Methods
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Molecule
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Molecule ( self )
Molecule() -> Molecule
Molecule constructor documentation.
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__hash__
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__hash__ ( self )
arguments/return value unknown
hash instance
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addAssociatedModel
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addAssociatedModel ( self, model )
addAssociatedModel(Model* model)
addAssociatedModel documentation.
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allRings
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allRings (
self,
crossResidues,
allSizeThreshold,
)
allRings(bool crossResidues, int allSizeThreshold) -> std::set<Ring>
allRings documentation.
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associatedModels
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associatedModels ( self )
associatedModels() -> std::vector<Model*>
associatedModels documentation.
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atomGroups
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atomGroups ( self, numAtoms )
atomGroups(int numAtoms) -> std::vector<Molecule::AtomGroup>
atomGroups documentation.
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bbox
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bbox ( self )
bbox() -> bool, otf::Geom3d::BBox
bbox documentation.
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computeIdatmTypes
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computeIdatmTypes ( self )
computeIdatmTypes()
computeIdatmTypes documentation.
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computeSecondaryStructure
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computeSecondaryStructure (
self,
energyCutoff,
minHelixLength,
minStrandLength,
)
computeSecondaryStructure(float energyCutoff, int minHelixLength, int minStrandLength)
computeSecondaryStructure documentation.
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deleteAtom
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deleteAtom ( self, element )
deleteAtom(Atom* element)
deleteAtom documentation.
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deleteBond
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deleteBond ( self, element )
deleteBond(Bond* element)
deleteBond documentation.
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deleteCoordSet
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deleteCoordSet ( self, element )
deleteCoordSet(CoordSet* element)
deleteCoordSet documentation.
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deleteResidue
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deleteResidue ( self, element )
deleteResidue(Residue* element)
deleteResidue documentation.
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destroy
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destroy ( self )
destroy()
destroy documentation.
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findCoordSet
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findCoordSet ( self, csi )
findCoordSet(int csi) -> CoordSet*
findCoordSet documentation.
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findResidue
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findResidue ( self, ri )
findResidue(int ri) -> Residue*
findResidue(otf::MolResId id, char* type) -> Residue*
findResidue documentation.
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idatmValid
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idatmValid ( self )
idatmValid() -> bool
idatmValid documentation.
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invalidateIdatm
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invalidateIdatm ( self )
invalidateIdatm()
invalidateIdatm documentation.
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minimumRings
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minimumRings ( self, crossResidues )
minimumRings(bool crossResidues) -> std::set<Ring>
minimumRings documentation.
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moveResAfter
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moveResAfter (
self,
from_,
to,
)
moveResAfter(Residue* from, Residue* to)
moveResAfter documentation.
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newAtom
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newAtom (
self,
n,
element,
)
newAtom(otf::Symbol n, otf::Element element) -> Atom*
newAtom documentation.
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newBond
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newBond (
self,
a0,
a1,
)
newBond(Atom* a0, Atom* a1) -> Bond*
newBond(Atom* a0, Atom* a1, float o) -> Bond*
newBond documentation.
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newCoordSet
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newCoordSet ( self, k )
newCoordSet(int k) -> CoordSet*
newCoordSet(int k, int size) -> CoordSet*
newCoordSet documentation.
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newResidue
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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.
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oslChildren
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oslChildren ( self )
oslChildren() -> std::vector<Selectable*>
oslChildren documentation.
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oslIdent
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oslIdent (
self,
start,
end,
)
oslIdent(enum Selector start, enum Selector end) -> std::string
oslIdent documentation.
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oslLevel
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oslLevel ( self )
oslLevel() -> enum Selector
oslLevel documentation.
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oslParents
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oslParents ( self )
oslParents() -> std::vector<Selectable*>
oslParents documentation.
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oslTestAbbr
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oslTestAbbr ( self, a )
oslTestAbbr(OSLAbbreviation* a) -> bool
oslTestAbbr documentation.
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printComponents
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printComponents ( self )
printComponents()
printComponents documentation.
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pseudoBondMgr
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pseudoBondMgr ( self, cs )
pseudoBondMgr(CoordSet* cs) -> PseudoBondMgr*
pseudoBondMgr documentation.
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removeAssociatedModel
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removeAssociatedModel ( self, model )
removeAssociatedModel(Model* model)
removeAssociatedModel documentation.
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rootForAtom
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rootForAtom (
self,
a,
ignoreBreakPoints,
)
rootForAtom(Atom* a, bool ignoreBreakPoints) -> Root*
rootForAtom documentation.
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roots
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roots ( self, ignoreBreakPoints )
roots(bool ignoreBreakPoints) -> std::vector<Root>
roots documentation.
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traverseAtoms
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traverseAtoms ( self, root )
traverseAtoms(Root* root) -> std::pair<Molecule::Atoms::const_iterator,Molecule::Atoms::const_iterator>
traverseAtoms documentation.
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traverseBonds
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traverseBonds ( self, root )
traverseBonds(Root* root) -> std::pair<Molecule::Bonds::const_iterator,Molecule::Bonds::const_iterator>
traverseBonds documentation.
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updateRibbonData
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updateRibbonData ( self )
updateRibbonData()
updateRibbonData documentation.
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useAsRoot
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useAsRoot ( self, newRoot )
useAsRoot(Atom* newRoot)
useAsRoot documentation.
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