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Pydoc: module atomProbTools

atomProbTools

index

Functions to create and access different types of atomProb.AtomProb objects.

Functions

create_AtomProb(selection, mapType='density'): Create an appropirate atomProb.AtomProb obj given the specified
mapType.

create_Mask(grid, molOrientationSels, mapOrientation=[ 1.000, 0.000, 0.000] [ 0.000, 1.000, 0.000] [ 0.000, 0.000, 1.000], molPlaneSel='not PSEUDO', zDirSels=None, mapCenter='centroid', referenceGrid=None, is2D=None): Given a densityGrid.DensityGrid, create an atomProb.Mask
object.

molOrientationSels - a sequence of two or four atomSel.AtomSel
                     objects. The first two specify map direction (within
                     the map plane), and (if specified) the second two
                     unambiguously specify the z-direction.

mapOrientation     - a mat3.Mat3 specifying the mask orientation.

molPlaneSel        - an atomSel.AtomSel specifying atoms defining
                     the mask plane.

mapCenter can be a vec3.Vec3, or is computed the strings:
  'center'   - the center of grid
  'centroid' - the centroid of the grid (position weighted by image
               value).
  'zero'     - (0,0,0).

is2D is specified to indicate a 2D map. By default (is2D=None), a
2D mask is detected if grid.znum=1.

generateAtomProb(term): Choose and return the correct AtomProb subclass, based on term.mapType()

maskInfo(atomProb): Return string containing formatted summary of mask info.

setVdWRadii(aProb, radiusScale=1.0): Given a atomProb.AtomProb, set atomic radii to
Van der Waal values in the module-local dictionary radiusMap.

transformedMask(mask): Return densityGrid.DensityGrid object corresponding to the
mask transformed by Mask::apply.

weightByAtomElectrons(aProb): Set the per-atom weights in AtomProb as the number of electrons in
each atom.

weightByResidueElectrons(aProb): Set the per-atom weights in the AtomProb as the number of electrons in
the respective containg residue.

Data
		radiusMap = {'C': 1.75, 'CO': 1.65, 'H': 1.17, 'HH': 1.0, 'N': 1.55, 'O': 1.4, 'P': 1.8, 'S': 1.8}