,2%,1%,5%,2%,-85,-85,66,65,45 to 105,11,14,,,,,
-mt,1548,59%,62%,46%,66%,-65,-65,174,175, ,11,11,,,,,
- , ,93%,95%,93%,93%, , , , , , , ,,,,,
- ,2431/2602, ,836,644,951, , , , , , , ,,,,,
-Histidine, , , , , , , , , , , , ,,,,,
-p-80°,51,9%,0%,6%,13%,60,62,-75,-75,-120 to -50,10,12,,,,,
-p80°,26,4%,0%,4%,6%,61,62,78,80,50 to 120,13,10,,,,,
-t-160°,31,5%,5%,14%,1%,-178,-177,-163,-165,150 to -120,12,20,,,,,
-t-80°,64,11%,17%,9%,9%,-173,-177,-81,-80,-120 to -50,10,22,,,,,
-t60°,94,16%,24%,17%,12%,-178,-177,62,60,50 to 120,13,19,,,,,
-m-70°,174,29%,26%,30%,30%,-60,-65,-69,-70,-120 to -30,11,23,,,,,
-m170°,44,7%,9%,3%,9%,-63,-65,165,165,120 to -160,10,16,,,,,
-m80°,78,13%,14%,10%,14%,-66,-65,83,80,50 to 120,11,18,,,,,
- , ,94%,94%,92%,95%, , , , , , , ,,,,,
- ,562/598, ,124,143,295, , , , , , , ,,,,,
-Tryptophan, , , , , , , , , , , , ,,,,,
-p-90°,67,11%,2%,13%,14%,58,62,-87,-90,-130 to -60,12,10,,,,,
-p90°,34,6%,1%,9%,6%,60,62,92,90,60 to 130,12,8,,,,,
-t-105°,100,16%,27%,10%,14%,178,-177,-105,-105,-130 to -60,16,14,,,,,
-t90°,109,18%,28%,14%,15%,-178,-177,88,90,0 to 100,10,11,,,,,
-m-90°,31,5%,0%,7%,7%,-70,-65,-87,-90,-130 to -60,9,12,,,,,
-m0°,48,8%,15%,2%,8%,-66,-65,-4,-5,-40 to 20,9,20,,,,,
-m95°,195,32%,22%,43%,29%,-69,-65,95,95,60 to 130,11,19,,,,,
- , ,94%,95%,98%,92%, , , , , , , ,,,,,
- ,584/618, ,140,175,269, , , , , , , ,,,,,
-Tyrosine, , , , , , , , , , , , ,,,,,
-p90°,182,13%,1%,21%,12%,63,62,89,90,"60 to 90 -90 to -60",13,13,,,,,
-t80°,486,34%,55%,25%,30%,176,-177,77,80,"20 to 90 -90 to -75",11,14,,,,,
-m-85°,618,43%,26%,50%,45%,-65,-65,-87,-85,"50 to 90 -90 to -50",11,21,,,,,
-m-30°,124,9%,15%,4%,9%,-64,-65,-42,-30,"-50 to 0 0 to 50",11,18,,,,,
- , ,98%,97%,99%,97%, , , , , , , ,,,,,
- ,1410/1443, ,290,468,652, , , , ,"(for Tyr, Phe 90° = -90°)",, ,,,,,
-Phenylalanine, , , , , , , , , , , , ,,,,,
-p90°,202,13%,1%,24%,11%,59,62,88,90,"60 to 90 -90 to -60",11,11,,,,,
-t80°,522,33%,57%,18%,29%,177,-177,80,80,"20 to 90 -90 to -75",13,17,,,,,
-m-85°,697,44%,29%,51%,47%,-64,-65,-83,-85,"50 to 90 -90 to -50",12,17,,,,,
-m-30°,149,9%,12%,5%,11%,-64,-65,-19,-30,"-50 to 0 0 to 50",9,20,,,,,
- , ,98%,97%,99%,98%, , , , , , , ,,,,,
- ,1570/1599, ,389,514,667, , , , , , , ,,,,,
-Proline, , , , , , , , , , , , ,,,,,
-Cγ endo,379,44%,23%,54%,43%,30,30, , ,15 to 60,7, ,,,,,
-Cγ exo,372,43%,68%,28%,44%,-29,-30, , ,-60 to -15,6, ,,,,,
-"cis Cγ endo",56,6%,0%,1%,7%,31,30, , ,15 to 60,5, ,,,,,
- , ,93%,91%,84%,94%, , , , , , , ,,,,,
- ,807/928, ,20,57,730,,,,,,,,,,,,
-Threonine, , , , , , , , , ,,,,,,,,
-p,1200,49%,25%,31%,65%,59,62, ,10,,,,,,,,
-t,169,7%,0%,13%,6%,-171,-175, ,6,,,,,,,,
-m,1062,43%,74%,55%,29%,-61,-65, ,7,,,,,,,,
- , ,99%,100%,99%,99%, , , ,,,,,,,,,
- ,2431/2447, ,395,672,1364, , , ,,,,,,,,,
-Valine, , , , , , , , ,,,,,,,,,
-p,169,6%,2%,8%,8%,63,63,=“177”f,8,,,,,,,,
-t,1931,73%,90%,72%,63%,175,175,Err:501,8,,,,,,,,
-m,526,20%,7%,20%,28%,-64,-60,Err:501,7,,,,,,,,
- , ,99%,100%,99%,99%, , , ,,,,,,,,,
- ,2626/2649, ,622,1080,924, , , ,,,,,,,,,
-Serine, , , , , , , , ,,,,,,,,,
-p,1201,48%,33%,36%,55%,64,62, ,10,,,,,,,,
-t,541,22%,22%,34%,18%,178,-177, ,11,,,,,,,,
-m,714,29%,44%,29%,25%,-65,-65, ,9,,,,,,,,
- , ,98%,98%,100%,98%, , , ,,,,,,,,,
- ,2456/2498, ,350,485,1621, , , ,,,,,,,,,
-Cysteine, , , , , , , , ,,,,,,,,,
-p,64,23%,5%,23%,34%,55,62, ,14,,,,,,,,
-t,74,26%,20%,45%,21%,-177,-177, ,10,,,,,,,,
-m,142,50%,75%,32%,43%,-65,-65, ,11,,,,,,,,
- , ,99%,100%,100%,98%, , , ,,,,,,,,,
- ,280/285, ,85,65,130,,,,,,,,,,,,
diff --git a/extras/data_generation/rotamer_library/rotamer_lib_creation.cmd b/extras/data_generation/rotamer_library/rotamer_lib_creation.cmd
new file mode 100644
index 0000000000000000000000000000000000000000..f1cb87ee6eb730145a73cc09292d5b12a2090e98
--- /dev/null
+++ b/extras/data_generation/rotamer_library/rotamer_lib_creation.cmd
@@ -0,0 +1,22 @@
+ost do_bbdep_lib.py raw_data.csv ARG
+ost do_bbdep_lib.py raw_data.csv ASN
+ost do_bbdep_lib.py raw_data.csv ASP
+ost do_bbdep_lib.py raw_data.csv GLN
+ost do_bbdep_lib.py raw_data.csv GLU
+ost do_bbdep_lib.py raw_data.csv LYS
+ost do_bbdep_lib.py raw_data.csv SER
+ost do_bbdep_lib.py raw_data.csv CYH
+ost do_bbdep_lib.py raw_data.csv CYD
+ost do_bbdep_lib.py raw_data.csv CYS
+ost do_bbdep_lib.py raw_data.csv MET
+ost do_bbdep_lib.py raw_data.csv TRP
+ost do_bbdep_lib.py raw_data.csv TYR
+ost do_bbdep_lib.py raw_data.csv THR
+ost do_bbdep_lib.py raw_data.csv VAL
+ost do_bbdep_lib.py raw_data.csv ILE
+ost do_bbdep_lib.py raw_data.csv LEU
+ost do_bbdep_lib.py raw_data.csv CPR
+ost do_bbdep_lib.py raw_data.csv TPR
+ost do_bbdep_lib.py raw_data.csv PRO
+ost do_bbdep_lib.py raw_data.csv HIS
+ost do_bbdep_lib.py raw_data.csv PHE
diff --git a/extras/data_generation/structure_db/README b/extras/data_generation/structure_db/README
index f86fa19e8c37a82083e61ecc780679ff606a4dbb..2286f335b4c01c5f7b6350327db905617bc151d7 100644
--- a/extras/data_generation/structure_db/README
+++ b/extras/data_generation/structure_db/README
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
We provide several scripts to obtain a StructureDB.
More information regarding the different steps you'll find in the comments
in the corresponding scripts.
diff --git a/extras/data_generation/structure_db/assign_structure_profiles.py b/extras/data_generation/structure_db/assign_structure_profiles.py
index 2c14c44087fbd2a84be740c1f626565cfae81dd4..ed1b57098a16902876dc0085fc08d1e8f3f05f3b 100644
--- a/extras/data_generation/structure_db/assign_structure_profiles.py
+++ b/extras/data_generation/structure_db/assign_structure_profiles.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os
from promod3 import loop
from ost import seq
diff --git a/extras/data_generation/structure_db/build_structure_db.py b/extras/data_generation/structure_db/build_structure_db.py
index 450899c4e2d2f9e95ee001cbaf19f6e2032543e5..a4b6252a1f68498713bee4d127b227a9d0051f1a 100644
--- a/extras/data_generation/structure_db/build_structure_db.py
+++ b/extras/data_generation/structure_db/build_structure_db.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
import os
import traceback
diff --git a/extras/data_generation/structure_db/create_structure_profiles.py b/extras/data_generation/structure_db/create_structure_profiles.py
index a0e335925a4ed4fa5ced2e07a44bd0b379da4bb8..eb00492e24de84e80509522a402a7f57aaf20997 100644
--- a/extras/data_generation/structure_db/create_structure_profiles.py
+++ b/extras/data_generation/structure_db/create_structure_profiles.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os
import sys
from promod3 import loop
diff --git a/extras/data_generation/structure_db/get_data_from_smtl.py b/extras/data_generation/structure_db/get_data_from_smtl.py
index 7965046a728bd55260ab275073d7449ce7147db7..48806e713c9677b8ff8c4c35761f141793cdece3 100644
--- a/extras/data_generation/structure_db/get_data_from_smtl.py
+++ b/extras/data_generation/structure_db/get_data_from_smtl.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import time
import os
import pickle
diff --git a/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py b/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py
index d982a468161a2ccfbcceb994961f4f7e706f543d..d0e195c9555dbcea76b74d0e1fbcb4a4ec0bea86 100644
--- a/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py
+++ b/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
import os
diff --git a/extras/data_generation/torsion_sampler/train_torsion_sampler.py b/extras/data_generation/torsion_sampler/train_torsion_sampler.py
index 1c6eb9d809068664075f554c9aa8a1dde93db2f1..5e1181b51a80ab88bfee2b020a7ceffd52bfd1cc 100644
--- a/extras/data_generation/torsion_sampler/train_torsion_sampler.py
+++ b/extras/data_generation/torsion_sampler/train_torsion_sampler.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import loop
from ost import mol
import os
diff --git a/extras/pre_commit/pm3_csc/__init__.py b/extras/pre_commit/pm3_csc/__init__.py
index 5c7540fe7a00cb9de5098adefb7e591f53f77673..d526e2ccc561f65cb13374753646fb3b92a63d0e 100644
--- a/extras/pre_commit/pm3_csc/__init__.py
+++ b/extras/pre_commit/pm3_csc/__init__.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Module to enforce ProMod3's coding policy.
"""
diff --git a/extras/pre_commit/pm3_csc/base.py b/extras/pre_commit/pm3_csc/base.py
index 4b0bc2efaf2f57f9b6e089a38006a6b96c5989ad..17a763716534776a87b9463189a966a0ec0875e7 100644
--- a/extras/pre_commit/pm3_csc/base.py
+++ b/extras/pre_commit/pm3_csc/base.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
This is a bunch of default functions for the coding style checker.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/__init__.py b/extras/pre_commit/pm3_csc/filecheck/__init__.py
index 5ba0033bb887a15c1215a16c3588dcfed4ffb9a8..1d614bb5528fbe5dd31812b610874762f48b3943 100644
--- a/extras/pre_commit/pm3_csc/filecheck/__init__.py
+++ b/extras/pre_commit/pm3_csc/filecheck/__init__.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Module hosting the code/ file check system.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/base.py b/extras/pre_commit/pm3_csc/filecheck/base.py
index 134a5069a9cdd868b2d190555411f84381b5dd72..95ab2274f992a4e2b9322eb87db537431dbd55a1 100644
--- a/extras/pre_commit/pm3_csc/filecheck/base.py
+++ b/extras/pre_commit/pm3_csc/filecheck/base.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Generic class for checking code from files.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/ccode.py b/extras/pre_commit/pm3_csc/filecheck/ccode.py
index 6ac3e170c696cac9fed2f8809fa7410a1aa95a33..e5bfe8be8a20cbd45e975be1fdf79e43eb9225ed 100644
--- a/extras/pre_commit/pm3_csc/filecheck/ccode.py
+++ b/extras/pre_commit/pm3_csc/filecheck/ccode.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking C/ C++ code.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/cmake.py b/extras/pre_commit/pm3_csc/filecheck/cmake.py
index 9bc06c24f7c5315da19f9ce9f17896929ea7538f..fde92de2138f904f40e9ce3d5a333942ebdae0de 100644
--- a/extras/pre_commit/pm3_csc/filecheck/cmake.py
+++ b/extras/pre_commit/pm3_csc/filecheck/cmake.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking CMake files.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/python.py b/extras/pre_commit/pm3_csc/filecheck/python.py
index b307d84acd15b0479697dc3b10cd0654e517a7b8..692c42e03cd1621966938b9df5788caab116f49c 100644
--- a/extras/pre_commit/pm3_csc/filecheck/python.py
+++ b/extras/pre_commit/pm3_csc/filecheck/python.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking Python code.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/rest.py b/extras/pre_commit/pm3_csc/filecheck/rest.py
index 315c2f86dfde1eb55012e147454bf298adcb6391..a3e5a4c62e0e6101da5cb7f47d3d8dfb3f47e0a2 100644
--- a/extras/pre_commit/pm3_csc/filecheck/rest.py
+++ b/extras/pre_commit/pm3_csc/filecheck/rest.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking reStructuredText docmentation files.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/shellscript.py b/extras/pre_commit/pm3_csc/filecheck/shellscript.py
index 0175f25c0d8bee28783b851f441c99f37e938a7e..73a958957c95817d0d0f7c98a97c7b3a3c1f2f95 100644
--- a/extras/pre_commit/pm3_csc/filecheck/shellscript.py
+++ b/extras/pre_commit/pm3_csc/filecheck/shellscript.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking shell code files.
"""
diff --git a/extras/pre_commit/pm3_csc/filecheck/text.py b/extras/pre_commit/pm3_csc/filecheck/text.py
index 5ff81c3233f77677cc83cc759733dc1afb4b7a5f..d4b59f3721589d10b424f232e7897e24bff9aae3 100644
--- a/extras/pre_commit/pm3_csc/filecheck/text.py
+++ b/extras/pre_commit/pm3_csc/filecheck/text.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Checking just text.
"""
diff --git a/extras/pre_commit/pm3_csc/git.py b/extras/pre_commit/pm3_csc/git.py
index cba5c9c5f91667483144c0354737533470b9e0fe..cebe8327860f2dbffff7541d141ce816db0fd25d 100644
--- a/extras/pre_commit/pm3_csc/git.py
+++ b/extras/pre_commit/pm3_csc/git.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Keep all the functions calling git in one place.
"""
diff --git a/extras/pre_commit/pre-commit b/extras/pre_commit/pre-commit
index 1c216048ca4d9596f273ae5bcdd5c38414d1ad52..df8eb506803ee6c928d7451a5e359cd30fe95925 100644
--- a/extras/pre_commit/pre-commit
+++ b/extras/pre_commit/pre-commit
@@ -1,6 +1,22 @@
#!/usr/bin/env python
# pylint: disable=invalid-name
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import subprocess, sys, re, os, difflib
# prevent creating .pyc files in the source directory
diff --git a/extras/sanity_checks/Makefile b/extras/sanity_checks/Makefile
index 454cab058d2dafb2d214cbdc1dc5f96382581e81..79d2b5862144b7926d6ba11628ad060085e67d85 100644
--- a/extras/sanity_checks/Makefile
+++ b/extras/sanity_checks/Makefile
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
########
# SETUP
########
diff --git a/extras/sanity_checks/README b/extras/sanity_checks/README
index 28977485bcb889baf193bd940597244513fdbec4..81bbd702a922c5ba1504ec3ab355ca54b25265e4 100644
--- a/extras/sanity_checks/README
+++ b/extras/sanity_checks/README
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
Check installation of PM3:
==========================
diff --git a/extras/sanity_checks/run_pipeline.py b/extras/sanity_checks/run_pipeline.py
index 4fd77a97db72a32b82ede9b5a164b121cf69f1a7..556ea8f82304f97e6172d9302ece99e87cd4a893 100644
--- a/extras/sanity_checks/run_pipeline.py
+++ b/extras/sanity_checks/run_pipeline.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import ost
from ost import io, mol
from promod3 import modelling
diff --git a/extras/sanity_checks/test_all.py b/extras/sanity_checks/test_all.py
index 73161a29ac9406235f447b77b25dac9717beadd1..d528c7a0acd0e7c826688bcd73c1b86cc6969b62 100644
--- a/extras/sanity_checks/test_all.py
+++ b/extras/sanity_checks/test_all.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os
import sys
import unittest
diff --git a/extras/sanity_checks/test_cpp.cc b/extras/sanity_checks/test_cpp.cc
index 1d4a18c232ca7e8b4aa1fb2f4a7337d5546e038b..9c8e3365517e69d0dcf73637e9308cf2b4b8a6fe 100644
--- a/extras/sanity_checks/test_cpp.cc
+++ b/extras/sanity_checks/test_cpp.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
// Test code for low-level ProMod3 features
#include <ost/base.hh>
diff --git a/extras/sanity_checks/test_module.py b/extras/sanity_checks/test_module.py
index 78437c9e362c62d8852d3bd4a0a0b21e36369fe8..db97a6d249431ce36feb6f82e0fa32d7a7c4a661 100644
--- a/extras/sanity_checks/test_module.py
+++ b/extras/sanity_checks/test_module.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import promod3
print "ProMod3-version =", promod3.__version__
diff --git a/extras/scoring_weight_training/README b/extras/scoring_weight_training/README
index 523a8ecd3bc4c03f70ce43b2a2d4b7885b3c0004..3c6db6b77663e2fe55690fe2586d0d444eb758a6 100644
--- a/extras/scoring_weight_training/README
+++ b/extras/scoring_weight_training/README
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
This folder contains scripts that were used to train weights for the scoring
functions used in loop selection in the pipeline. You need a compiled and
working version of ProMod3 to run these scripts. Scripts are provided as-is!
diff --git a/extras/scoring_weight_training/analyze_bft_candidates.py b/extras/scoring_weight_training/analyze_bft_candidates.py
index 27a12999478a9c75aba44878f20e02f187ba654f..1c1d28690117b22c9320356ef0d9b66fbbd48a4f 100644
--- a/extras/scoring_weight_training/analyze_bft_candidates.py
+++ b/extras/scoring_weight_training/analyze_bft_candidates.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: analyze number of loop candidates in BFT (also considering within_bounds)
IN:
diff --git a/extras/scoring_weight_training/analyze_bft_score_correlations.py b/extras/scoring_weight_training/analyze_bft_score_correlations.py
index c066cdbc6fdee0ba5be883529f91ad2a22d68cfc..a399df014ca329be042963d464bed0afa88833af 100644
--- a/extras/scoring_weight_training/analyze_bft_score_correlations.py
+++ b/extras/scoring_weight_training/analyze_bft_score_correlations.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: analyze correlation of scores to ca_rmsd
IN:
diff --git a/extras/scoring_weight_training/analyze_bft_scores.py b/extras/scoring_weight_training/analyze_bft_scores.py
index 423f9d92b3a08ea45ff92406368dc5097a4d64b0..a8abdf597f7ea63cbbc0db5fddb494f3d67f77c6 100644
--- a/extras/scoring_weight_training/analyze_bft_scores.py
+++ b/extras/scoring_weight_training/analyze_bft_scores.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: analyze performance of single scores and effect of within_bounds
-> need to manually tune wb_mode variable below to check within_bounds
diff --git a/extras/scoring_weight_training/analyze_weights.py b/extras/scoring_weight_training/analyze_weights.py
index 719bdc7354bdb2ef9ff122efda90ad5be1c61219..d04d40a776bdcec8ef8bd921cff45cf7b24452f9 100644
--- a/extras/scoring_weight_training/analyze_weights.py
+++ b/extras/scoring_weight_training/analyze_weights.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: analyze optimized scoring weights
IN:
diff --git a/extras/scoring_weight_training/collect_optimized_weights.py b/extras/scoring_weight_training/collect_optimized_weights.py
index 66c0dfba8b32d90d5e64641441c47977cf4c3f10..02544620abec130adbf7f33310a271a3f81c25bc 100644
--- a/extras/scoring_weight_training/collect_optimized_weights.py
+++ b/extras/scoring_weight_training/collect_optimized_weights.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: collect optimized weights from run_all_optimizations*.py
IN:
diff --git a/extras/scoring_weight_training/common.py b/extras/scoring_weight_training/common.py
index a46c419d7b54d331265e7a6040c52fdbee9f2135..f0bcf55b2a0c8e0a167907ee7528693962fdf91f 100644
--- a/extras/scoring_weight_training/common.py
+++ b/extras/scoring_weight_training/common.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Common functionality for analysis scripts.'''
import json, random
diff --git a/extras/scoring_weight_training/generate_bft.py b/extras/scoring_weight_training/generate_bft.py
index f7ae946a07b6c3fedd151dcd3f95d712fae25d8d..1687e0e24f9653fee838b68017c088ccb3393004 100644
--- a/extras/scoring_weight_training/generate_bft.py
+++ b/extras/scoring_weight_training/generate_bft.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: combine chunks into a single BFT
IN:
diff --git a/extras/scoring_weight_training/generate_bft_chunks.py b/extras/scoring_weight_training/generate_bft_chunks.py
index c31ca52f887e7e6704e7a053a67d2ef4102cf17f..ef0bcdf35e0e7878feae0af1a52f67a46a06e000 100644
--- a/extras/scoring_weight_training/generate_bft_chunks.py
+++ b/extras/scoring_weight_training/generate_bft_chunks.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: extract a chunk of the BFT
IN:
diff --git a/extras/scoring_weight_training/generate_bft_dbs.py b/extras/scoring_weight_training/generate_bft_dbs.py
index f6f931b357207094a059f8e42e70c8b7c99b90a5..863f922125b1a2b80d1aef301462b3ca83697be4 100644
--- a/extras/scoring_weight_training/generate_bft_dbs.py
+++ b/extras/scoring_weight_training/generate_bft_dbs.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: extract subset of DBs for clean scoring
IN: fragments.json from generate_bft_testset.py
diff --git a/extras/scoring_weight_training/generate_bft_testset.py b/extras/scoring_weight_training/generate_bft_testset.py
index d7fc423f3eba8c0bb8b908ed2bd9268def37a135..ac46ce477ced492e7964d76e6844631dbbc6ee7c 100644
--- a/extras/scoring_weight_training/generate_bft_testset.py
+++ b/extras/scoring_weight_training/generate_bft_testset.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: extract loop examples from structure DB
OUT: fragments.json: list of fragment infos ([chain_idx, offset, length])
diff --git a/extras/scoring_weight_training/generate_training_bft.py b/extras/scoring_weight_training/generate_training_bft.py
index bf46da2c4eb1390c01aeb10e6e665d3a37f9a40c..3d4b5984321db8a0bb54c73ee7167a34227f0e71 100644
--- a/extras/scoring_weight_training/generate_training_bft.py
+++ b/extras/scoring_weight_training/generate_training_bft.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: split BFT into training and test data
IN:
diff --git a/extras/scoring_weight_training/get_weights_code.py b/extras/scoring_weight_training/get_weights_code.py
index d83bf463e77f272b7c053a48294b197a21759f7d..1716a2c340b8a848ba0e3b58acc5a66be53d8134 100644
--- a/extras/scoring_weight_training/get_weights_code.py
+++ b/extras/scoring_weight_training/get_weights_code.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: get code snippets for weights of interest
IN:
diff --git a/extras/scoring_weight_training/optimize_weights.py b/extras/scoring_weight_training/optimize_weights.py
index 06ab7039bd71ecd10ae38db2fb4be8efa0b54973..e6c339c8f31aad2514edf2b251770bcf5902de4d 100644
--- a/extras/scoring_weight_training/optimize_weights.py
+++ b/extras/scoring_weight_training/optimize_weights.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: optimize weights for best possible AUC using Nelder-Mead method
IN:
diff --git a/extras/scoring_weight_training/optimize_weights_cma.py b/extras/scoring_weight_training/optimize_weights_cma.py
index a1372aec26d59a02ef05e2700a458f7f897d6ff3..88870e37cf908fb163582d1540718256e0a1326d 100644
--- a/extras/scoring_weight_training/optimize_weights_cma.py
+++ b/extras/scoring_weight_training/optimize_weights_cma.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
GOAL: optimize weights for best possible AUC using CMA-ES
IN:
diff --git a/extras/scoring_weight_training/run_all_optimizations.py b/extras/scoring_weight_training/run_all_optimizations.py
index 50d186251a41835ac948824572169b707c657e00..e979fc6d4e01a214a6f163da03817e6817adbbe2 100644
--- a/extras/scoring_weight_training/run_all_optimizations.py
+++ b/extras/scoring_weight_training/run_all_optimizations.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import os, json
###############################################################################
diff --git a/extras/scoring_weight_training/run_array_job.sh b/extras/scoring_weight_training/run_array_job.sh
index 1790bdc13352764f1fb3a39de1389215c8e841ff..7ea7ef6ac67b1fffc005c1de5615efcd4871cc75 100644
--- a/extras/scoring_weight_training/run_array_job.sh
+++ b/extras/scoring_weight_training/run_array_job.sh
@@ -11,7 +11,6 @@ ml Boost/1.53.0-goolf-1.4.10-Python-2.7.5
ml Python/2.7.5-goolf-1.4.10
ml numpy/1.9.1-goolf-1.4.10-Python-2.7.5
ml OpenMM/6.1-Linux64
-ml dssp/2.2.1-goolf-1.4.10-Boost-1.53.0
export PROMOD3_ROOT=/scicore/home/schwede/taurielg/ProMod3/build/stage
diff --git a/extras/test_code/test.cc b/extras/test_code/test.cc
index 59d7963bd48741d4c57b693d97ca869db0b36f19..7920788f06cdfa792e9a8ece3ac9d212a3c26083 100644
--- a/extras/test_code/test.cc
+++ b/extras/test_code/test.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
// Test code for low-level ProMod3 features
#include <ost/base.hh>
diff --git a/loop/data/convert_binaries.py b/loop/data/convert_binaries.py
index 8c2653f6abbf7f3b4fa759d22829cb8ebcb43b31..57171075c54e59cc990517f200765c43ee95a347 100644
--- a/loop/data/convert_binaries.py
+++ b/loop/data/convert_binaries.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Convert files from portable to raw.'''
import sys
import os
diff --git a/loop/doc/all_atom.rst b/loop/doc/all_atom.rst
index b2f19a81997933e3ac1815f2a7759cb0f8b06613..eaeb294774c88c8f4c239fc493e2eb641ee7408f 100644
--- a/loop/doc/all_atom.rst
+++ b/loop/doc/all_atom.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Handling All Atom Positions
================================================================================
diff --git a/loop/doc/backbone.rst b/loop/doc/backbone.rst
index 15288fb3c55e5af3ff5a698fc8fc41a9223778a4..3acc2f8e1a2b74a97e559c050e71eb97c777802e 100644
--- a/loop/doc/backbone.rst
+++ b/loop/doc/backbone.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Representing Loops
================================================================================
@@ -143,7 +159,8 @@ The BackboneList class
:type sequence: :class:`str`
:raises: :exc:`~exceptions.RuntimeError` if *sequence* contains a one letter
- code which is not one of the 20 default amino acids.
+ code which is not one of the 20 default amino acids or size of
+ *sequence* does not match.
.. method:: Extract(from, to)
@@ -450,8 +467,8 @@ The BackboneList class
.. method:: SetBackrub(index, primary_rot_angle, flanking_rot_angle_one, flanking_rot_angle_two)
- Applies a backrub motion at residue defined by **index**. The first
- rotation axis is defined by the CA positions from residues at
+ Applies a backrub motion [davis2006]_ at residue defined by **index**.
+ The first rotation axis is defined by the CA positions from residues at
**index** -1 and **index** +1. All atoms in between get rotated around this
axis by **primary_rot_angle**. To restore the the hydrogen bond network
of the two transformed oxygens, the backrub motion gets completed by
diff --git a/loop/doc/index.rst b/loop/doc/index.rst
index f60393092beaea6d8315036c82ee7dfb02b267d7..1b4199c068f6532d019465b011fb112ef140443f 100644
--- a/loop/doc/index.rst
+++ b/loop/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.loop` - Loop Handling
================================================================================
diff --git a/loop/doc/load_loop_objects.rst b/loop/doc/load_loop_objects.rst
index 00365ca9dcbf02c832bd8ea7c018b31f5e99a78f..a8410bea4fa9ec2f5a7ff3ac96ed26d06f707aea 100644
--- a/loop/doc/load_loop_objects.rst
+++ b/loop/doc/load_loop_objects.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Loading Precomputed Objects
================================================================================
@@ -10,7 +26,7 @@ Several data objects are used throughout the loop module.
