Setup and Installation¶
Dependencies¶
E3FP is compatible with Python 2.7.x and 3.x. It additionally has the following dependencies:
Installation¶
The following installation approaches are listed in order of recommendation. All but the first of these approaches requires a prior installation of RDKit.
Option 1: Install with Conda¶
E3FP is on the Anaconda distribution. Conda is a cross-platform package manager. This approach is highly recommended as it installs all required packages.
$ conda create -c keiserlab -c rdkit -c sdaxen --name e3fp_env e3fp
Warning
Due to a potential bug in some versions of conda, rdkit may not import on some systems. If this is the case, simply upgrade to the latest version of conda before creating the above environment:
conda update conda
To get the latest version of E3FP, follow Option 3: Clone the Repository.
Option 2: Install with Pip¶
Install with
$ pip install e3fp
To install the optional Python dependencies, run
$ pip install mpi4py futures standardiser h5py
Option 3: Clone the Repository¶
Install any of the optional dependencies above.
Note
- The easiest way to install the dependencies is with conda using Option 1 above.
If e3fp is also installed with conda, you will need to uninstall it before continuing below with
conda uninstall e3fp
Download this repository to your machine.
Clone this repository to your machine with
$ git clone https://github.com/keiserlab/e3fp.git
OR download an archive by navigating to the repository and clicking “Download ZIP”. Extract the archive.
Install with
$ cd e3fp $ python setup.py build_ext --inplace $ python setup.py install
Testing¶
After installation, it is recommended to run all tests with nose
,
$ pip install nose
$ nosetests e3fp