1# -*- coding: utf-8 -*- 

2# 

3# Copyright (c) 2017, the cclib development team 

4# 

5# This file is part of cclib (http://cclib.github.io) and is distributed under 

6# the terms of the BSD 3-Clause License. 

7"""Bridge for using cclib data in biopython (http://biopython.org).""" 

8 

9from cclib.parser.utils import PeriodicTable 

10from cclib.parser.utils import find_package 

11 

12_found_biopython = find_package("Bio") 

13if _found_biopython: 

14 from Bio.PDB.Atom import Atom 

15 

16 

17def makebiopython(atomcoords, atomnos): 

18 """Create a list of BioPython Atoms. 

19 

20 This creates a list of BioPython Atoms suitable for use by 

21 Bio.PDB.Superimposer, for example. 

22 """ 

23 if not _found_biopython: 

24 raise ImportError("You must install `biopython` to use this function") 

25 pt = PeriodicTable() 

26 bioatoms = [] 

27 for coords, atomno in zip(atomcoords, atomnos): 

28 symbol = pt.element[atomno] 

29 bioatoms.append(Atom(symbol, coords, 0, 0, 0, symbol, 0, symbol.upper())) 

30 return bioatoms 

31 

32 

33del find_package