biotite.structure.info.standardize_order

biotite.structure.info.standardize_order(atoms)

Get an index array for an input AtomArray or AtomArrayStack that reorders the atoms for each residue to obtain the standard RCSB PDB atom order.

The standard atom order is determined from the reference residues in the official Chemical Component Dictionary. If a residue of the input structure contains additional atoms that are not present in the reference residue, these indices to these atoms are appended to the end of the respective residue. A example for this are optional hydrogen atoms, that appear due to protonation.

Parameters

atomsAtomArray, shape=(n,) or AtomArrayStack, shape=(m,n)

Input structure with atoms that are potentially not in the standard order.

Returns

indicesndarray, dtype=int, shape=(n,)

When this index array is applied on the input atoms, the atoms for each residue are reordered to obtain the standard RCSB PDB atom order.

Raises

BadStructureError

If the input atoms have duplicate atoms (same atom name) within a residue.

Examples

Use as single residue as example.

>>> residue = atom_array[atom_array.res_id == 1]
>>> print(residue)
    A       1  ASN N      N        -8.901    4.127   -0.555
    A       1  ASN CA     C        -8.608    3.135   -1.618
    A       1  ASN C      C        -7.117    2.964   -1.897
    A       1  ASN O      O        -6.634    1.849   -1.758
    A       1  ASN CB     C        -9.437    3.396   -2.889
    A       1  ASN CG     C       -10.915    3.130   -2.611
    A       1  ASN OD1    O       -11.269    2.700   -1.524
    A       1  ASN ND2    N       -11.806    3.406   -3.543
    A       1  ASN H1     H        -8.330    3.957    0.261
    A       1  ASN H2     H        -8.740    5.068   -0.889
    A       1  ASN H3     H        -9.877    4.041   -0.293
    A       1  ASN HA     H        -8.930    2.162   -1.239
    A       1  ASN HB2    H        -9.310    4.417   -3.193
    A       1  ASN HB3    H        -9.108    2.719   -3.679
    A       1  ASN HD21   H       -11.572    3.791   -4.444
    A       1  ASN HD22   H       -12.757    3.183   -3.294

Reverse the atom array. Consequently, this also changes the atom order within the residue.

>>> reordered = residue[np.arange(len(residue))[::-1]]
>>> print(reordered)
    A       1  ASN HD22   H       -12.757    3.183   -3.294
    A       1  ASN HD21   H       -11.572    3.791   -4.444
    A       1  ASN HB3    H        -9.108    2.719   -3.679
    A       1  ASN HB2    H        -9.310    4.417   -3.193
    A       1  ASN HA     H        -8.930    2.162   -1.239
    A       1  ASN H3     H        -9.877    4.041   -0.293
    A       1  ASN H2     H        -8.740    5.068   -0.889
    A       1  ASN H1     H        -8.330    3.957    0.261
    A       1  ASN ND2    N       -11.806    3.406   -3.543
    A       1  ASN OD1    O       -11.269    2.700   -1.524
    A       1  ASN CG     C       -10.915    3.130   -2.611
    A       1  ASN CB     C        -9.437    3.396   -2.889
    A       1  ASN O      O        -6.634    1.849   -1.758
    A       1  ASN C      C        -7.117    2.964   -1.897
    A       1  ASN CA     C        -8.608    3.135   -1.618
    A       1  ASN N      N        -8.901    4.127   -0.555

The order is restored with the exception of the N-terminus protonation.

>>> restored = reordered[info.standardize_order(reordered)]
>>> print(restored)
    A       1  ASN N      N        -8.901    4.127   -0.555
    A       1  ASN CA     C        -8.608    3.135   -1.618
    A       1  ASN C      C        -7.117    2.964   -1.897
    A       1  ASN O      O        -6.634    1.849   -1.758
    A       1  ASN CB     C        -9.437    3.396   -2.889
    A       1  ASN CG     C       -10.915    3.130   -2.611
    A       1  ASN OD1    O       -11.269    2.700   -1.524
    A       1  ASN ND2    N       -11.806    3.406   -3.543
    A       1  ASN H2     H        -8.740    5.068   -0.889
    A       1  ASN HA     H        -8.930    2.162   -1.239
    A       1  ASN HB2    H        -9.310    4.417   -3.193
    A       1  ASN HB3    H        -9.108    2.719   -3.679
    A       1  ASN HD21   H       -11.572    3.791   -4.444
    A       1  ASN HD22   H       -12.757    3.183   -3.294
    A       1  ASN H3     H        -9.877    4.041   -0.293
    A       1  ASN H1     H        -8.330    3.957    0.261

Gallery

Docking biotin to streptavidin

Docking biotin to streptavidin