.. method:: LoadTorsionSampler(seed=0)
Loads and returns a torsion sampler with an amino acid grouping
- as defined by Solis & Rachovsky [1] that has been trained on
+ as defined by [solis2006]_ that has been trained on
non-redundant protein structures.
:param seed: Seed for internal random number generator
@@ -24,7 +40,7 @@ Several data objects are used throughout the loop module.
.. method:: LoadTorsionSamplerCoil(seed=0)
Loads and returns a torsion sampler with an amino acid grouping
- as defined by Solis & Rachovsky [1] that has been trained on coil
+ as defined by [solis2006]_ that has been trained on coil
residues of non-redundant protein structures.
:param seed: Seed for internal random number generator
@@ -38,7 +54,7 @@ Several data objects are used throughout the loop module.
.. method:: LoadTorsionSamplerHelical(seed=0)
Loads and returns a torsion sampler with an amino acid grouping
- as defined by Solis & Rachovsky [1] that has been trained on helical
+ as defined by [solis2006]_ that has been trained on helical
residues of non-redundant protein structures.
:param seed: Seed for internal random number generator
@@ -52,7 +68,7 @@ Several data objects are used throughout the loop module.
.. method:: LoadTorsionSamplerExtended(seed=0)
Loads and returns a torsion sampler with an amino acid grouping
- as defined by Solis & Rachovsky [1] that has been trained on extended
+ as defined by [solis2006]_ that has been trained on extended
residues of non-redundant protein structures.
:param seed: Seed for internal random number generator
@@ -63,28 +79,22 @@ Several data objects are used throughout the loop module.
:rtype: :class:`TorsionSampler`
-.. method:: LoadFragDB()
-
- Loads and returns a FragDB containing fragments up to the length of 14,
- therefore capable of bridging gaps up to the length of 12.
+.. method:: LoadStructureDB()
- :returns: The Fragment database
- :rtype: :class:`FragDB`
+ Loads and returns a structure db containing roughly 21000 chains form the
+ PDB with seqid redundancy cutoff of 60%
-.. method:: LoadStructureDB(load_frequencies=True)
+ :returns: The structure db
+ :rtype: :class:`StructureDB`
- Loads and returns a structure db containing roughly 24000 chains form the
- PDB with redundancy cutoff of 90%
- :param load_frequencies: If True, the full database including profile
- information gets loaded (see
- :meth:`StructureDB.Load`).
- :type load_frequencies: :class:`bool`
+.. method:: LoadFragDB()
- :returns: The structure db
- :rtype: :class:`StructureDB`
-
+ Loads and returns a FragDB containing fragments up to the length of 14,
+ therefore capable of bridging gaps up to the length of 12. The returned
+ databases contains the location of fragments in the :class:`StructureDB`
+ returned by :meth:`LoadStructureDB`.
-[1] A. D. Solis and S. Rackovsky. Improvement of statistical potentials and
- threading score functions using information maximization.
- Proteins, 62(4):892–908, Mar 2006.
+ :returns: The Fragment database
+ :rtype: :class:`FragDB`
+
\ No newline at end of file
diff --git a/loop/doc/mm_system_creation.rst b/loop/doc/mm_system_creation.rst
index 7ad0c03a88e75d071685fbee47a3d5f88dcc6530..87b6fb05808a9d70e5e489638d087cd99d95c46c 100644
--- a/loop/doc/mm_system_creation.rst
+++ b/loop/doc/mm_system_creation.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Generate :mod:`ost.mol.mm` systems
================================================================================
diff --git a/loop/doc/structure_db.rst b/loop/doc/structure_db.rst
index a967d08a3823e6ae0eba26410ba7bdfa313ba358..b3089c7248bc40d5f4bd292125795b2edde82204 100644
--- a/loop/doc/structure_db.rst
+++ b/loop/doc/structure_db.rst
@@ -1,9 +1,25 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Structural Data
================================================================================
.. currentmodule:: promod3.loop
-The structural database serves as a container for structural backbone and
+The :class:`StructureDB` serves as a container for structural backbone and
sequence data. Custom accessor objects can be implemented that relate
arbitrary features to structural data. Examples provided by ProMod3 include
accession using matching stem geometry (see: :class:`FragDB`) or sequence
@@ -41,7 +57,7 @@ Defining Chains and Fragments
.. class:: CoordInfo()
The CoordInfo gets automatically generated when new chains are added to
- the structural database. It contains internal information of how a
+ a :class:`StructureDB`. It contains internal information of how a
connected stretch of residues is stored in the database.
.. attribute:: id
@@ -68,17 +84,17 @@ Defining Chains and Fragments
Residue number of first residue in the added stretch. The residue number
is relative to the SEQRES provided in the input profile when adding the
- stuff to the structure db.
+ stuff to the structure db. (:class:`int`)
.. attribute:: shift
Translation from original coordinates that has been applied before storing
- structural information in db.
+ structural information in db. (:class:`ost.geom.Vec3`)
.. class:: FragmentInfo(chain_index, offset, length)
- The FragmentInfo defines any fragment in the structural database. If you
+ The FragmentInfo defines any fragment in the :class:`StructureDB`. If you
implement your own accessor object, thats the information you want to store.
:param chain_index: Fills :attr:`chain_index`
@@ -89,8 +105,8 @@ Defining Chains and Fragments
.. attribute:: chain_index
- The index of the chain (defined by :class:`CoordInfo`) in the structure db
- this particle belongs to. (:class:`int`)
+ The index of the chain (defined by :class:`CoordInfo`) in the
+ :class:`StructureDB` this particle belongs to. (:class:`int`)
.. attribute:: offset
@@ -127,7 +143,7 @@ database, you might want to consider two things:
to backbone coordinates and sequence.
If you want to store all data possible, use All. If you only want a subset,
you can combine some of the datatypes with a bitwise or operation
- (see example script for StructureDB). One important note:
+ (see example script for :class:`StructureDB`). One important note:
If you enable AAFrequenciesStruct, the actual information is not automatically
assigned. Only the according memory is allocated and set to zero, the actual
information must be assigned manually (see example script again...).
@@ -138,8 +154,8 @@ database, you might want to consider two things:
.. class:: StructureDB(data_to_store)
- Generates an empty StructureDB that can be filled with content through
- :func:`AddCoordinates`. The information extracted there is defined by
+ Generates an empty :class:`StructureDB` that can be filled with content
+ through :func:`AddCoordinates`. The information extracted there is defined by
*data_to_store*. Have a look at the :class:`StructureDBDataType`
documentation and at the example script...
@@ -263,7 +279,7 @@ database, you might want to consider two things:
.. method:: GetCoordIdx(id, chain_name)
- :returns: The StructureDB indices (in [0, :meth:`GetNumCoords`-1]) of
+ :returns: The :class:`StructureDB` indices (in [0, :meth:`GetNumCoords`-1])
of all coords (connected stretches) with matching
*id* / *chain_name*.
:rtype: :class:`list` of :class:`int`
@@ -281,7 +297,7 @@ database, you might want to consider two things:
index *idx*.
:rtype: :class:`CoordInfo`
- :param idx: The StructureDB index (in [0, :meth:`GetNumCoords`-1])
+ :param idx: The :class:`StructureDB` index (in [0, :meth:`GetNumCoords`-1])
:type idx: :class:`int`
@@ -379,7 +395,8 @@ database, you might want to consider two things:
.. method:: GetSolventAccessibilitites(fragment)
:returns: Solvent accessibility for each residue of *fragment* in square A
- as calculated by dssp.
+ as calculated by :meth:`~ost.mol.alg.Accessibility` when adding
+ the structure to the database.
:rtype: :class:`list` of :class:`float`
:param fragment: Fragment definition from which to extract the solvent
@@ -472,7 +489,7 @@ database, you might want to consider two things:
to make sure that you have no close homologue in the database.
:rtype: :class:`StructureDB`
- :param indices: StructureDB indices to be added to the sub database (in [0,
+ :param indices: Indices of chains to be added to the sub database (in [0,
:meth:`GetNumCoords`-1])
:type indices: :class:`list`
@@ -532,14 +549,16 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
.. method:: GetAngularBinSize()
- The size of the bins for the 4 angles describing the stem geometry and used to organize the fragments in the database.
+ The size of the bins for the 4 angles describing the stem geometry and used
+ to organize the fragments in the database.
:return: The bin size in degrees
:rtype: :class:`int`
.. method:: GetDistBinSize()
- The size of the bins for the distance describing the stem geometry and used to organize the fragments in the database.
+ The size of the bins for the distance describing the stem geometry and used
+ to organize the fragments in the database.
:return: The bin size
:rtype: :class:`float`
@@ -547,8 +566,13 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
.. method:: AddFragments(fragment_length, rmsd_cutoff, structure_db)
- Iterates over all fragments of length **fragment_length** in the given structural database and adds them to the fragment database. Fragments will be skipped if there is already a fragment in the database that has an RMSD to the one being added smaller than **rmsd_cutoff**.
- As the fragments are added they are organized in bins described by their length and the geometry of their N and C stem.
+ Iterates over all fragments of length **fragment_length** in
+ **structure_db** and adds them to the fragment database.
+ Fragments will be skipped if there is already a fragment in the database
+ that has an RMSD smaller than **rmsd_cutoff**, where RMSD is calculated
+ upon superposing the stem residues.
+ As the fragments are added they are organized in bins described by their
+ length and the geometry of their N and C stem.
:param fragment_length: The length of the fragments that should be added to the databse
:param rmsd_cutoff: The minimal RMSD between two fragments in the fragment database
@@ -560,7 +584,7 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
.. method:: PrintStatistics()
- Prints statistics about the fragment databse, notably:
+ Prints statistics about the fragment database, notably:
1. the number of different stem groups (number of bins used to group the
fragments according to the geometry of their stem residues)
@@ -598,12 +622,12 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
:param loop_length: The length of the fragments
:type loop_length: :class:`int`
- :returns: True if fragments of given length exist. This function is quick.
+ :returns: True if fragments of given length exist.
:rtype: :class:`bool`
.. method:: MaxFragLength()
- :returns: Maximal fragment length contained in db. This function is quick.
+ :returns: Maximal fragment length contained in db.
:rtype: :class:`int`
.. method:: SearchDB(n_stem, c_stem, frag_size, extra_bins=0)
@@ -635,7 +659,7 @@ In some cases you might want to use the :class:`StructureDB` to search
for fragments that possibly represent the structural conformation of interest.
The :class:`Fragger` searches a :class:`StructureDB` for n fragments,
that maximize a certain score and gathers a set of fragments with a guaranteed
-structural diversity based on an rmsd_threshold. You can use the :class:`Fragger`
+structural diversity based on an rmsd threshold. You can use the :class:`Fragger`
wrapped in a full fletched pipeline implemented in
:class:`~promod3.modelling.FraggerHandle` or search for fragments from scratch
using an arbitrary linear combination of scores:
@@ -882,7 +906,7 @@ The PsipredPrediction class
.. class:: PsipredPrediction
- A container for the secondary structure prediction by Psipred.
+ A container for the secondary structure prediction by PSIPRED [Jones1999]_.
.. method:: PsipredPrediction()
@@ -974,11 +998,3 @@ The PsipredPrediction class
.. method:: __len__()
:returns: Number of elements in container
-
-
-
-.. [soding2005] Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.
-.. [chakravarty1999] Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.
-.. [zhou2005] Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.
-.. [Jones1999] Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.
-.. [kabsch1983] Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 2577-2637.
diff --git a/loop/doc/torsion_sampler.rst b/loop/doc/torsion_sampler.rst
index 0962c3563d62638c5948f7d6f08189b2fcf6a95b..8344079a5065f12c19e844f50be70636032ba365 100644
--- a/loop/doc/torsion_sampler.rst
+++ b/loop/doc/torsion_sampler.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Sampling Dihedral Angles
================================================================================
diff --git a/loop/pymod/__init__.py b/loop/pymod/__init__.py
index fc70505fd93e0ec4f2cfe0b6286935732beb3457..3d3a8d1f0794350f978d5a05ca341d721d226018 100644
--- a/loop/pymod/__init__.py
+++ b/loop/pymod/__init__.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Initialise the loop module."""
# geom needed for export_backbone
from ost import geom
diff --git a/loop/pymod/export_all_atom_env.cc b/loop/pymod/export_all_atom_env.cc
index 8ebdf1229c8137bf69435b1c65b38f409c016c4c..552bc6135a4b9d328d13f7f6809b8f254245b3cd 100644
--- a/loop/pymod/export_all_atom_env.cc
+++ b/loop/pymod/export_all_atom_env.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_all_atom_positions.cc b/loop/pymod/export_all_atom_positions.cc
index d161f4b05551ca743457a978735e2d363d96dcf4..143020cdec7b2291c50c6e337e3ecfbfc47967e0 100644
--- a/loop/pymod/export_all_atom_positions.cc
+++ b/loop/pymod/export_all_atom_positions.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_amino_acid_atoms.cc b/loop/pymod/export_amino_acid_atoms.cc
index 5efcbd77c6b95be25b330f9dda5687a59b98934a..bd163ca2698cf0365de13dbd1fd9a14fb31e8c96 100644
--- a/loop/pymod/export_amino_acid_atoms.cc
+++ b/loop/pymod/export_amino_acid_atoms.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/message.hh>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_backbone.cc b/loop/pymod/export_backbone.cc
index 6d97c8a7eddf9dc0544697e1e00c486e58d323b5..61265152fa088f9c7a2b91c633b8485f32a93c4c 100644
--- a/loop/pymod/export_backbone.cc
+++ b/loop/pymod/export_backbone.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/register_ptr_to_python.hpp>
diff --git a/loop/pymod/export_forcefield_lookup.cc b/loop/pymod/export_forcefield_lookup.cc
index e1405f83bcbe27c0c3329726a3cd330be90c8847..7d56ce4239db3cbb8e9207bf5e4f2dc0a450edda 100644
--- a/loop/pymod/export_forcefield_lookup.cc
+++ b/loop/pymod/export_forcefield_lookup.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/message.hh>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_frag_db.cc b/loop/pymod/export_frag_db.cc
index c4fc17f0fcf24c15a2e25c78483095c1c0d0bee0..c5b7c59925cec905fc7e1e2c0ba2869a5b34db9e 100644
--- a/loop/pymod/export_frag_db.cc
+++ b/loop/pymod/export_frag_db.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_fragger.cc b/loop/pymod/export_fragger.cc
index 4c4f8b5903eefddfaddefa6f7696de4a26c45f31..d6afcf0f9f0d07785046f02de58510865395dcb3 100644
--- a/loop/pymod/export_fragger.cc
+++ b/loop/pymod/export_fragger.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
diff --git a/loop/pymod/export_loop_object_loader.cc b/loop/pymod/export_loop_object_loader.cc
index fb6cb09087e4950cb473d4255fd2dc1ad5731ccb..48dcf12c5cb99e4e4d62390d6861ad30ea062285 100644
--- a/loop/pymod/export_loop_object_loader.cc
+++ b/loop/pymod/export_loop_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/loop/loop_object_loader.hh>
diff --git a/loop/pymod/export_mm_system_creator.cc b/loop/pymod/export_mm_system_creator.cc
index a4f316c01ff0cc4ec4d1daed11625cb0e4cfb3c9..cffb7509271404be2fb8d39a9a83819da368fc02 100644
--- a/loop/pymod/export_mm_system_creator.cc
+++ b/loop/pymod/export_mm_system_creator.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_psipred_prediction.cc b/loop/pymod/export_psipred_prediction.cc
index fcdbb64b959b90b964898583d634ae54dba3b5a0..18eca538596823bd5ebe1bc3d6e5fc24c24e1a3d 100644
--- a/loop/pymod/export_psipred_prediction.cc
+++ b/loop/pymod/export_psipred_prediction.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
diff --git a/loop/pymod/export_structure_db.cc b/loop/pymod/export_structure_db.cc
index 954614498a7b99168f1c1598211a7be1e7a86889..a9f96d4629a10e8f32dbbc2915a63b94012f7c02 100644
--- a/loop/pymod/export_structure_db.cc
+++ b/loop/pymod/export_structure_db.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/loop/pymod/export_torsion_sampler.cc b/loop/pymod/export_torsion_sampler.cc
index 286a70302f7be6f0c4ad3f350b078db0fb39fb6f..ead2f96d30e09d41df6ce5e14a86a11d228b3f27 100644
--- a/loop/pymod/export_torsion_sampler.cc
+++ b/loop/pymod/export_torsion_sampler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
diff --git a/loop/pymod/wrap_loop.cc b/loop/pymod/wrap_loop.cc
index fd8a344e9450630fc028a11bb8d589996e2fb6a8..39aa16aeaa5ac7ada91bc8dc37904ccddad25c41 100644
--- a/loop/pymod/wrap_loop.cc
+++ b/loop/pymod/wrap_loop.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
void export_FragDB();
diff --git a/loop/src/all_atom_env.cc b/loop/src/all_atom_env.cc
index cef7b4eca18ebfd5ada74f84012cfd95807185f2..991e90c777445cdc80dd3328c1f41bf55a41a614 100644
--- a/loop/src/all_atom_env.cc
+++ b/loop/src/all_atom_env.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/all_atom_env.hh>
#include <promod3/core/message.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/loop/src/all_atom_env.hh b/loop/src/all_atom_env.hh
index 66ead82b0d564e81dcf86b571823d6fbf5486080..f39cf74347df2bf7c99f104721f1e45470f79ed9 100644
--- a/loop/src/all_atom_env.hh
+++ b/loop/src/all_atom_env.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_LOOP_ALL_ATOM_ENV_HH
#define PROMOD3_LOOP_ALL_ATOM_ENV_HH
diff --git a/loop/src/all_atom_positions.cc b/loop/src/all_atom_positions.cc
index 2dad21d0e0c802bd81cc771af31c4de0127a6db5..38976fed98a1016fc5cfd77397a1680bf1497c17 100644
--- a/loop/src/all_atom_positions.cc
+++ b/loop/src/all_atom_positions.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/all_atom_positions.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/geom_base.hh>
diff --git a/loop/src/all_atom_positions.hh b/loop/src/all_atom_positions.hh
index 3947d788eb5a91ad70927955eea94dc01f236b3f..03a2c2c9c952326b5629a8a269afc0943c6a1fba 100644
--- a/loop/src/all_atom_positions.hh
+++ b/loop/src/all_atom_positions.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_LOOP_ALL_ATOM_POSITIONS_HH
#define PROMOD3_LOOP_ALL_ATOM_POSITIONS_HH
diff --git a/loop/src/amino_acid_atoms.cc b/loop/src/amino_acid_atoms.cc
index 9924dbbaa67cf73e7b83212aad05a2d1170c0590..66e5c3364e3f6739052cd60b30de3dd46a9cbc5c 100644
--- a/loop/src/amino_acid_atoms.cc
+++ b/loop/src/amino_acid_atoms.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/amino_acid_atoms.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/message.hh>
diff --git a/loop/src/amino_acid_atoms.hh b/loop/src/amino_acid_atoms.hh
index 7de3f538be80ba8100911f3719d3c19e562f0397..44b32de1d16f15f5f298dabd718fc906b965e0e2 100644
--- a/loop/src/amino_acid_atoms.hh
+++ b/loop/src/amino_acid_atoms.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines functionality to deal with all atoms of amino acids.
///
/// - ...AtomIndex are used to index atoms of each amino acid. The backbone atom
diff --git a/loop/src/backbone.cc b/loop/src/backbone.cc
index edb4dd63c7dbbf09997f30d0395166e21a9104ad..35bc7e86a0de04cdf761e2fc71c3ec5057aea6d7 100644
--- a/loop/src/backbone.cc
+++ b/loop/src/backbone.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/backbone.hh>
#include <promod3/loop/density_creator.hh>
#include <ost/conop/processor.hh>
diff --git a/loop/src/backbone.hh b/loop/src/backbone.hh
index 70e3cb15fe838860bc2d5a4ad506475dc376c4b8..253bcd429305548c0c58b728921c43141eab658f 100644
--- a/loop/src/backbone.hh
+++ b/loop/src/backbone.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_BACKBONE_HH
#define PM3_BACKBONE_HH
diff --git a/loop/src/bb_trace_param.cc b/loop/src/bb_trace_param.cc
index aa8dabef0de6ad1fb1db65f05ef9ba19a62ab748..9a3fa35e869e729da119fa9c7d13e76f756f3439 100644
--- a/loop/src/bb_trace_param.cc
+++ b/loop/src/bb_trace_param.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/bb_trace_param.hh>
#include <promod3/core/message.hh>
diff --git a/loop/src/bb_trace_param.hh b/loop/src/bb_trace_param.hh
index 392eb19657c5682efbc799fab50293cccff4912e..821e1ea7fefa7761ce36cb26164cd473dca52ca5 100644
--- a/loop/src/bb_trace_param.hh
+++ b/loop/src/bb_trace_param.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_BB_TRACE_PARAM_HH
#define PM3_BB_TRACE_PARAM_HH
diff --git a/loop/src/data_bag.hh b/loop/src/data_bag.hh
index f6fa5919024bdcfa32dc9a54e896b85ca66ba1ad..f9926a483b11cb740bcc685e818b8df2a88ad4aa 100644
--- a/loop/src/data_bag.hh
+++ b/loop/src/data_bag.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_CORE_DATA_BAG_HH
#define PM3_CORE_DATA_BAG_HH
diff --git a/loop/src/dense_hash_table.hh b/loop/src/dense_hash_table.hh
index 884c7c3fa5ae9831dd4a2052cca832f9f047c046..ec9f573a09688bcf7f69dcd5ee0e204f360e2bc6 100644
--- a/loop/src/dense_hash_table.hh
+++ b/loop/src/dense_hash_table.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_DENSE_HASH_TABLE_HH
#define PROMOD_LOOP_DENSE_HASH_TABLE_HH
diff --git a/loop/src/dense_map.hh b/loop/src/dense_map.hh
index 189c688cd1a76f70da9fa2a4e0a89c68306a15fb..b0ab0c0fd1fea31ce879553b158c404aa9f2fa10 100644
--- a/loop/src/dense_map.hh
+++ b/loop/src/dense_map.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_DENSE_MAP_HH
#define PROMOD_LOOP_DENSE_MAP_HH
diff --git a/loop/src/density_creator.cc b/loop/src/density_creator.cc
index 6e6d8575159c876b2a3faef9f3c851689f3af3f8..48ba28c5d3e3759b6a5472399b9cc237e41b8343 100644
--- a/loop/src/density_creator.cc
+++ b/loop/src/density_creator.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/density_creator.hh>
#include <promod3/core/message.hh>
diff --git a/loop/src/density_creator.hh b/loop/src/density_creator.hh
index e317ef62d0c819c237c91e210d947c722989fd74..c65a8742bf00bcf8854818076cea9b8fe796a19d 100644
--- a/loop/src/density_creator.hh
+++ b/loop/src/density_creator.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_LOOP_DENSITY_CREATOR_HH
#define PM3_LOOP_DENSITY_CREATOR_HH
diff --git a/loop/src/forcefield_lookup.cc b/loop/src/forcefield_lookup.cc
index e662afe4e529d2f6da17487e95290e40a5ea2062..0dbf5a57ec8d04dffaeef4df4cdde807d11356bf 100644
--- a/loop/src/forcefield_lookup.cc
+++ b/loop/src/forcefield_lookup.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <fstream>
#include <promod3/loop/forcefield_lookup.hh>
#include <promod3/core/portable_binary_serializer.hh>
diff --git a/loop/src/forcefield_lookup.hh b/loop/src/forcefield_lookup.hh
index f0d08b8975d0483c75dc36654cd6a769c0ca87eb..cf043ace433fd53e548bee7d244d1e334ed0dece 100644
--- a/loop/src/forcefield_lookup.hh
+++ b/loop/src/forcefield_lookup.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines functionality to deal with force fields.
///
/// Here, we define:
diff --git a/loop/src/frag_db.cc b/loop/src/frag_db.cc
index 73f75b903efc17f72edbf402f63acd58e989ec9c..8bbe44523a4b37d6c73b555d1d4f084f79d4c25a 100644
--- a/loop/src/frag_db.cc
+++ b/loop/src/frag_db.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <fstream>
#include <limits>
#include <ost/mol/mol.hh>
diff --git a/loop/src/frag_db.hh b/loop/src/frag_db.hh
index 6bb3134df3e2084734a02dd8b5b27573ffa5b120..8df2c8b4cc3c76ee78d2388bb816b5d03053a198 100644
--- a/loop/src/frag_db.hh
+++ b/loop/src/frag_db.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_FRAG_DB_HH
#define PROMOD_LOOP_FRAG_DB_HH
diff --git a/loop/src/fragger.cc b/loop/src/fragger.cc
index aa6bc18dd72ad8699eddf2493eac9dfc2353ef48..e9db9731f8d5c171005b5665763f509ce8980fd5 100644
--- a/loop/src/fragger.cc
+++ b/loop/src/fragger.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/fragger.hh>
// for raw serialization
diff --git a/loop/src/fragger.hh b/loop/src/fragger.hh
index b109770cc5d2ace6a75d4da6d08e24d8355a8c04..c83d7df913459205c33a3aa8a68973363fef04e2 100644
--- a/loop/src/fragger.hh
+++ b/loop/src/fragger.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_FRAGGER_HH
#define PROMOD_LOOP_FRAGGER_HH
diff --git a/loop/src/hydrogen_constructor.cc b/loop/src/hydrogen_constructor.cc
index 27718a746a1f408dcf3158e99da99ba779034114..3df6326d6a173e8a0b30049c29688ae5a694c76a 100644
--- a/loop/src/hydrogen_constructor.cc
+++ b/loop/src/hydrogen_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/hydrogen_constructor.hh>
namespace promod3 { namespace loop {
diff --git a/loop/src/hydrogen_constructor.hh b/loop/src/hydrogen_constructor.hh
index 966a3a2064b19cfd258f6a67594aaee29d5d18b8..3ad2d3a97d28c712dab8c1c969d40887fff2dc9a 100644
--- a/loop/src/hydrogen_constructor.hh
+++ b/loop/src/hydrogen_constructor.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines functionality to construct hydrogens for amino acids.
#ifndef PROMOD3_HYDROGEN_CONSTRUCTOR_HH
diff --git a/loop/src/hydrogen_rule_lookup.cc b/loop/src/hydrogen_rule_lookup.cc
index f1201c9f9b227a53df5517cb5c52eac0b44ba670..af209a9058eb8cd8e7307de287db4f5979424f9d 100644
--- a/loop/src/hydrogen_rule_lookup.cc
+++ b/loop/src/hydrogen_rule_lookup.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/hydrogen_rule_lookup.hh>
namespace promod3 { namespace loop {
diff --git a/loop/src/hydrogen_rule_lookup.hh b/loop/src/hydrogen_rule_lookup.hh
index 43300434aeadc64c94725f152a28cb62b2fb8275..1114e3554f89812893b0c2237d6c332568ccc8fb 100644
--- a/loop/src/hydrogen_rule_lookup.hh
+++ b/loop/src/hydrogen_rule_lookup.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines rules to construct hydrogens for amino acids.
