biotite.structure.get_residues¶

biotite.structure.get_residues(array)[source]¶

Get the residue IDs and names of an atom array (stack).

The residues are listed in the same order they occur in the array (stack).

Parameters

arrayAtomArray or AtomArrayStack: The atom array (stack) to determine the residues from.

Returns

idsndarray, dtype=int: List of residue IDs.
namesndarray, dtype=”U5”: List of residue names.

Examples

Get the residue names of a 20 residue peptide.

>>> print(atom_array.res_name)
['ASN' 'ASN' 'ASN' 'ASN' 'ASN' 'ASN' 'ASN' 'ASN' 'ASN' 'ASN' 'ASN' 'ASN'
 'ASN' 'ASN' 'ASN' 'ASN' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU'
 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'TYR'
 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'TYR'
 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'TYR' 'ILE' 'ILE' 'ILE' 'ILE'
 'ILE' 'ILE' 'ILE' 'ILE' 'ILE' 'ILE' 'ILE' 'ILE' 'ILE' 'ILE' 'ILE' 'ILE'
 'ILE' 'ILE' 'ILE' 'GLN' 'GLN' 'GLN' 'GLN' 'GLN' 'GLN' 'GLN' 'GLN' 'GLN'
 'GLN' 'GLN' 'GLN' 'GLN' 'GLN' 'GLN' 'GLN' 'GLN' 'TRP' 'TRP' 'TRP' 'TRP'
 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'TRP'
 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'TRP' 'LEU' 'LEU' 'LEU' 'LEU'
 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU' 'LEU'
 'LEU' 'LEU' 'LEU' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS'
 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS' 'LYS'
 'LYS' 'ASP' 'ASP' 'ASP' 'ASP' 'ASP' 'ASP' 'ASP' 'ASP' 'ASP' 'ASP' 'ASP'
 'ASP' 'GLY' 'GLY' 'GLY' 'GLY' 'GLY' 'GLY' 'GLY' 'GLY' 'GLY' 'GLY' 'GLY'
 'GLY' 'GLY' 'GLY' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO'
 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER'
 'SER' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER'
 'SER' 'SER' 'SER' 'GLY' 'GLY' 'GLY' 'GLY' 'GLY' 'GLY' 'GLY' 'ARG' 'ARG'
 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG'
 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'ARG' 'PRO' 'PRO'
 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO'
 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO'
 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO' 'PRO'
 'PRO' 'PRO' 'PRO' 'PRO' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER' 'SER'
 'SER' 'SER' 'SER' 'SER']
>>> ids, names = get_residues(atom_array)
>>> print(names)
['ASN' 'LEU' 'TYR' 'ILE' 'GLN' 'TRP' 'LEU' 'LYS' 'ASP' 'GLY' 'GLY' 'PRO'
 'SER' 'SER' 'GLY' 'ARG' 'PRO' 'PRO' 'PRO' 'SER']

Gallery¶

Contact sites of protein-DNA interaction

Determination of amino acid enantiomers