mmLib.Structure.Residue

Package mmLib :: Module Structure :: Class Residue

[show private | hide private]

Class Residue

object --+    
         |    
  Fragment --+
             |
            Residue

Known Subclasses:: AminoAcidResidue, NucleicAcidResidue

A subclass of Fragment representing one residue in a polymer chain.

Method Summary
	`__str__(self)`
	`create_bonds(self)` Contructs bonds within a fragment.
	`get_offset_residue(self, offset)` Returns the residue along the chain at the given integer offset from self.
Inherited from Fragment
	`__init__(self, model_id, chain_id, fragment_id, res_name, **args)`
	`__contains__(self, atom_idx)` Return True if the Atom object is contained in the fragment.
	`__deepcopy__(self, memo)`
	`__ge__(self, other)`
	`__getitem__(self, name_idx)` Lookup a atom contained in a fragment by its name, or by its index within the fragment's private atom_list.
	`__gt__(self, other)`
	`__iter__(self)` Iterates the atoms within the fragment.
	`__le__(self, other)`
	`__len__(self)`
	`__lt__(self, other)`
	`add_atom(self, atom)` Adds a atom to the fragment, and sets the atom's atom.fragment attribute to the fragment.
	`count_all_atoms(self)` Counts all Atom objects including Atoms in alternate conformations.
	`count_atoms(self)` Counts Atom objects.
	`get_atom(self, name, alt_loc)` Returns the matching Atom object contained in the Fragment.
	`get_chain(self)` Returns the parent Chain object.
	`get_model(self)` Returns the parent Chain object.
	`get_offset_fragment(self, offset)` Returns the fragment in the same chain at integer offset from self.
	`get_structure(self)` Returns the parent Structure object.
	`index(self, atom)` Returns the sequential index of the atom.
	`is_amino_acid(self)` Returns True if the Fragment is a Amino Acid residue.
	`is_nucleic_acid(self)` Returns True if the Fragment is a Nucleic Acid residue.
	`is_standard_residue(self)` Returns True if the Fragment/Residue object is one of the PDB defined standard residues.
	`is_water(self)` Returns True if the Fragment is a water molecule, returns False otherwise.
	`iter_all_atoms(self)` Iterates of all Atoms in the Fragment includeing Altlocs.
	`iter_atoms(self)` Iterates over all Atom objects contained in the Fragment matching the current model and default alt_loc.
	`iter_bonds(self)` Iterates over all Bond objects.
	`remove_atom(self, atom)` Finish Me
	`set_default_alt_loc(self, alt_loc)` Sets the default alt_loc of the Fragment.
	`set_fragment_id(self, fragment_id)` Sets a new ID for the Fragment object, updating the fragment_id for all objects in the Structure hierarchy.
Inherited from object
	`__delattr__(...)` x.__delattr__('name') <==> del x.name
	`__getattribute__(...)` x.__getattribute__('name') <==> x.name
	`__hash__(x)` x.__hash__() <==> hash(x)
	`__reduce__(...)` helper for pickle
	`__reduce_ex__(...)` helper for pickle
	`__repr__(x)` x.__repr__() <==> repr(x)
	`__setattr__(...)` x.__setattr__('name', value) <==> x.name = value
Inherited from type
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T

Method Details

create_bonds(self)

Contructs bonds within a fragment. Bond definitions are retrieved from the monomer library. This version also constructs the bonds between adjectent residues.

Overrides:: mmLib.Structure.Fragment.create_bonds

get_offset_residue(self, offset)

Returns the residue along the chain at the given integer offset from self. Returns None if there is no residue at that offset, or if the fragment found is not the same type of residue as self.

Generated by Epydoc 2.0 on Wed Nov 24 17:34:57 2004

http://epydoc.sf.net