#ifndef PROMOD3_HYDROGEN_RULE_LOOKUP_HH
diff --git a/loop/src/idx_handler.cc b/loop/src/idx_handler.cc
index dfc50c26c159112638e248fde20750fa17ba362c..688fdbbeb2104c7368a8e1f9effab2c9643ab78e 100644
--- a/loop/src/idx_handler.cc
+++ b/loop/src/idx_handler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/idx_handler.hh>
#include <promod3/core/message.hh>
#include <ost/log.hh>
diff --git a/loop/src/idx_handler.hh b/loop/src/idx_handler.hh
index 193520286029bdf138bbd6c738a37405ef905d27..9cecb881e5f8f2338b03710371afb296d0117a31 100644
--- a/loop/src/idx_handler.hh
+++ b/loop/src/idx_handler.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_LOOP_IDX_HANDLER_HH
#define PROMOD3_LOOP_IDX_HANDLER_HH
diff --git a/loop/src/loop_object_loader.cc b/loop/src/loop_object_loader.cc
index 4eeff56860e15a6603312f8fa62104ad1e3f87af..f05bd9dbc45bfb244fb1b5538daa3acd5198fb9a 100644
--- a/loop/src/loop_object_loader.cc
+++ b/loop/src/loop_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/loop_object_loader.hh>
#include <promod3/config.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/loop/src/loop_object_loader.hh b/loop/src/loop_object_loader.hh
index 0b89e68a50ba2f96e453d3a3d1aab52b2fbe6d21..b42a2ffe249c768fcc422391b3e76ab3f4954f68 100644
--- a/loop/src/loop_object_loader.hh
+++ b/loop/src/loop_object_loader.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_LOOP_OBJECT_LOADER_HH
#define PROMOD3_LOOP_OBJECT_LOADER_HH
diff --git a/loop/src/mm_system_creator.cc b/loop/src/mm_system_creator.cc
index fdda4908ddbd0edaede2c01afc5e69f8caeb0f0b..6bdc36a4dd64e6b9407a81ac515ddfaeb975aa1e 100644
--- a/loop/src/mm_system_creator.cc
+++ b/loop/src/mm_system_creator.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/mm_system_creator.hh>
#include <promod3/loop/hydrogen_constructor.hh>
diff --git a/loop/src/mm_system_creator.hh b/loop/src/mm_system_creator.hh
index 2602a27e8f752223f2aedc905a3b7b9f80d07318..dd4a41713e3d6103b3a275f14c1baf1cd5283913 100644
--- a/loop/src/mm_system_creator.hh
+++ b/loop/src/mm_system_creator.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_MM_SYSTEM_CREATOR_HH
#define PROMOD3_MM_SYSTEM_CREATOR_HH
diff --git a/loop/src/paged_array.hh b/loop/src/paged_array.hh
index 3591e2915fb9b3acc07ce9ffd10720860ada420c..21c2cce8418d50494075cb01eb507e229876e13b 100644
--- a/loop/src/paged_array.hh
+++ b/loop/src/paged_array.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef OST_PAGED_ARRAY_HH
#define OST_PAGED_ARRAY_HH
diff --git a/loop/src/psipred_prediction.cc b/loop/src/psipred_prediction.cc
index 00b3f460be3e9564c5d7eda160cbc9b31440ccb3..08251013ca1bebf8cbf3f112388d6e6f9ad405c0 100644
--- a/loop/src/psipred_prediction.cc
+++ b/loop/src/psipred_prediction.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/psipred_prediction.hh>
namespace promod3{ namespace loop{
diff --git a/loop/src/psipred_prediction.hh b/loop/src/psipred_prediction.hh
index 31ff335c15ee553b6443a44f1b3addd75fb9276d..1b32ef591b21412aef43c05540b445d1ba5a262a 100644
--- a/loop/src/psipred_prediction.hh
+++ b/loop/src/psipred_prediction.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_PSIPRED_PREDICTION_HH
#define PROMOD_LOOP_PSIPRED_PREDICTION_HH
diff --git a/loop/src/sidechain_atom_constructor.cc b/loop/src/sidechain_atom_constructor.cc
index 0fb09cefbb5367fd9b24103448f62ee32a3db2dc..e1832ae3bb90d43df3acd79cfe118ee53a30aea9 100644
--- a/loop/src/sidechain_atom_constructor.cc
+++ b/loop/src/sidechain_atom_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/sidechain_atom_constructor.hh>
#include <promod3/core/geom_base.hh>
diff --git a/loop/src/sidechain_atom_constructor.hh b/loop/src/sidechain_atom_constructor.hh
index 92b97f100d88fecb35447b9354991b2daaa0a9a9..0c6679e3a8d8e56623b383995db2275562eba768 100644
--- a/loop/src/sidechain_atom_constructor.hh
+++ b/loop/src/sidechain_atom_constructor.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines functionality to construct sidechain heavy atoms based on
/// dihedral angles for amino acids.
diff --git a/loop/src/sidechain_atom_rule_lookup.cc b/loop/src/sidechain_atom_rule_lookup.cc
index 27d0b4f86b16d6eafd758e87bc4760c170e9bb56..70afd99afd898359ab34c39fd9780c8a2bced0aa 100644
--- a/loop/src/sidechain_atom_rule_lookup.cc
+++ b/loop/src/sidechain_atom_rule_lookup.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/sidechain_atom_rule_lookup.hh>
#include <promod3/loop/amino_acid_atoms.hh>
#include <ost/conop/amino_acids.hh>
diff --git a/loop/src/sidechain_atom_rule_lookup.hh b/loop/src/sidechain_atom_rule_lookup.hh
index 71805709bdccb274bf9a2c9d77f8f93ac785102d..38a35491938c689a1ee8ce69bbd93e9d7c50379a 100644
--- a/loop/src/sidechain_atom_rule_lookup.hh
+++ b/loop/src/sidechain_atom_rule_lookup.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
/// \brief Defines rules to construct sidechain heavy atoms from dihedral angles.
#ifndef PROMOD3_SIDECHAIN_ATOM_RULE_LOOKUP_HH
diff --git a/loop/src/stem_geom.hh b/loop/src/stem_geom.hh
index a1d123c5375634eef346ea388a2e357ed8587441..b29565dacfa02f04db8e3fb982e76e3ed203d1a5 100644
--- a/loop/src/stem_geom.hh
+++ b/loop/src/stem_geom.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_MELD_FRAGMENT_HH
#define PM3_MELD_FRAGMENT_HH
diff --git a/loop/src/structure_db.cc b/loop/src/structure_db.cc
index 7eb3fe33e6c722c526f44403d9f1c727c1c30cd1..b78558c11193b8b0af934e3183c26c7ee7afa71a 100644
--- a/loop/src/structure_db.cc
+++ b/loop/src/structure_db.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/structure_db.hh>
#include <promod3/core/portable_binary_serializer.hh>
#include <promod3/core/check_io.hh>
@@ -1331,8 +1347,41 @@ StructureDBPtr StructureDB::GetSubDB(const std::vector<uint>& indices) const{
}
void StructureDB::PrintStatistics() const{
- std::cout << "number of chains : " << coord_toc_.size() << std::endl;
- std::cout << "number of backbone coords :" << coords_.size() << std::endl;
+
+ std::cout << "db summary:" << std::endl << std::endl;
+ std::cout << "number of chains : " << coord_toc_.size() << std::endl;
+ std::cout << "number of backbone coords : " << coords_.size() << std::endl;
+ std::cout << std::endl;
+
+ if(stored_data_ == 0) {
+ return;
+ }
+
+ std::cout << "db contains following optional data: " << std::endl << std::endl;
+
+ if(this->HasData(Dihedrals)) {
+ std::cout << "- backbone dihedral angles" << std::endl;
+ }
+
+ if(this->HasData(SolventAccessibilities)) {
+ std::cout << "- solvent accessibilities" << std::endl;
+ }
+
+ if(this->HasData(ResidueDepths)) {
+ std::cout << "- residue depths" << std::endl;
+ }
+
+ if(this->HasData(DSSP)) {
+ std::cout << "- dssp secondary structure assignments" << std::endl;
+ }
+
+ if(this->HasData(AAFrequencies)) {
+ std::cout << "- sequence profiles" << std::endl;
+ }
+
+ if(this->HasData(AAFrequenciesStruct)) {
+ std::cout << "- structure profiles" << std::endl;
+ }
}
ost::seq::ProfileHandlePtr StructureDB::GenerateStructureProfile(
diff --git a/loop/src/structure_db.hh b/loop/src/structure_db.hh
index a11db69ef12d31a3669ea5c986933ebadd94e640..228785d6c19ab6084783272cd5f9fff86deffefd 100644
--- a/loop/src/structure_db.hh
+++ b/loop/src/structure_db.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_STRUCTURE_DB_HH
#define PROMOD_LOOP_STRUCTURE_DB_HH
diff --git a/loop/src/structure_db_custom_types.hh b/loop/src/structure_db_custom_types.hh
index d636c7dbd21edb8a335fb91f51f4d2003a064548..49ec68b4867e0a95382d14fa83b09c37bf606c01 100644
--- a/loop/src/structure_db_custom_types.hh
+++ b/loop/src/structure_db_custom_types.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_STRUCTURE_DB_CUSTOM_TYPES
#define PROMOD_LOOP_STRUCTURE_DB_CUSTOM_TYPES
diff --git a/loop/src/torsion_sampler.cc b/loop/src/torsion_sampler.cc
index 11ee9137e8e5cd8d1af6b493d5f5f380bf28cb65..70d32064a3c7638d394b25209cbdb0ba670fc2d1 100644
--- a/loop/src/torsion_sampler.cc
+++ b/loop/src/torsion_sampler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/torsion_sampler.hh>
#include <promod3/core/check_io.hh>
#include <promod3/core/portable_binary_serializer.hh>
diff --git a/loop/src/torsion_sampler.hh b/loop/src/torsion_sampler.hh
index d489e35c5fba307bf1fcb21bd92dba6c98d19bd3..4e5c9fd2f10fb3f5062319eac1f018e5ee32f759 100644
--- a/loop/src/torsion_sampler.hh
+++ b/loop/src/torsion_sampler.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_LOOP_TORSION_SAMPLER_HH
#define PROMOD_LOOP_TORSION_SAMPLER_HH
diff --git a/loop/src/ushort_vec.hh b/loop/src/ushort_vec.hh
index 9016eff2fcdf4cc8d9c6e6ff2581542f4320ae65..6339c2ce524570f8b57b9c01afc4e2db3d7da30a 100644
--- a/loop/src/ushort_vec.hh
+++ b/loop/src/ushort_vec.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_USHORT_VEC_HH
#define PROMOD_USHORT_VEC_HH
diff --git a/loop/tests/test_all_atom_env.cc b/loop/tests/test_all_atom_env.cc
index a3ecc8205a1916fee6c43c010102248c5128c706..0c2a45d3c4c1a7f2fc1965c4aec7e0922dbacabe 100644
--- a/loop/tests/test_all_atom_env.cc
+++ b/loop/tests/test_all_atom_env.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/all_atom_env.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_all_atom_positions.cc b/loop/tests/test_all_atom_positions.cc
index 14a21edaf8b21eb69c372bec36a20722c8880a6a..f50d5c5b40ee476385049e66059eca9857a1d71d 100644
--- a/loop/tests/test_all_atom_positions.cc
+++ b/loop/tests/test_all_atom_positions.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/all_atom_positions.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_amino_acid_atoms.cc b/loop/tests/test_amino_acid_atoms.cc
index a8b55b9d4829bb8cb54823816f66ac01ed4ecf7e..d4723925bbd0510426e36bf78a66ffea69145bf6 100644
--- a/loop/tests/test_amino_acid_atoms.cc
+++ b/loop/tests/test_amino_acid_atoms.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/amino_acid_atoms.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_backbone.cc b/loop/tests/test_backbone.cc
index 4b82781ca072c3ebd504f4a502a59e13a30a4958..8b7e31c938c78d32ce1d9d336436776960f1661f 100644
--- a/loop/tests/test_backbone.cc
+++ b/loop/tests/test_backbone.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/backbone.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_forcefield.cc b/loop/tests/test_forcefield.cc
index 1c7c54b9bf830681165657207ffb161522893fad..8c0722a397b01412f1413b52d43d3095836b25c2 100644
--- a/loop/tests/test_forcefield.cc
+++ b/loop/tests/test_forcefield.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/forcefield_lookup.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_hydrogens.cc b/loop/tests/test_hydrogens.cc
index 5d24f74da614f648defab26a9998fe61042263a1..523d10128b8df758752d9809dee468c4e2ffbeb9 100644
--- a/loop/tests/test_hydrogens.cc
+++ b/loop/tests/test_hydrogens.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/hydrogen_rule_lookup.hh>
#include <promod3/loop/hydrogen_constructor.hh>
diff --git a/loop/tests/test_idx_handler.cc b/loop/tests/test_idx_handler.cc
index 1ae50995d44229053a85ea9c7280fef941d13726..a726fc2be0e34be231d4b60e6eed1b53d44121dd 100644
--- a/loop/tests/test_idx_handler.cc
+++ b/loop/tests/test_idx_handler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/idx_handler.hh>
#include <promod3/loop/backbone.hh>
diff --git a/loop/tests/test_mm_system_creator.cc b/loop/tests/test_mm_system_creator.cc
index b02651f48ec964ad680fda776d40e02125d595c1..0077c2a900b6d35f51ed7ec7ee2c95acfcd99d38 100644
--- a/loop/tests/test_mm_system_creator.cc
+++ b/loop/tests/test_mm_system_creator.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/mm_system_creator.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_psipred_prediction.cc b/loop/tests/test_psipred_prediction.cc
index 7053e5a1dc6eaf2f60ab062fca6765b0d13e632e..5dbc83c7ba8d5a08970886598342c328b733aa32 100644
--- a/loop/tests/test_psipred_prediction.cc
+++ b/loop/tests/test_psipred_prediction.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/psipred_prediction.hh>
#include <promod3/core/message.hh>
#define BOOST_TEST_DYN_LINK
diff --git a/loop/tests/test_sidechain_construction.cc b/loop/tests/test_sidechain_construction.cc
index 70c4ea2eaaff04530ffe3fdc2c613abc3a43d46b..2e65c53c7d40efce1db613e4d2836969429d6421 100644
--- a/loop/tests/test_sidechain_construction.cc
+++ b/loop/tests/test_sidechain_construction.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/sidechain_atom_rule_lookup.hh>
#include <promod3/loop/sidechain_atom_constructor.hh>
diff --git a/loop/tests/test_structuredb.cc b/loop/tests/test_structuredb.cc
index 01cf26055402ab8a89363d2426287329d48a3dff..69715800d0b4bcbda3a3c70fef82a4d162cce1eb 100644
--- a/loop/tests/test_structuredb.cc
+++ b/loop/tests/test_structuredb.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/structure_db.hh>
#include <promod3/core/message.hh>
diff --git a/loop/tests/test_torsion_sampler.cc b/loop/tests/test_torsion_sampler.cc
index e956f094da3786b7a783e34f1d057e97598af5d6..af517a90beb8e9c6d989083895e71239757c4f6d 100644
--- a/loop/tests/test_torsion_sampler.cc
+++ b/loop/tests/test_torsion_sampler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/loop/torsion_sampler.hh>
#include <promod3/core/message.hh>
#include <promod3/loop/loop_object_loader.hh>
diff --git a/loop/tests/tests.cc b/loop/tests/tests.cc
index 1ba3edee29d4c0accae2178df7e5dc482f294322..5757e0a2c6da50f5d690c41365dbb0913543503e 100644
--- a/loop/tests/tests.cc
+++ b/loop/tests/tests.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_loop
#define BOOST_AUTO_TEST_MAIN
diff --git a/modelling/doc/algorithms.rst b/modelling/doc/algorithms.rst
index 7ff5ae3a33e08ccccdf6d98f87abe2748e1d0d19..51357bc0615a49e58f2ef12f3efad67eeb3b003d 100644
--- a/modelling/doc/algorithms.rst
+++ b/modelling/doc/algorithms.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Modelling Algorithms
================================================================================
diff --git a/modelling/doc/gap_handling.rst b/modelling/doc/gap_handling.rst
index e939f9f60fa779b43bfdb196e0649ebd28306a08..b70d39a57558559a9ee4f6240384ffdbeb4df34c 100644
--- a/modelling/doc/gap_handling.rst
+++ b/modelling/doc/gap_handling.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Handling Gaps
================================================================================
diff --git a/modelling/doc/index.rst b/modelling/doc/index.rst
index 27ed61013a17190ebef7f0afb0027241c0e19294..ce9be313f8c26c747a5e1d711c9bf44751ac8587 100644
--- a/modelling/doc/index.rst
+++ b/modelling/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.modelling` - Protein Modelling
================================================================================
diff --git a/modelling/doc/loop_candidates.rst b/modelling/doc/loop_candidates.rst
index d0711c5a7c89292a61e3f1547ed28af62841382b..927107a0ddaa78b2bb6efe78b80c0f1dbc5aae1e 100644
--- a/modelling/doc/loop_candidates.rst
+++ b/modelling/doc/loop_candidates.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Handling Loop Candidates
================================================================================
diff --git a/modelling/doc/loop_closing.rst b/modelling/doc/loop_closing.rst
index 7ec7230b20a4e32fd9cc1f15a9e84ea7b549c113..21b842f5d1e25b00dc2f2cb863bf8124ccfb8f81 100644
--- a/modelling/doc/loop_closing.rst
+++ b/modelling/doc/loop_closing.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Fitting Loops Into Gaps
================================================================================
@@ -7,7 +23,7 @@ Loops often need to undergo conformational changes to fit into gaps defined by
stem residues. |project| implements two algorithms performing this task:
* Cyclic coordinate descent (CCD) [canutescu2003]_
- * Kinematic closure (KIC) [mandell2009]_
+ * Kinematic closure (KIC) [coutsias2005]_
In case of small gaps or small issues in the loop you might also consider the
:class:`BackboneRelaxer`.
@@ -374,8 +390,4 @@ Example usage:
:rtype: :class:`~promod3.loop.MmSystemCreator`
-.. rubric:: Citations
-
-.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003). Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12(5):963–972.
-.. [mandell2009] Mandell DJ, Coutsias EA and Kortemme T (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 6(8):551-2.
diff --git a/modelling/doc/model_checking.rst b/modelling/doc/model_checking.rst
index 97d7f69a83735d2757ede0afee224f181afdd6d5..03763e178971929ce13573f5ac8d72dc6624434d 100644
--- a/modelling/doc/model_checking.rst
+++ b/modelling/doc/model_checking.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Model Checking
================================================================================
diff --git a/modelling/doc/monte_carlo.rst b/modelling/doc/monte_carlo.rst
index 56e572a8788749bde35c415893a964126c5e67b9..1cb924b406ab017598f909d34872c0394697cb72 100644
--- a/modelling/doc/monte_carlo.rst
+++ b/modelling/doc/monte_carlo.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Generating Loops De Novo
================================================================================
@@ -21,46 +37,7 @@ Carlo sampling to the N-terminal part of crambin:
.. literalinclude:: ../../../tests/doc/scripts/modelling_monte_carlo.py
-.. method:: SampleMonteCarlo(sampler, closer, scorer, cooler, steps,\
- bb_list, initialize=True, seed=0,\
- lowest_energy_conformation=True)
-
- A convenient function to perform Monte Carlo sampling using a simulated
- annealing scheme. In every iteration, a new loop conformation gets proposed by
- the provided *sampler* and closed by the *closer*. Upon scoring, this new
- conformation gets accepted/rejected using a metropolis criterion based on the
- temperature given by the *cooler*
- => acceptance probability: exp(-delta_score/T).
- The result is stored in *bb_list* and is either the lowest energy conformation
- ever encountered or the last accepted proposal.
-
- :param sampler: Sampler object capable of initializing and altering
- conformations.
- :param closer: Closer object to adapt a new conformation to
- the environment.
- :param scorer: Scorer object to score new loop conformations.
- :param cooler: Cooler object to control the temperature of the
- Monte Carlo trajectory.
- :param steps: Number of Monte Carlo iterations to be performed.
- :param bb_list: The chosen conformation gets stored here.
- :param initialize: Whether a new bb_list should be generated as starting
- point, based on the samplers Initialize function.
- The input *bb_list* gets used otherwise.
- :param seed: Seed for internal random number generator.
- :param lowest_energy_conformation: If True, we choose the lowest scoring
- conformation of the trajectory. Otherwise,
- the last accepted proposal.
-
- :type sampler: :ref:`mc-sampler-object`
- :type closer: :ref:`mc-closer-object`
- :type scorer: :ref:`mc-scorer-object`
- :type cooler: :ref:`mc-cooler-object`
- :type steps: :class:`int`
- :type bb_list: :class:`~promod3.loop.BackboneList`
- :type initialize: :class:`bool`
- :type seed: :class:`int`
- :type lowest_energy_conformation: :class:`bool`
-
+.. autofunction:: SampleMonteCarlo
.. _mc-sampler-object:
@@ -69,7 +46,46 @@ Sampler Object
The sampler objects can be used to generate initial conformations and
propose new conformations for a sequence of interest. They build the basis
-for any Monte Carlo sampling pipeline.
+for any Monte Carlo sampling pipeline. You can either use one of the
+provided samplers or any object that implements the functionality of
+:class:`SamplerBase`.
+
+
+.. class:: SamplerBase
+
+ Abstract base class defining the functions that must be implemented by any
+ sampler.
+
+ .. method:: Initialize(bb_list)
+
+ Supposed to initialize structural information from scratch. The sequence
+ of the generated :class:`promod3.loop.BackboneList` is taken from *bb_list*.
+
+ :param bb_list: Passed by reference, so the resulting
+ :class:`promod3.loop.BackboneList` is assigned to this
+ parameter. Sequence / length stay the same.
+
+ :type bb_list: :class:`promod3.loop.BackboneList`
+
+ :returns: None
+
+ .. method:: ProposeStep(actual_positions, proposed_positions)
+
+ Takes current positions and proposes a new conformation. There is no
+ guarantee on maintining any special RT state. The :ref:`mc-closer-object`
+ is supposed to sort that out.
+
+ :param actual_positions: Starting point, must not change when calling this
+ function.
+ :param proposed_positions: Passed by reference, so the resulting
+ :class:`promod3.loop.BackboneList` is assigned to
+ this parameter.
+
+ :type actual_positions: :class:`promod3.loop.BackboneList`
+ :type proposed_positions: :class:`promod3.loop.BackboneList`
+
+ :returns: None
+
.. class:: PhiPsiSampler(sequence, torsion_sampler, n_stem_phi=-1.0472,\
c_stem_psi=-0.78540, prev_aa='A', next_aa='A', seed=0)
@@ -237,9 +253,9 @@ for any Monte Carlo sampling pipeline.
:param seed: Seed for the internal random number generators
:type sequence: :class:`str`
- :type fraggers: :class:`str`
+ :type fraggers: :class:`list`
:type init_bb_list: :class:`~promod3.loop.BackboneList`
- :type samplint_start_index: :class:`int`
+ :type sampling_start_index: :class:`int`
:type init_fragments: :class:`int`
:type seed: :class:`int`
@@ -276,7 +292,32 @@ After the proposal of new conformations by the sampler objects, the
conformations typically have to undergo some structural changes, so they
fit to a given environment. This can either be structural changes, that
the stems of the sampled conformation overlap with given stem residues or
-or simple stem superposition in case of terminal sampling.
+or simple stem superposition in case of terminal sampling. You can either
+use any of the provided closers or any object that implements the
+functionality of :class:`CloserBase`.
+
+.. class:: CloserBase
+
+ Abstract base class defining the functions that must be implemented by any
+ closer.
+
+ .. method:: Close(actual_positions, closed_positions)
+
+ Takes current positions and proposes a new conformation that fits to a
+ given environment.
+
+ :param actual_positions: Starting point, must not change when calling this
+ function.
+ :param closed_positions: Passed by reference, so the resulting
+ :class:`promod3.loop.BackboneList` is assigned to
+ this parameter.
+
+ :type actual_positions: :class:`promod3.loop.BackboneList`
+ :type closed_positions: :class:`promod3.loop.BackboneList`
+
+ :returns: Whether closing procedure was successful
+ :rtype: :class:`bool`
+
.. class:: CCDCloser(n_stem, c_stem, sequence, torsion_sampler, seed)
@@ -305,7 +346,7 @@ or simple stem superposition in case of terminal sampling.
of :class:`~promod3.loop.TorsionSampler`
:type seed: :class:`int`
- .. method:: Close(actual_positions,closed_positions)
+ .. method:: Close(actual_positions, closed_positions)
:param actual_positions: Conformation to be closed.
:param closed_positions: Closed conformation gets stored in here.
@@ -320,7 +361,8 @@ or simple stem superposition in case of terminal sampling.
The DirtyCCDCloser applies the CCD algorithm to the sampled conformation
to enforce the match between the conformations stem residue and
- the stems given by the closer.
+ the stems given by the closer. There is no check for reasonable backbone
+ dihedral angles as it is the case for the :class:`CCDCloser`.
:param n_stem: Defining stem positions the closed conformation
should adapt.
@@ -331,7 +373,7 @@ or simple stem superposition in case of terminal sampling.
:type n_stem: :class:`ost.mol.ResidueHandle`
:type c_stem: :class:`ost.mol.ResidueHandle`
- .. method:: Close(actual_positions,closed_positions)
+ .. method:: Close(actual_positions, closed_positions)
:param actual_positions: Conformation to be closed.
:param closed_positions: Closed conformation gets stored in here.
@@ -355,10 +397,10 @@ or simple stem superposition in case of terminal sampling.
:param seed: Seed for internal random generators.
:type n_stem: :class:`ost.mol.ResidueHandle`
- :type n_stem: :class:`ost.mol.ResidueHandle`
+ :type c_stem: :class:`ost.mol.ResidueHandle`
:type seed: :class:`int`
- .. method:: Close(actual_positions,closed_positions)
+ .. method:: Close(actual_positions, closed_positions)
:param actual_positions: Conformation to be closed.
:param closed_positions: Closed conformation gets stored in here.
@@ -371,26 +413,60 @@ or simple stem superposition in case of terminal sampling.
.. class:: NTerminalCloser(c_stem)
- The NTerminalCloser simply takes the conformation and closes by superposing
- the c_stem with the desired positions.
+ The :class:`NTerminalCloser` simply takes the conformation and closes by
+ superposing the c_stem with the desired positions.
:param c_stem: Defining stem positions the closed conformation should
adapt.
:type c_stem: :class:`ost.mol.ResidueHandle`
- :returns: Whether closing was successful
+
+ .. method:: Close(actual_positions, closed_positions)
+
+ :param actual_positions: Conformation to be closed (or in this case
+ transformed in space).
+ :param closed_positions: Closed (transformed) conformation gets stored in
+ here.
+
+ :type actual_positions: :class:`~promod3.loop.BackboneList`
+ :type closed_positions: :class:`~promod3.loop.BackboneList`
+
+ :returns: Whether closing was successful
.. class:: CTerminalCloser(n_stem)
- The CTerminalCloser simply takes the conformation and closes by superposing
- the n_stem with the desired positions.
+ The :class:`CTerminalCloser` simply takes the conformation and closes by
+ superposing the n_stem with the desired positions.
:param n_stem: Defining stem positions the closed conformation should
adapt.
:type n_stem: :class:`ost.mol.ResidueHandle`
- :returns: Whether closing was successful
+ .. method:: Close(actual_positions,closed_positions)
+
+ :param actual_positions: Conformation to be closed (or in this case
+ transformed in space).
+ :param closed_positions: Closed (transformed) conformation gets stored in
+ here.
+
+ :type actual_positions: :class:`~promod3.loop.BackboneList`
+ :type closed_positions: :class:`~promod3.loop.BackboneList`
+
+ :returns: Whether closing was successful
+
+
+.. class:: DeNovoCloser
+
+ In case of sampling a full stretch, you dont have external constraints. The
+ closer has a rather boring job in this case.
+
+ .. method:: Close(actual_positions,closed_positions)
+
+ Does absolutely nothing, except copying over the coordinates from
+ *actual_positions* to *closed_positions* and return true.
+
+
.. _mc-scorer-object:
@@ -399,10 +475,27 @@ Scorer Object
--------------------------------------------------------------------------------
The scorer asses a proposed conformation and are intended to return a pseudo
-energy, the lower the better.
+energy, the lower the better. You can either use the provided scorer or any
+object implementing the functionality defined in :class:`ScorerBase`.
+
+
+.. class:: ScorerBase
+ Abstract base class defining the functions that must be implemented by any
+ scorer.
+
+ .. method:: GetScore(bb_list)
-.. class:: LinearScorer(scorer, scorer_env, start_resnum, num_residues,
+ Takes coordinates and spits out a score given some internal structural
+ environment.
+
+ :param bb_list: Coordinates to be scored
+ :type bb_list: :class:`promod3.loop.BackboneList`
+
+ :returns: The score
+ :rtype: :class:`float`
+
+.. class:: LinearScorer(scorer, scorer_env, start_resnum, num_residues,\
chain_idx, linear_weights)
The LinearScorer allows to combine the scores available from
@@ -450,13 +543,31 @@ Cooler Object
The cooler objects control the temperature of the Monte Carlo trajectory.
They're intended to deliver steadily decreasing temperatures with calls
-to their GetTemperature function.
+to their GetTemperature function. You can either use the provided cooler
+or any object implementing the functionality defined in
+:class:`CoolerBase`.
+
+.. class:: CoolerBase
+
+ Abstract base class defining the functions that must be implemented by any
+ cooler.
+
+ .. method:: GetTemperature()
+
+ :returns: The Temperature
+ :rtype: :class:`float`
+
+ .. method:: Reset()
+
+ Resets to original state, so a new Monte Carlo trajectory can be generated
+
.. class:: ExponentialCooler(change_frequency, start_temperature, cooling_factor)
The exponential cooler starts with a given *start_temperature* and counts the
- calls to its GetTemperature function. According to the *change_frequency*,
- the returned temperature gets multiplied by the *cooling_factor*.
+ calls to its :meth:`GetTemperature` function. According to the
+ *change_frequency*, the returned temperature gets multiplied by the
+ *cooling_factor*.
:param change_frequency: Frequency to change temperature
:param start_temperature: temperature to start with
@@ -472,4 +583,5 @@ to their GetTemperature function.
.. method:: Reset()
- Sets current temperature back to *start_temperature*
+ Sets current temperature back to *start_temperature* and the
+ internal counter to 0
diff --git a/modelling/doc/pipeline.rst b/modelling/doc/pipeline.rst
index 175b65c5d6554d15f76076e3bd3c530595a7cf64..54d86037d316ed87434fea7ae1cca2e3a2ae11d0 100644
--- a/modelling/doc/pipeline.rst
+++ b/modelling/doc/pipeline.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Modelling Pipeline
================================================================================
diff --git a/modelling/doc/sidechain_reconstruction.rst b/modelling/doc/sidechain_reconstruction.rst
index 72e93a0a96a3f793542c32062748295655c010b7..f6a076c6b780c809d729bf52882d7e7e1fc04cb0 100644
--- a/modelling/doc/sidechain_reconstruction.rst
+++ b/modelling/doc/sidechain_reconstruction.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Sidechain Reconstruction
================================================================================
@@ -144,9 +160,9 @@ SidechainReconstructor Class
:param use_frm: If True, use flexible rotamer model, else rigid.
:type use_frm: :class:`bool`
:param use_bbdep_lib: If True, use default backbone dependent rot. library
- (:meth:`Dunbrack <LoadDunbrackLib>`), else use
+ (:meth:`LoadBBDepLib`), else use
backbone independent one
- (:meth:`Penultimate <LoadPenultimateLib>`).
+ (:meth:`LoadLib`).
:type use_bbdep_lib: :class:`bool`
:param rotamer_library: Custom rotamer library to be used.
