diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index d5a2c7632e717937308cdc6de08d08933ddbb7ef..d555dbf5163fbd73ad4b63f5bddb64d591ff0c61 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,11 +1,14 @@
-Changes in Release 2.2.x
+Changes in Release 2.3.0
--------------------------------------------------------------------------------
* Add AAindex databases (Kawashima et al., 2000)
* Added experimental molecular structure format OMF (OpenStructure Minimal
Format)
* Removed GUI components in containers
- * DSSP 4.0 support in DSSP binding (https://github.com/PDB-REDO/dssp)
+ * Support to call external DSSP program has been deprecated.
+ ost.bindings.dssp.AssignDSSP still exists with the "old" interface but mimics
+ the equivalent behaviour with the OpenStructure internal secondary structure
+ and solvent accessibility algorithms.
* mol.alg.PDBize does not turn plain polymer chains (not marked peptide or
nucleotide) into ligand chains anymore
* Remove ENABLE_IMG flag in cmake build system - img module is always built now
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ba6cfe36f4e204a17cc4bd53e33e9c55cf021599..c118d3d0a100c940124a48699f21918d43dc815a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -14,7 +14,7 @@ cmake_policy(SET CMP0060 NEW)
project(OpenStructure CXX C)
set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
set (OST_VERSION_MAJOR 2)
-set (OST_VERSION_MINOR 2)
+set (OST_VERSION_MINOR 3)
set (OST_VERSION_PATCH 0)
set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index ed7b8286f28749ab09d157bf5621664443257119..0711b1a5aad8bf01ebfc501c57bf0f2f77269d6a 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -2,7 +2,7 @@ FROM ubuntu:20.04
# ARGUMENTS
###########
-ARG OPENSTRUCTURE_VERSION="2.2.0"
+ARG OPENSTRUCTURE_VERSION="2.3.0"
ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=2
ARG MSMS_VERSION="2.6.1"
@@ -32,7 +32,6 @@ RUN apt-get update -y && apt-get install -y cmake \
doxygen \
swig \
clustalw \
- dssp \
locales && \
# CLEANUP
rm -rf /var/lib/apt/lists/*
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 6c9a039f91430512bd800a3c82a51d9d02b047cd..1e20e4eae4100d265a6e7c3c008d9216a4e1516a 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -2959,10 +2959,11 @@ Statistics for column %(col)s
plt.title(title, size='x-large', fontweight='bold')
plt.ylabel(y_title, size='x-large')
plt.xlabel(x_title, size='x-large')
-
- plt.xscale('log', basex=10)
+ try:
+ plt.xscale('log', basex=10)
+ except:
+ plt.xscale('log', base=10) # breaking change in matplotlib 3.5
plt.xlim(0.001, 1.0)
-
if save:
plt.savefig(save)
diff --git a/modules/bindings/doc/dssp.rst b/modules/bindings/doc/dssp.rst
index 3a51a870c9c740b495baa5caa53c0d1475818d77..1a087bcfae35cbdab99549f234fd6e2fe4dd5667 100644
--- a/modules/bindings/doc/dssp.rst
+++ b/modules/bindings/doc/dssp.rst
@@ -13,6 +13,18 @@ hydrogen bonding patterns and geometric features.
The program can be downloaded from `<http://swift.cmbi.ru.nl/gv/dssp/>`_.
+.. warning::
+ Support of the DSSP program has been deprecated. OpenStructure provides
+ functionality to assign equivalent secondary structures
+ (:func:`ost.mol.alg.AssignSecStruct`) and solvent accessibility
+ (:func:`ost.mol.alg.Accessibility`). You're advised to use these
+ algorithms.
+
+ :func:`AssignDSSP` still exists and provides the "old" interface but
+ internally uses the OpenStructure impmlementations and does not call
+ an external program anymore.
