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
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(
f"Unknown residue(s) {np.unique(unknownres)} 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"))
if len(missingparam):
errors.append(
MissingParameterError(
f"Missing parameters for atom {missingparam} and type {missingparam}"
))
if len(missingtorsion):
errors.append(
MissingTorsionError(f"Missing torsion terms for {missingtorsion}"))
if len(missingbond):
errors.append(
MissingBondError(f"Missing bond parameters for {missingbond}"))
if len(missingangle):
errors.append(
MissingAngleError(f"Missing angle parameters for {missingangle}"))
if len(missingatomtype):
errors.append(
MissingAtomTypeError(f"Missing atom type for {missingatomtype}"))
return errors