def bond_order_tag(molecule, atom_map, bond_order_array): """ Add psi bond order to bond in molecule. This function adds a tag to the GetData dictionary in bond.GetData() Parameters ---------- molecule: OEMol This molecule must have tags that corresponds to the atom_map atom_map: dict dictionary that maps atom tag to atom index bond_order_array: dict maps Wiberg and Meyer bond indices to N x N numpy arrays. N - atoms in molecule. This array contains the bond order for bond(i,j) where i,j correspond to tag on atom and index in bond_order_array """ wiberg_bond_order = bond_order_array['Wiberg_psi4'] mayer_bond_order = bond_order_array['Mayer_psi4'] # Sanity check, both arrays are same shape for i, j in itertools.combinations(range(wiberg_bond_order.shape[0]), 2): idx_1 = atom_map[i + 1] idx_2 = atom_map[j + 1] atom_1 = molecule.GetAtom(oechem.OEHasAtomIdx(idx_1)) atom_2 = molecule.GetAtom(oechem.OEHasAtomIdx(idx_2)) bond = molecule.GetBond(atom_1, atom_2) if bond: wbo = wiberg_bond_order[i][j] mbo = mayer_bond_order[i][j] tag = oechem.OEGetTag('Wiberg_psi4') bond.SetData(tag, wbo) tag = oechem.OEGetTag('Mayer_psi4') bond.SetData(tag, mbo)
def DumpGroups(mol): print("groups of", mol.GetTitle()) print("number of atom groups", oechem.OECount(mol, IsAtomGroup())) print("number of bond groups", oechem.OECount(mol, IsBondGroup())) print("number of aromatic atoms groups", oechem.OECount(mol, oechem.OEHasGroupType(oechem.OEGetTag("aromatic atoms")))) print("number of aromatic bonds groups", oechem.OECount(mol, oechem.OEHasGroupType(oechem.OEGetTag("aromatic bonds")))) # loop over groups for g in mol.GetGroups(): DumpGroup(g) print()
def packMDData(self, mol): """ This method attached the Parmed structure to the passed OEMol() Parameters ---------- mol : OEMol() OpenEye Molecule object the molecular system Returns ------- mol : OeMol() the changed in place molecule """ try: # Try to attach the Parmed structure to the molecule. The molecule is changed in place mol = PackageOEMol.pack(mol, self.__parmed_structure__) except Exception as e: raise RuntimeError( 'It was not possible to attached ' 'the parmed structure to the molecule {}'.format(e)) if self.ref_positions: packedpos = PackageOEMol.encodePyObj(self.ref_positions) mol.SetData(oechem.OEGetTag('OEMDDataRefPositions'), packedpos) return mol
def SetPartialCharge(mol, tagname): oechem.OEMMFFAtomTypes(mol) oechem.OEMMFF94PartialCharges(mol) tag = oechem.OEGetTag(tagname) for atom in mol.GetAtoms(): atom.SetData(tag, atom.GetPartialCharge())
def _tag_fgroups(mol, fgroups_smarts=None): """ This function tags atoms and bonds of functional groups defined in fgroup_smarts. fgroup_smarts is a dictionary that maps functional groups to their smarts pattern. It can be user generated or from yaml file. Parameters ---------- mol: Openeye OEMolGraph frgroups_smarts: dictionary of functional groups mapped to their smarts pattern. Default is None. It uses 'fgroup_smarts.yaml' Returns ------- fgroup_tagged: dict a dictionary that maps indexed functional groups to corresponding atom and bond indices in mol """ if not fgroups_smarts: # Load yaml file fn = resource_filename('fragmenter', os.path.join('data', 'fgroup_smarts.yml')) f = open(fn, 'r') fgroups_smarts = yaml.safe_load(f) f.close() fgroup_tagged = {} for f_group in fgroups_smarts: qmol = oechem.OEQMol() if not oechem.OEParseSmarts(qmol, fgroups_smarts[f_group]): print('OEParseSmarts failed') ss = oechem.OESubSearch(qmol) oechem.OEPrepareSearch(mol, ss) for i, match in enumerate(ss.Match(mol, True)): fgroup_atoms = set() for ma in match.GetAtoms(): fgroup_atoms.add(ma.target.GetIdx()) tag = oechem.OEGetTag('fgroup') ma.target.SetData(tag, '{}_{}'.format(f_group, str(i))) fgroup_bonds = set() for ma in match.GetBonds(): #if not ma.target.IsInRing(): fgroup_bonds.add(ma.target.GetIdx()) tag =oechem.OEGetTag('fgroup') ma.target.SetData(tag, '{}_{}'.format(f_group, str(i))) fgroup_tagged['{}_{}'.format(f_group, str(i))] = (fgroup_atoms, fgroup_bonds) return fgroup_tagged
def mol_from_json(symbols, connectivity, geometry, permute_xyz=False): """ Generate OEMol from QCSchema molecule specs Parameters ---------- inp_molecule: dict Must have symbols and connectivity and/or geometry Note: If geometry is given, the molecule will have a tag indicating that the goemetry came from QCSchema. This will ensure that the order of the atoms and configuration is not change for generation of mapped SMILES and isomeric SMILES. Returns ------- molecule: OEMol """ molecule = oechem.OEMol() for s in symbols: molecule.NewAtom(_symbols[s]) # Add connectivity for bond in connectivity: a1 = molecule.GetAtom(oechem.OEHasAtomIdx(bond[0])) a2 = molecule.GetAtom(oechem.OEHasAtomIdx(bond[1])) bond_order = bond[-1] if not isinstance(bond_order, int) and not bond_order.is_integer(): raise ValueError( "bond order must be a whole number. A bond order of 1.5 is not allowed" ) molecule.NewBond(a1, a2, int(bond_order)) # Add geometry if molecule.NumAtoms() != geometry.shape[0] / 3: raise ValueError( "Number of atoms in molecule does not match length of position array" ) molecule.SetCoords(oechem.OEFloatArray(geometry)) molecule.SetDimension(3) if not permute_xyz: # Add tag that the geometry is from JSON and shouldn't be changed. geom_tag = oechem.OEGetTag("json_geometry") molecule.SetData(geom_tag, True) oechem.OEDetermineConnectivity(molecule) oechem.OEFindRingAtomsAndBonds(molecule) # No need to perceive Bond Order because the information was added from the connectivity table. Apparently, this # function does many different perceptions under the hood and it can add implicit hydrogens to divalent N that should be negatively charged. #oechem.OEPerceiveBondOrders(molecule) # This seems to add hydrogens that are not in the json #oechem.OEAssignImplicitHydrogens(molecule) oechem.OEAssignFormalCharges(molecule) oechem.OEAssignAromaticFlags(molecule) oechem.OEPerceiveChiral(molecule) oechem.OE3DToAtomStereo(molecule) oechem.OE3DToBondStereo(molecule) return molecule
def pack(cls, molecule, data): """ Encodes the ParmEd Structure or if provided the OpenMM Simulation object, this will extract the State and the log file from the state reporter and attach them to the OEMol as generic data. Returns the OEMol with attached data.""" tag_data = {} # Attach (base64) encoded ParmEd Structure. if isinstance(data, parmed.structure.Structure): molecule.SetData(oechem.OEGetTag('Structure'), cls.encodeStruct(data)) # Attach the encoded OpenMM State and log file from the Simulation. if isinstance(data, openmm.app.simulation.Simulation): tag_data = cls.encodeSimData(data) for k, v in tag_data.items(): molecule.SetData(oechem.OEGetTag(k), v) return molecule
def SetPartialCharge(mol, tagname, minvalue, maxvalue): oechem.OEMMFFAtomTypes(mol) oechem.OEMMFF94PartialCharges(mol) tag = oechem.OEGetTag(tagname) for atom in mol.GetAtoms(): charge = atom.GetPartialCharge() atom.SetData(tag, charge) minvalue = min(minvalue, charge) maxvalue = max(maxvalue, charge) return minvalue, maxvalue
def DumpGroup(group): print("type \"%s\"" % oechem.OEGetTag(group.GetGroupType()), end=" ") if group.NumAtoms() > 0: print("atom indices:", end=" ") for atom in group.GetAtoms(): print(atom.GetIdx(), end=" ") print() if group.NumBonds() > 0: print("bond indices:", end=" ") for bond in group.GetBonds(): print(bond.GetIdx(), end=" ") print()
