From 569a55824526841c2492b959cedc9736c119b103 Mon Sep 17 00:00:00 2001
From: kieferf <kieferf@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Wed, 24 Mar 2010 14:18:36 +0000
Subject: [PATCH] Add attach_asa parameter to the CalculateSurfaceArea method,
attach_asa specifies the name of the FloatProperty which the asa is attached
(on atom level)
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1879 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/bindings/pymod/msms.py | 36 +++++++++++++++++++++++++++++-----
1 file changed, 31 insertions(+), 5 deletions(-)
diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index bd9f5a8f1..9ae73f78a 100644
--- a/modules/bindings/pymod/msms.py
+++ b/modules/bindings/pymod/msms.py
@@ -59,7 +59,27 @@ def _SetupFiles(entity, selection):
tmp_file_handle.close()
return (tmp_dir_name, tmp_file_name)
-
+## \brief Reads Area file (-af) and attach sasa and sesa per atom to an entitiy
+#
+# \param entity EntityHandle or EntityView for attaching sasa and sesa on atom level
+# \param file Filename of area file
+# \param property Name of the float property
+# \exception RuntimeError if number of atoms in file != number of atoms in entity
+
+def _ParseAreaFile(entity,file, property):
+ area_fh = open(file)
+ area_lines = area_fh.readlines()
+ area_fh.close()
+ # shift first line
+ area_lines = area_lines[1:]
+ if entity.GetAtomCount() != len(area_lines):
+ raise RuntimeError, "Atom count (%d) unequeal to number of atoms in area file (%d)" % (entity.GetAtomCount(), len(area_lines))
+ for l in area_lines:
+ atom_no, sesa, sasa = l.split()
+ a = entity.atoms[int(atom_no)]
+ a.SetGenericFloatProperty(property, float(sasa))
+
+
## \brief Method which recursively deletes a directory
#
# \warning This method removes also non-empty directories without asking, so
@@ -109,7 +129,8 @@ def _RunMSMS(command):
# \return Touplet of lists for (SES, SAS)
def CalculateSurfaceArea(entity, density=1.0, radius=1.5, all_surf=False,
no_hydrogens=False, selection="",
- msms_exe=None, msms_env=None, keep_files=False):
+ msms_exe=None, msms_env=None, keep_files=False,
+ attach_asa = None):
import re
# check if msms executable is specified
@@ -127,10 +148,15 @@ def CalculateSurfaceArea(entity, density=1.0, radius=1.5, all_surf=False,
(msms_executable, msms_data_file, msms_data_file, density, radius)
if all_surf:
command+=" -all"
-
+ if attach_asa != None:
+ command+=" -af %s" % os.path.join(msms_data_dir, "asa_atom")
# run msms
stdout_value=_RunMSMS(command)
-
+
+ # add sesa and asa to entity if attach_asa is specified
+ if attach_asa != None:
+ _ParseAreaFile(entity, os.path.join(msms_data_dir, "asa_atom.area"), attach_asa)
+
# parse MSMS output
msms_ases=[]
msms_asas=[]
@@ -185,7 +211,7 @@ def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
selection+=" and ele!=H"
# setup files for msms
- print selection
+
(msms_data_dir, msms_data_file)=_SetupFiles(entity, selection)
# set command line
--
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