def _logParser(fname):
import re
unknownres_regex = re.compile('Unknown residue:\s+(\w+)')
missingparam_regex = re.compile(
'For atom: (.*) Could not find vdW \(or other\) parameters for type:\s+(\w+)'
)
missingtorsion_regex = re.compile('No torsion terms for\s+(.*)$')
missingbond_regex = re.compile(
'Could not find bond parameter for:\s+(.*)$')
missingangle_regex = re.compile('Could not find angle parameter:\s+(.*)$')
missingatomtype_regex = re.compile(
'FATAL:\s+Atom (.*) does not have a type')
unknownres = []
missingparam = []
missingtorsion = []
missingbond = []
missingangle = []
missingatomtype = []
with open(fname, 'r') as f:
for line in f:
if unknownres_regex.search(line):
unknownres.append(unknownres_regex.findall(line)[0])
if missingparam_regex.search(line):
missingparam.append(missingparam_regex.findall(line)[0])
if missingtorsion_regex.search(line):
missingtorsion.append(missingtorsion_regex.findall(line)[0])
if missingbond_regex.search(line):
missingbond.append(missingbond_regex.findall(line)[0])
if missingangle_regex.search(line):
missingangle.append(missingangle_regex.findall(line)[0])
if missingatomtype_regex.search(line):
missingatomtype.append(missingatomtype_regex.findall(line)[0])
errors = []
if len(unknownres):
errors.append(
UnknownResidueError(
'Unknown residue(s) {} found in the input structure. '
'You are either missing a topology definition for the residue or you need to '
'rename it to the correct residue name'.format(
np.unique(unknownres))))
if len(missingparam):
errors.append(
MissingParameterError(
'Missing parameters for atom {} and type {}'.format(
missingparam, missingparam)))
if len(missingtorsion):
errors.append(
MissingTorsionError(
'Missing torsion terms for {}'.format(missingtorsion)))
if len(missingbond):
errors.append(
MissingBondError(
'Missing bond parameters for {}'.format(missingbond)))
if len(missingangle):
errors.append(
MissingAngleError(
'Missing angle parameters for {}'.format(missingangle)))
if len(missingatomtype):
errors.append(
MissingAtomTypeError(
'Missing atom type for {}'.format(missingatomtype)))
return errors