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topdownproteomics / sdk

Software solution for common top-down proteomics tasks
http://www.topdownproteomics.org/
MIT License
9 stars 4 forks source link

Chemical formula api #40

Closed rfellers closed 6 years ago

rfellers commented 6 years ago

Adding simple chemical formula API for starters. I tried to take some parts of both NU and UW existing chemical formula APIs.

Here, as with most things in this library, I am making heavy use of interfaces. While this is my practice in general, I think it will also make it easier to incorporate this SDK into many diverse codebases (given a lack of multiple inheritance in .NET).

rfellers commented 6 years ago

Thanks. I am curious what requirements others might have for a chemical formula interface. I was only focused on ProForma, but that stills means that we need to handle regular elements, pure isotopes of elements (e.g. C13), and Unimod "atoms" (which can additionally represent glycan residues and common molecules). Should we add to the benchmarking app to include chemical formulas? How important is performance?

acesnik commented 6 years ago

I moved this discussion to here: https://github.com/topdownproteomics/sdk/issues/41