schrodinger.application.desmond.packages.analysis.RMSD

Class RMSD

object --+ | GeomAnalyzerBase --+ | _MaestroAnalysis --+ | PosAlign --+ | RMSD

Known Subclasses:

LigandRMSD

Root Mean Square Deviation from reference positions, with optional alignment fitting.

Instance Methods

__init__(self, msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None, in_place=False)
See L{PosAlign} for parameters.

_precalc(self, calc)
Reusable intermediate data saved in calc: We use the _center function, and create one copy of the trajectory frame and one copy of the full-system CT.

_postcalc(self, calc, _, fr)

Inherited from _MaestroAnalysis (private): _getCentered

Inherited from GeomAnalyzerBase: __call__

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

init(self, msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None, in_place=False)
(Constructor)


See L{PosAlign} for parameters.

@param     ref_pos: positions of reference conformer structure
@type      ref_pos: Nx3 C{numpy.ndarray}
@type     fit_aids: C{list} of C{int}s or C{None}. If C{None}, it is set
                    to aids, and fit_ref_pos is set to ref_pos.
@param    in_place: if C{True}, calculate RMSD without applying
                    transformations on C{ref_pos}

Typically, C{aids} and C{fit_aids} come from a common source whereas
C{ref_pos} and C{fit_ref_pos} come from another common source.

Parameters:

fit_ref_pos - positions of reference conformer structure for translation/rotation calculation

Overrides: object.__init__

_precalc(self, calc)

Reusable intermediate data saved in calc: We use the _center function, and create one copy of the trajectory frame and one copy of the full-system CT. In both, the solute atoms are centered.

Overrides: GeomAnalyzerBase._precalc: (inherited documentation)

_postcalc(self, calc, _, fr)

Overrides: GeomAnalyzerBase._postcalc: (inherited documentation)

Class RMSD

__init__(self, msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None, in_place=False) (Constructor)

_precalc(self, calc)

_postcalc(self, calc, _, fr)

init(self, msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None, in_place=False)
(Constructor)