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

[Peter S. S. <sh...@gm...>]

Hi, Dimitri,

I have two questions about your code.

1. Why are you incrementing the atom index by 1? Are there functions in
RDKit, for example, that use atom indices using index-origin 1? Or is it
rather because chemists in your target audience will be thinking of the
first atom in, say, a structure from an sd file as atom #1?

2. Regarding the last line, most of the RDKit code I've seen in past
examples displays the molecule using code like the following. When is it
necessary/not necessary to remove the "svg" string from the results of
GetDrawingText()?

svg = drawer.GetDrawingText().replace('svg:','')
SVG(svg)

Thanks,
-P.

On Mon, Oct 24, 2016 at 2:31 PM, Dimitri Maziuk <dm...@bm...>
wrote:

> 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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