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Merge pull request #84 from molssi-seamm/dev
Added access to OpenEye mols and SMILES
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,184 @@ | ||
| # -*- coding: utf-8 -*- | ||
|
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||
| """Interface to OpenEye OEChem.""" | ||
|
|
||
| import logging | ||
|
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||
| try: | ||
| from openeye import oechem | ||
| except ModuleNotFoundError: | ||
| oechem_available = False | ||
| oechem_licensed = False | ||
| else: | ||
| oechem_available = True | ||
| oechem_licensed = oechem.OEChemIsLicensed() | ||
|
|
||
| logger = logging.getLogger(__name__) | ||
|
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||
|
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| def check_openeye_license(): | ||
| if not oechem_available: | ||
| raise RuntimeError( | ||
| "OpenEye OEChem is not installed! See " | ||
| "https://docs.eyesopen.com/toolkits/python/index.html for detail" | ||
| ) | ||
| if not oechem_licensed: | ||
| raise RuntimeError( | ||
| "Cannot find a license for OpenEye OEChem! See " | ||
| "https://docs.eyesopen.com/toolkits/python/index.html for detail" | ||
| ) | ||
|
|
||
|
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| class OpenEyeMixin: | ||
| """A mixin for handling OpenEye's software via its Python interface.""" | ||
|
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| def to_OEGraphMol(self, properties=None): | ||
| """Return an OEGraphMol object for the configuration, template, or subset.""" | ||
| check_openeye_license() | ||
| oe_mol = oechem.OEGraphMol() | ||
|
|
||
| if self.__class__.__name__ == "_Configuration": | ||
| oe_mol.SetIntData("net charge", self.charge) | ||
| oe_mol.SetIntData("spin multiplicity", self.spin_multiplicity) | ||
|
|
||
| # Create the atoms | ||
| oe_atoms = [] | ||
| if "charge" in self.atoms: | ||
| charges = self.atoms.get_column_data("charge") | ||
| for atno, xyz, q in zip( | ||
| self.atoms.atomic_numbers, self.atoms.coordinates, charges | ||
| ): | ||
| oe_atom = oe_mol.NewAtom(atno) | ||
| oe_mol.SetCoords(oe_atom, xyz) | ||
| oe_atom.SetPartialCharge(q) | ||
| oe_atoms.append(oe_atom) | ||
| else: | ||
| for atno, xyz in zip(self.atoms.atomic_numbers, self.atoms.coordinates): | ||
| oe_atom = oe_mol.NewAtom(atno) | ||
| oe_mol.SetCoords(oe_atom, xyz) | ||
| oe_atoms.append(oe_atom) | ||
|
|
||
| # and bonds | ||
| index = {j: i for i, j in enumerate(self.atoms.ids)} | ||
| for row in self.bonds.bonds(): | ||
| oe_mol.NewBond( | ||
| oe_atoms[index[row["i"]]], oe_atoms[index[row["j"]]], row["bondorder"] | ||
| ) | ||
|
|
||
| if properties == "all": | ||
| data = self.properties.get("all", include_system_properties=True) | ||
| for key, value in data.items(): | ||
| _type = self.properties.type(key) | ||
| if _type == "int": | ||
| oe_mol.SetIntData(key, value) | ||
| elif _type == "float": | ||
| oe_mol.SetDoubleData(key, value) | ||
| elif _type == "str": | ||
| oe_mol.SetStringData(key, value) | ||
| else: | ||
| raise ValueError(f"Can't handle property of type '{_type}'") | ||
|
|
||
| # Units, if any | ||
| units = self.properties.units(key) | ||
