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Clean line breaks.

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See https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
2020-05-25 19:21:56 -07:00
parent 5242366006
commit 72851b5498
1 changed files with 40 additions and 38 deletions
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74
propka/ligand_pka_values.py
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@@ -37,8 +37,10 @@ class LigandPkaValues:
location of program location of program
""" """
path = os.environ.get('PATH').split(os.pathsep) path = os.environ.get('PATH').split(os.pathsep)
locs = [i for i in filter(lambda loc: os.access(loc, os.F_OK), \ locs = [
map(lambda dir: os.path.join(dir, program), path))] i for i in filter(lambda loc: os.access(loc, os.F_OK),
map(lambda dir: os.path.join(dir, program),
path))]
if len(locs) == 0: if len(locs) == 0:
str_ = "'Error: Could not find %s." % program str_ = "'Error: Could not find %s." % program
str_ += ' Please make sure that it is found in the path.' str_ += ' Please make sure that it is found in the path.'
@@ -46,7 +48,8 @@ class LigandPkaValues:
sys.exit(-1) sys.exit(-1)
return locs[0] return locs[0]
def get_marvin_pkas_for_pdb_file(self, pdbfile, num_pkas=10, min_ph=-10, max_ph=20): def get_marvin_pkas_for_pdb_file(self, pdbfile, num_pkas=10, min_ph=-10,
max_ph=20):
"""Use Marvin executables to get pKas for a PDB file. """Use Marvin executables to get pKas for a PDB file.
Args: Args:
@@ -56,12 +59,11 @@ class LigandPkaValues:
max_ph: maximum pH value max_ph: maximum pH value
""" """
molecule = propka.molecular_container.Molecular_container(pdbfile) molecule = propka.molecular_container.Molecular_container(pdbfile)
self.get_marvin_pkas_for_molecular_container(molecule, self.get_marvin_pkas_for_molecular_container(
num_pkas=num_pkas, molecule, num_pkas=num_pkas, min_ph=min_ph, max_ph=max_ph)
min_ph=min_ph,
max_ph=max_ph)
def get_marvin_pkas_for_molecular_container(self, molecule, num_pkas=10, min_ph=-10, max_ph=20): def get_marvin_pkas_for_molecular_container(self, molecule, num_pkas=10,
min_ph=-10, max_ph=20):
"""Use Marvin executables to calculate pKas for a molecular container. """Use Marvin executables to calculate pKas for a molecular container.
Args: Args:
@@ -72,13 +74,10 @@ class LigandPkaValues:
""" """
for name in molecule.conformation_names: for name in molecule.conformation_names:
filename = '%s_%s' % (molecule.name, name) filename = '%s_%s' % (molecule.name, name)
self.get_marvin_pkas_for_conformation_container(molecule.conformations[name], self.get_marvin_pkas_for_conformation_container(
name=filename, molecule.conformations[name], name=filename,
reuse=molecule.\ reuse=molecule.options.reuse_ligand_mol2_file,
options.reuse_ligand_mol2_file, num_pkas=num_pkas, min_ph=min_ph, max_ph=max_ph)
num_pkas=num_pkas,
min_ph=min_ph,
max_ph=max_ph)
def get_marvin_pkas_for_conformation_container(self, conformation, def get_marvin_pkas_for_conformation_container(self, conformation,
name='temp', reuse=False, name='temp', reuse=False,
@@ -95,10 +94,9 @@ class LigandPkaValues:
max_ph: maximum pH value max_ph: maximum pH value
""" """
conformation.marvin_pkas_calculated = True conformation.marvin_pkas_calculated = True
self.get_marvin_pkas_for_atoms(conformation.get_heavy_ligand_atoms(), self.get_marvin_pkas_for_atoms(
name=name, reuse=reuse, conformation.get_heavy_ligand_atoms(), name=name, reuse=reuse,
num_pkas=num_pkas, min_ph=min_ph, num_pkas=num_pkas, min_ph=min_ph, max_ph=max_ph)
max_ph=max_ph)
def get_marvin_pkas_for_atoms(self, atoms, name='temp', reuse=False, def get_marvin_pkas_for_atoms(self, atoms, name='temp', reuse=False,
