{"id":37610880,"url":"https://github.com/brsynth/molecule-signature","last_synced_at":"2026-01-16T10:20:39.830Z","repository":{"id":273900911,"uuid":"718567935","full_name":"brsynth/molecule-signature","owner":"brsynth","description":"Signature based molecule enumeration from morgan fingerprints","archived":false,"fork":false,"pushed_at":"2025-06-17T12:29:15.000Z","size":41718,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-12-14T12:59:57.709Z","etag":null,"topics":["chemoinformatics","fingerprint","generative-ai","synthetic-biology"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/brsynth.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-11-14T10:59:24.000Z","updated_at":"2025-06-17T12:18:29.000Z","dependencies_parsed_at":"2025-01-23T17:22:59.025Z","dependency_job_id":"f6b7eed3-6275-4e83-b96a-36a94bbb8094","html_url":"https://github.com/brsynth/molecule-signature","commit_stats":null,"previous_names":["brsynth/signature","brsynth/molecule-signature"],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/brsynth/molecule-signature","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Fmolecule-signature","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Fmolecule-signature/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Fmolecule-signature/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Fmolecule-signature/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brsynth","download_url":"https://codeload.github.com/brsynth/molecule-signature/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Fmolecule-signature/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478049,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["chemoinformatics","fingerprint","generative-ai","synthetic-biology"],"created_at":"2026-01-16T10:20:39.284Z","updated_at":"2026-01-16T10:20:39.818Z","avatar_url":"https://github.com/brsynth.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Molecule Signature\n\n[![Github Version](https://img.shields.io/github/v/release/brsynth/molecule-signature?display_name=tag\u0026sort=semver\u0026logo=github)](version)\n[![Github Licence](https://img.shields.io/github/license/brsynth/molecule-signature?logo=github)](LICENSE.md)\n[![Coveralls](https://img.shields.io/coverallsCoverage/github/brsynth/molecule-signature?logo=coveralls\u0026color=green)](https://coveralls.io/github/brsynth/molecule-signature)\n[![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/molecule-signature?logo=condaforge\u0026color=green)](https://anaconda.org/conda-forge/molecule-signature)\n\nSignature-based enumeration of molecules from morgan fingerprints.\n\n## Table of Contents\n\n- [Installation](#installation)\n  - [From conda package](#from-conda-package)\n  - [From source code](#from-source-code)\n- [Usage](#usage)\n  - [Build a signature from SMILES](#build-a-signature-from-smiles)\n  - [Build an alphabet from a set of SMILES](#build-an-alphabet-from-a-set-of-smiles)\n  - [Enumerate molecules from a ECFP fingerprint](#enumerate-molecules-from-a-ecfp-fingerprint)\n- [Citation](#citation)\n\n## Installation\n\n### From conda package\n\nInstallation using conda is the easiest way to get started. First, install Conda\nand then install the package from the conda-forge channel.\n\n1. **Install Conda:**\n   Download the installer for your operating system from the [Conda Installation\n   page](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html).\n   Follow the instructions on the page to install Conda. For example, on\n   Windows, you would download the installer and run it. On macOS and Linux, you\n   might use a command like:\n\n    ```bash\n    bash ~/Downloads/Miniconda3-latest-Linux-x86_64.sh\n    ```\n\n    Follow the prompts on the installer to complete the installation.\n\n2. **Install signature from conda-forge:**\n\n    ```bash\n    conda install -c conda-forge signature\n    ```\n\n### From source code\n\nOne can also install the tool from the source code. This method is useful for\ndevelopment purposes.\n\n1. **Install dependencies:**\n\n    ```bash\n    conda env create -f environment.yml\n    ```\n\n2. **Add the signature to conda:**\n\n    ```bash\n    conda activate sig\n    pip install -e .  # From the root of the repository\n    ```\n\n3. **Add development dependencies:**\n\n    ```bash\n    conda activate sig\n    conda env update -n sig -f environment-dev.yml\n    ```\n\n## Usage\n\n### Build a signature from SMILES\n\n- **From Python**\n\n    Below a simple example showing how to build a signature from a SMILES string. For\n    more example, one can refer to the [signature-basics](notebooks/signature-basics.ipynb) notebook.\n\n    ```python\n    from rdkit import Chem\n    from molsig.Signature import MoleculeSignature\n\n    mol = Chem.MolFromSmiles(\"CCO\")\n    mol_sig = MoleculeSignature(mol)\n    mol_sig.to_list()\n    # [\n    #  '80-1410 ## [C;H3;h3;D1;X4]-[C;H2;h2;D2;X4:1]-[O;H1;h1;D1;X2]',\n    #  '807-222 ## [C;H3;h3;D1;X4]-[C;H2;h2;D2;X4]-[O;H1;h1;D1;X2:1]',\n    #  '1057-294 ## [O;H1;h1;D1;X2]-[C;H2;h2;D2;X4]-[C;H3;h3;D1;X4:1]'\n    # ]\n    ```\n\n- **From the command line**\n\n    Getting help:\n\n    ```sh\n    molsig signature --help\n    ```\n\n    Run:\n\n    ```sh\n    molsig signature\n        --smiles \u003cSMILES\u003e\n        --output \u003cOutput file, tsv\u003e\n    ```\n\n### Build an alphabet from a set of SMILES\n\n- **From Python**\n\n    Alphabet makes use of signatures to create a collection of *morgan bits*-to-*atom signature* mappings.\n\n    See the [creating-alphabet-basics](notebooks/creating-alphabet-basics.ipynb) notebook.\n\n- **From the command line**\n\n    Getting help:\n\n    ```sh\n    molsig alphabet --help\n    ```\n\n    Run:\n\n    ```sh\n    molsig alphabet\n      --smiles \u003cInput file, txt\u003e\n      --output \u003cOutput file, npz\u003e\n    ```\n\n### Enumerate molecules from a ECFP fingerprint\n\n- **From Python**:\n\n    See the [enumeration-basics](notebooks/enumeration-basics.ipynb) notebook.\n\n- **From the command line**:\n\n    Getting help:\n\n    ```sh\n    molsig enumerate --help\n    ```\n\n    Run:\n\n    ```sh\n    molsig enumerate\n      --smiles \u003cSMILES\u003e\n      --alphabet \u003cInput alphabet file, npz\u003e\n      --output \u003cOutput file, tsv\u003e\n    ```\n\n## Citation\n\nIf you use this software, please cite it as below.\n\n\u003e Meyer, P., Duigou, T., Gricourt, G., Faulon, J. L. (2025). Reverse engineering molecules from fingerprints through deterministic enumeration and generative models. Journal of Cheminformatics, 17(1), 157. https://doi.org/10.1186/s13321-025-01074-5\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Fmolecule-signature","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrsynth%2Fmolecule-signature","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Fmolecule-signature/lists"}