Package MolKit :: Module protein :: Class ProteinMolecule

Class ProteinMolecule

tree.TreeNode --+    
                |    
molecule.Molecule --+
                    |
                   ProteinMolecule

Known Subclasses:: Protein, Chain, Residue

Instance Methods

[hide private]

findType(self, _type, uniq=0)
go down the tree until we find Nodes of the given type

isBelow(self, Klass)
go up the tree until we find Nodes of the given type return the number of level above self at which we find Klass, else 0 is retuned

Inherited from molecule.Molecule: __init__, addBond, attach_nonbonded_fragments, buildBondsBhtree, buildBondsByDistance, buildBondsByDistanceOnAtoms, buildBrokenBonds, closerThan, configureProgressBar, defaultRadii, getAtoms, getCenter, getNbrAtoms, getTypeList, mergeNPH, read, removeAllHydrogens, removeBond, subTree, updateProgressBar, write

Inherited from molecule.Molecule (private): _MarkTree, _atomRadius

Inherited from tree.TreeNode: NodesFromName, __cmp__, __eq__, __hash__, __ne__, __repr__, __str__, adopt, assignUniqIndex, compare, deleteSubTree, dump, findLevels, full_name, get, getNext, getParentOfType, getPrevious, getRoot, isAbove, makeNameUniq, merge, remove, split

Inherited from tree.TreeNode (private): _copyNode

Class Variables

[hide private]

Inherited from molecule.Molecule: compiled_patterns, p

Inherited from tree.TreeNode (private): _numberOfDeletedNodes

Method Details

[hide private]

findType(self, _type, uniq=0)

source code

go down the tree until we find Nodes of the given type

Overrides: tree.TreeNode.findType: (inherited documentation)

isBelow(self, Klass)

source code

go up the tree until we find Nodes of the given type return the number of level above self at which we find Klass, else 0 is retuned

Overrides: tree.TreeNode.isBelow: (inherited documentation)