:type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib`
diff --git a/modelling/pymod/CMakeLists.txt b/modelling/pymod/CMakeLists.txt
index 3f6e6f13be2079f47e8a11c1ffb979971cfb5534..5e44247d6bd03f7f80cbaee99fe973700ce4dcda 100644
--- a/modelling/pymod/CMakeLists.txt
+++ b/modelling/pymod/CMakeLists.txt
@@ -22,6 +22,7 @@ set(MODELLING_PYMOD
_denovo.py
_fragger_handle.py
_reconstruct_sidechains.py
+ _monte_carlo.py
)
pymod(NAME modelling
diff --git a/modelling/pymod/__init__.py b/modelling/pymod/__init__.py
index cdd41d485e453d2089b76a5a34c710559cd86a87..d81fc6ee63f97c01c6810036749a957c53f35205 100644
--- a/modelling/pymod/__init__.py
+++ b/modelling/pymod/__init__.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""Initialise the modelling module."""
from _modelling import *
from _closegaps import *
@@ -7,3 +23,4 @@ from _reconstruct_sidechains import *
from _ring_punches import *
from _denovo import *
from _fragger_handle import *
+from _monte_carlo import *
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index aa857023be8b7543a56670d0b8db6e340a4edcf1..167379a70fa81bbfaa400f65050d617655b0664b 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''High-level functionality for modelling module to close gaps. Added in the
__init__.py file. To be used directly by passing a ModellingHandle instance
as argument.
diff --git a/modelling/pymod/_denovo.py b/modelling/pymod/_denovo.py
index 51dd26d0ca0b540c9b6523c66337f5aa0a96fa52..445c9574c829b4bc02f3eed107e68586bacdff34 100644
--- a/modelling/pymod/_denovo.py
+++ b/modelling/pymod/_denovo.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from promod3 import scoring, loop
from _modelling import *
diff --git a/modelling/pymod/_fragger_handle.py b/modelling/pymod/_fragger_handle.py
index 95dee6db0f9c33dcdaf0bd3f5e78ba31c5202487..50ba6e50e6f3c7f000b90c0687cfcf83d864c79c 100644
--- a/modelling/pymod/_fragger_handle.py
+++ b/modelling/pymod/_fragger_handle.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Python functionality to generate fraggers.'''
from promod3.loop import *
diff --git a/modelling/pymod/_molprobity.py b/modelling/pymod/_molprobity.py
index ad431058365f6a80c702a9518fe237e2ac860adb..8f583e6ee2e90a2741c20d21394fa23d0a0a0ddb 100644
--- a/modelling/pymod/_molprobity.py
+++ b/modelling/pymod/_molprobity.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Binding to external MolProbity tool to get scores.'''
import ost
diff --git a/modelling/pymod/_monte_carlo.py b/modelling/pymod/_monte_carlo.py
new file mode 100644
index 0000000000000000000000000000000000000000..13a085ccac3c4cac8b8727540f62671f0bfc43f9
--- /dev/null
+++ b/modelling/pymod/_monte_carlo.py
@@ -0,0 +1,106 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+import random
+import math
+
+
+def SampleMonteCarlo(sampler, closer, scorer, cooler, steps, bb_list,
+ initialize, seed = 0, lowest_energy_conformation = True):
+ ''' A convenient function to perform Monte Carlo sampling using a simulated
+ annealing scheme. In every iteration, a new loop conformation gets proposed
+ by the provided *sampler* and closed by the *closer*. Upon scoring, this new
+ conformation gets accepted/rejected using a metropolis criterion based on
+ the temperature given by the *cooler*
+ => acceptance probability: exp(-delta_score/T).
+ The result is stored in *bb_list* (passed by reference, so NO return value)
+ and is either the lowest energy conformation ever encountered or the last
+ accepted proposal.
+
+ :param sampler: Sampler object capable of initializing and altering
+ conformations.
+ :param closer: Closer object to adapt a new conformation to
+ the environment.
+ :param scorer: Scorer object to score new loop conformations.
+ :param cooler: Cooler object to control the temperature of the
+ Monte Carlo trajectory.
+ :param steps: Number of Monte Carlo iterations to be performed.
+ :param bb_list: The chosen conformation gets stored here.
+ :param initialize: Whether a new bb_list should be generated as starting
+ point, based on the samplers Initialize function.
+ The input *bb_list* gets used otherwise.
+ :param seed: Seed for internal random number generator.
+ :param lowest_energy_conformation: If True, we choose the lowest scoring
+ conformation of the trajectory.
+ Otherwise, the last accepted proposal.
+
+ :type sampler: :ref:`mc-sampler-object`
+ :type closer: :ref:`mc-closer-object`
+ :type scorer: :ref:`mc-scorer-object`
+ :type cooler: :ref:`mc-cooler-object`
+ :type steps: :class:`int`
+ :type bb_list: :class:`~promod3.loop.BackboneList`
+ :type initialize: :class:`bool`
+ :type seed: :class:`int`
+ :type lowest_energy_conformation: :class:`bool`
+ '''
+
+ # Initialize from scratch if necessary
+ if initialize:
+ initialized = False
+ for i in range(100):
+ sampler.Initialize(bb_list)
+ if closer.Close(bb_list, bb_list):
+ initialized = True
+ break
+ if not initialized:
+ raise RuntimeError("Failed to initialize monte carlo protocol!")
+
+ # setup
+ random.seed(seed)
+ score = scorer.GetScore(bb_list)
+ closed = False
+ min_score = score
+ min_score_bb_list = bb_list.Copy()
+ proposed_bb_list = bb_list.Copy()
+
+ for i in range(steps):
+
+ # try several proposals (we might not be able to close at first attempt)
+ closed = False
+ for j in range(3):
+ sampler.ProposeStep(bb_list, proposed_bb_list)
+ if closer.Close(proposed_bb_list, proposed_bb_list):
+ closed = True
+ break
+
+ # check for success, try again in next step in case of failure
+ if not closed:
+ continue
+
+ # accept / reject based on Metropolis criterion
+ temperature = cooler.GetTemperature()
+ new_score = scorer.GetScore(proposed_bb_list)
+
+ if math.exp(-(new_score-score)/temperature) > random.random():
+ positions = proposed_bb_list.Copy()
+ score = new_score
+ if lowest_energy_conformation and score < min_score:
+ min_score = score
+ min_score_bb_list = positions
+
+ if lowest_energy_conformation:
+ bb_list = min_score_bb_list
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index fdea48505c30f4bb49832cd1182c89babe04acd0..56cc847c61da1238af93114613208ab3061fe2a6 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''High-level functionality for modelling module to build pipelines. Added in
the __init__.py file. To be used directly by passing a ModellingHandle instance
as argument.
@@ -164,7 +180,8 @@ def _GetSimEntity(sim):
def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
- structure_db=None, torsion_sampler=None):
+ structure_db=None, torsion_sampler=None,
+ rotamer_library=None):
'''Build sidechains for model.
This is a wrapper for :func:`promod3.modelling.ReconstructSidechains`,
@@ -190,10 +207,16 @@ def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
if ring punches are found. A default one is loaded
if None.
:type torsion_sampler: :class:`~promod3.loop.TorsionSampler`
+ :param rotamer_library: Used as parameter for
+ :func:`modelling.ReconstructSidechains`, a default
+ one is loaded if None.
+ :type rotamer_library: :class:`~promod3.sidechain.RotamerLib` or
+ :class:`~promod3.sidechain.BBDepRotamerLib`
'''
prof = core.StaticRuntimeProfiler.StartScoped('pipeline::BuildSidechains')
ost.LogInfo("Rebuilding sidechains.")
- ReconstructSidechains(mhandle.model, keep_sidechains=True)
+ ReconstructSidechains(mhandle.model, keep_sidechains=True,
+ rotamer_library=rotamer_library)
# check for ring punches
rings = GetRings(mhandle.model)
ring_punches = GetRingPunches(rings, mhandle.model)
@@ -221,7 +244,8 @@ def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
FillLoopsByDatabase(mhandle, fragment_db, structure_db,
torsion_sampler, ring_punch_detection=2)
# re-build sidechains
- ReconstructSidechains(mhandle.model, keep_sidechains=True)
+ ReconstructSidechains(mhandle.model, keep_sidechains=True,
+ rotamer_library=rotamer_library)
# restore gaps
mhandle.gaps = StructuralGapList()
for g in old_gaps:
@@ -459,6 +483,7 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list()):
fragment_db = loop.LoadFragDB()
structure_db = loop.LoadStructureDB()
torsion_sampler = loop.LoadTorsionSamplerCoil()
+ rotamer_library = sidechain.LoadBBDepLib()
merge_distance = 4
# remove terminal gaps
@@ -471,7 +496,7 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list()):
# build sidechains
BuildSidechains(mhandle, merge_distance, fragment_db,
- structure_db, torsion_sampler)
+ structure_db, torsion_sampler, rotamer_library)
# minimize energy of final model using molecular mechanics
MinimizeModelEnergy(mhandle, use_amber_ff=use_amber_ff,
diff --git a/modelling/pymod/_reconstruct_sidechains.py b/modelling/pymod/_reconstruct_sidechains.py
index cc465d832149d465348823cbfc67db6386235b93..d9a7dbd5541b9e7ca3102bf9e8cc78bda4b8f1e6 100644
--- a/modelling/pymod/_reconstruct_sidechains.py
+++ b/modelling/pymod/_reconstruct_sidechains.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from ost import geom, mol, conop
from promod3 import core, sidechain
import traceback
@@ -396,8 +412,7 @@ def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
:type consider_ligands: :class:`bool`
:param rotamer_library: A rotamer library to extract the rotamers from. The
- default is the :meth:`Dunbrack <LoadDunbrackLib>`
- library.
+ default is to call :meth:`<LoadBBDepLib>`.
:type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib`
:param optimize_subrotamers: Only considered when *rotamer_model*
@@ -427,7 +442,7 @@ def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
raise RuntimeError("Only \"rrm\" and \"frm\" allowed for rotamer_model!")
if rotamer_library == None:
- rotamer_library = sidechain.LoadDunbrackLib()
+ rotamer_library = sidechain.LoadBBDepLib()
bbdep = False
if type(rotamer_library) is sidechain.BBDepRotamerLib:
bbdep = True
diff --git a/modelling/pymod/_ring_punches.py b/modelling/pymod/_ring_punches.py
index 969aca39d8b7daabb2dc354350314bc18ac13f80..2efed0c1cd7c479abc6c397ea2ab141d0b8301ae 100644
--- a/modelling/pymod/_ring_punches.py
+++ b/modelling/pymod/_ring_punches.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Helper functions to deal with ring punchings.'''
import ost
from ost import geom
diff --git a/modelling/pymod/export_extension_scheme.cc b/modelling/pymod/export_extension_scheme.cc
index 56e96be00216cd1a66c624fdd95accf7325dadd1..26298341987427308fb16d1f70a2503c561ad6fd 100644
--- a/modelling/pymod/export_extension_scheme.cc
+++ b/modelling/pymod/export_extension_scheme.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include <promod3/modelling/extension_scheme.hh>
diff --git a/modelling/pymod/export_gap.cc b/modelling/pymod/export_gap.cc
index d2c8d07ff216564bb8e71d33c823a4399b095654..de39d2c23324a7d0c0d3fd2724272600ae7d454d 100644
--- a/modelling/pymod/export_gap.cc
+++ b/modelling/pymod/export_gap.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include <promod3/modelling/gap.hh>
diff --git a/modelling/pymod/export_gap_extender.cc b/modelling/pymod/export_gap_extender.cc
index 5c27c41b33ea38fbc8fa4789ebef5cc9ca093b35..3d530e190333a71ae9d1cdd01bed9ba059350596 100644
--- a/modelling/pymod/export_gap_extender.cc
+++ b/modelling/pymod/export_gap_extender.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/modelling/gap_extender.hh>
#include <promod3/core/export_helper.hh>
diff --git a/modelling/pymod/export_loop_candidate.cc b/modelling/pymod/export_loop_candidate.cc
index 7bb657db9d310ff2319217e054fa184b6f2df44d..564395002d68cfbf3699526ef35e0cfa10b08611 100644
--- a/modelling/pymod/export_loop_candidate.cc
+++ b/modelling/pymod/export_loop_candidate.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
diff --git a/modelling/pymod/export_loop_closure.cc b/modelling/pymod/export_loop_closure.cc
index a6aa1a0da761152f0fab494f034725b1746c7205..0a28b6bea9201f6e848a5493c2d88f4135c69330 100644
--- a/modelling/pymod/export_loop_closure.cc
+++ b/modelling/pymod/export_loop_closure.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/register_ptr_to_python.hpp>
diff --git a/modelling/pymod/export_model.cc b/modelling/pymod/export_model.cc
index db325e3d416a5b436da212f4ee0f550ac222a106..589242c563e995db7f7d96dd55f90e6c1ecf34b6 100644
--- a/modelling/pymod/export_model.cc
+++ b/modelling/pymod/export_model.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include <promod3/modelling/model.hh>
diff --git a/modelling/pymod/export_monte_carlo.cc b/modelling/pymod/export_monte_carlo.cc
index 7d296ccf9550ec7db9ebf53c06aa4e4792370e0f..32950cdbb17e2ada13c0772bfdb72ec50d5bcb62 100644
--- a/modelling/pymod/export_monte_carlo.cc
+++ b/modelling/pymod/export_monte_carlo.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/python/raw_function.hpp>
@@ -236,31 +252,6 @@ LinearScorerPtr LinearScorerInitWrapper(scoring::BackboneOverallScorerPtr scorer
return p;
}
-void MonteCarloWithoutRelaxer(MonteCarloSamplerPtr sampler,
- MonteCarloCloserPtr closer,
- MonteCarloScorerPtr scorer,
- MonteCarloCoolerPtr cooler,
- uint steps, loop::BackboneList& backbone_list,
- bool initialize, uint seed,
- bool lowest_energy_conformation) {
- SampleMonteCarlo(sampler, closer, scorer, cooler, steps, backbone_list,
- initialize, seed, lowest_energy_conformation);
-}
-
-void MonteCarloWithRelaxer(MonteCarloSamplerPtr sampler,
- MonteCarloCloserPtr closer,
- MonteCarloScorerPtr scorer,
- MonteCarloCoolerPtr cooler,
- uint steps, loop::BackboneList& backbone_list,
- BackboneRelaxerPtr relaxer, uint relaxer_frequency,
- uint relaxer_steps, bool initialize, uint seed,
- bool lowest_energy_conformation) {
- SampleMonteCarlo(sampler, closer, scorer, cooler, steps, backbone_list,
- relaxer, relaxer_frequency, relaxer_steps, initialize,
- seed, lowest_energy_conformation);
-}
-
-
}
void export_monte_carlo() {
@@ -357,18 +348,4 @@ void export_monte_carlo() {
register_ptr_to_python<NTerminalCloserPtr>();
register_ptr_to_python<CTerminalCloserPtr>();
register_ptr_to_python<MonteCarloCloserPtr>();
-
- // export monte carlo sampler
- def("SampleMonteCarlo", &MonteCarloWithoutRelaxer,
- (arg("sampler"), arg("closer"), arg("scorer"), arg("cooler"),
- arg("steps"), arg("backbone"), arg("initialize")=true, arg("seed")=0,
- arg("lowest_energy_conformation")=true));
-
- def("SampleMonteCarlo", &MonteCarloWithRelaxer,
- (arg("sampler"), arg("closer"), arg("scorer"), arg("cooler"),
- arg("steps"), arg("backbone"), arg("backbone_relaxer"),
- arg("relaxer_frequency"), arg("relaxer_steps"), arg("initialize")=true,
- arg("seed")=0, arg("lowest_energy_conformation")=true));
-
-
}
diff --git a/modelling/pymod/export_rigid_blocks.cc b/modelling/pymod/export_rigid_blocks.cc
index 3c7584d80b6f39ca036dfe616d15f86a6ed59274..36763f3a089dc775e3cdbe21f5091dc1e3c0b7c7 100644
--- a/modelling/pymod/export_rigid_blocks.cc
+++ b/modelling/pymod/export_rigid_blocks.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/modelling/pymod/export_score_container.cc b/modelling/pymod/export_score_container.cc
index 237e1d415f0dc52125c369ad2b5aebbde1c5d6ad..4afef319bfd48498b6929b542a1afd561b893066 100644
--- a/modelling/pymod/export_score_container.cc
+++ b/modelling/pymod/export_score_container.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/message.hh>
#include <promod3/core/export_helper.hh>
diff --git a/modelling/pymod/export_scoring_weights.cc b/modelling/pymod/export_scoring_weights.cc
index 11e3c18eb54a48f5162e88bab3c0286d4f8aca55..c100ec806c7ae8a888b567d526729b75696a345e 100644
--- a/modelling/pymod/export_scoring_weights.cc
+++ b/modelling/pymod/export_scoring_weights.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/message.hh>
#include <promod3/core/export_helper.hh>
diff --git a/modelling/pymod/export_sidechain_reconstructor.cc b/modelling/pymod/export_sidechain_reconstructor.cc
index 5c8306f3becb3f13b9c99b3ac0e5906ebf7895a9..0d270147df0de325c646d536ca627b307476ac9b 100644
--- a/modelling/pymod/export_sidechain_reconstructor.cc
+++ b/modelling/pymod/export_sidechain_reconstructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/modelling/sidechain_reconstructor.hh>
diff --git a/modelling/pymod/wrap_modelling.cc b/modelling/pymod/wrap_modelling.cc
index 72125d290d12735a145389f9d47b30a9eca7366e..7e4affa848f8deca25c2f428db14751cc328d533 100644
--- a/modelling/pymod/wrap_modelling.cc
+++ b/modelling/pymod/wrap_modelling.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
void export_gap();
diff --git a/modelling/src/all_atom_relaxer.cc b/modelling/src/all_atom_relaxer.cc
index 9fe1dc51136b70c71d5b4945978375c06f00d0e5..a7dd1ab6922425971a8afe85a1f20ace74b4e3e8 100644
--- a/modelling/src/all_atom_relaxer.cc
+++ b/modelling/src/all_atom_relaxer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/all_atom_relaxer.hh>
#include <promod3/loop/hydrogen_constructor.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/modelling/src/all_atom_relaxer.hh b/modelling/src/all_atom_relaxer.hh
index 9235a13f7980d05b37a06d51ef09c41637bd39ed..1e594df529d38a0a9656e4fd9d5d7ddae72d0ce8 100644
--- a/modelling/src/all_atom_relaxer.hh
+++ b/modelling/src/all_atom_relaxer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_MODELLING_ALL_ATOM_RELAXER_HH
#define PROMOD3_MODELLING_ALL_ATOM_RELAXER_HH
diff --git a/modelling/src/backbone_relaxer.cc b/modelling/src/backbone_relaxer.cc
index ded52f6a222d2cf2135de02027563fdc94ce9a13..c2212c9289fd13882973879164ab080461b883d2 100644
--- a/modelling/src/backbone_relaxer.cc
+++ b/modelling/src/backbone_relaxer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/backbone_relaxer.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/loop/amino_acid_atoms.hh>
diff --git a/modelling/src/backbone_relaxer.hh b/modelling/src/backbone_relaxer.hh
index 78d142e43c207597bf9e7fb127ffe3706ebda1cd..0d5499a3e2403536537ae8e373872646270320e3 100644
--- a/modelling/src/backbone_relaxer.hh
+++ b/modelling/src/backbone_relaxer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_BACKBONE_RELAXER_HH
#define PROMOD_MODELLING_BACKBONE_RELAXER_HH
diff --git a/modelling/src/ccd.cc b/modelling/src/ccd.cc
index bc913bba3f4b76fec10cc5f2a3fd513d6acbc006..10ffafaed32c2ff836f26c1cbaee253149e7152a 100644
--- a/modelling/src/ccd.cc
+++ b/modelling/src/ccd.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/ccd.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/geom_base.hh>
diff --git a/modelling/src/ccd.hh b/modelling/src/ccd.hh
index 344228a1391ee488b43d1e1a595e36dd332638f1..4d82a32f07e3a58b6aa2ea6d19fbfda348a1fbdd 100644
--- a/modelling/src/ccd.hh
+++ b/modelling/src/ccd.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_CCD_HH
#define PROMOD_MODELLING_CCD_HH
diff --git a/modelling/src/extension_scheme.cc b/modelling/src/extension_scheme.cc
index da4fd528548047fc800ade063867ff3850557d89..5e3535a83815df1fa3b6735f1a0b23e26fe86e1c 100644
--- a/modelling/src/extension_scheme.cc
+++ b/modelling/src/extension_scheme.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/extension_scheme.hh>
namespace promod3 { namespace modelling{
diff --git a/modelling/src/extension_scheme.hh b/modelling/src/extension_scheme.hh
index c9f183ded6c881c67757a5812b13dde3232f02f6..46de03491585b5bf5db1203bb50709d807eb5ecc 100644
--- a/modelling/src/extension_scheme.hh
+++ b/modelling/src/extension_scheme.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_EXTENSION_SCHEME_HH
#define PROMOD_MODELLING_EXTENSION_SCHEME_HH
diff --git a/modelling/src/gap.cc b/modelling/src/gap.cc
index df052586abaab7fa9dea6db806a4f713647a4ed8..5c13071eaff51ce8f8dd708f17feb17fdf11a78e 100644
--- a/modelling/src/gap.cc
+++ b/modelling/src/gap.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <ost/log.hh>
#include <promod3/modelling/gap.hh>
diff --git a/modelling/src/gap.hh b/modelling/src/gap.hh
index 4bbe3347fb9819619e4f9c09661c35a63c232919..b8bb9d5ec0ccfcbc616b2ef1e33a1b99a78263a5 100644
--- a/modelling/src/gap.hh
+++ b/modelling/src/gap.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_MODELLING_GAP_HH
#define PM3_MODELLING_GAP_HH
diff --git a/modelling/src/gap_extender.cc b/modelling/src/gap_extender.cc
index 02492976d7c358524506d21166eee585647b6272..2d723c4a5a31476c9814fdcee3a3cb789f43f003 100644
--- a/modelling/src/gap_extender.cc
+++ b/modelling/src/gap_extender.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/gap_extender.hh>
#include <algorithm>
diff --git a/modelling/src/gap_extender.hh b/modelling/src/gap_extender.hh
index 63217f96e04ee0042b54052c35c69b69fdc70d48..625b6f5877bff9d0aece6039d1a06d042c25cf2d 100644
--- a/modelling/src/gap_extender.hh
+++ b/modelling/src/gap_extender.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_MODELLING_GAP_EXTENDER_HH
#define PM3_MODELLING_GAP_EXTENDER_HH
diff --git a/modelling/src/kic.cc b/modelling/src/kic.cc
index fb7005aedd659dd59c21dbb7513657945e62726a..8571fa0759d1e63ef531b5ebd7b535ba0d017e79 100644
--- a/modelling/src/kic.cc
+++ b/modelling/src/kic.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/kic.hh>
#include <promod3/core/eigen_types.hh>
#include <promod3/core/message.hh>
diff --git a/modelling/src/kic.hh b/modelling/src/kic.hh
index 367e7969828f5fc8bccb8b86ef3ce75a79e05dcc..02166346104e1a054768c06664839d921cc8d457 100644
--- a/modelling/src/kic.hh
+++ b/modelling/src/kic.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_KIC_HH
#define PROMOD_MODELLING_KIC_HH
diff --git a/modelling/src/loop_candidate.cc b/modelling/src/loop_candidate.cc
index 5aa7cccee59836bc3589f851f741bf1e158c6a4e..8539705677d6bec217f1d4869f8ef662fc2768b1 100644
--- a/modelling/src/loop_candidate.cc
+++ b/modelling/src/loop_candidate.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/loop_candidate.hh>
#include <promod3/modelling/kic.hh>
#include <promod3/modelling/scoring_weights.hh>
diff --git a/modelling/src/loop_candidate.hh b/modelling/src/loop_candidate.hh
index 0b30ecf4bf2b51c2422ca0b26ec7607d805be3e0..14c6accf2145747158a2bad14165b1ac98e7d8bf 100644
--- a/modelling/src/loop_candidate.hh
+++ b/modelling/src/loop_candidate.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_MODELLING_LOOP_CANDIDATE_HH
#define PM3_MODELLING_LOOP_CANDIDATE_HH
diff --git a/modelling/src/model.cc b/modelling/src/model.cc
index 5740b93207b3c9d07a9dc790c1fe63f457609ad3..a4ef588ead11793811ba8b82a636adf7271c888f 100644
--- a/modelling/src/model.cc
+++ b/modelling/src/model.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <ctype.h>
#include <ost/log.hh>
#include <ost/dyn_cast.hh>
@@ -973,8 +989,6 @@ void BuildRawChain(const ost::seq::AlignmentHandle& aln,
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"modelling::BuildRawChain", 2);
- // FIXME: While conseptually simple, this function is way too long for my
- // taste. It should be chopped into smaller pieces.
if (aln.GetCount()!=2) {
throw promod3::Error("alignment must contain exactly two sequences");
}
@@ -1036,7 +1050,7 @@ void BuildRawChain(const ost::seq::AlignmentHandle& aln,
String name=conop::OneLetterCodeToResidueName(col[0]);
ResidueHandle dst_res=edi.AppendResidue(chain, name, ResNum(res_num));
dst_res.SetIsProtein(true);
- bool form_peptide_bond=false;
+ bool consecutive_residues=false;
if (last_num+1!=res_num) {
// that's an insertion
gap_list.push_back(StructuralGap(before, dst_res, gap_seq));
@@ -1044,12 +1058,9 @@ void BuildRawChain(const ost::seq::AlignmentHandle& aln,
} else if (last_index > -1 && last_index+1 != i) {
// that's a deletion
gap_list.push_back(StructuralGap(before, dst_res, ""));
- //form_peptide_bond=true;
} else {
- form_peptide_bond=true;
+ consecutive_residues=true;
}
- last_num=res_num;
- last_index=i;
bool has_cbeta=false;
if (toupper(col[0])==toupper(col[1])) {
CopyConserved(src_res, dst_res, edi, has_cbeta);
@@ -1072,13 +1083,21 @@ void BuildRawChain(const ost::seq::AlignmentHandle& aln,
if (spdbv_style) {
InsertDummyAtoms(dst_res, edi);
}
- if (form_peptide_bond && before.IsValid()) {
+ if (consecutive_residues && before.IsValid()) {
AtomHandle c_before=before.FindAtom("C");
AtomHandle n_this=dst_res.FindAtom("N");
- edi.Connect(c_before, n_this);
+ if(ost::conop::IsBondFeasible(c_before, n_this)) {
+ edi.Connect(c_before, n_this);
+ } else {
+ // not possible to generate feasible peptide bond
+ // add gap to enforce rebuilding during the modelling process
+ gap_list.push_back(StructuralGap(before, dst_res, ""));
+ }
}
- before=dst_res;
+ last_num=res_num;
+ last_index=i;
+ before=dst_res;
}
// check if we have added anything at all
if (last_num == 0) {
diff --git a/modelling/src/model.hh b/modelling/src/model.hh
index e42a2c8db6ee029ad4f7547faf6511b9f5be4fd2..e7503d8a3bbac7a73579d55b477eb8aaa63c03db 100644
--- a/modelling/src/model.hh
+++ b/modelling/src/model.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_MODELLING_MODEL_HH
#define PM3_MODELLING_MODEL_HH
diff --git a/modelling/src/monte_carlo.cc b/modelling/src/monte_carlo.cc
index 374fb05206799ba3106d26b95c173f8e018d4039..3c9782d12104409fedb32ff17ad2784c69f31cac 100644
--- a/modelling/src/monte_carlo.cc
+++ b/modelling/src/monte_carlo.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/monte_carlo.hh>
namespace promod3 { namespace modelling {
@@ -63,72 +79,5 @@ void SampleMonteCarlo(MonteCarloSamplerPtr sampler, MonteCarloCloserPtr closer,
if (lowest_energy_conformation) positions = min_score_bb_list;
}
-void SampleMonteCarlo(MonteCarloSamplerPtr sampler, MonteCarloCloserPtr closer,
- MonteCarloScorerPtr scorer, MonteCarloCoolerPtr cooler,
- uint steps, loop::BackboneList& positions,
- BackboneRelaxerPtr relaxer, uint relaxer_frequency,
- uint relaxer_steps, bool initialize, uint seed,
- bool lowest_energy_conformation) {
-
- loop::BackboneList proposed_positions;
-
- boost::mt19937 rgen(seed);
- boost::uniform_01<boost::mt19937> zeroone(rgen);
-
- Real score, new_score, temperature;
-
- if (initialize) {
- //try to initialize
- bool initialized = false;
- for (int i = 0; i < 100; ++i) {
- sampler->Initialize(positions);
- if (closer->Close(positions, positions)) {
- initialized = true;
- break;
- }
- }
- if (!initialized) {
- throw promod3::Error("Failed to initialize monte carlo sampling protocol!");
- }
- }
-
- score = scorer->GetScore(positions);
- bool closed = false;
-
- uint successful_steps = 0;
- Real min_score = score;
- loop::BackboneList min_score_bb_list = positions;
-
- for (uint i = 0; i < steps; ++i) {
- //try several proposals!
