From da57a1f6a1c3a884321c27b438a8329725e546a5 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 5 Jan 2021 23:30:52 +0100
Subject: [PATCH] Fallback if dssp binding is used with dssp 4
(https://github.com/PDB-REDO/dssp)
---
modules/bindings/pymod/dssp.py | 104 +++++++++++++++++----------------
1 file changed, 55 insertions(+), 49 deletions(-)
diff --git a/modules/bindings/pymod/dssp.py b/modules/bindings/pymod/dssp.py
index d52b49412..5eb5e294d 100644
--- a/modules/bindings/pymod/dssp.py
+++ b/modules/bindings/pymod/dssp.py
@@ -38,27 +38,11 @@ def _SkipHeader(stream):
line=stream.readline()
return False
-def _Cleanup(pdb_path, temp_path, entity_saved):
- if entity_saved and os.path.exists(pdb_path):
+def _Cleanup(temp_dssp_path, pdb_path):
+ if os.path.exists(temp_dssp_path):
+ os.remove(temp_dssp_path)
+ if os.path.exists(pdb_path):
os.remove(pdb_path)
- if os.path.exists(temp_path):
- os.remove(temp_path)
-
-def _ExecuteDSSP(path, dssp_bin, temp_dir=None):
- # use of mktemp is a safty problem (use mkstemp and provide file handle to
- # subsequent process
- temp_dssp_path=tempfile.mktemp(suffix=".out",prefix="dssp", dir=temp_dir)
- 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)
-
- subprocess.run([dssp_abs_path, path, temp_dssp_path])
-
- return temp_dssp_path
-
def _CalcRelativeSA(residue_type, absolute_sa):
solvent_max_list=[118,317,238,243,183,262,286,154,258,228,
@@ -98,36 +82,58 @@ def AssignDSSP(ent, pdb_path="", extract_burial_status=False, tmp_dir=None,
in the path.
:raises: :class:`RuntimeError` when dssp is executed with errors
"""
- entity_saved = False
- # use of mktemp is a safty problem (use mkstemp and provide file handle to
- # subsequent process
- pdb_path=tempfile.mktemp(suffix=".pdb",prefix="temp_entity",
- dir=tmp_dir)
- io.SavePDB(ent, pdb_path)
- entity_saved = True
-
- #TODO: exception handling (currently errors occuring here
- # are handled in the parser LoadDSSP)
- temp_dssp_path=_ExecuteDSSP(pdb_path, dssp_bin)
- if not os.path.exists(temp_dssp_path):
- _Cleanup(pdb_path, temp_dssp_path, entity_saved)
- raise RuntimeError('DSSP output file does not exist.')
- # assign DSSP to entity
- try:
- LoadDSSP(temp_dssp_path, ent, extract_burial_status,
- entity_saved)
- except Exception as e:
- # clean up
- print("Exception in DSSP:", e)
- _Cleanup(pdb_path, temp_dssp_path, entity_saved)
- raise RuntimeError(e)
-
- # clean up
- #print pdb_path, temp_dssp_path
- _Cleanup(pdb_path, temp_dssp_path, entity_saved)
-
- return ent
+ 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, capture_output=True)
+ 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, capture_output=True)
+
+ 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 LoadDSSP(file_name, model, extract_burial_status=False,
--
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