HappyDoc Generated Documentation Class: Molecule

. / _chimera / Molecule 

Methods   
  oslTestAbbr 
oslTestAbbr ( self,  a )
  newCoordSet 
newCoordSet ( self,  key )
  intersects 
intersects (
        self,
        p,
        lens,
        )
  setAllPDBHeaders 
setAllPDBHeaders ( self,  hs )
  bsphere 
bsphere ( self,  lens )
  residueBefore 
residueBefore ( self,  r )
  sequences 
sequences ( self )
  primaryAtoms 
primaryAtoms ( self )
  traverseAtoms 
traverseAtoms ( self,  root )
  decrHyds 
decrHyds ( self )
  deleteCoordSet 
deleteCoordSet ( self,  element )
  findAtom 
findAtom ( self,  i )
  findResidue 
findResidue ( self,  i )
  deleteBond 
deleteBond ( self,  element )
  oslChildren 
oslChildren ( self )
  roots 
roots ( self,  ignoreBreakPoints )
  ribbonCoordinates 
ribbonCoordinates ( self,  a )
  setPDBHeader 
setPDBHeader (
        self,
        k,
        v,
        )
  addPDBHeader 
addPDBHeader (
        self,
        k,
        h,
        )
  newAtom 
newAtom (
        self,
        n,
        e,
        )
  computeBounds 
computeBounds ( self,  lens )
  sequence 
sequence ( self )
  allRings 
allRings (
        self,
        crossResidues,
        allSizeThreshold,
        )
  removeAssociatedModel 
removeAssociatedModel ( self,  model )
  deleteResidue 
deleteResidue ( self,  element )
  deleteAtom 
deleteAtom ( self,  element )
  printComponents 
printComponents ( self )
  computeIdatmTypes 
computeIdatmTypes ( self )
  useAsRoot 
useAsRoot ( self,  newRoot )
  destroy 
destroy ( self )
  newBond 
newBond (
        self,
        a0,
        a1,
        )
  addAssociatedModel 
addAssociatedModel ( self,  model )
  pseudoBondMgr 
pseudoBondMgr ( self,  cs )
  oslParents 
oslParents ( self )
  oslIdent 
oslIdent (
        self,
        start,
        end,
        )
  moveResAfter 
moveResAfter (
        self,
        from_,
        to,
        )
  findCoordSet 
findCoordSet ( self,  i )
  sortedAtoms 
sortedAtoms ( self )
  computeSecondaryStructure 
computeSecondaryStructure (
        self,
        energyCutoff,
        minHelixLength,
        minStrandLength,
        )
  associatedModels 
associatedModels ( self )
  bbox 
bbox ( self,  lens )
  newResidue 
newResidue (
        self,
        t,
        rid,
        )
  incrHyds 
incrHyds ( self )
  count 
count ( self )
  updateRibbonData 
updateRibbonData ( self )
  pruneShortBonds 
pruneShortBonds ( self )
  traverseBonds 
traverseBonds ( self,  root )
  rootForAtom 
rootForAtom (
        self,
        a,
        ignoreBreakPoints,
        )
  numHyds 
numHyds ( self )
  minimumRings 
minimumRings ( self,  crossResidues )
  oslLevel 
oslLevel ( self )
  atomGroups 
atomGroups ( self,  numAtoms )
  findBond 
findBond ( self,  i )
  residueAfter 
residueAfter ( self,  r )

This document was automatically generated Wed Jul 9 15:49:00 2008 by HappyDoc version 3.1