Table of Contents

Class: Molecule _chimera/__init__.py

Molecule documentation

attributes:

  • activeCoordSet

  • atoms

  • autochain

  • ballFract

  • bonds

  • color

  • coordSets

  • explicitHydrogens

  • lineWidth

  • mol2comments

  • mol2data

  • pdbHeaders

  • pointSize

  • residues

  • showStubBonds

  • sortedAtoms

  • stickSize

  • structureAssigned

  • surfaceColor

  • vdwDensity

  • wireStipple

Methods   
Molecule
__hash__
addAssociatedModel
allRings
associatedModels
atomGroups
bbox
computeIdatmTypes
computeSecondaryStructure
deleteAtom
deleteBond
deleteCoordSet
deleteResidue
destroy
findCoordSet
findResidue
idatmValid
invalidateIdatm
minimumRings
moveResAfter
newAtom
newBond
newCoordSet
newResidue
oslChildren
oslIdent
oslLevel
oslParents
oslTestAbbr
printComponents
pseudoBondMgr
removeAssociatedModel
rootForAtom
roots
traverseAtoms
traverseBonds
updateRibbonData
useAsRoot
  Molecule 
Molecule ( self )

Molecule() -> Molecule

Molecule constructor documentation.

  __hash__ 
__hash__ ( self )

arguments/return value unknown

hash instance

  addAssociatedModel 
addAssociatedModel ( self,  model )

addAssociatedModel(Model* model)

addAssociatedModel documentation.

  allRings 
allRings (
        self,
        crossResidues,
        allSizeThreshold,
        )

allRings(bool crossResidues, int allSizeThreshold) -> std::set<Ring>

allRings documentation.

  associatedModels 
associatedModels ( self )

associatedModels() -> std::vector<Model*>

associatedModels documentation.

  atomGroups 
atomGroups ( self,  numAtoms )

atomGroups(int numAtoms) -> std::vector<Molecule::AtomGroup>

atomGroups documentation.

  bbox 
bbox ( self )

bbox() -> bool, otf::Geom3d::BBox

bbox documentation.

  computeIdatmTypes 
computeIdatmTypes ( self )

computeIdatmTypes()

computeIdatmTypes documentation.

  computeSecondaryStructure 
computeSecondaryStructure (
        self,
        energyCutoff,
        minHelixLength,
        minStrandLength,
        )

computeSecondaryStructure(float energyCutoff, int minHelixLength, int minStrandLength)

computeSecondaryStructure documentation.

  deleteAtom 
deleteAtom ( self,  element )

deleteAtom(Atom* element)

deleteAtom documentation.

  deleteBond 
deleteBond ( self,  element )

deleteBond(Bond* element)

deleteBond documentation.

  deleteCoordSet 
deleteCoordSet ( self,  element )

deleteCoordSet(CoordSet* element)

deleteCoordSet documentation.

  deleteResidue 
deleteResidue ( self,  element )

deleteResidue(Residue* element)

deleteResidue documentation.

  destroy 
destroy ( self )

destroy()

destroy documentation.

  findCoordSet 
findCoordSet ( self,  csi )

findCoordSet(int csi) -> CoordSet*

findCoordSet documentation.

  findResidue 
findResidue ( self,  ri )

findResidue(int ri) -> Residue* findResidue(otf::MolResId id, char* type) -> Residue*

findResidue documentation.

  idatmValid 
idatmValid ( self )

idatmValid() -> bool

idatmValid documentation.

  invalidateIdatm 
invalidateIdatm ( self )

invalidateIdatm()

invalidateIdatm documentation.

  minimumRings 
minimumRings ( self,  crossResidues )

minimumRings(bool crossResidues) -> std::set<Ring>

minimumRings documentation.

  moveResAfter 
moveResAfter (
        self,
        from_,
        to,
        )

moveResAfter(Residue* from, Residue* to)

moveResAfter documentation.

  newAtom 
newAtom (
        self,
        n,
        element,
        )

newAtom(otf::Symbol n, otf::Element element) -> Atom*

newAtom documentation.

  newBond 
newBond (
        self,
        a0,
        a1,
        )

newBond(Atom* a0, Atom* a1) -> Bond* newBond(Atom* a0, Atom* a1, float o) -> Bond*

newBond documentation.

  newCoordSet 
newCoordSet ( self,  k )

newCoordSet(int k) -> CoordSet* newCoordSet(int k, int size) -> CoordSet*

newCoordSet documentation.

  newResidue 
newResidue (
        self,
        t,
        rid,
        )

newResidue(otf::Symbol t, otf::MolResId rid) -> Residue* newResidue(otf::Symbol t, otf::Symbol chain, int pos, char insert) -> Residue*

newResidue documentation.

  oslChildren 
oslChildren ( self )

oslChildren() -> std::vector<Selectable*>

oslChildren documentation.

  oslIdent 
oslIdent (
        self,
        start,
        end,
        )

oslIdent(enum Selector start, enum Selector end) -> std::string

oslIdent documentation.

  oslLevel 
oslLevel ( self )

oslLevel() -> enum Selector

oslLevel documentation.

  oslParents 
oslParents ( self )

oslParents() -> std::vector<Selectable*>

oslParents documentation.

  oslTestAbbr 
oslTestAbbr ( self,  a )

oslTestAbbr(OSLAbbreviation* a) -> bool

oslTestAbbr documentation.

  printComponents 
printComponents ( self )

printComponents()

printComponents documentation.

  pseudoBondMgr 
pseudoBondMgr ( self,  cs )

pseudoBondMgr(CoordSet* cs) -> PseudoBondMgr*

pseudoBondMgr documentation.

  removeAssociatedModel 
removeAssociatedModel ( self,  model )

removeAssociatedModel(Model* model)

removeAssociatedModel documentation.

  rootForAtom 
rootForAtom (
        self,
        a,
        ignoreBreakPoints,
        )

rootForAtom(Atom* a, bool ignoreBreakPoints) -> Root*

rootForAtom documentation.

  roots 
roots ( self,  ignoreBreakPoints )

roots(bool ignoreBreakPoints) -> std::vector<Root>

roots documentation.

  traverseAtoms 
traverseAtoms ( self,  root )

traverseAtoms(Root* root) -> std::pair<Molecule::Atoms::const_iterator,Molecule::Atoms::const_iterator>

traverseAtoms documentation.

  traverseBonds 
traverseBonds ( self,  root )

traverseBonds(Root* root) -> std::pair<Molecule::Bonds::const_iterator,Molecule::Bonds::const_iterator>

traverseBonds documentation.

  updateRibbonData 
updateRibbonData ( self )

updateRibbonData()

updateRibbonData documentation.

  useAsRoot 
useAsRoot ( self,  newRoot )

useAsRoot(Atom* newRoot)

useAsRoot documentation.


Table of Contents

This document was automatically generated on Wed Mar 26 19:02:47 2003 by HappyDoc version 2.1