HappyDoc Generated Documentation Class: Atom

. / _chimera / Atom 

Not instantiable from Python

constants:
  • Ball = 3
  • Dot = 0
  • EndCap = 2
  • Ion = 0
  • Linear = 2
  • Planar = 3
  • Single = 1
  • Sphere = 1
  • Tetrahedral = 4
  • UNASSIGNED = -1
  • selLevel = 3
attributes:
  • altLoc: str
  • bonds: list of Bond
  • bondsMap: dict of (Atom, Bond)
  • color: Color
  • coordIndex: unsigned int
  • defaultRadius: float
  • display: bool
  • drawMode: int
  • element: Element
  • hide: bool
  • idatmIsExplicit: bool
  • idatmType: str
  • label: str
  • labelColor: Color
  • labelOffset: Vector
  • molecule: Molecule
  • name: str
  • neighbors: list of Atom
  • pseudoBonds: list of PseudoBond
  • radius: float
  • residue: Residue
  • surfaceCategory: str
  • surfaceColor: Color
  • surfaceDisplay: bool
  • surfaceOpacity: float
  • vdw: bool
  • vdwColor: Color
Methods   
  oslTestAbbr 
oslTestAbbr ( self,  a )

oslTestAbbr(a: OSLAbbreviation) -> bool

  findPseudoBond 
findPseudoBond ( self,  i )

findPseudoBond(i: int) -> PseudoBond

  associated 
associated (
        self,
        otherAtom,
        category,
        )

associated(otherAtom: Atom, category: str) -> bool

  setCoord 
setCoord ( self,  c )

setCoord(c: Point) setCoord(c: Point, cs: CoordSet)

  primaryBonds 
primaryBonds ( self )

primaryBonds() -> list of Bond

  oslChildren 
oslChildren ( self )

oslChildren() -> list of Selectable

  coordination 
coordination ( self,  valueIfUnknown )

coordination(valueIfUnknown: int = 0) -> int

  shown 
shown ( self )

shown() -> bool

  rootAtom 
rootAtom ( self,  ignoreBreakPoints )

rootAtom(ignoreBreakPoints: bool) -> Atom

  minimumRings 
minimumRings ( self,  crossResidues )

minimumRings(crossResidues: bool = false) -> list of Ring

  allRings 
allRings (
        self,
        crossResidues,
        sizeThreshold,
        )

allRings(crossResidues: bool = false, sizeThreshold: int = 0) -> list of Ring

  getIdatmInfoMap 
getIdatmInfoMap ( self )

getIdatmInfoMap() -> dict of (str, Atom.IdatmInfo)

  connectsTo 
connectsTo ( self,  a )

connectsTo(a: Atom) -> Bond

  vdwPoints 
vdwPoints ( self )

vdwPoints() -> list of tuple(Point, Vector)

  traverseFrom 
traverseFrom ( self,  ignoreBreakPoints )

traverseFrom(ignoreBreakPoints: bool) -> Atom

  associations 
associations (
        self,
        category,
        otherAtom,
        )

associations(category: str, otherAtom: Atom = None) -> list of PseudoBond

  oslParents 
oslParents ( self )

oslParents() -> list of Selectable

  revertDefaultRadius 
revertDefaultRadius ( self )

revertDefaultRadius()

  oslIdent 
oslIdent (
        self,
        start,
        end,
        )

oslIdent(start: int = SelDefault, end: int = SelDefault) -> str

  addBond 
addBond ( self,  element )

addBond(element: Bond)

  IdatmInfo 
IdatmInfo ( self )

IdatmInfo() -> IdatmInfo IdatmInfo(_x: Atom.IdatmInfo) -> IdatmInfo

  allLocations 
allLocations ( self )

allLocations() -> list of Atom

  count 
count ( self )

count() -> int

  removePseudoBond 
removePseudoBond ( self,  element )

removePseudoBond(element: PseudoBond)

  clearVdwPoints 
clearVdwPoints ( self )

clearVdwPoints()

  primaryNeighbors 
primaryNeighbors ( self )

primaryNeighbors() -> list of Atom

  xformCoord 
xformCoord ( self )

xformCoord() -> Point xformCoord(cs: CoordSet) -> Point

  coord 
coord ( self )

coord() -> Point coord(cs: CoordSet) -> Point

  removeBond 
removeBond ( self,  element )

removeBond(element: Bond)

  oslLevel 
oslLevel ( self )

oslLevel() -> int

  addPseudoBond 
addPseudoBond ( self,  element )

addPseudoBond(element: PseudoBond)

  findBond 
findBond ( self,  a )

findBond(a: Atom) -> Bond


This document was automatically generated Thu Nov 09 13:33:32 2006 by HappyDoc version 3.0.a1