Pmv.computeIsovalue

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.

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)

source code

blur a set of coordinates with radii

computeMSMSvolume(atmCoords, atmRadii, pRadius, dens)

source code

None

meshArea(verts, tri)

source code

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)

source code

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)

source code

None

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

source code

None

computeBlurCurvature(radii, coords, blobbiness, points)

source code

None

Module computeIsovalue

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)

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

computeMSMSvolume(atmCoords, atmRadii, pRadius, dens)

meshArea(verts, tri)

normalCorrection(norms, faces)

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

computeIsocontour(isovalue, data)

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

computeBlurCurvature(radii, coords, blobbiness, points)