Python Bindings

molex provides Python bindings via PyO3, enabled with the python feature flag. The module is built with maturin.

Installation

cd crates/molex
maturin develop --release --features python

Core functions

pdb_to_coords(pdb_string) → bytes

Parse a PDB string and return COORDS01 binary bytes.

mmcif_to_coords(cif_string) → bytes

Parse an mmCIF string and return COORDS01 binary bytes.

coords_to_pdb(coords_bytes) → str

Convert COORDS01 bytes back to a PDB-format string.

deserialize_coords(coords_bytes) → dict

Deserialize COORDS01 bytes into a Python dictionary with NumPy arrays:

result = molex.deserialize_coords(coords_bytes)
# result["num_atoms"]: int
# result["x"], result["y"], result["z"]: np.ndarray[f32]

AtomWorks adapters

For ML model pipelines that use Biotite AtomArray objects:

entities_to_atom_array(assembly_bytes) → AtomArray

Convert ASSEM01 bytes to a Biotite AtomArray with standard and AtomWorks-specific annotations (entity_id, mol_type, chain_type).

entities_to_atom_array_plus(assembly_bytes) → AtomArray

Like entities_to_atom_array but also populates bonds via distance inference.

atom_array_to_entities(atom_array) → bytes

Convert a Biotite AtomArray back to ASSEM01 bytes.

entities_to_atom_array_parsed(assembly_bytes, filename) → AtomArray

Convert via the full AtomWorks cleaning pipeline (leaving group removal, charge correction, missing atom imputation).

parse_file_to_entities(path) → bytes

Parse a structure file (PDB/mmCIF) directly to ASSEM01 bytes.

parse_file_full(path) → AtomArray

Parse a structure file through the full AtomWorks pipeline.

coords_to_atom_array(coords_bytes) → AtomArray

Convert single-molecule COORDS01 bytes to AtomArray.

coords_to_atom_array_plus(coords_bytes) → AtomArray

Like coords_to_atom_array with bond inference.

atom_array_to_coords(atom_array) → bytes

Convert AtomArray to single-molecule COORDS01 bytes.