Metadata-Version: 2.1
Name: xlms-tools
Version: 1.0.0
Summary: xlms-tools is a set of command line tools to apply crosslinking mass spectrometry (XL-MS) data to protein structure models.
Author-email: Topf Lab <karen.manalastas-cantos@cssb-hamburg.de>
Project-URL: Homepage, https://gitlab.com/topf-lab/xlms-tools
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython>=1.78
Requires-Dist: numpy>=1.19.2
Requires-Dist: scipy>=1.5.2

# xlms-tools

## Description
xlms-tools is a set of command line tools to apply crosslinking mass spectrometry (XL-MS) data to protein structure models.

## Setting up xlms-tools
After downloading or cloning this repository, download dependencies by running the following from the project directory:
```bash
$ pip3 install -r requirements.txt
```

## Using xlms-tools
Currently, xlms-tools can be run in two modes. The first is to score how well a protein structure model agrees with XL-MS data, specified as a list crosslinks and monolinks derived from a XL-MS experiment.


### To score how well a protein structure agrees with XL-MS data
1. Format crosslinks and monolinks into a text file with the following format:


2. Score protein structure model/s:
```bash
$ python xlms-tools.py -m score -l [list of crosslinks and/or monolinks] [PDB file]
```

## Citations
When using xlms-tools, please cite:
Manalastas-Cantos, K. et al. (2023) Modeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry. BioRxiv. https://doi.org/10.1101/2023.09.11.557128 
