Merge pull request #17 from martimunicoy/docs

Documentation development

docs/charge.rst

@@ -0,0 +1,20 @@
+.. _charge ::
+
+Charge methods
+==============
+
+This module provides different methods to calculate partial charges
+for PELE.
+
+.. currentmodule:: offpele.charge
+
+Primary objects
+---------------
+
+.. autosummary::
+    :nosignatures:
+    :toctree: api/autogenerated
+    :template: class.rst
+
+    Am1bccCalculator
+    GasteigerCalculator

docs/index.rst

@@ -13,6 +13,7 @@ User guide
   :maxdepth: 1
 
   installation
+  releasehistory
 
 
 API documentation
@@ -24,3 +25,4 @@ API documentation
   topology
   template
   solvent
+  charge

docs/installation.rst

@@ -3,11 +3,81 @@
 Installation
 ************
 
-Installing via PyPI
-===================
+Installing via `conda`
+======================
+The more straightforward way to install `offpele` along with the required
+dependencies is through the `conda <http://www.continuum.io/blog/conda>`_
+package manager.
 
-It can be easily install through PyPI with the following command:
+First, you need to install the
+`miniconda <http://conda.pydata.org/miniconda.html>`_ distribution, which is
+the minimal installation of the Anaconda Python package.
+
+To install the Python 3 version on ``linux`` (on ``bash`` systems):
+
+.. code-block:: bash
+
+   $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+   $ bash ./Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3
+
+It can also be installed on ``osx`` with:
+
+.. code-block:: bash
+
+   $ curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O
+   $ bash ./Miniconda3-latest-MacOSX-x86_64.sh -b -p $HOME/miniconda3
+
+Once installed, the bases environment of `conda` can be loaded with
+the following commands:
+
+.. code-block:: bash
+
+   $ source ~/miniconda3/etc/profile.d/conda.sh
+   $ conda activate base
+
+You can also create a custom conda environment to handle offpele:
+
+.. code-block:: bash
+
+   $ conda create --name offpele_env
+
+which can be activated and deactivated with the two commands from below:
+
+.. code-block:: bash
+
+   $ conda activate offpele_env
+   $ conda deactivate
+
+To install de dependencies of offpele, the following `conda` channels need
+to be added and updated:
+
+.. code-block:: bash
+
+   $ conda config --add channels omnia --add channels conda-forge --add channels martimunicoy
+   $ conda update --all
+
+Finally, you can install the latest stable build of `offpele`
+
+.. code-block:: bash
+
+   $ conda install offpele
+
+
+Installing via `PyPI`
+=====================
+
+`offpele` can also be installed through `PyPI <https://pypi.org>`_
+with the following command:
 
 .. code-block:: bash
 
    $ pip install offpele
+
+However, with `PyPI` some of the required dependencies of `offpele` are not
+installed and have to be installed manually such as:
+
+- Open Force Field Toolkit
+- RDKit
+- AmberTools
+
+For this reason, the installation through `conda` is recommended.