Metadata-Version: 2.1
Name: pyXLMS
Version: 0.0.1
Summary: A python package to process protein cross-linking data.
Author-email: Micha Johannes Birklbauer <micha.birklbauer@fh-hagenberg.at>
Maintainer-email: Micha Johannes Birklbauer <micha.birklbauer@fh-hagenberg.at>
License: MIT License
        
        Copyright (c) 2024 Micha Johannes Birklbauer
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Homepage, https://github.com/hgb-bin-proteomics/pyXLMS
Project-URL: Documentation, https://hgb-bin-proteomics.github.io/pyXLMS
Project-URL: Issues, https://github.com/hgb-bin-proteomics/pyXLMS/issues
Keywords: crosslink,crosslinker,crosslinking,mass spectrometry,proteomics
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas
Provides-Extra: gui
Requires-Dist: streamlit ; extra == 'gui'

# pyXLMS

Supported search engines:
- MS Annika
- xiSearch / xiFDR
- MaxLynx
- ?

General interface with csv input

Packages to include:
- Export to xiNET
  - Req:
  - fasta file
  - Crosslink:
    - Sequence
    - XL position in peptide
    - protein accession
    - XL position in protein
    - Score
- Export to xiVIEW
  - Req: cover by xiNET Req
- Export to xiFDR
  - Req:
  - CSM:
    - Spectrum File
    - Scan Nr
    - Sequence
    - XL position in peptide
    - Precursor charge
    - Score CSM
    - Score peptide
    - protein accession
    - position of peptide in protein
    - decoy peptide
- Export to pyXlinkViewer
  - Req: all covered
- Export to XMAS
  - Req: all covered
- Export to Spectral Library
  - Req:
  - MGF
  - CSM:
    - Modification
    - RT
    - Ion Mobility / Compensation Voltage  
- MS Annika FDR
  - Req: all covered
- MS Annika Combine Results
  - Req: all covered
- CSM Annotation
  - Req: this is probably MS Annika only, as it requires doublet information
