Metadata-Version: 1.1
Name: OpenSMOG
Version: 0.0.2
Summary: Structure-based Models for Biomolecules using OpenMM
Home-page: https://github.com/junioreif/OpenSMOG
Author: ['Antonio Bento de Oliveira Junior', 'Vinicius de Godoi Contessoto']
Author-email: antonio.oliveira@rice.edu,contessoto@rice.edu
License: UNKNOWN
Description: ========
        OpenSMOG
        ========
        
        |Citing OpenSMOG|
        |PyPI|
        |conda-forge|
        |ReadTheDocs|
        |SMOG server|
        |Update|
        |GitHub-Stars|
        
        .. |Citing OpenSMOG| image:: https://img.shields.io/badge/cite-OpenSMOG-informational
           :target: https://opensmog.readthedocs.io/en/latest/Reference/citing.html
        .. |PyPI| image:: https://img.shields.io/pypi/v/OpenSMOG.svg
           :target: https://pypi.org/project/OpenSMOG/
        .. |conda-forge| image:: https://img.shields.io/conda/vn/conda-forge/OpenSMOG.svg
           :target: https://anaconda.org/conda-forge/OpenSMOG
        .. |ReadTheDocs| image:: https://readthedocs.org/projects/opensmog/badge/?version=latest
           :target: https://opensmog.readthedocs.io/en/latest/
        .. |SMOG server| image:: https://img.shields.io/badge/SMOG-Server-informational
           :target: https://smog-server.org/
        .. |Update| image:: https://anaconda.org/conda-forge/opensmog/badges/latest_release_date.svg
           :target: https://anaconda.org/conda-forge/opensmog
        .. |GitHub-Stars| image:: https://img.shields.io/github/stars/junioreif/OpenSMOG.svg?style=social
           :target: https://github.com/junioreif/OpenSMOG
        
        
        `Documentation <https://opensmog.readthedocs.io/>`__
        | `Install <https://opensmog.readthedocs.io/en/latest/GettingStarted/install.html>`__
        | `Tutorials <https://opensmog.readthedocs.io/en/latest/Tutorials/SBM_CA.html>`__
        
        Overview
        ========
        
        OpenSMOG is a Python library for performing molecular dynamics simulations using Structure-Based Models. OpenSMOG uses the  `OpenMM <http://openmm.org/>`__. Python API employing a wide variety of potential forms, including the most commonly employed models such as the C-alpha and All-Atoms.
        The input files are generated using SMOG2 software with the flag :code:`-openSMOG`. Details on how to create the files can be found in the `SMOG2 User Manual <https://smog-server.org/smog2/>`__.
        
        
        Resources
        =========
        
        - `Reference Documentation <https://opensmog.readthedocs.io/>`__: Examples, tutorials, and class details.
        - `Installing OpenSMOG <https://opensmog.readthedocs.io/en/latest/GettingStarted/install.html#installing-opensmog>`__: Instructions for installing **OpenSMOG**.
        - `Installing SMOG2 <https://opensmog.readthedocs.io/en/latest/GettingStarted/install.html#installing-smog2>`__: Instructions for installing **SMOG2**.
        - `GitHub repository <https://github.com/junioreif/OpenSMOG/>`__: Download the **OpenMiChroM** source code.
        - `Issue tracker <https://github.com/junioreif/OpenSMOG/issues>`__: Report issues/bugs or request features.
        
        
        Citation
        ========
        
        When using **OpenSMOG** to perform chromatin dynamics simulations or analyses, please `use this citation
        <https://opensmog.readthedocs.io/en/latest/Reference/citing.html>`__.
        
        
        
        Installation
        ============
        
        The **OpenSMOG** library can be installed via `conda <https://conda.io/projects/conda/>`__ or `pip <https://pypi.org/>`__, or compiled from `source (GitHub) <https://github.com/junioreif/OpenSMOG>`__.
        
        Install via conda
        -----------------
        
        The code below will install **OpenSMOG** from `conda-forge <https://anaconda.org/conda-forge/OpenSMOG>`__.
        
        .. code-block:: bash
        
            conda install -c conda-forge OpenSMOG
        
        Install via pip
        -----------------
        
        The code below will install **OpenSMOG** from `PyPI <https://pypi.org/project/OpenSMOG/>`__.
        
        .. code-block:: bash
        
            pip install OpenSMOG
        
        Install OpenMM
        --------------
        
        The **OpenSMOG** library uses `OpenMM <http://openmm.org/>`_ API to run the molecular dynamics simulations.
        These requirements can be met by installing the following packages from the `conda-forge channel <https://conda-forge.org/>`__:
        
        .. code-block:: bash
        
            conda install -c conda-forge openmm
            
        The following are libraries **required** for installing **OpenSMOG**:
        
            - `Python <https://www.python.org/>`__ (>=3.6)
            - `NumPy <https://www.numpy.org/>`__ (>=1.14)
            - `ElementTree XML <https://docs.python.org/3/library/xml.etree.elementtree.html>`__ (>=2.2.0)
        
        Installing SMOG2
        ================
        
        The inputs **OpenSMOG** simulations are generated using `SMOG2 <https://smog-server.org/smog2>`__ > 2.4. Here, there is a quick installation guide based on `conda <https://conda.io/projects/conda/>`_.
        
        First, just create a new environment and activate it:
        
        .. code-block:: bash
        
            conda create --name smog2.4 perl
            
        .. code-block:: bash
        
            conda activate smog2.4
        
        Next, it is necessary an installation of a few **Perl** modules:
        
        .. code-block:: bash
        
            conda install -c bioconda perl-xml-simple perl-xml-libxml java-jdk
        
        .. code-block:: bash
        
            conda install -c eumetsat perl-pdl
        
        .. code-block:: bash
        
            perl -MCPAN -e 'install XML::Validator::Schema'
        
        Add the **Perl** and **smog2** path into the configure.smog2 file.
        
        .. hint:: Use the following command line to find out which installed **Perl** is being used.
        
        .. code-block:: bash
        
            which perl
        
        Then load and test the **smog2** installation:
        
        .. code-block:: bash
        
            source configure.smog2
            
        .. code-block:: bash
        
            ./test-config
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Natural Language :: English
