From 1e817071b9155bd98a0137a8a5e68a0658bc3b4e Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@stud.unibas.ch>
Date: Fri, 20 Sep 2013 14:42:57 +0200
Subject: [PATCH] Map ASA/ESA onto atoms
Allows to map the asa and esa values calculated by msms onto
the atoms with generic properties using the CalculateSurface
function.
---
modules/bindings/pymod/msms.py | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index 60009f607..534cd3d8e 100644
--- a/modules/bindings/pymod/msms.py
+++ b/modules/bindings/pymod/msms.py
@@ -332,7 +332,8 @@ def CalculateSurfaceVolume(entity, density=1.0, radius=1.5, all_surf=False,
def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
no_hydrogens=False, no_hetatoms=False, no_waters=False,
selection='',
- msms_exe=None, msms_env=None, keep_files=False):
+ msms_exe=None, msms_env=None, keep_files=False,
+ attach_asa=None, attach_esa=None):
"""
Calculates molecular surface by using the external MSMS program
@@ -353,6 +354,8 @@ def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
:param msms_exe: msms executable (full path to executable)
:param msms_env: msms environment variable
:param keep_files: Do not delete temporary files
+ :param attach_asa: Attaches per atom SASA to specified FloatProp at atom level
+ :param attach_esa: Attaches per atom SESA to specified FloatProp at atom level
:returns: list of :class:`~ost.mol.SurfaceHandle` objects
"""
import os
@@ -385,10 +388,17 @@ def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
msms_data_file, msms_data_file, density, radius)
if all_surf:
command+=" -all"
+ if attach_asa != None or attach_esa != 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 or attach_esa != None:
+ _ParseAreaFile(entity, selection, os.path.join(msms_data_dir, "asa_atom.area"),
+ attach_asa, attach_esa)
+
# parse msms output
num_surf=0
for line in stdout_value.splitlines():
--
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