Package Pmv :: Module computeIsovalue
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Module computeIsovalue

source code

Functions [hide private]
  computeIsovalue(nodes, blobbyness, densityList=3.0, gridResolution=0.5, criteria="Volume", radiiSet="united", msmsProbeRadius=1.4, computeWeightOption=0, resolutionLevel=None, gridDims=None, padding=0.0)
This function is based on shapefit/surfdock.py blurSurface() by Qing Zhang.
  blurCoordsRadii(coords, radii, blobbyness=-0.1, res=0.5, weights=None, dims=None, padding=0.0)
blur a set of coordinates with radii
  computeMSMSvolume(atmCoords, atmRadii, pRadius, dens)
  meshArea(verts, tri)
Compute the surface area of a surface as the sum of the area of its triangles.
  normalCorrection(norms, faces)
Replace any normal, which is equal to zero, with the average of its triangle neighbors' non-zero normals (triangle neighbors, as the edge partners, can be derived from the faces)
  findIsoValueMol(radii, coords, blobbyness, data, isoDensity, targetValue, target)
Find the best isocontour value (isovalue) for a molecule...
  computeIsocontour(isovalue, data)
  decimate(vert, tri, normals, density=1.0)
  computeBlurCurvature(radii, coords, blobbiness, points)

Function Details [hide private]

computeIsovalue(nodes, blobbyness, densityList=3.0, gridResolution=0.5, criteria="Volume", radiiSet="united", msmsProbeRadius=1.4, computeWeightOption=0, resolutionLevel=None, gridDims=None, padding=0.0)

source code 
This function is based on shapefit/surfdock.py blurSurface() by Qing Zhang.

INPUT:
        nodes           
        blobbyness:             blobbyness
        densityList:            A list of vertex densities (or just a single density value) for blur surfaces
                                        e.g. [1.0, 2.0, 3.0] or 1.0 or [1.0]
        gridResolution:         Resolution of grid used for blurring
                                        0.5  gives surface vertex density >  5 dots/Angstrom^2
                                        0.25 gives surface vertex density > 20 dots/Angstrom^2
                                        0.2  gives surface vertex density > 40 dots/Angstrom^2
        radiiSet:               Radii set for computing both MSMS and blur surfaces
        msmsProbeRadius:        Probe radius for computing MSMS
        resolutionLevel:        Level of surface resolution
                = None:                 using the given blobbyness value
                = 1 or 'very low'       blobbyness = -0.1
                = 2 or 'low'            blobbyness = -0.3
                = 3 or 'medium'         blobbyness = -0.5
                = 4 or 'high'           blobbyness = -0.9
                = 5 or 'very high'      blobbyness = -3.0

        padding : size of the padding around the molecule

                

blurCoordsRadii(coords, radii, blobbyness=-0.1, res=0.5, weights=None, dims=None, padding=0.0)

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blur a set of coordinates with radii

computeMSMSvolume(atmCoords, atmRadii, pRadius, dens)

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None

meshArea(verts, tri)

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Compute the surface area of a surface as the sum of the area of its triangles. The surface is specified by vertices, indices of triangular faces

normalCorrection(norms, faces)

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Replace any normal, which is equal to zero, with the average of its triangle neighbors' non-zero normals (triangle neighbors, as the edge partners, can be derived from the faces)

findIsoValueMol(radii, coords, blobbyness, data, isoDensity, targetValue, target)

source code 
Find the best isocontour value (isovalue) for a molecule
at one specific blobbyness by reproducing the targetValue
for a target (area or volume)
INPUT:
        mol:            molecule recognizable by MolKit
        blobbyness:     blobbyness
        data:           blurred data
        isoDensity:     density of surface vertices for finding isovalue only
        targetValue:    value of the target, to be reproduced
        target:         Area or Volume
OUTPUT:
        target:         (as input)
        targetValue:    (as input)
        value:          reproduced value of target
        isovalue:       the best isocontour value
        v1d:            vertices of generated blur surface
        t1d:            faces of generated blur surface
        n1d:            normals of the vertices

computeIsocontour(isovalue, data)

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None

decimate(vert, tri, normals, density=1.0)

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None

computeBlurCurvature(radii, coords, blobbiness, points)

source code 
None