Re: [Rdkit-discuss] Hiding/removing specific atoms in a RDKit molecule

[Paolo T. <pao...@gm...>]

Hi Gianmarco,

I am not aware of a method to simply hide atoms: here's a method t remove
atoms given a list of indices, which should be what you need.
Note that remove_selected_hs() replaces the "real" hydrogen with an
implicit H on the parent atom, which I believe is what you want.

from rdkit import Chem
from rdkit.Chem import rdDistGeom

mol = Chem.MolFromSmiles("OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O")
mol_h = Chem.AddHs(mol)
rdDistGeom.EmbedMolecule(mol_h)
0
mol_h
[image: image.png]
hs = [a.GetIdx() for a in mol_h.GetAtoms() if a.GetAtomicNum() == 1]
hs
[12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]
# Let's remove any second H as an example
hs_to_remove = [hs[i] for i in range(0, len(hs), 2)]
hs_to_remove
[12, 14, 16, 18, 20, 22]

def remove_selected_hs(mol, hs_to_remove):
    def fix_explicit_hs(mol, ai):
        oa = mol.GetAtomWithIdx(ai)
        if oa.GetAtomicNum() > 1:
            oa.SetNumExplicitHs(oa.GetNumExplicitHs() + 1)

    if not hs_to_remove:
        return mol
    rwmol = Chem.RWMol(mol)
    ai_to_remove = []
    for bond_idx in reversed(range(rwmol.GetNumBonds())):
        b = rwmol.GetBondWithIdx(bond_idx)
        bidx = b.GetBeginAtomIdx()
        remove_bidx = bidx in hs_to_remove
        eidx = b.GetEndAtomIdx()
        remove_eidx = eidx in hs_to_remove
        if (remove_bidx or remove_eidx):
            if remove_bidx:
                ai_to_remove.append(bidx)
                fix_explicit_hs(rwmol, eidx)
            if remove_eidx:
                ai_to_remove.append(eidx)
                fix_explicit_hs(rwmol, bidx)
            rwmol.RemoveBond(bidx, eidx)
    for atom_idx in sorted(ai_to_remove, reverse=True):
        rwmol.RemoveAtom(atom_idx)
    Chem.SanitizeMol(rwmol)
    return rwmol.GetMol()
remove_selected_hs(mol_h, hs_to_remove)
[image: image.png]
Cheers,
p.

On Thu, Dec 2, 2021 at 1:19 PM Gianmarco Ghiandoni <ghi...@gm...>
wrote:

> Hi all,
>
> I have been working on a library that computes properties for molecules
> where hydrogens are explicit. These properties are then saved into a
> dictionary where keys are indices, then I am using the dictionary to depict
> these properties on their corresponding hydrogens - also according to some
> thresholds, which means that not all hydrogens are labelled. The result is
> something like this:
>
> [image: image.png]
>
> Now my question is: How do I hide/remove the hydrogens that are not
> labelled? I am storing their indices while iterating to append their labels
> but there seem not to be a straightforward way to get rid of them.
>
> Thanks,
>
> Giammy
>
> --
> *Gianmarco*
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