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Fixed missing mdtraj.utils.six error #34

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Fixed missing mdtraj.utils.six error #34

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390cad1
Fixed missing mdtraj.utils.six error
thelostscout Jun 3, 2024
f1d218b
replaced basestring with string
thelostscout Jun 3, 2024
47b0db8
removed dependency `mdtraj.utils.six.string_types`.
thelostscout Jun 3, 2024
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8 changes: 2 additions & 6 deletions bgmol/tpl/hdf5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,12 +27,8 @@
from mdtraj import version
from mdtraj.core.topology import _topology_from_subset, Topology
from mdtraj.utils import unitcell
from mdtraj.utils.six import PY3
if PY3:
basestring = str
import mdtraj.core.element as elem
from mdtraj.utils import in_units_of, ensure_type, import_, cast_indices
from mdtraj.utils.six import string_types
from ..util.importing import import_openmm

try:
Expand Down Expand Up @@ -94,7 +90,7 @@ def load_hdf5(filename, stride=None, atom_indices=None, frame=None):
--------
mdtraj.HDF5TrajectoryFile : Low level interface to HDF5 files
"""
if not isinstance(filename, string_types):
if not isinstance(filename, str):
raise TypeError('filename must be of type string for load_lh5. '
'you supplied %s' % type(filename))

Expand Down Expand Up @@ -1027,7 +1023,7 @@ def __init__(self, file, reportInterval, coordinates=True, time=True,
temperature=True, velocities=False, forces=False, atomSubset=None):
"""Create a HDF5Reporter.
"""
if isinstance(file, basestring):
if isinstance(file, str):
self._traj_file = self.backend(file, 'w')
elif isinstance(file, self.backend):
self._traj_file = file
Expand Down