From 940efe8ede7bf49e1f1f19d395eca626ca68a2c6 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 10 Dec 2015 14:58:30 +0100
Subject: [PATCH] refactor - move rawmodel to modelling
---
CHANGELOG | 1 +
CMakeLists.txt | 2 +-
actions/doc/index_dev.rst | 2 +-
actions/pm-build-rawmodel | 4 +-
doc/contributing.rst | 4 +-
doc/developers.rst | 2 +-
doc/gettingstarted.rst | 2 +-
loop/pymod/__init__.py | 10 +--
loop/pymod/export_monte_carlo.cc | 1 -
loop/src/CMakeLists.txt | 2 +-
loop/src/backbone_loop_score.hh | 2 +-
loop/src/loop_candidate.hh | 2 +-
loop/src/monte_carlo_sampler.hh | 2 +-
loop/src/monte_carlo_scorer.hh | 2 +-
{rawmodel => modelling}/CMakeLists.txt | 0
modelling/doc/CMakeLists.txt | 5 ++
{rawmodel => modelling}/doc/index.rst | 26 ++++----
modelling/pymod/CMakeLists.txt | 16 +++++
modelling/pymod/__init__.py | 5 ++
{rawmodel => modelling}/pymod/_closegaps.py | 61 +++++++++---------
{rawmodel => modelling}/pymod/export_gap.cc | 6 +-
.../pymod/export_gap_extender.cc | 4 +-
{rawmodel => modelling}/pymod/export_model.cc | 4 +-
.../pymod/wrap_modelling.cc | 2 +-
{rawmodel => modelling}/src/CMakeLists.txt | 10 +--
{rawmodel => modelling}/src/gap.cc | 2 +-
{rawmodel => modelling}/src/gap.hh | 6 +-
{rawmodel => modelling}/src/gap_extender.cc | 8 +--
{rawmodel => modelling}/src/gap_extender.hh | 8 +--
{rawmodel => modelling}/src/model.cc | 2 +-
{rawmodel => modelling}/src/model.hh | 6 +-
modelling/tests/CMakeLists.txt | 25 +++++++
.../tests/data}/1mcg.pdb | 0
.../tests/data}/2dbs.pdb | 0
.../tests/data}/cbeta.fasta | 0
.../tests/data}/cbeta.pdb | 0
.../tests/data}/compounds.chemlib | Bin
.../tests/data}/del.fasta | 0
.../loop => modelling/tests/data}/ext.pdb | 0
.../tests/data}/gly.pdb | 0
.../tests/data}/ins.fasta | 0
.../tests/data}/sep.fasta | 0
.../tests/data}/sep.pdb | 0
.../tests/data}/seq.fasta | 0
.../tests/data}/ter.fasta | 0
.../tests/test_close_gaps.py | 34 +++++-----
.../tests/test_gap_extension.py | 8 +--
.../tests/test_modelling.py | 46 ++++++-------
pipeline/pymod/CMakeLists.txt | 2 +-
pipeline/pymod/run_engine.py | 32 ++++-----
pipeline/tests/test_run_engine.py | 6 +-
rawmodel/doc/CMakeLists.txt | 5 --
rawmodel/pymod/CMakeLists.txt | 16 -----
rawmodel/pymod/__init__.py | 5 --
rawmodel/tests/CMakeLists.txt | 25 -------
sidechain/pymod/_reconstruct_sidechains.py | 2 +
56 files changed, 209 insertions(+), 206 deletions(-)
rename {rawmodel => modelling}/CMakeLists.txt (100%)
create mode 100644 modelling/doc/CMakeLists.txt
rename {rawmodel => modelling}/doc/index.rst (94%)
create mode 100644 modelling/pymod/CMakeLists.txt
create mode 100644 modelling/pymod/__init__.py
rename {rawmodel => modelling}/pymod/_closegaps.py (92%)
rename {rawmodel => modelling}/pymod/export_gap.cc (90%)
rename {rawmodel => modelling}/pymod/export_gap_extender.cc (91%)
rename {rawmodel => modelling}/pymod/export_model.cc (95%)
rename rawmodel/pymod/wrap_rawmodel.cc => modelling/pymod/wrap_modelling.cc (83%)
rename {rawmodel => modelling}/src/CMakeLists.txt (54%)
rename {rawmodel => modelling}/src/gap.cc (98%)
rename {rawmodel => modelling}/src/gap.hh (97%)
rename {rawmodel => modelling}/src/gap_extender.cc (93%)
rename {rawmodel => modelling}/src/gap_extender.hh (88%)
rename {rawmodel => modelling}/src/model.cc (99%)
rename {rawmodel => modelling}/src/model.hh (98%)
create mode 100644 modelling/tests/CMakeLists.txt
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/1mcg.pdb (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/2dbs.pdb (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/cbeta.fasta (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/cbeta.pdb (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/compounds.chemlib (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/del.fasta (100%)
rename {rawmodel/tests/data/loop => modelling/tests/data}/ext.pdb (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/gly.pdb (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/ins.fasta (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/sep.fasta (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/sep.pdb (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/seq.fasta (100%)
rename {rawmodel/tests/data/raw-modeling => modelling/tests/data}/ter.fasta (100%)
rename {rawmodel => modelling}/tests/test_close_gaps.py (83%)
rename {rawmodel => modelling}/tests/test_gap_extension.py (87%)
rename rawmodel/tests/test_raw_modeling.py => modelling/tests/test_modelling.py (73%)
delete mode 100644 rawmodel/doc/CMakeLists.txt
delete mode 100644 rawmodel/pymod/CMakeLists.txt
delete mode 100644 rawmodel/pymod/__init__.py
delete mode 100644 rawmodel/tests/CMakeLists.txt
diff --git a/CHANGELOG b/CHANGELOG
index 9c9ba86d..b50334fa 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -19,5 +19,6 @@ Changes in Release 0.2
Changes in Release 0.3 (to be released)
-------------------------------------------------------------------------------
* merged argcheck into the helper module
+ * rawmodel renamed to modelling and including high-level modelling functions
.. LocalWords: Changelog reStructuredText changelog txt
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f27f785a..36e9b1a4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -103,7 +103,7 @@ set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
add_subdirectory(config)
add_subdirectory(core)
-add_subdirectory(rawmodel)
+add_subdirectory(modelling)
add_subdirectory(sidechain)
add_subdirectory(loop)
add_subdirectory(pipeline)
diff --git a/actions/doc/index_dev.rst b/actions/doc/index_dev.rst
index d392fe26..d88a7075 100644
--- a/actions/doc/index_dev.rst
+++ b/actions/doc/index_dev.rst
@@ -363,4 +363,4 @@ Unit Test Actions API
.. LocalWords: userlevel RunExitStatusTest testExit ost testutils RunTests
.. LocalWords: stdout stderr testcode nobytecode testsetup actiontest os
.. LocalWords: getcwd pardir builtin testoutput NORMALIZE WHITESPACE API
-.. LocalWords: rawmodel autoclass
+.. LocalWords: autoclass
diff --git a/actions/pm-build-rawmodel b/actions/pm-build-rawmodel
index 464dd164..a6d8f2c1 100755
--- a/actions/pm-build-rawmodel
+++ b/actions/pm-build-rawmodel
@@ -1,6 +1,6 @@
import os, argparse
from ost import io
-from promod3 import rawmodel
+from promod3 import modelling
from promod3.core import helper
### CHANGELOG - START
@@ -67,7 +67,7 @@ aln = io.LoadAlignment(opts.alignment_file)
# how can we do multi-whatever things?
aln.AttachView(1, tpl.CreateFullView())
-result = rawmodel.BuildRawModel(aln)
+result = modelling.BuildRawModel(aln)
io.SavePDB(result.model, opts.model_file)
if not os.path.isfile(opts.model_file):
helper.MsgErrorAndExit("Failed to write model file '%s'." % opts.model_file, 5)
diff --git a/doc/contributing.rst b/doc/contributing.rst
index 451b6f71..d47ca142 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -517,7 +517,7 @@ top level :file:`CMakeLists.txt`:
## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
add_subdirectory(config)
add_subdirectory(core)
- add_subdirectory(rawmodel)
+ add_subdirectory(modelling)
add_subdirectory(sidechains)
add_subdirectory(loop)
add_subdirectory(scripts)
@@ -830,7 +830,7 @@ contributions to web pages using |project|.
