def loopmodel_template(template, missing_residues, overwrite_structures=False):
template_filepath = os.path.abspath(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, template.id + '-pdbfixed.pdb'))
output_pdb_filepath = os.path.abspath(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, template.id + '.pdb'))
loop_filepath = os.path.abspath(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, template.id + '.loop'))
output_score_filepath = os.path.abspath(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, template.id + '-loopmodel-score.sc'))
log_filepath = os.path.abspath(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, template.id + '-loopmodel-log.yaml'))
if not overwrite_structures:
if os.path.exists(log_filepath):
return
logfile = ensembler.core.LogFile(log_filepath)
write_loop_file(template, missing_residues)
starttime = datetime.datetime.utcnow()
if len(missing_residues) == 0:
loopmodel_output = LoopmodelOutput(successful=True, no_missing_residues=True)
else:
loopmodel_output = run_loopmodel(template_filepath, loop_filepath, output_pdb_filepath, output_score_filepath)
if not loopmodel_output.successful:
logger.error('MPI rank %d Loopmodel error for template %s - see logfile' % (mpistate.rank, template.id))
timedelta = datetime.datetime.utcnow() - starttime
logfile.log({
'templateid': str(template.id),
'no_missing_residues': loopmodel_output.no_missing_residues,
'loopmodel_output': loopmodel_output.output_text,
'mpi_rank': mpistate.rank,
'successful': loopmodel_output.successful,
'exception': loopmodel_output.exception,
'loopmodel_exception': loopmodel_output.loopmodel_exception,
'traceback': loopmodel_output.traceback,
'timing': ensembler.core.strf_timedelta(timedelta),
})
def loopmodel_template(template, missing_residues, overwrite_structures=False):
template_filepath = os.path.abspath(
os.path.join(
ensembler.core.default_project_dirnames.
templates_structures_modeled_loops, template.id + '-pdbfixed.pdb'))
output_pdb_filepath = os.path.abspath(
os.path.join(
ensembler.core.default_project_dirnames.
templates_structures_modeled_loops, template.id + '.pdb'))
loop_filepath = os.path.abspath(
os.path.join(
ensembler.core.default_project_dirnames.
templates_structures_modeled_loops, template.id + '.loop'))
output_score_filepath = os.path.abspath(
os.path.join(
ensembler.core.default_project_dirnames.
templates_structures_modeled_loops,
template.id + '-loopmodel-score.sc'))
log_filepath = os.path.abspath(
os.path.join(
ensembler.core.default_project_dirnames.
templates_structures_modeled_loops,
template.id + '-loopmodel-log.yaml'))
if not overwrite_structures:
if os.path.exists(log_filepath):
return
logfile = ensembler.core.LogFile(log_filepath)
write_loop_file(template, missing_residues)
starttime = datetime.datetime.utcnow()
if len(missing_residues) == 0:
loopmodel_output = LoopmodelOutput(successful=True,
no_missing_residues=True)
else:
loopmodel_output = run_loopmodel(template_filepath, loop_filepath,
output_pdb_filepath,
output_score_filepath)
if not loopmodel_output.successful:
logger.error(
'MPI rank %d Loopmodel error for template %s - see logfile' %
(mpistate.rank, template.id))
timedelta = datetime.datetime.utcnow() - starttime
logfile.log({
'templateid': str(template.id),
'no_missing_residues': loopmodel_output.no_missing_residues,
'loopmodel_output': loopmodel_output.output_text,
'mpi_rank': mpistate.rank,
'successful': loopmodel_output.successful,
'exception': loopmodel_output.exception,
'loopmodel_exception': loopmodel_output.loopmodel_exception,
'traceback': loopmodel_output.traceback,
'timing': ensembler.core.strf_timedelta(timedelta),
})
def pdbfix_template(template_full_seq, overwrite_structures=False):
"""
Parameters
----------
template_full_seq: BioPython SeqRecord
full UniProt sequence for span of the template (including unresolved residues)
overwrite_structures: bool
Returns
-------
fixer.missingResidues
"""
try:
template_pdbfixed_filepath = os.path.join(
ensembler.core.default_project_dirnames.templates_structures_modeled_loops,
template_full_seq.id + '-pdbfixed.pdb'
)
seq_pdbfixed_filepath = os.path.join(
ensembler.core.default_project_dirnames.templates_structures_modeled_loops,
template_full_seq.id + '-pdbfixed.fasta'
)
import pdbfixer
import simtk.openmm.app
template_filepath = os.path.join(
ensembler.core.default_project_dirnames.templates_structures_resolved,
