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/ . / _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 = 4294967295
- 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
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Methods
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oslTestAbbr
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oslTestAbbr ( self, a )
oslTestAbbr(a: OSLAbbreviation) -> bool
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findPseudoBond
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findPseudoBond ( self, i )
findPseudoBond(i: int) -> PseudoBond
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associated
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associated (
self,
otherAtom,
category,
)
associated(otherAtom: Atom, category: str) -> bool
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setCoord
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setCoord ( self, c )
setCoord(c: Point)
setCoord(c: Point, cs: CoordSet)
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primaryBonds
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primaryBonds ( self )
primaryBonds() -> list of Bond
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oslChildren
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oslChildren ( self )
oslChildren() -> list of Selectable
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coordination
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coordination ( self, valueIfUnknown )
coordination(valueIfUnknown: int = 0) -> int
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shown
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shown ( self )
shown() -> bool
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rootAtom
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rootAtom ( self, ignoreBreakPoints )
rootAtom(ignoreBreakPoints: bool) -> Atom
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minimumRings
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minimumRings ( self, crossResidues )
minimumRings(crossResidues: bool = false) -> list of Ring
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allRings
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allRings (
self,
crossResidues,
sizeThreshold,
)
allRings(crossResidues: bool = false, sizeThreshold: int = 0) -> list of Ring
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getIdatmInfoMap
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getIdatmInfoMap ( self )
getIdatmInfoMap() -> dict of (str, Atom.IdatmInfo)
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connectsTo
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connectsTo ( self, a )
connectsTo(a: Atom) -> Bond
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vdwPoints
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vdwPoints ( self )
vdwPoints() -> list of tuple(Point, Vector)
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traverseFrom
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traverseFrom ( self, ignoreBreakPoints )
traverseFrom(ignoreBreakPoints: bool) -> Atom
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associations
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associations (
self,
category,
otherAtom,
)
associations(category: str, otherAtom: (Atom|None) = None) -> list of PseudoBond
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oslParents
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oslParents ( self )
oslParents() -> list of Selectable
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revertDefaultRadius
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revertDefaultRadius ( self )
revertDefaultRadius()
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oslIdent
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oslIdent (
self,
start,
end,
)
oslIdent(start: int = SelDefault, end: int = SelDefault) -> str
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addBond
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addBond ( self, element )
addBond(element: Bond)
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IdatmInfo
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IdatmInfo ( self )
IdatmInfo() -> IdatmInfo
IdatmInfo(_x: Atom.IdatmInfo) -> IdatmInfo
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allLocations
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allLocations ( self )
allLocations() -> list of Atom
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count
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count ( self )
count() -> int
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removePseudoBond
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removePseudoBond ( self, element )
removePseudoBond(element: PseudoBond)
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clearVdwPoints
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clearVdwPoints ( self )
clearVdwPoints()
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primaryNeighbors
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primaryNeighbors ( self )
primaryNeighbors() -> list of Atom
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xformCoord
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xformCoord ( self )
xformCoord() -> Point
xformCoord(cs: CoordSet) -> Point
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coord
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coord ( self )
coord() -> Point
coord(cs: CoordSet) -> Point
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removeBond
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removeBond ( self, element )
removeBond(element: Bond)
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oslLevel
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oslLevel ( self )
oslLevel() -> int
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addPseudoBond
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addPseudoBond ( self, element )
addPseudoBond(element: PseudoBond)
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findBond
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findBond ( self, a )
findBond(a: Atom) -> Bond
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