+
+
Examples
--------------------------------------------------------------------------------
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 2cff9231cffc91418d604e2caabb0c57292f647a..ba82c33973b12cb7989ae7130fcd6b48ec4d4a4a 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -148,12 +148,12 @@ def CreateDB(infasta, dbout, mkdb_cmd=None):
"""
if mkdb_cmd==None:
try:
- exe=settings.Locate('formatdb')
- args=[exe, '-i', infasta, '-n', dbout]
+ exe=settings.Locate('makeblastdb')
+ args=[exe, '-in', infasta, '-out', dbout, '-dbtype', 'prot']
except:
try:
- exe=settings.Locate('makeblastdb')
- args=[exe, '-in', infasta, '-out', dbout, '-dbtype', 'prot']
+ exe=settings.Locate('formatdb')
+ args=[exe, '-i', infasta, '-n', dbout]
except:
raise RuntimeError('could not find makeblastdb/formatdb executable')
else:
@@ -177,10 +177,10 @@ def BlastVersion(blast_location=None):
"""
try:
- blast_exe=settings.Locate('blastall',explicit_file_name=blast_location)
+ blast_exe=settings.Locate('blastp',explicit_file_name=blast_location)
except:
try:
- blast_exe=settings.Locate('blastp', explicit_file_name=blast_location)
+ blast_exe=settings.Locate('blastall', explicit_file_name=blast_location)
except:
raise RuntimeError('could not find blast executable')
@@ -242,10 +242,10 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
if blast_location==None:
try:
- blast_exe=settings.Locate('blastall')
+ blast_exe=settings.Locate('blastp')
except:
try:
- blast_exe=settings.Locate('blastp')
+ blast_exe=settings.Locate('blastall')
except:
raise RuntimeError('could not find blast executable')
else:
diff --git a/modules/bindings/pymod/dssp.py b/modules/bindings/pymod/dssp.py
index 803ea195004b440212604c5f1d494a53962bdb24..ee179c9a6966283027f5ef93d8c704bc5ba7e8ea 100644
--- a/modules/bindings/pymod/dssp.py
+++ b/modules/bindings/pymod/dssp.py
@@ -59,12 +59,94 @@ def _CalcRelativeSA(residue_type, absolute_sa):
rel=float(absolute_sa)/(solvent_max_list[residue_indices.find(residue_type)])
return rel
+#
+#def AssignDSSP(ent, pdb_path="", extract_burial_status=False, tmp_dir=None,
+# dssp_bin=None):
+# """
+# Assign secondary structure states to peptide residues in the structure. This
+# function uses the DSSP command line program.
+#
+# If you already have a DSSP output file and would like to assign the secondary
+# structure states to an entity, use :func:`LoadDSSP`.
+#
+# :param ent: The entity for which the secondary structure should be calculated
+# :type ent: :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
+# :param extract_burial_status: If true, also extract burial status and store
+# as float-property
+# ``relative_solvent_accessibility`` at residue
+# level
+# :param tmp_dir: If set, overrides the default tmp directory of the
+# operating system
+# :param dssp_bin: The path to the DSSP executable
+# :raises: :class:`~ost.settings.FileNotFound` if the dssp executable is not
+# in the path.
+# :raises: :class:`RuntimeError` when dssp is executed with errors
+# """
+#
+# if not ent.IsValid():
+# raise ValueError('model entity is not valid')
+# if ent.atom_count==0:
+# raise ValueError('model entity does not contain any atoms')
+#
+# dssp_abs_path=settings.Locate(['dsspcmbi','dssp','mkdssp'], env_name='DSSP_EXECUTABLE',
+# explicit_file_name=dssp_bin)
+# if os.path.isdir(dssp_abs_path):
+# raise RuntimeError('"%s" is a directory. Specify path to DSSP binary' % dssp_abs_path)
+# if not os.access(dssp_abs_path, os.X_OK):
+# raise RuntimeError('"%s" is not executable' % dssp_abs_path)
+#
+# pdb_path=tempfile.mktemp(suffix=".pdb",prefix="temp_entity", dir=tmp_dir)
+# io.SavePDB(ent, pdb_path)
+# temp_dssp_path=tempfile.mktemp(suffix=".out",prefix="dssp", dir=tmp_dir)
+#
+# cmd = [dssp_abs_path, pdb_path, temp_dssp_path]
+# s = subprocess.run(cmd, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+# if s.returncode == 0:
+# try:
+# LoadDSSP(temp_dssp_path, ent, extract_burial_status)
+# _Cleanup(temp_dssp_path, pdb_path)
+# return ent
+# except:
+# pass # continue with dssp 4 fallback
+#
+# # either dssp execution failed or output file cannot be loaded
+# # both can be the result of using dssp 4 (https://github.com/PDB-REDO/dssp)
+# # => try fallback
+#
+# # dssp 4 desperately wants a CRYST1 record (REMOVE IF NOT NEEDED ANYMORE!)
+# # Be aware, Even more stuff is needed if you don't set the CLIBD_MON env var
+# # The dssp binding has therefore been deprecated and we mimic to "old" interface
+# # using OpenStructure internal functionality
+# with open(pdb_path, 'r') as fh:
+# file_content = fh.read()
+# with open(pdb_path, 'w') as fh:
+# fh.write('CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ' +
+# os.linesep + file_content)
+#
+# # explicitely request dssp output format
+# cmd = [dssp_abs_path, '--output-format', 'dssp', pdb_path, temp_dssp_path]
+# s_fallback = subprocess.run(cmd, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+#
+# if s_fallback.returncode == 0:
+# try:
+# LoadDSSP(temp_dssp_path, ent, extract_burial_status)
+# _Cleanup(temp_dssp_path, pdb_path)
+# return ent
+# except:
+# pass # continue with cleanup and raise error
+#
+# _Cleanup(temp_dssp_path, pdb_path)
+# raise RuntimeError('Failed to assign DSSP')
+
def AssignDSSP(ent, pdb_path="", extract_burial_status=False, tmp_dir=None,
dssp_bin=None):
"""
Assign secondary structure states to peptide residues in the structure. This
- function uses the DSSP command line program.
+ function replaces the "old" AssignDSSP which relies on the DSSP command line
+ program and uses OpenStructure internal functionality only. The sole purpose
+ is to retain the "old" interface and you're adviced to directly use
+ :func:`ost.mol.alg.AssignSecStruct` and :func:`ost.mol.alg.Accessibility`.
If you already have a DSSP output file and would like to assign the secondary
structure states to an entity, use :func:`LoadDSSP`.
@@ -76,11 +158,8 @@ def AssignDSSP(ent, pdb_path="", extract_burial_status=False, tmp_dir=None,
``relative_solvent_accessibility`` at residue
level
:param tmp_dir: If set, overrides the default tmp directory of the
- operating system
- :param dssp_bin: The path to the DSSP executable
- :raises: :class:`~ost.settings.FileNotFound` if the dssp executable is not
- in the path.
- :raises: :class:`RuntimeError` when dssp is executed with errors
+ operating system - deprecated, has no effect
+ :param dssp_bin: The path to the DSSP executable - deprecated, has no effect
"""
if not ent.IsValid():
@@ -88,52 +167,24 @@ def AssignDSSP(ent, pdb_path="", extract_burial_status=False, tmp_dir=None,
if ent.atom_count==0:
raise ValueError('model entity does not contain any atoms')
- dssp_abs_path=settings.Locate(['dsspcmbi','dssp','mkdssp'], env_name='DSSP_EXECUTABLE',
- explicit_file_name=dssp_bin)
- if os.path.isdir(dssp_abs_path):
- raise RuntimeError('"%s" is a directory. Specify path to DSSP binary' % dssp_abs_path)
- if not os.access(dssp_abs_path, os.X_OK):
- raise RuntimeError('"%s" is not executable' % dssp_abs_path)
-
- pdb_path=tempfile.mktemp(suffix=".pdb",prefix="temp_entity", dir=tmp_dir)
- io.SavePDB(ent, pdb_path)
- temp_dssp_path=tempfile.mktemp(suffix=".out",prefix="dssp", dir=tmp_dir)
-
- cmd = [dssp_abs_path, pdb_path, temp_dssp_path]
- s = subprocess.run(cmd, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
- if s.returncode == 0:
- try:
- LoadDSSP(temp_dssp_path, ent, extract_burial_status)
- _Cleanup(temp_dssp_path, pdb_path)
- return ent
- except:
- pass # continue with dssp 4 fallback
-
- # either dssp execution failed or output file cannot be loaded
- # both can be the result of using dssp 4 (https://github.com/PDB-REDO/dssp)
- # => try fallback
-
- # dssp 4 desperately wants a CRYST1 record (REMOVE IF NOT NEEDED ANYMORE!)