| if units is not None and units != "": | ||
| tmp = key.split("#", maxsplit=1) | ||
| if len(tmp) > 1: | ||
| oe_mol.SetStringData(tmp[0] + ",units" + "#" + tmp[1], units) | ||
| else: | ||
| oe_mol.SetStringData(key + ",units", units) | ||
| return oe_mol | ||
|
|
||
| def from_OEMol( | ||
| self, oe_mol, properties="all", atoms=True, coordinates=True, bonds=True | ||
| ): | ||
| """Transform an OpenEye molecule into the current object.""" | ||
| check_openeye_license() | ||
|
|
||
| atnos = [] | ||
| Xs = [] | ||
| Ys = [] | ||
| Zs = [] | ||
| qs = [] | ||
| for oe_atom in oe_mol.GetAtoms(): | ||
| atno = oe_atom.GetAtomicNum() | ||
| atnos.append(atno) | ||
| x, y, z = oe_mol.GetCoords(oe_atom) | ||
| Xs.append(x) | ||
| Ys.append(y) | ||
| Zs.append(z) | ||
| qs.append(oe_atom.GetPartialCharge()) | ||
|
|
||
| index = {at: i for i, at in enumerate(oe_mol.GetAtoms())} | ||
| Is = [] | ||
| Js = [] | ||
| BondOrders = [] | ||
| for oe_bond in oe_mol.GetBonds(): | ||
| oe_i = oe_bond.GetBgn() | ||
| oe_j = oe_bond.GetEnd() | ||
| i = index[oe_i] | ||
| j = index[oe_j] | ||
| bondorder = oe_bond.GetOrder() | ||
| Is.append(i) | ||
| Js.append(j) | ||
| BondOrders.append(bondorder) | ||
| logger.debug(f"bond {i} - {j} {bondorder}") | ||
|
|
||
| if atoms: | ||
| self.clear() | ||
|
|
||
| # Get the property data, cast to correct type | ||
| data = {} | ||
| for tmp in oe_mol.GetDataIter(): | ||
| tag = tmp.GetTag() | ||
| attribute = oechem.OEGetTag(tag) | ||
| value = oe_mol.GetData(tag) | ||
| data[attribute] = value | ||
|
|
||
| # Check for property items for charge and multiplicity | ||
| if self.__class__.__name__ == "_Configuration": | ||
| if "net charge" in data: | ||
| self.charge = int(data["net charge"]) | ||
| if "spin multiplicity" in data: | ||
| self.spin_multiplicity = int(data["spin multiplicity"]) | ||
|
|
||
| if atoms: | ||
| if any([i != 0.0 for i in qs]): | ||
| if "formal_charge" not in self.atoms: | ||
| self.atoms.add_attribute("charge", coltype="float", default=0) | ||
| ids = self.atoms.append(x=Xs, y=Ys, z=Zs, atno=atnos, charge=qs) | ||
| else: | ||
| ids = self.atoms.append(x=Xs, y=Ys, z=Zs, atno=atnos) | ||
| else: | ||
| ids = self.atoms.ids | ||
|
|
||
| if coordinates: | ||
| xyz = [[x, y, z] for x, y, z in zip(Xs, Ys, Zs)] | ||
| self.atoms.coordinates = xyz | ||
|
|
||
| if atoms or bonds: | ||
| i = [ids[x] for x in Is] | ||
| j = [ids[x] for x in Js] | ||
| self.bonds.append(i=i, j=j, bondorder=BondOrders) | ||
|
|
||
| # Record any properties in the database if desired | ||
| if properties == "all": | ||
| for key, value in data.items(): | ||
| if ",units" not in key and key not in [ | ||
| "", | ||
| "net charge", | ||
| "spin multiplicity", | ||
| ]: | ||
| if not self.properties.exists(key): | ||
| tmp = key.split("#", maxsplit=1) | ||
| if len(tmp) > 1: | ||
| units_key = tmp[0] + ",units" + "#" + tmp[1] | ||
| else: | ||
| units_key = key + ",units" | ||
| _type = value.__class__.__name__ | ||
| if units_key in data: | ||
| units = data[units_key] | ||
| self.properties.add(key, _type, units=units) | ||
| else: | ||
| self.properties.add(key, _type) | ||
| self.properties.put(key, value) | ||
| return self |
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