biotite

What problem does it solve?

Biotite provides a fast, NumPy-backed toolkit to read, manipulate, analyze, and fetch biomolecular structures and sequences, serving as the connective tissue between design predictors, structure analysis tools, and data sources.

Core Features & Use Cases

• Read/write PDB/mmCIF/BinaryCIF structures and trajectories; convert between AtomArray and AtomArrayStack; fetch data from sources such as RCSB PDB, AlphaFold DB, UniProt, NCBI Entrez, and PubChem.
• Structural analysis and transformation: RMSD, TM-score, lDDT, SASA, hydrogen bonds, secondary structure, and alignment of designs with predictions.
• Interoperability: thin wrappers and bridges to external tools (RDKit, OpenMM, PyMOL) to prepare inputs, refine models, and automate pipelines.
• Use case: design-validation workflows that combine predictor outputs with structural analyses to rank survivors.

Quick Start

Install Biotite and run a quick check: fetch a PDB by its id, load it, and compute a simple RMSD against a rotated copy.