.. NBD documentation master file, created by
   sphinx-quickstart on Mon Dec  4 11:58:09 2017.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Software
=========

Summary
----------

NBD main technologies are:

- PELE++ (`PELE docs <https://nostrumbiodiscovery.github.io/pele_docs/>`_)

- PELE Platform (`PELE Platform <https://nostrumbiodiscovery.github.io/pele_platform/>`_)

- Adaptive PELE Simulation (`Adaptive PELE docs <https://adaptivepele.github.io/AdaptivePELE/>`_)

- Frag PELE Simulation (`FrAG PELE docs <https://carlesperez94.github.io/frag_pele/>`_)

- MSM PELE Simulation (`MSM PELE docs <https://nostrumbiodiscovery.github.io/msm_pele/>`_)

- NAMD Molecular Dynamics (`NAMD docs <http://www.ks.uiuc.edu/Research/namd/>`_)

- analogs finder  (`analogs finder docs <https://nostrumbiodiscovery.github.io/analogs_finder/>`_)

- modtox AI (`modtox AI docs  <https://nostrumbiodiscovery.github.io/modtox/>`_)

- schrodinger platform (`schrodinger docs  <https://www.schrodinger.com/>`_)

- GROMACS (`GROMACS docs <https://manual.gromacs.org/documentation/>`_)

- PLUMED (`PLUMED docs <https://www.plumed.org/doc>`_)


Job Launching Templates
-------------------------

.. toctree::
   templates/documentation

PELE
---------

Pele is our in-house commercial software that we sell and use for speeding up DD projects

.. toctree::
   pele/documentation

.. toctree::
   peleplatform/documentation

.. toctree::
   adaptive/documentation

NAMD
----------

NAMD is used to perform molecular dynamics over several systems to study their dynamics over time

.. toctree::
   MD/documentation

Schrodinger
------------------

Schrodinger is used for virtual screening purposes and system preparation. 

.. toctree::
   Schrodinger/documentation

Python packages
---------------------

A miscelaneous of several Python Packages built along the years

.. toctree::
   python/packages

GROMACS
------------------
GROMACS is a versatile package to perform molecular dynamics.

.. toctree::
   GROMACS/documentation

PLUMED
------------------
PLUMED is a plugin that works with a large number of molecular dynamics codes. PLUMED can also work as a Command Line Tool to perform analysis on trajectories saved in most of the existing formats.

.. toctree::
   PLUMED/documentation

PSI4
----
PSI4 is the latest in the family of PSI Quantum Chemistry programs, it's mainly developed at Dave Scherrill's lab. at Georgia Tech. It's focused on the highest levels of Quantum Chemistry calculations such as fullCI, Coupled Cluster Theory and various DFT recipes.

.. toctree::
   PSI4/documentation


Nice DCV
------------

NICE DCV is the remote 3D visualization technology that enables Technical Computing users to connect to OpenGL applications running in a data center. (https://aws.amazon.com/es/hpc/dcv/)

.. toctree::
   Nice/nice

Tests
----------

Here you will find information of the automatic tests
run on nbdcalc01 computer


.. toctree::
   tests/index

New Comers
-------------

Here you will find how to set up your laptop to access NBD facilities

.. toctree::
   new_comers/index

AlphaFold
------------
Here you will find how to run AlphaFold

.. toctree::
   alphafold/alphafold

Structure Filtering
----------------------
Here you will find how to run a structure filtering

.. toctree::
   filtering/filtering

Dabble
------
Here you will find how to run Dabble

.. toctree::
   dabble/dabble

Protein-protein docking
-----------------------
Here you will find information about several PPI software installed in our cluster

.. toctree::
   ppi/ppi