diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 5872b48efc776fc573c8086b1ebd3ef8224f42d0..d555dbf5163fbd73ad4b63f5bddb64d591ff0c61 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -5,7 +5,10 @@ Changes in Release 2.3.0
* 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/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/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,