def test_set_protein_traj(self):
oetraj_record = self.record.get_value(OEField('OETraj', Types.Record))
prot_mol = oetraj_record.get_value(Fields.protein_traj_confs)
mdrecord = MDDataRecord(oetraj_record)
oetraj_record.delete_field(Fields.protein_traj_confs)
with self.assertRaises(ValueError):
mdrecord.get_protein_traj
self.assertTrue(mdrecord.set_protein_traj(prot_mol))
def process(self, record, port):
try:
# The copy of the dictionary option as local variable
# is necessary to avoid filename collisions due to
# the parallel cube processes
opt = dict(self.opt)
# Create the MD record to use the MD Record API
mdrecord = MDDataRecord(record)
# Logger string
opt['Logger'].info(' ')
system_title = mdrecord.get_title
#sys_id = mdrecord.get_flask_id
opt['Logger'].info(
'{}: Attempting MD Traj conversion into OEMols'.format(
system_title))
traj_fn = mdrecord.get_stage_trajectory()
opt['Logger'].info('{} Temp Directory: {}'.format(
system_title, os.path.dirname(traj_fn)))
opt['Logger'].info('{} Trajectory filename: {}'.format(
system_title, traj_fn))
# Generate multi-conformer protein and ligand OEMols from the trajectory
opt['Logger'].info(
'{} Generating protein and ligand trajectory OEMols'.format(
system_title))
flask = mdrecord.get_flask
md_components = record.get_value(Fields.md_components)
# opt['Logger'].info(md_components.get_info)
# Check Ligand Isomeric Smiles
lig_comp = md_components.get_ligand
lig_ref = record.get_value(Fields.ligand)
smi_lig_comp = oechem.OECreateSmiString(lig_comp)
smi_lig_ref = oechem.OECreateSmiString(lig_ref)
if smi_lig_ref != smi_lig_comp:
raise ValueError(
"Ligand Isomeric Smiles String check failure: {} vs {}".
format(smi_lig_comp, smi_lig_ref))
ptraj, ltraj, wtraj = utl.extract_aligned_prot_lig_wat_traj(
md_components,
flask,
traj_fn,
opt,
water_cutoff=opt['water_cutoff'])
ltraj.SetTitle(record.get_value(Fields.ligand_name))
ptraj.SetTitle(record.get_value(Fields.protein_name))
opt['Logger'].info(
'{} #atoms, #confs in protein traj OEMol: {}, {}'.format(
system_title, ptraj.NumAtoms(), ptraj.NumConfs()))
opt['Logger'].info(
'{} #atoms, #confs in ligand traj OEMol: {}, {}'.format(
system_title, ltraj.NumAtoms(), ltraj.NumConfs()))
opt['Logger'].info(
'{} #atoms, #confs in water traj OEMol: {}, {}'.format(
system_title, wtraj.NumAtoms(), wtraj.NumConfs()))
# Create new record with OETraj results
oetrajRecord = OERecord()
oetrajRecord.set_value(OEField('LigTraj', Types.Chem.Mol), ltraj)
if wtraj:
oetrajRecord.set_value(OEField('WatTraj', Types.Chem.Mol),
wtraj)
if in_orion():
oetrajRecord.set_value(Fields.collection,
mdrecord.collection_id)
mdrecord_traj = MDDataRecord(oetrajRecord)
mdrecord_traj.set_protein_traj(ptraj,
shard_name="ProteinTrajConfs_")
record.set_value(Fields.Analysis.oetraj_rec, oetrajRecord)
# update or initiate the list of analyses that have been done
if record.has_value(Fields.Analysis.analysesDone):
analysesDone = utl.RequestOEFieldType(
record, Fields.Analysis.analysesDone)
analysesDone.append('OETraj')
else:
analysesDone = ['OETraj']
record.set_value(Fields.Analysis.analysesDone, analysesDone)
opt['Logger'].info(
'{}: saved protein, ligand and water traj OEMols'.format(
system_title))
self.success.emit(record)
del mdrecord
del mdrecord_traj
except Exception as e:
print("Failed to complete", str(e), flush=True)
self.log.error(traceback.format_exc())
# Return failed mol
self.failure.emit(record)
return
def process(self, record, port):
try:
# The copy of the dictionary option as local variable
# is necessary to avoid filename collisions due to
# the parallel cube processes
opt = dict(self.opt)
# Logger string
opt['Logger'].info(' Beginning ConfTrajsToLigTraj')
system_title = utl.RequestOEFieldType(record, Fields.title)
opt['Logger'].info(
'{} Attempting to combine conf traj OEMols into ligand traj OEMol'
.format(system_title))
# Go find the ligand and LigTraj fields in each of the conformer records
if not record.has_field(Fields.Analysis.oetrajconf_rec):
raise ValueError(
'{} could not find the conformer record'.format(
system_title))
else:
opt['Logger'].info(
'{} found the conformer record'.format(system_title))
# set up ligand and LigTraj lists then loop over conformer records
poseIdVec = []
ligTrajConfs = []
protTrajConfs = []
watTrajConfs = []
list_conf_rec = record.get_value(Fields.Analysis.oetrajconf_rec)
for confrec in list_conf_rec:
confid = utl.RequestOEFieldType(confrec, Fields.confid)
if not confrec.has_field(Fields.Analysis.oetraj_rec):
raise ValueError(
'{} confID {}: could not find traj record'.format(
system_title, confid))
oetrajRecord = confrec.get_value(Fields.Analysis.oetraj_rec)
# Extract the ligand traj OEMol from the OETraj record
ligTraj = utl.RequestOEField(oetrajRecord, 'LigTraj',
Types.Chem.Mol)
poseIdVec += [confid] * ligTraj.NumConfs()
ligTrajConfs.append(ligTraj)
opt['Logger'].info(
'{} confID {}: adding ligTraj with {} atoms, {} confs'.