def mol_from_json(symbols, connectivity, geometry, permute_xyz=False): """ Generate OEMol from QCSchema molecule specs Parameters ---------- inp_molecule: dict Must have symbols and connectivity and/or geometry Note: If geometry is given, the molecule will have a tag indicating that the goemetry came from QCSchema. This will ensure that the order of the atoms and configuration is not change for generation of mapped SMILES and isomeric SMILES. Returns ------- molecule: OEMol """ molecule = oechem.OEMol() for s in symbols: molecule.NewAtom(_symbols[s]) # Add connectivity for bond in connectivity: a1 = molecule.GetAtom(oechem.OEHasAtomIdx(bond[0])) a2 = molecule.GetAtom(oechem.OEHasAtomIdx(bond[1])) molecule.NewBond(a1, a2, bond[-1]) # Add geometry if molecule.NumAtoms() != geometry.shape[0] / 3: raise ValueError( "Number of atoms in molecule does not match length of position array" ) molecule.SetCoords(oechem.OEFloatArray(geometry)) molecule.SetDimension(3) if not permute_xyz: # Add tag that the geometry is from JSON and shouldn't be changed. geom_tag = oechem.OEGetTag("json_geometry") molecule.SetData(geom_tag, True) oechem.OEDetermineConnectivity(molecule) oechem.OEFindRingAtomsAndBonds(molecule) oechem.OEPerceiveBondOrders(molecule) # This seems to add hydrogens that are not in the json #oechem.OEAssignImplicitHydrogens(molecule) oechem.OEAssignFormalCharges(molecule) oechem.OEAssignAromaticFlags(molecule) oechem.OEPerceiveChiral(molecule) oechem.OE3DToAtomStereo(molecule) oechem.OE3DToBondStereo(molecule) return molecule
def _tag_rings(mol): """ This function tags ring atom and bonds with ringsystem index Parameters ---------- mol: OpenEye OEMolGraph Returns ------- tagged_rings: dict maps ringsystem index to ring atom and bond indices """ tagged_rings = {} nringsystems, parts = oechem.OEDetermineRingSystems(mol) for ringidx in range(1, nringsystems +1): ringidx_atoms = set() for atom in mol.GetAtoms(): if parts[atom.GetIdx()] == ringidx: ringidx_atoms.add(atom.GetIdx()) tag = oechem.OEGetTag('ringsystem') atom.SetData(tag, ringidx) # Find bonds in ring and tag ringidx_bonds = set() for a_idx in ringidx_atoms: atom = mol.GetAtom(oechem.OEHasAtomIdx(a_idx)) for bond in atom.GetBonds(): nbrAtom = bond.GetNbr(atom) nbrIdx = nbrAtom.GetIdx() if nbrIdx in ringidx_atoms and nbrIdx != a_idx: ringidx_bonds.add(bond.GetIdx()) tag = oechem.OEGetTag('ringsystem') bond.SetData(tag, ringidx) tagged_rings[ringidx] = (ringidx_atoms, ringidx_bonds) return tagged_rings
def process(self, system, port): try: # Solvate the system sol_system = utils.hydrate(system, self.opt) sol_system.SetTitle(system.GetTitle()) # Attached the original system to the solvated one if self.opt['ref_structure']: sol_system.SetData(oechem.OEGetTag("RefStructure"), system) self.success.emit(sol_system) except Exception as e: # Attach error message to the molecule that failed self.log.error(traceback.format_exc()) system.SetData('error', str(e)) # Return failed mol self.failure.emit(system) return
def __init__(self, infileName, tagname): self.pattyTag = oechem.OEGetTag(tagname) self.smartsList = [] ifs = open(infileName) lines = ifs.readlines() for line in lines: # Strip trailing comments index = line.find('%') if index != -1: line = line[0:index] # Split into tokens. toks = string.split(line) if len(toks) == 2: smarts, type = toks pat = oechem.OESubSearch() pat.Init(smarts) pat.SetMaxMatches(0) self.smartsList.append([pat, type, smarts])
def prep_mols_for_vis(wbo_dict, fgroup): # first sort wbo wbo_keys = sorted(list(wbo_dict.keys())) molecules = [] bond_map_idx = [(4,5)]*len(wbo_keys) wbos = [] for bo in wbo_keys: drop = False mol = oechem.OEMol(wbo_dict[bo][0]) name = mol.GetTitle().split('_') if fgroup == name[-1]: map_idx = [1] elif fgroup == name[1]: map_idx = [2, 3] for bond in mol.GetBonds(): a1 = bond.GetBgn() a2 = bond.GetEnd() m1 = a1.GetMapIdx() m2 = a2.GetMapIdx() if name[-1] == fgroup: to_check_ortho = [1, 4, 5] elif name[1] == fgroup: to_check_ortho = [2, 3, 4, 5] if (m1 in to_check_ortho or m2 in to_check_ortho) and bond.IsInRing(): if a1.GetAtomicNum() == 7 or a2.GetAtomicNum() == 7: # The N is ortho to the bond. drop out from list drop = True if (m1 in map_idx or m2 in map_idx) and not bond.IsInRing(): bond.GetBgn().SetMapIdx(4) bond.GetEnd().SetMapIdx(5) wbo = bond.GetData('WibergBondOrder') else: # Remove wbo so that only R1 WBO is generated in visualization to_delete = bond.GetData('WibergBondOrder') tag = oechem.OEGetTag('WibergBondOrder') bond.DeleteData(tag) if not drop: molecules.append(mol) wbos.append(wbo) return molecules, bond_map_idx, wbos
def tag_conjugated_bond(mol, tautomers=None, tag=None, threshold=1.05): """ Add conjugated bond data tag. If the bond order is above the threshold, this tag will be True, otherwise it will be False Parameters ---------- mol: OEMol tautomers: list of OEMols, optional, Default None If a list is provided, the conjugation tag will be true if the bond in any of the set of molecules is double. The list should consist of resonance structures of the molecules. You can get that from oequacpac.EnumerateTautomres tag: str, optional, Default None If provided, will use that bond order. Options are WibergBondOrder, Wiberg_psi4, Mayer_psi4 threshold: int, optional, Default is 1.05 The fractional bond order threshold above which the bond will be considered conjugated. Returns ------- atom_indices: list of atom indices in conjugated bonds. """ atom_indices = [] for bond in mol.GetBonds(): resonance = False if tautomers is not None: for tmol in tautomers: t_bond = tmol.GetBond(oechem.OEHasBondIdx(bond.GetIdx())) if t_bond.GetOrder() > 1: resonance = True break elif bond.GetData()[tag] >= threshold: resonance = True # Add tag to bond conj_tag = oechem.OEGetTag("conjugated") bond.SetData(conj_tag, resonance) if resonance: a1 = bond.GetBgnIdx() a2 = bond.GetEndIdx() atom_indices.extend([a1, a2]) return atom_indices
def test_failure(self): print('Testing cube:', self.cube.name) # Read a molecule mol = oechem.OEMol() ifs = oechem.oemolistream( get_data_filename('uranium-hexafluoride.sdf')) # Test a single molecule if not oechem.OEReadMolecule(ifs, mol): raise Exception('Cannot read molecule') ifs.close() # Process the molecules self.cube.process(mol, self.cube.intake.name) # Assert that one molecule was emitted on the success port self.assertEqual(self.runner.outputs['success'].qsize(), 0) # Assert that zero molecules were emitted on the failure port self.assertEqual(self.runner.outputs['failure'].qsize(), 1) outmol = self.runner.outputs["failure"].get() # Check that the number of atoms in input and output molecules match. self.assertEqual(outmol.NumAtoms(), mol.NumAtoms()) # Check that an error message has been attached self.assertTrue(outmol.HasData(oechem.OEGetTag('error')))
def __iter__(self): max_idx = self.args.limit if max_idx is not None: max_idx = int(max_idx) count = 0 self.config = config_from_env() in_orion = self.config is not None if not in_orion: with oechem.oemolistream(str(self.args.data_in)) as ifs: for mol in ifs.GetOEMols(): mol.SetData(oechem.OEGetTag('prefix'), self.opt['prefix']) mol.SetData(oechem.OEGetTag('suffix'), self.opt['suffix']) for at in mol.GetAtoms(): residue = oechem.OEAtomGetResidue(at) residue.SetName(self.opt['type']) oechem.OEAtomSetResidue(at, residue) if self.opt['IDTag']: mol.SetData(oechem.OEGetTag('IDTag'), 'l' + mol.GetTitle()[0:12] + '_' + str(count)) yield mol count += 1 if max_idx is not None and count == max_idx: break else: stream = StreamingDataset(self.args.data_in, input_format=self.args.download_format) for mol in stream: mol.SetData(oechem.OEGetTag('prefix'), self.opt['prefix']) mol.SetData(oechem.OEGetTag('suffix'), self.opt['suffix']) for at in mol.GetAtoms(): residue = oechem.OEAtomGetResidue(at) residue.SetName(self.opt['type']) oechem.OEAtomSetResidue(at, residue) if self.opt['IDTag']: mol.SetData(oechem.OEGetTag('IDTag'), 'l' + mol.GetTitle()[0:12] + '_'+str(count)) yield mol count += 1 if max_idx is not None and count == max_idx: break
