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OpenSMOG-1.1.1rc1
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مشاهده بیشترتوضیحات
Structure-based Models for Biomolecules using OpenMM
| ویژگی | مقدار |
|---|---|
| سیستم عامل | OS Independent |
| نام فایل | OpenSMOG-1.1.1rc1 |
| نام | OpenSMOG |
| نسخه کتابخانه | 1.1.1rc1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | ['Antonio Bento de Oliveira Junior', 'Vinicius de Godoi Contessoto'] |
| ایمیل نویسنده | antonio.oliveira@rice.edu,contessoto@rice.edu |
| آدرس صفحه اصلی | https://github.com/junioreif/OpenSMOG |
| آدرس اینترنتی | https://pypi.org/project/OpenSMOG/ |
| مجوز | - |
========
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, which supports a wide variety of potential energy functions, including those that are commonly employed in C-alpha and all-atom models.
While it is possible to use this library in a standalone fashion, it is expected that users will generate input files using the SMOG2 software (version 2.4, or later, with the flag :code:`-OpenSMOG`). Details on how to generate OpenSMOG-compatible force fields files can be found in the `SMOG2 User Manual <https://smog-server.org/smog2/>`__.
Citation
========
When using **OpenSMOG** and **SMOG2**, please `use the following references
<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)
- `lxml <https://lxml.de/>`__ (>=4.6.2)
Installing SMOG2
================
The inputs **OpenSMOG** simulations are generated using `SMOG2 <https://smog-server.org/smog2>`_ (version 2.4 and later). Here, there is a quick installation guide based on `conda <https://conda.io/projects/conda/>`_ (Linux and Windows-WSL only).
First, download SMOG 2 (v2.4, or later) at `smog-server.org <https://smog-server.org/smog2/>`__
Second, create a new conda environment and activate it (called smog2.4, but name as appropriate):
.. code-block:: bash
conda create --name smog2.4 perl
.. code-block:: bash
conda activate smog2.4
Next, it is necessary to install 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 (described in the README that comes with SMOG 2).
.. 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
As described in the SMOG 2 manual, it is highly recommended that you also download smog-check and run all checks before using the SMOG 2 software.
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**.
- `Issue tracker <https://github.com/smog-server/OpenSMOG/issues>`__: Report issues/bugs or request features.
نحوه نصب
نصب پکیج whl OpenSMOG-1.1.1rc1:
pip install OpenSMOG-1.1.1rc1.whl
نصب پکیج tar.gz OpenSMOG-1.1.1rc1:
pip install OpenSMOG-1.1.1rc1.tar.gz