standardize script of mol file without rdkit or openbabel
khoivan88 opened this issue · 2 comments
Hi, thank you for this super userful library as well as others (Pubchempy, Chemspipy, CIRPy).
I have a python script for a chemical inventory program (Open Enventory) that scrapes mol files from various websites. The scraping file is doing a pretty good job but a small percentage of the mol files (mostly from pubchem) have explicit hydrogens and I want the mol files to have implicit hydrogens. I have discovered rdkit, and open babel to be able to clean the mol file (convert explixit hydrogens to implicit hydrogens). Your molvs is exactly what I am looking for and more (the standardize module). However, I want my python scraping code to be more portable and usable for non technical people and I am just looking for a small library or code that can do the "standardize" function without installing rdkit or open babel.
I was wondering if you might know of such library or maybe you could direct me to some direction.
Thank you very much!
Best regards,
Khoi Van
Doing chemoinformatics without using one of the available toolkits (CDK, OpenBabel or RDKit) is probably a lot of work. And, to program parts of it you will need to be a computational chemist...
@UnixJunkie Thank you for your info!