.. LocalWords: unittest TestCase nameattr testcode staticmethod builtin cp
.. LocalWords: SomethingTests testFileExistsFalse testutils RunTests DQMEAN
.. LocalWords: pre API inline CMake hh ProMod Bienchen OST OPENSTRUCTURE os
-.. LocalWords: mol alg conop QMEAN KIC eigen eigenvectors Lapack rawmodel
+.. LocalWords: mol alg conop QMEAN KIC eigen eigenvectors Lapack
.. LocalWords: OpenStructure ost pylint chmod sys pyc dont bytecode args
.. LocalWords: AwesomeActionTests ActionTestCase kwargs testExit getcwd
.. LocalWords: RunExitStatusTest DoAwesomeActionTests pardir mainattr alot
diff --git a/doc/developers.rst b/doc/developers.rst
index dff31849..c467ed1e 100644
--- a/doc/developers.rst
+++ b/doc/developers.rst
@@ -13,7 +13,7 @@ Contents:
core/setcompoundschemlib
core/index
pipeline/index
- rawmodel/index
+ modelling/index
loop/index
sidechain/index
actions/index_dev
diff --git a/doc/gettingstarted.rst b/doc/gettingstarted.rst
index 070ac0fe..696d3827 100644
--- a/doc/gettingstarted.rst
+++ b/doc/gettingstarted.rst
@@ -41,7 +41,7 @@ Modelling pipeline
Commonly, your input is a template structure and an alignment of the template to
the desired target sequence. The modelling steps then are:
-- Build a raw model from the template (see :func:`~promod3.rawmodel.BuildRawModel` function)
+- Build a raw model from the template (see :func:`~promod3.modelling.BuildRawModel` function)
- Perform loop modelling to close all gaps (see :mod:`~promod3.loop` module)
- Reconstruct sidechains (see :mod:`~promod3.sidechain` module)
- Minimize energy of final model using molecular mechanics
diff --git a/loop/pymod/__init__.py b/loop/pymod/__init__.py
index c95bece0..afe579e8 100644
--- a/loop/pymod/__init__.py
+++ b/loop/pymod/__init__.py
@@ -5,21 +5,21 @@ from _loop import *
# not the best style, but as long as we only have a single function in
# __init__.py lets ignore this flaw... if there are more general functions
# coming up, start sth like a 'base.py' and import here properly
-def SetupBackboneScorer(raw_model):
+def SetupBackboneScorer(mhandle):
'''Get a scorer for medling with backbones.
This one is already tailored towards a certain modelling job.
- :param raw_model: The raw model this scorer should be dedicated to.
- :type raw_model: :class:`~promod3.rawmodel.ModellingHandle`
+ :param mhandle: The modelling handle this scorer should be dedicated to.
+ :type mhandle: :class:`~promod3.modelling.ModellingHandle`
:return: A scorer instance.
:rtype: :class:`~promod3.loop.BackboneLoopScorer`
'''
scorer = LoadBackboneLoopScorer()
seqres = list()
- for s in raw_model.seqres:
+ for s in mhandle.seqres:
seqres.append(s.GetString())
scorer.Initialize(seqres)
- scorer.SetEnvironment(raw_model.model)
+ scorer.SetEnvironment(mhandle.model)
return scorer
diff --git a/loop/pymod/export_monte_carlo.cc b/loop/pymod/export_monte_carlo.cc
index 2938c720..ce4a3f23 100644
--- a/loop/pymod/export_monte_carlo.cc
+++ b/loop/pymod/export_monte_carlo.cc
@@ -8,7 +8,6 @@
#include <promod3/loop/monte_carlo_scorer.hh>
#include <promod3/loop/monte_carlo_sampler.hh>
#include <promod3/loop/monte_carlo_closer.hh>
-#include <promod3/rawmodel/gap.hh>
using namespace promod3;
using namespace promod3::loop;
diff --git a/loop/src/CMakeLists.txt b/loop/src/CMakeLists.txt
index ce925776..eb2d6980 100644
--- a/loop/src/CMakeLists.txt
+++ b/loop/src/CMakeLists.txt
@@ -47,5 +47,5 @@ backbone_relaxer.cc
)
module(NAME loop HEADERS ${LOOP_HEADERS} SOURCES ${LOOP_SOURCES} DEPENDS_ON
- promod3_core promod3_rawmodel promod3_sidechain LINK ${OST_LIBRARIES} ${BOOST_LIBRARIES} ${LAPACK_LIBRARIES})
+ promod3_core promod3_modelling promod3_sidechain LINK ${OST_LIBRARIES} ${BOOST_LIBRARIES} ${LAPACK_LIBRARIES})
diff --git a/loop/src/backbone_loop_score.hh b/loop/src/backbone_loop_score.hh
index 56ce6db2..af6a4dc6 100644
--- a/loop/src/backbone_loop_score.hh
+++ b/loop/src/backbone_loop_score.hh
@@ -6,7 +6,7 @@
#include <ost/geom/vecmat3_op.hh>
#include <ost/mol/view_op.hh>
#include <promod3/loop/backbone.hh>
-#include <promod3/rawmodel/gap.hh>
+#include <promod3/modelling/gap.hh>
#include <promod3/loop/dynamic_spatial_organizer.hh>
#include <boost/shared_ptr.hpp>
diff --git a/loop/src/loop_candidate.hh b/loop/src/loop_candidate.hh
index da784743..273ede5e 100644
--- a/loop/src/loop_candidate.hh
+++ b/loop/src/loop_candidate.hh
@@ -3,7 +3,7 @@
#include <promod3/loop/backbone.hh>
#include <promod3/loop/frag_db.hh>
-#include <promod3/rawmodel/gap.hh>
+#include <promod3/modelling/gap.hh>
#include <promod3/loop/monte_carlo.hh>
#include <promod3/loop/flame.hh>
#include <promod3/loop/backbone_loop_score.hh>
diff --git a/loop/src/monte_carlo_sampler.hh b/loop/src/monte_carlo_sampler.hh
index dcfa4754..196f3dc1 100644
--- a/loop/src/monte_carlo_sampler.hh
+++ b/loop/src/monte_carlo_sampler.hh
@@ -11,7 +11,7 @@
#include <ost/mol/residue_handle.hh>
#include <ost/mol/atom_handle.hh>
-#include <promod3/rawmodel/gap.hh>
+#include <promod3/modelling/gap.hh>
#include <promod3/loop/backbone.hh>
#include <promod3/loop/torsion_sampler.hh>
#include <promod3/core/message.hh>
diff --git a/loop/src/monte_carlo_scorer.hh b/loop/src/monte_carlo_scorer.hh
index f46e1ae4..0785fe3e 100644
--- a/loop/src/monte_carlo_scorer.hh
+++ b/loop/src/monte_carlo_scorer.hh
@@ -6,7 +6,7 @@
#include <ost/mol/mol.hh>
-#include <promod3/rawmodel/gap.hh>
+#include <promod3/modelling/gap.hh>
#include <promod3/loop/backbone_loop_score.hh>
diff --git a/rawmodel/CMakeLists.txt b/modelling/CMakeLists.txt
similarity index 100%
rename from rawmodel/CMakeLists.txt
rename to modelling/CMakeLists.txt
diff --git a/modelling/doc/CMakeLists.txt b/modelling/doc/CMakeLists.txt
new file mode 100644
index 00000000..082558a1
--- /dev/null
+++ b/modelling/doc/CMakeLists.txt
@@ -0,0 +1,5 @@
+set(MODELLING_RST
+index.rst
+)
+
+add_doc_source(NAME modelling RST ${MODELLING_RST})
diff --git a/rawmodel/doc/index.rst b/modelling/doc/index.rst
similarity index 94%
rename from rawmodel/doc/index.rst
rename to modelling/doc/index.rst
index b36f700a..390a66d7 100644
--- a/rawmodel/doc/index.rst
+++ b/modelling/doc/index.rst
@@ -1,10 +1,10 @@
-:mod:`~promod3.rawmodel` - Protein Modelling
+:mod:`~promod3.modelling` - Protein Modelling
================================================================================
-.. module:: promod3.rawmodel
+.. module:: promod3.modelling
:synopsis: Protein Modelling
-.. currentmodule:: promod3.rawmodel
+.. currentmodule:: promod3.modelling
High-level functionality for protein modelling.
