# -*- coding: utf-8 -*-
"""Interface to OpenEye OEChem."""
import logging
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__)
[docs]
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"
)
[docs]
def openeye_version():
"""The version of the OpenEye OEChem toolkit."""
if not oechem_available:
return None
return oechem.OEChemGetVersion()
[docs]
class OpenEyeMixin:
"""A mixin for handling OpenEye's software via its Python interface."""
[docs]
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
[docs]
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
