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Improve the performance of ParmEd converter. (Fix #3028) #3029

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Merged
IAlibay merged 4 commits into from
Nov 19, 2020
Merged

Improve the performance of ParmEd converter. (Fix #3028) #3029

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6cdb64b
Improve the performance of ParmEd converter. (Fix #3028)
HanatoK Nov 17, 2020
ec12676
Fix a PEP 8 warning in the previous commit.
HanatoK Nov 17, 2020
7d36d8b
Update AUTHORS and CHANGELOG.
HanatoK Nov 18, 2020
72c94e0
Update CHANGELOG.
HanatoK Nov 19, 2020
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1 change: 1 addition & 0 deletions package/AUTHORS
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Original file line number Diff line number Diff line change
Expand Up @@ -150,6 +150,7 @@ Chronological list of authors
- Edis Jakupovic
- Nicholas Craven
- Mieczyslaw Torchala
- Haochuan Chen

External code
-------------
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4 changes: 3 additions & 1 deletion package/CHANGELOG
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Expand Up @@ -15,7 +15,8 @@ The rules for this file:
------------------------------------------------------------------------------
??/??/?? tylerjereddy, richardjgowers, IAlibay, hmacdope, orbeckst, cbouy,
lilyminium, daveminh, jbarnoud, yuxuanzhuang, VOD555, ianmkenney,
calcraven，xiki-tempula, mieczyslaw, manuel.nuno.melo, PicoCentauri
calcraven，xiki-tempula, mieczyslaw, manuel.nuno.melo, PicoCentauri,
hanatok

* 2.0.0

Expand Down Expand Up @@ -73,6 +74,7 @@ Fixes
would create a test artifact (Issue #2979, PR #2981)

Enhancements
* Improved performance of the ParmEd converter (Issue #3028, PR #3029)
* Improved analysis class docstrings, and added missing classes to the
`__all__` list (PR #2998)
* The PDB writer gives more control over how to write the atom ids
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6 changes: 4 additions & 2 deletions package/MDAnalysis/coordinates/ParmEd.py
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Expand Up @@ -132,7 +132,7 @@ def _read_first_frame(self):
}

def get_indices_from_subset(i, atomgroup=None, universe=None):
return atomgroup.index(universe.atoms[i])
return atomgroup[universe.atoms[i]]

class ParmEdConverter(base.ConverterBase):
"""Convert MDAnalysis AtomGroup or Universe to ParmEd :class:`~parmed.structure.Structure`.
Expand Down Expand Up @@ -262,8 +262,10 @@ def convert(self, obj):
struct.box = None

if hasattr(ag_or_ts, 'universe'):
atomgroup = {atom: index for index,
atom in enumerate(list(ag_or_ts))}
get_atom_indices = functools.partial(get_indices_from_subset,
atomgroup=list(ag_or_ts),
atomgroup=atomgroup,
universe=ag_or_ts.universe)
else:
get_atom_indices = lambda x: x
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