From 3c38ce98b798db12bc7a2adad5ccf72b30b1deaf Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Wed, 18 May 2011 19:25:04 +0200
Subject: [PATCH] Allow to pass dssp binary path to AssignDSSP; alternative
binary name for dssp used on Locate
While we are in there, also fix BZDNG-235 by checking that
DSSP is executable and not a directory and making sure the
output file exists before continuing.
Conflicts:
modules/bindings/pymod/dssp.py
---
modules/bindings/pymod/dssp.py | 42 +++++++++++++++++++++++++++-------
1 file changed, 34 insertions(+), 8 deletions(-)
diff --git a/modules/bindings/pymod/dssp.py b/modules/bindings/pymod/dssp.py
index 234ba7406..05236eadc 100644
--- a/modules/bindings/pymod/dssp.py
+++ b/modules/bindings/pymod/dssp.py
@@ -39,13 +39,19 @@ def _SkipHeader(stream):
return False
-def _ExecuteDSSP(path, temp_dir=None):
+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('dssp', env_name='DSSP_EXECUTABLE')
- command=dssp_abs_path+" "+path+" "+temp_dssp_path
- ps=subprocess.Popen(command, shell=True, stderr=subprocess.PIPE)
+ dssp_abs_path=settings.Locate(['dsspcmbi','dssp'], 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)
+
+ ps=subprocess.Popen([dssp_abs_path, path, temp_dssp_path],
+ stderr=subprocess.PIPE)
err_lines=ps.stderr.readlines()
return temp_dssp_path
@@ -64,8 +70,27 @@ def _CalcRelativeSA(residue_type, absolute_sa):
return rel
-def AssignDSSP(ent, pdb_path="", extract_burial_status_flag=0, tmp_dir=None):
- entity_saved_flag = 0
+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
+ :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
+ """
+ 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",
@@ -75,8 +100,9 @@ def AssignDSSP(ent, pdb_path="", extract_burial_status_flag=0, tmp_dir=None):
#TODO: exception handling (currently errors occuring here
# are handled in the parser LoadDSSP)
- temp_dssp_path=_ExecuteDSSP(pdb_path)
-
+ temp_dssp_path=_ExecuteDSSP(pdb_path, dssp_bin)
+ if not os.path.exists(temp_dssp_path):
+ raise RuntimeEror('DSSP output file does not exist.')
# assign DSSP to entity
try:
LoadDSSP(temp_dssp_path, ent, extract_burial_status_flag,
--
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