def DepictMoleculeWithFragmentCombinations(report, mol, frags, opts): #fragcombs, opts): """ This function was taken from https://docs.eyesopen.com/toolkits/cookbook/python/depiction/enumfrags.html with some modification """ stag = "fragment idx" itag = oechem.OEGetTag(stag) for fidx, frag in enumerate(frags): for bond in frags[frag].GetBonds(): bond.SetData(itag, fidx) # setup depiction styles nrfrags = len(frags) colors = [c for c in oechem.OEGetLightColors()] if len(colors) < nrfrags: colors = [c for c in oechem.OEGetColors(oechem.OEYellowTint, oechem.OEDarkOrange, nrfrags)] bondglyph = ColorBondByFragmentIndex(colors, itag) lineWidthScale = 0.75 fadehighlight = oedepict.OEHighlightByColor(oechem.OEGrey, lineWidthScale) # depict each fragment combinations for frag in frags: cell = report.NewCell() disp = oedepict.OE2DMolDisplay(mol, opts) fragatoms = oechem.OEIsAtomMember(frags[frag].GetAtoms()) fragbonds = oechem.OEIsBondMember(frags[frag].GetBonds()) notfragatoms = oechem.OENotAtom(fragatoms) notfragbonds = oechem.OENotBond(fragbonds) oedepict.OEAddHighlighting(disp, fadehighlight, notfragatoms, notfragbonds) bond = mol.GetBond(oechem.OEHasBondIdx(frag)) atomBondSet = oechem.OEAtomBondSet() atomBondSet.AddBond(bond) atomBondSet.AddAtom(bond.GetBgn()) atomBondSet.AddAtom(bond.GetEnd()) hstyle = oedepict.OEHighlightStyle_BallAndStick hcolor = oechem.OEColor(oechem.OELightBlue) oedepict.OEAddHighlighting(disp, hcolor, hstyle, atomBondSet) #oegrapheme.OEAddGlyph(disp, bondglyph, fragbonds) oedepict.OERenderMolecule(cell, disp) # depict original fragmentation in each header cellwidth, cellheight = report.GetHeaderWidth(), report.GetHeaderHeight() opts.SetDimensions(cellwidth, cellheight, oedepict.OEScale_AutoScale) opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome) bondlabel = LabelBondOrder() opts.SetBondPropertyFunctor(bondlabel) disp = oedepict.OE2DMolDisplay(mol, opts) #oegrapheme.OEAddGlyph(disp, bondglyph, oechem.IsTrueBond()) headerpen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGrey, oedepict.OEFill_Off, 2.0) for header in report.GetHeaders(): oedepict.OERenderMolecule(header, disp) oedepict.OEDrawBorder(header, headerpen)
def _file_processing(**opt): """ This supporting function compresses the produced trajectory and supporting files in a .tar file (if required ) and eventually uploaded them to Orion. If not .tar file is selected then all the generated files are eventually uploaded in Orion Parameters ---------- opt: python dictionary A dictionary containing all the MD setting info """ # Set the trajectory file name if opt['trajectory_filetype'] == 'NetCDF': trj_fn = opt['outfname'] +'.nc' elif opt['trajectory_filetype'] == 'DCD': trj_fn = opt['outfname'] +'.dcd' elif opt['trajectory_filetype'] == 'HDF5': trj_fn = opt['outfname'] + '.hdf5' else: oechem.OEThrow.Fatal("The selected trajectory filetype is not supported: {}" .format(opt['trajectory_filetype'])) # Set .pdb file names pdb_fn = opt['outfname'] + '.pdb' pdb_order_fn = opt['outfname'] + '_ordering_test' + '.pdb' log_fn = opt['outfname'] + '.log' # List all the file names fnames = [trj_fn, pdb_fn, pdb_order_fn, log_fn] ex_files = [] # Check which file names are actually produced files for fn in fnames: if os.path.isfile(fn): ex_files.append(fn) # Tar the outputted files if required if opt['tar']: tarname = opt['outfname'] + '.tar' opt['Logger'].info('Creating tar file: {}'.format(tarname)) tar = tarfile.open(tarname, "w") for name in ex_files: opt['Logger'].info('Adding {} to {}'.format(name, tarname)) tar.add(name) tar.close() opt['molecule'].SetData(oechem.OEGetTag("Tar_fname"), tarname) if in_orion(): upload_file(tarname, tarname, tags=['TRJ_INFO']) # Clean up files that have been added to tar. for tmp in ex_files: try: os.remove(tmp) except: pass else: # If not .tar file is required the files are eventually uploaded in Orion if in_orion(): for fn in ex_files: upload_file(fn, fn, tags=['TRJ_INFO']) return
def process(self, mol, port): try: # Split the complex in components in order to apply the FF protein, ligand, water, excipients = utils.split(mol) # Unique prefix name used to output parametrization files self.opt['prefix_name'] = mol.GetTitle() # Apply FF to the Protein protein_structure = utils.applyffProtein(protein, self.opt) # Apply FF to water molecules water_structure = utils.applyffWater(water, self.opt) # Apply FF to the excipients if excipients.NumAtoms() > 0: excipient_structure = utils.applyffExcipients(excipients, self.opt) # The excipient order is set equal to the order in related # parmed structure to avoid possible atom index mismatching excipients = oeommutils.openmmTop_to_oemol(excipient_structure.topology, excipient_structure.positions, verbose=False) # Apply FF to the ligand ligand_structure = utils.applyffLigand(ligand, self.opt) # Build the Parmed structure if excipients.NumAtoms() > 0: complex_structure = protein_structure + ligand_structure + \ excipient_structure + water_structure else: complex_structure = protein_structure + ligand_structure + water_structure num_atom_system = protein.NumAtoms() + ligand.NumAtoms() + excipients.NumAtoms() + water.NumAtoms() if not num_atom_system == complex_structure.topology.getNumAtoms(): oechem.OEThrow.Fatal("Parmed and OE topologies mismatch atom number error") # Assemble a new OEMol complex in a specific order # to match the defined Parmed structure complex complx = protein.CreateCopy() oechem.OEAddMols(complx, ligand) oechem.OEAddMols(complx, excipients) oechem.OEAddMols(complx, water) complx.SetTitle(mol.GetTitle()) # Set Parmed structure box_vectors vec_data = pack_utils.PackageOEMol.getData(complx, tag='box_vectors') vec = pack_utils.PackageOEMol.decodePyObj(vec_data) complex_structure.box_vectors = vec # Attach the Parmed structure to the complex packed_complex = pack_utils.PackageOEMol.pack(complx, complex_structure) # Attach the reference positions to the complex ref_positions = complex_structure.positions packedpos = pack_utils.PackageOEMol.encodePyObj(ref_positions) packed_complex.SetData(oechem.OEGetTag('OEMDDataRefPositions'), packedpos) # Set atom serial numbers, Ligand name and HETATM flag # oechem.OEPerceiveResidues(packed_complex, oechem.OEPreserveResInfo_SerialNumber) for at in packed_complex.GetAtoms(): thisRes = oechem.OEAtomGetResidue(at) thisRes.SetSerialNumber(at.GetIdx()) if thisRes.GetName() == 'UNL': thisRes.SetName("LIG") thisRes.SetHetAtom(True) oechem.OEAtomSetResidue(at, thisRes) if packed_complex.GetMaxAtomIdx() != complex_structure.topology.getNumAtoms(): raise ValueError("OEMol complex and Parmed structure mismatch atom numbers") # Check if it is possible to create the OpenMM System system = complex_structure.createSystem(nonbondedMethod=app.CutoffPeriodic, nonbondedCutoff=10.0 * unit.angstroms, constraints=app.HBonds, removeCMMotion=False) self.success.emit(packed_complex) except Exception as e: # Attach error message to the molecule that failed self.log.error(traceback.format_exc()) mol.SetData('error', str(e)) # Return failed mol self.failure.emit(mol) return
