Coverage for local_installation/dynasor/trajectory/atomic_indices.py: 100%

1import os 

2import re 

3import numpy as np 

4from dynasor.logging_tools import logger 

5 

6 

7def parse_gromacs_index_file(fname): 

8 """ 

9 Parses a gromacs style index (ndx) file. 

10 Returns a dict with key values as 

11 group-name: [1, 3, 8] 

12 

13 Note that atomic indices in gromacs-ndx file starts with 1, but the returned dict starts with 0 

14 """ 

15 

16 if not os.path.isfile(fname): 

17 raise ValueError('Index file not found') 

18 

19 atomic_indices = dict() 

20 header_re = re.compile(r'^ *\[ *([a-zA-Z0-9_.-]+) *\] *$') 

21 with open(fname, 'r') as fobj: 

22 for line in fobj.readlines(): 

23 match = header_re.match(line) 

24 if match is not None: # get name of group 

25 name = match.group(1) 

26 if name in atomic_indices.keys(): 

27 logger.warning(f'Group name {name} appears twice in index file, only one used.') 

28 atomic_indices[name] = [] 

29 else: # get indices for group 

30 indices = [int(i) for i in line.split()] 

31 atomic_indices[name].extend(indices) 

32 

33 # cast to indices to numpy arrays and shift so indices start with 0 

34 for name, indices in atomic_indices.items(): 

35 atomic_indices[name] = np.array(indices) - 1 

36 

37 return atomic_indices