Package MolKit :: Module protein :: Class Chain

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Class Chain

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

Class to represent chains or residues. Inherits from tree element

Instance Methods

__init__(self, id=None, parent=None, elementType=<class MolKit.protein.Residue at 0xb7bb8a4c>, list=None, childrenName='residues', setClass=<class MolKit.protein.ChainSet at 0xb7bb8aac>, childrenSetClass=<class MolKit.protein.ResidueSet at 0xb7bb8a1c>, top=None, childIndex=None, assignUniqIndex=1)
Chain constructor.

shortestDist(self, atoms1, atoms2)

connectResidues(self, res1, res2, cut_off=1.85)
Connect residues based on distance

buildBondsByDistance(self, cut_off=1.85)
Build bonds between atoms inside this chain, based on distance

isDna(self)
checks if the chain is DNA or not.

isProteic(self)
checks if the chain is proteic or not.

isHetatmChain(self)
checks if is whole chain of hetatms

secondaryStructure(self, ssBuilder)
create a secondarystructureset.

Inherited from ProteinMolecule: findType, isBelow

Inherited from molecule.Molecule: addBond, attach_nonbonded_fragments, buildBondsBhtree, 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

Inherited from molecule.Molecule: compiled_patterns, p

Inherited from tree.TreeNode (private): _numberOfDeletedNodes

Method Details

init(self, id=None, parent=None, elementType=<class MolKit.protein.Residue at 0xb7bb8a4c>, list=None, childrenName='residues', setClass=<class MolKit.protein.ChainSet at 0xb7bb8aac>, childrenSetClass=<class MolKit.protein.ResidueSet at 0xb7bb8a1c>, top=None, childIndex=None, assignUniqIndex=1)
(Constructor)

Chain constructor. Arguments: id (string) optional parent (instance of a TreeNode) optional elementType (instance of class inheriting from TreeNode)

Overrides: molecule.Molecule.__init__

shortestDist(self, atoms1, atoms2)

None

connectResidues(self, res1, res2, cut_off=1.85)

Connect residues based on distance

buildBondsByDistance(self, cut_off=1.85)

Build bonds between atoms inside this chain, based on distance

Overrides: molecule.Molecule.buildBondsByDistance

isDna(self)

checks if the chain is DNA or not.

isProteic(self)

checks if the chain is proteic or not.

isHetatmChain(self)

checks if is whole chain of hetatms

secondaryStructure(self, ssBuilder)

create a secondarystructureset. If secondarystructureset can't be obtained, none is created and a warning is printed.