def _autoDetectTopology(folder):
from htmd.molecule.readers import _TOPOLOGY_READERS
topotypes = ['pdb', 'prmtop', 'psf'] + list(_TOPOLOGY_READERS.keys()) # Prepending PDB, PSF, PRMTOP so that they are the default
topo = None
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 = files[0]
break
if topo is None:
raise RuntimeError('No topology file found in folder {}. '
'Supported extensions are {}'.format(folder, list(_TOPOLOGY_READERS.keys())))
return topo
def _autoDetectTopology(folder):
from htmd.molecule.readers import _TOPOLOGY_READERS
topotypes = ['pdb', 'prmtop', 'psf'] + list(_TOPOLOGY_READERS.keys(
)) # Prepending PDB, PSF, PRMTOP so that they are the default
topo = None
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 = files[0]
break
if topo is None:
raise RuntimeError('No topology file found in folder {}. '
'Supported extensions are {}'.format(
folder, list(_TOPOLOGY_READERS.keys())))
return topo
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 _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())
logger.warning(
'Filtering was not able to write {} due to error: {}'.
format(filttopo, e))
def _autoDetectTrajectories(folder):
from htmd.molecule.readers import _TRAJECTORY_READERS
import natsort
for tt in _TRAJECTORY_READERS:
trajectories = glob(path.join(folder, '*.{}'.format(tt)))
if len(trajectories) > 0:
return natsort.natsorted(trajectories)
from htmd.molecule.readers import _TOPOLOGY_READERS
__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]))
topo[tt] = files[0]
mol.write(filttopo, filtsel)
except Exception as e:
logger.warning('Filtering was not able to write {} due to error: {}'.format(filttopo, e))
def _autoDetectTrajectories(folder):
from htmd.molecule.readers import _TRAJECTORY_READERS
import natsort
for tt in _TRAJECTORY_READERS:
trajectories = glob(path.join(folder, '*.{}'.format(tt)))
if len(trajectories) > 0:
return natsort.natsorted(trajectories)
from htmd.molecule.readers import _TOPOLOGY_READERS
__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]))
topo[tt] = files[0]
if len(topo) == 0:
raise RuntimeError('No topology file found in folder {}. '