schrodinger.pipeline.stages.rmsd module

A stage for calculating RMSDs for structures in two sets.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.pipeline.stages.rmsd.RmsdStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for calculating RMSDs for structures in two sets.

First set - original structures Second set - new conformations

The keywords specific to this stage are…

UNIQUEFIELD_REF - Property in the reference set used to match

structures for comparison. If unset, it defaults to the UNIQUEFIELD property. The RMSD is calculated for pairs in which the UNIQUEFIELD_REF value in the reference ligand matches the UNIQUEFIELD value in the modified ligand.

UNIQUEFIELD - Property in the modified set used to match

structures for comparison.

RMSDFIELD - Property to save RMSDs into in the output file

RENUMBER_STRUCTURES - Should be False if atom numbering is the same

between same structure in two input sets

IGNORE_STATES - If True, ignore hydrogens and treat all bonds

as single order.

The stage takes two input structure file sets and generates one output structure file set.

operate()

Algorithm: Compare each structure in the original (first) ligands set to every structure in the modified (second) set. If their corresponding UNIQUEFIELD_* properties are the same, calculate RMS for the structure, save it to RMSDFIELD, and write out the structure to the output file.