- closed = false;
- for (int j = 0; j < 3; ++j) {
- sampler->ProposeStep(positions, proposed_positions);
- if (closer->Close(proposed_positions, proposed_positions)) {
- closed = true;
- break;
- }
- }
- if (!closed) continue;
- temperature = cooler->GetTemperature();
- new_score = scorer->GetScore(proposed_positions);
- if (std::exp(-(new_score-score)/temperature) > zeroone()) {
- positions.swap(proposed_positions);
- score = new_score;
- ++successful_steps;
- if (successful_steps % relaxer_frequency == 0) {
- relaxer->Run(positions, relaxer_steps);
- }
- if (lowest_energy_conformation && score < min_score) {
- min_score = score;
- min_score_bb_list = positions;
- }
- }
- }
-
- // update return value if needed
- if (lowest_energy_conformation) positions = min_score_bb_list;
-}
-
}}//ns
diff --git a/modelling/src/monte_carlo.hh b/modelling/src/monte_carlo.hh
index 8f6d82c32d13329b191fe0001573dfd4c291a21c..1e573957efa0ace1aa8fcd4c999e89a4ed5a686a 100644
--- a/modelling/src/monte_carlo.hh
+++ b/modelling/src/monte_carlo.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_MONTE_CARLO_HH
#define PROMOD_MODELLING_MONTE_CARLO_HH
@@ -18,14 +34,6 @@ namespace promod3 { namespace modelling {
uint steps, loop::BackboneList& backbone_list,
bool initialize = true, uint seed = 0,
bool lowest_energy_conformation = true);
-
- void SampleMonteCarlo(MonteCarloSamplerPtr sampler, MonteCarloCloserPtr closer,
- MonteCarloScorerPtr scorer, MonteCarloCoolerPtr cooler,
- uint steps, loop::BackboneList& backbone_list,
- BackboneRelaxerPtr relaxer, uint relaxer_frequency,
- uint relaxer_steps, bool initialize = true, uint seed = 0,
- bool lowest_energy_conformation = true);
-
}}
#endif
diff --git a/modelling/src/monte_carlo_closer.cc b/modelling/src/monte_carlo_closer.cc
index 3d3090efb57e5cb1b63841523bc5e2edc7b82516..02d20b40c2d288eb4463852b8af83bf8df38fd07 100644
--- a/modelling/src/monte_carlo_closer.cc
+++ b/modelling/src/monte_carlo_closer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/monte_carlo_closer.hh>
#include <promod3/modelling/kic.hh>
#include <promod3/modelling/ccd.hh>
diff --git a/modelling/src/monte_carlo_closer.hh b/modelling/src/monte_carlo_closer.hh
index 239f11c93701ec2947f7084aed5bb7e8dadcbf0c..28feb029c3e847bc1018553f06aa4e7b99699de9 100644
--- a/modelling/src/monte_carlo_closer.hh
+++ b/modelling/src/monte_carlo_closer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_MONTE_CARLO_CLOSER_HH
#define PROMOD_MODELLING_MONTE_CARLO_CLOSER_HH
diff --git a/modelling/src/monte_carlo_cooler.cc b/modelling/src/monte_carlo_cooler.cc
index 1a99a55d1281b031ae61858f952b9c98ffae31a0..1b50af2133687bd419a3c3c00a6c6594d0b61005 100644
--- a/modelling/src/monte_carlo_cooler.cc
+++ b/modelling/src/monte_carlo_cooler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/monte_carlo_cooler.hh>
namespace promod3 { namespace modelling {
diff --git a/modelling/src/monte_carlo_cooler.hh b/modelling/src/monte_carlo_cooler.hh
index acf12e5f2e7573b824ec8bffa706152c52046390..8906e454ec90c02fb9dfab4747103298431aa45d 100644
--- a/modelling/src/monte_carlo_cooler.hh
+++ b/modelling/src/monte_carlo_cooler.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_MONTE_CARLO_COOLER_HH
#define PROMOD_MODELLING_MONTE_CARLO_COOLER_HH
diff --git a/modelling/src/monte_carlo_sampler.cc b/modelling/src/monte_carlo_sampler.cc
index e2d69b7675523fa369504003e2a9e12e25385393..31e398be7b38a72144447a14908d89705b2748e8 100644
--- a/modelling/src/monte_carlo_sampler.cc
+++ b/modelling/src/monte_carlo_sampler.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/monte_carlo_sampler.hh>
diff --git a/modelling/src/monte_carlo_sampler.hh b/modelling/src/monte_carlo_sampler.hh
index e80478fd2e9629e8a26e485df6d90bd628f85781..e3e7223c9f2f229b858672ce6ffed92f769322d3 100644
--- a/modelling/src/monte_carlo_sampler.hh
+++ b/modelling/src/monte_carlo_sampler.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_MONTE_CARLO_SAMPLER_HH
#define PROMOD_MODELLING_MONTE_CARLO_SAMPLER_HH
diff --git a/modelling/src/monte_carlo_scorer.cc b/modelling/src/monte_carlo_scorer.cc
index ba536e7d772fc8b8d506c8375269e4d9fb528da1..e13fb44305136f832ec8b885b4ab80cfdbe18029 100644
--- a/modelling/src/monte_carlo_scorer.cc
+++ b/modelling/src/monte_carlo_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/monte_carlo_scorer.hh>
namespace promod3 { namespace modelling {
diff --git a/modelling/src/monte_carlo_scorer.hh b/modelling/src/monte_carlo_scorer.hh
index a6707b359e0a138f296120815e524bfd9f4488b8..b478805833423e8246510fd02a2de3b1a08b87ec 100644
--- a/modelling/src/monte_carlo_scorer.hh
+++ b/modelling/src/monte_carlo_scorer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_MONTE_CARLO_SCORER_HH
#define PROMOD_MODELLING_MONTE_CARLO_SCORER_HH
diff --git a/modelling/src/rigid_blocks.cc b/modelling/src/rigid_blocks.cc
index df46c90fc4195cf3c47b6f4bb09a2b9ec5301e7f..d334a932ce55795573d6a857d9da314ac5710910 100644
--- a/modelling/src/rigid_blocks.cc
+++ b/modelling/src/rigid_blocks.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/rigid_blocks.hh>
#include <promod3/core/cluster.hh>
diff --git a/modelling/src/rigid_blocks.hh b/modelling/src/rigid_blocks.hh
index a210c6e77ab0e4b9aba403f09420d37145b2561d..9cddf9254d38c8a4bd11ebdfdcd1609da244f131 100644
--- a/modelling/src/rigid_blocks.hh
+++ b/modelling/src/rigid_blocks.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD_MODELLING_RIGID_BLOCKS_HH
#define PROMOD_MODELLING_RIGID_BLOCKS_HH
diff --git a/modelling/src/score_container.cc b/modelling/src/score_container.cc
index 5cbaf767239e742459ba58096debc49ee7113ca3..0a707265a03cae4f76d129685f7c52cedb85c385 100644
--- a/modelling/src/score_container.cc
+++ b/modelling/src/score_container.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/score_container.hh>
namespace promod3 { namespace modelling {
diff --git a/modelling/src/score_container.hh b/modelling/src/score_container.hh
index cd5b235b6c8b15966eb2cb971785955ecdd95d56..08ba76781e32113371941d02731ef68d1070a4a4 100644
--- a/modelling/src/score_container.hh
+++ b/modelling/src/score_container.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_MODELLING_SCORE_CONTAINER_HH
#define PROMOD3_MODELLING_SCORE_CONTAINER_HH
diff --git a/modelling/src/scoring_weights.cc b/modelling/src/scoring_weights.cc
index ac8ad4f8fd8408a604842f5c54744ed6a1e50f05..aa484910b25a2926bbef7775795e5c61191c9864 100644
--- a/modelling/src/scoring_weights.cc
+++ b/modelling/src/scoring_weights.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/scoring_weights.hh>
#include <promod3/core/message.hh>
diff --git a/modelling/src/scoring_weights.hh b/modelling/src/scoring_weights.hh
index b51158e330ef1f476c266751f4cdbf9a9f872406..72f59dc84b018be59b454c40c26822ddb78093cc 100644
--- a/modelling/src/scoring_weights.hh
+++ b/modelling/src/scoring_weights.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_MODELLING_SCORING_WEIGHTS_HH
#define PROMOD3_MODELLING_SCORING_WEIGHTS_HH
diff --git a/modelling/src/sidechain_env_listener.cc b/modelling/src/sidechain_env_listener.cc
index d72e09f30a9c918c87d1569aabe9be055c6de17f..19d97aa12f345b8c6b81bc184457b9c7cb7e7226 100644
--- a/modelling/src/sidechain_env_listener.cc
+++ b/modelling/src/sidechain_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/sidechain_env_listener.hh>
#include <promod3/sidechain/sidechain_object_loader.hh>
#include <promod3/core/runtime_profiling.hh>
@@ -14,11 +30,11 @@ SidechainEnvListener::SidechainEnvListener(bool use_frm, bool use_bbdep_lib,
, env_(20.0), env_data_(NULL) {
// check
if (use_frm_ && !use_bbdep_lib_) {
- throw promod3::Error("Cannot use PenultimateLib with FRMRotamers!");
+ throw promod3::Error("Cannot use non backbone dependent lib with FRMRotamers!");
}
// setup library
- if (use_bbdep_lib_) bbdep_library_ = sidechain::LoadDunbrackLib();
- else library_ = sidechain::LoadPenultimateLib();
+ if (use_bbdep_lib_) bbdep_library_ = sidechain::LoadBBDepLib();
+ else library_ = sidechain::LoadLib();
}
diff --git a/modelling/src/sidechain_env_listener.hh b/modelling/src/sidechain_env_listener.hh
index 2f8c14a1349f80b6d36464debc298b7aa3161d01..309930e65e0b0db0469a36c1338e7c39db22a118 100644
--- a/modelling/src/sidechain_env_listener.hh
+++ b/modelling/src/sidechain_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SIDECHAIN_ENV_LISTENER_HH
#define PM3_SIDECHAIN_ENV_LISTENER_HH
diff --git a/modelling/src/sidechain_reconstructor.cc b/modelling/src/sidechain_reconstructor.cc
index 9bc1dabac79df3bc9474f41108bf61e1ac12f887..3e63c3221e189cb5cca392298fcc34545581e971 100644
--- a/modelling/src/sidechain_reconstructor.cc
+++ b/modelling/src/sidechain_reconstructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/sidechain_reconstructor.hh>
#include <promod3/sidechain/disulfid.hh>
#include <promod3/sidechain/rotamer_graph.hh>
diff --git a/modelling/src/sidechain_reconstructor.hh b/modelling/src/sidechain_reconstructor.hh
index 6c1a4ac06e05a0683a960579b39883d7007c39e4..167493b0ecae058728ba4a02ce9584658d6e4d96 100644
--- a/modelling/src/sidechain_reconstructor.hh
+++ b/modelling/src/sidechain_reconstructor.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SIDECHAIN_RECONSTRUCTOR_HH
#define PM3_SIDECHAIN_RECONSTRUCTOR_HH
diff --git a/modelling/tests/CMakeLists.txt b/modelling/tests/CMakeLists.txt
index 41792a8b7cd90a6cec0593b801e8cd39df877696..be4d60a8f70218533b3bcd555da3114454075299 100644
--- a/modelling/tests/CMakeLists.txt
+++ b/modelling/tests/CMakeLists.txt
@@ -55,6 +55,7 @@ set(MODELLING_TEST_DATA
data/del.fasta
data/ff_NAD.dat
data/gly.pdb
+ data/gly_shifted_nter.pdb
data/hetero-punched.pdb
data/ins.fasta
data/modelCApartial-5tgl1A.pdb
diff --git a/modelling/tests/data/gly_shifted_nter.pdb b/modelling/tests/data/gly_shifted_nter.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..bc8949cdf00fcc944fccf1f1d7fdad9b7ce6daf6
--- /dev/null
+++ b/modelling/tests/data/gly_shifted_nter.pdb
@@ -0,0 +1,81 @@
+ATOM 1 N GLY A 1 -9.301 13.863 14.812 1.00 46.35 N
+ATOM 2 CA GLY A 1 -8.174 14.241 15.713 1.00 45.84 C
+ATOM 3 C GLY A 1 -7.595 13.051 16.465 1.00 44.35 C
+ATOM 4 O GLY A 1 -8.219 11.989 16.526 1.00 46.54 O
+ATOM 9 N GLY A 2 -6.383 13.240 16.995 1.00 42.02 N
+ATOM 10 CA GLY A 2 -5.611 12.243 17.755 1.00 39.04 C
+ATOM 11 C GLY A 2 -5.093 11.042 16.960 1.00 35.73 C
+ATOM 12 O GLY A 2 -5.875 10.322 16.336 1.00 35.25 O
+ATOM 18 N GLY A 3 -5.757 8.838 14.934 1.00 32.59 N
+ATOM 19 CA GLY A 3 -5.167 7.704 14.210 1.00 30.22 C
+ATOM 20 C GLY A 3 -5.475 6.389 14.924 1.00 28.03 C
+ATOM 21 O GLY A 3 -5.774 6.389 16.125 1.00 25.91 O
+ATOM 25 N GLY A 4 -5.434 5.288 14.176 1.00 26.73 N
+ATOM 26 CA GLY A 4 -5.705 3.960 14.726 1.00 26.95 C
+ATOM 27 C GLY A 4 -4.622 3.524 15.706 1.00 27.12 C
+ATOM 28 O GLY A 4 -3.426 3.545 15.366 1.00 27.18 O
+ATOM 35 N GLY A 5 -5.020 3.161 16.948 1.00 27.05 N
+ATOM 36 CA GLY A 5 -4.064 2.725 17.976 1.00 26.49 C
+ATOM 37 C GLY A 5 -3.515 1.307 17.792 1.00 25.98 C
+ATOM 38 O GLY A 5 -2.801 0.795 18.659 1.00 26.77 O
+ATOM 42 N GLY A 6 -3.807 0.705 16.641 1.00 23.73 N
+ATOM 43 CA GLY A 6 -3.371 -0.650 16.363 1.00 22.05 C
+ATOM 44 C GLY A 6 -2.311 -0.858 15.292 1.00 21.12 C
+ATOM 45 O GLY A 6 -1.814 -1.970 15.124 1.00 19.47 O
+ATOM 56 N GLY A 7 -1.980 0.191 14.544 1.00 22.58 N
+ATOM 57 CA GLY A 7 -0.962 0.055 13.501 1.00 20.39 C
+ATOM 58 C GLY A 7 0.393 0.457 14.047 1.00 22.27 C
+ATOM 59 O GLY A 7 0.645 1.639 14.340 1.00 22.00 O
+ATOM 67 N GLY A 8 1.271 -0.539 14.140 1.00 21.40 N
+ATOM 68 CA GLY A 8 2.612 -0.344 14.678 1.00 21.91 C
+ATOM 69 C GLY A 8 3.734 -0.393 13.645 1.00 22.34 C
+ATOM 70 O GLY A 8 4.910 -0.258 13.998 1.00 24.21 O
+ATOM 78 N GLY A 9 3.365 -0.539 12.371 1.00 20.22 N
+ATOM 79 CA GLY A 9 4.342 -0.585 11.293 1.00 20.67 C
+ATOM 80 C GLY A 9 5.264 -1.780 11.345 1.00 20.79 C
+ATOM 81 O GLY A 9 4.834 -2.874 11.700 1.00 19.22 O
+ATOM 82 N GLY A 10 6.545 -1.555 11.072 1.00 20.29 N
+ATOM 83 CA GLY A 10 7.521 -2.635 11.071 1.00 22.16 C
+ATOM 84 C GLY A 10 8.055 -3.014 12.464 1.00 23.01 C
+ATOM 85 O GLY A 10 9.266 -3.098 12.676 1.00 23.84 O
+ATOM 91 N GLY A 11 7.141 -3.248 13.409 1.00 24.30 N
+ATOM 92 CA GLY A 11 7.527 -3.666 14.757 1.00 23.54 C
+ATOM 93 C GLY A 11 7.811 -5.171 14.643 1.00 23.07 C
+ATOM 94 O GLY A 11 7.027 -5.913 14.030 1.00 23.44 O
+ATOM 99 N GLY A 12 9.005 -5.608 15.082 1.00 23.03 N
+ATOM 100 CA GLY A 12 9.328 -7.039 15.000 1.00 23.30 C
+ATOM 101 C GLY A 12 8.373 -7.936 15.805 1.00 22.52 C
+ATOM 102 O GLY A 12 7.733 -7.476 16.760 1.00 21.80 O
+ATOM 106 N GLY A 13 8.271 -9.196 15.382 1.00 22.06 N
+ATOM 107 CA GLY A 13 7.433 -10.219 16.020 1.00 22.83 C
+ATOM 108 C GLY A 13 7.699 -10.347 17.529 1.00 24.10 C
+ATOM 109 O GLY A 13 6.768 -10.261 18.334 1.00 23.86 O
+ATOM 117 N GLY A 14 8.974 -10.480 17.898 1.00 22.59 N
+ATOM 118 CA GLY A 14 9.386 -10.612 19.299 1.00 23.66 C
+ATOM 119 C GLY A 14 9.109 -9.356 20.121 1.00 23.97 C
+ATOM 120 O GLY A 14 8.824 -9.445 21.320 1.00 21.85 O
+ATOM 122 N GLY A 15 9.149 -8.199 19.455 1.00 23.41 N
+ATOM 123 CA GLY A 15 8.880 -6.917 20.103 1.00 25.09 C
+ATOM 124 C GLY A 15 7.378 -6.717 20.320 1.00 23.56 C
+ATOM 125 O GLY A 15 6.968 -6.064 21.278 1.00 23.45 O
+ATOM 131 N GLY A 16 6.569 -7.318 19.442 1.00 21.80 N
+ATOM 132 CA GLY A 16 5.106 -7.272 19.532 1.00 20.39 C
+ATOM 133 C GLY A 16 4.711 -8.157 20.718 1.00 20.37 C
+ATOM 134 O GLY A 16 3.856 -7.788 21.511 1.00 18.06 O
+ATOM 136 N GLY A 17 5.429 -9.273 20.876 1.00 20.11 N
+ATOM 137 CA GLY A 17 5.215 -10.213 21.983 1.00 21.59 C
+ATOM 138 C GLY A 17 5.492 -9.561 23.332 1.00 22.42 C
+ATOM 139 O GLY A 17 4.665 -9.622 24.238 1.00 23.01 O
+ATOM 145 N GLY A 18 6.639 -8.890 23.414 1.00 24.69 N
+ATOM 146 CA GLY A 18 7.114 -8.182 24.603 1.00 26.91 C
+ATOM 147 C GLY A 18 6.147 -7.077 25.056 1.00 26.71 C
+ATOM 148 O GLY A 18 5.800 -7.000 26.231 1.00 27.59 O
+ATOM 154 N GLY A 19 5.683 -6.273 24.099 1.00 25.69 N
+ATOM 155 CA GLY A 19 4.764 -5.161 24.348 1.00 25.99 C
+ATOM 156 C GLY A 19 3.375 -5.643 24.772 1.00 23.81 C
+ATOM 157 O GLY A 19 2.828 -5.155 25.769 1.00 24.09 O
+ATOM 162 N GLY A 20 2.830 -6.601 24.019 1.00 19.41 N
+ATOM 163 CA GLY A 20 1.496 -7.148 24.282 1.00 21.16 C
+ATOM 164 C GLY A 20 1.366 -8.006 25.540 1.00 20.66 C
+ATOM 165 O GLY A 20 0.301 -8.035 26.151 1.00 20.51 O
+END
diff --git a/modelling/tests/test_close_gaps.py b/modelling/tests/test_close_gaps.py
index 988cb6078aac2da0ad8a19ba9441ce4fbe2c8aec..43a2e2d599f62613f9f8379f996112b2f9242627 100644
--- a/modelling/tests/test_close_gaps.py
+++ b/modelling/tests/test_close_gaps.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for modelling components to close gaps.
"""
diff --git a/modelling/tests/test_gap_extension.py b/modelling/tests/test_gap_extension.py
index a5504bc191c8b534112c47444a6ae217b2fe8618..2c7b5d93665cfbf7ac70df1b741d3f374ad2fcd6 100644
--- a/modelling/tests/test_gap_extension.py
+++ b/modelling/tests/test_gap_extension.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import unittest
from promod3 import modelling
from ost import io,seq
diff --git a/modelling/tests/test_loop_candidates.cc b/modelling/tests/test_loop_candidates.cc
index 70c92d55fb35c002c0d3077aaaa1c334b9df29b5..f82acf29f4c931c589960898fa936d53c5fdf290 100644
--- a/modelling/tests/test_loop_candidates.cc
+++ b/modelling/tests/test_loop_candidates.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/loop_candidate.hh>
diff --git a/modelling/tests/test_loop_closing.cc b/modelling/tests/test_loop_closing.cc
index 5a7b9d475f651dd39a955400f2fb8264e3c3c555..7d1c163f405f0a512ced58284e38f92ba90858d5 100644
--- a/modelling/tests/test_loop_closing.cc
+++ b/modelling/tests/test_loop_closing.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/kic.hh>
#include <promod3/modelling/ccd.hh>
diff --git a/modelling/tests/test_modelling.py b/modelling/tests/test_modelling.py
index 7e1bebee4221149467c1cb435103ab598968bdc2..f7169d4d60577dddc3fd54429d67627e49765343 100644
--- a/modelling/tests/test_modelling.py
+++ b/modelling/tests/test_modelling.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for modelling.
"""
@@ -51,6 +67,7 @@ class ModellingTests(unittest.TestCase):
aln.AttachView(1, tpl.CreateFullView())
result = modelling.BuildRawModel(aln)
seq1 = seq.SequenceFromChain('MODEL', result.model.chains[0])
+ self.assertEqual(len(result.gaps), 0)
self.assertEqual(seq1.string, aln.sequences[0].string)
def testDeletion(self):
@@ -77,6 +94,19 @@ class ModellingTests(unittest.TestCase):
self.assertEqual(result.gaps[0].after, residues[2])
self.assertEqual(result.gaps[0].seq, 'AV')
+ def testNonFeasiblePeptideBond(self):
+ # test if the result contains a gap when two residues cannot be
+ # connected with a feasible peptide bond
+ tpl = io.LoadPDB('data/gly_shifted_nter.pdb')
+ aln = io.LoadAlignment('data/seq.fasta')
+ aln.AttachView(1, tpl.CreateFullView())
+ result = modelling.BuildRawModel(aln)
+ residues = result.model.residues
+ self.assertEqual(len(result.gaps), 1)
+ self.assertEqual(result.gaps[0].before, residues[1])
+ self.assertEqual(result.gaps[0].after, residues[2])
+ self.assertEqual(result.gaps[0].seq, '')
+
def testTer(self):
# test if the result contains two terminal gaps, one at the beginning,
# one at the end
diff --git a/modelling/tests/test_pipeline.py b/modelling/tests/test_pipeline.py
index b43d05a308e0530df362d3b3e4e2018b31cba31f..0654915a03a25ef84c71702846839c7c85b4a517 100644
--- a/modelling/tests/test_pipeline.py
+++ b/modelling/tests/test_pipeline.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests for modelling pipeline components.
We go from a fake cut in crambin to reconstruct that same protein.
diff --git a/modelling/tests/test_ring_punches.py b/modelling/tests/test_ring_punches.py
index 901cfbc04e10a7dedbb7e7ebb3f5e1e738cacd2a..64d1b1b80cbd8a6bfda65f14f6d051366f939cc4 100644
--- a/modelling/tests/test_ring_punches.py
+++ b/modelling/tests/test_ring_punches.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
"""
Unit tests to detect ring punchings.
"""
diff --git a/modelling/tests/test_sidechain_reconstruction.py b/modelling/tests/test_sidechain_reconstruction.py
index 37c82e652036a155f409d6f1e7ce4c9f45e88d4d..7b5a988ff484b7513187db97dc4e00da246c7d86 100644
--- a/modelling/tests/test_sidechain_reconstruction.py
+++ b/modelling/tests/test_sidechain_reconstruction.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
import unittest
from ost import io, mol, geom
from promod3 import loop, sidechain, modelling
@@ -8,8 +24,8 @@ class SidechainTests(unittest.TestCase):
@classmethod
def setUpClass(cls):
'''Load libs here for all tests.'''
- cls.bbdep_rotamer_library = sidechain.LoadDunbrackLib() # DEFAULT
- cls.rotamer_library = sidechain.LoadPenultimateLib()
+ cls.bbdep_rotamer_library = sidechain.LoadBBDepLib() # DEFAULT
+ cls.rotamer_library = sidechain.LoadLib()
#######################################################################
# HELPERs
diff --git a/modelling/tests/test_sidechain_reconstructor.cc b/modelling/tests/test_sidechain_reconstructor.cc
index e6f9a9a2ee5f6e5ead668361f4e00857e284feca..7e730c697d6401bc8170bac20f3bdea6f33cd573 100644
--- a/modelling/tests/test_sidechain_reconstructor.cc
+++ b/modelling/tests/test_sidechain_reconstructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/modelling/sidechain_reconstructor.hh>
#include <promod3/core/message.hh>
diff --git a/modelling/tests/tests.cc b/modelling/tests/tests.cc
index 956b0f2712eee2fcb1cc6ae9b9f183a4caa360cb..b497ab9838fe7aeeb97fcc164d0fa443164c0a06 100644
--- a/modelling/tests/tests.cc
+++ b/modelling/tests/tests.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_modelling
#define BOOST_AUTO_TEST_MAIN
diff --git a/scoring/data/convert_binaries.py b/scoring/data/convert_binaries.py
index d7b5ff7c2978492f5bc0902ce706ac32921e4ae5..4a6210bf1a76efad00ab6768f686166e1515ec87 100644
--- a/scoring/data/convert_binaries.py
+++ b/scoring/data/convert_binaries.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Convert files from portable to raw.'''
import sys
import os
diff --git a/scoring/doc/all_atom_scorers.rst b/scoring/doc/all_atom_scorers.rst
index 0a1b39b1613522dd671df0b73b32e98dcaac55eb..bcb3cdc43ed0e78becf8a07467928571d60bf604 100644
--- a/scoring/doc/all_atom_scorers.rst
+++ b/scoring/doc/all_atom_scorers.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
All Atom Scorers
================================================================================
diff --git a/scoring/doc/backbone_score_env.rst b/scoring/doc/backbone_score_env.rst
index 25980a4d34ba90890e7686c87838fa8dcd0f1679..11ea33ce9e947a60b120cc82e658231249e48082 100644
--- a/scoring/doc/backbone_score_env.rst
+++ b/scoring/doc/backbone_score_env.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Backbone Score Environment
================================================================================
@@ -187,9 +203,9 @@ Pairwise function classes
Inherits all functionality of :class:`PairwiseFunction`.
Defines a constraint function. The score for a distance between *min_dist* and
- *max_dist* is determined by liner interpolation assuming the first and last
- value exactly lying on *min_dist* ang *max_dist*. For distances outside the
- range defined by *min_dist* and *max_dist*, the score is 0.0.
+ *max_dist* is determined by linear interpolation assuming the first and last
+ value exactly lying on *min_dist* and *max_dist*. For distances outside the
+ range defined by *min_dist* and *max_dist*, the returned score is 0.0.
:param min_dist: Minimal distance to be considered
:param max_dist: Maximal distance to be considered
@@ -200,9 +216,6 @@ Pairwise function classes
:type max_dist: :class:`float`
:type values: :class:`list` of :class:`float`
-
- :returns: Index of added constraint definition
-
:raises: :exc:`~exceptions.RuntimeError` if *min_dist* >= *max_dist* or when
*min_dist* or *max_dist* are negative or when *values* contains no
elements
@@ -211,7 +224,7 @@ Pairwise function classes
Inherits all functionality of :class:`PairwiseFunction`.
Defines a simple contact function. The score value is *score* if
- distance < *max_dist* and 0 otherwise.
+ distance < *max_dist* and 0.0 otherwise.
:param max_dist: Maximal distance to be in contact
:param score: Value that gets returned if in contact
diff --git a/scoring/doc/backbone_scorers.rst b/scoring/doc/backbone_scorers.rst
index 55a07ec77cc2e0ebc0b619c90c4ebaf824e9531a..68a45cab6d736cc1963c245bb0c5cf1e0e140e08 100644
--- a/scoring/doc/backbone_scorers.rst
+++ b/scoring/doc/backbone_scorers.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Backbone Scorers
================================================================================
@@ -249,10 +265,10 @@ CBetaScorer class
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadCBetaScorer`) or by setting all energies (see :meth:`SetEnergy`).
- :param cutoff: Radius in which other cbeta atoms are counted.
+ :param cutoff: Radius in which other cbeta atoms are considered.
:type cutoff: :class:`float`
:param bins: Number of equally sized bins to discretize distances (range
- of [0,*cutoff*]).
+ of [0, *cutoff*]).
:type bins: :class:`int`
:param seq_sep: Minimal separation in sequence two cbeta atoms must have to
be considered.
diff --git a/scoring/doc/index.rst b/scoring/doc/index.rst
index 983d6b5587c5f70fc9088e6bdac386567fef16c3..d21154f06951fcdb6bbbe1c11f329f69f24bd57c 100644
--- a/scoring/doc/index.rst
+++ b/scoring/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.scoring` - Loop Scoring
================================================================================
@@ -7,7 +23,11 @@
.. currentmodule:: promod3.scoring
Tools and algorithms to score loops. The scoring system is split between an
-environment which contains model-specific data and scorers which evaluate loops.
+environment and scorers.
+Several scorers can be attached to the same environment containing the
+actual structural data of the current modelling problem.
+The environment is updated as the modelling proceeds and manages efficient
+spatial lookups to be used by the attached scorers.