num_pkas=10, min_ph=-10, max_ph=20): num_pkas=10, min_ph=-10, max_ph=20):
@@ -116,8 +114,8 @@ class LigandPkaValues:
molecules = propka.lib.split_atoms_into_molecules(atoms) molecules = propka.lib.split_atoms_into_molecules(atoms)
for i, molecule in enumerate(molecules): for i, molecule in enumerate(molecules):
filename = '%s_%d.mol2'%(name, i+1) filename = '%s_%d.mol2'%(name, i+1)
self.get_marvin_pkas_for_molecule(molecule, filename=filename, self.get_marvin_pkas_for_molecule(
reuse=reuse, num_pkas=num_pkas, molecule, filename=filename, reuse=reuse, num_pkas=num_pkas,
min_ph=min_ph, max_ph=max_ph) min_ph=min_ph, max_ph=max_ph)
def get_marvin_pkas_for_molecule(self, atoms, filename='__tmp_ligand.mol2', def get_marvin_pkas_for_molecule(self, atoms, filename='__tmp_ligand.mol2',
@@ -138,25 +136,28 @@ class LigandPkaValues:
propka.pdb.write_mol2_for_atoms(atoms, filename) propka.pdb.write_mol2_for_atoms(atoms, filename)
# check that we actually have a file to work with # check that we actually have a file to work with
if not os.path.isfile(filename): if not os.path.isfile(filename):
errstr = "Didn't find a user-modified file '%s' - generating one" \ errstr = ("Didn't find a user-modified file '%s' - generating one"
% filename % filename)
warning(errstr) warning(errstr)
propka.pdb.write_mol2_for_atoms(atoms, filename) propka.pdb.write_mol2_for_atoms(atoms, filename)
# Marvin calculate pKa values # Marvin calculate pKa values
options = 'pka -a %d -b %d --min %f --max %f -d large' % (num_pkas, options = ('pka -a %d -b %d --min %f --max %f -d large'
num_pkas, % (num_pkas, num_pkas, min_ph, max_ph))
min_ph, (output, errors) = subprocess.Popen(
max_ph) [self.cxcalc, filename]+options.split(), stdout=subprocess.PIPE,
(output, errors) = subprocess.Popen([self.cxcalc, filename]+options.split(),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate() stderr=subprocess.PIPE).communicate()
if len(errors) > 0: if len(errors) > 0:
info('********************************************************************************************************') info('***********************************************************'
info('* Warning: Marvin execution failed: *') '*********************************************')
info('* Warning: Marvin execution failed: '
' *')
info('* %-100s *' % errors) info('* %-100s *' % errors)
info('* *') info('* '
info('* Please edit the ligand mol2 file and re-run PropKa with the -l option: %29s *' % filename) ' *')
info('********************************************************************************************************') info('* Please edit the ligand mol2 file and re-run PropKa with '
'the -l option: %29s *' % filename)
info('***********************************************************'
'*********************************************')
sys.exit(-1) sys.exit(-1)
# extract calculated pkas # extract calculated pkas
indices, pkas, types = self.extract_pkas(output) indices, pkas, types = self.extract_pkas(output)
@@ -182,8 +183,9 @@ class LigandPkaValues:
tags = tags.split('\t') tags = tags.split('\t')
values = values.split('\t') values = values.split('\t')
# format values # format values
types = [tags[i][0] for i in range(1, len(tags)-1) if len(values) > i \ types = [
and values[i] != ''] 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 != ''] indices = [int(a)-1 for a in values[-1].split(',') if a != '']
values = [float(v.replace(',', '.')) for v in values[1:-1] if v != ''] values = [float(v.replace(',', '.')) for v in values[1:-1] if v != '']
if len(indices) != len(values) != len(types): if len(indices) != len(values) != len(types):