Datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults.
Install
npx skills add K-Dense-AI/scientific-agent-skills --skill datamol -g -a claude-code -y- Repository
- K-Dense-AI/scientific-agent-skills55.7k
- Category
- Media
- Updated
- 9d ago
- License
- Apache-2.0 license
- Context cost
- Mediumabout 2,542 tokens
- Runs scripts
- No, instructions only
What it does
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
Datamol Cheminformatics Skill
Overview
Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. Simplify complex molecular operations with sensible defaults, efficient parallelization, and modern I/O capabilities. All molecular objects are native rdkit.Chem.Mol instances, ensuring full compatibility with the RDKit ecosystem.
Verified target: datamol 0.13.0, released September 9, 2026. Local checks used Python 3.13 and RDKit 2026.03.6. Python 3.11+ and RDKit 2024.09+ are required. The 0.13 distribution includes SELFIES, visualization, cloud, Excel and Parquet runtime dependencies. Current API examples and verification limits are recorded in references/review.md. Pin the environment: RDKit upgrades can change canonical representations and retained conformers. Compare chemical invariants, not a fixed conformer count or an exact version-dependent canonical string.
Key capabilities:
- Molecular format conversion (SMILES, SELFIES, InChI)
- Structure standardization and sanitization
- Molecular descriptors and fingerprints
- 3D conformer generation and analysis
- Clustering and diversity selection
- Scaffold and fragment analysis
- Chemical reaction application
- Visualization and alignment
- Batch processing with parallelization
- Cloud storage support via fsspec
Installation and Setup
Guide users to install datamol:
uv pip install "datamol==0.13.0"
RDKit and the S3/GCS, Excel/Parquet, visualization and SELFIES dependencies are installed by the current distribution; separate feature extras are not required. Use an isolated environment to avoid conflicting scientific-package requirements.
Import convention:
import datamol as dm
Core Workflows
Ten workflow areas, each with worked code, are documented in references/core_workflows.md:
