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