Commonly, your input is a template structure and an alignment of the template to
@@ -48,32 +48,32 @@ Modelling API
The returned :class:`ModellingHandle` stores the obtained raw model as well
as information about insertions and deletions in the gaps list.
- .. testcode:: rawmodel
+ .. testcode:: modelling
:hide:
import os
import tempfile
from ost import io
- from promod3 import rawmodel
+ from promod3 import modelling
- aln = io.LoadAlignment('../tests/rawmodel/data/raw-modeling/seq.fasta')
- template_structure = io.LoadPDB('../tests/rawmodel/data/raw-modeling/gly.pdb',
+ aln = io.LoadAlignment('../tests/modelling/data/seq.fasta')
+ template_structure = io.LoadPDB('../tests/modelling/data/gly.pdb',
restrict_chains='A')
aln.AttachView(1, template_structure.Select('peptide=true'))
- result = rawmodel.BuildRawModel(aln)
+ result = modelling.BuildRawModel(aln)
(fh, fn) = tempfile.mkstemp(suffix='.pdb')
io.SavePDB(result.model, fn)
os.remove(fn)
- .. doctest:: rawmodel
+ .. doctest:: modelling
from ost import io
- from promod3 import rawmodel
+ from promod3 import modelling
aln = io.LoadAlignment('seq.fasta')
template_structure = io.LoadPDB('gly.pdb', restrict_chains='A')
aln.AttachView(1, template_structure.Select('peptide=true'))
- result = rawmodel.BuildRawModel(aln)
+ result = modelling.BuildRawModel(aln)
io.SavePDB(result.model, 'model.pdb')
:param alignment: Single alignment handle for raw model.
@@ -135,7 +135,7 @@ Modelling Handle class
.. class:: ModellingHandle
Handles the result for structure model building and provides high-level methods
- to turn an initial raw model (see :func:`~promod3.rawmodel.BuildRawModel`)
+ to turn an initial raw model (see :func:`~promod3.modelling.BuildRawModel`)
into a complete protein model by removing any existing gaps.
.. attribute:: model
@@ -336,7 +336,7 @@ False if no new extension possible.
:rtype: :class:`bool`
.. LocalWords: currentmodule promod aln AttachView BuildRawModel pdb calpha
-.. LocalWords: ModellingHandle StructuralGapList rawmodel Modelling os ost
+.. LocalWords: ModellingHandle StructuralGapList modelling Modelling os ost
.. LocalWords: testcode tempfile io LoadAlignment LoadPDB fh fn doctest API
.. LocalWords: modelling phosphoserine param exc RuntimeError automethod
.. LocalWords: CloseSmallDeletions
diff --git a/modelling/pymod/CMakeLists.txt b/modelling/pymod/CMakeLists.txt
new file mode 100644
index 00000000..9c8e1260
--- /dev/null
+++ b/modelling/pymod/CMakeLists.txt
@@ -0,0 +1,16 @@
+set(MODELLING_CPP
+wrap_modelling.cc
+export_model.cc
+export_gap.cc
+export_gap_extender.cc
+)
+
+set(MODELLING_PYMOD
+ __init__.py
+ _closegaps.py
+)
+
+pymod(NAME modelling
+ CPP ${MODELLING_CPP}
+ PY ${MODELLING_PYMOD}
+ DEPENDS_ON core_pymod)
diff --git a/modelling/pymod/__init__.py b/modelling/pymod/__init__.py
new file mode 100644
index 00000000..f71871e7
--- /dev/null
+++ b/modelling/pymod/__init__.py
@@ -0,0 +1,5 @@
+"""
+Initialise the modelling module.
+"""
+from _modelling import *
+from _closegaps import *
diff --git a/rawmodel/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
similarity index 92%
rename from rawmodel/pymod/_closegaps.py
rename to modelling/pymod/_closegaps.py
index 6792787e..f32d39f9 100644
--- a/rawmodel/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -5,7 +5,7 @@ as argument.
import ost
#pylint: disable=no-name-in-module
-from . import _rawmodel as rawmodel
+from . import _modelling as modelling
from promod3 import loop
def CloseSmallDeletions(mhandle, scorer, extension_steps=9, clash_thresh=1.0,
@@ -23,31 +23,31 @@ def CloseSmallDeletions(mhandle, scorer, extension_steps=9, clash_thresh=1.0,
.. testcode:: closesmalldel
:hide:
- from promod3 import rawmodel
+ from promod3 import modelling
from promod3 import loop
- tpl = ost.io.LoadPDB('../tests/rawmodel/data/raw-modeling/gly.pdb')
+ tpl = ost.io.LoadPDB('../tests/modelling/data/gly.pdb')
aln = ost.seq.CreateAlignment(ost.seq.CreateSequence('trg', 'GGG-GGG'),
ost.seq.CreateSequence('tpl', 'GGGAGGG'))
aln.AttachView(1, tpl.CreateFullView())
- mhandle = rawmodel.BuildRawModel(aln)
+ mhandle = modelling.BuildRawModel(aln)
assert len(mhandle.gaps) == 1
scorer = loop.SetupBackboneScorer(mhandle)
- rawmodel.CloseSmallDeletions(mhandle, scorer)
+ modelling.CloseSmallDeletions(mhandle, scorer)
assert len(mhandle.gaps) == 0
.. doctest:: closesmalldel
import ost
- from promod3 import rawmodel
+ from promod3 import modelling
from promod3 import loop
tpl = ost.io.LoadPDB('gly.pdb')
aln = ost.io.LoadAlignment('seq.fasta')
aln.AttachView(1, tpl.CreateFullView())
- mhandle = rawmodel.BuildRawModel(aln)
+ mhandle = modelling.BuildRawModel(aln)
scorer = loop.SetupBackboneScorer(mhandle)
- rawmodel.CloseSmallDeletions(mhandle, scorer)
+ modelling.CloseSmallDeletions(mhandle, scorer)
:param mhandle: Modelling handle on which to apply change.
