mmLib.Structure.Fragment

Package mmLib :: Module Structure :: Class Fragment

[show private | hide private]

Type Fragment

object --+
         |
        Fragment

Known Subclasses:: Residue

Fragment objects are a basic unit for organizing small groups of Atoms. Amino acid residues are fragments, as well as nucleic acids and other small molecules. In terms of a PDB file, they are all the atoms from a unique residue in a chain. Fragments have the following attributes:

Fragment.res_name - the fragment/residue name Fragment.res_seq - the sequence id of the fragment/residue Fragment.chain_id - the ID of the chain containing this fragment

Method Summary
	`__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)`
	`__str__(self)`
	`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.
	`create_bonds(self)` Contructs bonds within a fragment.
	`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

contains(self, atom_idx)
(In operator)

Return True if the Atom object is contained in the fragment.

getitem(self, name_idx)
(Indexing operator)

Lookup a atom contained in a fragment by its name, or by its index within the fragment's private atom_list. If the atom is not found, a exception is raised. The type of exception depends on the argument type. If the argument was a integer, then a IndexError is raised. If the argument was a string, then a KeyError is raised.

iter(self)

Iterates the atoms within the fragment. If the fragment contains atoms in alternate conformations, only the atoms with the structure's default_alt_loc are iterated.

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.

create_bonds(self)

Contructs bonds within a fragment. Bond definitions are retrieved from the monomer library.

get_atom(self, name, alt_loc=None)

Returns the matching Atom instance contained in the Fragment. Returns None if a match is not found. If alt_loc is not given, then the default alt_loc is used.

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. Returns None if no fragment is found.

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. PDB standard residues are amino and nucleic acid 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. The iteration is preformed by iterating over all Atom objects in the same order as iter_atoms(), then iterating over each Atom's 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.

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