template_full_seq.id + '.pdb'
)
fixer = pdbfixer.PDBFixer(filename=template_filepath)
chainid = next(fixer.structure.iter_chains()).chain_id
seq_obj = simtk.openmm.app.internal.pdbstructure.Sequence(chainid)
for r in template_full_seq.seq:
resi3 = Bio.SeqUtils.seq3(r).upper()
seq_obj.residues.append(resi3)
fixer.structure.sequences.append(seq_obj)
fixer.findMissingResidues()
remove_missing_residues_at_termini(fixer, len_full_seq=len(template_full_seq.seq))
if not overwrite_structures and os.path.exists(template_pdbfixed_filepath):
return fixer.missingResidues
fixer.findMissingAtoms()
(newTopology, newPositions, newAtoms, existingAtomMap) = fixer._addAtomsToTopology(True, True)
fixer.topology = newTopology
fixer.positions = newPositions
with open(template_pdbfixed_filepath, 'w') as template_pdbfixed_file:
simtk.openmm.app.PDBFile.writeFile(
fixer.topology, fixer.positions, file=template_pdbfixed_file
)
# Write sequence to file
seq_pdbfixed = ''.join([Bio.SeqUtils.seq1(r.name) for r in fixer.topology.residues()])
seq_record_pdbfixed = SeqRecord(Seq(seq_pdbfixed), id=template_full_seq.id, description=template_full_seq.id)
Bio.SeqIO.write([seq_record_pdbfixed], seq_pdbfixed_filepath, 'fasta')
return fixer.missingResidues
except (KeyboardInterrupt, ImportError):
raise
except Exception as e:
trbk = traceback.format_exc()
log_filepath = os.path.abspath(os.path.join(
ensembler.core.default_project_dirnames.templates_structures_modeled_loops,
template_full_seq.id + '-pdbfixer-log.yaml'
))
logfile = ensembler.core.LogFile(log_filepath)
logfile.log({
'templateid': str(template_full_seq.id),
'exception': e,
'traceback': ensembler.core.literal_str(trbk),
'mpi_rank': mpistate.rank,
})
logger.error(
'MPI rank %d pdbfixer error for template %s - see logfile' %
(mpistate.rank, template_full_seq.id)
)
logger.debug(e)
logger.debug(trbk)
def pdbfix_template(template_full_seq, overwrite_structures=False):
"""
Parameters
----------
template_full_seq: BioPython SeqRecord
full UniProt sequence for span of the template (including unresolved residues)
overwrite_structures: bool
Returns
-------
fixer.missingResidues
"""
try:
template_pdbfixed_filepath = os.path.join(
ensembler.core.default_project_dirnames.
templates_structures_modeled_loops,
template_full_seq.id + '-pdbfixed.pdb')
seq_pdbfixed_filepath = os.path.join(
ensembler.core.default_project_dirnames.
templates_structures_modeled_loops,
template_full_seq.id + '-pdbfixed.fasta')
import pdbfixer
import simtk.openmm.app
template_filepath = os.path.join(
ensembler.core.default_project_dirnames.
templates_structures_resolved, template_full_seq.id + '.pdb')
fixer = pdbfixer.PDBFixer(filename=template_filepath)
chainid = next(fixer.topology.chains()).id
sequence = [
Bio.SeqUtils.seq3(r).upper() for r in template_full_seq.seq
]
seq_obj = pdbfixer.pdbfixer.Sequence(chainid, sequence)
fixer.sequences.append(seq_obj)
fixer.findMissingResidues()
remove_missing_residues_at_termini(fixer,
len_full_seq=len(
template_full_seq.seq))
if not overwrite_structures and os.path.exists(
template_pdbfixed_filepath):
return fixer.missingResidues
fixer.findMissingAtoms()
(newTopology, newPositions, newAtoms,
existingAtomMap) = fixer._addAtomsToTopology(True, True)
fixer.topology = newTopology
fixer.positions = newPositions
with open(template_pdbfixed_filepath, 'w') as template_pdbfixed_file:
simtk.openmm.app.PDBFile.writeFile(fixer.topology,
fixer.positions,
file=template_pdbfixed_file)
# Write sequence to file
seq_pdbfixed = ''.join(
[Bio.SeqUtils.seq1(r.name) for r in fixer.topology.residues()])
seq_record_pdbfixed = SeqRecord(Seq(seq_pdbfixed),
id=template_full_seq.id,
description=template_full_seq.id)
Bio.SeqIO.write([seq_record_pdbfixed], seq_pdbfixed_filepath, 'fasta')
return fixer.missingResidues
except (KeyboardInterrupt, ImportError):
raise
except Exception as e:
trbk = traceback.format_exc()
log_filepath = os.path.abspath(
os.path.join(
ensembler.core.default_project_dirnames.
templates_structures_modeled_loops,
template_full_seq.id + '-pdbfixer-log.yaml'))
logfile = ensembler.core.LogFile(log_filepath)
logfile.log({
'templateid': str(template_full_seq.id),
'exception': e,
'traceback': ensembler.core.literal_str(trbk),
'mpi_rank': mpistate.rank,
})
logger.error(
'MPI rank %d pdbfixer error for template %s - see logfile' %
(mpistate.rank, template_full_seq.id))
logger.debug(e)
logger.debug(trbk)
