molecule-signature

Signature based molecule enumeration from morgan fingerprints

https://github.com/brsynth/molecule-signature

Science Score: 44.0%

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Low similarity (13.2%) to scientific vocabulary

Keywords

chemoinformatics fingerprint generative-ai synthetic-biology

Last synced: 6 months ago · JSON representation ·

Repository

Signature based molecule enumeration from morgan fingerprints

Basic Info

Host: GitHub
Owner: brsynth
License: mit
Language: Python
Default Branch: main
Homepage:
Size: 39.8 MB

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Forks: 0
Open Issues: 0
Releases: 4

Topics

chemoinformatics fingerprint generative-ai synthetic-biology

Created over 2 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog License Citation

README.md

Molecule Signature

Signature-based enumeration of molecules from morgan fingerprints.

Installation
- From conda package
- From source code
Usage
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.

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

Follow the prompts on the installer to complete the installation.
Install signature from conda-forge:

bash 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.

Install dependencies:

bash conda env create -f environment.yml
Add the signature to conda:

bash conda activate sig pip install -e . # From the root of the repository
Add development dependencies:

bash 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.

```python from rdkit import Chem from molsig.Signature import MoleculeSignature

mol = Chem.MolFromSmiles("CCO") molsig = MoleculeSignature(mol) molsig.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:

sh molsig signature --help

Run:

sh 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:

sh molsig alphabet --help

Run:

sh 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:

sh molsig enumerate --help

Run:

sh 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.

Owner

Name: BioRetroSynth
Login: brsynth
Kind: organization

Website: http://www.jfaulon.com
Repositories: 33
Profile: https://github.com/brsynth

Our group is interested in synthetic biology and systems metabolic engineering in whole-cell and cell-free systems.

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite it as below.
authors:
  - family-names: "Meyer"
    given-names: "Philippe"
    orcid: "https://orcid.org/0000-0002-0618-2947"
  - family-names: "Duigou"
    given-names: "Thomas"
    orcid: "https://orcid.org/0000-0002-2649-2950"
  - family-names: "Gricourt"
    given-names: "Guillaume"
    orcid: "https://orcid.org/0000-0003-0143-5535"
  - family-names: "Faulon"
    given-names: "Jean-Loup"
    orcid: "https://orcid.org/0000-0003-4274-2953"
title: "The Molecule Signature package: Signature-based enumeration of molecules from morgan fingerprints."
version: 2.0.1
doi: TO DEFINE
date-released: 2025-01-30
url: "https://github.com/brsynth/molecule-signature"
preferred-citation:
  type: article
  authors:
  - family-names: "Meyer"
    given-names: "Philippe"
    orcid: "https://orcid.org/0000-0002-0618-2947"
  - family-names: "Duigou"
    given-names: "Thomas"
    orcid: "https://orcid.org/0000-0002-2649-2950"
  - family-names: "Gricourt"
    given-names: "Guillaume"
    orcid: "https://orcid.org/0000-0003-0143-5535"
  - family-names: "Faulon"
    given-names: "Jean-Loup"
    orcid: "https://orcid.org/0000-0003-4274-2953"
  doi:
  journal: in preparation
  month:
  start:
  end:
  title: "Reverse Engineering Molecules from Fingerprints through Deterministic Enumeration and Generative Models."
  issue:
  volume:
  year:

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