:type mhandle: :class:`ModellingHandle`
@@ -96,7 +96,7 @@ def CloseSmallDeletions(mhandle, scorer, extension_steps=9, clash_thresh=1.0,
# the gap, we get the backbone to be stretched. If no more extension
# is possible, break out. On first successful relaxation for an
# extension, we successfully stop.
- extender = rawmodel.GapExtender(current_gap)
+ extender = modelling.GapExtender(current_gap)
for _ in range(extension_steps):
if not extender.Extend():
break
@@ -141,7 +141,7 @@ def CloseSmallDeletions(mhandle, scorer, extension_steps=9, clash_thresh=1.0,
scorer.SetEnvironment(\
bb_list,
current_gap.before.GetNumber().GetNum())
- rawmodel.ClearGaps(mhandle, current_gap)
+ modelling.ClearGaps(mhandle, current_gap)
success = True
break
@@ -164,29 +164,29 @@ def MergeGapsByDistance(mhandle, distance):
.. testcode:: mergegapsbydist
:hide:
- from promod3 import rawmodel
+ from promod3 import modelling
- tpl = ost.io.LoadPDB('../tests/rawmodel/data/raw-modeling/1mcg.pdb')
+ tpl = ost.io.LoadPDB('../tests/modelling/data/1mcg.pdb')
aln = ost.seq.CreateAlignment(ost.seq.CreateSequence('trg',
'DDFAGDTKNLGHN'),
ost.seq.CreateSequence('tpl',
'NN----A----LF'))
aln.AttachView(1, tpl.CreateFullView())
- mhandle = rawmodel.BuildRawModel(aln)
+ mhandle = modelling.BuildRawModel(aln)
assert len(mhandle.gaps) == 2
- rawmodel.MergeGapsByDistance(mhandle, 0)
+ modelling.MergeGapsByDistance(mhandle, 0)
assert len(mhandle.gaps) == 1
.. doctest:: mergegapsbydist
import ost
- from promod3 import rawmodel
+ from promod3 import modelling
tpl = ost.io.LoadPDB('1mcg.pdb')
aln = ost.io.LoadAlignment('1mcg_aln.fasta')
aln.AttachView(1, tpl.CreateFullView())
- mhandle = rawmodel.BuildRawModel(aln)
- rawmodel.MergeGapsByDistance(mhandle, 0)
+ mhandle = modelling.BuildRawModel(aln)
+ modelling.MergeGapsByDistance(mhandle, 0)
:param mhandle: Modelling handle on which to apply change.
:type mhandle: :class:`ModellingHandle`
@@ -223,7 +223,7 @@ def MergeGapsByDistance(mhandle, distance):
- current_gap.after.GetNumber().GetNum()
if dist <= distance:
# gaps are close enough, combine! combine!
- rawmodel.MergeGaps(mhandle, i)
+ modelling.MergeGaps(mhandle, i)
ost.LogVerbose("Merged gap %s and %s into %s" % \
(current_gap, next_gap, mhandle.gaps[i]))
try_again = True
@@ -241,36 +241,36 @@ def FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
.. testcode:: fillloopsbydb
:hide:
- from promod3 import rawmodel
+ from promod3 import modelling
from promod3 import loop
- tpl = ost.io.LoadPDB('../tests/rawmodel/data/raw-modeling/2dbs.pdb')
+ tpl = ost.io.LoadPDB('../tests/modelling/data/2dbs.pdb')
aln = ost.seq.CreateAlignment(
ost.seq.CreateSequence('trg', 'TLNGFTVPAGNTLV--LNPDKGATVTMA'),
ost.seq.CreateSequence('tpl', 'NGGTLLIPNGTYHFLGIQMKSNVHIRVE'))
aln.AttachView(1, tpl.CreateFullView())
- mhandle = rawmodel.BuildRawModel(aln)
+ mhandle = modelling.BuildRawModel(aln)
assert len(mhandle.gaps) == 1
scorer = loop.SetupBackboneScorer(mhandle)
- rawmodel.FillLoopsByDatabase(mhandle, scorer, loop.LoadFragDB(),
+ modelling.FillLoopsByDatabase(mhandle, scorer, loop.LoadFragDB(),
loop.LoadStructureDB(),
loop.LoadTorsionSamplerCoil())
assert len(mhandle.gaps) == 0
.. doctest:: fillloopsbydb
- from promod3 import rawmodel
+ from promod3 import modelling
from promod3 import loop
tpl = io.LoadPDB('2dbs.pdb')
aln = ost.io.LoadAlignment('2dbs.fasta')
aln.AttachView(1, tpl.CreateFullView())
- mhandle = rawmodel.BuildRawModel(aln)
+ mhandle = modelling.BuildRawModel(aln)
scorer = loop.SetupBackboneScorer(mhandle)
- scorer = rawmodel.FillLoopsByDatabase(mhandle, scorer, loop.LoadFragDB(),
+ scorer = modelling.FillLoopsByDatabase(mhandle, scorer, loop.LoadFragDB(),
loop.LoadStructureDB(),
loop.LoadTorsionSamplerCoil())
@@ -355,7 +355,7 @@ def FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
# get info on current gap
actual_gap = mhandle.gaps[gap_idx].Copy()
actual_length = actual_gap.length
- actual_extender = rawmodel.GapExtender(actual_gap)
+ actual_extender = modelling.GapExtender(actual_gap)
min_before_resnum = 100000000000
max_after_resnum = -100000000000
actual_candidates = list()
@@ -481,7 +481,7 @@ def FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
actual_chain_idx)
ost.LogVerbose("Resolved %s by filling %s" % \
(str(actual_gap), str(actual_extended_gaps[idx_a])))
- next_gap = rawmodel.ClearGaps(mhandle, actual_extended_gaps[idx_a])
+ next_gap = modelling.ClearGaps(mhandle, actual_extended_gaps[idx_a])
if next_gap == -1:
break
else:
@@ -491,11 +491,12 @@ def FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
gap_idx += 1
return scorer
-__all__ = ['CloseSmallDeletions', 'MergeGapsByDistance',
- 'FillLoopsByDatabase']
+# these methods will be exported into module
+__all__ = ('CloseSmallDeletions', 'MergeGapsByDistance',
+ 'FillLoopsByDatabase',)
# LocalWords: modeling stereochemically param idx init
-# LocalWords: py ost pylint rawmodel promod CloseSmallDeletions testcode
+# LocalWords: py ost pylint modelling promod CloseSmallDeletions testcode
# LocalWords: fillloopsbydb tpl aln trg TLNGFTVPAGNTLV LNPDKGATVTMA mhandle
# LocalWords: NGGTLLIPNGTYHFLGIQMKSNVHIRVE AttachView CreateFullView len
# LocalWords: BuildRawModel SetupBackboneScorer FillLoopsByDatabase doctest
diff --git a/rawmodel/pymod/export_gap.cc b/modelling/pymod/export_gap.cc
similarity index 90%
rename from rawmodel/pymod/export_gap.cc
rename to modelling/pymod/export_gap.cc
index 27192da4..71df386b 100644
--- a/rawmodel/pymod/export_gap.cc
+++ b/modelling/pymod/export_gap.cc
@@ -1,13 +1,13 @@
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-#include <promod3/rawmodel/gap.hh>
+#include <promod3/modelling/gap.hh>
using namespace ost;
using namespace boost::python;
-using namespace promod3::rawmodel;
+using namespace promod3::modelling;
namespace{
- promod3::rawmodel::StructuralGap WrapGetItem(promod3::rawmodel::StructuralGapList& l, int i){
+ promod3::modelling::StructuralGap WrapGetItem(promod3::modelling::StructuralGapList& l, int i){
return l.at(i);
}
}
diff --git a/rawmodel/pymod/export_gap_extender.cc b/modelling/pymod/export_gap_extender.cc
similarity index 91%
rename from rawmodel/pymod/export_gap_extender.cc
rename to modelling/pymod/export_gap_extender.cc
index 3f9e1448..ee56ba8a 100644
--- a/rawmodel/pymod/export_gap_extender.cc
+++ b/modelling/pymod/export_gap_extender.cc
@@ -1,9 +1,9 @@
#include <boost/python.hpp>
-#include <promod3/rawmodel/gap_extender.hh>
+#include <promod3/modelling/gap_extender.hh>
using namespace ost;
