Now that I have a wide enough data set to look at all common groups relevant to a subsection of a community. We can start to elucidate common scaffolds that exist between diverse communities. So let’s begin, here is the demo so you can follow along: !pip install -q global-chem[cheminformatics]…

I have just realized I am my own best user. I forgot why I was interested in organic chemistry in the first place. Pihkal was such an awesome book because of how acute and kind of whimsical the science was. I’ve always loved the cloud in the air organic chemistry…

Chemical Diversity is hard to define, and for a list of SMILES it can be ever increasing to understand what that really means. Fingerprinting is alternative method of converting a SMILES into a bit representation that has different features of that chemical compound. Unfortunately, when the conversion happens we lose…

I guess this was something I wanted to talk about for awhile. My grandad died. During all this madness I lost someone I loved. I don’t have many people in my family and most likely in my defense only my mom and sister will be there. A couple of months…

There was a time where I needed to download the zinc database rapidly because we made some earlier mistakes in some downstream pipelines and was approaching a deadline. The entire pipeline needed to be restarted and thus from downloading the zinc database. The Zinc Database has two major versions, 2015…

I wanted to see the performance of the SMILES I wrote in GlobalChem to see how well different algorithms of validation perform on a common basis set of molecules. The four main packages I chose (also ease of implementation) is RDKit, PartialSMILES, PySMILES, and MolVS. There’s a couple of others…

One day during graduate school I was assigned to process ~1.7 billion compounds in SMILES format(The EnamineDB) through a data pipeline and get the resulting output. To actually accomplish this, I realized I needed a robust pipeline data management system that will help me navigate large chunks of data with…

Recently, a co-worker challenged me draw a molecule and predict the pKa using just reasoning. Let’s look at a simple example of acetic acid to butyric acid where we subsequently add a carbon can we predict the protonation of the carboxylic acid hydrogen? This raised an interesting data connection for…

Most often I have a new SMARTS string I need to test against a range of chemical environments to see if the string reasonably captures the chemical environment described by it’s functional group. I had a friend right a partial working flask app for me and I’m distributing it global-chem…