Question: SDF data from pubchem database by entering SID or CID of molecule
0
gravatar for sana.mystudies
24 months ago by
India
sana.mystudies60 wrote:

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

ADD COMMENTlink modified 24 months ago by mgab40 • written 24 months ago by sana.mystudies60
1
gravatar for Gungor Budak
24 months ago by
Gungor Budak230
Ankara/Turkey
Gungor Budak230 wrote:

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.

ADD COMMENTlink modified 24 months ago • written 24 months ago by Gungor Budak230

Thank you. i will work on it

ADD REPLYlink written 24 months ago by sana.mystudies60
1
gravatar for mgab
24 months ago by
mgab40
Germany
mgab40 wrote:

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

pcp.download('SDF', '134310260.sdf', 134310260, 'sid')
ADD COMMENTlink written 24 months ago by mgab40
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