In this example, we load a structure, setup a score environment, link a few
scorers to it and finally score some loops:
diff --git a/scoring/doc/other_scoring_functions.rst b/scoring/doc/other_scoring_functions.rst
index f505232e026655cdebf83d068269e805eb99fedd..80487531f986d6004e6764b8a8575be11b8bf6de 100644
--- a/scoring/doc/other_scoring_functions.rst
+++ b/scoring/doc/other_scoring_functions.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Other Scoring Functions
================================================================================
@@ -53,4 +69,3 @@ Scoring Functions from SCWRL3
-.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
diff --git a/scoring/pymod/__init__.py b/scoring/pymod/__init__.py
index 9a977e84016d8b94a0396beac02175298fa2cbb8..e00f68205fd1fecacb0edb1d4e8582ca3323e9c5 100644
--- a/scoring/pymod/__init__.py
+++ b/scoring/pymod/__init__.py
@@ -1 +1,17 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from _scoring import *
diff --git a/scoring/pymod/export_all_atom_score.cc b/scoring/pymod/export_all_atom_score.cc
index ddaa3f50594fadf0dad1e71ee833d26e1d970777..a3990a887e39b885b65d9f6f319f216fd0e926bb 100644
--- a/scoring/pymod/export_all_atom_score.cc
+++ b/scoring/pymod/export_all_atom_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/scoring/all_atom_score_base.hh>
diff --git a/scoring/pymod/export_backbone_score.cc b/scoring/pymod/export_backbone_score.cc
index 8bc2b5800aac45118768dc14f9f0a44427bf0b36..78722280ad48d79749bb8a778d3fbd7b839782b5 100644
--- a/scoring/pymod/export_backbone_score.cc
+++ b/scoring/pymod/export_backbone_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/scoring/backbone_score_base.hh>
diff --git a/scoring/pymod/export_constraint_constructor.cc b/scoring/pymod/export_constraint_constructor.cc
index 2de16edbb11164c91ee0604a102ab8e0c9ecc78a..0005e736b693643f62f44b68b5e2abf82aa81241 100644
--- a/scoring/pymod/export_constraint_constructor.cc
+++ b/scoring/pymod/export_constraint_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/core/export_helper.hh>
#include <promod3/scoring/constraint_constructor.hh>
diff --git a/scoring/pymod/export_density_scorer.cc b/scoring/pymod/export_density_scorer.cc
index f022f963aee63b41120ca950a1db90d89b14ffec..b887a2daf1c6ea65c228ca23cbd1bd5c37f152a0 100644
--- a/scoring/pymod/export_density_scorer.cc
+++ b/scoring/pymod/export_density_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/scoring/density_score.hh>
diff --git a/scoring/pymod/export_object_loader.cc b/scoring/pymod/export_object_loader.cc
index 73e8909c4ad1e7912773065470191c24f90e85a7..7c4791327e1fde416bcb15960eb2e5c2c65ca517 100644
--- a/scoring/pymod/export_object_loader.cc
+++ b/scoring/pymod/export_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/scoring/scoring_object_loader.hh>
diff --git a/scoring/pymod/export_pairwise_functions.cc b/scoring/pymod/export_pairwise_functions.cc
index b43f195c41a12ff6c293699127bd54be882de60d..4aa5bfc121d8166367db1da217f5dd0ac7765716 100644
--- a/scoring/pymod/export_pairwise_functions.cc
+++ b/scoring/pymod/export_pairwise_functions.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/scoring/pairwise_scoring_function.hh>
#include <promod3/core/export_helper.hh>
diff --git a/scoring/pymod/export_scwrl3_energy_functions.cc b/scoring/pymod/export_scwrl3_energy_functions.cc
index 54c5a8e1e8155b575dc8d0971eeaee102c683a89..58136cc8d88d6483fcd9eeaaf7188c7cfb2fc9b4 100644
--- a/scoring/pymod/export_scwrl3_energy_functions.cc
+++ b/scoring/pymod/export_scwrl3_energy_functions.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/scoring/scwrl3_energy_functions.hh>
#include <promod3/core/export_helper.hh>
diff --git a/scoring/pymod/wrap_scoring.cc b/scoring/pymod/wrap_scoring.cc
index 4b717f9cbc40743c1e84fcef141dc8e95bdb874f..a162eec0d2403fe153587642000859552249934e 100644
--- a/scoring/pymod/wrap_scoring.cc
+++ b/scoring/pymod/wrap_scoring.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
void export_BackboneScore();
diff --git a/scoring/src/all_atom_clash_score.cc b/scoring/src/all_atom_clash_score.cc
index eb011421297ff1de8c10f6fbd5a14533c2c2706e..de47faeaf2bbd6c0c3569c73c9699d2789941db9 100644
--- a/scoring/src/all_atom_clash_score.cc
+++ b/scoring/src/all_atom_clash_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/all_atom_clash_score.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/check_io.hh>
diff --git a/scoring/src/all_atom_clash_score.hh b/scoring/src/all_atom_clash_score.hh
index df69a60646241c8a1c563c8234b7bc30283ee193..39f0ae6bbc80448e9ab25c048bff543933deb27a 100644
--- a/scoring/src/all_atom_clash_score.hh
+++ b/scoring/src/all_atom_clash_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_CLASH_SCORE_HH
#define PM3_SCORING_ALL_ATOM_CLASH_SCORE_HH
diff --git a/scoring/src/all_atom_interaction_env_listener.cc b/scoring/src/all_atom_interaction_env_listener.cc
index 122ab3a28456c0fdacc1d1a5465414ceb98d0e4e..c5cff244cb8cf863e2661a2fe7a0478cbf10673d 100644
--- a/scoring/src/all_atom_interaction_env_listener.cc
+++ b/scoring/src/all_atom_interaction_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/all_atom_interaction_env_listener.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/scoring/src/all_atom_interaction_env_listener.hh b/scoring/src/all_atom_interaction_env_listener.hh
index f97a9da63f065f0be185e992a423724c1acaca49..bf6f800b0d4a7c9ab18d9db9a35a802b0cc62313 100644
--- a/scoring/src/all_atom_interaction_env_listener.hh
+++ b/scoring/src/all_atom_interaction_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_SCORE_ENV_LISTENER_HH
#define PM3_SCORING_ALL_ATOM_SCORE_ENV_LISTENER_HH
diff --git a/scoring/src/all_atom_interaction_score.cc b/scoring/src/all_atom_interaction_score.cc
index 35c9f4955e2a13070a4b6ff4fa3b93731a90ac4f..2ccc192e07d4b74e807ebd8d6774db4c0dd3fa8c 100644
--- a/scoring/src/all_atom_interaction_score.cc
+++ b/scoring/src/all_atom_interaction_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/all_atom_interaction_score.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/check_io.hh>
diff --git a/scoring/src/all_atom_interaction_score.hh b/scoring/src/all_atom_interaction_score.hh
index 5aadd05c56ca9b67ac8f86259ef6e06d9350c1fa..0e2166a1c1ed5a020cfbfd3a480dd23fd8c286d4 100644
--- a/scoring/src/all_atom_interaction_score.hh
+++ b/scoring/src/all_atom_interaction_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_INTERACTION_SCORE_HH
#define PM3_SCORING_ALL_ATOM_INTERACTION_SCORE_HH
diff --git a/scoring/src/all_atom_overall_scorer.cc b/scoring/src/all_atom_overall_scorer.cc
index 314f22d7c5e5336bc30fe62b09af20e414561489..891fa9448fa0373eefbcf04feacae82a951cb343 100644
--- a/scoring/src/all_atom_overall_scorer.cc
+++ b/scoring/src/all_atom_overall_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/all_atom_overall_scorer.hh>
namespace promod3 { namespace scoring {
diff --git a/scoring/src/all_atom_overall_scorer.hh b/scoring/src/all_atom_overall_scorer.hh
index ac090a46f7f55b58aba5dd27a09f4a9c0c6c04a1..81770d349d0d94da8b24456b3c92c60221771090 100644
--- a/scoring/src/all_atom_overall_scorer.hh
+++ b/scoring/src/all_atom_overall_scorer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_OVERALL_SCORER_HH
#define PM3_SCORING_ALL_ATOM_OVERALL_SCORER_HH
diff --git a/scoring/src/all_atom_packing_score.cc b/scoring/src/all_atom_packing_score.cc
index aef0d0a0ee488290b48cf5546d863f761c640cdb..786ba8601894329127dc9fd32ee015129efc604e 100644
--- a/scoring/src/all_atom_packing_score.cc
+++ b/scoring/src/all_atom_packing_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/all_atom_packing_score.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/check_io.hh>
diff --git a/scoring/src/all_atom_packing_score.hh b/scoring/src/all_atom_packing_score.hh
index 71cf70ea1a9359398923571105c41bd6e7a6b71f..899b6b1ccd8ab0e6d1989fbdc7966a6c16230246 100644
--- a/scoring/src/all_atom_packing_score.hh
+++ b/scoring/src/all_atom_packing_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_PACKING_SCORE_HH
#define PM3_SCORING_ALL_ATOM_PACKING_SCORE_HH
diff --git a/scoring/src/all_atom_score_base.hh b/scoring/src/all_atom_score_base.hh
index ba17cb0843b8523633bdcb24d530d3a53f89cfcb..abf7100ee54d1e805402f10bf5a99ca21958122a 100644
--- a/scoring/src/all_atom_score_base.hh
+++ b/scoring/src/all_atom_score_base.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_ALL_ATOM_SCORE_BASE_HH
#define PM3_SCORING_ALL_ATOM_SCORE_BASE_HH
diff --git a/scoring/src/backbone_overall_scorer.cc b/scoring/src/backbone_overall_scorer.cc
index bfa296653be248bcbdca2e27ebe81328abe01840..5af0d12fde653c8dea2a1c4595dd512a7e060152 100644
--- a/scoring/src/backbone_overall_scorer.cc
+++ b/scoring/src/backbone_overall_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/backbone_overall_scorer.hh>
namespace promod3 { namespace scoring {
diff --git a/scoring/src/backbone_overall_scorer.hh b/scoring/src/backbone_overall_scorer.hh
index 94af847f50e8e9bcd99414526e420cdc33da6902..61db071b109699502779aa38506338b692c20f87 100644
--- a/scoring/src/backbone_overall_scorer.hh
+++ b/scoring/src/backbone_overall_scorer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_BACKBONE_OVERALL_SCORER_HH
#define PM3_SCORING_BACKBONE_OVERALL_SCORER_HH
diff --git a/scoring/src/backbone_score_base.cc b/scoring/src/backbone_score_base.cc
index 30888ec88eac26787f32d63406ea5f686404ae07..05ab62387a203e50e5b5607c736c8c356b971f1c 100644
--- a/scoring/src/backbone_score_base.cc
+++ b/scoring/src/backbone_score_base.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/backbone_score_base.hh>
diff --git a/scoring/src/backbone_score_base.hh b/scoring/src/backbone_score_base.hh
index 8631f8a888f3cea59db7c5c4ba5638723c17d2e1..0b8ad73d8cae64341db1b66644d24586aff3335d 100644
--- a/scoring/src/backbone_score_base.hh
+++ b/scoring/src/backbone_score_base.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_BACKBONE_SCORE_HH
#define PM3_SCORING_BACKBONE_SCORE_HH
diff --git a/scoring/src/cb_packing_score.cc b/scoring/src/cb_packing_score.cc
index 0f0b307df7677da899b0d155d7ced9cd72775f56..5d98abc3cda936181be58e2b68741957a5a7a73a 100644
--- a/scoring/src/cb_packing_score.cc
+++ b/scoring/src/cb_packing_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/cb_packing_score.hh>
diff --git a/scoring/src/cb_packing_score.hh b/scoring/src/cb_packing_score.hh
index 0f3e5518e8a17eb2c9eaf7b041a3deafe6c337fb..97772e275154cb1b9f8dd59e48022df843b59b2a 100644
--- a/scoring/src/cb_packing_score.hh
+++ b/scoring/src/cb_packing_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CB_PACKING_SCORE_HH
#define PM3_SCORING_CB_PACKING_SCORE_HH
diff --git a/scoring/src/cbeta_env_listener.cc b/scoring/src/cbeta_env_listener.cc
index 6b8092f5c7ca8d6c93cc9b0cbe1208e48e88b044..9bb3021a9cc222bb69276766ae30aa83412821cb 100644
--- a/scoring/src/cbeta_env_listener.cc
+++ b/scoring/src/cbeta_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/cbeta_env_listener.hh>
diff --git a/scoring/src/cbeta_env_listener.hh b/scoring/src/cbeta_env_listener.hh
index af07e116c9f8386fa9db2313f8ea8b31d5e3ed9c..fd86b4e0a18785332e85eb85677429c82db93d6e 100644
--- a/scoring/src/cbeta_env_listener.hh
+++ b/scoring/src/cbeta_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CBETA_ENV_LISTENER_HH
#define PM3_SCORING_CBETA_ENV_LISTENER_HH
diff --git a/scoring/src/cbeta_score.cc b/scoring/src/cbeta_score.cc
index 1932a20038350aa5d03f1f9c898abd8b62070de3..17eb90f88ce95b67a761477f3b47901d70c71636 100644
--- a/scoring/src/cbeta_score.cc
+++ b/scoring/src/cbeta_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/cbeta_score.hh>
diff --git a/scoring/src/cbeta_score.hh b/scoring/src/cbeta_score.hh
index c2686975efc7e187710954e1d3d32952c35134b2..2a4cb7b629b6c1194d814fcbab80061c1d9108ea 100644
--- a/scoring/src/cbeta_score.hh
+++ b/scoring/src/cbeta_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CBETA_SCORE_HH
#define PM3_SCORING_CBETA_SCORE_HH
diff --git a/scoring/src/clash_env_listener.cc b/scoring/src/clash_env_listener.cc
index 3bf1c656436207a3eb23c2d551d83cb9ed7fe838..f9ff06382e686b1d94a00d2447a244eb05fd732e 100644
--- a/scoring/src/clash_env_listener.cc
+++ b/scoring/src/clash_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/clash_env_listener.hh>
diff --git a/scoring/src/clash_env_listener.hh b/scoring/src/clash_env_listener.hh
index cb4ee362b1d30c99823e6e3517879a7c56103fa7..3d8c121c8f6f7c03fdd2bcf20a0486424fa39075 100644
--- a/scoring/src/clash_env_listener.hh
+++ b/scoring/src/clash_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CLASH_ENV_LISTENER_HH
#define PM3_SCORING_CLASH_ENV_LISTENER_HH
diff --git a/scoring/src/clash_score.cc b/scoring/src/clash_score.cc
index c7c2849124252180da3e5af0f76a4b63dc4f632f..f0589dc74a28a4fc4ba94650b8f6bb220e9e72fc 100644
--- a/scoring/src/clash_score.cc
+++ b/scoring/src/clash_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/clash_score.hh>
#include <promod3/scoring/scwrl3_energy_functions.hh>
diff --git a/scoring/src/clash_score.hh b/scoring/src/clash_score.hh
index 2a06194ca6bb549c887f362bcb18641dc132511c..23251cc607083e34f1e8277e2430efa04c24ff97 100644
--- a/scoring/src/clash_score.hh
+++ b/scoring/src/clash_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CLASH_SCORE_HH
#define PM3_SCORING_CLASH_SCORE_HH
diff --git a/scoring/src/constraint_constructor.cc b/scoring/src/constraint_constructor.cc
index 15e200177219085de069322553b78a6615bd9ba3..127b78aef46598d94336df7d502cf27108f41bea 100644
--- a/scoring/src/constraint_constructor.cc
+++ b/scoring/src/constraint_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/constraint_constructor.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/cluster.hh>
diff --git a/scoring/src/constraint_constructor.hh b/scoring/src/constraint_constructor.hh
index e722bf6c694596bd39d7094dd6058b86ca833bbf..75e2b393032c419cce6a7f63dbe6047fd567e724 100644
--- a/scoring/src/constraint_constructor.hh
+++ b/scoring/src/constraint_constructor.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_CONSTRAINT_CONSTRUCTOR_HH
#define PM3_SCORING_CONSTRAINT_CONSTRUCTOR_HH
diff --git a/scoring/src/density_score.cc b/scoring/src/density_score.cc
index 803a843b68e1dd8396d27b3cd67ef916c5232649..7ad2daac39745dc1d4f3f1efc24d759438c42822 100644
--- a/scoring/src/density_score.cc
+++ b/scoring/src/density_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/density_score.hh>
namespace promod3{ namespace scoring{
diff --git a/scoring/src/density_score.hh b/scoring/src/density_score.hh
index d5e5123c3f733f2976e47c8928d32b6d11dc8f57..fe698cd36eaa5a1b79d52f7357840839be8eb823 100644
--- a/scoring/src/density_score.hh
+++ b/scoring/src/density_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_DENSITY_SCORE_HH
#define PM3_SCORING_DENSITY_SCORE_HH
diff --git a/scoring/src/hbond_env_listener.cc b/scoring/src/hbond_env_listener.cc
index 08a64dce7b0f74939f5d6b7e04580e54038891e2..afe63391a632ba1d1260b7ee6350d73bb95df854 100644
--- a/scoring/src/hbond_env_listener.cc
+++ b/scoring/src/hbond_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/hbond_env_listener.hh>
#include <set>
diff --git a/scoring/src/hbond_env_listener.hh b/scoring/src/hbond_env_listener.hh
index d5e6ea01849d5de7f3d08abfe36652040bccfee5..7b45cdc6eeea1cc8c7aa8a88866928ff0caaff1f 100644
--- a/scoring/src/hbond_env_listener.hh
+++ b/scoring/src/hbond_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_HBOND_ENV_LISTENER_HH
#define PM3_SCORING_HBOND_ENV_LISTENER_HH
diff --git a/scoring/src/hbond_score.cc b/scoring/src/hbond_score.cc
index 19940c002455a7087c7966fbbdcbe7e1bfef8dd8..e7955422b6cf9ee7aaf668040e101a44e0c141b0 100644
--- a/scoring/src/hbond_score.cc
+++ b/scoring/src/hbond_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/hbond_score.hh>
namespace promod3{ namespace scoring{
diff --git a/scoring/src/hbond_score.hh b/scoring/src/hbond_score.hh
index e8211fd43cc83e65585c049b9485c704ed17aa9b..895e93d4f37bfde32cc7221c66fb387f7164284b 100644
--- a/scoring/src/hbond_score.hh
+++ b/scoring/src/hbond_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_HBOND_SCORE_HH
#define PM3_SCORING_HBOND_SCORE_HH
diff --git a/scoring/src/pairwise_score.cc b/scoring/src/pairwise_score.cc
index 1a0ef644e17b316b17ab735e0d34576efa8b2962..fd8f6c421317b2c9961a40393783bf906487ef0e 100644
--- a/scoring/src/pairwise_score.cc
+++ b/scoring/src/pairwise_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/pairwise_score.hh>
namespace promod3{ namespace scoring{
diff --git a/scoring/src/pairwise_score.hh b/scoring/src/pairwise_score.hh
index dcd712e8d3e8ef3564d04252e7a73d2d73435826..60c59f869f3b38974569405c79c5b8502b98f03e 100644
--- a/scoring/src/pairwise_score.hh
+++ b/scoring/src/pairwise_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_PAIRWISE_SCORE_HH
#define PM3_PAIRWISE_SCORE_HH
diff --git a/scoring/src/pairwise_scoring_function.hh b/scoring/src/pairwise_scoring_function.hh
index 5edcf6af1ba5e860429261463b83fe0872963ec0..823f445510f57d7d901616935c3da1801def55bd 100644
--- a/scoring/src/pairwise_scoring_function.hh
+++ b/scoring/src/pairwise_scoring_function.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_PAIRWISE_SCORING_FUNCTION_HH
#define PM3_PAIRWISE_SCORING_FUNCTION_HH
diff --git a/scoring/src/reduced_env_listener.cc b/scoring/src/reduced_env_listener.cc
index 14025821515000582ab9144edf70db3abe4e6f31..1d52b029c1d4d83c7f7ab4154b717cd8e051b27d 100644
--- a/scoring/src/reduced_env_listener.cc
+++ b/scoring/src/reduced_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/reduced_env_listener.hh>
diff --git a/scoring/src/reduced_env_listener.hh b/scoring/src/reduced_env_listener.hh
index 52d405e2ac27c5e427f85e1a5e0b9ea5308bd872..1cfce4d80f5aa91efc64bc6d543d0db68d6fcc56 100644
--- a/scoring/src/reduced_env_listener.hh
+++ b/scoring/src/reduced_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_REDUCED_ENV_LISTENER_HH
#define PM3_SCORING_REDUCED_ENV_LISTENER_HH
diff --git a/scoring/src/reduced_score.cc b/scoring/src/reduced_score.cc
index a8e992ae8a68642a34d5fdf864ca5e6376945d91..c0b9b245ebe2d467274b488daadf3b21f59c5140 100644
--- a/scoring/src/reduced_score.cc
+++ b/scoring/src/reduced_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/reduced_score.hh>
diff --git a/scoring/src/reduced_score.hh b/scoring/src/reduced_score.hh
index e41f784c28bfba0b9e053e11e594eb4105b9f24f..bcfa027202dacc3d58fd0da4455a20c4341bd34c 100644
--- a/scoring/src/reduced_score.hh
+++ b/scoring/src/reduced_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_REDUCED_SCORE_HH
#define PM3_SCORING_REDUCED_SCORE_HH
diff --git a/scoring/src/scoring_object_loader.cc b/scoring/src/scoring_object_loader.cc
index fff223a9fb260b0b4eddbad3d6fae500a45a42b5..563e679bd0a6e77c5f443f5246e17d45970d37ea 100644
--- a/scoring/src/scoring_object_loader.cc
+++ b/scoring/src/scoring_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/scoring_object_loader.hh>
#include <promod3/config.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/scoring/src/scoring_object_loader.hh b/scoring/src/scoring_object_loader.hh
index b406f72dd735e51ff470f34326c4cd8095603c07..62ab321c9855c8f63e15b0f3355e95788b9070d4 100644
--- a/scoring/src/scoring_object_loader.hh
+++ b/scoring/src/scoring_object_loader.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SCORING_OBJECT_LOADER_HH
#define PROMOD3_SCORING_OBJECT_LOADER_HH
diff --git a/scoring/src/scwrl3_energy_functions.hh b/scoring/src/scwrl3_energy_functions.hh
index 7db72ebf5611fd7424e940a63f26c1de8b49222d..2829e91b3e085ef30f3c402ef559f4a4f930575a 100644
--- a/scoring/src/scwrl3_energy_functions.hh
+++ b/scoring/src/scwrl3_energy_functions.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCWRL3_ENERGY_FUNCTIONS_HH
#define PM3_SCWRL3_ENERGY_FUNCTIONS_HH
diff --git a/scoring/src/ss_agreement_env_listener.cc b/scoring/src/ss_agreement_env_listener.cc
index e9a090ee09d03511f421b2d052773ae9798cb647..5350a8ba15e64b74a461aacfec6e23b7fd4c4f99 100644
--- a/scoring/src/ss_agreement_env_listener.cc
+++ b/scoring/src/ss_agreement_env_listener.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/ss_agreement_env_listener.hh>
namespace promod3{ namespace scoring{
diff --git a/scoring/src/ss_agreement_env_listener.hh b/scoring/src/ss_agreement_env_listener.hh
index ad87b4e96753def90f56ff538fa63db1dc30361d..775099fc69e2f704e3ca91a6788d8685a02a168e 100644
--- a/scoring/src/ss_agreement_env_listener.hh
+++ b/scoring/src/ss_agreement_env_listener.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_SSAGREEMENT_ENV_LISTENER_HH
#define PM3_SCORING_SSAGREEMENT_ENV_LISTENER_HH
diff --git a/scoring/src/ss_agreement_score.cc b/scoring/src/ss_agreement_score.cc
index be4d6640415ed05e6074a9fcdda8e5af5d2677d2..cf92f38ef370e6025d262d929b7417b0d5054d04 100644
--- a/scoring/src/ss_agreement_score.cc
+++ b/scoring/src/ss_agreement_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/ss_agreement_score.hh>
namespace promod3 { namespace scoring {
diff --git a/scoring/src/ss_agreement_score.hh b/scoring/src/ss_agreement_score.hh
index 7e9960cffd65184225e68480da4755be32444282..a34698d840731163620bde3ee985825bd1302ff0 100644
--- a/scoring/src/ss_agreement_score.hh
+++ b/scoring/src/ss_agreement_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_SS_AGREEMENT_SCORE_HH
#define PM3_SCORING_SS_AGREEMENT_SCORE_HH
diff --git a/scoring/src/torsion_score.cc b/scoring/src/torsion_score.cc
index 65cca939dda0a6a59d7ce1bf057a8b9e6329f5bb..22907b1543197ee8f193a07169f2b0dee9296601 100644
--- a/scoring/src/torsion_score.cc
+++ b/scoring/src/torsion_score.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/torsion_score.hh>
namespace promod3{ namespace scoring{
diff --git a/scoring/src/torsion_score.hh b/scoring/src/torsion_score.hh
index 4cd298c83dab5097d0544b8825e636b540064a3d..d80c42d599a317d0d7b9e64bf56453b07f49bbcb 100644
--- a/scoring/src/torsion_score.hh
+++ b/scoring/src/torsion_score.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PM3_SCORING_TORSION_SCORE_HH
#define PM3_SCORING_TORSION_SCORE_HH
diff --git a/scoring/tests/test_all_atom_scorer.cc b/scoring/tests/test_all_atom_scorer.cc
index e1736b216d42e8cd8d70ef564a89e74f45bdcf2c..cf5ac6c945ce52b05d5bd32dde2fef8865c4eb27 100644
--- a/scoring/tests/test_all_atom_scorer.cc
+++ b/scoring/tests/test_all_atom_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/core/message.hh>
#include <promod3/loop/all_atom_env.hh>
#include <promod3/scoring/scoring_object_loader.hh>
diff --git a/scoring/tests/test_backbone_score_base.cc b/scoring/tests/test_backbone_score_base.cc
index 3706e45ab0cd23c3a05e689ebf2d12a4acfb7a44..b9e5e1d2eb3138e1ff6d4c035270f56a61931867 100644
--- a/scoring/tests/test_backbone_score_base.cc
+++ b/scoring/tests/test_backbone_score_base.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/backbone_score_base.hh>
#define BOOST_TEST_DYN_LINK
diff --git a/scoring/tests/test_backbone_scorer.cc b/scoring/tests/test_backbone_scorer.cc
index 49922b4b65c3292dcf9b519bb4d96c2b0d80ba4c..56e8be5a3afcd8aa6e7807aa0fcd602f4176177d 100644
--- a/scoring/tests/test_backbone_scorer.cc
+++ b/scoring/tests/test_backbone_scorer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/scoring/backbone_score_base.hh>
#include <promod3/scoring/backbone_overall_scorer.hh>
diff --git a/scoring/tests/tests.cc b/scoring/tests/tests.cc
index 9ef67f35e664a43f5b72a48108fe82cef9747477..afe7f82308e8672d821fb286ec92f9c02481bc35 100644
--- a/scoring/tests/tests.cc
+++ b/scoring/tests/tests.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_scoring
#define BOOST_AUTO_TEST_MAIN
diff --git a/scripts/pm.in b/scripts/pm.in
index 84618642d6816343ed92a8c0a9ad7d93ad246519..3bafd55c7c8985fdd1c678d90ea82aed4275973f 100755
--- a/scripts/pm.in
+++ b/scripts/pm.in
@@ -1,5 +1,20 @@
#!/bin/bash
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
# Wrapper script that dispatches the actions to the actual Python script. It
# autodetects the most important directories and sets LD_LIBRARY_PATH and
# friends.
diff --git a/sidechain/data/CMakeLists.txt b/sidechain/data/CMakeLists.txt
index 5af403815d4d5139f71becbfabe6fd1e9bb21ffe..c8224cba31cbdd8fd99abe5e3696f8aae0c4cb72 100644
--- a/sidechain/data/CMakeLists.txt
+++ b/sidechain/data/CMakeLists.txt
@@ -1,5 +1,5 @@
# convert files
-convert_module_data(MODULE sidechain FILE 2010DunbrackLib.dat
- SCRIPT convert_lib.py ARGS BBDepRotamerLib)
-convert_module_data(MODULE sidechain FILE PenultimateLib.dat
+convert_module_data(MODULE sidechain FILE lib.dat
SCRIPT convert_lib.py ARGS RotamerLib)
+convert_module_data(MODULE sidechain FILE bb_dep_lib.dat
+ SCRIPT convert_lib.py ARGS BBDepRotamerLib)
diff --git a/sidechain/data/convert_lib.py b/sidechain/data/convert_lib.py
index 56082fa17e686e9df0883933c8e35bc8ccd59f2c..515dc9280f5d3894bdc89f5233633f779cdab8d3 100644
--- a/sidechain/data/convert_lib.py
+++ b/sidechain/data/convert_lib.py
@@ -1,3 +1,19 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
'''Convert files from portable to raw.'''
import sys
import os
diff --git a/sidechain/data/portable_PenultimateLib.dat b/sidechain/data/portable_PenultimateLib.dat
deleted file mode 100644
index 67f192bc441a000d7d004990dc05c02f1211e959..0000000000000000000000000000000000000000
Binary files a/sidechain/data/portable_PenultimateLib.dat and /dev/null differ
diff --git a/sidechain/data/portable_2010DunbrackLib.dat b/sidechain/data/portable_bb_dep_lib.dat
similarity index 68%
rename from sidechain/data/portable_2010DunbrackLib.dat
rename to sidechain/data/portable_bb_dep_lib.dat
index 17b0544726980826dd8cad59b17f024796a58370..800aa84be0fc4b8f88856633f64d06ce575b4a42 100644
Binary files a/sidechain/data/portable_2010DunbrackLib.dat and b/sidechain/data/portable_bb_dep_lib.dat differ
diff --git a/sidechain/data/portable_lib.dat b/sidechain/data/portable_lib.dat
new file mode 100644
index 0000000000000000000000000000000000000000..38bf7f375c233b919fcb606507f26bb63dca4da1
Binary files /dev/null and b/sidechain/data/portable_lib.dat differ
diff --git a/sidechain/doc/disulfid.rst b/sidechain/doc/disulfid.rst
index 1cee3075640728b8c205c8bf9d9ff0128d6eeb9d..d078a6c5a65e20f2b4fc682f26a1e5b7853d6a92 100644
--- a/sidechain/doc/disulfid.rst
+++ b/sidechain/doc/disulfid.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Disulfid Bond Evaluation
================================================================================
diff --git a/sidechain/doc/frame.rst b/sidechain/doc/frame.rst
index d5e355915971ca7a0cd140036d366d9812f777e3..d8365f4a5316d2efebaaaafb50a87238b1b3ac2d 100644
--- a/sidechain/doc/frame.rst
+++ b/sidechain/doc/frame.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Frame
================================================================================
diff --git a/sidechain/doc/graph.rst b/sidechain/doc/graph.rst
index 118c72eabb98ed98acdc13eafcb6f3af4bbbb867..44606b2766a57c90bfa7f74d86cfc720ddf4ed71 100644
--- a/sidechain/doc/graph.rst
+++ b/sidechain/doc/graph.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamer Graph
================================================================================
@@ -6,7 +22,7 @@ Rotamer Graph
Once having a frame representing the rigid parts, the internal energies in
rotamer groups can be calculated. To come to a final solution of the sidechain
modelling problem, the pairwise energies also have to be evaluated and an
-overall solution has to be found. PROMOD3 implements a
+overall solution has to be found. ProMod3 implements a
:class:`promod3.core.GraphMinimizer` that allows to find solutions using
tree decomposition, A* and Monte Carlo algorithms.
diff --git a/sidechain/doc/index.rst b/sidechain/doc/index.rst
index c0a24dce4ca854bcd16c85d29094dcd1ff799f71..aeac7212ce7a9232b81c95d2178cb32d07ff6595 100644
--- a/sidechain/doc/index.rst
+++ b/sidechain/doc/index.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
:mod:`~promod3.sidechain` - Sidechain Modelling
================================================================================
@@ -9,7 +25,7 @@
Tools and algorithms to model sidechains given backbone coordinates. The full
module is heavily based on SCWRL4 [krivov2009]_ . The according paper describes
the modelling of sidechains using two different rotamer models. A rigid model,
-as well as a flexible model. Both models are implemented in PROMOD3 and can be
+as well as a flexible model. Both models are implemented in ProMod3 and can be
applied in flexible ways.
