def get_secondary_structure(self, chain_id):
if self.template_obj is None:
raise ModelRunError("template object is not set")
return ''.join(
self.yasara.SecStrRes('obj %i and protein and mol %s' %
(self.template_obj, chain_id)))
def get_chain_ids(self):
if self.template_obj is None:
raise ModelRunError("template object is not set")
chain_ids = self.yasara.ListMol(
'obj %i and protein' % self.template_obj, 'MOL')
return chain_ids
def _pick_identical_chains(self, main_chain_id, context):
identical_chain_groups = self._group_identical_chains(context)
for group in identical_chain_groups:
if main_chain_id in group:
return group
raise ModelRunError("chain not found in identical groups: {}".format(main_chain_id))
def residue_interacts_with(self, residue, interacting_residues):
if self.template_obj is None:
raise ModelRunError("template object is not set")
if 'CA' not in residue.atom_numbers:
return False
interacting_residues = list(
filter(lambda res: 'CA' in res.atom_numbers, interacting_residues))
atoms = self.yasara.ListAtom(
"CA and atom %i-%i and obj %i with distance<6 from %i" %
(interacting_residues[0].atom_numbers['CA'],
interacting_residues[-1].atom_numbers['CA'], self.template_obj,
residue.atom_numbers['CA']))
return len(atoms) > 0
def get_residues(self, chain_id):
if self.template_obj is None:
raise ModelRunError("template object is not set")
residues = []
for s in self.yasara.ListAtom(
"obj %i and mol %s and protein" %
(self.template_obj, chain_id), "RESNUM RESNAME ATOMNAME ATOMNUM"):
resnum, resname, atomname, atomnum = s.split()
if len(residues) <= 0 or residues[-1].residue_number != resnum:
amino_acid = AminoAcid.from_three_letter_code(resname)
residues.append(ModelingResidue(resnum, amino_acid))
residues[-1].atom_numbers[atomname] = int(atomnum)
return residues
def _handle_error_txt(self, error_path, work_dir_path, context, main_domain_alignment):
with open(error_path, 'r') as f:
msg = f.read()
if 'reward for reporting' in msg.lower():
model_name = model_storage.get_model_name(context.get_main_target_sequence(),
context.target_species_id,
main_domain_alignment,
TemplateID(context.template_pdbid,
context.main_target_chain_id))
tar_path = model_storage.get_error_tar_path(context.get_main_target_sequence(),
context.target_species_id,
main_domain_alignment,
TemplateID(context.template_pdbid,
context.main_target_chain_id))
with tarfile.open(tar_path, mode="w:gz") as ar:
ar.add(work_dir_path, arcname=model_name)
raise ModelRunError(msg)
def _model_run(self, main_domain_alignment, chain_alignments, context, main_target_sequence, require_resnum):
model_name = model_storage.get_model_name(context.get_main_target_sequence(),
context.target_species_id,
main_domain_alignment,
TemplateID(context.template_pdbid,
context.main_target_chain_id))
work_dir_path = tempfile.mkdtemp()
full_target_path = os.path.join(work_dir_path, 'target.fa')
align_fasta_path = os.path.join(work_dir_path, 'align.fa')
output_yob_path = os.path.join(work_dir_path, 'target.yob')
error_path = os.path.join(work_dir_path, 'errorexit.txt')
error_scene_path = os.path.join(work_dir_path, 'errorexit.sce')
before_scene_path = os.path.join(work_dir_path, 'beforemodel.sce')
write_fasta(full_target_path, {'target': context.get_main_target_sequence()})
try:
context.yasara.CD(work_dir_path)
context.yasara.SaveSce(before_scene_path)
chain_ids_before_model = context.get_chain_ids()
sequences_before_model = {chain_id: context.get_sequence(chain_id) for chain_id in chain_ids_before_model}
self._write_model_alignment_fasta(context, chain_alignments, align_fasta_path)
context.yasara.Processors(1)
context.yasara.ExperimentHomologyModeling(templateobj=context.template_obj,
alignfile=align_fasta_path,
templates="1, sameseq = 1",
alignments=1,
termextension=0,
oligostate=32,
looplenmax=10,
animation='fast',
speed='fast',
loopsamples=20,
resultfile='target')
context.yasara.Experiment("On")
context.yasara.Wait("Expend")
if os.path.isfile(error_path):
self._handle_error_txt(error_path, work_dir_path, context, main_domain_alignment)
elif os.path.isfile(error_scene_path):
raise ModelRunError("yasara exited with an error")
if not os.path.isfile(output_yob_path):
chain_ids_after_failure = context.get_chain_ids()
if chain_ids_before_model != chain_ids_after_failure:
raise ModelRunError("During modeling, yasara changed the chains {} to {}"
.format(chain_ids_before_model, chain_ids_after_failure))
for chain_id in chain_ids_before_model:
sequence_after_failure = context.get_sequence(chain_id)
if sequence_after_failure != sequences_before_model[chain_id]:
raise ModelRunError("During modeling, yasara changed chain {} sequence {} to {}"
.format(chain_id, sequences_before_model[chain_id], sequence_after_failure))
raise ModelRunError("yasara generated no output yob, check the console for further details")
chain_ids_after_build = context.get_chain_ids()
if context.main_target_chain_id not in chain_ids_after_build:
raise ModelRunError(f"The chain {context.main_target_chain_id} is not in the final model output by yasara")
_log.debug("after modeling {}".format([(chain_id, context.get_sequence(chain_id))
for chain_id in context.get_chain_ids()]))
_log.debug("input target aligned sequence:\n{}".format(main_domain_alignment.get_target_sequence_without_insertions()))
if not any([context.get_sequence(chain_id) == main_domain_alignment.get_target_sequence_without_insertions()
for chain_id in context.get_chain_ids()]):
if require_resnum is not None and not self._model_covers_residue(context, main_target_sequence, require_resnum):
raise ModelRunError("yasara generated a model that doesn't match the input alignment")
model_path = os.path.join(work_dir_path, 'target.pdb')
context.yasara.SavePDB(context.template_obj, model_path)
self._write_selected_targets(chain_alignments, os.path.join(work_dir_path, 'selected-targets.txt'))
log_path = os.path.join(work_dir_path, 'model.log')
ModelLogger.get_current().write(log_path)
tar_path = model_storage.get_tar_path(context.get_main_target_sequence(),
context.target_species_id,
main_domain_alignment,
TemplateID(context.template_pdbid,
context.main_target_chain_id))
with tarfile.open(tar_path, mode="w:gz") as ar:
ar.add(work_dir_path, arcname=model_name)
return tar_path
except RuntimeError as e:
self._log_additional_error_info(e, chain_alignments, context)
if os.path.isfile(error_path):
self._handle_error_txt(error_path, work_dir_path, context, main_domain_alignment)
elif os.path.isfile(error_scene_path):
raise ModelRunError("yasara exited with an error")
else:
raise e
finally:
if os.path.isdir(work_dir_path):
shutil.rmtree(work_dir_path)
def _model_run(self, main_domain_alignment, chain_alignments, context):
model_name = model_storage.get_model_name(
context.get_main_target_sequence(), context.target_species_id,
main_domain_alignment,
TemplateID(context.template_pdbid, context.main_target_chain_id))
work_dir_path = tempfile.mkdtemp()
align_fasta_path = os.path.join(work_dir_path, 'align.fa')
output_yob_path = os.path.join(work_dir_path, 'target.yob')
error_path = os.path.join(work_dir_path, 'errorexit.txt')
error_scene_path = os.path.join(work_dir_path, 'errorexit.sce')
before_scene_path = os.path.join(work_dir_path, 'beforemodel.sce')
try:
context.yasara.CD(work_dir_path)
context.yasara.SaveSce(before_scene_path)
self._write_model_alignment_fasta(context, chain_alignments,
align_fasta_path)
context.yasara.Processors(1)
context.yasara.ExperimentHomologyModeling(
templateobj=context.template_obj,
alignfile=align_fasta_path,
templates="1, sameseq = 1",
alignments=1,
termextension=0,
oligostate=32,
looplenmax=10,
animation='fast',
speed='fast',
loopsamples=20,
resultfile='target')
context.yasara.Experiment("On")
context.yasara.Wait("Expend")
if os.path.isfile(error_path):
self._handle_error_txt(error_path, work_dir_path, context,
main_domain_alignment)
elif os.path.isfile(error_scene_path):
raise ModelRunError("yasara exited with an error")
if not os.path.isfile(output_yob_path):
raise ModelRunError("yasara generated no output yob")
model_path = os.path.join(work_dir_path, 'target.pdb')
context.yasara.SavePDB(context.template_obj, model_path)
self._write_selected_targets(
chain_alignments,
os.path.join(work_dir_path, 'selected-targets.txt'))
tar_path = model_storage.get_tar_path(
context.get_main_target_sequence(), context.target_species_id,
main_domain_alignment,
TemplateID(context.template_pdbid,
context.main_target_chain_id))
with tarfile.open(tar_path, mode="w:gz") as ar:
ar.add(work_dir_path, arcname=model_name)
return tar_path
except RuntimeError as e:
self._log_additional_error_info(e, chain_alignments, context)
if os.path.isfile(error_path):
self._handle_error_txt(error_path, work_dir_path, context,
main_domain_alignment)
elif os.path.isfile(error_scene_path):
raise ModelRunError("yasara exited with an error")
else:
raise e
finally:
if os.path.isdir(work_dir_path):
shutil.rmtree(work_dir_path)
def delete_chain(self, chain_id):
if self.template_obj is None:
raise ModelRunError("template object is not set")
self.yasara.DelMol('obj %i and protein and mol %s' %
(self.template_obj, chain_id))