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

Class ConformerRmsdX

                    object --+    
                             |    
structutils.rmsd.ConformerRmsd --+
                                 |
                                ConformerRmsdX

Instance Methods

[hide private]

__init__(self, reference_structure, *args, **kwargs)
x.__init__(...) initializes x; see help(type(x)) for signature

renumberBySymmetry(self)
Disables renumbering using symmetry, if we are brute forcing the solution.

renumberWorkingStructures(self, has_hydrogens)
Renumber the working structures to give them identical numbering.

_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)
This is not currently being used and has been superseded by use of mmstereo with mmstereo_new_anc.

Inherited from structutils.rmsd.ConformerRmsd: __str__, calculate, evaluateAsl, getRmsdDataname, populatePatternDict, writeCommand, writeStructures

Inherited from structutils.rmsd.ConformerRmsd (private): _encodeOriginalAtomNumbers, _extractSuperimposeAslStructure, _getReducedStructure, _prepareStructures, _superimpose

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Instance Variables

[hide private]

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

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

x.__init__(...) initializes x; see help(type(x)) for signature

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: object.__init__

renumberBySymmetry(self)

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

Overrides: structutils.rmsd.ConformerRmsd.renumberBySymmetry

renumberWorkingStructures(self, has_hydrogens)

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

Overrides: structutils.rmsd.ConformerRmsd.renumberWorkingStructures

_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)

This is not currently being used and has been superseded by use of mmstereo with mmstereo_new_anc. It will be left here temporarily for potential use. Use with care.

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)

renumberBySymmetry(self)

renumberWorkingStructures(self, has_hydrogens)

_getRenumberedStructureWithComparison(self, st1, st2)

_align_hydrogens(self, st1, st2)

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