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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. |
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blurCoordsRadii(coords,
radii,
blobbyness=-0.1,
res=0.5,
weights=None,
dims=None,
padding=0.0) blur a set of coordinates with radii |
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| computeMSMSvolume(atmCoords, atmRadii, pRadius, dens) | ||
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meshArea(verts,
tri) Compute the surface area of a surface as the sum of the area of its triangles. |
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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) |
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findIsoValueMol(radii,
coords,
blobbyness,
data,
isoDensity,
targetValue,
target) Find the best isocontour value (isovalue) for a molecule... |
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| computeIsocontour(isovalue, data) | ||
| decimate(vert, tri, normals, density=1.0) | ||
| computeBlurCurvature(radii, coords, blobbiness, points) |
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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 |
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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 |
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