format(system_title, confid, ligTraj.NumAtoms(),
ligTraj.NumConfs()))
# Extract the activeSite water traj OEMol from the OETraj record
watTraj = utl.RequestOEField(oetrajRecord, 'WatTraj',
Types.Chem.Mol)
watTrajConfs.append(watTraj)
opt['Logger'].info(
'{} confID {}: adding watTraj with {} atoms, {} confs'.
format(system_title, confid, watTraj.NumAtoms(),
watTraj.NumConfs()))
# Extract the protTraj OEMol from the OETraj record
mdtrajrecord = MDDataRecord(oetrajRecord)
protTraj = mdtrajrecord.get_protein_traj
protTrajConfs.append(protTraj)
opt['Logger'].info(
'{} confID {}: adding protTraj with {} atoms, {} confs'.
format(system_title, confid, protTraj.NumAtoms(),
protTraj.NumConfs()))
del mdtrajrecord
if len(ligTrajConfs) < 1 or len(protTrajConfs) < 1:
raise ValueError(
'{} empty list of lig or protein trajectory OEMols'.format(
system_title))
ligTraj = oechem.OEMol(ligTrajConfs[0])
xyz = oechem.OEFloatArray(3 * ligTraj.GetMaxAtomIdx())
for trajMol in ligTrajConfs[1:]:
for conf in trajMol.GetConfs():
conf.GetCoords(xyz)
ligTraj.NewConf(xyz)
opt['Logger'].info(
'{} composite ligTraj has {} atoms, {} confs'.format(
system_title, ligTraj.NumAtoms(), ligTraj.NumConfs()))
watTraj = oechem.OEMol(watTrajConfs[0])
xyz = oechem.OEFloatArray(3 * watTraj.GetMaxAtomIdx())
for trajMol in watTrajConfs[1:]:
for conf in trajMol.GetConfs():
conf.GetCoords(xyz)
watTraj.NewConf(xyz)
opt['Logger'].info(
'{} composite watTraj has {} atoms, {} confs'.format(
system_title, watTraj.NumAtoms(), watTraj.NumConfs()))
protTraj = protTrajConfs[0]
xyz = oechem.OEFloatArray(3 * protTraj.GetMaxAtomIdx())
for trajMol in protTrajConfs[1:]:
for conf in trajMol.GetConfs():
conf.GetCoords(xyz)
protTraj.NewConf(xyz)
opt['Logger'].info(
'{} composite protTraj has {} atoms, {} confs'.format(
system_title, protTraj.NumAtoms(), protTraj.NumConfs()))
record.set_value(Fields.Analysis.poseIdVec, poseIdVec)
# Create new record with OETraj results
oetrajRecord = OERecord()
oetrajRecord.set_value(OEField('LigTraj', Types.Chem.Mol), ligTraj)
if watTraj:
oetrajRecord.set_value(OEField('WatTraj', Types.Chem.Mol),
watTraj)
if in_orion():
collection_id = utl.RequestOEFieldType(record,
Fields.collection)
oetrajRecord.set_value(Fields.collection, collection_id)
mdrecord_traj = MDDataRecord(oetrajRecord)
mdrecord_traj.set_protein_traj(protTraj,
shard_name="ProteinTrajConfs_")
record.set_value(Fields.Analysis.oetraj_rec, oetrajRecord)
self.success.emit(record)
except Exception as e:
print("Failed to complete", str(e), flush=True)
opt['Logger'].info(
'Exception {} in ConfTrajsToLigTraj on {}'.format(
str(e), system_title))
self.log.error(traceback.format_exc())
# Return failed mol
self.failure.emit(record)
return
