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import os
import re
import numpy as np
from dynasor.logging_tools import logger
def parse_gromacs_index_file(fname):
"""
Parses a gromacs style index (ndx) file.
Returns a dict with key values as
group-name: [1, 3, 8]
Note that atomic indices in gromacs-ndx file starts with 1, but the returned dict starts with 0
"""
if not os.path.isfile(fname):
raise ValueError('Index file not found')
atomic_indices = dict()
header_re = re.compile(r'^ *\[ *([a-zA-Z0-9_.-]+) *\] *$')
with open(fname, 'r') as fobj:
for line in fobj.readlines():
match = header_re.match(line)
if match is not None: # get name of group
name = match.group(1)
if name in atomic_indices.keys():
logger.warning(f'Group name {name} appears twice in index file, only one used.')
atomic_indices[name] = []
else: # get indices for group
indices = [int(i) for i in line.split()]
atomic_indices[name].extend(indices)
# cast to indices to numpy arrays and shift so indices start with 0
for name, indices in atomic_indices.items():
atomic_indices[name] = np.array(indices) - 1
return atomic_indices
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