1. Installing the Library

Below are two currently available methods of installation.

Note

As of yet, the library is only available for the Linux platform and will only run on 64-bit systems. However, other platforms will probably be supported in the future as well.

1.1. Installation with Anaconda

This is probably the easiest and preferred way to install the library and the associated Python package. All you need to do is just either get the full Anaconda distribution or its lightweight variant, Miniconda.

Anaconda is essentially a Python distribution, package manager and virtual environment in one and makes setting up a development environment for your project very easy. After installing Anaconda/Miniconda all you need to do is to run the following in the terminal:

conda install -c lich molpher-lib

This will automatically download the latest version of the library and the corresponding Python package and install in the currently active environment (for more information on environments and the conda command see Conda Test Drive in the official documentation).

1.2. Building and Installing from source

If you are a developer and want to build the most recent version from source, you will need build everything from scratch. This section describes how to do that on the Linux platform and hints at possible problems one might encounter. If you want to build the library on a different platform, this section might provide useful information as well.

1.2.1. Prerequisites

Before you start building, there are a few prerequisites that need to be satisfied on your system:

  • build-essential – You will need this package to be able to build the software. It contains a compiler and other tools important for the build.
  • swig – Used to generate the Python wrapping code (at least version 3.0 or later).
  • bison and flex – Required by the rdkit toolkit.
  • setuptools and pip – If you want to use pip to install the Python package, you will need this to be installed in your Python distribution.
  • python{version}-dev – You will need this package in order to build the Python bindings for the particular Python version.

When those requirements are satisfied you can clone the source code from the repository:

git clone https://{username}@bitbucket.org/Krwemil/molpher-lib.git # (replace {username} with your Bitbucket username)

and start building.

Note

The repository is currently private and you will need the authorization of the author to access it.

1.2.2. Building Molpher and Its Dependencies

First, download the Molpher Dependency Bundle and extract the contents to a directory called deps/ of the repository root. This bundle contains all the source code and binaries of the dependencies that you will need to build and use the library on the Linux platform.

When it’s done, just run:

make CONF=Release_Linux_amd64

to build the release version of the library (no debugging symbols SWIG code is not generated) or:

make CONF=Debug_SWIG

to build the development version with debug symbols and the SWIG code regenerated.

If you want to build the conda packages as well you can use the following python script in the repository root:

python build_conda.py

Attention

You will need the jinja2 Python library to do that.

You can then install the packages by running:

conda install --use-local molpher-lib

You can also install the Python package directly with pip:

pip install .

in the repository root. This will install the Python package to the currently active Python distribution and links the compiled extension against the compiled library in the lib/ directory generated previously by make.