schrodinger.application.jaguar.rmsd module

This module is a subclass of schrodinger.structutils.rmsd to provide ability to do searching over more permutations of possible renumbering.

class schrodinger.application.jaguar.rmsd.JaguarConformerRmsdX(reference_structure, *args, **kwargs)

Bases: schrodinger.structutils.rmsd.ConformerRmsd

calculate()

Returns:Root-mean-squared difference of atom coordinates. Type:float Raise:ValueError if working versions of the reference and test structures don’t have the same shape (non-confs).

The order of operations:

• prepare working copies of the reference and test structures.

  ** copy the structures. ** encode the original atom indexes as atom properties. ** extract substructure of the atoms matching the ASL. ** reduce to heavy atom graph (instance option, non-default). ** normalize numbering scheme (instance option, default).

• determine molecular symmetry mapping (optional, default).
• create a numpy coordinate array for the working structures.

• numpy linear algebra SVD to superimpose (instance option).

  ** transform test_structure

• numpy array used to calculate RMSD, and max_dist.
• decode original indexes to identify atoms involve in max dist.

renumberBySymmetry()

Disables renumbering using symmetry, if we are brute forcing the solution.

renumberWorkingStructures(has_hydrogens)

Renumber the working structures to give them identical numbering. If search_permutations is set, a custom renumbering method is used.