biochem

Cheminformatics and structural biology tools for BioChemAIgent and Drug Discovery Platform.

Install

micromamba env create -f environment.yml -y
micromamba env create -f environment.yml -y --prefix ~/env/bcai
pip install -e .

Key tools

• render_structures — render PDB/CIF/SDF/MOL2 files to interactive 3D HTML (py3Dmol). Exposes style_rules, surface_rules, label_rules, chain_color_map, interaction_tables, box constraint overlay.
• get_protein_ligand_interaction / interaction_plot — compute and visualise protein-ligand interaction networks.
• run_af3 / run_esm3 — AlphaFold3 and ESM3 structure prediction.
• molecular_docking tools — protein/ligand preparation, VINA/SMINA/GNINA/DiffDock docking.
• protein_ligand_basics — SMILES→3D, protonation, PDB extraction, ADMET prediction.

Notes

• render_structures.style_rules and surface_rules use TypedDict (StyleRule, SurfaceRule) so FastMCP generates a schema with named properties. This is required for LLMs to correctly populate nested selection/style dicts — bare Dict[str, Any] causes models to emit empty {} objects.
• Cartoon style without an explicit color renders white on the default white background. Always include "color": "spectrum" or another colour when specifying cartoon style rules.

License

This software is licensed under the GNU Affero General Public License v3.0 (AGPL-3.0).

You are free to use, modify, and distribute this software for non-commercial purposes, provided that any derivative works are also licensed under AGPL-3.0 and made publicly available.

Commercial use — including use in proprietary pipelines, SaaS products, or any revenue-generating activity — requires a separate commercial license. Contact: yousefi.bme@gmail.com, sbonn@uke.de

SPDX-License-Identifier: AGPL-3.0-only