E3FP is compatible with Python 3.x. It additionally has the following dependencies:
The following packages are required for the specified features:
- parallelization:
- molecular standardisation:
- protonation states:
- storing conformer energies:
The following installation approaches are listed in order of recommendation. All but the first of these approaches requires a prior installation of RDKit.
E3FP is on the Anaconda distribution. Conda is a cross-platform package manager. This approach is highly recommended as it installs all required packages.
Install with
$ conda create -c conda-forge --name e3fp_env e3fp $ conda activate e3fp_env
To install the optional Python dependencies, run
$ conda install -c conda-forge mpi4py h5py standardiser
To get the latest version of E3FP, follow Option 3: Clone the Repository
.
Install with
$ pip install e3fp
To install the optional Python dependencies, run
$ pip install mpi4py h5py standardiser
- Download this repository to your machine.
Clone this repository to your machine with
$ git clone https://github.com/keiserlab/e3fp.git $ cd e3fp
- OR download an archive by navigating to the repository and clicking "Download ZIP". Extract the archive.
- Install the optional dependencies and any required ones using pip or conda.
Note
The easiest way to install the dependencies is with
$ conda env create --name e3fp_env --file environment.yml $ conda activate e3fp_env
Install with
$ python setup.py build_ext --inplace $ python setup.py install
After installation, it is recommended to run all tests with pytest
. After running pip install pytest
or conda install -c conda-forge pytest
, run
$ pytest e3fp