Molecule Signature

Signature-based enumeration of molecules from morgan fingerprints.

Table of Contents

• Installation
  • From conda package
  • From source code
• Usage
  • Build a signature from SMILES
  • Build an alphabet from a set of SMILES
  • Enumerate molecules from a ECFP fingerprint
• Citation

Installation

From conda package

Installation using conda is the easiest way to get started. First, install Conda and then install the package from the conda-forge channel.

1. Install Conda: Download the installer for your operating system from the Conda Installation page. Follow the instructions on the page to install Conda. For example, on Windows, you would download the installer and run it. On macOS and Linux, you might use a command like:

   bash ~/Downloads/Miniconda3-latest-Linux-x86_64.sh

   Follow the prompts on the installer to complete the installation.

2. Install signature from conda-forge:

   conda install -c conda-forge signature

From source code

One can also install the tool from the source code. This method is useful for development purposes.

1. Install dependencies:

   conda env create -f environment.yml

2. Add the signature to conda:

   conda activate sig
   pip install -e .  # From the root of the repository

3. Add development dependencies:

   conda activate sig
   conda env update -n sig -f environment-dev.yml

Usage

Build a signature from SMILES

• From Python

  Below a simple example showing how to build a signature from a SMILES string. For more example, one can refer to the signature-basics notebook.

  from rdkit import Chem
  from molsig.Signature import MoleculeSignature
  
  mol = Chem.MolFromSmiles("CCO")
  mol_sig = MoleculeSignature(mol)
  mol_sig.to_list()
  # [
  #  '80-1410 ## [C;H3;h3;D1;X4]-[C;H2;h2;D2;X4:1]-[O;H1;h1;D1;X2]',
  #  '807-222 ## [C;H3;h3;D1;X4]-[C;H2;h2;D2;X4]-[O;H1;h1;D1;X2:1]',
  #  '1057-294 ## [O;H1;h1;D1;X2]-[C;H2;h2;D2;X4]-[C;H3;h3;D1;X4:1]'
  # ]

• From the command line

  Getting help:

  molsig signature --help

  Run:

  molsig signature
      --smiles <SMILES>
      --output <Output file, tsv>

Build an alphabet from a set of SMILES

• From Python

  Alphabet makes use of signatures to create a collection of morgan bits-to-atom signature mappings.

  See the creating-alphabet-basics notebook.

• From the command line

  Getting help:

  molsig alphabet --help

  Run:

  molsig alphabet
    --smiles <Input file, txt>
    --output <Output file, npz>

Enumerate molecules from a ECFP fingerprint

• From Python:

  See the enumeration-basics notebook.

• From the command line:

  Getting help:

  molsig enumerate --help

  Run:

  molsig enumerate
    --smiles <SMILES>
    --alphabet <Input alphabet file, npz>
    --output <Output file, tsv>

Citation

If you use this software, please cite it as below.

Meyer, P., Duigou, T., Gricourt, G., & Faulon, J.-L. Reverse Engineering Molecules from Fingerprints through Deterministic Enumeration and Generative Models. In preparation.