def calculate_t142_central_wbo(mol: oechem.OEMol,
params: Dict[str, List[List[int]]]) -> float:
"""Calculates the WBO between the central atoms in the t142 param in the molecule.
(WBO is Wiberg Bond Order.)
The `params` argument contains the parameters of the molecule (see
`calculate_mol_params`).
Returns -1 if the calculation fails.
"""
# Only use first occurrence of the parameter.
indices = params['t142'][0]
# For torsion parameters such as t142, the central atoms should be at the
# second and third index.
central_indices = [indices[1], indices[2]]
# Generate molecule conformer.
oechem.OEAddExplicitHydrogens(mol)
omega = oeomega.OEOmega()
omega.SetMaxConfs(1)
omega.SetCanonOrder(False)
omega.SetSampleHydrogens(True)
omega.SetEnergyWindow(15.0) #unit?
omega.SetRMSThreshold(1.0)
# Don't generate random stereoisomer if not specified.
omega.SetStrictStereo(True)
status = omega(mol)
if status is False:
omega.SetStrictStereo(False)
new_status = omega(mol)
if new_status is False:
logger.error("Failed to generate conformer for %s",
oechem.OEMolToSmiles(mol))
return -1
# Calculate the WBO between the two central atoms.
conf = next(iter(mol.GetConfs()))
charged_copy = oechem.OEMol(conf)
results = oequacpac.OEAM1Results()
if not AM1_CALCULATOR.CalcAM1(results, charged_copy):
logger.error("Failed to assign partial charges to %s",
oechem.OEMolToSmiles(mol))
return -2
return results.GetBondOrder(central_indices[0], central_indices[1])
def _calc_properties(mol: oechem.OEMol) -> danceprops.DanceProperties:
"""
Calculates properties of the given molecule and returns a
DanceProperties object holding them.
Based on Victoria Lim's am1wib.py - see
https://github.com/vtlim/misc/blob/master/oechem/am1wib.py
"""
props = danceprops.DanceProperties()
for conf in mol.GetConfs():
charged_copy = oechem.OEMol(conf)
results = oequacpac.OEAM1Results()
if not AM1.CalcAM1(results, charged_copy):
logging.debug(
f"failed to assign partial charges to {mol.GetTitle()}")
return props
DanceGenerator._add_charge_props(mol, charged_copy, results)
# Sum bond orders, bond lengths, and bond angles
for atom in charged_copy.GetAtoms(oechem.OEIsInvertibleNitrogen()):
nbors = list(atom.GetAtoms()) # (neighbors)
ang1 = math.degrees(
oechem.OEGetAngle(charged_copy, nbors[0], atom, nbors[1]))
ang2 = math.degrees(
oechem.OEGetAngle(charged_copy, nbors[1], atom, nbors[2]))
ang3 = math.degrees(
oechem.OEGetAngle(charged_copy, nbors[2], atom, nbors[0]))
props.tri_n_bond_angle = ang1 + ang2 + ang3
for nbor in nbors:
bond_order = results.GetBondOrder(atom.GetIdx(),
nbor.GetIdx())
bond_length = oechem.OEGetDistance(charged_copy, atom,
nbor)
element = nbor.GetAtomicNum()
props.tri_n_bonds.append(
danceprops.DanceTriNBond(bond_order, bond_length,
element))
props.tri_n_bond_order += bond_order
props.tri_n_bond_length += bond_length
break # terminate after one trivalent nitrogen
break # terminate after one conformation
return props