b928c18bab
* 'python setup.py install' will install
- a package 'propka' (which contains everything that 'Source' contained
in the original distribution)
- an executable script 'propka31' (which is identical to the original
'propka.py' script but it is automatically generated via the setuptools
mechanism; it uses propka.run.main().
* 'pip install' will also work
* the README.md file was changed to reflect the alterations
* metadata in the setup.py file was added
NOTE: The licence is still unclear!
122 lines
5.2 KiB
Python
122 lines
5.2 KiB
Python
#!/usr/bin/env python
|
|
|
|
from __future__ import division
|
|
from __future__ import print_function
|
|
|
|
import propka.molecular_container, propka.calculations, propka.calculations, propka.parameters, propka.pdb, propka.lib, os, subprocess, sys
|
|
|
|
class ligand_pka_values:
|
|
def __init__(self, parameters):
|
|
self.parameters = parameters
|
|
|
|
# attempt to find Marvin executables in the path
|
|
self.molconvert = self.find_in_path('molconvert')
|
|
self.cxcalc = self.find_in_path('cxcalc')
|
|
print('Found Marvin executables:')
|
|
print(self.cxcalc)
|
|
print(self.molconvert)
|
|
|
|
return
|
|
|
|
|
|
def find_in_path(self, program):
|
|
path = os.environ.get('PATH').split(os.pathsep)
|
|
|
|
l = [i for i in filter(lambda loc: os.access(loc, os.F_OK),
|
|
map(lambda dir: os.path.join(dir, program),path))]
|
|
|
|
if len(l) == 0:
|
|
print('Error: Could not find %s. Please make sure that it is found in the path.'%program)
|
|
sys.exit(-1)
|
|
|
|
return l[0]
|
|
|
|
def get_marvin_pkas_for_pdb_file(self, file, no_pkas=10, min_pH =-10, max_pH=20):
|
|
molecule = propka.molecular_container.Molecular_container(file)
|
|
self.get_marvin_pkas_for_molecular_container(molecule, no_pkas=no_pkas, min_pH =min_pH, max_pH=max_pH)
|
|
return
|
|
|
|
def get_marvin_pkas_for_molecular_container(self, molecule, no_pkas=10, min_pH =-10, max_pH=20):
|
|
for name in molecule.conformation_names:
|
|
filename = '%s_%s'%(molecule.name,name)
|
|
self.get_marvin_pkas_for_conformation_container(molecule.conformations[name], name=filename, reuse=molecule.options.reuse_ligand_mol2_file,
|
|
no_pkas=no_pkas, min_pH =min_pH, max_pH=max_pH)
|
|
|
|
return
|
|
|
|
def get_marvin_pkas_for_conformation_container(self, conformation, name = 'temp', reuse=False, no_pkas=10, min_pH =-10, max_pH=20):
|
|
conformation.marvin_pkas_calculated = True
|
|
self.get_marvin_pkas_for_atoms(conformation.get_heavy_ligand_atoms(), name=name, reuse=reuse,
|
|
no_pkas=no_pkas, min_pH =min_pH, max_pH=max_pH)
|
|
|
|
return
|
|
|
|
def get_marvin_pkas_for_atoms(self, atoms, name='temp', reuse=False, no_pkas=10, min_pH =-10, max_pH=20):
|
|
# do one molecule at the time so we don't confuse marvin
|
|
molecules = propka.lib.split_atoms_into_molecules(atoms)
|
|
for i in range(len(molecules)):
|
|
filename = '%s_%d.mol2'%(name, i+1)
|
|
self.get_marvin_pkas_for_molecule(molecules[i], filename=filename, reuse=reuse, no_pkas=no_pkas, min_pH =min_pH, max_pH=max_pH)
|
|
|
|
return
|
|
|
|
|
|
def get_marvin_pkas_for_molecule(self, atoms, filename='__tmp_ligand.mol2', reuse=False, no_pkas=10, min_pH =-10, max_pH=20):
|
|
# print out structure unless we are using user-modified structure
|
|
if not reuse:
|
|
propka.pdb.write_mol2_for_atoms(atoms, filename)
|
|
# check that we actually have a file to work with
|
|
if not os.path.isfile(filename):
|
|
print('Warning: Didn\'t find a user-modified file \'%s\' - generating one'%filename)
|
|
propka.pdb.write_mol2_for_atoms(atoms, filename)
|
|
|
|
|
|
|
|
# Marvin
|
|
# calculate pKa values
|
|
options = 'pka -a %d -b %d --min %f --max %f -d large'%(no_pkas, no_pkas, min_pH, max_pH)
|
|
(output,errors) = subprocess.Popen([self.cxcalc, filename]+options.split(),
|
|
stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
|
|
|
|
if len(errors)>0:
|
|
print('********************************************************************************************************')
|
|
print('* Warning: Marvin execution failed: *')
|
|
print('* %-100s *'%errors)
|
|
print('* *')
|
|
print('* Please edit the ligand mol2 file and re-run PropKa with the -l option: %29s *'%filename)
|
|
print('********************************************************************************************************')
|
|
sys.exit(-1)
|
|
|
|
# extract calculated pkas
|
|
indices,pkas,types = self.extract_pkas(output)
|
|
|
|
# store calculated pka values
|
|
for i in range(len(indices)):
|
|
atoms[indices[i]].marvin_pka = pkas[i]
|
|
atoms[indices[i]].charge = {'a':-1,'b':+1}[types[i]]
|
|
print('%s model pKa: %.2f'%(atoms[indices[i]],pkas[i]))
|
|
|
|
return
|
|
|
|
def extract_pkas(self, output):
|
|
# split output
|
|
[tags, values,empty_line] = output.decode().split('\n')
|
|
#print(tags)
|
|
#print(values)
|
|
tags = tags.split('\t')
|
|
values = values.split('\t')
|
|
|
|
# format values
|
|
types = [tags[i][0] for i in range(1,len(tags)-1) if len(values)>i and values[i] != '']
|
|
indices = [int(a)-1 for a in values[-1].split(',') if a !='']
|
|
values = [float(v.replace(',','.')) for v in values[1:-1] if v != '']
|
|
|
|
if len(indices) != len(values) != len(types):
|
|
raise Exception('Lengths of atoms and pka values mismatch')
|
|
|
|
return indices, values, types
|
|
|
|
|
|
|
|
|