192 lines
8.3 KiB
Python
192 lines
8.3 KiB
Python
"""Ligand pKa values"""
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import os
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import subprocess
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import sys
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import propka.molecular_container
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import propka.calculations
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import propka.parameters
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import propka.pdb
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import propka.lib
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from propka.lib import info, warning
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class LigandPkaValues:
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"""Ligand pKa value class."""
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def __init__(self, parameters):
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"""Initialize object with parameters.
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Args:
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parameters: parameters
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"""
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self.parameters = parameters
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# attempt to find Marvin executables in the path
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self.molconvert = self.find_in_path('molconvert')
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self.cxcalc = self.find_in_path('cxcalc')
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info('Found Marvin executables:')
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info(self.cxcalc)
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info(self.molconvert)
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@staticmethod
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def find_in_path(program):
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"""Find a program in the system path.
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Args:
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program: program to find
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Returns:
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location of program
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"""
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path = os.environ.get('PATH').split(os.pathsep)
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locs = [i for i in filter(lambda loc: os.access(loc, os.F_OK), \
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map(lambda dir: os.path.join(dir, program), path))]
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if len(locs) == 0:
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str_ = "'Error: Could not find %s." % program
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str_ += ' Please make sure that it is found in the path.'
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info(str_)
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sys.exit(-1)
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return locs[0]
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def get_marvin_pkas_for_pdb_file(self, pdbfile, num_pkas=10, min_ph=-10, max_ph=20):
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"""Use Marvin executables to get pKas for a PDB file.
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Args:
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pdbfile: PDB file
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num_pkas: number of pKas to get
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min_ph: minimum pH value
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max_ph: maximum pH value
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"""
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molecule = propka.molecular_container.Molecular_container(pdbfile)
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self.get_marvin_pkas_for_molecular_container(molecule,
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num_pkas=num_pkas,
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min_ph=min_ph,
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max_ph=max_ph)
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def get_marvin_pkas_for_molecular_container(self, molecule, num_pkas=10, min_ph=-10, max_ph=20):
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"""Use Marvin executables to calculate pKas for a molecular container.
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Args:
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molecule: molecular container
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num_pkas: number of pKas to calculate
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min_ph: minimum pH value
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max_ph: maximum pH value
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"""
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for name in molecule.conformation_names:
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filename = '%s_%s' % (molecule.name, name)
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self.get_marvin_pkas_for_conformation_container(molecule.conformations[name],
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name=filename,
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reuse=molecule.\
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options.reuse_ligand_mol2_file,
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num_pkas=num_pkas,
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min_ph=min_ph,
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max_ph=max_ph)
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def get_marvin_pkas_for_conformation_container(self, conformation,
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name='temp', reuse=False,
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num_pkas=10, min_ph=-10,
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max_ph=20):
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"""Use Marvin executables to calculate pKas for a conformation container.
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Args:
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conformation: conformation container
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name: filename
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reuse: flag to reuse the structure files
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num_pkas: number of pKas to calculate
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min_ph: minimum pH value
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max_ph: maximum pH value
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"""
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conformation.marvin_pkas_calculated = True
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self.get_marvin_pkas_for_atoms(conformation.get_heavy_ligand_atoms(),
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name=name, reuse=reuse,
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num_pkas=num_pkas, min_ph=min_ph,
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max_ph=max_ph)
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def get_marvin_pkas_for_atoms(self, atoms, name='temp', reuse=False,
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num_pkas=10, min_ph=-10, max_ph=20):
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"""Use Marvin executables to calculate pKas for a list of atoms.
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Args:
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atoms: list of atoms
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name: filename
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reuse: flag to reuse the structure files
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num_pkas: number of pKas to calculate
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min_ph: minimum pH value
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max_ph: maximum pH value
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"""
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# do one molecule at the time so we don't confuse marvin
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molecules = propka.lib.split_atoms_into_molecules(atoms)
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for i, molecule in enumerate(molecules):
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filename = '%s_%d.mol2'%(name, i+1)
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self.get_marvin_pkas_for_molecule(molecule, filename=filename,
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reuse=reuse, num_pkas=num_pkas,
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min_ph=min_ph, max_ph=max_ph)
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def get_marvin_pkas_for_molecule(self, atoms, filename='__tmp_ligand.mol2',
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reuse=False, num_pkas=10, min_ph=-10,
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max_ph=20):
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"""Use Marvin executables to calculate pKas for a molecule.
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Args:
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molecule: the molecule
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name: filename
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reuse: flag to reuse the structure files
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num_pkas: number of pKas to calculate
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min_ph: minimum pH value
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max_ph: maximum pH value
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"""
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# print out structure unless we are using user-modified structure
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if not reuse:
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propka.pdb.write_mol2_for_atoms(atoms, filename)
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# check that we actually have a file to work with
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if not os.path.isfile(filename):
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errstr = "Didn't find a user-modified file '%s' - generating one" \
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% filename
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warning(errstr)
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propka.pdb.write_mol2_for_atoms(atoms, filename)
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# Marvin calculate pKa values
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options = 'pka -a %d -b %d --min %f --max %f -d large' % (num_pkas,
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num_pkas,
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min_ph,
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max_ph)
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(output, errors) = subprocess.Popen([self.cxcalc, filename]+options.split(),
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE).communicate()
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if len(errors) > 0:
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info('********************************************************************************************************')
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info('* Warning: Marvin execution failed: *')
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info('* %-100s *' % errors)
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info('* *')
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info('* Please edit the ligand mol2 file and re-run PropKa with the -l option: %29s *' % filename)
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info('********************************************************************************************************')
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sys.exit(-1)
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# extract calculated pkas
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indices, pkas, types = self.extract_pkas(output)
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# store calculated pka values
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for i, index in enumerate(indices):
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atoms[index].marvin_pka = pkas[i]
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atoms[index].charge = {'a': -1, 'b': 1}[types[i]]
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info('%s model pKa: %.2f' % (atoms[index], pkas[i]))
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@staticmethod
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def extract_pkas(output):
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"""Extract pKa value from output.
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Args:
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output: output string to parse
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Returns:
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1. Indices
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2. Values
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3. Types
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"""
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# split output
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[tags, values, _] = output.decode().split('\n')
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tags = tags.split('\t')
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values = values.split('\t')
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# format values
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types = [tags[i][0] for i in range(1, len(tags)-1) if len(values) > i \
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and values[i] != '']
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indices = [int(a)-1 for a in values[-1].split(',') if a != '']
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values = [float(v.replace(',', '.')) for v in values[1:-1] if v != '']
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if len(indices) != len(values) != len(types):
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raise Exception('Lengths of atoms and pka values mismatch')
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return indices, values, types
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