/ . / PipesAndPlanks / base.py
Functions
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getEndNormals
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getEndNormals (
c0,
c1,
c2,
)
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displayStrands
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displayStrands (
mol,
color,
fixedWidth,
width,
fixedThickness,
thickness,
split,
splitRatio,
)
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minimizeTwist
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minimizeTwist (
d,
nn,
nb,
on,
ob,
)
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showTurn
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showTurn (
turn,
color,
width,
thickness,
)
Create a VRML node representing a turn
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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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findTurns
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findTurns ( mol )
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findHelices
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findHelices ( mol )
Find helices and sheets in model
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addEdges
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addEdges (
edges,
offsets,
coord,
normal,
binormal,
)
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determinant
|
determinant ( mat )
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deinitialize
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deinitialize ()
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initialize
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initialize ()
initialize and deinitialize are called before
and after calls to displayHelices, displayStrands
and displayTurns. displayTurns should be called
last because it uses data populated by the first
two routines.
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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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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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displayTurns
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displayTurns (
mol,
color,
width,
thickness,
)
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getInteriorNormals
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getInteriorNormals (
c0,
cb,
ca,
)
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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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displayHelices
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displayHelices (
mol,
color,
fixedRadius,
radius,
split,
splitRatio,
)
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findStrands
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findStrands ( mol )
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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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findAxes
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findAxes ( resList, atomNames )
Calculate orthonormal basis vectors via principal component analysis
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