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# -*- coding: utf-8 -*-
#
# Copyright (c) 2018, 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.
"""Generic file writer and related tools"""
import logging
import sys
from abc import ABCMeta, abstractmethod
from six import add_metaclass
if sys.version_info <= (3, 3):
from collections import Iterable
else:
from collections.abc import Iterable
import numpy
from cclib.parser.utils import PeriodicTable
from cclib.parser.utils import find_package
_has_openbabel = find_package("openbabel")
if _has_openbabel:
from cclib.bridge import makeopenbabel
import openbabel as ob
import openbabel.pybel as pb
class MissingAttributeError(Exception):
pass
@add_metaclass(ABCMeta)
class Writer:
"""Abstract class for writer objects."""
required_attrs = ()
def __init__(self, ccdata, jobfilename=None, indices=None, terse=False,
*args, **kwargs):
"""Initialize the Writer object.
This should be called by a subclass in its own __init__ method.
Inputs:
ccdata - An instance of ccData, parsed from a logfile.
jobfilename - The filename of the parsed logfile.
indices - One or more indices for extracting specific geometries/etc. (zero-based)
terse - Whether to print the terse version of the output file - currently limited to cjson/json formats
"""
self.ccdata = ccdata
self.jobfilename = jobfilename
self.indices = indices
self.terse = terse
self.ghost = kwargs.get("ghost")
self.pt = PeriodicTable()
self._check_required_attributes()
# Open Babel isn't necessarily present.
if _has_openbabel:
# Generate the Open Babel/Pybel representation of the molecule.
# Used for calculating SMILES/InChI, formula, MW, etc.
self.obmol, self.pbmol = self._make_openbabel_from_ccdata()
self.bond_connectivities = self._make_bond_connectivity_from_openbabel(self.obmol)
self._fix_indices()
@abstractmethod
def generate_repr(self):
"""Generate the written representation of the logfile data."""
def _calculate_total_dipole_moment(self):
"""Calculate the total dipole moment."""
# ccdata.moments may exist, but only contain center-of-mass coordinates
if len(getattr(self.ccdata, 'moments', [])) > 1:
return numpy.linalg.norm(self.ccdata.moments[1])
def _check_required_attributes(self):
"""Check if required attributes are present in ccdata."""
missing = [x for x in self.required_attrs
if not hasattr(self.ccdata, x)]
if missing:
missing = ' '.join(missing)
raise MissingAttributeError(
'Could not parse required attributes to write file: ' + missing)
def _make_openbabel_from_ccdata(self):
"""Create Open Babel and Pybel molecules from ccData."""
if not hasattr(self.ccdata, 'charge'):
logging.warning("ccdata object does not have charge, setting to 0")
_charge = 0
else:
_charge = self.ccdata.charge
if not hasattr(self.ccdata, 'mult'):
logging.warning("ccdata object does not have spin multiplicity, setting to 1")
_mult = 1
else:
_mult = self.ccdata.mult
obmol = makeopenbabel(self.ccdata.atomcoords,
self.ccdata.atomnos,
charge=_charge,
mult=_mult)
if self.jobfilename is not None:
obmol.SetTitle(self.jobfilename)
return (obmol, pb.Molecule(obmol))
def _make_bond_connectivity_from_openbabel(self, obmol):
"""Based upon the Open Babel/Pybel molecule, create a list of tuples
to represent bonding information, where the three integers are
the index of the starting atom, the index of the ending atom,
and the bond order.
"""
bond_connectivities = []
for obbond in ob.OBMolBondIter(obmol):
bond_connectivities.append((obbond.GetBeginAtom().GetIndex(),
obbond.GetEndAtom().GetIndex(),
obbond.GetBondOrder()))
return bond_connectivities
def _fix_indices(self):
"""Clean up the index container type and remove zero-based indices to
prevent duplicate structures and incorrect ordering when
indices are later sorted.
"""
if not self.indices:
self.indices = set()
elif not isinstance(self.indices, Iterable):
self.indices = set([self.indices])
# This is the most likely place to get the number of
# geometries from.
if hasattr(self.ccdata, 'atomcoords'):
lencoords = len(self.ccdata.atomcoords)
indices = set()
for i in self.indices:
if i < 0:
i += lencoords
indices.add(i)
self.indices = indices
return
del find_package
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