Coverage for /builds/debichem-team/python-ase/ase/io/cjson.py: 100.00%

1"""Module to read atoms in chemical json file format. 

2 

3https://wiki.openchemistry.org/Chemical_JSON 

4""" 

5import json 

6 

7import numpy as np 

8 

9from ase import Atoms 

10from ase.cell import Cell 

11 

12 

13# contract and lower case string 

14def contract(dictionary): 

15 dcopy = {key.replace(' ', '').lower(): dictionary[key] for key in 

16 dictionary} 

17 return dcopy 

18 

19 

20def read_cjson(fileobj): 

21 """Read a Chemical Json file as written by avogadro2 (>=1.93.0) 

22 

23 See https://wiki.openchemistry.org/Chemical_JSON 

24 """ 

25 data = contract(json.load(fileobj)) 

26 atoms = Atoms() 

27 datoms = data['atoms'] 

28 

29 atoms = Atoms(datoms['elements']['number']) 

30 

31 if 'unitcell' in data: 

32 cell = data['unitcell'] 

33 a = cell['a'] 

34 b = cell['b'] 

35 c = cell['c'] 

36 alpha = cell['alpha'] 

37 beta = cell['beta'] 

38 gamma = cell['gamma'] 

39 atoms.cell = Cell.fromcellpar([a, b, c, alpha, beta, gamma]) 

40 atoms.pbc = True 

41 

42 coords = contract(datoms['coords']) 

43 if '3d' in coords: 

44 positions = np.array(coords['3d']).reshape(len(atoms), 3) 

45 atoms.set_positions(positions) 

46 else: 

47 positions = np.array(coords['3dfractional']).reshape(len(atoms), 3) 

48 atoms.set_scaled_positions(positions) 

49 

50 yield atoms