Metadata-Version: 2.1
Name: mass2chem
Version: 0.3.0
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


## Included or work in progress

* Handling chemical formula 

* A list of common mass values, including contaminants

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


## to include

* 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/rounding 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.
It may be removed completely in future versions.

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 

Third party:

https://github.com/domdfcoding/chemistry_tools



## Dev note

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

