Package mmLib :: Module Structure :: Class AminoAcidResidue
[show private | hide private]
[frames | no frames]

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

Generated by Epydoc 2.1 on Sun Apr 23 22:08:39 2006 http://epydoc.sf.net