Convert from HMDB, ChEBI, etc. to molecular formula?

[Former user]

I'm trying to find a tool to do this for batch files (formulas are needed for use in El-MAVEN; it doesn't use the database IDs in compound lists). Surprisingly, CTS and the others I've tried don't do it.

[Khoi Van]

Hi, I am not too familiar with HMDB or ChEBI database. I wonder if pubchem can do what you are asking? However, I believe pubchem has limit of not more than 5 requests per seconds. One thing you can do, perhaps is write a simple python program to read through a list of files and then submit and get return result from CTS or cactus chemical identidifier resolver (https://cactus.nci.nih.gov/chemical/structure) or pubchem (https://pubchem.ncbi.nlm.nih.gov/)

[Diego Pedrosa]

Hello, If you batch convert your IDs to Inchi Code, you will get the formulas on the 2nd layer:

InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1

After that, a simple python script or excel formula can extract the desired data