"""Determine the atoms and sum up the occurences of sp3 hybridized atoms.

This Jupyter notebook was written and tested for Python 3.9.2, 
RDKit 2020.09.4, and Jupyter-notebook 6.2.0 in Linux Debian 11 / bullseye,
branch testing on August 8th, 2021."""

from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D

from IPython.display import SVG
IPythonConsole.ipython_useSVG=True  


def mol_with_atom_index(mol):
    for atom in mol.GetAtoms():
        atom.SetAtomMapNum(atom.GetIdx())
    return mol


mol = Chem.MolFromSmiles("COc(cccc1)c1Nc1nnc(CC(Nc(cc2)ccc2OC(F)(F)F)=O)s1")
mol = mol_with_atom_index(mol)
mc = Chem.Mol(mol.ToBinary())


drawer = rdMolDraw2D.MolDraw2DSVG(450, 200) 
drawer.DrawMolecule(mc)
drawer.FinishDrawing()

svg = drawer.GetDrawingText()
display(SVG(svg.replace('svg:','')))

# eventually report the assigned hybridizations
sp3_counter = 0

for atom in mol.GetAtoms():
   
    from_data = str("{:2} {:2} {} {}".format(atom.GetIdx(),
                                             atom.GetSymbol(),
                                             atom.GetTotalNumHs(),
                                             atom.GetHybridization()))

    if str(atom.GetHybridization()) == str("SP3"):
        retain = " ".join([from_data, "*"])
        sp3_counter += 1
    else:
        retain = from_data
    print(retain)
    
print("RDKit assigns {} atoms with SP3 hybridization".format(sp3_counter))        

 0 C  3 SP3 *
 1 O  0 SP2
 2 C  0 SP2
 3 C  1 SP2
 4 C  1 SP2
 5 C  1 SP2
 6 C  1 SP2
 7 C  0 SP2
 8 N  1 SP2
 9 C  0 SP2
10 N  0 SP2
11 N  0 SP2
12 C  0 SP2
13 C  2 SP3 *
14 C  0 SP2
15 N  1 SP2
16 C  0 SP2
17 C  1 SP2
18 C  1 SP2
19 C  1 SP2
20 C  1 SP2
21 C  0 SP2
22 O  0 SP2
23 C  0 SP3 *
24 F  0 SP3 *
25 F  0 SP3 *
26 F  0 SP3 *
27 O  0 SP2
28 S  0 SP2
RDKit assigns 6 atoms with SP3 hybridization