From 034099f19120848eeb97acd47371921af638fcaa Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sun, 21 Nov 2021 11:40:52 +0100
Subject: [PATCH] Deprecate calling external dssp program
Support for DSSP 4.0 (https://github.com/PDB-REDO/dssp) has been
enabled in commit da57a1f6a1c3a884321c27b438a8329725e546a5.
This worked if CLIBD_MON env var points to some CCP4 related
compound library. In the example of dssp shipped with Debian
bullseye, that's not the case. The observation there:
It works if applied on a PDB file downloaded from RCSB with all bells
and whistles but it doesn't work if only the fix from the above commit
is applied. As OpenStructure implements all functionality from DSSP
(secondary structure and solvent accessibility), the binding to an
external program has been deprecated. dssp.AssignDSSP still exists,
but mimics the old behaviour using OpenStructure internal implementations.
---
CHANGELOG.txt | 5 +-
modules/bindings/doc/dssp.rst | 12 +++
modules/bindings/pymod/dssp.py | 155 ++++++++++++++++++++++-----------
3 files changed, 119 insertions(+), 53 deletions(-)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 5872b48ef..d555dbf51 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 3a51a870c..1a087bcfa 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 803ea1950..ee179c9a6 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,
--
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