IPKM/mdevaluate
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Removed cached from open

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This commit is contained in:
Sebastian Kloth 2023-11-10 15:19:44 +01:00
parent a75091aa95
commit 2904d1e4d8
1 changed files with 2 additions and 8 deletions
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10
src/mdevaluate/__init__.py
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@ -20,7 +20,6 @@ def open(
directory="", directory="",
topology="*.tpr", topology="*.tpr",
trajectory="*.xtc", trajectory="*.xtc",
cached=False,
nojump=False, nojump=False,
index_file=None, index_file=None,
charges=None, charges=None,
@ -32,13 +31,9 @@ def open(
Args: Args:
directory: Directory of the simulation. directory: Directory of the simulation.
topology (opt.): topology (opt.):
Descriptor of the topology file (tpr or gro). By default a tpr file is Descriptor of the topology file (tpr or gro). By default, a tpr file is
used, if there is exactly one in the directoy. used, if there is exactly one in the directoy.
trajectory (opt.): Descriptor of the trajectory (xtc file). trajectory (opt.): Descriptor of the trajectory (xtc file).
cached (opt.):
If the trajectory reader should be cached. Can be True, an integer or None.
If this is True maxsize is 128, otherwise this is used as maxsize for
the cache, None means infinite cache (this is a potential memory leak!).
nojump (opt.): If nojump matrixes should be generated. They will alwyas be loaded if present nojump (opt.): If nojump matrixes should be generated. They will alwyas be loaded if present
Returns: Returns:
@ -82,7 +77,6 @@ def open(
atom_set, frames = reader.open_with_mdanalysis( atom_set, frames = reader.open_with_mdanalysis(
top_file, top_file,
traj_file, traj_file,
cached=cached,
index_file=index_file, index_file=index_file,
charges=charges, charges=charges,
masses=masses, masses=masses,
@ -97,7 +91,7 @@ def open(
def open_energy(file): def open_energy(file):
"""Reads an gromacs energy file and output the data in a pandas DataFrame. """Reads a gromacs energy file and output the data in a pandas DataFrame.
Args: Args:
file: Filename of the energy file file: Filename of the energy file
""" """