pemsley/coot/rdkit

import coot_headless_api
from rdkit import Chem
from rdkit.Chem import AllChem

import coot_headless_api
import base64
from rdkit import Chem
# Initialize molecules container
molecules = coot_headless_api.molecules_container_t(False)  # False = not verbose
# Get monomer from Coot's library
imol = molecules.get_monomer("AMP")  # or any other monomer code
# Get RDKit molecule as pickled base64
pickle_base64_str = molecules.get_rdkit_mol_pickle_base64("AMP", imol)
# Decode and create RDKit molecule
pickle_bytes = base64.b64decode(pickle_base64_str)
rdkit_mol = Chem.Mol(pickle_bytes)  # Use Chem.Mol(), NOT pickle.loads()

from rdkit import Chem
# Make editable copy
mol_edit = Chem.RWMol(rdkit_mol)
# Replace atom (e.g., phosphorus to sulfur)
for atom in mol_edit.GetAtoms():
    if atom.GetSymbol() == 'P':
        atom.SetAtomicNum(16)  # 16 = sulfur
        break
# Convert back to read-only molecule
modified_mol = mol_edit.GetMol()
Chem.SanitizeMol(modified_mol)

from rdkit.Chem import AllChem
# Remove hydrogens
mol_no_h = Chem.RemoveHs(mol)
# IMPORTANT: Regenerate 2D coords AFTER removing hydrogens
AllChem.Compute2DCoords(mol_no_h)
# Now generate visualization

from rdkit.Chem.Draw import rdMolDraw2D
drawer = rdMolDraw2D.MolDraw2DSVG(400, 400)
drawer.DrawMolecule(mol_no_h)
drawer.FinishDrawing()
svg_string = drawer.GetDrawingText()
# Save without displaying (see Data Handling below)

svg_data  # This displays all the text - SLOW!

# Just save directly without displaying
# (use len() to verify if needed, though even this may not return properly)

svg_content = drawer.GetDrawingText()
# Don't display svg_content - just reference it

# Use the variable directly without echoing/catting the content

Chem.MolToSmiles(mol)  # Returns SMILES string

x = 5
y = 10
x + y  # Won't return the value

# Call 1: Define
def my_function():
    x = 5
    y = 10
    return x + y
# Call 2: Execute
my_function()  # Now returns 15