search

mcs07 / PubChemPy

Python wrapper for the PubChem PUG REST API.
http://pubchempy.readthedocs.io
MIT License
379 stars 106 forks source link

pubchempy missing results available on the pubchem web page #68

Open drmatthewclark opened 2 years ago

drmatthewclark commented 2 years ago

pubchempy.get_compounds('NSC231854', 'name') results in an empty list, yet searching the same string on the pubchem web page gives

NSC231854; NSC-231854 Substance SID: 567558
Data Source: DTP/NCI External ID: 231854
Data Source Category: Governmental Organizations
Deposit Date: 2005-03-26 Last Modified Date: 2011-12-19

nbehrnd commented 2 years ago

A brief /manual/ consultation of the record page in question, with specific attention to the section /2D structure/.[1] This is the formula of an ester of benzoic acid, though the former alcohol is not specified (label R). So it could be a methyl, an ethyl, a propyl chain, etc. Maybe R isn't about an alkyl chain and a representative including H so that the formula equally applies to plain benzoic acid.

With this variation at disposition, how to name and assign properties? Here, PubChem could better report the SMARTS string about this residue (as in «fragment»). However, I'm not aware if a /search by motif of a sub structure/ expressed in SMARTS (instead of SMILES) may be relayed successfully to pubchem by pubchempy.

[1] https://pubchem.ncbi.nlm.nih.gov/substance/567558#section=2D-Structure

xruifan commented 6 months ago

try get_substances('NSC231854', 'name')? It is a substance record on pubchem website.