def main(argv=[__name__]): """ itf = oechem.OEInterface() oechem.OEConfigure(itf, InterfaceData) if not oechem.OEParseCommandLine(itf, argv): return 1 oname = itf.GetString("-out") iname = itf.GetString("-in") ext = oechem.OEGetFileExtension(oname) if not oedepict.OEIsRegisteredImageFile(ext): oechem.OEThrow.Fatal("Unknown image type!") ofs = oechem.oeofstream() if not ofs.open(oname): oechem.OEThrow.Fatal("Cannot open output file!") ## INPUT PARAMETERS ######################################################### ######################################################### mm = 'tyk2/og_pdbs' qml = 'tyk2/forward_snapshots' phase = 'solvent' which_ligand = 'old' dir_name = iname ligand_pdbs_mm = glob.glob(f"{mm}/{dir_name}/{which_ligand}*{phase}.pdb") print(len(ligand_pdbs_mm)) ligand_pdbs_qml = glob.glob(f"{qml}/{dir_name}/{which_ligand}*{phase}.pdb") print(len(ligand_pdbs_qml)) #d = np.load('full_data_dict.npy', allow_pickle=True) from_ligand, to_ligand = iname.replace('from', '').replace('to', '').replace('lig', '') print(from_ligand) print(to_ligand) #key1 = (1, 8) #key2 = ('solvent', which_ligand) ######################################################### ######################################################### #d = d.flatten()[0] #work = d[key1][key2] #print(work) for i, (mm_pdb_path, ani_pdb_path) in enumerate(zip(ligand_pdbs_mm, ligand_pdbs_qml)): print(mm_pdb_path, ani_pdb_path) if i == 0: MM_mol = createOEMolFromSDF(mm_pdb_path, 0) ANI_mol = createOEMolFromSDF(ani_pdb_path, 0) else: # there absolutely must be a better/faster way of doing this because this is ugly and slow MM_mol.NewConf(createOEMolFromSDF(mm_pdb_path, 0)) ANI_mol.NewConf(createOEMolFromSDF(ani_pdb_path, 0)) """ ofs = oechem.oeofstream() oname = f"tor_out" ext = oechem.OEGetFileExtension(oname) mm_pdb_path = f"og_lig0_solvent.pdb" ani_pdb_path = f"forward_lig0.solvent.pdb" MM_mol = createOEMolFromSDF(mm_pdb_path, 0) ANI_mol = createOEMolFromSDF(ani_pdb_path, 0) mol = MM_mol mol2 = ANI_mol for m in [mol, mol2]: oechem.OESuppressHydrogens(m) oechem.OECanonicalOrderAtoms(m) oechem.OECanonicalOrderBonds(m) m.Sweep() refmol = None stag = "dihedral_histogram" itag = oechem.OEGetTag(stag) nrbins = 20 print(mol.NumConfs()) print(mol2.NumConfs()) get_dihedrals(mol, itag) set_dihedral_histograms(mol, itag, nrbins) get_dihedrals(mol2, itag) #set_weighted_dihedral_histograms(mol2, itag, work, nrbins) set_dihedral_histograms(mol2, itag, nrbins) width, height = 800, 400 image = oedepict.OEImage(width, height) moffset = oedepict.OE2DPoint(0, 0) mframe = oedepict.OEImageFrame(image, width * 0.70, height, moffset) doffset = oedepict.OE2DPoint(mframe.GetWidth(), height * 0.30) dframe = oedepict.OEImageFrame(image, width * 0.30, height * 0.5, doffset) flexibility = True colorg = get_color_gradient(nrbins, flexibility) opts = oedepict.OE2DMolDisplayOptions(mframe.GetWidth(), mframe.GetHeight(), oedepict.OEScale_AutoScale) depict_dihedrals(mframe, dframe, mol, mol2, refmol, opts, itag, nrbins, colorg) if flexibility: lopts = oedepict.OELegendLayoutOptions( oedepict.OELegendLayoutStyle_HorizontalTopLeft, oedepict.OELegendColorStyle_LightBlue, oedepict.OELegendInteractiveStyle_Hover) lopts.SetButtonWidthScale(1.2) lopts.SetButtonHeightScale(1.2) lopts.SetMargin(oedepict.OEMargin_Right, 40.0) lopts.SetMargin(oedepict.OEMargin_Bottom, 80.0) legend = oedepict.OELegendLayout(image, "Legend", lopts) legend_area = legend.GetLegendArea() draw_color_gradient(legend_area, colorg) oedepict.OEDrawLegendLayout(legend) iconscale = 0.5 oedepict.OEAddInteractiveIcon(image, oedepict.OEIconLocation_TopRight, iconscale) oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 10.0) oedepict.OEWriteImage(ofs, ext, image) return 0
def hydrate(system, opt): """ This function solvates the system by using PDBFixer Parameters: ----------- system: OEMol molecule The system to solvate opt: python dictionary The parameters used to solvate the system Return: ------- oe_mol: OEMol The solvated system """ def BoundingBox(molecule): """ This function calculates the Bounding Box of the passed molecule molecule: OEMol return: bb (numpy array) the calculated bounding box is returned as numpy array: [(xmin,ymin,zmin), (xmax,ymax,zmax)] """ coords = [v for k, v in molecule.GetCoords().items()] np_coords = np.array(coords) min_coord = np_coords.min(axis=0) max_coord = np_coords.max(axis=0) bb = np.array([min_coord, max_coord]) return bb # Create a system copy sol_system = system.CreateCopy() # Calculate system BoundingBox (Angstrom units) BB = BoundingBox(sol_system) # Estimation of the box cube length in A box_edge = 2.0 * opt['solvent_padding'] + np.max(BB[1] - BB[0]) # BB center xc = (BB[0][0]+BB[1][0])/2. yc = (BB[0][1]+BB[1][1])/2. zc = (BB[0][2]+BB[1][2])/2. delta = np.array([box_edge/2., box_edge/2., box_edge/2.]) - np.array([xc, yc, zc]) sys_coord_dic = {k: (v+delta) for k, v in sol_system.GetCoords().items()} sol_system.SetCoords(sys_coord_dic) # Load a fake system to initialize PDBfixer filename = resource_filename('pdbfixer', 'tests/data/test.pdb') fixer = PDBFixer(filename=filename) # Convert between OE and OpenMM topology omm_top, omm_pos = oeommutils.oemol_to_openmmTop(sol_system) chain_names = [] for chain in omm_top.chains(): chain_names.append(chain.id) # Set the correct topology to the fake system fixer.topology = omm_top fixer.positions = omm_pos # Solvate the system fixer.addSolvent(padding=unit.Quantity(opt['solvent_padding'], unit.angstroms), ionicStrength=unit.Quantity(opt['salt_concentration'], unit.millimolar)) # The OpenMM topology produced by the solvation fixer has missing bond # orders and aromaticity. The following section is creating a new openmm # topology made of just water molecules and ions. The new topology is then # converted in an OEMol and added to the passed molecule to produce the # solvated system wat_ion_top = app.Topology() # Atom dictionary between the the PDBfixer topology and the water_ion topology fixer_atom_to_wat_ion_atom = {} for chain in fixer.topology.chains(): if chain.id not in chain_names: n_chain = wat_ion_top.addChain(chain.id) for res in chain.residues(): n_res = wat_ion_top.addResidue(res.name, n_chain) for at in res.atoms(): n_at = wat_ion_top.addAtom(at.name, at.element, n_res) fixer_atom_to_wat_ion_atom[at] = n_at for bond in fixer.topology.bonds(): at0 = bond[0] at1 = bond[1] try: wat_ion_top.addBond(fixer_atom_to_wat_ion_atom[at0], fixer_atom_to_wat_ion_atom[at1], type=None, order=1) except: pass wat_ion_pos = fixer.positions[len(omm_pos):] oe_mol = oeommutils.openmmTop_to_oemol(wat_ion_top, wat_ion_pos) # Setting the box vectors omm_box_vectors = fixer.topology.getPeriodicBoxVectors() box_vectors = utils.PackageOEMol.encodePyObj(omm_box_vectors) oe_mol.SetData(oechem.OEGetTag('box_vectors'), box_vectors) oechem.OEAddMols(oe_mol, sol_system) return oe_mol
def process(self, mol, port): try: if port == 'system_port': self.system = mol self.check_system = True return if self.check_system: num_conf = 0 name = 'p' + self.system.GetTitle() + '_l' + mol.GetTitle()[0:12] + '_' + str(self.count) for conf in mol.GetConfs(): conf_mol = oechem.OEMol(conf) complx = self.system.CreateCopy() oechem.OEAddMols(complx, conf_mol) # Split the complex in components protein, ligand, water, excipients = utils.split(complx) # If the protein does not contain any atom emit a failure if not protein.NumAtoms(): # Error: protein molecule is empty oechem.OEThrow.Fatal("The protein molecule does not contains atoms") # If the ligand does not contain any atom emit a failure if not ligand.NumAtoms(): # Error: ligand molecule is empty oechem.OEThrow.Fatal("The Ligand molecule does not contains atoms") # If the water does not contain any atom emit a failure if not water.NumAtoms(): # Error: water molecule is empty oechem.OEThrow.Fatal("The water does not contains atoms. This could happen if not" "solvation process has occurred") # Check if the ligand is inside the binding site. Cutoff distance 3A if not oeommutils.check_shell(ligand, protein, 3): oechem.OEThrow.Fatal("The ligand is probably outside the protein binding site") # Removing possible clashes between the ligand and water or excipients water_del = oeommutils.delete_shell(ligand, water, 1.5, in_out='in') excipient_del = oeommutils.delete_shell(ligand, excipients, 1.5, in_out='in') # Reassemble the complex new_complex = protein.CreateCopy() oechem.OEAddMols(new_complex, ligand) oechem.OEAddMols(new_complex, excipient_del) oechem.OEAddMols(new_complex, water_del) name_c = name if mol.GetMaxConfIdx() > 1: name_c = name + '_c' + str(num_conf) new_complex.SetData(oechem.OEGetTag('IDTag'), name_c) new_complex.SetTitle(name_c) num_conf += 1 self.success.emit(new_complex) self.count += 1 except Exception as e: # Attach error message to the molecule that failed self.log.error(traceback.format_exc()) mol.SetData('error', str(e)) # Return failed mol self.failure.emit(mol) return
def main(argv=[__name__]): itf = oechem.OEInterface() oechem.OEConfigure(itf, InterfaceData) oedepict.OEConfigureImageWidth(itf, 600.0) oedepict.OEConfigureImageHeight(itf, 600.0) oedepict.OEConfigure2DMolDisplayOptions(itf, oedepict.OE2DMolDisplaySetup_AromaticStyle) oechem.OEConfigureSplitMolComplexOptions(itf, oechem.OESplitMolComplexSetup_LigName) if not oechem.OEParseCommandLine(itf, argv): return 1 iname = itf.GetString("-complex") oname = itf.GetString("-out") ifs = oechem.oemolistream() if not ifs.open(iname): oechem.OEThrow.Fatal("Cannot open input file!") ext = oechem.OEGetFileExtension(oname) if not oedepict.OEIsRegisteredImageFile(ext): oechem.OEThrow.Fatal("Unknown image type!") ofs = oechem.oeofstream() if not ofs.open(oname): oechem.OEThrow.Fatal("Cannot open output file!") complexmol = oechem.OEGraphMol() if not oechem.OEReadMolecule(ifs, complexmol): oechem.OEThrow.Fatal("Unable to read molecule from %s" % iname) if not oechem.OEHasResidues(complexmol): oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All) # Separate ligand and protein sopts = oechem.OESplitMolComplexOptions() oechem.OESetupSplitMolComplexOptions(sopts, itf) ligand = oechem.OEGraphMol() protein = oechem.OEGraphMol() water = oechem.OEGraphMol() other = oechem.OEGraphMol() oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts) if ligand.NumAtoms() == 0: oechem.OEThrow.Fatal("Cannot separate complex!") # Calculate average BFactor of the whole complex avgbfactor = GetAverageBFactor(complexmol) # Calculate minimum and maximum BFactor of the ligand and its environment minbfactor, maxbfactor = GetMinAndMaxBFactor(ligand, protein) # Attach to each ligand atom the average BFactor of the nearby protein atoms stag = "avg residue BFfactor" itag = oechem.OEGetTag(stag) SetAverageBFactorOfNearbyProteinAtoms(ligand, protein, itag) oechem.OEThrow.Info("Average BFactor of the complex = %+.3f" % avgbfactor) oechem.OEThrow.Info("Minimum BFactor of the ligand and its environment = %+.3f" % minbfactor) oechem.OEThrow.Info("Maximum BFactor of the ligand and its environment = %+.3f" % maxbfactor) # Create image imagewidth, imageheight = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf) image = oedepict.OEImage(imagewidth, imageheight) mframe = oedepict.OEImageFrame(image, imagewidth, imageheight * 0.90, oedepict.OE2DPoint(0.0, 0.0)) lframe = oedepict.OEImageFrame(image, imagewidth, imageheight * 0.10, oedepict.OE2DPoint(0.0, imageheight * 0.90)) opts = oedepict.OE2DMolDisplayOptions(mframe.GetWidth(), mframe.GetHeight(), oedepict.OEScale_AutoScale) oedepict.OESetup2DMolDisplayOptions(opts, itf) opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome) # Create BFactor color gradient colorg = oechem.OELinearColorGradient() colorg.AddStop(oechem.OEColorStop(0.0, oechem.OEDarkBlue)) colorg.AddStop(oechem.OEColorStop(10.0, oechem.OELightBlue)) colorg.AddStop(oechem.OEColorStop(25.0, oechem.OEYellowTint)) colorg.AddStop(oechem.OEColorStop(50.0, oechem.OERed)) colorg.AddStop(oechem.OEColorStop(100.0, oechem.OEDarkRose)) # Prepare ligand for depiction oegrapheme.OEPrepareDepictionFrom3D(ligand) arcfxn = BFactorArcFxn(colorg, itag) for atom in ligand.GetAtoms(): oegrapheme.OESetSurfaceArcFxn(ligand, atom, arcfxn) opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(ligand, opts)) # Render ligand and visualize BFactor disp = oedepict.OE2DMolDisplay(ligand, opts) colorbfactor = ColorLigandAtomByBFactor(colorg) oegrapheme.OEAddGlyph(disp, colorbfactor, oechem.OEIsTrueAtom()) oegrapheme.OEDraw2DSurface(disp) oedepict.OERenderMolecule(mframe, disp) # Draw color gradient opts = oegrapheme.OEColorGradientDisplayOptions() opts.SetColorStopPrecision(1) opts.AddMarkedValue(avgbfactor) opts.SetBoxRange(minbfactor, maxbfactor) oegrapheme.OEDrawColorGradient(lframe, colorg, opts) oedepict.OEWriteImage(oname, image) return 0
def process(self, mol, port): try: # Split the complex in components in order to apply the FF protein, ligand, water, excipients = oeommutils.split( mol, ligand_res_name=self.opt['ligand_res_name']) self.log.info( "\nComplex name: {}\nProtein atom numbers = {}\nLigand atom numbers = {}\n" "Water atom numbers = {}\nExcipients atom numbers = {}".format( mol.GetTitle(), protein.NumAtoms(), ligand.NumAtoms(), water.NumAtoms(), excipients.NumAtoms())) # Unique prefix name used to output parametrization files self.opt['prefix_name'] = mol.GetTitle() oe_mol_list = [] par_mol_list = [] # Apply FF to the Protein if protein.NumAtoms(): oe_mol_list.append(protein) protein_structure = utils.applyffProtein(protein, self.opt) par_mol_list.append(protein_structure) # Apply FF to the ligand if ligand.NumAtoms(): oe_mol_list.append(ligand) ligand_structure = utils.applyffLigand(ligand, self.opt) par_mol_list.append(ligand_structure) # Apply FF to water molecules if water.NumAtoms(): oe_mol_list.append(water) water_structure = utils.applyffWater(water, self.opt) par_mol_list.append(water_structure) # Apply FF to the excipients if excipients.NumAtoms(): excipient_structure = utils.applyffExcipients( excipients, self.opt) par_mol_list.append(excipient_structure) # The excipient order is set equal to the order in related # parmed structure to avoid possible atom index mismatching excipients = oeommutils.openmmTop_to_oemol( excipient_structure.topology, excipient_structure.positions, verbose=False) oechem.OEPerceiveBondOrders(excipients) oe_mol_list.append(excipients) # Build the overall Parmed structure complex_structure = parmed.Structure() for struc in par_mol_list: complex_structure = complex_structure + struc complx = oe_mol_list[0].CreateCopy() num_atom_system = complx.NumAtoms() for idx in range(1, len(oe_mol_list)): oechem.OEAddMols(complx, oe_mol_list[idx]) num_atom_system += oe_mol_list[idx].NumAtoms() if not num_atom_system == complex_structure.topology.getNumAtoms(): oechem.OEThrow.Fatal( "Parmed and OE topologies mismatch atom number error") complx.SetTitle(mol.GetTitle()) # Set Parmed structure box_vectors is_periodic = True try: vec_data = pack_utils.PackageOEMol.getData(complx, tag='box_vectors') vec = pack_utils.PackageOEMol.decodePyObj(vec_data) complex_structure.box_vectors = vec except: is_periodic = False self.log.warn( "System has been parametrize without periodic box vectors for vacuum simulation" ) # Attach the Parmed structure to the complex packed_complex = pack_utils.PackageOEMol.pack( complx, complex_structure) # Attach the reference positions to the complex ref_positions = complex_structure.positions packedpos = pack_utils.PackageOEMol.encodePyObj(ref_positions) packed_complex.SetData(oechem.OEGetTag('OEMDDataRefPositions'), packedpos) # Set atom serial numbers, Ligand name and HETATM flag # oechem.OEPerceiveResidues(packed_complex, oechem.OEPreserveResInfo_SerialNumber) for at in packed_complex.GetAtoms(): thisRes = oechem.OEAtomGetResidue(at) thisRes.SetSerialNumber(at.GetIdx()) if thisRes.GetName() == 'UNL': # thisRes.SetName("LIG") thisRes.SetHetAtom(True) oechem.OEAtomSetResidue(at, thisRes) if packed_complex.GetMaxAtomIdx( ) != complex_structure.topology.getNumAtoms(): raise ValueError( "OEMol complex and Parmed structure mismatch atom numbers") # Check if it is possible to create the OpenMM System if is_periodic: complex_structure.createSystem( nonbondedMethod=app.CutoffPeriodic, nonbondedCutoff=10.0 * unit.angstroms, constraints=app.HBonds, removeCMMotion=False) else: complex_structure.createSystem(nonbondedMethod=app.NoCutoff, constraints=app.HBonds, removeCMMotion=False) self.success.emit(packed_complex) except Exception as e: # Attach error message to the molecule that failed self.log.error(traceback.format_exc()) mol.SetData('error', str(e)) # Return failed mol self.failure.emit(mol) return
