##############################
Installation and Prerequisites
##############################

Software Prequisites
--------------------

The following commands should be in your path:

1. ``antechamber``, ``parmchk2``, and ``tleap`` (`AmberTools <https://ambermd.org/GetAmber.php#ambertools>`_, version 22 or higher); preferred installation via ``conda``.
2. ``gmx`` or ``gmx_mpi`` (`Gromacs <https://manual.gromacs.org/documentation/current/index.html>`_, version 2022.1 or higher); preferred installation via compiling from source.
3. ``obabel`` (`OpenBabel <https://github.com/openbabel/openbabel>`_); preferred installation via Linux distribution package.  Note that ``htpolynet`` itself does not require OpenBabel, but we show in the examples how to build input monomer structures from SMILES strings using OpenBabel, so it is recommended that you have it installed.

Installation
------------

If you use conda/anaconda, we recommended that you create a separate Python environment running ``htpolynet``:

.. code-block:: console

    $ conda create --name mol-env python
    $ conda activate mol-env

Once this environment is created and activated, you can install ``ambertools``, ``gromacs``, and ``htpolynet`` from ``conda-forge``:

.. code-block:: console

    $ conda install -c conda-forge ambertools
    $ conda install -c conda-forge gromacs
    $ conda install -c conda-forge htpolynet

If you are not a conda user, you can install ``htpolynet`` from PyPI.

.. code-block:: console

    $ pip install htpolynet

Note that you will have to install ``ambertools`` and ``gromacs`` some other way.

Again, to use the examples as provided, you will need to have OpenBabel installed.  We recommend installing OpenBabel from your Linux distribution's package management system.

To install a development version of ``htpolynet`` you can instal from a freshly cloned Github repository:

.. code-block:: console

    $ git clone git@github.com:AbramsGroup/htpolynet.git
    $ cd htpolynet
    $ pip install -e .

Note here that you will need to have all other prequisites installed as mentioned above, *plus* a conda-based installation of ``parmed``.

Notes
-----

If you prefer to use more recent versions of AmberTools, Gromacs, or OpenBabel than your system currently provides, you can compile the latest versions from source.  **It is recommended that you deactivate any conda environment before performing any of these compilations.**

Compilation of AmberTools
#########################

Compilation of AmberTools requires ``csh``, ``flex``, and ``bison``:

.. code-block:: console

    $ tar jxf AmberTools21.tar.bz2
    $ cd amber_src
    $ ./configure --no-X11 --skip-python gnu
    $ source amber.sh
    $ make install

Compilation of Gromacs
######################

You can also compile Gromacs from source, if your Linux distibution doesn't include it in its package management, or you are on a big supercomputer.  The example below builds Gromacs with CUDA but without MPI (assuming you have CUDA installed):

.. code-block:: console

    $ tar xfz gromacs-2022.1.tar.gz
    $ cd gromacs-2022.1
    $ mkdir build
    $ cd build
    $ cmake ..  -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs
    $ make
    $ make check
    $ sudo make install

And add to your ``~/.bashrc``:

.. code-block:: console

    source /usr/local/gromacs/bin/GMXRC

This should provide access to the ``gmx`` command.  If you additionally compiled an MPI version (using ``-DGMX_MPI=on`` in the ``cmake`` command), you will also have access to ``gmx_mpi``; either of these commands can be used by htpolynet.  Note that Gromacs 2016 and below have a version of ``gmx distance`` that limits the number of distances that can be calculated, so we (always) recommend using the latest Gromacs.

Compilation of ``obabel``
#########################

If your system does not have ``obabel`` installed and your Linux distribution doesn't offer a package for it (or you are not root!), you can compile it from source.  Be sure to unpack `Eigen <https://eigen.tuxfamily.org/index.php?title=Main_Page>`_ first so that the ``conformer`` plug-in for ``obabel`` will work.  Below I demonstrate a session in which both the Eigen and OpenBabel source packages are downloaded to ``~/Downloads`` and are unpacked in the directory ``~/build/``, and the OpenBabel installation directory is ``~/opt/obabel``.

.. code-block:: console

    $ cd ~/build
    $ tar jxf ~/Downloads/eigen-3.4.0.tar.bz2  # unpack only -- no need to compile
    $ tar jxf ~/Downloads/openbabel-3.1.1.tar.bz2
    $ cd openbabel-3.1.1
    $ mkdir build
    $ cd build
    $ cmake .. -DEIGEN3_INCLUDE_DIR=${HOME}/build/eigen-3.4.0/ -DCMAKE_INSTALL_PREFIX=${HOME}/opt/obabel
    $ make
    $ make test
    $ make install

You will need to ensure that ``${HOME}/opt/babel/bin`` is in your ``PATH``, ``${HOME}/opt/babel/lib`` is in your ``LD_LIBRARY_PATH``, and that the environment variable ``BABEL_LIBDIR`` is set to ``${HOME}/opt/babel/lib``.

Other Prequisites
-----------------

In order to use ``htpolynet`` effectively, it is recommended that you have good working knowledge of the following:

1. MD simulation in general and Gromacs specifically;
2. the General Amber Force Field (GAFF), including in particular

   a. how to use ``antechamber``, ``tleap``, and ``parmchk2`` to generate GAFF parameterizations; and
   b. how to use these parameterizations inside Gromacs; and

3. Polymer chemistry, at least for the systems you are interested in simulating.