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Pydoc: module densityGridTools

densityGridTools

index

Tools to help create, manipulate and plot densityGrid.DensityGrid objects used to represent electron density maps, projections and atomic force height maps.

Functions

covarianceValues(map): Return the principal components of the covariance matrix, sorted in
order of largest to smallest.

create_DensityGrid(filename=None, slice=None, delta=None, verbose=False): Read the specified EDM file. Supported formats are MRC, MRCS and CCP4.
The slice argument can be used to specify a slice containing a 2D
projection.

The optional delta argument will override the grid spacing members of the
returned DensityGrid object - i.e. xdelta, ydelta, and (for 3D maps only)
zdelta.

mergedSlicesAsImage(dmap1, dmap2, imgFilename, sliceNum=0, offset=None, verbose=False): Given two projections, given as sliceNum slices of dmap1 and dmap2
arguments, create an output image named imgFilename in which dmap1 and
dmap2 are represented as the colors magenta and green, respectively.
Regions in which the projections have the same (nonzero) value appear
white.

mergedSlicesToImage(dmap1, dmap2, sliceNum=0, offset=None, flip=True, verbose=False): Given two projections, given as sliceNum slices of dmap1 and
dmap2 arguments, return a PIL.Image in which dmap1 and dmap2 are
represented as the colors magenta and green, respectively.
Regions in which the projections have the same (nonzero) value
appear white.

Because DensityGrid slice data is filled bottom to top, and PIL
Image data is filled top to bottom, image data is flipped after creation
unless the flip argument is set to False.

openImageOrDensityGrid(filename, omap=None, flip=True): Open a MRCS or image file, and return a densityGrid.DensityGrid
object.

If specified, the omap argument should be a slice (znum=1) DensityGrid
object used to fill in grid information when an image is specified. If
this argument is omitted, then grid value information for the returned
object is bogus.

Because DensityGrid slice data is filled bottom to top, and PIL
Image data is filled top to bottom, image data is flipped after
being read, and before copying the data to the DensityGrid. This
action can be disabled by setting flip to False.

sliceAsImage(dmap, imgFilename, sliceNum=0, usePalette=False): Given a densityGrid.DensityGrid object, write out the specified slice
(grid number in the z-dimension) to the specified file. File type is
determined by the suffix given in imgFilename.

sliceToBytes(dmap, sliceNum=0): Given a densityGrid.DensityGrid object, return a tuple containing
(xsize,ysize,dataInBytes), with byte data corresponding to slice given by
sliceNum. Normalized pixel intensity is computed as
2558(sliceData -minVal) / (maxVal-minVal), where minVal and maxVal are
the minimal and maximal values in the slice.

sliceToImage(dmap, sliceNum=0, usePalette=False, flip=True): Given a densityGrid.DensityGrid object, return a PIL.Image with
a grayscale image corresponding to slice given by sliceNum, as returned
by sliceToBytes.

Because DensityGrid slice data is filled bottom to top, and PIL Image
data is filled top to bottom, image data is flipped after creation unless
the flip argument is set of False.

The optional usePalette argument can be set to produce a black,red->blue
colormapped image instead of a black->white intensity image.

trimDensityGrid(dmap, pad=0.5, sel='not pseudo', algorithm='rectangle', percent=None, verbose=False): Return a new DensityGrid object whose grid is a subregion of
the input atomic density map around atom coordinates specified by sel. In
this way the DensityGrid can be reduced in size. The trimming can be
specified relative to atomic coordinates, or as a fraction of the input
grid size.

If the percent argument is specified, the map is trimmed as a percent of
the input grid. This pargument can be specified as a tuple of 6
percentages specifying, in percent, (xmin, xmax, ymin, ymax, zmin, zmax),
or as a single or three number(s), specifying percent about the center.

If percent is not specified, then atomic coordinates are used to trim the
map as follows:

  Given the current atomic coordinates defined by sel (an atom selection
  string or atomSel.AtomSel object) and an atomic density map, dmap
  (a string with the filename path of a ccp4 or mrc file or, alternatively,
  an atomDensity.DensityGrid instance), return a subregion of dmap
  (an atomDensity.DensityGrid instance) around the coordinates.

  The method used to determine the subregion is specified by the
  algorithm argument: either "sphere", where the subregion is
  defined by the smallest sphere (of radius r) that envelops all the
  coordinates, with r augmented by the multiplier specified by the
  pad argument (i.e., the sphere has a radius r + pad * r, centered
  around the centroid of the coordinates). or "rectangle" whereby a
  rectangular prism is selected using the same mechanism, but different
  values are determined in each dimension. If the region exceeds the
  dimensions of the map in one dimension, the map is truncated to
  the bounds of the original map.