Package schrodinger :: Package application :: Package jaguar :: Module rmsd :: Class ConformerRmsdX

Class ConformerRmsdX

structutils.rmsd.ConformerRmsdX --+
                                  |
                                 ConformerRmsdX

Instance Methods

[hide private]

__init__(self, reference_structure, *args, **kwargs)

_prepareStructures(self)
Returns: a working copy of the reference and test structures, renumbered and/or reduced as needed.

_getRenumberedStructureWithComparison(self, st1, st2)
Returns: new structures with normalized atomic orders, based upon the reference set of SMARTS patterns in self._mol_pattern_dict.

tuple

_align_hydrogens(self, st1, st2)
align the hydrogens to get correct chirality this is done by finding the permutation of hydrogens about each heavy atom that minimizes rmsd computed using only the heavy atom and attached hydrogens

Inherited from structutils.rmsd.ConformerRmsdX: __str__, calculate, getRmsdDataname, writeCommand, writeStructures

Inherited from structutils.rmsd.ConformerRmsdX (private): _encodeOriginalAtomNumbers, _extractSuperimposeAslStructure, _getReducedStructure, _getRenumberedStructure, _superimpose

Instance Variables

[hide private]

Inherited from structutils.rmsd.ConformerRmsdX: max_distance, max_distance_atom_1, max_distance_atom_2, max_permutations, orig_index_prop, precision, renumber_structures, rmsd, rmsd_str, use_heavy_atom_graph, use_symmetry

Method Details

[hide private]

init(self, reference_structure, *args, **kwargs)
(Constructor)

Parameters:

search_permutations (Boolean) - If True, computes the rmsd between all possible atom renumberings between test and reference structures, as defined by evaluating the matching smarts pattern. Uses the renumbering with minimal rsmd. Can be (very!) expensive.
search_chirality (Boolean) - If True, search for permutations of hydrogens that preserve the chirality of numbering around a chiral center with 3 or 4 neighbors.

Overrides: structutils.rmsd.ConformerRmsdX.__init__

_prepareStructures(self)

Parameters:

reference - If true, seed the renumbering pattern dictionary.

Returns:

a working copy of the reference and test structures, renumbered and/or reduced as needed. The original atom index is saved as atom level properties in the working structure. A substructure of just the atoms specified for superposition via ASL.

Overrides: structutils.rmsd.ConformerRmsdX._prepareStructures

(inherited documentation)

_getRenumberedStructureWithComparison(self, st1, st2)

Parameters:

st1 (structure.Structure) - The first structure to renumber.
st2 (structure.Structure) - The second structure to renumber.

Returns:

new structures with normalized atomic orders, based upon the reference set of SMARTS patterns in self._mol_pattern_dict. this version minimizes the RMSD between st1 and st2 by comparing all atomic renumberings of st2 returned when evaluating the smarts pattern

_align_hydrogens(self, st1, st2)

align the hydrogens to get correct chirality this is done by finding the permutation of hydrogens about each heavy atom that minimizes rmsd computed using only the heavy atom and attached hydrogens

assumes that the numbering is consistent with the connectivity of the structure

This method has been extended to treat chirality of all terminal CX3 groups so that includes things like CF3, for example. So, in what follows 'hydrogen' just means an atom having only one bond and 'heavy' is everything else.

Parameters:

st1 (schrodinger.structure.Structure) - structure 1
st2 (schrodinger.structure.Structure) - structure 1

Returns: tuple

the two renumbered structures

Class ConformerRmsdX

__init__(self, reference_structure, *args, **kwargs) (Constructor)

_prepareStructures(self)

_getRenumberedStructureWithComparison(self, st1, st2)

_align_hydrogens(self, st1, st2)

init(self, reference_structure, *args, **kwargs)
(Constructor)