using namespace boost::python;
-using namespace promod3::rawmodel;
+using namespace promod3::modelling;
namespace{
diff --git a/rawmodel/pymod/export_model.cc b/modelling/pymod/export_model.cc
similarity index 95%
rename from rawmodel/pymod/export_model.cc
rename to modelling/pymod/export_model.cc
index 7cce1771..daee7499 100644
--- a/rawmodel/pymod/export_model.cc
+++ b/modelling/pymod/export_model.cc
@@ -1,9 +1,9 @@
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-#include <promod3/rawmodel/model.hh>
+#include <promod3/modelling/model.hh>
using namespace boost::python;
-using namespace promod3::rawmodel;
+using namespace promod3::modelling;
ModellingHandle (*BuildRawModelHandle)(const ost::seq::AlignmentHandle&,
bool,
diff --git a/rawmodel/pymod/wrap_rawmodel.cc b/modelling/pymod/wrap_modelling.cc
similarity index 83%
rename from rawmodel/pymod/wrap_rawmodel.cc
rename to modelling/pymod/wrap_modelling.cc
index b2d88e81..ebfa07ba 100644
--- a/rawmodel/pymod/wrap_rawmodel.cc
+++ b/modelling/pymod/wrap_modelling.cc
@@ -4,7 +4,7 @@ void export_gap();
void export_model();
void export_gap_extender();
-BOOST_PYTHON_MODULE(_rawmodel)
+BOOST_PYTHON_MODULE(_modelling)
{
export_gap();
export_model();
diff --git a/rawmodel/src/CMakeLists.txt b/modelling/src/CMakeLists.txt
similarity index 54%
rename from rawmodel/src/CMakeLists.txt
rename to modelling/src/CMakeLists.txt
index a1f86282..6abdad56 100644
--- a/rawmodel/src/CMakeLists.txt
+++ b/modelling/src/CMakeLists.txt
@@ -1,17 +1,17 @@
-set(RAWMODEL_SOURCES
+set(MODELLING_SOURCES
gap.cc
gap_extender.cc
model.cc
)
-set(RAWMODEL_HEADERS
+set(MODELLING_HEADERS
gap.hh
gap_extender.hh
model.hh
)
-module(NAME rawmodel
- HEADERS ${RAWMODEL_HEADERS}
- SOURCES ${RAWMODEL_SOURCES}
+module(NAME modelling
+ HEADERS ${MODELLING_HEADERS}
+ SOURCES ${MODELLING_SOURCES}
DEPENDS_ON promod3_core
LINK ${OST_LIBRARIES} ${BOOST_LIBRARIES})
diff --git a/rawmodel/src/gap.cc b/modelling/src/gap.cc
similarity index 98%
rename from rawmodel/src/gap.cc
rename to modelling/src/gap.cc
index af3d103d..5a7016ee 100644
--- a/rawmodel/src/gap.cc
+++ b/modelling/src/gap.cc
@@ -5,7 +5,7 @@
using namespace ost::mol;
using namespace ost;
-namespace promod3 { namespace rawmodel {
+namespace promod3 { namespace modelling {
String StructuralGap::GetChainName() const
{
diff --git a/rawmodel/src/gap.hh b/modelling/src/gap.hh
similarity index 97%
rename from rawmodel/src/gap.hh
rename to modelling/src/gap.hh
index 86f85236..3c506a8c 100644
--- a/rawmodel/src/gap.hh
+++ b/modelling/src/gap.hh
@@ -1,10 +1,10 @@
-#ifndef PM3_RAWMODEL_GAP_HH
-#define PM3_RAWMODEL_GAP_HH
+#ifndef PM3_MODELLING_GAP_HH
+#define PM3_MODELLING_GAP_HH
#include <ost/mol/mol.hh>
#include <promod3/core/message.hh>
-namespace promod3 { namespace rawmodel {
+namespace promod3 { namespace modelling {
/// Describes a structural gap, i.e. a loop to be modeled. The gap may either be
/// terminal or between two defined regions. The gap stores information of the
diff --git a/rawmodel/src/gap_extender.cc b/modelling/src/gap_extender.cc
similarity index 93%
rename from rawmodel/src/gap_extender.cc
rename to modelling/src/gap_extender.cc
index acd1cef3..601f585f 100644
--- a/rawmodel/src/gap_extender.cc
+++ b/modelling/src/gap_extender.cc
@@ -1,19 +1,19 @@
-#include <promod3/rawmodel/gap_extender.hh>
+#include <promod3/modelling/gap_extender.hh>
using namespace ost::mol;
using namespace ost;
namespace{
- bool CompareScoredElements(const std::pair<promod3::rawmodel::StructuralGap,Real>& a,
- const std::pair<promod3::rawmodel::StructuralGap,Real>& b){
+ bool CompareScoredElements(const std::pair<promod3::modelling::StructuralGap,Real>& a,
+ const std::pair<promod3::modelling::StructuralGap,Real>& b){
return a.second < b.second;
}
}
-namespace promod3{ namespace rawmodel{
+namespace promod3{ namespace modelling{
bool GapExtender::Extend()
{
diff --git a/rawmodel/src/gap_extender.hh b/modelling/src/gap_extender.hh
similarity index 88%
rename from rawmodel/src/gap_extender.hh
rename to modelling/src/gap_extender.hh
index c8656355..82d1bf6b 100644
--- a/rawmodel/src/gap_extender.hh
+++ b/modelling/src/gap_extender.hh
@@ -1,13 +1,13 @@
-#ifndef PM3_RAWMODEL_GAP_EXTENDER_HH
-#define PM3_RAWMODEL_GAP_EXTENDER_HH
+#ifndef PM3_MODELLING_GAP_EXTENDER_HH
+#define PM3_MODELLING_GAP_EXTENDER_HH
#include <ost/mol/mol.hh>
#include <promod3/core/message.hh>
-#include <promod3/rawmodel/gap.hh>
+#include <promod3/modelling/gap.hh>
#include <ost/mol/mol.hh>
#include <algorithm>
-namespace promod3 { namespace rawmodel {
+namespace promod3 { namespace modelling {
class GapExtender;
class ScoringGapExtender;
diff --git a/rawmodel/src/model.cc b/modelling/src/model.cc
similarity index 99%
rename from rawmodel/src/model.cc
rename to modelling/src/model.cc
index 6c6729bc..12379bca 100644
--- a/rawmodel/src/model.cc
+++ b/modelling/src/model.cc
@@ -17,7 +17,7 @@ using namespace ost;
using namespace ost::seq;
using namespace ost::conop;
-namespace promod3 { namespace rawmodel {
+namespace promod3 { namespace modelling {
namespace {
diff --git a/rawmodel/src/model.hh b/modelling/src/model.hh
similarity index 98%
rename from rawmodel/src/model.hh
rename to modelling/src/model.hh
index fa421338..f6fe2908 100644
--- a/rawmodel/src/model.hh
+++ b/modelling/src/model.hh
@@ -1,5 +1,5 @@
-#ifndef PM3_MODEL_HH
-#define PM3_MODEL_HH
+#ifndef PM3_MODELLING_MODEL_HH
+#define PM3_MODELLING_MODEL_HH
#include <ost/seq/alignment_handle.hh>
#include <ost/seq/sequence_list.hh>
@@ -8,7 +8,7 @@
#include "gap.hh"
-namespace promod3 { namespace rawmodel {
+namespace promod3 { namespace modelling {
struct ModellingHandle {
diff --git a/modelling/tests/CMakeLists.txt b/modelling/tests/CMakeLists.txt
new file mode 100644
index 00000000..f879c051
--- /dev/null
+++ b/modelling/tests/CMakeLists.txt
@@ -0,0 +1,25 @@
+set(MODELLING_UNIT_TESTS
+ test_modelling.py
+ test_gap_extension.py
+ test_close_gaps.py
+)
+
+set(MODELLING_TEST_DATA
+ data/ext.pdb
+ data/compounds.chemlib
+ data/gly.pdb
+ data/ter.fasta
+ data/sep.pdb
+ data/sep.fasta
+ data/seq.fasta
+ data/ins.fasta
+ data/del.fasta
+ data/cbeta.pdb
+ data/cbeta.fasta
+ data/1mcg.pdb
+ data/2dbs.pdb
+)
+
+promod3_unittest(MODULE modelling
+ SOURCES "${MODELLING_UNIT_TESTS}"
+ DATA "${MODELLING_TEST_DATA}")
diff --git a/rawmodel/tests/data/raw-modeling/1mcg.pdb b/modelling/tests/data/1mcg.pdb
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/1mcg.pdb
rename to modelling/tests/data/1mcg.pdb
