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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 for using cclib data in biopython (http://biopython.org)."""
from cclib.parser.utils import PeriodicTable
from cclib.parser.utils import find_package
_found_biopython = find_package("Bio")
if _found_biopython:
from Bio.PDB.Atom import Atom
def makebiopython(atomcoords, atomnos):
"""Create a list of BioPython Atoms.
This creates a list of BioPython Atoms suitable for use by
Bio.PDB.Superimposer, for example.
"""
if not _found_biopython:
raise ImportError("You must install `biopython` to use this function")
pt = PeriodicTable()
bioatoms = []
for coords, atomno in zip(atomcoords, atomnos):
symbol = pt.element[atomno]
bioatoms.append(Atom(symbol, coords, 0, 0, 0, symbol, 0, symbol.upper()))
return bioatoms
del find_package
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