Package MolKit :: Module protein :: Class Residue

Class Residue

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

Class to represent an amino acide. Inherits from tree element

Instance Methods

[hide private]

__init__(self, type='UNK', number=-1, icode='', parent=None, elementType=<class MolKit.molecule.Atom at 0xb7b9789c>, list=None, childrenName='atoms', setClass=<class MolKit.protein.ResidueSet at 0xb7bb8a1c>, childrenSetClass=<class MolKit.molecule.AtomSet at 0xb7b9780c>, top=None, childIndex=None, assignUniqIndex=1)
Residue constructor.

getPsi(self)
compute PSI N(i),CA(i),C(i),N(i+1)

getPhi(self)
compute PHI C(i-1),N(i),CA(i),c(i)

buildBondsByDistance(self)
Build bonds between atoms inside this residue, based on distance WARNING this is a n^2 process, should only be used for small molecules like residues

backbone(self)
Return atomset containing backbone atoms

sidechain(self)
Return atomset containing sidechain atoms

getAtmsAndCoords(self, atmNames)
Function returning the coords of all the atoms of the given atom name or None if one is not in the atoms residues

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

[hide private]

_bbname = ['N', 'CA', 'C', 'O']

_bbtype = ['N', 'C', 'C', 'O']

Inherited from molecule.Molecule: compiled_patterns, p

Inherited from tree.TreeNode (private): _numberOfDeletedNodes

Method Details

[hide private]

init(self, type='UNK', number=-1, icode='', parent=None, elementType=<class MolKit.molecule.Atom at 0xb7b9789c>, list=None, childrenName='atoms', setClass=<class MolKit.protein.ResidueSet at 0xb7bb8a1c>, childrenSetClass=<class MolKit.molecule.AtomSet at 0xb7b9780c>, top=None, childIndex=None, assignUniqIndex=1)
(Constructor)

source code

Residue constructor. Arguments: type (string) number (integer or string) icode (1character) insertion code optional parent (instance of a TreeNode) optional elementType (instance of class inheriting from TreeNode)