Metadata-Version: 2.1
Name: mass2chem
Version: 0.0.5
Summary: Common utilities for interpreting mass spectrometry data
Home-page: https://github.com/shuzhao-li/mass2chem
Author: Shuzhao Li
Author-email: shuzhao.li@gmail.com
License: BSD
Keywords: chemistry,bioinformatics,mass spectrometry
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3
Description-Content-Type: text/markdown
License-File: LICENSE

# 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

E.g. in pychemy.adducts, it's wrong to use ('M+3H', 0.33,  1.0073),
because the computing error in 0.33 (correct is 1/3) is far too large for mass precision.

Pychemy is included as stripped version in "mass2chem.chem" for now, but only used for formula handling.

For high-resolution measurements, electrons should be considered too.


## 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 

## Dev note

The organization of this repo will change, after compatibility check on application packages.
 

