Edit the structure annotation using an atom

[dargen3]

Hello,

I would like to please ask if there is any way to modify the structure using an atom in the biotite? I know that the data of individual atoms can be accessed via indexing. For example, if I want to change the charge of the n-th atom to -1:

import biotite.structure.io.pdbx as mmCIF
import biotite.structure as biotite_structure

mmCIF_file = mmCIF.CIFFile.read("9bfl.cif")
protein = mmCIF.get_structure(mmCIF_file,
                              model=1,
                              extra_fields=["charge"],
                              include_bonds=True)

protein.charge[10] = -1

But I would like to ask if it is possible to access/change values for an atom without knowing its index? For example, if I want to iterate over residues and then over their atoms:

import biotite.structure.io.pdbx as mmCIF
import biotite.structure as biotite_structure

mmCIF_file = mmCIF.CIFFile.read("9bfl.cif")
protein = mmCIF.get_structure(mmCIF_file,
                              model=1,
                              extra_fields=["charge"],
                              include_bonds=True)

for res in biotite_structure.residue_iter(protein):
    for atom in res:
        if some_nontrivial_magic_function(atom):
            atom.charge = -1

The problem with the code above is that if I store a value in atom.charge, that value is not written to protein.charge.

[padix-key]

No, unfortunately this is not possible. If would propose to rewrite your snippet similar to the following:

for res_start_i, res_stop_i in itertools.pairwise(biotite_structure.get_residue_starts(protein, add_exclusive_stop=True)):
    for atom_i in range(res_start_i, res_stop_i):
        if some_nontrivial_magic_function(protein[atom_i]):
            protein.charge[atom_i] = -1

Using residue-wise iteration is not necessary in this snippet, but I suppose in your actual application it is.

Whenever possible, I recommend vectorized operations over the entire AtomArray or at least slices of it for performance reasons, though I do not know if this is possible for your some_nontrivial_magic_function().

[dargen3]

Thank you for quick help!