diff --git a/rawmodel/tests/data/raw-modeling/2dbs.pdb b/modelling/tests/data/2dbs.pdb
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/2dbs.pdb
rename to modelling/tests/data/2dbs.pdb
diff --git a/rawmodel/tests/data/raw-modeling/cbeta.fasta b/modelling/tests/data/cbeta.fasta
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/cbeta.fasta
rename to modelling/tests/data/cbeta.fasta
diff --git a/rawmodel/tests/data/raw-modeling/cbeta.pdb b/modelling/tests/data/cbeta.pdb
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/cbeta.pdb
rename to modelling/tests/data/cbeta.pdb
diff --git a/rawmodel/tests/data/raw-modeling/compounds.chemlib b/modelling/tests/data/compounds.chemlib
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/compounds.chemlib
rename to modelling/tests/data/compounds.chemlib
diff --git a/rawmodel/tests/data/raw-modeling/del.fasta b/modelling/tests/data/del.fasta
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/del.fasta
rename to modelling/tests/data/del.fasta
diff --git a/rawmodel/tests/data/loop/ext.pdb b/modelling/tests/data/ext.pdb
similarity index 100%
rename from rawmodel/tests/data/loop/ext.pdb
rename to modelling/tests/data/ext.pdb
diff --git a/rawmodel/tests/data/raw-modeling/gly.pdb b/modelling/tests/data/gly.pdb
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/gly.pdb
rename to modelling/tests/data/gly.pdb
diff --git a/rawmodel/tests/data/raw-modeling/ins.fasta b/modelling/tests/data/ins.fasta
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/ins.fasta
rename to modelling/tests/data/ins.fasta
diff --git a/rawmodel/tests/data/raw-modeling/sep.fasta b/modelling/tests/data/sep.fasta
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/sep.fasta
rename to modelling/tests/data/sep.fasta
diff --git a/rawmodel/tests/data/raw-modeling/sep.pdb b/modelling/tests/data/sep.pdb
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/sep.pdb
rename to modelling/tests/data/sep.pdb
diff --git a/rawmodel/tests/data/raw-modeling/seq.fasta b/modelling/tests/data/seq.fasta
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/seq.fasta
rename to modelling/tests/data/seq.fasta
diff --git a/rawmodel/tests/data/raw-modeling/ter.fasta b/modelling/tests/data/ter.fasta
similarity index 100%
rename from rawmodel/tests/data/raw-modeling/ter.fasta
rename to modelling/tests/data/ter.fasta
diff --git a/rawmodel/tests/test_close_gaps.py b/modelling/tests/test_close_gaps.py
similarity index 83%
rename from rawmodel/tests/test_close_gaps.py
rename to modelling/tests/test_close_gaps.py
index c4b0155f..d833591e 100644
--- a/rawmodel/tests/test_close_gaps.py
+++ b/modelling/tests/test_close_gaps.py
@@ -1,7 +1,7 @@
import unittest
import ost
from ost import io, seq
-from promod3 import rawmodel
+from promod3 import modelling
from promod3 import loop
# setting up an OST LogSink to capture messages
@@ -25,18 +25,18 @@ class CloseGapsTests(unittest.TestCase):
def testClosesmalldel(self):
# check that very small gaps are closed
- # create a rawmodel to work with (which actually is a bit dangerous:
+ # create a raw model to work with (which actually is a bit dangerous:
# the PDB file has nothing to do with the alignment...)
- tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
+ tpl = io.LoadPDB('data/gly.pdb')
# switch target and template in this alignment to get a deletion
aln = seq.CreateAlignment(seq.CreateSequence('trg', 'GGG-GGG'),
seq.CreateSequence('tpl', 'GGGAGGG'))
aln.AttachView(1, tpl.CreateFullView())
- rmodel = rawmodel.BuildRawModel(aln)
+ rmodel = modelling.BuildRawModel(aln)
self.assertEqual(len(rmodel.gaps), 1)
# obtain the scorer
scorer = loop.SetupBackboneScorer(rmodel)
- rawmodel.CloseSmallDeletions(rmodel, scorer)
+ modelling.CloseSmallDeletions(rmodel, scorer)
self.assertEqual(len(rmodel.gaps), 0)
self.assertEqual(self.log.messages['VERBOSE'],
['Assigning MOL_IDs',
@@ -47,15 +47,15 @@ class CloseGapsTests(unittest.TestCase):
def testMergeGapsByDistance(self):
# test that merging two close gaps works
- tpl = io.LoadPDB('data/raw-modeling/1mcg.pdb')
+ tpl = io.LoadPDB('data/1mcg.pdb')
aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGDTKNLGHN'),
seq.CreateSequence('tpl', 'NN----A----LF'))
aln.AttachView(1, tpl.CreateFullView())
- rmodel = rawmodel.BuildRawModel(aln)
+ rmodel = modelling.BuildRawModel(aln)
self.assertEqual(len(rmodel.gaps), 2)
self.assertEqual(str(rmodel.gaps[0]), 'A.ASP2-(FAGD)-A.THR7')
self.assertEqual(str(rmodel.gaps[1]), 'A.THR7-(KNLG)-A.HIS12')
- rawmodel.MergeGapsByDistance(rmodel,0)
+ modelling.MergeGapsByDistance(rmodel,0)
self.assertEqual(len(rmodel.gaps), 1)
self.assertEqual(str(rmodel.gaps[0]), 'A.ASP2-(FAGDTKNLG)-A.HIS12')
self.assertEqual(self.log.messages['VERBOSE'],
@@ -68,38 +68,38 @@ class CloseGapsTests(unittest.TestCase):
def testMergeGapsByDistanceBothTerminals(self):
# test that we do not delete the whole thing for gaps at terminals
- tpl = io.LoadPDB('data/raw-modeling/1mcg.pdb')
+ tpl = io.LoadPDB('data/1mcg.pdb')
aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGDTKNLGHN'),
seq.CreateSequence('tpl', '----NNALF----'))
aln.AttachView(1, tpl.CreateFullView())
- rmodel = rawmodel.BuildRawModel(aln)
+ rmodel = modelling.BuildRawModel(aln)
self.assertEqual(len(rmodel.gaps), 2)
- rawmodel.MergeGapsByDistance(rmodel,4)
+ modelling.MergeGapsByDistance(rmodel,4)
self.assertEqual(len(rmodel.gaps), 2)
def testMergeGapsByDistanceOneTerminal(self):
# test that we do not delete the whole thing for gaps at terminals
- tpl = io.LoadPDB('data/raw-modeling/1mcg.pdb')
+ tpl = io.LoadPDB('data/1mcg.pdb')
aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGDTKNLGHN'),
seq.CreateSequence('tpl', 'NN----ALF----'))
aln.AttachView(1, tpl.CreateFullView())
- rmodel = rawmodel.BuildRawModel(aln)
+ rmodel = modelling.BuildRawModel(aln)
self.assertEqual(len(rmodel.gaps), 2)
- rawmodel.MergeGapsByDistance(rmodel,2)
+ modelling.MergeGapsByDistance(rmodel,2)
self.assertEqual(len(rmodel.gaps), 1)
def testFillGapsByDatabase(self):
# get rid of gaps by db
- tpl = io.LoadPDB('data/raw-modeling/2dbs.pdb')
+ tpl = io.LoadPDB('data/2dbs.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'TLNGFTVPAGNTLV--LNPDKGATVTMA'),
seq.CreateSequence('tpl', 'NGGTLLIPNGTYHFLGIQMKSNVHIRVE'))
aln.AttachView(1, tpl.CreateFullView())
- rmodel = rawmodel.BuildRawModel(aln)
+ rmodel = modelling.BuildRawModel(aln)
self.assertEqual(len(rmodel.gaps), 1)
scorer = loop.SetupBackboneScorer(rmodel)
- rawmodel.FillLoopsByDatabase(rmodel, scorer, loop.LoadFragDB(),
