biomol.core.IndexTable

class IndexTable(atom_to_res, res_to_chain, res_atom_indptr, res_atom_indices, chain_res_indptr, chain_res_indices)

Bases: object

Index mapping between structural levels.

This class stores forward parent mappings and reverse CSR mappings to efficiently move between atoms, residues, and chains.

Parameters:

• atom_to_res (NDArray[np.integer]) – 1D array mapping each atom index to its parent residue index.

• res_to_chain (NDArray[np.integer]) – 1D array mapping each residue index to its parent chain index.

• res_atom_indptr (NDArray[np.integer]) – CSR index pointer array for residues to atoms mapping.

• res_atom_indices (NDArray[np.integer]) – CSR indices array for residues to atoms mapping.

• chain_res_indptr (NDArray[np.integer]) – CSR index pointer array for chains to residues mapping.

• chain_res_indices (NDArray[np.integer]) – CSR indices array for chains to residues mapping.

Examples

>>> table = IndexTable.from_parents(
...     atom_to_res=np.array([0, 0, 1, 1, 2]),
...     res_to_chain=np.array([0, 0, 1]),
... )

>>> table.atoms_to_residues(np.array([0, 2, 4]))
array([0, 1, 2])

>>> table.residues_to_chains(np.array([0, 2]))
array([0, 1])

>>> table.chains_to_residues(np.array([0, 1]))
array([0, 1, 2])

Attributes

atom_to_res	1D array mapping each atom index to its parent residue index.
res_to_chain	1D array mapping each residue index to its parent chain index.
res_atom_indptr	CSR index pointer array for residues to atoms mapping.
res_atom_indices	CSR indices array for residues to atoms mapping.
chain_res_indptr	CSR index pointer array for chains to residues mapping.
chain_res_indices	CSR indices array for chains to residues mapping.

Methods

atoms_to_chains	Map atom indices to chain indices.
atoms_to_residues	Map atom indices to residue indices.
chains_to_atoms	Map chain indices to concatenated atom indices.
chains_to_residues	Map chain indices to concatenated residue indices.
convert	Convert indices between structural levels.
copy	Create a deep copy of the IndexTable.
from_dict	Create IndexTable from a dictionary.
from_parents	Create IndexTable from forward parent mappings.
residues_to_atoms	Map residue indices to concatenated atom indices.
residues_to_chains	Map residue indices to chain indices.
to_dict	Convert IndexTable to a JSON-serializable dictionary.