HappyDoc Generated Documentation ./PipesAndPlanks/base.py

. / PipesAndPlanks / base.py 

Functions   
  getEndNormals 
getEndNormals (
        c0,
        c1,
        c2,
        )
  displayStrands 
displayStrands (
        mol,
        color,
        fixedWidth,
        width,
        fixedThickness,
        thickness,
        split,
        splitRatio,
        )
  minimizeTwist 
minimizeTwist (
        d,
        nn,
        nb,
        on,
        ob,
        )
  showTurn 
showTurn (
        turn,
        color,
        width,
        thickness,
        )

Create a VRML node representing a turn

  showHelix 
showHelix (
        helix,
        color,
        fixedRadius,
        radius,
        split,
        splitRatio,
        )

Create a VRML node representing a helix

  findTurns 
findTurns ( mol )
  findHelices 
findHelices ( mol )

Find helices and sheets in model

  addEdges 
addEdges (
        edges,
        offsets,
        coord,
        normal,
        binormal,
        )
  determinant 
determinant ( mat )
  deinitialize 
deinitialize ()
  initialize 
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.

  splitResidues 
splitResidues ( residues,  atomNames )

Split a list of residues by finding the pair that has the most divergent axes

  matrixNormalize 
matrixNormalize ( m )

Chimera is very picky about its matrices

Routine below normalizes a 3x3 matrix to the acceptable tolerance

  displayTurns 
displayTurns (
        mol,
        color,
        width,
        thickness,
        )
  getInteriorNormals 
getInteriorNormals (
        c0,
        cb,
        ca,
        )
  parametricVars 
parametricVars (
        base,
        axes,
        c,
        )

Compute the parametric variables from "base" to "c" using orthonormal bases of "axes"

  displayHelices 
displayHelices (
        mol,
        color,
        fixedRadius,
        radius,
        split,
        splitRatio,
        )
  findStrands 
findStrands ( mol )
  showStrand 
showStrand (
        strand,
        color,
        fixedWidth,
        width,
        fixedThickness,
        thickness,
        split,
        splitRatio,
        )

Create a VRML node representing a sheet

  findAxes 
findAxes ( resList,  atomNames )

Calculate orthonormal basis vectors via principal component analysis

Classes   

This document was automatically generated Wed Jul 9 15:49:39 2008 by HappyDoc version 3.1