def getData(molecule, tag): return molecule.GetData(oechem.OEGetTag(str(tag)))
def getReporters(totalSteps=None, outfname=None, **opt): """ Creates 3 OpenMM Reporters for the simulation. Parameters ---------- totalSteps : int The total number of simulation steps reportInterval : (opt), int, default=1000 Step frequency to write to reporter file. outfname : str Specifies the filename prefix for the reporters. Returns ------- reporters : list of three openmm.app.simulation.reporters (0) state_reporter: writes energies to '.log' file. (1) progress_reporter: prints simulation progress to 'sys.stdout' (2) traj_reporter: writes trajectory to file. Supported format .nc, .dcd, .hdf5 """ if totalSteps is None: totalSteps = opt['steps'] if outfname is None: outfname = opt['outfname'] reporters = [] if opt['reporter_interval']: state_reporter = app.StateDataReporter(outfname+'.log', separator="\t", reportInterval=opt['reporter_interval'], step=True, potentialEnergy=True, totalEnergy=True, volume=True, density=True, temperature=True) reporters.append(state_reporter) progress_reporter = app.StateDataReporter(stdout, separator="\t", reportInterval=opt['reporter_interval'], step=True, totalSteps=totalSteps, time=True, speed=True, progress=True, elapsedTime=True, remainingTime=True) reporters.append(progress_reporter) if opt['trajectory_interval']: trj_fname = outfname # Trajectory file format selection if opt['trajectory_filetype'] == 'NetCDF': trj_fname += '.nc' traj_reporter = mdtraj.reporters.NetCDFReporter(trj_fname, opt['trajectory_interval']) elif opt['trajectory_filetype'] == 'DCD': trj_fname += '.dcd' traj_reporter = app.DCDReporter(trj_fname, opt['trajectory_interval']) elif opt['trajectory_filetype'] == 'HDF5': trj_fname += '.hdf5' mdtraj.reporters.HDF5Reporter(trj_fname, opt['trajectory_interval']) else: oechem.OEThrow.Fatal("The selected trajectory file format is not supported: {}" .format(opt['trajectory_filetype'])) opt['molecule'].SetData(oechem.OEGetTag("Trj_fname"), trj_fname) reporters.append(traj_reporter) return reporters
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved. # # TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is # provided to current licensees or subscribers of OpenEye products or # SaaS offerings (each a "Customer"). # Customer is hereby permitted to use, copy, and modify the Sample Code, # subject to these terms. OpenEye claims no rights to Customer's # modifications. Modification of Sample Code is at Customer's sole and # exclusive risk. Sample Code may require Customer to have a then # current license or subscription to the applicable OpenEye offering. # THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT # NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A # PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be # liable for any damages or liability in connection with the Sample Code # or its use. # @ <SNIPPET> from openeye import oechem mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C1CCCC(C(=O)O)C1") # @ <SNIPPET-TYPE-MISMATCH> tag = oechem.OEGetTag("MolWeight") weight = oechem.OECalculateMolecularWeight(mol) mol.SetData(tag, float(weight)) mol.SetData(tag, int(weight)) # @ </SNIPPET-TYPE-MISMATCH> # @ </SNIPPET>
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT # NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A # PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be # liable for any damages or liability in connection with the Sample Code # or its use. from __future__ import print_function from openeye import oechem qmol = oechem.OEGraphMol() oechem.OESmilesToMol(qmol, "c1ccccc1") # create a substructure search object # @ <SNIPPET> itag = oechem.OEGetTag("__origr_idx") for ai in qmol.GetAtoms(): ai.SetData(itag, ai.GetIdx()) ss = oechem.OESubSearch(qmol, oechem.OEExprOpts_DefaultAtoms, oechem.OEExprOpts_DefaultBonds) tmol = oechem.OEGraphMol() oechem.OESmilesToMol(tmol, "Cc1ccccc1") oechem.OEPrepareSearch(tmol, ss) for mi in ss.Match(tmol, True): match = oechem.OEMatch() for apairi in mi.GetAtoms(): pidx = apairi.pattern.GetData(itag) pattern = qmol.GetAtom(oechem.OEHasAtomIdx(pidx)) match.AddPair(pattern, apairi.target)
def oesolvate(solute, density=1.0, padding_distance=10.0, distance_between_atoms=2.5, solvents='tip3p', molar_fractions='1.0', geometry='box', close_solvent=True, salt='[Na+], [Cl-]', salt_concentration=0.0, neutralize_solute=True, verbose=False, return_components=False, **kargs): """ This function solvates the passed solute in a cubic box or a sphere by using Packmol. Packmol creates an initial point for molecular dynamics simulations by packing molecule in defined regions of space. For additional info: http://www.ime.unicamp.br/~martinez/packmol/home.shtml The geometry volume is estimated by the using the padding parameter and the solute size. The number of solvent molecules is calculated by using the specified density and volume. Solvent molecules are specified as comma separated smiles strings. The molar fractions of each solvent molecule are specified in a similar fashion. By default if the solute is charged counter ions are added to neutralize it Parameters: ----------- solute: OEMol molecule The solute to solvate density: float The solution density in g/ml padding_distance: float The largest dimension of the solute (along the x, y, or z axis) is determined (in A), and a cubic box of size (largest dimension)+2*padding is used distance_between_atoms: float The minimum distance between atoms in A solvents: python string A comma separated smiles string or keywords for the solvent molecules. Special water models can be selected by using the keywords: tip3p for TIP3P water model geometry molar_fractions: python string A comma separated molar fraction string of the solvent molecules close_solvent: boolean If True solvent molecules will be placed very close to the solute salt: python string A comma separated string of the dissociated salt in solution salt_concentration: float Salt concentration in millimolar neutralize_solute: boolean If True counter-ions will be added to the solution to neutralize the solute verbose: Bool If True verbose mode is enabled return_components: Bool If True the added solvent molecules are also returned as OEMol Return: ------- oe_mol: OEMol The solvated system. If the selected geometry is a box a SD tag with name 'box_vector' is attached the output molecule containing the system box vectors. oe_mol_components: OEMol If the return_components flag is True the added solvent molecules are returned as an additional OEMol """ def BoundingBox(molecule): """ This function calculates the Bounding Box of the passed molecule molecule: OEMol return: bb (numpy array) the calculated bounding box is returned as numpy array: [(xmin,ymin,zmin), (xmax,ymax,zmax)] """ coords = [v for k, v in molecule.GetCoords().items()] np_coords = np.array(coords) min_coord = np_coords.min(axis=0) max_coord = np_coords.max(axis=0) bb = np.array([min_coord, max_coord]) return bb if shutil.which("packmol") is None: raise (IOError("Packmol executable not found")) # Extract solvent smiles strings and mole fractions solvents = [sm.strip() for sm in solvents.split(',')] fractions = [float(mf) for mf in molar_fractions.split(',')] # If the smiles string and mole fractions lists have different lengths raise an error if len(solvents) != len(fractions): raise ValueError( "Selected solvent number and selected molar fraction number mismatch: {} vs {}" .format(len(solvents), len(fractions))) # Remove smiles string with 0.0 mole fraction solvent_smiles = [ solvents[i] for i, v in enumerate(fractions) if fractions[i] ] mol_fractions = [mf for mf in fractions if mf] # Mole fractions are non-negative numbers if any([v < 0.0 for v in