# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk) # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. # NACCESS interface adapted from Bio/PDB/DSSP.py from __future__ import print_function import os import tempfile import shutil import subprocess from Bio.PDB.PDBIO import PDBIO from Bio.PDB.AbstractPropertyMap import AbstractResiduePropertyMap, AbstractAtomPropertyMap """Interface for the program NACCESS. See: http://wolf.bms.umist.ac.uk/naccess/ errors likely to occur with the binary: default values are often due to low default settings in accall.pars - e.g. max cubes error: change in accall.pars and recompile binary use naccess -y, naccess -h or naccess -w to include HETATM records """ def run_naccess(model, pdb_file, probe_size=None, z_slice=None, naccess='naccess', temp_path='/tmp/'): # make temp directory; tmp_path = tempfile.mkdtemp(dir=temp_path) # file name must end with '.pdb' to work with NACCESS # -> create temp file of existing pdb # or write model to temp file handle, tmp_pdb_file = tempfile.mkstemp('.pdb', dir=tmp_path) os.close(handle) if pdb_file: pdb_file = os.path.abspath(pdb_file) shutil.copy(pdb_file, tmp_pdb_file) else: writer = PDBIO() writer.set_structure(model.get_parent()) writer.save(tmp_pdb_file) # chdir to temp directory, as NACCESS writes to current working directory old_dir = os.getcwd() os.chdir(tmp_path) # create the command line and run # catch standard out & err command = [naccess, tmp_pdb_file] if probe_size: command.extend(['-p', probe_size]) if z_slice: command.extend(['-z', z_slice]) p = subprocess.Popen(command, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = p.communicate() os.chdir(old_dir) # get the output, then delete the temp directory rsa_file = tmp_pdb_file[:-4] + '.rsa' with open(rsa_file) as rf: rsa_data = rf.readlines() asa_file = tmp_pdb_file[:-4] + '.asa' with open(asa_file) as af: asa_data = af.readlines() shutil.rmtree(tmp_path, ignore_errors=True) return rsa_data, asa_data def process_rsa_data(rsa_data): # process the .rsa output file: residue level SASA data naccess_rel_dict = {} for line in rsa_data: if line.startswith('RES'): res_name = line[4:7] chain_id = line[8] resseq = int(line[9:13]) icode = line[13] res_id = (' ', resseq, icode) naccess_rel_dict[(chain_id, res_id)] = { 'res_name': res_name, 'all_atoms_abs': float(line[16:22]), 'all_atoms_rel': float(line[23:28]), 'side_chain_abs': float(line[29:35]), 'side_chain_rel': float(line[36:41]), 'main_chain_abs': float(line[42:48]), 'main_chain_rel': float(line[49:54]), 'non_polar_abs': float(line[55:61]), 'non_polar_rel': float(line[62:67]), 'all_polar_abs': float(line[68:74]), 'all_polar_rel': float(line[75:80])} return naccess_rel_dict def process_asa_data(rsa_data): # process the .asa output file: atomic level SASA data naccess_atom_dict = {} for line in rsa_data: atom_serial = line[6:11] full_atom_id = line[12:16] atom_id = full_atom_id.strip() altloc = line[16] resname = line[17:20] chainid = line[21] resseq = int(line[22:26]) icode = line[26] res_id = (' ', resseq, icode) id = (chainid, res_id, atom_id) asa = line[54:62] # solvent accessibility in Angstrom^2 vdw = line[62:68] # van der waal radius naccess_atom_dict[id] = asa return naccess_atom_dict class NACCESS(AbstractResiduePropertyMap): def __init__(self, model, pdb_file=None, naccess_binary='naccess', tmp_directory='/tmp'): res_data, atm_data = run_naccess(model, pdb_file, naccess=naccess_binary, temp_path=tmp_directory) naccess_dict = process_rsa_data(res_data) res_list = [] property_dict = {} property_keys = [] property_list = [] # Now create a dictionary that maps Residue objects to accessibility for chain in model: chain_id = chain.get_id() for res in chain: res_id = res.get_id() if (chain_id, res_id) in naccess_dict: item = naccess_dict[(chain_id, res_id)] res_name = item['res_name'] assert (res_name == res.get_resname()) property_dict[(chain_id, res_id)] = item property_keys.append((chain_id, res_id)) property_list.append((res, item)) res.xtra["EXP_NACCESS"] = item else: pass AbstractResiduePropertyMap.__init__(self, property_dict, property_keys, property_list) class NACCESS_atomic(AbstractAtomPropertyMap): def __init__(self, model, pdb_file=None, naccess_binary='naccess', tmp_directory='/tmp'): res_data, atm_data = run_naccess(model, pdb_file, naccess=naccess_binary, temp_path=tmp_directory) self.naccess_atom_dict = process_asa_data(atm_data) property_dict = {} property_keys = [] property_list = [] # Now create a dictionary that maps Atom objects to accessibility for chain in model: chain_id = chain.get_id() for residue in chain: res_id = residue.get_id() for atom in residue: atom_id = atom.get_id() full_id = (chain_id, res_id, atom_id) if full_id in self.naccess_atom_dict: asa = self.naccess_atom_dict[full_id] property_dict[full_id] = asa property_keys.append((full_id)) property_list.append((atom, asa)) atom.xtra['EXP_NACCESS'] = asa AbstractAtomPropertyMap.__init__(self, property_dict, property_keys, property_list) if __name__ == "__main__": import sys from Bio.PDB import PDBParser p = PDBParser() s = p.get_structure('X', sys.argv[1]) model = s[0] n = NACCESS(model, sys.argv[1]) for e in n: print(e)