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 
# \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, scratch_dir, max_number_of_atoms):
  # create temporary directory
  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) > 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)
  
  # 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
      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)
      if(a.IsValid()):
        a.SetFloatProp(asa_atom, float(asa))
      else:
        print chain_id, resNum, atom_name
      
## \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
# \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", scratch_dir = None, max_number_of_atoms=50000):
  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, scratch_dir)

  # 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