From d1052ecfb93fd67f477c05fc2160111c67009295 Mon Sep 17 00:00:00 2001
From: Florian Kiefer <florian.kiefer@unibas.ch>
Date: Tue, 10 Jul 2012 09:44:20 +0200
Subject: [PATCH] workaround for naccess
naccess does not like dots in path names. Some temporary directories
contain dots, which causes naccess to fail. We now provide a scratch_dir
option, which allows to specify a temporary directory.
Also, allow to set the maximal number of atoms supported by naccess.
---
modules/bindings/pymod/naccess.py | 21 +++++++++++++++------
1 file changed, 15 insertions(+), 6 deletions(-)
diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index afb58c4ba..f9f2e5703 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -35,16 +35,22 @@ def _GetExecutable(naccess_exe):
#
# \param entity EntityHandle or EntityView to calculate surface
# \param selection Calculate surface for subset of entity
+# \param scratch_dir Directory for temporary files (NACCESS is sensitive to "." in directory names
+# \param max_number_of_atoms Max Number of atoms in the entity (i.e. is limited in the default NACCESS version to 50 000)
# \return array containing temporary directory, input filename for naccess and directory of the input file
# \exception RuntimeError if selection is not valid
-def _SetupFiles(entity, selection):
+def _SetupFiles(entity, selection, scratch_dir, max_number_of_atoms):
# create temporary directory
- tmp_dir_name=tempfile.mkdtemp()
+ tmp_dir_name=""
+ if scratch_dir!=None:
+ tmp_dir_name=tempfile.mkdtemp(dir=scratch_dir)
+ else:
+ tmp_dir_name=tempfile.mkdtemp()
# select only heavy atoms if no_hydrogens is true
entity_view=entity.Select(selection)
- if len(entity_view.atoms) > 50000:
- raise RuntimeError, "Too much atoms for NACCESS (> 50 000)"
+ if len(entity_view.atoms) > max_number_of_atoms:
+ raise RuntimeError, "Too much atoms for NACCESS (> %s)" % max_number_of_atoms
if not entity_view.IsValid():
raise RuntimeError, "Could not create view for selection (%s)"%(selection)
@@ -184,11 +190,14 @@ def _RunNACCESS(command, temp_dir):
# \param asa_abs Attaches per residue absolute SASA to specified FloatProp on residue level
# \param asa_rel Attaches per residue relative SASA to specified FloatProp on residue level
# \param asa_atom Attaches per atom SASA to specified FloatProp at atom level
+# \param scratch_dir Directory for temporary files (NACCESS is sensitive to "." in directory names
+# \param max_number_of_atoms Max Number of atoms in the entity (i.e. is limited in the default NACCESS version to 50 000)
+
# \return absolute SASA calculated using asa_atom
def CalculateSurfaceArea(entity, radius=1.4,
include_hydrogens=False, include_hetatm = False,
include_water = False, selection="",
- naccess_exe=None, keep_files=False , asa_abs= "asaAbs", asa_rel="asaRel", asa_atom="asaAtom"):
+ naccess_exe=None, keep_files=False , asa_abs= "asaAbs", asa_rel="asaRel", asa_atom="asaAtom", scratch_dir = None, max_number_of_atoms=50000):
import re
# check if msms executable is specified
@@ -196,7 +205,7 @@ def CalculateSurfaceArea(entity, radius=1.4,
# parse selection
# setup files for msms
- (naccess_data_dir, naccess_data_file,naccess_data_base )=_SetupFiles(entity, selection)
+ (naccess_data_dir, naccess_data_file,naccess_data_base )=_SetupFiles(entity, selection, scratch_dir)
# set command line
command="%s %s -p %f " % \
--
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