oslTestAbbr ( self,  a )

oslTestAbbr(a: OSLAbbreviation) -> bool

newCoordSet ( self,  key )

newCoordSet(key: int) -> CoordSet newCoordSet(key: int, size: int) -> CoordSet

oslChildren ( self )

oslChildren() -> list of Selectable

setAllPDBHeaders ( self,  hs )

setAllPDBHeaders(hs: dict of (str, list of str))

bsphere ( self,  lens )

bsphere(lens: Lens = NULL) -> bool, Sphere

residueBefore ( self,  r )

residueBefore(r: Residue) -> Residue

sequences ( self )

arguments/return value unknown

return all non-trivial sequences in a molecule

This function is also available as molecule.sequences(...)

returns a list of sequences for the given molecule, one sequence per multi-residue chain. The sequence name is "Chain X" where X is the chain ID, or "Principal chain" if there is no chain ID.

The residues attribute of each sequence is a list of the residues for that sequence, and the attribute resmap is a dictionary that maps residue to sequence position (zero-based). The residues attribute will self-delete if the corresponding model is closed.

If asDict is true, return a dictionary of Sequences keyed on chain ID (can throw AssertionError if multiple chains have same ID), otherwise return a list.

primaryAtoms ( self )

primaryAtoms() -> list of Atom

traverseAtoms ( self,  root )

traverseAtoms(root: Root) -> list of Atom

decrHyds ( self )

decrHyds()

deleteCoordSet ( self,  element )

deleteCoordSet(element: CoordSet)

findAtom ( self,  i )

findAtom(i: int) -> Atom

findResidue ( self,  i )

findResidue(i: int) -> Residue findResidue(rid: MolResId, type: str = NULL) -> Residue

deleteBond ( self,  element )

deleteBond(element: Bond)

roots ( self,  ignoreBreakPoints )

roots(ignoreBreakPoints: bool) -> list of Root

setPDBHeader (
        self,
        k,
        v,
        )

setPDBHeader(k: str, v: list of str)

addPDBHeader (
        self,
        k,
        h,
        )

addPDBHeader(k: str, h: str)

newAtom (
        self,
        n,
        e,
        )

newAtom(n: str, e: Element) -> Atom

computeBounds ( self,  lens )

computeBounds(lens: Lens = NULL) -> bool, Sphere, BBox

sequence ( self )

arguments/return value unknown

Get the Sequence of the specified chain

Uses the getSequences function (below) and accepts the same keywords. Throws KeyError if the specified chain isn't found, and AssertionError if there are multiple chains with the specified ID.

allRings (
        self,
        crossResidues,
        allSizeThreshold,
        )

allRings(crossResidues: bool, allSizeThreshold: int) -> set of Ring

removeAssociatedModel ( self,  model )

removeAssociatedModel(model: Model)

deleteResidue ( self,  element )

deleteResidue(element: Residue)

deleteAtom ( self,  element )

deleteAtom(element: Atom)

printComponents ( self )

printComponents()

computeIdatmTypes ( self )

computeIdatmTypes()

useAsRoot ( self,  newRoot )

useAsRoot(newRoot: Atom)

destroy ( self )

destroy()

newBond (
        self,
        a0,
        a1,
        )

newBond(a0: Atom, a1: Atom) -> Bond

addAssociatedModel ( self,  model )

addAssociatedModel(model: Model)

pseudoBondMgr ( self,  cs )

pseudoBondMgr(cs: CoordSet = NULL) -> PseudoBondMgr

oslParents ( self )

oslParents() -> list of Selectable

oslIdent (
        self,
        start,
        end,
        )

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

moveResAfter (
        self,
        from_,
        to,
        )

moveResAfter(from: Residue, to: Residue)

findCoordSet ( self,  i )

findCoordSet(i: int) -> CoordSet

sortedAtoms ( self )

sortedAtoms() -> list of Atom

computeSecondaryStructure (
        self,
        energyCutoff,
        minHelixLength,
        minStrandLength,
        )

computeSecondaryStructure(energyCutoff: float = -0.5, minHelixLength: int = 3, minStrandLength: int = 3)

associatedModels ( self )

associatedModels() -> list of Model

bbox ( self,  lens )

bbox(lens: Lens = NULL) -> bool, BBox

newResidue (
        self,
        t,
        rid,
        )

newResidue(t: str, rid: MolResId) -> Residue newResidue(t: str, chain: str, pos: int, insert: str) -> Residue

incrHyds ( self )

incrHyds()

count ( self )

count() -> int

updateRibbonData ( self )

updateRibbonData()

pruneShortBonds ( self )

pruneShortBonds()

traverseBonds ( self,  root )

traverseBonds(root: Root) -> list of Bond

rootForAtom (
        self,
        a,
        ignoreBreakPoints,
        )

rootForAtom(a: Atom, ignoreBreakPoints: bool) -> Root

numHyds ( self )

numHyds() -> int

minimumRings ( self,  crossResidues )

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

oslLevel ( self )

oslLevel() -> int

atomGroups ( self,  numAtoms )

atomGroups(numAtoms: int) -> list of list of Atom

findBond ( self,  i )

findBond(i: int) -> Bond

residueAfter ( self,  r )

residueAfter(r: Residue) -> Residue