mol_fractions]): raise ValueError("Error: Mole fractions are non-negative real numbers") # Mole fractions must sum up to 1.0 if abs(sum(mol_fractions) - 1.0) > 0.001: oechem.OEThrow.Error("Error: Mole fractions do not sum up to 1.0") if geometry not in ['box', 'sphere']: raise ValueError( "Error geometry: the supported geometries are box and sphere not {}" .format(geometry)) # Set Units density = density * unit.grams / unit.milliliter padding_distance = padding_distance * unit.angstrom salt_concentration = salt_concentration * unit.millimolar # Calculate the Solute Bounding Box BB_solute = BoundingBox(solute) # Estimate of the box cube length box_edge = 2.0 * padding_distance + np.max(BB_solute[1] - BB_solute[0]) * unit.angstrom if geometry == 'box': # Box Volume Volume = box_edge**3 if geometry == 'sphere': Volume = (4.0 / 3.0) * 3.14159265 * (0.5 * box_edge)**3 # Omega engine is used to generate conformations omegaOpts = oeomega.OEOmegaOptions() omegaOpts.SetMaxConfs(1) omegaOpts.SetStrictStereo(False) omega = oeomega.OEOmega(omegaOpts) # Create a string code to identify the solute residues. The code ID used is based # on the residue number id, the residue name and the chain id: # id+resname+chainID hv_solute = oechem.OEHierView( solute, oechem.OEAssumption_BondedResidue + oechem.OEAssumption_ResPerceived) solute_resid_list = [] for chain in hv_solute.GetChains(): for frag in chain.GetFragments(): for hres in frag.GetResidues(): oe_res = hres.GetOEResidue() solute_resid_list.append( str(oe_res.GetResidueNumber()) + oe_res.GetName() + chain.GetChainID()) # Solvent component list_names solvent_resid_dic_names = dict() # Neutralize solute ion_sum_wgt_n_ions = 0.0 * unit.grams / unit.mole if neutralize_solute: # Container for the counter-ions oe_ions = [] # Container for the ion smiles strings ions_smiles = [] solute_formal_charge = 0 for at in solute.GetAtoms(): solute_formal_charge += at.GetFormalCharge() if solute_formal_charge > 0: ions_smiles.append("[Cl-]") elif solute_formal_charge < 0: ions_smiles.append("[Na+]") else: pass # Total number of counter-ions to neutralize the solute n_ions = abs(solute_formal_charge) # print("Counter ions to add = {} of {}".format(n_ions, ions_smiles[0])) # Ions if n_ions >= 1: for sm in ions_smiles: mol = oechem.OEMol() if not oechem.OESmilesToMol(mol, sm): raise ValueError( "Error counter ions: SMILES string parsing fails for the string: {}" .format(sm)) # Generate conformer if not omega(mol): raise ValueError( "Error counter ions: Conformer generation fails for the molecule with " "smiles string: {}".format(sm)) oe_ions.append(mol) if sm == '[Na+]': solvent_resid_dic_names[' NA'] = mol else: solvent_resid_dic_names[' CL'] = mol ion_sum_wgt = 0.0 * unit.grams / unit.mole for ion in oe_ions: # Molecular weight ion_sum_wgt += oechem.OECalculateMolecularWeight( ion) * unit.grams / unit.mole ion_sum_wgt_n_ions = ion_sum_wgt * n_ions # Create ions .pdb files ions_smiles_pdbs = [] for i in range(0, len(ions_smiles)): pdb_name = os.path.basename(tempfile.mktemp(suffix='.pdb')) pdb_name = ions_smiles[i] + '_' + pdb_name ions_smiles_pdbs.append(pdb_name) for i in range(0, len(ions_smiles)): ofs = oechem.oemolostream(ions_smiles_pdbs[i]) oechem.OEWriteConstMolecule(ofs, oe_ions[i]) # Add salts to the solution # Solvent smiles string parsing char_set = string.ascii_uppercase salt_sum_wgt_n_salt = 0.0 * unit.grams / unit.mole if salt_concentration > 0.0 * unit.millimolar: salt_smiles = [sm.strip() for sm in salt.split(',')] # Container list of oemol salt molecules generated by using smiles strings oe_salt = [] for sm in salt_smiles: mol_salt = oechem.OEMol() if not oechem.OESmilesToMol(mol_salt, sm): raise ValueError( "Error salt: SMILES string parsing fails for the string: {}" .format(sm)) # Generate conformer if not omega(mol_salt): raise ValueError( "Error salt: Conformer generation fails for the " "molecule with smiles string: {}".format(sm)) # Unique 3 code letter are set as solvent residue names solv_id = ''.join(random.sample(char_set * 3, 3)) # Try to recognize the residue name oechem.OEPerceiveResidues(mol_salt) for atmol in mol_salt.GetAtoms(): res = oechem.OEAtomGetResidue(atmol) if res.GetName() == 'UNL': res.SetName(solv_id) oechem.OEAtomSetResidue(atmol, res) if solv_id not in solvent_resid_dic_names: solvent_resid_dic_names[solv_id] = mol_salt else: if res.GetName() not in solvent_resid_dic_names: solvent_resid_dic_names[res.GetName()] = mol_salt break oe_salt.append(mol_salt) n_salt = int( round(unit.AVOGADRO_CONSTANT_NA * salt_concentration * Volume.in_units_of(unit.liter))) # for i in range(0, len(salt_smiles)): # print("Number of molecules for the salt component {} = {}".format(salt_smiles[i], n_salt)) salt_sum_wgt = 0.0 * unit.grams / unit.mole for salt in oe_salt: # Molecular weight salt_sum_wgt += oechem.OECalculateMolecularWeight( salt) * unit.grams / unit.mole salt_sum_wgt_n_salt = salt_sum_wgt * n_salt # Create salt .pdb files if n_salt >= 1: salt_pdbs = [] for i in range(0, len(salt_smiles)): pdb_name = os.path.basename(tempfile.mktemp(suffix='.pdb')) # pdb_name = salt_smiles[i] + '_' + pdb_name salt_pdbs.append(pdb_name) for i in range(0, len(salt_smiles)): ofs = oechem.oemolostream(salt_pdbs[i]) oechem.OEWriteConstMolecule(ofs, oe_salt[i]) # Container list of oemol solvent molecules generated by using smiles strings oe_solvents = [] for sm in solvent_smiles: if sm == 'tip3p': tip3p_fn = os.path.join(PACKAGE_DIR, 'oeommtools', 'data', 'tip3p.pdb') ifs = oechem.oemolistream(tip3p_fn) mol_sol = oechem.OEMol() if not oechem.OEReadMolecule(ifs, mol_sol): raise IOError( "It was not possible to read the tip3p molecule file") else: mol_sol = oechem.OEMol() if not oechem.OESmilesToMol(mol_sol, sm): raise ValueError( "Error solvent: SMILES string parsing fails for the string: {}" .format(sm)) # Generate conformer if not omega(mol_sol): raise ValueError( "Error solvent: Conformer generation fails for " "the molecule with smiles string: {}".format(sm)) # Unique 3 code letter are set as solvent residue names solv_id = ''.join(random.sample(char_set * 3, 3)) # Try to recognize the residue name oechem.OEPerceiveResidues(mol_sol) for atmol in mol_sol.GetAtoms(): res = oechem.OEAtomGetResidue(atmol) if res.GetName() == 'UNL': res.SetName(solv_id) oechem.OEAtomSetResidue(atmol, res) if solv_id not in solvent_resid_dic_names: solvent_resid_dic_names[solv_id] = mol_sol else: if res.GetName() not in solvent_resid_dic_names: solvent_resid_dic_names[res.GetName()] = mol_sol break oe_solvents.append(mol_sol) # Sum of the solvent molecular weights solvent_sum_wgt_frac = 0.0 * unit.grams / unit.mole for idx in range(0, len(oe_solvents)): # Molecular weight wgt = oechem.OECalculateMolecularWeight( oe_solvents[idx]) * unit.grams / unit.mole solvent_sum_wgt_frac += wgt * mol_fractions[idx] # Solute molecular weight solute_wgt = oechem.OECalculateMolecularWeight( solute) * unit.gram / unit.mole # Estimate of the number of each molecular species present in the solution accordingly # to their molar fraction fi: # # ni = fi*(density*volume*NA - wgt_solute - sum_k(wgt_salt_k*nk) - wgt_ion*n_ion)/sum_j(wgt_nj * fj) # # where ni is the number of molecule of specie i, density the mixture density, volume the # mixture volume, wgt_solute the molecular weight of the solute, wgt_salt_k the molecular # weight of the salt component k, nk the number of molecule of salt component k, wgt_ion # the counter ion molecular weight, n_ions the number of counter ions and wgt_nj the molecular # weight of the molecule specie j with molar fraction fj div = (unit.AVOGADRO_CONSTANT_NA * density * Volume - (solute_wgt + salt_sum_wgt_n_salt + ion_sum_wgt_n_ions)) / solvent_sum_wgt_frac # Solvent number of monomers n_monomers = [int(round(mf * div)) for mf in mol_fractions] if not all([nm > 0 for nm in n_monomers]): raise ValueError( "Error negative number of solvent components: the density could be too low" ) # for i in range(0, len(solvent_smiles)): # print("Number of molecules for the component {} = {}".format(solvent_smiles[i], n_monomers[i])) # Packmol Configuration file setting if close_solvent: header_template = """\n# Mixture\ntolerance {}\nfiletype pdb\noutput {}\nadd_amber_ter\navoid_overlap no""" else: header_template = """\n# Mixture\ntolerance {}\nfiletype pdb\noutput {}\nadd_amber_ter\navoid_overlap yes""" # Templates strings solute_template = """\n\n# Solute\nstructure {}\nnumber 1\nfixed 0. 