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Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
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2.2 years ago

Hi,

I am trying to generate SMILES for a set of molecules. As shown below, I have the sample _ID, name, Pubchem_SID (which looks funny) and CAS. I tried using Pubchempy to extract SMILES using Pubchem_SID but it failed. Given the fields below, I'd appreciate some direction on how I can generate SMILES for these molecules. Thanks!

**SAMPLE_ID**
NCGC00013369-03
NCGC00013556-01
NCGC00016522-05
NCGC00016544-01

**SAMPLE_NAME**
Pamoic acid
3,5,3'-Triiodothyronine
Bisacodyl
Dehydroepiandrosterone acetate

**PUBCHEM_SID**
144206996
144203580
144204023
144204036

**CAS**
130-85-8
6893-02-03
603-50-9
853-23-6
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12 months ago
prasundutta87 • 330

Many ways to achieve what you want-

1) Pubchem_SID is Pubchem Substance ID..so if you go to the Pubchem homepage, select 'Substance' instead of 'Compound' in the Search bar and search for, for example, '144206996', you will get Pamoic acid. You can download the 2D SDF and then convert it to SMILES for any of your downstream analysis using OpenBabel or any format converter that you possess..

Furthermore, if you want to download all the SIDs at once, you can write a small perl script based on this example command:

wget -O 144206996.sdf https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/sid/144206996/record/SDF

You can write a loop to change the SIDs and all your SDFs will be downloaded at once that you can convert into SMILES...

2) Go to https://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch.cgi, choose 'Pubchem Substance' as the database, give a list of SIDs in 'Enter IDs' or upload the list, select SMILES in 'choose a format', and click 'Download'..you will get what you want..

3) If you want to continue using Pubchempy, check this out: https://pubchempy.readthedocs.io/en/latest/guide/substance.html#retrieving-substances

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Thank you so so much! I think I'd go with the Pubchempy

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