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# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Bridge between cclib data and openbabel (http://openbabel.org)."""
from cclib.parser.data import ccData
from cclib.parser.utils import find_package
_found_openbabel = find_package("openbabel")
if _found_openbabel:
import openbabel as ob
def _check_openbabel(found_openbabel):
if not found_openbabel:
raise ImportError("You must install `openbabel` to use this function")
def makecclib(mol):
"""Create cclib attributes and return a ccData from an OpenBabel molecule.
Beyond the numbers, masses and coordinates, we could also set the total charge
and multiplicity, but often these are calculated from atomic formal charges
so it is better to assume that would not be correct.
"""
_check_openbabel(_found_openbabel)
attributes = {
'atomcoords': [],
'atommasses': [],
'atomnos': [],
'natom': mol.NumAtoms(),
}
for atom in ob.OBMolAtomIter(mol):
attributes['atomcoords'].append([atom.GetX(), atom.GetY(), atom.GetZ()])
attributes['atommasses'].append(atom.GetAtomicMass())
attributes['atomnos'].append(atom.GetAtomicNum())
return ccData(attributes)
def makeopenbabel(atomcoords, atomnos, charge=0, mult=1):
"""Create an Open Babel molecule."""
_check_openbabel(_found_openbabel)
obmol = ob.OBMol()
for i in range(len(atomnos)):
# Note that list(atomcoords[i]) is not equivalent!!!
# For now, only take the last geometry.
# TODO: option to export last geometry or all geometries?
coords = atomcoords[-1][i].tolist()
atomno = int(atomnos[i])
obatom = ob.OBAtom()
obatom.SetAtomicNum(atomno)
obatom.SetVector(*coords)
obmol.AddAtom(obatom)
obmol.ConnectTheDots()
obmol.PerceiveBondOrders()
obmol.SetTotalSpinMultiplicity(mult)
obmol.SetTotalCharge(int(charge))
return obmol
def readfile(fname, format):
"""Read a file with OpenBabel and extract cclib attributes."""
_check_openbabel(_found_openbabel)
obc = ob.OBConversion()
if obc.SetInFormat(format):
mol = ob.OBMol()
obc.ReadFile(mol, fname)
return makecclib(mol)
else:
print("Unable to load the %s reader from OpenBabel." % format)
return {}
del find_package
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