IPKM/mdevaluate
6
1
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fixed index reader

Browse Source
This commit is contained in:
sebastiankloth 2022-05-03 15:15:12 +02:00
parent 6c54848105
commit c18a369473
2 changed files with 9 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
mdevaluate/__init__.py
View File

@ -53,6 +53,12 @@ def open(directory='', topology='*.tpr', trajectory='*.xtc', cached=False,
if top_glob is not None and len(top_glob) == 1: if top_glob is not None and len(top_glob) == 1:
top_file, = top_glob top_file, = top_glob
logger.info('Loading topology: {}'.format(top_file)) logger.info('Loading topology: {}'.format(top_file))
if index_file is not None:
index_glob = glob(os.path.join(directory, index_file), recursive=True)
if index_glob is not None:
index_file = index_glob[0]
else:
index_file = None
else: else:
raise FileNotFoundError('Topology file could not be identified.') raise FileNotFoundError('Topology file could not be identified.')

6
mdevaluate/reader.py
View File

@ -56,7 +56,7 @@ def open_with_mdanalysis(topology, trajectory, cached=False, index_file=None):
raise WrongTopologyError('Topology file should end with ".tpr" or ".gro"') raise WrongTopologyError('Topology file should end with ".tpr" or ".gro"')
indices = None indices = None
if index_file: if index_file:
indices = load_indices(indexfile) indices = load_indices(index_file)
atms = atoms.Atoms( atms = atoms.Atoms(
np.stack((uni.atoms.resids, uni.atoms.resnames, uni.atoms.names), axis=1), np.stack((uni.atoms.resids, uni.atoms.resnames, uni.atoms.names), axis=1),
@ -67,10 +67,10 @@ def open_with_mdanalysis(topology, trajectory, cached=False, index_file=None):
group_re = re.compile('\[ ([-+\w]+) \]') group_re = re.compile('\[ ([-+\w]+) \]')
def load_indices(indexfile): def load_indices(index_file):
indices = {} indices = {}
index_array = None index_array = None
with open(indexfile) as idx_file: with open(index_file) as idx_file:
for line in idx_file: for line in idx_file:
m = group_re.search(line) m = group_re.search(line)
if m is not None: if m is not None: