IPKM/mdevaluate
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Removed delayed reader.

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This commit is contained in:
sebastiankloth 2023-06-27 10:35:15 +02:00
parent ef125c2a89
commit 578d3638a4
1 changed files with 1 additions and 26 deletions
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27
mdevaluate/reader.py
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@ -39,7 +39,7 @@ class WrongTopologyError(Exception):
def open_with_mdanalysis(
topology, trajectory, cached=False, index_file=None, charges=None, masses=None
):
"""Open a the topology and trajectory with mdanalysis."""
"""Open the topology and trajectory with mdanalysis."""
uni = mdanalysis.Universe(topology, trajectory, convert_units=False)
if cached is not False:
if cached is True:
@ -373,28 +373,3 @@ class CachedReader(BaseReader):
def __getitem__(self, item):
return self._get_item(item)
class DelayedReader(BaseReader):
@property
def filename(self):
if self.rd is not None:
return self.rd.filename
else:
return self._filename
def __init__(self, filename, reindex=False, ignore_index_timestamps=False):
super().__init__(filename, reindex=False, ignore_index_timestamps=False)
self.natoms = len(self.rd[0].coordinates)
self.cache = self.rd.cache
self._filename = self.rd.filename
self.rd = None
def __len__(self):
return len(self.cache)
def _get_item(self, frame):
return read_xtcframe_delayed(self.filename, self.cache[frame], self.natoms)
def __getitem__(self, frame):
return self._get_item(frame)