mmLib.Structure.Residue

Package mmLib :: Module Structure :: Class Residue

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Type 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 instance contained in the Fragment.
	`get_chain(self)` Returns the parent Chain object.
	`get_equivalent_atom(self, atom)` Returns the atom with the same fragment_id and name as the argument atom, or None if it is not found.
	`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)` Removes the Atom instance from the Fragment.
	`set_chain_id(self, chain_id)` Sets the chain_id of the Fragment and all contained Atom objects.
	`set_default_alt_loc(self, alt_loc)` Sets the default alt_loc of the Fragment.
	`set_fragment_id(self, fragment_id)` Sets the fragment_id of the Fragment and all contained Atom objects.
	`set_model_id(self, model_id)` Sets the model_id of the Fragment and all contained Atom objects.
	`set_res_name(self, res_name)` Sets the res_name of the Fragment and all contained Atom objects.
Inherited from object
	`__delattr__(...)` x.__delattr__('name') <==> del x.name
	`__getattribute__(...)` x.__getattribute__('name') <==> x.name
	`__hash__(x)` x.__hash__() <==> hash(x)
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T
	`__reduce__(...)` helper for pickle
	`__reduce_ex__(...)` helper for pickle
	`__repr__(x)` x.__repr__() <==> repr(x)
	`__setattr__(...)` x.__setattr__('name', value) <==> x.name = value

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.

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