Metadata-Version: 2.1
Name: mscheck
Version: 0.1.7b0
Summary: Auto MS mass checker
Home-page: https://github.com/Waztom/mscheck
Author: Warren Thompson
Author-email: waztom@gmail.com
License: MIT
Description: # <a name="MScheck for locating target compound masses in mass spectra"></a>**MScheck for locating target compound masses in mass spectra**
        
        [//]: # "Badges"
        
        [![PyPI version](https://badge.fury.io/py/mscheck.svg)](https://badge.fury.io/py/mscheck)
        
        MScheck is a python package that hunts for a target compound mass + given ion mass (eg. H+, Na+).
        MScheck was created to assist with the automated mass spectrum analysis of target compounds synthesised using
        a high throughput approach.
        
        # <a name="MScheck installation"></a>**MScheck installation**
        
        MScheck relies on rdkit for generating molecule SVG images and for calculating molecular weights<br>
        Installing rdkit using conda works best followed by a pip install of MScheck<br>
        
        1. Create a conda environment with rdkit
        
           > `conda create -c conda-forge -n MScheck rdkit`
        
        2. Activate the MScheck conda environment created
        
           > `conda activate MScheck`
        
        3. Pip install MScheck
           > `pip install mscheck`
        
        # <a name="MScheck use"></a>**MScheck use**
        
        MScheck has been tested on using Agilent LCMS files (.D) as the starting file format. One challenge is to convert vendor file formats into
        a format with the binary decoded.
        
        1. Convert .D Agilent folder to a .d MassHunter format using Agilent's ChemStation to MassHunter Translator (B.04.00)
        2. Convert .d format into .mzML format using [ProteoWizard's](http://proteowizard.sourceforge.net/) MSConvert tool
        3. Finally - we have an file format that we can use!
        4. In your favourite IDE or Jupyter notebook - as basic example of using MSCheck is prvided below:<br>
        
        ```
        from mscheck.analyse import AnalyseSpectrum
        
        # Create MS scptrum object and find peaks
        test = AnalyseSpectrum("<path to .mzML file>", mode="Positive")
        
        # Analyse test spectrum
        test.analyse(compoundsmiles=target_compound,
                     ionstoadd=["[H]", "[Na]", "[K]", "[NH4+]"],
                     tolerance=1)test.analyse
        
        # Create a SVG report - if you do not give a compound_name
        # the ending leaf of the file name will be used
        test.create_report(compound_name="Test")
        ```
        
         <br>
        
        Example of report output:<br>
        
        <p align="center">
        <img src="images/report.svg" width="600px">
        </p>
        
        The .SVG report will be in a folder called Reports
        
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Description-Content-Type: text/markdown
