`get_atom_name_indices`#

biotite.structure.get_atom_name_indices(atoms, atom_names)[source]#

For each residue, get the index of the atom with the given atom name.

Parameters:

atomsAtomArray or AtomArrayStack: Search for the indices of the given atom names in this structure.
atom_nameslist of str, length=p: The names of the atoms to get the indices of.

Returns:

indicesndarray, dtype=int, shape=(k, p): For every residue and atom name, the return value contains the atom index in the AtomArray where the sought atom name is located. Where the atom name is not present in a residue, the array is filled with -1.

Examples

>>> indices = get_atom_name_indices(atom_array, ["CA", "CB"])
>>> print(indices)
[[  1   4]
 [ 17  20]
 [ 36  39]
 [ 57  60]
 [ 76  79]
 [ 93  96]
 [117 120]
 [136 139]
 [158 161]
 [170  -1]
 [177  -1]
 [184 187]
 [198 201]
 [209 212]
 [220  -1]
 [227 230]
 [251 254]
 [265 268]
 [279 282]
 [293 296]]
>>> for row in indices:
...     for index in row:
...         if index != -1:
...             print(atom_array[index])
...     print()
    A       1  ASN CA     C        -8.608    3.135   -1.618
    A       1  ASN CB     C        -9.437    3.396   -2.889

    A       2  LEU CA     C        -4.923    4.002   -2.452
    A       2  LEU CB     C        -4.411    5.450   -2.619

    A       3  TYR CA     C        -3.690    2.738    0.981
    A       3  TYR CB     C        -3.964    3.472    2.302

    A       4  ILE CA     C        -5.857   -0.449    0.613
    A       4  ILE CB     C        -7.386   -0.466    0.343

    A       5  GLN CA     C        -4.122   -1.167   -2.743
    A       5  GLN CB     C        -4.292   -0.313   -4.013

    A       6  TRP CA     C        -0.716   -0.631   -0.993
    A       6  TRP CB     C        -0.221    0.703   -0.417

    A       7  LEU CA     C        -1.641   -2.932    1.963
    A       7  LEU CB     C        -2.710   -2.645    3.033

    A       8  LYS CA     C        -3.024   -5.791   -0.269
    A       8  LYS CB     C        -4.224   -5.697   -1.232

    A       9  ASP CA     C         0.466   -6.016   -1.905
    A       9  ASP CB     C         1.033   -4.839   -2.724

    A      10  GLY CA     C         2.060   -6.618    1.593

    A      11  GLY CA     C         2.626   -2.967    2.723

    A      12  PRO CA     C         6.333   -2.533    3.806
    A      12  PRO CB     C         6.740   -2.387    5.279

    A      13  SER CA     C         7.049   -6.179    2.704
    A      13  SER CB     C         6.458   -7.371    3.472

    A      14  SER CA     C         6.389   -5.315   -1.015
    A      14  SER CB     C         4.914   -4.993   -1.265

    A      15  GLY CA     C         9.451   -3.116   -1.870

    A      16  ARG CA     C         7.289    0.084   -2.054
    A      16  ARG CB     C         6.110   -0.243   -2.994

    A      17  PRO CA     C         6.782    3.088    0.345
    A      17  PRO CB     C         7.554    4.394    0.119

    A      18  PRO CA     C         3.287    4.031    1.686
    A      18  PRO CB     C         3.035    4.190    3.187

    A      19  PRO CA     C         1.185    6.543   -0.353
    A      19  PRO CB     C         0.048    6.014   -1.229

    A      20  SER CA     C         0.852   10.027    1.285
    A      20  SER CB     C         1.972   11.071    1.284

get_atom_name_indices#

`get_atom_name_indices`#