def test_set_parmed(self):
new_record = OERecord(self.record)
new_mdrecord = MDDataRecord(new_record)
pmd = new_mdrecord.get_parmed()
new_mdrecord.delete_field(Fields.pmd_structure)
self.assertFalse(new_mdrecord.has_parmed)
new_mdrecord.set_parmed(pmd, sync_stage_name='last')
self.assertTrue(new_mdrecord.has_parmed)
def process(self, record, port):
try:
opt = self.opt
opt['CubeTitle'] = self.title
if not record.has_value(Fields.md_components):
raise ValueError("MD Components Field is missing")
md_components = record.get_value(Fields.md_components)
flask, map_comp = md_components.create_flask
opt['Logger'].info(md_components.get_info)
if not record.has_value(Fields.title):
self.log.warn("Missing record Title field")
flask_title = flask.GetTitle()[0:12]
else:
flask_title = record.get_value(Fields.title)
# Parametrize the whole flask
flask_pmd_structure = md_components.parametrize_components(protein_ff=opt['protein_forcefield'],
ligand_ff=opt['ligand_forcefield'])
# Set Parmed structure box_vectors
is_periodic = True
if md_components.get_box_vectors is not None:
flask_pmd_structure.box_vectors = md_components.get_box_vectors
else:
is_periodic = False
self.log.warn("Flask {} has been parametrize without periodic box vectors ".format(flask_title))
if flask.NumAtoms() != flask_pmd_structure.topology.getNumAtoms():
raise ValueError("The flask {} and the generated Parmed structure "
"have mismatch atom numbers: {} vs {}".
format(flask_title,
flask.NumAtoms(),
flask_pmd_structure.topology.getNumAtoms()))
# Check Formal vs Partial charges
flask_formal_charge = 0
for at in flask.GetAtoms():
flask_formal_charge += at.GetFormalCharge()
flask_partial_charge = 0.0
for at in flask_pmd_structure.atoms:
flask_partial_charge += at.charge
if abs(flask_formal_charge - flask_partial_charge) > 0.01:
raise ValueError("Flask Formal charge and flask Partial charge mismatch: {} vs {}".format(
flask_formal_charge, flask_partial_charge))
# Copying the charges between the parmed structure and the oemol
for parm_at, oe_at in zip(flask_pmd_structure.atoms, flask.GetAtoms()):
if parm_at.atomic_number != oe_at.GetAtomicNum():
raise ValueError(
"Atomic number mismatch between the Parmed and the OpenEye topologies: {} - {}".
format(parm_at.atomic_number, oe_at.GetAtomicNum()))
oe_at.SetPartialCharge(parm_at.charge)
# Set the component charges
for comp_name, comp in md_components.get_components.items():
for at_comp in comp.GetAtoms():
pred = oechem.OEHasAtomIdx(map_comp[comp_name][at_comp.GetIdx()])
at_flask = flask.GetAtom(pred)
if at_flask.GetAtomicNum() != at_comp.GetAtomicNum():
"Atomic number mismatch between the component {} atom {} and the flask atom {}".\
format(comp_name, at_comp, at_flask)
at_comp.SetPartialCharge(at_flask.GetPartialCharge())
md_components.set_component_by_name(comp_name, comp)
# Update the components after setting the charges
record.set_value(Fields.md_components, md_components)
# Check if it is possible to create the OpenMM System
if is_periodic:
omm_flask = flask_pmd_structure.createSystem(nonbondedMethod=app.CutoffPeriodic,
nonbondedCutoff=10.0 * unit.angstroms,
constraints=None,
removeCMMotion=False,
rigidWater=False)
else:
omm_flask = flask_pmd_structure.createSystem(nonbondedMethod=app.NoCutoff,
constraints=None,
removeCMMotion=False,
rigidWater=False)
mdrecord = MDDataRecord(record)
sys_id = mdrecord.get_flask_id
mdrecord.set_flask(flask)
mdrecord.set_parmed(flask_pmd_structure, shard_name="Parmed_" + flask_title + '_' + str(sys_id))
data_fn = os.path.basename(mdrecord.cwd) + '_' + flask_title+'_' + str(sys_id) + '-' + opt['suffix']+'.tar.gz'
if not mdrecord.add_new_stage(MDStageNames.ForceField,
MDStageTypes.SETUP,
flask,
MDState(flask_pmd_structure),
data_fn):
raise ValueError("Problems adding the new Parametrization Stage")
self.success.emit(mdrecord.get_record)
del mdrecord
except Exception as e:
print("Failed to complete", str(e), flush=True)
self.opt['Logger'].info('Exception {} {}'.format(str(e), self.title))
self.log.error(traceback.format_exc())
self.failure.emit(record)
return