0. 0. 0. 0. 0.\nresnumbers 1\nend structure""" if geometry == 'box': solvent_template = """\nstructure {}\nnumber {}\ninside box {:0.3f} {:0.3f} {:0.3f} {:0.3f} {:0.3f} {:0.3f}\ \nchain !\nresnumbers 3\nend structure""" if geometry == 'sphere': solvent_template = """\nstructure {}\nnumber {}\ninside sphere {:0.3f} {:0.3f} {:0.3f} {:0.3f}\ \nchain !\nresnumbers 3\nend structure""" # Create solvents .pdb files solvent_pdbs = [] for i in range(0, len(solvent_smiles)): pdb_name = os.path.basename(tempfile.mktemp(suffix='.pdb')) solvent_pdbs.append(pdb_name) for i in range(0, len(solvent_smiles)): ofs = oechem.oemolostream(solvent_pdbs[i]) oechem.OEWriteConstMolecule(ofs, oe_solvents[i]) solute_pdb = 'solute' + '_' + os.path.basename( tempfile.mktemp(suffix='.pdb')) ofs = oechem.oemolostream(solute_pdb) if solute.GetMaxConfIdx() > 1: raise ValueError("Solutes with multiple conformers are not supported") else: oechem.OEWriteConstMolecule(ofs, solute) # Write Packmol header section mixture_pdb = 'mixture' + '_' + os.path.basename( tempfile.mktemp(suffix='.pdb')) body = header_template.format(distance_between_atoms, mixture_pdb) # Write Packmol configuration file solute section body += solute_template.format(solute_pdb) # The solute is centered inside the box xc = (BB_solute[0][0] + BB_solute[1][0]) / 2. yc = (BB_solute[0][1] + BB_solute[1][1]) / 2. zc = (BB_solute[0][2] + BB_solute[1][2]) / 2. # Correct for periodic box conditions to avoid # steric clashes at the box edges pbc_correction = 1.0 * unit.angstrom xmin = xc - ((box_edge - pbc_correction) / 2.) / unit.angstrom xmax = xc + ((box_edge - pbc_correction) / 2.) / unit.angstrom ymin = yc - ((box_edge - pbc_correction) / 2.) / unit.angstrom ymax = yc + ((box_edge - pbc_correction) / 2.) / unit.angstrom zmin = zc - ((box_edge - pbc_correction) / 2.) / unit.angstrom zmax = zc + ((box_edge - pbc_correction) / 2.) / unit.angstrom # Packmol setting for the solvent section body += '\n\n# Solvent' for i in range(0, len(solvent_smiles)): if geometry == 'box': body += solvent_template.format(solvent_pdbs[i], n_monomers[i], xmin, ymin, zmin, xmax, ymax, zmax) if geometry == 'sphere': body += solvent_template.format(solvent_pdbs[i], n_monomers[i], xc, yc, zc, 0.5 * box_edge / unit.angstrom) # Packmol setting for the salt section if salt_concentration > 0.0 * unit.millimolar and n_salt >= 1: body += '\n\n# Salt' for i in range(0, len(salt_smiles)): if geometry == 'box': body += solvent_template.format(salt_pdbs[i], int(round(n_salt)), xmin, ymin, zmin, xmax, ymax, zmax) if geometry == 'sphere': body += solvent_template.format(salt_pdbs[i], int(round(n_salt)), xc, yc, zc, 0.5 * box_edge / unit.angstrom) # Packmol setting for the ions section if neutralize_solute and n_ions >= 1: body += '\n\n# Counter Ions' for i in range(0, len(ions_smiles)): if geometry == 'box': body += solvent_template.format(ions_smiles_pdbs[i], n_ions, xmin, ymin, zmin, xmax, ymax, zmax) if geometry == 'sphere': body += solvent_template.format(ions_smiles_pdbs[i], n_ions, xc, yc, zc, 0.5 * box_edge / unit.angstrom) # Packmol configuration file packmol_filename = os.path.basename(tempfile.mktemp(suffix='.inp')) with open(packmol_filename, 'w') as file_handle: file_handle.write(body) # Call Packmol if not verbose: mute_output = open(os.devnull, 'w') with open(packmol_filename, 'r') as file_handle: subprocess.check_call(['packmol'], stdin=file_handle, stdout=mute_output, stderr=mute_output) else: with open(packmol_filename, 'r') as file_handle: subprocess.check_call(['packmol'], stdin=file_handle) # Read in the Packmol solvated system solvated = oechem.OEMol() if os.path.exists(mixture_pdb + '_FORCED'): os.rename(mixture_pdb + '_FORCED', mixture_pdb) print("Warning: Packing solution is not optimal") ifs = oechem.oemolistream(mixture_pdb) oechem.OEReadMolecule(ifs, solvated) # To avoid to change the user oemol starting solute by reading in # the generated mixture pdb file and loosing molecule info, the # solvent molecules are extracted from the mixture system and # added back to the starting solute # Extract from the solution system the solvent molecules # by checking the previous solute generated ID: id+resname+chainID hv_solvated = oechem.OEHierView( solvated, oechem.OEAssumption_BondedResidue + oechem.OEAssumption_ResPerceived) # This molecule will hold the solvent molecules generated directly from # the omega conformers. This is useful to avoid problems related to read in # the solvent molecules from pdb files and triggering unwanted perceiving actions new_components = oechem.OEMol() bv = oechem.OEBitVector(solvated.GetMaxAtomIdx()) for chain in hv_solvated.GetChains(): for frag in chain.GetFragments(): for hres in frag.GetResidues(): oe_res = hres.GetOEResidue() if str(oe_res.GetResidueNumber()) + oe_res.GetName( ) + chain.GetChainID() not in solute_resid_list: oechem.OEAddMols(new_components, solvent_resid_dic_names[oe_res.GetName()]) atms = hres.GetAtoms() for at in atms: bv.SetBitOn(at.GetIdx()) pred = oechem.OEAtomIdxSelected(bv) components = oechem.OEMol() oechem.OESubsetMol(components, solvated, pred) new_components.SetCoords(components.GetCoords()) # This is necessary otherwise just one big residue is created oechem.OEPerceiveResidues(new_components) # Add the solvent molecules to the solute copy solvated_system = solute.CreateCopy() oechem.OEAddMols(solvated_system, new_components) # Set Title solvated_system.SetTitle(solute.GetTitle()) # Set ions resname to Na+ and Cl- for at in solvated_system.GetAtoms(): res = oechem.OEAtomGetResidue(at) if res.GetName() == ' NA': res.SetName("Na+") oechem.OEAtomSetResidue(atmol, res) elif res.GetName() == ' CL': res.SetName("Cl-") oechem.OEAtomSetResidue(atmol, res) else: pass # Cleaning to_delete = solvent_pdbs + [packmol_filename, solute_pdb, mixture_pdb] if salt_concentration > 0.0 * unit.millimolar and n_salt >= 1: to_delete += salt_pdbs if neutralize_solute and n_ions >= 1: to_delete += ions_smiles_pdbs for fn in to_delete: try: os.remove(fn) except: pass # Calculate the solution total density total_wgt = oechem.OECalculateMolecularWeight( solvated_system) * unit.gram / unit.mole density_mix = (1 / unit.AVOGADRO_CONSTANT_NA) * total_wgt / Volume print("Computed Solution Density = {}".format( density_mix.in_units_of(unit.gram / unit.milliliter))) # Threshold checking ths = 0.1 * unit.gram / unit.milliliter if not abs(density - density_mix.in_units_of(unit.gram / unit.milliliter)) < ths: raise ValueError( "Error: the computed density for the solute {} does not match the selected density {} vs {}" .format(solute.GetTitle(), density_mix, density)) if geometry == 'box': # Define the box vector and attached it as SD tag to the solvated system # with ID tag: 'box_vectors' box_vectors = (Vec3(box_edge / unit.angstrom, 0.0, 0.0), Vec3(0.0, box_edge / unit.angstrom, 0.0), Vec3(0.0, 0.0, box_edge / unit.angstrom)) * unit.angstrom box_vectors = data_utils.encodePyObj(box_vectors) solvated_system.SetData(oechem.OEGetTag('box_vectors'), box_vectors) if return_components: new_components.SetTitle(solute.GetTitle() + '_solvent_comp') return solvated_system, new_components else: return solvated_system