+ modelling.FillLoopsByDatabase(rmodel, scorer, loop.LoadFragDB(),
loop.LoadStructureDB(),
loop.LoadTorsionSamplerCoil())
self.assertEqual(len(rmodel.gaps), 0)
diff --git a/rawmodel/tests/test_gap_extension.py b/modelling/tests/test_gap_extension.py
similarity index 87%
rename from rawmodel/tests/test_gap_extension.py
rename to modelling/tests/test_gap_extension.py
index fecd7c3f..046446d3 100644
--- a/rawmodel/tests/test_gap_extension.py
+++ b/modelling/tests/test_gap_extension.py
@@ -1,15 +1,15 @@
import unittest
-from promod3 import rawmodel
+from promod3 import modelling
from ost import io
class GapExtension(unittest.TestCase):
def testGapExtender(self):
- ent = io.LoadPDB('data/loop/ext.pdb')
+ ent = io.LoadPDB('data/ext.pdb')
chain = ent.chains[0]
- gap = rawmodel.StructuralGap(chain.FindResidue(9),
+ gap = modelling.StructuralGap(chain.FindResidue(9),
chain.FindResidue(11),
'X')
- ext = rawmodel.GapExtender(gap)
+ ext = modelling.GapExtender(gap)
self.assertEqual(str(gap), 'A.PRO9-(X)-A.TRP11')
self.assertTrue(ext.Extend())
self.assertEqual(str(gap), 'A.THR8-(PX)-A.TRP11')
diff --git a/rawmodel/tests/test_raw_modeling.py b/modelling/tests/test_modelling.py
similarity index 73%
rename from rawmodel/tests/test_raw_modeling.py
rename to modelling/tests/test_modelling.py
index 3be952b7..69c79bf9 100644
--- a/rawmodel/tests/test_raw_modeling.py
+++ b/modelling/tests/test_modelling.py
@@ -1,14 +1,14 @@
"""
-Unit tests for rawmodel.
+Unit tests for modelling.
"""
import unittest
-from promod3 import rawmodel
+from promod3 import modelling
from ost import conop, seq, io, mol
-class RawModelingTests(unittest.TestCase):
+class ModellingTests(unittest.TestCase):
def setUp(self):
compound_lib = conop.CompoundLib.Load(
- 'data/raw-modeling/compounds.chemlib')
+ 'data/compounds.chemlib')
conop.SetDefaultLib(compound_lib)
io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(
compound_lib)
@@ -17,23 +17,23 @@ class RawModelingTests(unittest.TestCase):
# test that BuildRawModel throws exception when no view is attached
aln = seq.CreateAlignment(seq.CreateSequence('A', 'acdef'),
seq.CreateSequence('B', 'ac-ef'))
- self.assertRaises(RuntimeError, rawmodel.BuildRawModel, aln)
+ self.assertRaises(RuntimeError, modelling.BuildRawModel, aln)
def testModeledSequence(self):
# test if the model has the sequence we want.
- tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
- aln = io.LoadAlignment('data/raw-modeling/seq.fasta')
+ tpl = io.LoadPDB('data/gly.pdb')
+ aln = io.LoadAlignment('data/seq.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = rawmodel.BuildRawModel(aln)
+ result = modelling.BuildRawModel(aln)
seq1 = seq.SequenceFromChain('MODEL', result.model.chains[0])
self.assertEqual(seq1.string, aln.sequences[0].string)
def testDeletion(self):
# test if the result contains a "deletion" gap at the right spot.
- tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
- aln = io.LoadAlignment('data/raw-modeling/del.fasta')
+ tpl = io.LoadPDB('data/gly.pdb')
+ aln = io.LoadAlignment('data/del.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = rawmodel.BuildRawModel(aln)
+ result = modelling.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(result.gaps), 1)
self.assertEqual(result.gaps[0].before, residues[2])
@@ -42,10 +42,10 @@ class RawModelingTests(unittest.TestCase):
def testInsertion(self):
# test if the result contains an "insertion" gap at the right spot.
- tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
- aln = io.LoadAlignment('data/raw-modeling/ins.fasta')
+ tpl = io.LoadPDB('data/gly.pdb')
+ aln = io.LoadAlignment('data/ins.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = rawmodel.BuildRawModel(aln)
+ result = modelling.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(result.gaps), 1)
self.assertEqual(result.gaps[0].before, residues[1])
@@ -55,10 +55,10 @@ class RawModelingTests(unittest.TestCase):
def testTer(self):
# test if the result contains two terminal gaps, one at the beginning,
# one at the end
- tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
- aln = io.LoadAlignment('data/raw-modeling/ter.fasta')
+ tpl = io.LoadPDB('data/gly.pdb')
+ aln = io.LoadAlignment('data/ter.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = rawmodel.BuildRawModel(aln)
+ result = modelling.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(result.gaps), 2)
self.assertEqual(result.gaps[0].before, mol.ResidueHandle())
@@ -70,10 +70,10 @@ class RawModelingTests(unittest.TestCase):
def testModified(self):
# test if we correctly strip off modifications
- tpl = io.LoadPDB('data/raw-modeling/sep.pdb')
- aln = io.LoadAlignment('data/raw-modeling/sep.fasta')
+ tpl = io.LoadPDB('data/sep.pdb')
+ aln = io.LoadAlignment('data/sep.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = rawmodel.BuildRawModel(aln)
+ result = modelling.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(residues), 1)
self.assertEqual(len(residues[0].atoms), 6)
@@ -86,10 +86,10 @@ class RawModelingTests(unittest.TestCase):
def testInsertCBeta(self):
# test if the dst residues contain cbeta, unless they are glycines
- tpl = io.LoadPDB('data/raw-modeling/cbeta.pdb')
- aln = io.LoadAlignment('data/raw-modeling/cbeta.fasta')
+ tpl = io.LoadPDB('data/cbeta.pdb')
+ aln = io.LoadAlignment('data/cbeta.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = rawmodel.BuildRawModel(aln)
+ result = modelling.BuildRawModel(aln)
residues = result.model.residues
self.assertFalse(residues[0].FindAtom("CB").IsValid())
self.assertFalse(residues[1].FindAtom("CB").IsValid())
diff --git a/pipeline/pymod/CMakeLists.txt b/pipeline/pymod/CMakeLists.txt
index 5ed2ecba..2d94a5b1 100644
--- a/pipeline/pymod/CMakeLists.txt
+++ b/pipeline/pymod/CMakeLists.txt
@@ -3,4 +3,4 @@ set(PIPELINE_PYMOD
run_engine.py
)
-pymod(NAME pipeline PY ${PIPELINE_PYMOD} DEPENDS_ON _rawmodel rawmodel_pymod)
+pymod(NAME pipeline PY ${PIPELINE_PYMOD} DEPENDS_ON _modelling modelling_pymod)
diff --git a/pipeline/pymod/run_engine.py b/pipeline/pymod/run_engine.py
index a8e32b86..0acb61b2 100644
--- a/pipeline/pymod/run_engine.py
+++ b/pipeline/pymod/run_engine.py
@@ -4,16 +4,16 @@
import ost
from promod3 import loop
-from promod3 import rawmodel
+from promod3 import modelling
-def BuildFromRawModel(raw_model, structure_db=None, fragment_db=None,
+def BuildFromRawModel(mhandle, structure_db=None, fragment_db=None,
torsion_sampler=None, merge_distance=4):
'''Build a model starting with a
- :class:`RawModel <promod3.rawmodel.ModellingHandle>`.
