Re: [Rdkit-discuss] 2D drawing with atoms labeled by index

[Dimitri M. <dm...@bm...>]

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