rhdm / e3fp

3D molecular fingerprints

E3FP: Extended 3-Dimensional FingerPrint

E3FP¹ is a 3D molecular fingerprinting method inspired by Extended Connectivity FingerPrints (ECFP)².

Table of Contents

• Dependencies
  • Required
  • Optional
• Setup and Installation
• Usage and Overview
• References

Dependencies

e3fp is compatible with Python 2.7.x and 3.6.x. It additionally has the following dependencies:

Required

• NumPy
• SciPy
• RDKit
• mmh3
• python_utilities

Optional

The following packages are required for the specified features:

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

Setup and Installation

The following installation approaches are listed in order of recommendation. Each of these approaches first requires an installation of RDKit.

Option 1: Install with Pip

1. Install with

pip install e3fp

2. To install the optional Python dependencies, run

pip install mpi4py futures standardiser h5py

Option 2: Clone the repository

0. Install any of the optional dependencies above.
1. 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 https://github.com/keiserlab/e3fp and clicking "Download ZIP". Extract the archive.
2. Install with

   cd e3fp
   python setup.py install

Testing

After installation, it is recommended to run all tests with nose,

pip install nose
nosetests e3fp

Usage and Overview

To use E3FP in a python script, enter:

import e3fp

See pipeline.py for methods for generating conformers and E3FP fingerprints from various inputs.

Run python e3fp/conformer/generate.py --help for options for generating conformers.

Run python e3fp/fingerprint/generate.py --help for options for generating E3FP fingerprints.

See defaults.cfg for an example params file.

See the E3FP paper repo for an application of E3FP and all code used for the E3FP paper¹.

References

1. Axen SD, Huang XP, Caceres EL, Gendelev L, Roth BL, Keiser MJ. A Simple Representation Of Three-Dimensional Molecular Structure. bioRxiv (2017). doi: 10.1101/136705. (preprint)
2. Rogers D & Hahn M. Extended-connectivity fingerprints. J. Chem. Inf. Model. 50, 742-54 (2010). doi: 10.1021/ci100050t