def _autoDetectTopology(folder):
topo = {}
for tt in __topotypes:
files = glob(path.join(folder, '*.{}'.format(tt)))
if len(files) > 0:
if len(files) > 1:
logger.warning('Multiple "{}" files were found in folder {}. '
'Picking {} as the topology'.format(tt, folder, files[0]))
topo[tt] = files[0]
if len(topo) == 0:
raise RuntimeError('No topology file found in folder {}. '
'Supported extensions are {}'.format(folder, list(_TOPOLOGY_READERS.keys())))
return list(topo.values())
def _autoDetectTrajectories(folder):
from moleculekit.readers import _TRAJECTORY_READERS
import natsort
for tt in _TRAJECTORY_READERS:
if tt in (
"xsc",
): # Some trajectory readers don't really load trajectories like xsc
continue
trajectories = glob(path.join(folder, "*.{}".format(tt)))
if len(trajectories) > 0:
return natsort.natsorted(trajectories)
__readers = list(_TOPOLOGY_READERS.keys())
__defaultReaders = ["pdb", "prmtop", "psf"]
__otherReaders = list(np.setdiff1d(__readers, __defaultReaders))
__topotypes = (__defaultReaders + __otherReaders
) # Prepending PDB, PSF, PRMTOP so that they are the default
def _autoDetectTopology(folder):
topo = {}
for tt in __topotypes:
files = glob(path.join(folder, "*.{}".format(tt)))
if len(files) > 0:
if len(files) > 1:
logger.warning('Multiple "{}" files were found in folder {}. '
"Picking {} as the topology".format(
tt, folder, files[0]))