Since you already got your answer I'll just post this for posterity:
import sys import rdkit import rdkit.Chem import rdkit.Chem.AllChem import rdkit.Chem.Draw import rdkit.Chem.Draw.rdMolDraw2D mol=rdkit.Chem.SupplierFromFilename(sys.argv[1],removeHs=False).next() dr=rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG(800,800) dr.SetFontSize(0.3) op = dr.drawOptions() for i in range(mol.GetNumAtoms()) : op.atomLabels[i]=mol.GetAtomWithIdx(i).GetSymbol() + str((i+1)) rdkit.Chem.AllChem.Compute2DCoords(mol) dr.DrawMolecule(mol) dr.FinishDrawing() svg=dr.GetDrawingText() -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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