Metadata-Version: 2.1
Name: pymacroms
Version: 1.1.1
Summary: pyMacroMS - High performance quantification of complex high resolution polymer mass spectra
Home-page: http://macroarc.org/research/macroarc-pyMacroMS.html
Author: Kevin De Bruycker and Tim Krappitz
Author-email: kevindebruycker@gmail.com
License: MIT License
Description: # pyMacroMS
        ##### _High performance quantification of complex high resolution polymer mass spectra_
        
        The purpose of this program is to identify and quantify macromolecular species 
        in high resolution mass spectra based on the used monomer(s), possible end-groups 
        and the adduct ion. Experimental spectra are imported as a centroided peaklist
        from a comma-separated values (csv) file or directly from a Thermo RAW file (from v1.0.0). Please find code for example usage
         on our [webpage](http://macroarc.org/research/macroarc-pyMacroMS.html).
         
        From version 1.0.0, pyMacroMS requires a 64-bit version of Python. 
        
        ##### Dependencies
        
        pyMacroMS requires the following modules to be installed:
        * [IsoSpecPy](http://matteolacki.github.io/IsoSpec/) for the generation of isotopic patterns
        * numpy and pandas for data processing
        * sklearn for quantification via linear regression
        * matplotlib for quick representation of results
        * progressbar2 for feedback during the more time consuming steps 
        * reportlab and svglib for the generation of a PDF report
        * pythonnet for the interface with Thermo's RawFileReader
        
        ##### Citation
        
        Please refer to our publication for more details about the algorithm and 
        cite us when using pyMacroMS in your work:
        
        [K. De Bruycker, T. Krappitz, C. Barner-Kowollik, _ACS Macro Lett._ **2018**, 1443-1447.](http://dx.doi.org/10.1021/acsmacrolett.8b00804)
        
        ##### License
        
        * pyMacroMS is available free of charge under an MIT License. 
        See the LICENCE file for more details.
        * pyMacroMS uses the RawFileReader reading tool. Copyright Â© 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
        If you use pyMacroMS, you agree to the license agreement of RawFileReader, of which a copy is provided when installing pyMacroMS. 
        
        
        ##### Changelog
        
        ###### 1.1.1
        * Now works with IsoSpecPy 2.x, tested with 2.1.4, but does not work with IsoSpecPy 1.x any more.
        
        ###### 1.1.0
        * Speed improvements for assembling the possible monomer combinations in the polymer simulation. 
          Special thanks to Matthieu Soete for sharing his insights.
        * Preparations for a GUI
        
        ###### 1.0.9
        * Introduced basic support for Scan Filters (limit the imported data to 1 type of scan). Different scan types are detrimental for the averaging algorithm and probably don't make much sense anyway (?) 
        * Increase compatibility with Unix systems, installation of pythonnet package seems to be the major struggle though
        * MSData class now takes the argument mzOffset, an offset that is added to every m/z value when reading the spectrum. 
        * Speed improvements for a large amount of possible compositions
        * Minor bugfixes
        
        ###### 1.0.0
        * Thermo RAW files can now be used as input without any pre-processing
            * By default, all scans are imported separately
            * Scans can be averaged by providing a range of scans or retention times
        * New MSData class introduced
            * Handles reading of csv files (previously Spectrum class) and Thermo RAW files
            * Stores all imported spectra and corresponding processed results to allow for batch processing of multiple scans 
            * Post-processing of results still in Spectrum class, so on a per-scan base... Future problem
        * Version 1.0.0 and onwards are licensed under an MIT License (rather than a GNU GPL v3.0 for older versions) to comply with the license requirements of Thermo's RawFileReader
        
        ###### 0.2.0
        * Isobaric species are now pre-filtered, which leads to a significantly improved calculation time
        * Introduced the option to define a custom database of monomers/endgroups (with a higher priority than the built-in database)
        * Introduced the option to save the output as a PDF report
        
        ###### 0.1.2
        * Update code to use the new IsoSpecPy 1.9.X API
        
        ###### 0.1.1
        * Minor fixes to the interfacing with IsoSpecPy
        * Fixed compatibility with IsoSpecPy 1.9.X
        
        ###### 0.1.0
        * Initial release
        
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
