SDF data from pubchem database by entering SID or CID of molecule
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4.7 years ago
Sabine ▴ 70

Hi All, I want to download the SDF file data for a list of pubchem compounds. I have SID, CID information of all of the molecules. It will be difficult to retrieve the SDF one by one for all of these compounds. Is there any tools/softwares to collect the SDF data by entering these SID or CID? Thank you for suggestion

Pubchem SDF file of molecule SDF from Pubchem • 3.2k views
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4.7 years ago
Gungor Budak ▴ 250

You can use PubChemPy Python wrapper for PUG REST API:

import pubchempy as pcp
pcp.download('SDF', '5090.sdf', 5090, 'cid')

So above code downloads an SDF file for compound with CID 5090.

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Thank you. i will work on it

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4.7 years ago
mgab ▴ 60

I have tried using SID but it is not working, that is

pcp.download('SDF', '134310260.sdf', 134310260, 'sid')
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