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object --+ | Fragment --+ | Residue --+ | AminoAcidResidue
A subclass of Residue representing one amino acid residue in a polypeptide chain.
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Inherited from Inherited from Inherited from |
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Inherited from |
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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.
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Returns True if the Fragment is an Amino Acid residue.
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Returns True if the Fragment is a water molecule, returns False otherwise.
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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. |
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. |
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. |
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. |
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. |
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. |
Calculates the given torsion angle for the monomer. The torsion angles are defined by name in monomers.cif. |
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. |
Calculates the Pucker torsion of a ring system. Returns None for Amino Acids which do not have Pucker torsion angles. |
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