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#!/usr/bin/env python
from json import dumps
from rdkit import Chem, rdBase
from rdkit.Chem import AllChem, Draw, rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
COLS = [(1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0), (1.0, 0.55, 1.0)]
def get_hit_atoms_and_bonds(mol, smt):
alist = []
blist = []
q = Chem.MolFromSmarts(smt)
for match in mol.GetSubstructMatches(q):
alist.extend(match)
for ha1 in alist:
for ha2 in alist:
if ha1 > ha2:
b = mol.GetBondBetweenAtoms(ha1, ha2)
if b:
blist.append(b.GetIdx())
return alist, blist
def add_colours_to_map(els, cols, col_num):
for el in els:
if el not in cols:
cols[el] = []
if COLS[col_num] not in cols[el]:
cols[el].append(COLS[col_num])
def do_a_picture(smi, smarts, filename, label, fmt='svg'):
with rdDepictor.UsingCoordGen(True):
mol = Chem.MolFromSmiles(smi)
mol = Draw.PrepareMolForDrawing(mol)
acols = {}
bcols = {}
h_rads = {}
h_lw_mult = {}
for i, smt in enumerate(smarts):
alist, blist = get_hit_atoms_and_bonds(mol, smt)
col = i % 4
add_colours_to_map(alist, acols, col)
add_colours_to_map(blist, bcols, col)
if fmt == 'svg':
d = rdMolDraw2D.MolDraw2DSVG(300, 300)
mode = 'w'
elif fmt == 'png':
d = rdMolDraw2D.MolDraw2DCairo(300, 300)
mode = 'wb'
else:
print('unknown format {}'.format(fmt))
return
d.drawOptions().fillHighlights = False
d.DrawMoleculeWithHighlights(mol, label, acols, bcols, h_rads, h_lw_mult, -1)
d.FinishDrawing()
with open(filename, mode) as f:
f.write(d.GetDrawingText())
smi = 'CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]'
smarts = ['CONN', 'N#CC~CO', 'C=CON', 'CONNCN']
do_a_picture(smi, smarts, 'atom_highlights_3.png', '', fmt='png')
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