Chimie Théorique » scripts_chimie4psmn » DockOnSurf

Installation

============

Download the ``dockonsurf`` directory and place it somewhere in your computer,

by typing in your terminal: ::

    git clone http://forge.cbp.ens-lyon.fr/git/dockonsurf

In order to be able to execute DockOnSurf by simply typing ``dockonsurf.py`` You need 

to add the DockOnSurf directory in your ``PATH``. Assuming you download it in your ``$HOME``

directory, add ``$HOME/dockonsurf`` to your ``PATH`` variable by typing: ::

    PATH="$PATH:$HOME/dockonsurf/"

If you downloaded it elsewhere, replace ``$HOME`` for the actual path where your DockOnSurf is 

(where you did the ``git clone`` command).

If you want to permanently add the DockOnSurf directory in your ``PATH`` add 

``PATH="$PATH:$HOME/dockonsurf/"`` at the end of your ``$HOME/.bashrc`` file.

DockOnSurf needs the python libraries listed under **Requirements** to be installed 

and available. The easiest way to do this is with the ``conda`` package and environment 

manager (see https://docs.conda.io/en/latest/). You can alternatively install 

them using pip except from RDKit, which is not available as its core routines are 

written in C.

Requirements

^^^^^^^^^^^^

* `Python <http://www.python.org/>`_ >= 3.6

* `Matplotlib <https://matplotlib.org>`_ ~= 3.2.1

* `NumPy <http://docs.scipy.org/doc/numpy/reference/>`_ >= 1.16.6

* `RDKit <https://rdkit.org/>`_ ~= 2019.9.3

* `scikit-learn <https://scikit-learn.org/>`_ ~= 0.23.1

* `HDBSCAN <https://hdbscan.readthedocs.io/en/latest/basic_hdbscan.html>`_ ~= 0.8.26

* `ASE <https://wiki.fysik.dtu.dk/ase/>`_ ~= 3.19.1

* `NetworkX <https://networkx.org/>`_ >= 2.4

* `python-daemon <https://pypi.org/project/python-daemon/>`_ ~= 2.2.4

* `pymatgen <https://pymatgen.org/>`_ ~= 2020.11.11

* `pycp2k <https://github.com/SINGROUP/pycp2k>`_ ~= 0.2.2

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