+ :class:`raw model <promod3.modelling.ModellingHandle>`.
- :param raw_model: The prepared template coordinates loaded with the input
+ :param mhandle: The prepared template coordinates loaded with the input
alignment.
- :type raw_model: :class:`~promod3.rawmodel.ModellingHandle`
+ :type mhandle: :class:`~promod3.modelling.ModellingHandle`
:param structure_db: The structural database. Loads the default one shipped
with |project| if omitted.
@@ -49,34 +49,34 @@ def BuildFromRawModel(raw_model, structure_db=None, fragment_db=None,
if torsion_sampler == None:
torsion_sampler = loop.LoadTorsionSamplerCoil()
- scorer = loop.SetupBackboneScorer(raw_model)
+ scorer = loop.SetupBackboneScorer(mhandle)
# step 1: close small deletions in the raw model
ost.LogVerbose("Trying to close small deletions (no. of gaps: %d)." % \
- len(raw_model.gaps))
- scorer = rawmodel.CloseSmallDeletions(raw_model, scorer)
+ len(mhandle.gaps))
+ scorer = modelling.CloseSmallDeletions(mhandle, scorer)
# step 2: simple handling of further gaps: merge, then fill from db
for distance in range(merge_distance):
# step 2a: Combine gaps living close to each other
ost.LogVerbose("Trying to merge gaps (%d) with distance %d." % \
- (len(raw_model.gaps), distance))
- rawmodel.MergeGapsByDistance(raw_model, distance)
- ost.LogVerbose("%d gap(s) left after merging.\n" % len(raw_model.gaps)+
+ (len(mhandle.gaps), distance))
+ modelling.MergeGapsByDistance(mhandle, distance)
+ ost.LogVerbose("%d gap(s) left after merging.\n" % len(mhandle.gaps)+
"Trying to fill loops by database")
# step 2b: fit loops into the model
- scorer = rawmodel.FillLoopsByDatabase(raw_model, scorer, fragment_db,
+ scorer = modelling.FillLoopsByDatabase(mhandle, scorer, fragment_db,
structure_db, torsion_sampler,
max_loops_to_search=30)
ost.LogVerbose("%d gap(s) left after database search." % \
- len(raw_model.gaps))
- if len(raw_model.gaps) == 0:
+ len(mhandle.gaps))
+ if len(mhandle.gaps) == 0:
break
- return raw_model.model
+ return mhandle.model
__all__ = ('BuildProMod3Model')
# LocalWords: BuildProMod ProMod sticked ost promod BuildFromRawModel param
-# LocalWords: RawModel rtype bool LoadStructureDB LogVerbose LoadFragDB
+# LocalWords: rtype bool LoadStructureDB LogVerbose LoadFragDB
# LocalWords: LoadTorsionSamplerCoil SetupBackboneScorer
# LocalWords: CloseSmallDeletions
diff --git a/pipeline/tests/test_run_engine.py b/pipeline/tests/test_run_engine.py
index ea131abf..17b1ada4 100644
--- a/pipeline/tests/test_run_engine.py
+++ b/pipeline/tests/test_run_engine.py
@@ -3,7 +3,7 @@ import os
import ost
from promod3 import pipeline
-from promod3 import rawmodel
+from promod3 import modelling
class RunPipelineTests(unittest.TestCase):
def testBuildFromRawModel(self):
@@ -16,9 +16,9 @@ class RunPipelineTests(unittest.TestCase):
template = ost.io.LoadPDB(os.path.join("data", "2l4k_B.pdb.gz"))
aln = ost.io.LoadAlignment(os.path.join("data", "2l4k_B_aln.fasta"))
aln.AttachView(1, template.Select('peptide=true'))
- raw_model = rawmodel.BuildRawModel(aln)
+ mhandle = modelling.BuildRawModel(aln)
# run the pipeline
- self.assertTrue(pipeline.run_engine.BuildFromRawModel(raw_model))
+ self.assertTrue(pipeline.run_engine.BuildFromRawModel(mhandle))
if __name__ == "__main__":
from ost import testutils
diff --git a/rawmodel/doc/CMakeLists.txt b/rawmodel/doc/CMakeLists.txt
deleted file mode 100644
index 2f436174..00000000
--- a/rawmodel/doc/CMakeLists.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-set(RAWMODEL_RST
-index.rst
-)
-
-add_doc_source(NAME rawmodel RST ${RAWMODEL_RST})
diff --git a/rawmodel/pymod/CMakeLists.txt b/rawmodel/pymod/CMakeLists.txt
deleted file mode 100644
index 00f6f28f..00000000
--- a/rawmodel/pymod/CMakeLists.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-set(RAWMODEL_CPP
-wrap_rawmodel.cc
-export_model.cc
-export_gap.cc
-export_gap_extender.cc
-)
-
-set(RAWMODEL_PYMOD
- __init__.py
- _closegaps.py
-)
-
-pymod(NAME rawmodel
- CPP ${RAWMODEL_CPP}
- PY ${RAWMODEL_PYMOD}
- DEPENDS_ON core_pymod)
diff --git a/rawmodel/pymod/__init__.py b/rawmodel/pymod/__init__.py
deleted file mode 100644
index 78a1f850..00000000
--- a/rawmodel/pymod/__init__.py
+++ /dev/null
@@ -1,5 +0,0 @@
-"""
-Initialise the rawmodel module.
-"""
-from _rawmodel import *
-from _closegaps import *
diff --git a/rawmodel/tests/CMakeLists.txt b/rawmodel/tests/CMakeLists.txt
deleted file mode 100644
index d3005b81..00000000
--- a/rawmodel/tests/CMakeLists.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-set(RAWMODEL_UNIT_TESTS
- test_raw_modeling.py
- test_gap_extension.py
- test_close_gaps.py
-)
-
-set(RAWMODEL_TEST_DATA
- data/loop/ext.pdb
- data/raw-modeling/compounds.chemlib
- data/raw-modeling/gly.pdb
- data/raw-modeling/ter.fasta
- data/raw-modeling/sep.pdb
- data/raw-modeling/sep.fasta
- data/raw-modeling/seq.fasta
- data/raw-modeling/ins.fasta
- data/raw-modeling/del.fasta
- data/raw-modeling/cbeta.pdb
- data/raw-modeling/cbeta.fasta
- data/raw-modeling/1mcg.pdb
- data/raw-modeling/2dbs.pdb
-)
-
-promod3_unittest(MODULE rawmodel
- SOURCES "${RAWMODEL_UNIT_TESTS}"
- DATA "${RAWMODEL_TEST_DATA}")
diff --git a/sidechain/pymod/_reconstruct_sidechains.py b/sidechain/pymod/_reconstruct_sidechains.py
index 33f029cc..fabd97e5 100644
--- a/sidechain/pymod/_reconstruct_sidechains.py
+++ b/sidechain/pymod/_reconstruct_sidechains.py
@@ -360,3 +360,5 @@ def Reconstruct(ent, keep_sidechains = False, build_disulfids = True,
r.ApplyOnResidue(rh,True)
+# these methods will be exported into module
+__all__ = ('Reconstruct',)
--
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