The following code fragment shows an example of a basic sidechain reconstruction
@@ -37,4 +53,3 @@ Contents:
subrotamer_optimizer
-.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.
diff --git a/sidechain/doc/loading.rst b/sidechain/doc/loading.rst
index b795abc601ad9c617895d86a63316a14623727bf..83e9390b16d8b8726c23a58f79dfdbf0eff22790 100644
--- a/sidechain/doc/loading.rst
+++ b/sidechain/doc/loading.rst
@@ -1,32 +1,50 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Loading Rotamer Libraries
================================================================================
.. currentmodule:: promod3.sidechain
-Since the PROMOD3 sidechain modelling algorithms are mainly designed after the
-work of the Dunbrack lab [krivov2009]_ , their backbone dependent rotamer
-library is probably the way to go. There exists a binary version of their
-2010 libary [shapovalov2011]_ , that can
-directly be loaded. As an alternative, there is also a binary file containing
-the backbone independent Penultimate library [lovell2000]_ .
+There are several rotamer libraries that can be used in ProMod3. ProMod3
+is optimized for the use with backbone dependent rotamer libraries such
+as the 2010 library provided by the Dunbrack lab [shapovalov2011]_.
+You can request a licence `here <http://dunbrack.fccc.edu/bbdep2010/>`_
+and generate such a library as described in
+extras/data_generation/rotamer_library/README. Alternatively, ProMod3
+provides its own backbone dependent or backbone independent libraries
+that can be loaded with :meth:`LoadBBDepLib` / :meth:`LoadLib`.
-.. method:: LoadDunbrackLib()
+.. method:: LoadBBDepLib()
- Loads the 2010 backbone dependent rotamer library from the dunbrack lab.
- The library has been generated using the ReadDunbrackFile function
- using the file with smoothing factor 5 and nonrotameric dihedrals
- sampled in 20 degree steps.
+ A backbone dependent rotamer library shipped with ProMod3. You can find
+ details on how it is created in extras/data_generation/rotamer_library/README.
+ All scripts to build it are in the same directory as the README file and
+ build the basis for custom versions.
- :returns: The requested library
+ :returns: The requested Library
:rtype: :class:`BBDepRotamerLib`
-.. method:: LoadPenultimateLib()
+.. method:: LoadLib()
- Loads the backbone independent Penultimate library. The values for the dihedral
- angles are directly extracted from the publication without considering the
- probabilities specific for helices/sheets. Due to no assigned standard
- deviations, the flexible rotamer model won't produce meaningful results.
+ A backbone independent rotamer library shipped with ProMod3. You can find
+ details on how it is created in extras/data_generation/rotamer_library/README.
+ All scripts to build it are in the same directory as the README file and
+ build the basis for custom versions.
:returns: The requested library
:rtype: :class:`RotamerLib`
@@ -36,8 +54,9 @@ the backbone independent Penultimate library [lovell2000]_ .
Reads a file as it is provided when you get a licence for the 2010 library of
the Dunbrack lab. It can only read the classic version, where all rotamers
- are in a single file. Specific distributions of nonrotameric sidechains
- cannot be read.
+ are in a single file. Specific distributions of non-rotameric sidechains
+ cannot be read. You can find an example described in
+ extras/data_generation/rotamer_library/README
:param filename: Name of the file
:type param: :class:`str`
@@ -49,9 +68,3 @@ the backbone independent Penultimate library [lovell2000]_ .
:returns: The read library
:rtype: :class:`BBDepRotamerLib`
-
-
-.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011). A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure.
-
-.. [lovell2000] Lovell SC, Word JM, Richardson JS, Richardson DC (2000). The penultimate rotamer library. Proteins.
-
diff --git a/sidechain/doc/rotamer.rst b/sidechain/doc/rotamer.rst
index 40f882320bb51f59b604a6ea7de7106d8582ca2a..30b3c7ca3b06602a1fbade371a3abdbc5a4e9029 100644
--- a/sidechain/doc/rotamer.rst
+++ b/sidechain/doc/rotamer.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamers
================================================================================
@@ -7,7 +23,7 @@ A rotamer represents an amino acid sidechain and is basically a set of
:class:`Particle` objects. There exist two types. The :class:`RRMRotamer` and
:class:`FRMRotamer`.
To gather all possible rotamers for one particular sidechain position,
-PROMOD3 offers the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
+ProMod3 offers the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
Pairwise interactions between particles give raise to pairwise energies between
rotamers. Nevertheless, the energy calculation itself happens on the level
of RotamerGroups and is mostly hidden away in the construction of the
@@ -264,7 +280,7 @@ Rotamers
The FRMRotamer represents a rotamer of the so called flexible rotamer model,
where one rotamer gets represented by several subrotamers.
- The idea is, that all particles of all subrotamers are given at
+ The idea is that all particles of all subrotamers are given at
initialization. Subrotamers are then defined by providing lists of indices.
One particle can be part of several subrotamers.
diff --git a/sidechain/doc/rotamer_constructor.rst b/sidechain/doc/rotamer_constructor.rst
index 36c76a2c0857dc5bdbd5b3257e24e8b2bde5eaac..82f9626c2afedb57149fc5c55042ee13dcd8fcb8 100644
--- a/sidechain/doc/rotamer_constructor.rst
+++ b/sidechain/doc/rotamer_constructor.rst
@@ -1,10 +1,26 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamer Constructor
================================================================================
.. currentmodule:: promod3.sidechain
Instead of creating rotamers by yourself, you can simply use the convenient
-functionality provided by PROMOD3
+functionality provided by ProMod3
Constructing Rotamers and Frame Residues
diff --git a/sidechain/doc/rotamer_id.rst b/sidechain/doc/rotamer_id.rst
index 7eac7b85ca8de53c2ee27619089aa93a1907da66..746a51641352c7295152567a742eda8befedc803 100644
--- a/sidechain/doc/rotamer_id.rst
+++ b/sidechain/doc/rotamer_id.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
RotamerID
================================================================================
diff --git a/sidechain/doc/rotamer_lib.rst b/sidechain/doc/rotamer_lib.rst
index 21ca7e4e93a69de5fe2a556da1e1b66a128d4ab1..0069c3888b70f7ad37acbf984cd3c95470af9840 100644
--- a/sidechain/doc/rotamer_lib.rst
+++ b/sidechain/doc/rotamer_lib.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Rotamer Library
================================================================================
@@ -9,7 +25,7 @@ sidechain can completely be described in terms of dihedral angles. Preferred
combinations of such dihedral angles are a result of steric properties and
can be gathered in rotamer libraries. Different libraries exist in the field
and their main difference is, whether the provided sidechain conformations
-are dependent on their backbone or not. PROMOD3 provides you with a
+are dependent on their backbone or not. ProMod3 provides you with a
:class:`BBDepRotamerLib` organizing rotamers for the different aminoacids
in equidistant phi/psi bins, as well as a simple :class:`RotamerLib`.
Both libraries are containers for :class:`RotamerLibEntry` and are optimized
@@ -168,10 +184,12 @@ The Backbone Dependent Rotamer Library
added to the library or can be interpolated.
In the first option, *phi* and *psi* simply get transformed to the
according bin using following formalism: bin = round((angle + pi)/bin_size).
- In case of interpolation, the chi angles and the according standard
- deviations of the rotamers get bilinearly interpolated using the
- corresponding rotamers with same configuration from the neighbouring bins.
- This behaviour can be controlled with the SetInterpolate function.
+ In case of interpolation, the chi angles of rotameric dihedral angles and the
+ according standard deviations of the rotamers get bilinearly interpolated
+ using the corresponding rotamers with same configuration from the
+ neighbouring bins. No interplation is applied to non-rotameric dihedral
+ angles (chi2 in ASP, ASN, HIS, PHE, TRP, TYR; chi3 in GLU, GLN).
+ This behaviour can be controlled with :meth:`SetInterpolate`.
The query function follows following strategies in case of
special *id* requests.
@@ -220,7 +238,8 @@ The Backbone Dependent Rotamer Library
.. method:: SetInterpolate(interpolate)
- :param interpolate: Controls behaviour when QueryLib function gets called
+ :param interpolate: Controls behaviour when :meth:`QueryLib`
+ gets called
:type interpolate: :class:`bool`
@@ -302,9 +321,9 @@ functionalities.
Creates a :class:`RotamerLibEntry` from the given *res*.
The function tries to automatically identify the :class:`RotamerID` based
- on the residue name. The probability gets set to zero and the standard
- deviations to 0. All not required chi angles with their corresponding
- standard deviations are NaN.
+ on the residue name. The probability and standard deviations are set to 0.0,
+ all not required chi angles with their corresponding standard deviations to
+ NaN.
:param res: Source of dihedral angles
@@ -418,4 +437,55 @@ functionalities.
:returns: :class:`bool` Whether both dihedrals are defined
(not NaN) and within the specified threshold
+Rotamer Configurations
+--------------------------------------------------------------------------------
+
+In rotamers, one distinguishes between rotameric and non-rotameric sidechain
+dihedral angles. The rotameric ones are around SP3-SP3 hybridized bonds and
+typically have three distinct configurations (trans, gauche-, gauche+).
+The non-rotameric ones behave differently. ProMod3 offers some functionality
+to estimate those configurations.
+
+.. class:: DihedralConfiguration
+
+ Enumerates the possible sidechain dihedral configurations
+
+ .. hlist::
+ :columns: 1
+
+ * TRANS - Trans configuration (120 < angle < -120)
+ * GAUCHE_PLUS - Gauche+ configuration (0 < angle < 120)
+ * GAUCHE_MINUS - Gauce- configuration (-120 < angle < 0)
+ * NON_ROTAMERIC - Dihedral without SP3-SP3 bond
+ * INVALID - Invalid configuration, e.g. chi3 of ALA (doesnt exist...)
+
+.. method:: GetRotamericConfiguration(angle)
+
+ Evaluates the *angle* according to the ranges specified for
+ :class:`DihedralConfiguration`.
+
+ :param angle: Angle to be evaluated
+ :type angle: :class:`float`
+
+ :returns: TRANS, GAUCHE_PLUS or GAUCHE_MINUS.
+ INVALID if *angle* is NaN.
+
+.. method:: GetDihedralConfiguration(entry, id, dihedral_idx)
+
+ Estimates configuration of a sidechain dihedral angle in a specific
+ :class:`RotamerLibEntry` with the knowledge of its identity. This allows
+ to also return NON_ROTAMERIC (e.g. chi2 for ASN).
+
+ :param entry: Sidechain dihedral angle comes from here
+ :param id: Identity of rotamer
+ :param dihedral_idx: Specifies angle (0 => chi1, ..., 3 => chi4)
+
+ :type entry: :class:`RotamerLibEntry`
+ :type id: :class:`RotamerID`
+ :type dihedral_idx: :class:`int`
+
+ :returns: Result of :meth:`GetRotamericConfiguration` if specified
+ angle is Rotameric, NON_ROTAMERIC if specified angle is
+ valid and non rotameric, INVALID otherwise.
+
diff --git a/sidechain/doc/subrotamer_optimizer.rst b/sidechain/doc/subrotamer_optimizer.rst
index e4124466394f2bdc0248aa40056a590f5b556dcb..27315888d85598b7f8830e1241b5139c65af0db5 100644
--- a/sidechain/doc/subrotamer_optimizer.rst
+++ b/sidechain/doc/subrotamer_optimizer.rst
@@ -1,3 +1,19 @@
+.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+.. Biozentrum - University of Basel
+..
+.. Licensed under the Apache License, Version 2.0 (the "License");
+.. you may not use this file except in compliance with the License.
+.. You may obtain a copy of the License at
+..
+.. http://www.apache.org/licenses/LICENSE-2.0
+..
+.. Unless required by applicable law or agreed to in writing, software
+.. distributed under the License is distributed on an "AS IS" BASIS,
+.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+.. See the License for the specific language governing permissions and
+.. limitations under the License.
+
+
Subrotamer Optimization
================================================================================
diff --git a/sidechain/pymod/__init__.py b/sidechain/pymod/__init__.py
index a915c37e3d03af93e9e14a35f2d00d40c3deae7b..311426d9e13dc020e82e4f64a0afad86803bc11a 100644
--- a/sidechain/pymod/__init__.py
+++ b/sidechain/pymod/__init__.py
@@ -1,2 +1,18 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
from _sidechain import *
diff --git a/sidechain/pymod/export_connector.cc b/sidechain/pymod/export_connector.cc
index b1eaecfef8424924044036ebf0cb24659306f3da..39742c354089d84aab6bd8611ece0d8d4ad80009 100644
--- a/sidechain/pymod/export_connector.cc
+++ b/sidechain/pymod/export_connector.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/sidechain/sidechain_connector.hh>
diff --git a/sidechain/pymod/export_disulfid.cc b/sidechain/pymod/export_disulfid.cc
index b346dc8e834f462a09cdd0a0391775fba05df7d8..86fb589469481cb181736cab155a7455c6101724 100644
--- a/sidechain/pymod/export_disulfid.cc
+++ b/sidechain/pymod/export_disulfid.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/register_ptr_to_python.hpp>
diff --git a/sidechain/pymod/export_frame.cc b/sidechain/pymod/export_frame.cc
index 7d4beedc0938544dbe4abb911002026f5f6eb117..c1aec78b2b9ceeb50b9931fb6ebc2415882dafb5 100644
--- a/sidechain/pymod/export_frame.cc
+++ b/sidechain/pymod/export_frame.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/sidechain/frame.hh>
diff --git a/sidechain/pymod/export_particle.cc b/sidechain/pymod/export_particle.cc
index 7a94286d5652c3adce7a422fb36d15e5500b2d4a..64eb1a0660bcf678d29ebde03afe41d2e3e93377 100644
--- a/sidechain/pymod/export_particle.cc
+++ b/sidechain/pymod/export_particle.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/sidechain/particle.hh>
diff --git a/sidechain/pymod/export_rotamer.cc b/sidechain/pymod/export_rotamer.cc
index 77b138df2e3e5251483d8cca23531fdefe269c82..80468074311b622982c4326c50f579d8293ecf23 100644
--- a/sidechain/pymod/export_rotamer.cc
+++ b/sidechain/pymod/export_rotamer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/sidechain/pymod/export_rotamer_cruncher.cc b/sidechain/pymod/export_rotamer_cruncher.cc
index 0a1458d35f48dfe1d0b4f25727f4cb238182b683..c38ae85bdc4b6df92e2d571b83b8f4fd3470f592 100644
--- a/sidechain/pymod/export_rotamer_cruncher.cc
+++ b/sidechain/pymod/export_rotamer_cruncher.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/sidechain/rotamer_cruncher.hh>
diff --git a/sidechain/pymod/export_rotamer_density.cc b/sidechain/pymod/export_rotamer_density.cc
index 60b9a1eafe6b8178704b4062a7f9dc02f1e10836..942f5f50d3ffe23ee7a40365027f2b9384e92cd2 100644
--- a/sidechain/pymod/export_rotamer_density.cc
+++ b/sidechain/pymod/export_rotamer_density.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/sidechain/pymod/export_rotamer_graph.cc b/sidechain/pymod/export_rotamer_graph.cc
index 782d0e81d070cf83c1ee3220d5483f80e09e6998..001ba6cacb13a0a1284299ebb53b58b155cbf9f9 100644
--- a/sidechain/pymod/export_rotamer_graph.cc
+++ b/sidechain/pymod/export_rotamer_graph.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/graph_minimizer.hh>
diff --git a/sidechain/pymod/export_rotamer_ids.cc b/sidechain/pymod/export_rotamer_ids.cc
index 69988eab1a8b15dc3643bdcca12f0ee64c589d58..28fb24e7569c56611c92cb30f94c736e1b4cea19 100644
--- a/sidechain/pymod/export_rotamer_ids.cc
+++ b/sidechain/pymod/export_rotamer_ids.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/sidechain/rotamer_id.hh>
diff --git a/sidechain/pymod/export_rotamer_lib.cc b/sidechain/pymod/export_rotamer_lib.cc
index dbe530a62b0114d9642962fb2854fe5f2f2c183f..0e5286b7b09698e141e7b729fe015d2a350be95a 100644
--- a/sidechain/pymod/export_rotamer_lib.cc
+++ b/sidechain/pymod/export_rotamer_lib.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/register_ptr_to_python.hpp>
@@ -139,6 +155,20 @@ void export_RotamerLib(){
register_ptr_to_python<RotamerLibPtr>();
+ enum_<DihedralConfiguration>("DihedralConfiguration")
+ .value("INVALID", INVALID)
+ .value("TRANS", TRANS)
+ .value("GAUCHE_MINUS", GAUCHE_MINUS)
+ .value("GAUCHE_PLUS", GAUCHE_PLUS)
+ .value("NON_ROTAMERIC", NON_ROTAMERIC)
+ .export_values()
+ ;
+
+ def("GetRotamericConfiguration", &GetRotamericConfiguration, (arg("angle")));
+ def("GetDihedralConfiguration", &GetDihedralConfiguration, (arg("entry"),
+ arg("id"),
+ arg("dihedral_idx")));
+
def("ReadDunbrackFile",&ReadDunbrackFile,(arg("filename")));
def("ReadDaggetFile",&ReadDaggetFile,arg("filename"));
diff --git a/sidechain/pymod/export_scwrl_rotamer_constructor.cc b/sidechain/pymod/export_scwrl_rotamer_constructor.cc
index 539288e3e6363cee544e8815c484c83da32e6971..7b7bd10d64be7304ab9e22cce4f2b5a2f03fa76b 100644
--- a/sidechain/pymod/export_scwrl_rotamer_constructor.cc
+++ b/sidechain/pymod/export_scwrl_rotamer_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <promod3/core/export_helper.hh>
diff --git a/sidechain/pymod/export_sidechain_object_loader.cc b/sidechain/pymod/export_sidechain_object_loader.cc
index 98b539ce31f42ec1136f6fe4243352852fa920d3..ab7ce781a316d83f16ec05abc9fb20ac4e6e8899 100644
--- a/sidechain/pymod/export_sidechain_object_loader.cc
+++ b/sidechain/pymod/export_sidechain_object_loader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <promod3/sidechain/sidechain_object_loader.hh>
@@ -6,6 +22,6 @@ using namespace promod3::sidechain;
using namespace boost::python;
void export_SidechainObjectLoader(){
- def("LoadDunbrackLib", &LoadDunbrackLib);
- def("LoadPenultimateLib", &LoadPenultimateLib);
+ def("LoadBBDepLib", &LoadBBDepLib);
+ def("LoadLib", &LoadLib);
}
\ No newline at end of file
diff --git a/sidechain/pymod/export_subrotamer_optimizer.cc b/sidechain/pymod/export_subrotamer_optimizer.cc
index 1b168786700daca626ac00b535921e04c6808663..e562637a0cd94415809b7605c425e685c25e1afe 100644
--- a/sidechain/pymod/export_subrotamer_optimizer.cc
+++ b/sidechain/pymod/export_subrotamer_optimizer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
#include <boost/python/iterator.hpp>
#include <boost/python/register_ptr_to_python.hpp>
diff --git a/sidechain/pymod/wrap_sidechain.cc b/sidechain/pymod/wrap_sidechain.cc
index 840b5d3b405eab5f532b7f6cd2de1eccf1a34c4b..f74e4610bb543c1530f8b47e2489675da8f774fe 100644
--- a/sidechain/pymod/wrap_sidechain.cc
+++ b/sidechain/pymod/wrap_sidechain.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <boost/python.hpp>
void export_Connector();
diff --git a/sidechain/src/bb_dep_rotamer_lib.cc b/sidechain/src/bb_dep_rotamer_lib.cc
index 20bbe7ee31b36798e84440f46939eef176d00b86..e99ba2e96afdc414b5d66bba06792d767694640b 100644
--- a/sidechain/src/bb_dep_rotamer_lib.cc
+++ b/sidechain/src/bb_dep_rotamer_lib.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/bb_dep_rotamer_lib.hh>
#include <promod3/core/check_io.hh>
#include <promod3/core/runtime_profiling.hh>
@@ -8,7 +24,8 @@ namespace{
return a.probability > b.probability;
}
- inline Real BilinearInterpolation(Real f00, Real f10, Real f01, Real f11, Real x, Real y){
+ inline Real BilinearInterpolation(Real f00, Real f10, Real f01, Real f11,
+ Real x, Real y) {
return f00 + (f10-f00)*x + (f01-f00)*y + (f00-f10-f01+f11)*x*y;
}
@@ -18,7 +35,8 @@ namespace{
return a;
}
- inline Real CircularBilinearInterpolation(Real f00, Real f10, Real f01, Real f11, Real x, Real y){
+ inline Real CircularBilinearInterpolation(Real f00, Real f10, Real f01, Real f11,
+ Real x, Real y) {
Real interpol_one;
Real interpol_two;
@@ -33,6 +51,20 @@ namespace{
diff = BoundAngle(interpol_two-interpol_one);
return BoundAngle(interpol_one + diff*y);
}
+
+ inline Real NearestNeighbourInterpolation(Real f00, Real f10, Real f01, Real f11,
+ Real x, Real y) {
+ if(x > Real(0.5) && y > Real(0.5)) {
+ return f11;
+ }
+ if(x > Real(0.5)) {
+ return f10;
+ }
+ if(y > Real(0.5)) {
+ return f01;
+ }
+ return f00;
+ }
}
@@ -425,52 +457,125 @@ std::pair<RotamerLibEntry*,uint> BBDepRotamerLib::QueryLib(RotamerID id, Real ph
Real sig4;
for(uint i = 0; i < it->second.second; ++i){
- probability = BilinearInterpolation(static_data_[pos00].probability,
- static_data_[pos10].probability,
- static_data_[pos01].probability,
- static_data_[pos11].probability,
- x,y);
+
+ // Rotameric dihedral angles have clear configurations: GAUCHE_MINUS,
+ // GAUCHE_PLUS, TRANS etc. Its therefore possible to interpolate
+ // a dihedral angle of same configuration, even the probability in between
+ // them. However, in the non-rotameric case, this assignment is less
+ // clear. Therefore the messy interpolation.
