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Pydoc: module atomProbTools

atomProbTools

index

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

Functions

centerOnMap(atomProb, map, verbose=False): Given an AtomProb, and a densityGrid.DensityGrid,
adjust atom positions such that the atoms in atomProb's selection's
center of mass coincide with the center of the map.

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

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

The grid argumenet is a DensityGrid, or image filename. If an image,
the referenceGrid option much be specified to fill in the remaining
grid information. In this case the optional argument flip will be passed
to openImageOrDensityGrid.

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

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

molCenterSel        - an atomSel.AtomSel specifying atoms defining
                     the origin. Defaults to molPlaneSel.

mapOrientation     - a mat3.Mat3 specifying the mask orientation.

Briefly (and approximately):
  z-dir: perpendicular to molOrientationSels
  x-dir: difference of molOrientationSels
  y-dir: perpendicular to other two

mapOrientation rotates the coorindate system s.t. a different axis
is the z-axis.

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.

radiusByName(atom)

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}