Expand description
Molecule data structures for computational chemistry and drug discovery.
Where bio_files provides format-level types for reading and writing molecular files, this
library provides the application-level types those are loaded into: ones carrying inferred
properties, topology, and conformational data.
These types are shared between Molchanica and its ADME inference library; they live here so neither has to depend on the other.
The render feature adds surface-mesh generation, and the mesh and electron-density fields used
to draw molecules. It pulls in a GPU stack, so leave it off for headless use such as ML inference.
Modules§
- bond_
inference - mol_
components - Represents small organic molecules by breaking them down into components.
Components correspond to chemically meaningful subgraphs (functional groups, ring clusters,
chains), and are connected by
Connections that mirror the actual bonds that cross component boundaries. - molecules
- properties
- Properties inferred from a molecule’s structure.
- reflection
- Data types for electron density, as measured by crystallography and Cryo-EM reflection data.
- screening
- Types used when screening small molecules against a target.
- serialization
- Binary serialization of
MoleculeSmall. - sfc_
mesh - For calculating the accessible surface (AS), a proxy for accessibility of solvents to a molecule. Used for drawing surface, dots, and related meshes. Related to the van der Waals radius.
- smiles
- Convert between molecules and SMILES text todo: Consider moving this to bio_files. Although geometry considerations may be a better suit for here.
- tautomers
- For identifying Tautomers
- util
- Misc.
Macros§
- copy_le
- Write a primitive into a byte slice as little-endian. Used by our custom binary formats.
- parse_
le - Read a little-endian primitive out of a byte slice. Used by our custom binary formats.
Type Aliases§
- Color
- RGB, each channel in the range 0.0 to 1.0.