+
+ if(HasNonRotameric(id)) {
+ probability = NearestNeighbourInterpolation(static_data_[pos00].probability,
+ static_data_[pos10].probability,
+ static_data_[pos01].probability,
+ static_data_[pos11].probability,
+ x,y);
+
+ } else {
+ probability = BilinearInterpolation(static_data_[pos00].probability,
+ static_data_[pos10].probability,
+ static_data_[pos01].probability,
+ static_data_[pos11].probability,
+ x,y);
+ }
+
summed_probability += probability;
- chi1 = CircularBilinearInterpolation(static_data_[pos00].chi1,
- static_data_[pos10].chi1,
- static_data_[pos01].chi1,
- static_data_[pos11].chi1,
- x,y);
- chi2 = CircularBilinearInterpolation(static_data_[pos00].chi2,
- static_data_[pos10].chi2,
- static_data_[pos01].chi2,
- static_data_[pos11].chi2,
- x,y);
- chi3 = CircularBilinearInterpolation(static_data_[pos00].chi3,
- static_data_[pos10].chi3,
- static_data_[pos01].chi3,
- static_data_[pos11].chi3,
- x,y);
- chi4 = CircularBilinearInterpolation(static_data_[pos00].chi4,
- static_data_[pos10].chi4,
- static_data_[pos01].chi4,
- static_data_[pos11].chi4,
- x,y);
- sig1 = BilinearInterpolation(static_data_[pos00].sig1,
- static_data_[pos10].sig1,
- static_data_[pos01].sig1,
- static_data_[pos11].sig1,
- x,y);
- sig2 = BilinearInterpolation(static_data_[pos00].sig2,
- static_data_[pos10].sig2,
- static_data_[pos01].sig2,
- static_data_[pos11].sig2,
- x,y);
- sig3 = BilinearInterpolation(static_data_[pos00].sig3,
- static_data_[pos10].sig3,
- static_data_[pos01].sig3,
- static_data_[pos11].sig3,
- x,y);
- sig4 = BilinearInterpolation(static_data_[pos00].sig4,
- static_data_[pos10].sig4,
- static_data_[pos01].sig4,
- static_data_[pos11].sig4,
- x,y);
+
+ if(IsRotameric(id, 0)) {
+ chi1 = CircularBilinearInterpolation(static_data_[pos00].chi1,
+ static_data_[pos10].chi1,
+ static_data_[pos01].chi1,
+ static_data_[pos11].chi1,
+ x,y);
+ sig1 = BilinearInterpolation(static_data_[pos00].sig1,
+ static_data_[pos10].sig1,
+ static_data_[pos01].sig1,
+ static_data_[pos11].sig1,
+ x,y);
+ } else {
+ chi1 = NearestNeighbourInterpolation(static_data_[pos00].chi1,
+ static_data_[pos10].chi1,
+ static_data_[pos01].chi1,
+ static_data_[pos11].chi1,
+ x,y);
+ sig1 = NearestNeighbourInterpolation(static_data_[pos00].sig1,
+ static_data_[pos10].sig1,
+ static_data_[pos01].sig1,
+ static_data_[pos11].sig1,
+ x,y);
+ }
+
+ if(IsRotameric(id, 1)) {
+ chi2 = CircularBilinearInterpolation(static_data_[pos00].chi2,
+ static_data_[pos10].chi2,
+ static_data_[pos01].chi2,
+ static_data_[pos11].chi2,
+ x,y);
+ sig2 = BilinearInterpolation(static_data_[pos00].sig2,
+ static_data_[pos10].sig2,
+ static_data_[pos01].sig2,
+ static_data_[pos11].sig2,
+ x,y);
+ } else {
+ chi2 = NearestNeighbourInterpolation(static_data_[pos00].chi2,
+ static_data_[pos10].chi2,
+ static_data_[pos01].chi2,
+ static_data_[pos11].chi2,
+ x,y);
+ sig2 = NearestNeighbourInterpolation(static_data_[pos00].sig2,
+ static_data_[pos10].sig2,
+ static_data_[pos01].sig2,
+ static_data_[pos11].sig2,
+ x,y);
+ }
+
+ if(IsRotameric(id, 2)) {
+ chi3 = CircularBilinearInterpolation(static_data_[pos00].chi3,
+ static_data_[pos10].chi3,
+ static_data_[pos01].chi3,
+ static_data_[pos11].chi3,
+ x,y);
+ sig3 = BilinearInterpolation(static_data_[pos00].sig3,
+ static_data_[pos10].sig3,
+ static_data_[pos01].sig3,
+ static_data_[pos11].sig3,
+ x,y);
+ } else {
+ chi3 = NearestNeighbourInterpolation(static_data_[pos00].chi3,
+ static_data_[pos10].chi3,
+ static_data_[pos01].chi3,
+ static_data_[pos11].chi3,
+ x,y);
+ sig3 = NearestNeighbourInterpolation(static_data_[pos00].sig3,
+ static_data_[pos10].sig3,
+ static_data_[pos01].sig3,
+ static_data_[pos11].sig3,
+ x,y);
+ }
+
+ if(IsRotameric(id, 3)) {
+ chi4 = CircularBilinearInterpolation(static_data_[pos00].chi4,
+ static_data_[pos10].chi4,
+ static_data_[pos01].chi4,
+ static_data_[pos11].chi4,
+ x,y);
+ sig4 = BilinearInterpolation(static_data_[pos00].sig4,
+ static_data_[pos10].sig4,
+ static_data_[pos01].sig4,
+ static_data_[pos11].sig4,
+ x,y);
+ } else {
+ chi4 = NearestNeighbourInterpolation(static_data_[pos00].chi4,
+ static_data_[pos10].chi4,
+ static_data_[pos01].chi4,
+ static_data_[pos11].chi4,
+ x,y);
+ sig4 = NearestNeighbourInterpolation(static_data_[pos00].sig4,
+ static_data_[pos10].sig4,
+ static_data_[pos01].sig4,
+ static_data_[pos11].sig4,
+ x,y);
+ }
++pos00;
++pos01;
@@ -481,7 +586,6 @@ std::pair<RotamerLibEntry*,uint> BBDepRotamerLib::QueryLib(RotamerID id, Real ph
result_buffer_.push_back(RotamerLibEntry(probability, chi1, chi2, chi3, chi4,
sig1, sig2, sig3, sig4));
-
}
for(std::vector<RotamerLibEntry>::iterator i = result_buffer_.begin();
diff --git a/sidechain/src/bb_dep_rotamer_lib.hh b/sidechain/src/bb_dep_rotamer_lib.hh
index a01a042f4598998e1d3e48e4b29e98ce941e4df6..c88b19feabe09600944fa453fb675555ab92416a 100644
--- a/sidechain/src/bb_dep_rotamer_lib.hh
+++ b/sidechain/src/bb_dep_rotamer_lib.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_BB_DEP_ROTAMER_LIB_HH
#define PROMOD3_BB_DEP_ROTAMER_LIB_HH
diff --git a/sidechain/src/disulfid.cc b/sidechain/src/disulfid.cc
index 620658f2e17954b972d0b996dd3664a9db293b53..5cdb808cf97ab4b6dcba60b7d88b16419d51f00d 100644
--- a/sidechain/src/disulfid.cc
+++ b/sidechain/src/disulfid.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/disulfid.hh>
#include <promod3/sidechain/rotamer.hh>
#include <promod3/sidechain/particle.hh>
diff --git a/sidechain/src/disulfid.hh b/sidechain/src/disulfid.hh
index ac6aa87e196c4e4f0873c9068e7e932798021aca..6dd98a4ae27b14b2a4c6a624fb3bc57d9ccb7c30 100644
--- a/sidechain/src/disulfid.hh
+++ b/sidechain/src/disulfid.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SIDECHAIN_DISULFID_HH
#define PROMOD3_SIDECHAIN_DISULFID_HH
diff --git a/sidechain/src/frame.cc b/sidechain/src/frame.cc
index 6f79ead37f8ff176f441a7108915b7547b4b0c39..891e2959674a32fe2bfae76ef33fd636e5cddd42 100644
--- a/sidechain/src/frame.cc
+++ b/sidechain/src/frame.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/frame.hh>
#include <promod3/core/runtime_profiling.hh>
#include <ost/mol/xcs_editor.hh>
diff --git a/sidechain/src/frame.hh b/sidechain/src/frame.hh
index 1ba20cec8f4eae40a4b9cb03908ce52db20bbf8a..b073bb0989e60eb581a17f33d299de0bdc201368 100644
--- a/sidechain/src/frame.hh
+++ b/sidechain/src/frame.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_FRAME_HH
#define PROMOD3_FRAME_HH
diff --git a/sidechain/src/particle.cc b/sidechain/src/particle.cc
index 91fa11d16ce2d64ad14f47746da934174d4ee3e6..e4c79f01a01b4216a97b30cc3c53b0dedb2dc785 100644
--- a/sidechain/src/particle.cc
+++ b/sidechain/src/particle.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/particle.hh>
diff --git a/sidechain/src/particle.hh b/sidechain/src/particle.hh
index 663a37f676fa8a89c1567d807ee6927bf68afec9..9675e0ccf95afc8bd9682641c0e8673e0bcae711 100644
--- a/sidechain/src/particle.hh
+++ b/sidechain/src/particle.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_PARTICLE_HH
#define PROMOD3_PARTICLE_HH
diff --git a/sidechain/src/rotamer.cc b/sidechain/src/rotamer.cc
index 71443cb8feb51f25abc7805f41a5973777f51e99..41d1f9e2b4678ce83c72ff8b4368b43f4f5ab4d4 100644
--- a/sidechain/src/rotamer.cc
+++ b/sidechain/src/rotamer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/rotamer.hh b/sidechain/src/rotamer.hh
index 45ce313939a798828f47988b1158678907f7c0d2..068f3578fe5f0da278425c593d33a4db226c5d3b 100644
--- a/sidechain/src/rotamer.hh
+++ b/sidechain/src/rotamer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_HH
#define PROMOD3_ROTAMER_HH
diff --git a/sidechain/src/rotamer_cruncher.cc b/sidechain/src/rotamer_cruncher.cc
index f6769858fe96e0124513e3b61b0586ed2a975aab..dfe7c57ca9ca1092b69f81600f1b97b2e1b13242 100644
--- a/sidechain/src/rotamer_cruncher.cc
+++ b/sidechain/src/rotamer_cruncher.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_cruncher.hh>
diff --git a/sidechain/src/rotamer_cruncher.hh b/sidechain/src/rotamer_cruncher.hh
index fecff6096bf14f93d02e737f9ba3b943374a4793..bd4e6e95981342d5184252325309d8d46d5e25bd 100644
--- a/sidechain/src/rotamer_cruncher.hh
+++ b/sidechain/src/rotamer_cruncher.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_CRUNCHER_HH
#define PROMOD3_ROTAMER_CRUNCHER_HH
diff --git a/sidechain/src/rotamer_density.cc b/sidechain/src/rotamer_density.cc
index 92c1fd1fa056baf3e85342d6020cb0150537d504..c3502ef25841181adbc9641c5ea972b400b3570d 100644
--- a/sidechain/src/rotamer_density.cc
+++ b/sidechain/src/rotamer_density.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_density.hh>
namespace promod3{ namespace sidechain{
diff --git a/sidechain/src/rotamer_density.hh b/sidechain/src/rotamer_density.hh
index 3f9d4236cb69a6a15241d9d8294c6c1cca0763b1..acf38b55dda8d3b61a742db27256c19a6b4981bf 100644
--- a/sidechain/src/rotamer_density.hh
+++ b/sidechain/src/rotamer_density.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_DENSITY_HH
#define PROMOD3_ROTAMER_DENSITY_HH
diff --git a/sidechain/src/rotamer_graph.cc b/sidechain/src/rotamer_graph.cc
deleted file mode 100644
index dff604b654ce11ec96ba155db7812207cfd3330f..0000000000000000000000000000000000000000
--- a/sidechain/src/rotamer_graph.cc
+++ /dev/null
@@ -1,44 +0,0 @@
-#include <promod3/sidechain/rotamer_graph.hh>
-
-
-namespace promod3 { namespace sidechain {
-
-RotamerGraph::~RotamerGraph() { }
-
-template<typename RotamerGroupPtr>
-RotamerGraphPtr RotamerGraph::CreateFromList(
- const std::vector<RotamerGroupPtr>& rotamer_groups) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "RotamerGraph::CreateFromList", 2);
-
- RotamerGraphPtr graph(new RotamerGraph);
-
- // let's create the nodes
- uint counter = 0;
- std::vector<Real> self_energies;
- for(uint i = 0; i < rotamer_groups.size(); ++i) {
- RotamerGroupPtr rot_group = rotamer_groups[i];
- self_energies.resize(rot_group->size());
- for(uint j = 0; j < rot_group->size(); ++j){
- self_energies[j] = (*rot_group)[j]->GetSelfEnergy();
- }
- graph->AddNode(self_energies);
- }
-
- // let's create the edges
- for(uint i = 0; i < rotamer_groups.size(); ++i){
- for(uint j = i+1; j < rotamer_groups.size(); ++j){
- promod3::core::EMatXX emat;
- if(rotamer_groups[i]->CalculatePairwiseEnergies(rotamer_groups[j],
- 0.01, emat)) {
- graph->AddEdge(i, j, emat);
- }
- }
- }
-
- return graph;
-}
-
-}}//ns
-
diff --git a/sidechain/src/rotamer_graph.hh b/sidechain/src/rotamer_graph.hh
index 4e447b684191e0b33b7ab4ef4c8aae860ba3aebd..7ff2c37769467ebf5bc94625b410d91be2c9586e 100644
--- a/sidechain/src/rotamer_graph.hh
+++ b/sidechain/src/rotamer_graph.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_GRAPH_COMPONENTS_HH
#define PROMOD3_ROTAMER_GRAPH_COMPONENTS_HH
diff --git a/sidechain/src/rotamer_group.cc b/sidechain/src/rotamer_group.cc
index dd20d27cb85307258a8b00c7693430a018bf49ce..ed6fde6c96b03d07a152f5211bf6f9102ca55e05 100644
--- a/sidechain/src/rotamer_group.cc
+++ b/sidechain/src/rotamer_group.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_group.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/rotamer_group.hh b/sidechain/src/rotamer_group.hh
index 0ed5555e040b2a5f87c45dcdad5568b23ae90a08..b2556becc273619a187b085275e7fde33395dc08 100644
--- a/sidechain/src/rotamer_group.hh
+++ b/sidechain/src/rotamer_group.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_GROUP_HH
#define PROMOD3_ROTAMER_GROUP_HH
diff --git a/sidechain/src/rotamer_id.cc b/sidechain/src/rotamer_id.cc
index e5427def61b2a9256650f0c62060d9118c83ea5b..76a11c985ca94b97b74d59959017142ce96df195 100644
--- a/sidechain/src/rotamer_id.cc
+++ b/sidechain/src/rotamer_id.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_id.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/rotamer_id.hh b/sidechain/src/rotamer_id.hh
index 2ba2cb2e02701b758b1fd493140bb0dd97fe8a0b..407924d50f0170192ec3233d4040395d196b4a4b 100644
--- a/sidechain/src/rotamer_id.hh
+++ b/sidechain/src/rotamer_id.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_ID_HH
#define PROMOD3_ROTAMER_ID_HH
diff --git a/sidechain/src/rotamer_lib.cc b/sidechain/src/rotamer_lib.cc
index 10ae3e6438f212aaac69a6e9b7b893e604d0ddde..5c5fa4db1d322226dccd453f46e0798a8aefd0b3 100644
--- a/sidechain/src/rotamer_lib.cc
+++ b/sidechain/src/rotamer_lib.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_lib.hh>
#include <promod3/core/check_io.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/rotamer_lib.hh b/sidechain/src/rotamer_lib.hh
index f6fdbe02df6c48158ad1eda3e12e7114f8a07dd5..49e8fb7bce78fb5e0df9a95409240c865ac76b64 100644
--- a/sidechain/src/rotamer_lib.hh
+++ b/sidechain/src/rotamer_lib.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_LIB_HH
#define PROMOD3_ROTAMER_LIB_HH
diff --git a/sidechain/src/rotamer_lib_entry.cc b/sidechain/src/rotamer_lib_entry.cc
index 3ab17d9de0b06254b501b0e85c7352fb584c3e40..5379598395a65a9484c410714b45d3b3c5f39b27 100644
--- a/sidechain/src/rotamer_lib_entry.cc
+++ b/sidechain/src/rotamer_lib_entry.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_lib_entry.hh>
namespace{
@@ -33,7 +49,7 @@ promod3::sidechain::RotamerLibEntryPtr FromARG(const ost::mol::ResidueHandle& re
cd.IsValid() && ne.IsValid() && cz.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -61,7 +77,7 @@ promod3::sidechain::RotamerLibEntryPtr FromASN(const ost::mol::ResidueHandle& re
od1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -85,7 +101,7 @@ promod3::sidechain::RotamerLibEntryPtr FromASP(const ost::mol::ResidueHandle& re
od1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -110,7 +126,7 @@ promod3::sidechain::RotamerLibEntryPtr FromGLN(const ost::mol::ResidueHandle& re
cd.IsValid() && oe1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -137,7 +153,7 @@ promod3::sidechain::RotamerLibEntryPtr FromGLU(const ost::mol::ResidueHandle& re
cd.IsValid() && oe1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -165,7 +181,7 @@ promod3::sidechain::RotamerLibEntryPtr FromLYS(const ost::mol::ResidueHandle& re
cd.IsValid() && ce.IsValid() && nz.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -191,7 +207,7 @@ promod3::sidechain::RotamerLibEntryPtr FromSER(const ost::mol::ResidueHandle& re
if(!(n.IsValid() && ca.IsValid() && cb.IsValid() && og.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -211,7 +227,7 @@ promod3::sidechain::RotamerLibEntryPtr FromCYS(const ost::mol::ResidueHandle& re
if(!(n.IsValid() && ca.IsValid() && cb.IsValid() && sg.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -234,7 +250,7 @@ promod3::sidechain::RotamerLibEntryPtr FromMET(const ost::mol::ResidueHandle& re
sd.IsValid() && ce.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -260,7 +276,7 @@ promod3::sidechain::RotamerLibEntryPtr FromTRP(const ost::mol::ResidueHandle& re
cd1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -284,7 +300,7 @@ promod3::sidechain::RotamerLibEntryPtr FromTYR(const ost::mol::ResidueHandle& re
cd1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -306,7 +322,7 @@ promod3::sidechain::RotamerLibEntryPtr FromTHR(const ost::mol::ResidueHandle& re
if(!(n.IsValid() && ca.IsValid() && cb.IsValid() && og1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -326,7 +342,7 @@ promod3::sidechain::RotamerLibEntryPtr FromVAL(const ost::mol::ResidueHandle& re
if(!(n.IsValid() && ca.IsValid() && cb.IsValid() && cg1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -348,7 +364,7 @@ promod3::sidechain::RotamerLibEntryPtr FromILE(const ost::mol::ResidueHandle& re
cd1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -372,7 +388,7 @@ promod3::sidechain::RotamerLibEntryPtr FromLEU(const ost::mol::ResidueHandle& re
cd1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -396,7 +412,7 @@ promod3::sidechain::RotamerLibEntryPtr FromPRO(const ost::mol::ResidueHandle& re
cd.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -420,7 +436,7 @@ promod3::sidechain::RotamerLibEntryPtr FromHIS(const ost::mol::ResidueHandle& re
nd1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -444,7 +460,7 @@ promod3::sidechain::RotamerLibEntryPtr FromPHE(const ost::mol::ResidueHandle& re
cd1.IsValid())){
std::stringstream ss;
ss << "Could not find all atoms required to get ";
- ss << "all rotamer diheral angles!";
+ ss << "all rotamer dihedral angles!";
throw promod3::Error(ss.str());
}
@@ -698,4 +714,113 @@ bool RotamerLibEntry::SimilarDihedral(RotamerLibEntryPtr other, uint dihedral_id
return this->SimilarDihedral(other,dihedral_idx,thresh,id);
}
+bool HasNonRotameric(RotamerID id) {
+
+ return id == ASN || id == ASP || id == GLN || id == GLU || id == PHE ||
+ id == TYR || id == HIS || id == TRP;
+}
+
+bool IsRotameric(RotamerID id, int dihedral_idx) {
+
+ if(dihedral_idx == 0) {
+ return id!=GLY && id!=ALA && id!=XXX; // all others are rotameric
+ }
+
+ if(dihedral_idx == 1) {
+ return id == ARG || id == GLN || id == GLU || id == ILE || id == LEU ||
+ id == LYS || id == MET;
+ }
+
+ if(dihedral_idx == 2) {
+ return id == ARG || id == LYS || id == MET;
+ }
+
+ if(dihedral_idx == 3) {
+ return id == ARG || id == LYS;
+ }
+
+ return false;
+}
+
+DihedralConfiguration GetRotamericConfiguration(Real angle) {
+
+ if(angle != angle) {
+ return INVALID;
+ }
+
+ if(angle > Real(0.0) && angle < Real(2.09439510239)) {
+ return GAUCHE_PLUS;
+ }
+
+ if(angle < Real(0.0) && angle > Real(-2.09439510239)) {
+ return GAUCHE_MINUS;
+ }
+
+ return TRANS;
+}
+
+DihedralConfiguration GetDihedralConfiguration(const RotamerLibEntry& entry,
+ RotamerID id,
+ uint dihedral_idx) {
+
+ if(dihedral_idx > 3) {
+ return INVALID;
+ }
+
+ switch(dihedral_idx) {
+
+ case 0: {
+ if(entry.chi1 != entry.chi1) {
+ return INVALID;
+ }
+ if(id == GLY || id == ALA || id == XXX) {
+ return INVALID;
+ }
+ return GetRotamericConfiguration(entry.chi1);
+ }
+
+ case 1: {
+ if(entry.chi2 != entry.chi2) {
+ return INVALID;
+ }
+ if(id == ASN || id == ASP || id == PHE || id == TYR || id == HIS ||
+ id == TRP) {
+ return NON_ROTAMERIC;
+ }
+ if(id == ARG || id == GLN || id == GLU || id == ILE || id == LEU ||
+ id == LYS || id == MET) {
+ return GetRotamericConfiguration(entry.chi2);
+ }
+ return INVALID;
+ }
+
+ case 2: {
+ if(entry.chi3 != entry.chi3) {
+ return INVALID;
+ }
+ if(id == ARG || id == LYS || id == MET) {
+ return GetRotamericConfiguration(entry.chi3);
+ }
+ if(id == GLN || id == GLU) {
+ return NON_ROTAMERIC;
+ }
+ return INVALID;
+ }
+
+ case 3: {
+ if(entry.chi4 != entry.chi4) {
+ return INVALID;
+ }
+ if(id == ARG || id == LYS) {
+ return GetRotamericConfiguration(entry.chi4);
+ }
+ return INVALID;
+ }
+
+ default: {
+ throw promod3::Error("Invalid dihedral idx!");
+ }
+ }
+}
+
}} //ns
diff --git a/sidechain/src/rotamer_lib_entry.hh b/sidechain/src/rotamer_lib_entry.hh
index 7e8afd80771dbd5e55b40fc6572efacc2bfa42e2..45dc6bb826d419deee441d144c196ec9a19a3d10 100644
--- a/sidechain/src/rotamer_lib_entry.hh
+++ b/sidechain/src/rotamer_lib_entry.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_LIB_ENTRY_HH
#define PROMOD3_ROTAMER_LIB_ENTRY_HH
@@ -21,6 +37,7 @@ namespace promod3{ namespace sidechain{
struct RotamerLibEntry;
typedef boost::shared_ptr<RotamerLibEntry> RotamerLibEntryPtr;
+
struct RotamerLibEntry{
RotamerLibEntry(Real p, Real c1, Real c2, Real c3, Real c4,
@@ -96,6 +113,20 @@ struct RotamerLibEntry{
};
+enum DihedralConfiguration {
+ INVALID, TRANS, GAUCHE_MINUS, GAUCHE_PLUS, NON_ROTAMERIC
+};
+
+bool HasNonRotameric(RotamerID id);
+
+bool IsRotameric(RotamerID id, int dihedral_idx);
+
+DihedralConfiguration GetRotamericConfiguration(Real angle);
+
+DihedralConfiguration GetDihedralConfiguration(const RotamerLibEntry& entry,
+ RotamerID id,
+ uint dihedral_idx);
+
}} //ns
#endif
diff --git a/sidechain/src/rotamer_lib_reader.cc b/sidechain/src/rotamer_lib_reader.cc
index 4025bd4d502641685d443eff4dc66705a5c4d811..3f381fb2c335a9971c08fd00986da23a6bf75f8e 100644
--- a/sidechain/src/rotamer_lib_reader.cc
+++ b/sidechain/src/rotamer_lib_reader.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/rotamer_lib_reader.hh>
namespace promod3{ namespace sidechain{
diff --git a/sidechain/src/rotamer_lib_reader.hh b/sidechain/src/rotamer_lib_reader.hh
index 606a4c37787b436dde260e867758f034eac48880..1abcdd30fa16954877e4fd64aa8eaa8761fe5e9a 100644
--- a/sidechain/src/rotamer_lib_reader.hh
+++ b/sidechain/src/rotamer_lib_reader.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_ROTAMER_LIB_READER_HH
#define PROMOD3_ROTAMER_LIB_READER_HH
diff --git a/sidechain/src/scwrl_rotamer_constructor.cc b/sidechain/src/scwrl_rotamer_constructor.cc
index ed8d8da2f04790a7c2d7b72f5eb189de82c1a420..bb1ab96b5866998a0f6ec66d341905f830ca44e5 100644
--- a/sidechain/src/scwrl_rotamer_constructor.cc
+++ b/sidechain/src/scwrl_rotamer_constructor.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/scwrl_rotamer_constructor.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/message.hh>
@@ -602,7 +618,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup(bool cb_in_sidechain) {
AddFRMFixParticle(LYS, 3, 7);
}
- sidechain_infos_[LYS].has_hydrogens = true;
+ backbone_infos_[LYS].has_hydrogens = true;
AddBBInfo(LYS, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(LYS, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(LYS, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
@@ -1708,6 +1724,20 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructSidechainFrameResidue(
//set bb hydrogen
if(info.has_hydrogens){
+ // to construct hydrogens, we might also need backbone atoms in the buffer
+ const SCWRLRotamerInfo& bb_info = rotamer_lookup_.GetBackboneInfo(id);
+
+ for(uint i = 0; i < bb_info.particles.size(); ++i){
+ if(!bb_info.particles[i].is_hydrogen){
+ ost::mol::AtomHandle a = res.FindAtom(bb_info.particles[i].name);
+ if(!a.IsValid()){
+ throw promod3::Error("Expected atom " + bb_info.particles[i].name +
+ " to be present in input residue!");
+ }
+ pos_buffer_->SetPos(id, bb_info.particles[i].atom_idx, a.GetPos());
+ }
+ }
+
promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_, true,
promod3::loop::PROT_STATE_HISH);
}
@@ -1739,12 +1769,10 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructSidechainFrameResidue(
for(uint i = 0; i < info.particles.size(); ++i){
if(!info.particles[i].is_hydrogen){
-
if(!all_atom.IsSet(aa_res_idx, info.particles[i].atom_idx)){
throw promod3::Error("Expected atom " + info.particles[i].name +
" to be set in all_atom");
}
-
pos_buffer_->SetPos(id, info.particles[i].atom_idx,
all_atom.GetPos(aa_res_idx, info.particles[i].atom_idx));
}
@@ -1752,6 +1780,20 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructSidechainFrameResidue(
//set hydrogens
if(info.has_hydrogens){
+ // to construct hydrogens, we might also need backbone atoms in the buffer
+ const SCWRLRotamerInfo& bb_info = rotamer_lookup_.GetBackboneInfo(id);
+
+ for(uint i = 0; i < bb_info.particles.size(); ++i){
+ if(!bb_info.particles[i].is_hydrogen){
+ if(!all_atom.IsSet(aa_res_idx, bb_info.particles[i].atom_idx)){
+ throw promod3::Error("Expected atom " + bb_info.particles[i].name +
+ " to be set in all_atom");
+ }
+ pos_buffer_->SetPos(id, bb_info.particles[i].atom_idx,
+ all_atom.GetPos(aa_res_idx, bb_info.particles[i].atom_idx));
+ }
+ }
+
promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_, true,
promod3::loop::PROT_STATE_HISH);
}
diff --git a/sidechain/src/scwrl_rotamer_constructor.hh b/sidechain/src/scwrl_rotamer_constructor.hh
index 8beea0819bacefa5d12de50ce1500740b23c20ed..28915f2fa59bf841721061eaf45f76e7f87dc360 100644
--- a/sidechain/src/scwrl_rotamer_constructor.hh
+++ b/sidechain/src/scwrl_rotamer_constructor.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SCWRL_ROTAMER_CONSTRUCTOR_HH
#define PROMOD3_SCWRL_ROTAMER_CONSTRUCTOR_HH
diff --git a/sidechain/src/sidechain_connector.cc b/sidechain/src/sidechain_connector.cc
index c8e5c21966e75605c268289514016fbbc1beafae..ca9250bc5478bb77445205062345abc031075023 100644
--- a/sidechain/src/sidechain_connector.cc
+++ b/sidechain/src/sidechain_connector.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/sidechain_connector.hh>
#include <promod3/core/runtime_profiling.hh>
diff --git a/sidechain/src/sidechain_connector.hh b/sidechain/src/sidechain_connector.hh
index 4a74884544e0ea68cc52d148159d0b85e5e1e482..55617577d7708b5233afb38f94b8ef2d7ceb048e 100644
--- a/sidechain/src/sidechain_connector.hh
+++ b/sidechain/src/sidechain_connector.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SIDECHAIN_CONNECTOR_HH
#define PROMOD3_SIDECHAIN_CONNECTOR_HH
diff --git a/sidechain/src/sidechain_object_loader.cc b/sidechain/src/sidechain_object_loader.cc
index 9480ad2bc87050cef37b4f1c505c3c446d7c2881..62850f20a5f5142c475594a896efb41599e858e9 100644
--- a/sidechain/src/sidechain_object_loader.cc
+++ b/sidechain/src/sidechain_object_loader.cc
@@ -1,21 +1,37 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/sidechain_object_loader.hh>
#include <promod3/config.hh>
#include <promod3/core/runtime_profiling.hh>
namespace promod3{ namespace sidechain{
-BBDepRotamerLibPtr LoadDunbrackLib(){
+BBDepRotamerLibPtr LoadBBDepLib(){
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "sidechain::LoadDunbrackLib", 2);
- String path = GetProMod3BinaryPath("sidechain_data", "2010DunbrackLib.dat");
+ "sidechain::LoadBBDepLib", 2);
+ String path = GetProMod3BinaryPath("sidechain_data", "bb_dep_lib.dat");
BBDepRotamerLibPtr p = BBDepRotamerLib::Load(path);
return p;
}
-RotamerLibPtr LoadPenultimateLib(){
+RotamerLibPtr LoadLib(){
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "sidechain::LoadPenultimateLib", 2);
- String path = GetProMod3BinaryPath("sidechain_data", "PenultimateLib.dat");
+ "sidechain::LoadLib", 2);
+ String path = GetProMod3BinaryPath("sidechain_data", "lib.dat");
RotamerLibPtr p = RotamerLib::Load(path);
return p;
}
diff --git a/sidechain/src/sidechain_object_loader.hh b/sidechain/src/sidechain_object_loader.hh
index d7ece7bfa72e079e605114a5f1d9fe91d728f906..3a15201b437f8c40602bdbbd2e7e52456cd2fd70 100644
--- a/sidechain/src/sidechain_object_loader.hh
+++ b/sidechain/src/sidechain_object_loader.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SIDECHAIN_OBJECT_LOADER_HH
#define PROMOD3_SIDECHAIN_OBJECT_LOADER_HH
@@ -6,9 +22,8 @@
namespace promod3 { namespace sidechain{
-BBDepRotamerLibPtr LoadDunbrackLib();
-RotamerLibPtr LoadPenultimateLib();
-
+BBDepRotamerLibPtr LoadBBDepLib();
+RotamerLibPtr LoadLib();
}} //ns
#endif
diff --git a/sidechain/src/subrotamer_optimizer.cc b/sidechain/src/subrotamer_optimizer.cc
index 3594a5bcbe07e39b76c0e1098ac7eb440c031e15..3444eb3c5d4e3ced83bef7ad954f7f8374ff157c 100644
--- a/sidechain/src/subrotamer_optimizer.cc
+++ b/sidechain/src/subrotamer_optimizer.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/subrotamer_optimizer.hh>
namespace promod3{ namespace sidechain{
diff --git a/sidechain/src/subrotamer_optimizer.hh b/sidechain/src/subrotamer_optimizer.hh
index df415f00cadbaebca42f393dce66c7bb8e620d80..371c5e7763a50f86bce7526abbbfb9caa5737206 100644
--- a/sidechain/src/subrotamer_optimizer.hh
+++ b/sidechain/src/subrotamer_optimizer.hh
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#ifndef PROMOD3_SUBROTAMER_OPTIMIZER_HH
#define PROMOD3_SUBROTAMER_OPTIMIZER_HH
diff --git a/sidechain/tests/test_frame_construction.cc b/sidechain/tests/test_frame_construction.cc
index 5c6801168270bd96ee3ae08bde1c0486fa8ce8b0..0817985b9a9d2708693957562ac4f196fb4efeac 100644
--- a/sidechain/tests/test_frame_construction.cc
+++ b/sidechain/tests/test_frame_construction.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/scwrl_rotamer_constructor.hh>
#include <promod3/core/message.hh>
diff --git a/sidechain/tests/test_rotamers.cc b/sidechain/tests/test_rotamers.cc
index 0b49ec0bd4a76442941fdc4555df4ec18aa99c8d..11143888c2c85c246ee6c46c170560e5cfd045a0 100644
--- a/sidechain/tests/test_rotamers.cc
+++ b/sidechain/tests/test_rotamers.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#include <promod3/sidechain/scwrl_rotamer_constructor.hh>
#include <promod3/core/message.hh>
@@ -211,8 +227,8 @@ BOOST_AUTO_TEST_CASE(test_rotamer_group_consistency) {
ost::mol::ResidueHandleList res_list = test_ent.GetResidueList();
loop::AllAtomPositions all_atoms = GetAllAtomPos(res_list);
// get all frames without hbonds
- BBDepRotamerLibPtr bbd_rot_lib = LoadDunbrackLib();
- RotamerLibPtr rot_lib = LoadPenultimateLib();
+ BBDepRotamerLibPtr bbd_rot_lib = LoadBBDepLib();
+ RotamerLibPtr rot_lib = LoadLib();
CheckRotamerGroupConstruction(res_list, all_atoms, bbd_rot_lib,
rot_lib);
}
@@ -223,7 +239,7 @@ BOOST_AUTO_TEST_CASE(test_rotamer_apply_on_residue) {
ost::mol::ResidueHandleList res_list = test_ent.GetResidueList();
loop::AllAtomPositions all_atoms = GetAllAtomPos(res_list);
// check all frames without hbonds
- RotamerLibPtr rot_lib = LoadPenultimateLib();
+ RotamerLibPtr rot_lib = LoadLib();
CheckRotamerApplyOnResidue(res_list, all_atoms, rot_lib);
}
diff --git a/sidechain/tests/tests.cc b/sidechain/tests/tests.cc
index 70ebea3f331ef95dbb6c42b2a9a95646f9fb1259..bfcbfd198384cb41889ca820c948fa813c243dc6 100644
--- a/sidechain/tests/tests.cc
+++ b/sidechain/tests/tests.cc
@@ -1,3 +1,19 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_sidechain
#define BOOST_AUTO_TEST_MAIN