Toolomics

Pure Python geospatial computation without geopandas or shapely. Provides algorithms for point-in-polygon, distance calculations, GeoJSON reading, spatial joins, and buffer analysis using only numpy, pandas, math, and built-in modules.

Comprehensive guide to molecular networking analysis using the matchms Python library for mass spectrometry data

Covalent molecular docking for irreversible inhibitor design. Dock ligands with warheads to protein reactive residues (Cys, SeCys, Lys, Ser, Tyr). Multi-seed reproducibility assessment, contact analysis, de novo design workflows.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.