|
/ . / _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 )
|
|
|
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 )
|
|
|
newResidue
|
newResidue (
self,
t,
rid,
)
|
|
|
incrHyds
|
incrHyds ( self )
|
|
|
updateRibbonData
|
updateRibbonData ( self )
|
|
|
pruneShortBonds
|
pruneShortBonds ( self )
|
|
|
traverseBonds
|
traverseBonds ( self, root )
|
|
|
rootForAtom
|
rootForAtom (
self,
a,
ignoreBreakPoints,
)
|
|
|
minimumRings
|
minimumRings ( self, crossResidues )
|
|
|
oslLevel
|
oslLevel ( self )
|
|
|
atomGroups
|
atomGroups ( self, numAtoms )
|
|
|
findBond
|
findBond ( self, i )
|
|
|
residueAfter
|
residueAfter ( self, r )
|
|
|