mass2chem 0.0.4

Common utilities for interpreting mass spectrometry data

mass2chem - common utilities in interpreting mass spectrometry data

Annotation and Inferrence

to include

• Handling chemical formula via pychemy (which needs update to high res data)

• A list of common mass values, including contaminants

• A list of common adducts, rules, while they are more directly ready in future Azimuth

• Chemical similary computing

• Reaction inference, including mass diff corresponding to common reactions

• Annotation via in-house libraries

• hook/adaptor to other tools

Added basic formula based calculations

Note: RE based formula parsing is still limited.

Pychemy isn't good fit, as

1. high-resolution calculation needs update
2. Open babel binding is not worthy the trouble

Included as stripped version in "mass2chem.chem" for now.

Related

https://github.com/shuzhao-li/pychemy

https://github.com/opencobra/cobrapy/blob/devel/cobra/core/formula.py (they are using average molecular weight, not mass spec oriented)

https://github.com/shuzhao-li/Azimuth (Private)