Help on class Molecule in module _molecule:

class Molecule(_chimera.Model)
 |  Molecule() -> Molecule
 |  
 |  Method resolution order:
 |      Molecule
 |      _chimera.Model
 |      _chimera.Selectable
 |      libwrappy2.WrapPy
 |      __builtin__.object
 |  
 |  Methods defined here:
 |  
 |  __hash__(...)
 |      x.__hash__() <==> hash(x)
 |  
 |  __init__(...)
 |      x.__init__(...) initializes x; see help(type(x)) for signature
 |  
 |  addPDBHeader(...)
 |      addPDBHeader(k: unicode, h: unicode)
 |  
 |  allRings(...)
 |      allRings(crossResidues: bool, allSizeThreshold: int) -> set of Ring
 |  
 |  atomCoordinatesArray(...)
 |      atomCoordinatesArray() -> object
 |  
 |  atomGroups(...)
 |      atomGroups(numAtoms: int) -> list of list of Atom
 |  
 |  computeIdatmTypes(...)
 |      computeIdatmTypes()
 |  
 |  computeSecondaryStructure(...)
 |      computeSecondaryStructure(energyCutoff: float = -0.5, minHelixLength: int = 3, minStrandLength: int = 3, info: __unknown__ = None)
 |  
 |  decrHyds(...)
 |      decrHyds()
 |  
 |  deleteAtom(...)
 |      deleteAtom(element: Atom)
 |  
 |  deleteBond(...)
 |      deleteBond(element: Bond)
 |  
 |  deleteCoordSet(...)
 |      deleteCoordSet(element: CoordSet)
 |  
 |  deleteResidue(...)
 |      deleteResidue(element: Residue)
 |  
 |  findAtom(...)
 |      findAtom(i: int) -> Atom
 |  
 |  findBond(...)
 |      findBond(i: int) -> Bond
 |  
 |  findBondRot(...)
 |      findBondRot(bond: Bond) -> BondRot
 |  
 |  findCoordSet(...)
 |      findCoordSet(i: int) -> CoordSet
 |  
 |  findResidue(...)
 |      findResidue(i: int) -> Residue
 |      findResidue(rid: MolResId, type: (str|None) = None) -> Residue
 |  
 |  incrHyds(...)
 |      incrHyds()
 |  
 |  indexedAtoms(...)
 |      indexedAtoms(indices: object) -> list of Atom
 |  
 |  loadAllFrames lambda self
 |  
 |  metalComplexGroup = _getMetalPbg(mol, **kw)
 |  
 |  minimumRings(...)
 |      minimumRings(crossResidues: bool = false) -> set of Ring
 |  
 |  moveResAfter(...)
 |      moveResAfter(from: Residue, to: Residue)
 |  
 |  newAtom(...)
 |      newAtom(n: unicode, e: Element, coordIndex: int = -1) -> Atom
 |  
 |  newBond(...)
 |      newBond(a0: Atom, a1: Atom) -> Bond
 |  
 |  newCoordSet(...)
 |      newCoordSet(key: int) -> CoordSet
 |      newCoordSet(key: int, size: int) -> CoordSet
 |  
 |  newResidue(...)
 |      newResidue(t: unicode, rid: MolResId, neighbor: (Residue|None) = None, after: bool = true) -> Residue
 |      newResidue(t: unicode, chain: unicode, pos: int, insert: str, neighbor: (Residue|None) = None, after: bool = true) -> Residue
 |  
 |  numHyds(...)
 |      numHyds() -> int
 |  
 |  primaryAtoms(...)
 |      primaryAtoms() -> list of Atom
 |  
 |  printComponents(...)
 |      printComponents(os: writable file-like)
 |  
 |  pruneShortBonds(...)
 |      pruneShortBonds()
 |  
 |  pseudoBondMgr(...)
 |      pseudoBondMgr(cs: (CoordSet|None) = None) -> PseudoBondMgr
 |  
 |  reorderResidues(...)
 |      reorderResidues(residues: list of Residue)
 |  
 |  residueAfter(...)
 |      residueAfter(r: Residue) -> Residue
 |  
 |  residueBefore(...)
 |      residueBefore(r: Residue) -> Residue
 |  
 |  ribbonCoordinates(...)
 |      ribbonCoordinates(a: Atom) -> chimera.Point
 |  
 |  rootForAtom(...)
 |      rootForAtom(a: Atom, ignoreBreakPoints: bool) -> Root
 |  
 |  roots(...)
 |      roots(ignoreBreakPoints: bool) -> list of Root
 |  
 |  sequence = getSequence(molecule, chainID, **kw)
 |      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.
 |  
 |  sequences = getSequences(molecule, asDict=False)
 |      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.
 |  
 |  setAllPDBHeaders(...)
 |      setAllPDBHeaders(hs: dict of (unicode, list of unicode))
 |  
 |  setPDBHeader(...)
 |      setPDBHeader(k: unicode, v: list of unicode)
 |  
 |  traverseAtoms(...)
 |      traverseAtoms(root: Root) -> list of Atom
 |  
 |  traverseBonds(...)
 |      traverseBonds(root: Root) -> list of Bond
 |  
 |  updateRibbonData(...)
 |      updateRibbonData() -> bool
 |  
 |  useAsRoot(...)
