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