Hi,
I've got some problems generating the correct images of the molecules.
I'm new to Python and RDKit, so maybe I did something wrong.
Could someone help me and correct the code?
I've got a cluster of five compounds and I want to display them, but with
Draw.MolsToGridImage(mols) I didn't obtain correct images.
I've searched for another method, but I obtain again this image...
#now display structures from one of the clusters
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
m1 = ms[99]
m2 = ms[18]
m3 = ms[19]
m4 = ms[58]
m5 = ms[60]
mols=(m1,m2,m3,m4,m5)
smile1 = Chem.MolToSmiles(m1)
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from IPython.display import SVG
def moltosvg(mol, molSize = (300,300), kekulize = True):
mc = Chem.Mol(mol.ToBinary())
if kekulize:
try:
Chem.Kekulize(mc)
except:
mc = Chem.Mol(mol.ToBinary())
if not mc.GetNumConformers():
rdDepictor.Compute2DCoords(mc)
drawer = rdMolDraw2D.MolDraw2DSVG(molSize[0],molSize[1])
drawer.DrawMolecule(mc)
drawer.FinishDrawing()
svg = drawer.GetDrawingText()
return svg.replace('svg:','')
SVG(moltosvg(m1))
[cid:949a3b76-5d3b-4ed6-8c7a-2ea9a87e8f8b]
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