Overview

BioMol is a molecular data engine that brings PyMOL-like selections and NumPy-style operations into Python. It enables seamless navigation between atoms, residues, and chains, while providing efficient data structures for machine learning and large-scale analysis.

Key features

• Single Object Representation: Unified representation of molecular structures

• Flexible View: Navigate between atoms, residues, and chains easily

• Performance: Fast and memory-efficient data structures with NumPy-style operations

Core Philosophy

The core philosophy of BioMol is to provide a single object that can represent complex molecular structures with multiple levels of detail.

from biomol import BioMol

mol = BioMol(...)
mol.atoms  # Access atom-level data
mol.residues  # Access residue-level data
mol.chains  # Access chain-level

This unified approach allows users to handle molecular data more intuitively like PyMOL.

chain_a_atoms = mol.chains.select(id="A").atoms
chain_a_carbons = chain_a_atoms.select(element="C")
chain_a_non_carbons = chain_a_atoms - chain_a_carbons

Also, BioMol supports NumPy-style operations for efficient data manipulation.

chain_a_ca = chain_a_carbons[chain_a_carbons.name == "CA"]
first_five_ca = chain_a_ca[:5]

See also

BioMol

Dive deeper into the core concepts of BioMol, including Views and Features.