diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
new file mode 100644
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+++ b/modules/bindings/pymod/naccess.py
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+'''
+Naccess module
+
+Author: Florian Kiefer
+
+This module is for calculating surface areas
+from OpenStructure using the external program naccess
+
+How To Use This Module:
+ 1. Import it (e.g. as "from ost.bindings import naccess")
+ 2. Use it (e.g. as "sasa = naccess.CalculateSurfaceArea(entity)")
+
+Requirement:
+ - naccess installed
+'''
+
+import tempfile
+import subprocess
+import os
+import re
+from ost import io
+from ost import mol
+from ost import settings
+from ost import geom
+
+## \brief Method to check if naccess executable is present
+#
+# \param naccess Explicit path to msms executable
+# \return Path to the executable
+# \exception FileNotFound if executable is not found
+def _GetExecutable(naccess_exe):
+ return settings.Locate('naccess', explicit_file_name=naccess_exe)
+
+## \brief Setup files for naccess calculation in temporary directory
+#
+# \param entity EntityHandle or EntityView to calculate surface
+# \param selection Calculate surface for subset of entity
+# \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):
+ # create temporary directory
+ 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 not entity_view.IsValid():
+ raise RuntimeError, "Could not create view for selection (%s)"%(selection)
+
+ # write entity to tmp file
+ tmp_file_name=os.path.join(tmp_dir_name,"entity.pdb")
+ tmp_file_base = os.path.join(tmp_dir_name,"entity")
+ io.SavePDB(entity_view, tmp_file_name)
+ return (tmp_dir_name, tmp_file_name, tmp_file_base)
+
+## \brief Reads Area file (.asa) and attach asa per atom to an entitiy
+#
+# \param entity EntityHandle or EntityView for attaching sasa on atom level
+# \param file Filename of area file
+# \param asa_atom Name of the float property for SASA
+
+
+def _ParseAsaFile(entity, file, asa_atom):
+
+ asa_fh = open(file)
+ asa_lines = asa_fh.readlines()
+ asa_fh.close()
+
+ for l in asa_lines:
+ if l.startswith("ATOM"):
+ # get res_number, chain_id and atom name
+ atom_name = l[12:16]
+ chain_id = l[21]
+ res_number = l[22:27]
+ asa = l[54:63]
+ atom_name = atom_name.strip()
+ chain_id = chain_id.strip()
+ res_number = res_number.strip()
+ asa = asa.strip()
+ #print "res_number:", res_number
+ m=re.match(r'(?P<num>-?\d+)(?P<ins>\w)?', res_number)
+ di = m.groupdict()
+
+ if di["ins"] == None:
+ resNum = mol.ResNum(int(di["num"]))
+ else:
+ resNum = mol.ResNum(int(di["num"]), di["ins"])
+ #print res_number, resNum.num, resNum.ins
+ a = entity.FindAtom(chain_id, resNum, atom_name)
+ a.SetFloatProp(asa_atom, float(asa))
+
+## \brief Reads Area file (.rsa) and attach asa (absolute + relative) per residue to an entitiy
+#
+# \param entity EntityHandle or EntityView for attaching sasa on atom level
+# \param file Filename of .rsa file
+# \param asa_atom Name of the float property for absolute SASA
+# \param asa_atom Name of the float property for relative SASA
+# \exception RuntimeError if residue names are not the same
+
+def _ParseRsaFile(enti,file, asa_abs, asa_rel):
+ area_fh = open(file)
+ area_lines = area_fh.readlines()
+ area_fh.close()
+ # shift first line
+ area_lines = area_lines[4:]
+
+
+ for l in area_lines:
+ if l.startswith("RES"):
+ p = re.compile(r'\s+')
+ t = p.split(l)
+ #res_name, chain_id , res_number, abs_all, rel_all = t[1:6]
+ res_name = l[3:8]
+ res_name = res_name.strip()
+ chain_id = l[8:9]
+ res_number = l[9:14]
+ res_number= res_number.strip()
+ #print l[15:30]
+ abs_all, rel_all =l[15:28].strip().split()
+ m=re.match(r'(?P<num>-?\d+)(?P<ins>\w)?', res_number)
+ di = m.groupdict()
+ if di["ins"] == None:
+ resNum = mol.ResNum(int(di["num"]))
+ else:
+ resNum = mol.ResNum(int(di["num"]), di["ins"])
+
+ res = enti.handle.FindResidue(chain_id, resNum)
+ #res = entity.FindResidue(chain_id, mol.ResNum(int(res_number)))
+ #print res_name, chain_id, res_number
+ if res_name == res.name:
+ res.SetFloatProp(asa_rel, float(rel_all) )
+ res.SetFloatProp(asa_abs, float(abs_all) )
+ else:
+ raise RuntimeError, "Residue Names are not the same for ResNumb: %s (%s vs %s)" % (res_number, res.name, res_name)
+
+## \brief Method which recursively deletes a directory
+#
+# \warning This method removes also non-empty directories without asking, so
+# be careful!
+def __CleanupFiles(dir_name):
+ import shutil
+ shutil.rmtree(dir_name)
+
+## \brief Method to run the MSMS surface calculation
+#
+# This method starts the external MSMS executable and returns the stdout of MSMS
+#
+# \param command Command to execute
+# \return stdout of MSMS
+# \exception CalledProcessError for non-zero return value
+def _RunNACCESS(command, 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
+ if proc.returncode!=0:
+ print "WARNING: naccess error\n", stdout_value
+ raise subprocess.CalledProcessError(proc.returncode, command)
+
+ return stdout_value
+
+
+## \brief Calculates analytical the solvent accessible surface
+# area by using the external naccess program
+#
+# This method calculates the molecular surface areas by invoking the external
+# program naccess. First, it is checked if the naccess executable is present, then,
+# the necessary files are prepared in a temporary directory and naccess is
+# executed. The last step is to remove the temporary directory.
+#
+#
+# \param entity OST entity to calculate surface
+# \param radius Surface probe radius
+# \param include_hydrogens Calculate surface including hydrogens
+# \param include_hetatm Calculate surface including hetatms
+# \param include_water Calculate surface including water
+# \param selection Calculate surface for subset of entity
+# \param naccess _exe msms 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
+# \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"):
+ import re
+
+ # check if msms 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)
+
+ # set command line
+ 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)
+
+ 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:
+ 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
+