- with open(pdb_path, 'r') as fh:
- file_content = fh.read()
- with open(pdb_path, 'w') as fh:
- fh.write('CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ' +
- os.linesep + file_content)
-
- # explicitely request dssp output format
- cmd = [dssp_abs_path, '--output-format', 'dssp', pdb_path, temp_dssp_path]
- s_fallback = subprocess.run(cmd, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
-
- if s_fallback.returncode == 0:
- try:
- LoadDSSP(temp_dssp_path, ent, extract_burial_status)
- _Cleanup(temp_dssp_path, pdb_path)
- return ent
- except:
- pass # continue with cleanup and raise error
-
- _Cleanup(temp_dssp_path, pdb_path)
- raise RuntimeError('Failed to assign DSSP')
+ mol.alg.AssignSecStruct(ent)
+ if extract_burial_status:
+ mol.alg.Accessibility(ent, algorithm=mol.alg.DSSP)
+ # map float properties from Accessibility algorithm to the original
+ # properties that have been set in the binding
+ for r in ent.residues:
+ if r.HasProp("asaAbs"):
+ asa = round(r.GetFloatProp("asaAbs")) # original DSSP output is rounded
+ asa_rel = _CalcRelativeSA(r.one_letter_code, asa) # there would be the
+ # asaRel property but
+ # it relates to the
+ # non-rounded asa
+ r.SetFloatProp("solvent_accessibility", asa)
+ r.SetFloatProp("relative_solvent_accessibility", asa_rel)
+ if asa_rel < 0.25:
+ r.SetStringProp("burial_status", 'b')
+ else:
+ r.SetStringProp("burial_status", 'e')
def LoadDSSP(file_name, model, extract_burial_status=False,
diff --git a/modules/io/src/mol/omf.cc b/modules/io/src/mol/omf.cc
index 5d62e7fd1abd2e90da441f8baa54c2aaa0846e1b..3d3c144deb6d9a962c5178a1779c804fa2cb9705 100644
--- a/modules/io/src/mol/omf.cc
+++ b/modules/io/src/mol/omf.cc
@@ -1118,6 +1118,13 @@ ost::mol::EntityHandle OMF::GetBU(int bu_idx) const{
}
void OMF::ToStream(std::ostream& stream) const {
+
+ uint32_t magic_number = 42;
+ stream.write(reinterpret_cast<char*>(&magic_number), sizeof(uint32_t));
+
+ uint32_t version = 1;
+ stream.write(reinterpret_cast<char*>(&version), sizeof(uint32_t));
+
Dump(stream, residue_definitions_);
Dump(stream, biounit_definitions_);
Dump(stream, chain_data_);
@@ -1127,12 +1134,31 @@ void OMF::ToStream(std::ostream& stream) const {
}
void OMF::FromStream(std::istream& stream) {
+
+ uint32_t magic_number;
+ stream.read(reinterpret_cast<char*>(&magic_number), sizeof(uint32_t));
+ if(magic_number != 42) {
+ throw ost::Error("Cannot read corrupted OMF stream");
+ }
+
+ uint32_t version;
+ stream.read(reinterpret_cast<char*>(&version), sizeof(uint32_t));
+ if(version != 1) {
+ std::stringstream ss;
+ ss << "OST version only supports OMF version 1. Got "<<version;
+ throw ost::Error(ss.str());
+ }
+
Load(stream, residue_definitions_);
Load(stream, biounit_definitions_);
Load(stream, chain_data_);
Load(stream, bond_chain_names_);
Load(stream, bond_atoms_);
Load(stream, bond_orders_);
+
+ if(!stream.good()) {
+ throw ost::Error("Cannot read corrupted OMF stream");
+ }
}
void OMF::FillChain(ost::mol::ChainHandle& chain, ost::mol::XCSEditor& ed,
diff --git a/singularity/Singularity b/singularity/Singularity
index c36ec32d9f843842586c5415375a47a6d4118a21..dd26e2a39ff55ef5417c5f215ffc0bdcc5775a69 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -1,5 +1,5 @@
BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/openstructure:2.2.0-focal
+From: registry.scicore.unibas.ch/schwede/openstructure:2.3.0-focal
%post
##############################################################################
# POST