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Imported modules
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from CGLutil import vrml
import LinearAlgebra
import Numeric
import chimera
import math
import operator
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Functions
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determinant
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determinant ( mat )
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displayHelices
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displayHelices (
mol,
color,
fixedRadius,
radius,
split,
splitRatio,
)
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displayStrands
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displayStrands (
mol,
color,
fixedWidth,
width,
fixedThickness,
thickness,
split,
splitRatio,
)
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findAxes
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findAxes ( resList, atomNames )
Calculate orthonormal basis vectors from the eigenvectors of
the moment of inertia tensor of a set of coordinates
moment of inertia tensor components for an atom are:
I[i,j] = mass * (r * r * delta[i,j] - r[i] * r[j]
where
r = vector from center of mass to this atom
delta = delta function (1 if i == j, 0 otherwise)
See Kroto, H.W., Molecular Rotation Spectra, John Wiley and Sons, 1975, p 19
or http://www.phys.ufl.edu/~avery/course/3062_f96/home4/home4.htm
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findHelices
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findHelices ( mol )
Find helices and sheets in model
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findStrands
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findStrands ( mol )
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matrixNormalize
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matrixNormalize ( m )
Chimera is very picky about its matrices
Routine below normalizes a 3x3 matrix to the acceptable tolerance
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parametricVars
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parametricVars (
base,
axes,
c,
)
Compute the parametric variables from "base" to "c" using orthonormal
bases of "axes"
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showHelix
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showHelix (
helix,
color,
fixedRadius,
radius,
split,
splitRatio,
)
Create a VRML node representing a helix
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showStrand
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showStrand (
strand,
color,
fixedWidth,
width,
fixedThickness,
thickness,
split,
splitRatio,
)
Create a VRML node representing a sheet
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splitResidues
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splitResidues ( residues, atomNames )
Split a list of residues by finding the pair that has
the most divergent axes
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