Python: module atomProb

atomProb

represent ensemble of structures as a density map. See C.D. Schwieters and G.M. Clore, ``G.M. Reweighted atomic densities to represent ensembles of NMR structures,'' J. Biomol. NMR 23, 221-225 (2002). constructor: AtomProb(atomSel, atomPosList) - atomSel is a string or atomSel.AtomSel atomPosList is a list of atomic coordinates for the structures which will make up the map. If it is omitted, coordinates will be take from the coordinates assocated with the atomSel argument. methods: calc() - calculate density map writeEDM(filename) - write map to specified file in xplor edm format getGrid() - return the densityGrid.DensityGrid object generated by calc(). selection() - return atomSel given during construction. setAtomRadius(val) - set default atomic radius calc() - compute atomic probability calcGradient(derivList, - given a derivList.DerivList, and dFdRho_ijk, dFdRho ) compute the gradient of dFdq_l radiusGradient(dFdRho) - return a vector with the value of dFdr_l, given dFdRho_ijk. accessor pairs: verbose - boolean radii - vector of atomic radii- one per atom in selection's simulation. Default value is 1 Anstrom. atomWeights - vector of per-atom weights- one per atom in selection's simulation, and distinct from the weights member for per-structure weights. This defaults to 1, generateGrid - boolean. If true, calc() will regenerate the grid extent based on the gridVals member. distType - one of "quartic","gaussian" scaleType - one of "amplitude", "distribution", "normalize", "flat", "volume" or "off". This specifies the normalization of an atom's contribution to the distribution: off and flat -specify that no normalization be applied: for each atom contribution in the supplied atomPosList array a normalized distribution will be contributed to the grid. amplitude -contribution from each atom will be normalized by the maximum contribution from that atom. normalize -same as amplitude, but the prefactor is divided by an additional factor proportional to volume. volume -a normalized distribution is multiplied by the associated volume. With this scaleType, all atoms contribute constant density. distribution - FIX: ?? weights - a list of per structure weights which must be the same length as atomPosList. These weights are normalized. isProjection - if True, generate a 2D projection in a map which has znum=1. mapType - one of "density", "projection", or "height" [default: "density"] translation - translation vector for centering a projection. orientation - Rotation matrix defining orientation for projection. mapResolution - resolution (Gaussian width) of the experimental map which is fit to, used for Gaussian blurring. This is currently only used by AtomProbProjections, and defaults to 0 (no blurring). members: gridVals - a densityGrid.DensityGrid_Params object used to generate grid extents if generateGrid is True. d_dt - for projections and height maps, after calcGradient is called, this is filled with the gradient with respect to the translation vector. d_dR - for projections and height maps, after calcGradient is called, this is filled with the gradient with respect to the orientation matrix. # This file was automatically generated by SWIG (http://www.swig.org). # Version 4.0.2 # # Do not make changes to this file unless you know what you are doing--modify # the SWIG interface file instead.

Classes

builtins.object

AtomProb

class AtomProb(builtins.object)

AtomProb(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

atomRadius(self, *args, **kwargs) -> 'double'

atomWeights(self, *args, **kwargs) -> 'CDSVector< float_type > const'

calc(self, *args, **kwargs) -> 'void'

calcGradient(self, *args, **kwargs) -> 'void'

copyGrid(self, *args, **kwargs) -> 'void'

distType(self, *args, **kwargs) -> 'AtomProb::DistType'

generateGrid(self, *args, **kwargs) -> 'bool const'

getGrid(self, *args, **kwargs) -> 'DensityGrid *'

gridParams(self, *args, **kwargs) -> 'DensityGrid_Params const'

info(self, *args, **kwargs) -> 'String'

mapResolution(self, *args, **kwargs) -> 'float_type const'

mapType(self, *args, **kwargs) -> 'AtomProb::MapType'

modified(self, *args, **kwargs) -> 'bool'

orientation(self, *args, **kwargs) -> 'Mat3 const'

pyXplorHelp(self, *args, **kwargs) -> 'String'

radii(self, *args, **kwargs) -> 'CDSVector< float_type > const'

radiusGradient(self, *args, **kwargs) -> 'CDSVector< float_type >'

scaleType(self, *args, **kwargs) -> 'AtomProb::ScaleType'

selection(self, *args, **kwargs) -> 'AtomSel'

setAtomRadius(self, *args, **kwargs) -> 'void'

setAtomWeights(self, *args, **kwargs) -> 'void'

setDistType(self, *args, **kwargs) -> 'void'

setGenerateGrid(self, *args, **kwargs) -> 'void'

setGridParams(self, *args, **kwargs) -> 'void'

setIsProjection(s, isProjection): backwards compatibility

setMapResolution(self, *args, **kwargs) -> 'void'

setMapType(self, *args, **kwargs) -> 'void'

setOrientation(self, *args, **kwargs) -> 'void'

setRadii(self, *args, **kwargs) -> 'void'

setScaleType(self, *args, **kwargs) -> 'void'

setTranslation(self, *args, **kwargs) -> 'void'

setVerbose(self, *args, **kwargs) -> 'void'

setWeights(self, *args, **kwargs) -> 'void'

translation(self, *args, **kwargs) -> 'Vec3 const'

updateValues(self, *args, **kwargs) -> 'void'

val(self, *args, **kwargs) -> 'double'

verbose(self, *args, **kwargs) -> 'bool const'

weights(self, *args, **kwargs) -> 'CDSVector< float_type >'

writeEDM(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_AtomProb(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

d_dR

d_dt

thisown: The membership flag

Data and other attributes defined here:

AMPLITUDE = 0

DENSITY = 0

DISTRIBUTION = 1

FLAT = 3

GAUSSIAN = 1

HEIGHT = 2

NORMALIZE = 2

OFF = 4

PROJECTION = 1

QUARTIC = 0

QUARTICSPREAD = 2

VOLUME = 5

Functions
		pyXplorHelp(*args) -> 'String'

Data
		__CDSVector_hh__ = 1