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Make the TPR parser a bit faster #2804

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merged 3 commits into from
Jul 2, 2020
Merged

Make the TPR parser a bit faster #2804

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cb84a99
Make the TPR parser a bit faster
jbarnoud Jun 29, 2020
174dd40
Update changelog for #2804
jbarnoud Jun 29, 2020
2fc42b3
Merge branch 'develop' into slightly-faster-tpr
richardjgowers Jul 2, 2020
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4 changes: 3 additions & 1 deletion package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,8 @@ The rules for this file:

------------------------------------------------------------------------------
??/??/?? richardjgowers, IAlibay, hmacdope, orbeckst, cbouy, lilyminium,
daveminh
daveminh, jbarnoud


* 2.0.0

Expand All @@ -33,6 +34,7 @@ Enhancements
token (Issue #2468, PR #2707)
* Added the `from_smiles` classmethod to the Universe (Issue #2468, PR #2707)
* Added computation of Mean Squared Displacements (#2438, PR #2619)
* Improved performances when parsing TPR files (PR #2804)
* Added converter between Cartesian and Bond-Angle-Torsion coordinates (PR #2668)

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11 changes: 4 additions & 7 deletions package/MDAnalysis/topology/tpr/obj.py
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Expand Up @@ -125,10 +125,7 @@ def __init__(self, name, long_name, natoms):
self.natoms = natoms

def process(self, atom_ndx):
while atom_ndx:
# format for all info: (type, [atom1, atom2, ...])
# yield atom_ndx.pop(0), [atom_ndx.pop(0) for i in range(self.natoms)]

# but currently only [atom1, atom2, ...] is interested
atom_ndx.pop(0)
yield [atom_ndx.pop(0) for i in range(self.natoms)]
# The format for all record is (type, atom1, atom2, ...)
# but we are only interested in the atoms.
for cursor in range(0, len(atom_ndx), self.natoms + 1):
yield atom_ndx[cursor + 1: cursor + 1 + self.natoms]