For Fragmenstein. A draft of a potential way to remove atoms from a 3D embedded set of molecules, when 2D is too misleading and overlap is key.

pick_for_deletion.py

# NGLView is a great way to see a set of rdkit.Chem molecules in 3D.
# Right clicking gives green spheres by default. Right clicking on a sphere removes it. So nice way to keep track

# the `ModNGL` object contains the dynamic property `picked_atoms` which lists the atoms that were clicked.
# Clicked twice is removed. However, there is no way to determine the button integer (left, middle, wheel, right).

# Before loading the mols from rdkit it would be nice to fill the PDB info.
# As seen in https://blog.matteoferla.com/2020/03/atom-names-purely-in-rdkit.html
# once one has the atom names one can delete the atoms off a ``rdkit.Chem.RWMol`` making it nice and clear for Fragmenstein.

import nglview as nv
from io import StringIO
from typing import *
import json
from IPython.display import display
from collections import defaultdict

class ModNGL(nv.NGLWidget):
    
    picked_atoms = []

    @observe('picked')
    def my_picked(self, change):
        """
        This does not override the `_on_picked` method, that when initialised by
        `view.player._make_widget_picked` fills `view.player.widget_picked.value`.
        It however is strongly influenced by it!
        
        Unfortunately, there's no way to tell in Python if left or right was clicked.
        Technically in JS, the `buttons` integer passed to `clicked` controls this,
        but it is not stored.
        "picked" is a trait and is configured on both Python and JS. 
        So I doubt a pure Python solution is possible.
        """
        print(buttons)
        if change['new']:
            self.picked_atoms.append(change['new'])
        
    @property
    def picked_atoms(self) -> Dict[List[str]]:
        """
        Returns a dict with keys component indices and values a list of atom names sensu NGL
        
        ``[LIG]1:A.O1`` So [residue name] residue index : chain . atom name
        
        """
        compontent_atoms = defaultdict(list)
        for atom in self.picked_atoms:
            name = atom['atom1']['name']
            comp = compontent_atoms[atom['component']]
            if name in comp:
                del comp[comp.index(name)]
            else:
                comp.append(name)
        return compontent_atoms

# ------------------------------------------------------------------------------------------------------------------------
      
def show_mols(*mols: Chem.Mol) -> nv.NGLWidget:
    view = ModNGL()
    for mol in (acetyl, ethylamine):
        fh = StringIO(Chem.MolToPDBBlock(mol))
        view.add_component(fh, ext='pdb')
    #view.player._make_widget_picked()
    return view

view = show_mols(acetyl, ethylamine)
view