diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index 268b72ac141152bcbdb60be58be6dfb021b880b2..fc98f23f03104f2f8b47dd0c741c2862a3b37b32 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -1,7 +1,7 @@
'''
Naccess module
-Author: Florian Kiefer
+Author: Florian Kiefer, Gerardo Tauriello (cleanup/speedup)
This module is for calculating surface areas
from OpenStructure using the external program naccess
@@ -18,16 +18,13 @@ import tempfile
import subprocess
import os
import re
-from ost import io
-from ost import mol
-from ost import settings
-from ost import geom
+from ost import io, mol, settings, LogWarning
def _GetExecutable(naccess_exe):
"""
Method to check if naccess executable is present
- :param naccess: Explicit path to msms executable
+ :param naccess: Explicit path to naccess executable
:returns: Path to the executable
:exception: FileNotFound if executable is not found
"""
@@ -46,14 +43,14 @@ def _SetupFiles(entity, selection, scratch_dir, max_number_of_atoms):
"""
# create temporary directory
- tmp_dir_name=""
- if scratch_dir!=None:
- tmp_dir_name=tempfile.mkdtemp(dir=scratch_dir)
+ tmp_dir_name = ""
+ if scratch_dir != None:
+ tmp_dir_name = tempfile.mkdtemp(dir=scratch_dir)
else:
- tmp_dir_name=tempfile.mkdtemp()
+ tmp_dir_name = tempfile.mkdtemp()
- # select only heavy atoms if no_hydrogens is true
- entity_view=entity.Select(selection)
+ # select as specified by user
+ entity_view = entity.Select(selection)
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():
@@ -61,7 +58,7 @@ def _SetupFiles(entity, selection, scratch_dir, max_number_of_atoms):
# write entity to tmp file
tmp_file_name = "entity.pdb"
- tmp_file_base = os.path.join(tmp_dir_name,"entity")
+ tmp_file_base = os.path.join(tmp_dir_name, "entity")
io.SavePDB(entity_view, os.path.join(tmp_dir_name, tmp_file_name))
return (tmp_dir_name, tmp_file_name, tmp_file_base)
@@ -171,10 +168,11 @@ def _RunNACCESS(command, temp_dir):
:returns: stdout of MSMS
:exception: CalledProcessError for non-zero return value
"""
- proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, cwd = temp_dir)
+ proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
+ cwd=temp_dir)
stdout_value, stderr_value = proc.communicate()
- #check for successful completion of msms
+ # check for successful completion of naccess
if proc.returncode!=0:
print "WARNING: naccess error\n", stdout_value
raise subprocess.CalledProcessError(proc.returncode, command)
@@ -184,8 +182,10 @@ def _RunNACCESS(command, temp_dir):
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", scratch_dir = None, max_number_of_atoms=50000):
+ include_water=False, selection="", naccess_exe=None,
+ keep_files=False, asa_abs= "asaAbs", asa_rel="asaRel",
+ asa_atom="asaAtom", scratch_dir=None,
+ max_number_of_atoms=50000):
"""
Calculates analytical the solvent accessible surface area by using the
external naccess program
@@ -203,56 +203,55 @@ def CalculateSurfaceArea(entity, radius=1.4,
:param include_water: Calculate surface including water
:param selection: Calculate surface for subset of entity
:param naccess_exe: naccess executable (full path to executable)
- :param keep_files: Do not delete temporary files
- :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)
+ :param keep_files: If True, do not delete temporary files
+ :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: Scratch directory. A subfolder for temporary files
+ is created in there. If not specified, a default
+ directory is used (see :func:`tempfile.mkdtemp`).
+ :param max_number_of_atoms: Max Number of atoms in the entity (i.e. is limited
+ in the default NACCESS version to 50 000)
:returns: absolute SASA calculated using asa_atom
"""
-
- import re
- # check if msms executable is specified
+ # check if naccess executable is specified
naccess_executable=_GetExecutable(naccess_exe)
- # parse selection
- # setup files for msms
- (naccess_data_dir, naccess_data_file,naccess_data_base )=_SetupFiles(entity, selection, scratch_dir, max_number_of_atoms)
+ # setup files for naccess
+ (naccess_data_dir, naccess_data_file, naccess_data_base) \
+ = _SetupFiles(entity, selection, scratch_dir, max_number_of_atoms)
# set command line
- command="%s %s -p %f " % \
- (naccess_executable, naccess_data_file, radius)
+ command = "%s %s -p %f " % \
+ (naccess_executable, naccess_data_file, radius)
if include_hydrogens:
command = "%s -w" % command
if include_water:
command = "%s -y" % command
if include_hetatm:
command = "%s -h" % command
- #print command
- stdout_value=_RunNACCESS(command, naccess_data_dir)
+ # execute naccess
+ stdout_value = _RunNACCESS(command, naccess_data_dir)
+ # parse outout
new_asa= os.path.join(naccess_data_dir, "%s.asa" % naccess_data_base)
_ParseAsaFile(entity, new_asa, asa_atom)
new_rsa = os.path.join(naccess_data_dir, "%s.rsa" % naccess_data_base)
_ParseRsaFile(entity, new_rsa, asa_abs, asa_rel)
- # Calculate Asa for all atoms:
+ # sum up Asa for all atoms
sasa = 0.0
for a in entity.atoms:
sasa += a.GetFloatProp(asa_atom, 0.0)
-
- # first read in result_file
-
- # parse MSMS output
-
# clean up
if not keep_files:
__CleanupFiles(naccess_data_dir)
return sasa
-