Setup and Installation¶

Dependencies¶

E3FP is compatible with Python 2.7.x and 3.x. It additionally has the following dependencies:

Required¶

Optional¶

The following packages are required for the specified features:

parallelization:
- mpi4py
- futures
molecular standardisation:
- standardiser
protonation states:
- cxcalc
storing conformer energies:
- h5py

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