RMSD align breaks when aligning larger molecule to smaller molecule

QChASM / Aaron

AARON (An Automated Reaction Optimizer for New catalysts) automates DFT optimizations of TS structures for asymmetric catalytic reactions.

GNU General Public License v3.0

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RMSD align breaks when aligning larger molecule to smaller molecule #21

Closed vingman closed 6 years ago

vingman commented 6 years ago

Line 1160 in Geometry.pm _RMSD() loops over reference geometry atoms ($atom1_ref). However, if this is smaller than $atom2_ref, it tries to index out of bounds.

vingman commented 6 years ago

Fixed. It now trims the longer array to be the same size as the shorter one. Also added a reorder => 1/0 kwarg to RMSD. This will systematically try different atom orders to find the best overlap, for cases when the atom numberings are not conserved across files.