Metadata-Version: 2.1
Name: lightdock
Version: 0.9.1
Summary: A macromolecular docking framework
Home-page: https://lightdock.org/
License: GPLv3 License
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        <p align="center">
            <img src="https://lightdock.org/assets/images/lightdock_logo.png">
        </p>
        
        ## 1. Synopsis
        **LightDock** is a protein-protein, protein-peptide and protein-DNA docking framework based on the [Glowworm Swarm Optimization](https://link.springer.com/article/10.1007/s11721-008-0021-5) (GSO) algorithm.
        
        The LightDock framework is highly versatile, with many options that can be further developed and optimized by the users: it can accept any user-defined scoring function, can use local gradient-free minimization, the simulation can be restrained from the beginning to focus on user-assigned interacting regions, **it supports residue restraints in both receptor and ligand partners**.
        
        ## 2. Reference
        LightDock protocol and the updates to make use of residue restraints have been published in [Oxford Bioinformatics](https://academic.oup.com/bioinformatics) journal. Please cite these references if you use LightDock in your research:
        
        **LightDock: a new multi-scale approach to protein–protein docking**<br>
        [Brian Jiménez-García](http://bjimenezgarcia.com), Jorge Roel-Touris, Miguel Romero-Durana, Miquel Vidal, Daniel Jiménez-González and Juan Fernández-Recio<br>
        *Bioinformatics*, Volume 34, Issue 1, 1 January 2018, Pages 49–55, [https://doi.org/10.1093/bioinformatics/btx555](https://doi.org/10.1093/bioinformatics/btx555)
        
        **LightDock goes information-driven**<br>
        Jorge Roel-Touris, Alexandre M.J.J. Bonvin, [Brian Jiménez-García](http://bjimenezgarcia.com)<br>
        *Bioinformatics*, btz642; doi: [https://doi.org/10.1093/bioinformatics/btz642](https://doi.org/10.1093/bioinformatics/btz642)
        
        
        ## 3. Installation
        
        Lightdock software is compatible and it has been tested with the followings OS:
        
        * **macOS**: El Capitan, Sierra, High Sierra, Mojave, Catalina.
        * **GNU/Linux**: Ubuntu 16+, Debian Stretch+, Scientific Linux 6+, CentOS 6+.
        
        Microsoft Windows is not officially supported, despite many parts of the protocol might be able to run. Please use it at your own risk. If you wish to contribute testing and developing LightDock for Windows, please contact us.
        
        ### 3.1. Dependencies
        LightDock has the following dependencies:
        
        * NumPy (<http://www.numpy.org/>)
        * Scipy (<http://www.scipy.org/>)
        * Cython (<http://cython.org/>)
        * BioPython (<http://biopython.org>)
        * ProDy (<http://prody.csb.pitt.edu/>)
        * Freesasa (<http://freesasa.github.io/>)
        
        Optional dependencies are:
        
        * MPI4py (if you plan to use MPI support which is experimental at the moment, <http://pythonhosted.org/mpi4py/>)
        
        ### 3.2. Install LightDock
        The fastest way to install LightDock is to use `pip`:
        
        ```bash
        pip install lightdock
        ```
        
        ## 4. Development
        For development and extension of the LightDock code, please follow these instructions:
        
        ### 4.1. Clone
        Clone this repository:
        
        ```bash
        git clone https://github.com/lightdock/lightdock.git
        ```
        
        ### 4.2. Compile Python C and Cython extensions
        
        Please make sure dependencies are already installed (via pip, package manager, etc.):
        
        * numpy>=1.17.1
        * scipy>=1.3.1
        * cython>=0.29.13
        * biopython>=1.74
        * pyparsing>=2.4.2
        * prody>=1.10.11
        * freesasa>=2.0.3
        
        It is recommended to create a virtual environment and install it:
        
        ```bash
        virtualenv venv
        source venv/bin/activate
        cd lightdock
        pip install -e .
        ```
        
        If not using pip or setuptools for development, there is as bash script to compile all the extensions:
        
        ```bash
        cd lightdock
        ./setup.sh
        ```
        
        ### 4.3. Add Lightdock to your path
        
        Add the following lines to your `~/.bashrc` file, don't forget to change `/path/to/lightdock`:
        
        ```bash
        # LightDock
        export LIGHTDOCK_HOME="/path/to/lightdock"
        export PATH=$PATH:$LIGHTDOCK_HOME/bin
        export PYTHONPATH=$PYTHONPATH:$LIGHTDOCK_HOME
        ```
        
        Don't forget to apply the changes:
        
        ```bash
        source ~/.bashrc
        ```
        
        ### 4.4. Testing
        
        You can run LightDock tests:
        
        ```bash
        cd lightdock
        nosetests
        ```
        
        ## 5. Documentation
        
        The complete documentation about how to run the LightDock protocol and several tutorials and use cases can be found at [https://lightdock.org/tutorials](https://lightdock.org/tutorials).
        
        
        ## 6. Get Help
        
        LightDock is being actively developed and some issues may arise or you may need extra help to run LightDock. In those cases, there are two main ways to get help:
        
        1. Read the [FAQ](https://lightdock.org/tutorials/faq) in case your problem is known
        2. Open a [new issue in this repository](https://github.com/lightdock/lightdock/issues/new)
        3. Or write an email to <lightdocking@gmail.com>
        
        ## 7. LICENSE
        
        LightDock is available under GPLv3 License. See [LICENSE](LICENSE) document for more details.
        
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.6
Description-Content-Type: text/markdown
