mmLib.Structure.AminoAcidResidue

Package mmLib :: Module Structure :: Class AminoAcidResidue

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Type AminoAcidResidue

object --+        
         |        
  Fragment --+    
             |    
       Residue --+
                 |
                AminoAcidResidue

A subclass of Residue representing one amino acid residue in a polypeptide chain.

Method Summary
	`__deepcopy__(self, memo)`
	`calc_mainchain_bond_angle(self)` Calculates main chain bond angles (N-CA-C, N-CA-CB, CB-CA-C, CA-C-O, CA-C-(next)N, C-(next residue)N-(next residue)CA) and returnst the result as a 6-tuple in that order.
	`calc_mainchain_bond_length(self)` Calculates the main chain bond lengths: (N-CA, CA-C, C-O, CA-CB, CA-(next)N).
	`calc_pucker_torsion(self)` Calculates the Pucker torsion of a ring system.
	`calc_torsion(self, torsion_angle_name)` Calculates the given torsion angle for the monomer.
	`calc_torsion_chi(self)` Calculates CHI side-chain torsion angles according to the amino acid specific definitions in the AminoAcids library.
	`calc_torsion_chi1(self)`
	`calc_torsion_chi2(self)`
	`calc_torsion_chi3(self)`
	`calc_torsion_chi4(self)`
	`calc_torsion_omega(self)` Calculates the Omega torsion angle of the amino acid.
	`calc_torsion_phi(self)` Calculates the Phi torsion angle of the amino acid.
	`calc_torsion_psi(self)` Calculates the Psi torsion angle of the amino acid.
	`is_amino_acid(self)` Returns True if the Fragment is a Amino Acid residue.
	`is_cis(self)` Returns True if this is a CIS amino acid, otherwise returns False.
	`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.
Inherited from Residue
	`__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.
	`__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_nucleic_acid(self)` Returns True if the Fragment is a Nucleic Acid residue.
	`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

calc_mainchain_bond_angle(self)

Calculates main chain bond angles (N-CA-C, N-CA-CB, CB-CA-C, CA-C-O, CA-C-(next)N, C-(next residue)N-(next residue)CA) and returnst the result as a 6-tuple in that order. Angles involving missing atoms are returned as None in the tuple.

calc_mainchain_bond_length(self)

Calculates the main chain bond lengths: (N-CA, CA-C, C-O, CA-CB, CA-(next)N). The result is returned as a 5-tuple in that order. Bond lengths involving missing atoms are returned as None in the tuple.

calc_pucker_torsion(self)

Calculates the Pucker torsion of a ring system. Returns None for Amino Acids which do not have Pucker torsion angles.

calc_torsion(self, torsion_angle_name)

Calculates the given torsion angle for the monomer. The torsion angles are defined by name in monomers.cif.

calc_torsion_chi(self)

Calculates CHI side-chain torsion angles according to the amino acid specific definitions in the AminoAcids library. Returns the 4-tuple (CHI1, CHI2, CHI3, CHI4). Angles involving missing atoms, or angles which do not exist for the amino acid are returned as None in the tuple.

calc_torsion_omega(self)

Calculates the Omega torsion angle of the amino acid. Raises a CTerminal exception if called on a C-terminal residue which does not have a Omega torsion angle.

calc_torsion_phi(self)

Calculates the Phi torsion angle of the amino acid. Raises a NTerminal exception if called on a N-terminal residue which does not have a Phi torsion angle.

calc_torsion_psi(self)

Calculates the Psi torsion angle of the amino acid. Raises a CTerminal exception if called on a C-terminal residue which does not have a Psi torsion angle.

is_amino_acid(self)

Returns True if the Fragment is a Amino Acid residue.

Overrides:: mmLib.Structure.Fragment.is_amino_acid

is_cis(self)

Returns True if this is a CIS amino acid, otherwise returns False. It uses calc_torsion_omega, and if there are missing atoms this method will return None.

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.

Overrides:: mmLib.Structure.Fragment.is_standard_residue

is_water(self)

Returns True if the Fragment is a water molecule, returns False otherwise.

Overrides:: mmLib.Structure.Fragment.is_water

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