Package mmLib :: Module Structure :: Class AminoAcidResidue
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Class AminoAcidResidue

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

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

Instance Methods [hide private]
 
__deepcopy__(self, memo) source code
 
is_standard_residue(self)
Returns True if the Fragment/Residue object is one of the PDB defined standard residues.
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is_amino_acid(self)
Returns True if the Fragment is an Amino Acid residue.
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is_water(self)
Returns True if the Fragment is a water molecule, returns False otherwise.
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calc_mainchain_bond_length(self)
Calculates the main chain bond lengths: (N-CA, CA-C, C-O, CA-CB, CA-(next)N).
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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 returns the result as a 6-tuple in that order.
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calc_torsion_psi(self)
Calculates the Psi torsion angle of the amino acid.
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calc_torsion_phi(self)
Calculates the Phi torsion angle of the amino acid.
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calc_torsion_omega(self)
Calculates the Omega torsion angle of the amino acid.
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is_cis(self)
Returns True if this is a CIS amino acid, otherwise returns False.
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calc_torsion(self, torsion_angle_name)
Calculates the given torsion angle for the monomer.
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calc_torsion_chi1(self) source code
 
calc_torsion_chi2(self) source code
 
calc_torsion_chi3(self) source code
 
calc_torsion_chi4(self) source code
 
calc_torsion_chi(self)
Calculates CHI side-chain torsion angles according to the amino acid specific definitions in the AminoAcids library.
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calc_pucker_torsion(self)
Calculates the Pucker torsion of a ring system.
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Inherited from Residue: __str__, create_bonds, get_offset_residue

Inherited from Fragment: __contains__, __ge__, __getitem__, __gt__, __init__, __iter__, __le__, __len__, __lt__, add_atom, count_all_atoms, count_atoms, get_atom, get_chain, get_equivalent_atom, get_model, get_offset_fragment, get_structure, index, is_nucleic_acid, iter_all_atoms, iter_atoms, iter_bonds, remove_atom, set_chain_id, set_default_alt_loc, set_fragment_id, set_model_id, set_res_name

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__deepcopy__(self, memo)

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Overrides: Fragment.__deepcopy__

is_standard_residue(self)

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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: Fragment.is_standard_residue

is_amino_acid(self)

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Returns True if the Fragment is an Amino Acid residue.

Overrides: Fragment.is_amino_acid

is_water(self)

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

Overrides: Fragment.is_water

calc_mainchain_bond_length(self)

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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_mainchain_bond_angle(self)

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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 returns the result as a 6-tuple in that order. Angles involving missing atoms are returned as None in the tuple.

calc_torsion_psi(self)

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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.

calc_torsion_phi(self)

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

calc_torsion_omega(self)

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

is_cis(self)

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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.

calc_torsion(self, torsion_angle_name)

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

calc_torsion_chi(self)

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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_pucker_torsion(self)

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