 |      useAsRoot(newRoot: Atom)
 |  
 |  ----------------------------------------------------------------------
 |  Data descriptors defined here:
 |  
 |  __dict__
 |  
 |  activeCoordSet
 |      CoordSet
 |  
 |  aromaticColor
 |      chimera.Color
 |  
 |  aromaticDisplay
 |      bool
 |  
 |  aromaticLineType
 |      int
 |  
 |  aromaticMode
 |      int
 |  
 |  atoms
 |      list of Atom
 |  
 |  atomsMoved
 |      set of Atom
 |  
 |  autochain
 |      bool
 |  
 |  ballScale
 |      float
 |  
 |  bonds
 |      list of Bond
 |  
 |  coordSets
 |      dict of (int, CoordSet)
 |  
 |  idatmValid
 |      bool
 |  
 |  lineType
 |      int
 |  
 |  lineWidth
 |      float
 |  
 |  lowerCaseChains
 |      bool
 |  
 |  mol2comments
 |      list of unicode
 |  
 |  mol2data
 |      list of unicode
 |  
 |  numAtoms
 |      unsigned int
 |  
 |  numBonds
 |      unsigned int
 |  
 |  numResidues
 |      unsigned int
 |  
 |  pdbHeaders
 |      dict of (unicode, list of unicode)
 |  
 |  pdbVersion
 |      int
 |  
 |  pointSize
 |      float
 |  
 |  residueLabelPos
 |      int
 |  
 |  residues
 |      list of Residue
 |  
 |  ribbonHidesMainchain
 |      bool
 |  
 |  ribbonInsideColor
 |      chimera.Color
 |  
 |  ribbonSmoothing
 |      int
 |  
 |  ribbonStiffness
 |      float
 |  
 |  ribbonType
 |      int
 |  
 |  showStubBonds
 |      bool
 |  
 |  stickScale
 |      float
 |  
 |  structureAssigned
 |      bool
 |  
 |  surfaceColor
 |      chimera.Color
 |  
 |  surfaceOpacity
 |      float
 |  
 |  vdwDensity
 |      float
 |  
 |  wireStipple
 |      (int, int)
 |  
 |  ----------------------------------------------------------------------
 |  Data and other attributes defined here:
 |  
 |  CentroidAll = 0
 |  
 |  CentroidBackbone = 1
 |  
 |  Circle = 0
 |  
 |  DefaultBondRadius = 0.20000000298023224
 |  
 |  DefaultOffset = -1e+99
 |  
 |  Disk = 1
 |  
 |  PrimaryAtom = 2
 |  
 |  RSM_COIL = 2
 |  
 |  RSM_STRAND = 1
 |  
 |  RT_BSPLINE = 0
 |  
 |  RT_CARDINAL = 1
 |  
 |  __new__ = 
 |      T.__new__(S, ...) -> a new object with type S, a subtype of T
 |  
 |  ----------------------------------------------------------------------
 |  Methods inherited from _chimera.Model:
 |  
 |  __str__ = _labelFunc(item)
 |  
 |  addAssociatedModel(...)
 |      addAssociatedModel(model: Model, propagateAttrs: bool = true)
 |  
 |  associatedModels(...)
 |      associatedModels() -> list of Model
 |  
 |  bbox(...)
 |      bbox() -> bool, BBox
 |  
 |  bsphere(...)
 |      bsphere() -> bool, Sphere
 |  
 |  destroy(...)
 |      destroy()
 |  
 |  frontPoint(...)
 |      frontPoint(p1: Point, p2: Point) -> bool, float
 |  
 |  intersects(...)
 |      intersects(p: Plane) -> bool
 |  
 |  removeAssociatedModel(...)
 |      removeAssociatedModel(model: Model)
 |  
 |  ----------------------------------------------------------------------
 |  Data descriptors inherited from _chimera.Model:
 |  
 |  clipPlane
 |      Plane
 |  
 |  clipThickness
 |      float
 |  
 |  color
 |      Color
 |  
 |  display
 |      bool
 |  
 |  id
 |      int
 |  
 |  name
 |      unicode
 |  
 |  openState
 |      OpenState
 |  
 |  subid
 |      int
 |  
 |  useClipPlane
 |      bool
 |  
 |  useClipThickness
 |      bool
 |  
 |  ----------------------------------------------------------------------
 |  Data and other attributes inherited from _chimera.Model:
 |  
 |  selLevel = 1
 |  
 |  ----------------------------------------------------------------------
 |  Methods inherited from _chimera.Selectable:
 |  
 |  oslChildren(...)
 |      oslChildren() -> list of Selectable
 |  
 |  oslIdent(...)
 |      oslIdent(start: int = SelDefault, end: int = SelDefault) -> unicode
 |  
 |  oslLevel(...)
 |      oslLevel() -> int
 |  
 |  oslParents(...)
 |      oslParents() -> list of Selectable
 |  
 |  oslTestAbbr(...)
 |      oslTestAbbr(a: OSLAbbreviation) -> bool
 |  
 |  ----------------------------------------------------------------------
 |  Static methods inherited from _chimera.Selectable:
 |  
 |  count(...)
 |      count() -> int
 |  
 |  ----------------------------------------------------------------------
 |  Data descriptors inherited from libwrappy2.WrapPy:
 |  
 |  __destroyed__
 |      true if underlying C++ object has disappeared