Role system for Python3

decorators roles python3 role role-library role-api python-class python-metaclasses

• Updated Aug 28, 2021
• Python

A package to identify matched molecular pairs and use them to predict property changes.

entity-graph status-active role-library lang-python interface-cli role-application domain-cheminformatics task-structure-analysis method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery task-featurization ecosystem-rdkit

• Updated Jun 3, 2026
• Python

This repository contains code for the paper: Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules using SELFIES

entity-graph role-library lang-python status-archived domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api interface-jupyter status-published scope-focused domain-drug-discovery task-featurization task-molecular-generation

• Updated Aug 13, 2024
• Jupyter Notebook

Molsystem provides a general class for handling molecular and periodic systems

status-active role-library lang-python domain-cheminformatics method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi scope-focused method-physics domain-molecular-simulation task-system-model entity-crystal

• Updated Jun 30, 2026
• Python

Python wrapper for the PubChem PUG REST API.

status-active role-library lang-python domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery

• Updated Sep 8, 2025
• Python

Working with molecular structures in pandas DataFrames

status-active role-library lang-python domain-structural-biology domain-cheminformatics task-file-io task-structure-analysis method-chemoinformatics entity-protein entity-small-molecule interface-api interface-jupyter status-published status-packaged-pypi status-packaged-conda scope-focused

• Updated May 22, 2026
• Python

Generate Simple Pharmacophore Models with RDKit

status-active role-library lang-python domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api interface-jupyter status-packaged-pypi scope-focused domain-drug-discovery ecosystem-rdkit task-pharmacophore

• Updated Mar 10, 2026
• Jupyter Notebook

Contact map analysis for biomolecules; based on MDTraj

status-active role-library lang-python domain-structural-biology entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused entity-complex domain-molecular-simulation task-trajectory-analysis entity-trajectory method-rule-based task-interaction-analysis

• Updated May 9, 2026
• Python

BINANA (BINding ANAlyzer) analyzes the geometries of predicted ligand poses to identify molecular interactions that contribute to binding. It is useful because accurately characterizing these interactions allows medicinal chemists to assess whether a predicted ligand merits further study. We have also created a BINANA web-browser application.

status-active role-library lang-python lang-typescript interface-web interface-cli domain-structural-biology entity-protein entity-small-molecule interface-api status-published scope-focused domain-drug-discovery entity-complex method-rule-based task-interaction-analysis

• Updated Jun 30, 2025
• Jupyter Notebook

Python interface of cpptraj

status-active role-library lang-python lang-cpp task-file-io entity-protein interface-api status-published status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

• Updated Mar 6, 2026
• Jupyter Notebook

An automated framework for generating optimized partial charges for molecules

status-active role-library lang-python interface-cli domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics domain-molecular-simulation task-parameterization ecosystem-openff task-charge-assignment

• Updated Jul 6, 2026
• Python

a molecular descriptor calculator

entity-graph role-library lang-python status-archived interface-cli domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused task-featurization ecosystem-rdkit

• Updated Feb 7, 2024
• Python

pythonic interface to virtual screening software

status-active role-library lang-python interface-cli task-workflow role-application domain-cheminformatics method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery task-docking method-physics entity-complex

• Updated Sep 4, 2025
• Python

Annotated data.

status-active role-library lang-python domain-bioinformatics task-file-io interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-statistics task-system-model domain-single-cell entity-multi-omics ecosystem-scverse

• Updated Jul 29, 2026
• Python

Interface for AutoDock, molecule parameterization

status-active role-library lang-python interface-cli domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery task-docking entity-complex method-rule-based task-ligand-prep ecosystem-autodock task-parameterization ecosystem-rdkit

• Updated Jul 10, 2026
• Python

Robust representation of semantically constrained graphs, in particular for molecules in chemistry

entity-graph status-active role-library lang-python domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery task-featurization task-molecular-generation

• Updated May 17, 2025
• Python

Standalone charge assignment from Espaloma framework.

entity-graph status-active role-library lang-python interface-cli method-deep-learning domain-cheminformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-molecular-simulation task-charge-assignment method-geometric-learning

• Updated Oct 10, 2025
• Python

molfeat - the hub for all your molecular featurizers

entity-graph status-active role-library lang-python method-deep-learning domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery method-machine-learning task-featurization ecosystem-rdkit

• Updated May 27, 2025
• Python

MoleculeKit: Your favorite molecule manipulation kit

status-active role-library lang-python domain-structural-biology task-file-io method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-molecular-simulation task-system-model

• Updated Jul 29, 2026
• Python

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

status-active role-library lang-python lang-c domain-bioinformatics task-file-io method-chemoinformatics interface-api status-published status-packaged-pypi status-packaged-conda scope-focused entity-nucleic-acid entity-sequence domain-genomics

• Updated Jul 19, 2026
• Cython