Molecule definitions

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This library contains the molecule data structures used by Molchanica and its ADME inference library. bio_files provides simpler types for reading and writing molecular files; this one contains detailed ones with application-specific data.

Its fundamental types are Atom, Bond, Residue, and Chain. Built atop these are the molecule types: MoleculeSmall for small organics, MoleculePeptide for proteins, plus MoleculeNucleicAcid, MoleculeLipid, and Pocket. Each holds a MoleculeCommon, which carries the atoms, bonds, adjacency list, and identifiers shared by all of them.

It also includes derived characterizations of a molecule, which are the inputs to property inference:

• MolCharacterization — rings, functional groups, rotatable bonds, and molecular descriptors
• MolComponents — a decomposition of a molecule into chemically meaningful components and their connections
• Conformer — a sampled conformational ensemble, with per-atom motion statistics
• Pharmacophore — H-bond donors and acceptors, hydrophobic sites, and ring centres in 3D

See the docs for details on the data structures and functions available.

Features

• render — surface-mesh generation, and the mesh and electron-density fields used to draw molecules. Pulls in a GPU stack; leave it off for headless use such as ML inference.