Generate 2d images of molecules from PubChem FTP data

Question

Rather than crawl PubChem's website, I'd prefer to be nice and generate the images locally from the PubChem ftp site:

ftp://ftp.ncbi.nih.gov/pubchem/specifications/

The only problem is that I'm limited to OSX and Linux and I can't seem to find a way of programmatically generating the 2d images that they have on their site. See this example:

https://pubchem.ncbi.nlm.nih.gov/compound/6#section=Top

Under the heading "2D Structure" we have this image here:

https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=6&t=l

That is what I'm trying to generate.

Answer 1

If you want something working out of the box I would suggest using molconvert from ChemAxon's Marvin (https://www.chemaxon.com/products/marvin/), which is free for academics. It can be used easily from the command line and it supports plenty of input and output formats. So for your example it would be:

molconvert "png" -s "C1=CC(=C(C=C1[N+](=O)[O-])[N+](=O)[O-])Cl" -o cdnb.png

Resulting in the following image:

It also allows you to set parameters such as width, height, quality, background color and so on.

---

However, if you are a programmer I would definitely recommend RDKit. Follows a code which generates images for a pair of compounds given as smiles.

from rdkit import Chem
from rdkit.Chem import Draw

ms_smis = [["C1=CC(=C(C=C1[N+](=O)[O-])[N+](=O)[O-])Cl", "cdnb"],
           ["C1=CC(=CC(=C1)N)C(=O)N", "3aminobenzamide"]]
ms = [[Chem.MolFromSmiles(x[0]), x[1]] for x in ms_smis]

for m in ms: Draw.MolToFile(m[0], m[1] + ".svg", size=(800, 800))

This gives you following images:

Answer 2

So I also emailed the PubChem guys and they got back to me very quickly with this response:

The only bulk access we have to images is through the download service: https://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch.cgi
You can request up to 50,000 images at a time.

Which is better than I was expecting, but still not amazing since it requires downloading things that I in theory could generate locally. So I'm leaving this question open until some kind soul writes an open source library to do the same.

Edit:

I figure I might as well save people some time if they are doing the same thing as I am. I've created a Ruby Gem backed on Mechanize to automate the downloading of images. Please be kind to their servers and only download what you need.

https://github.com/zachaysan/pubchem

gem install pubchem