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from collections.abc import Sequence
import numpy as np
from flax_model.alphafold3.cpp import cif_dict
from flax_model.alphafold3.structure.python import mmcif_layout
def filter(
mmcif: cif_dict.CifDict,
include_nucleotides: bool,
include_ligands: bool = ...,
include_water: bool = ...,
include_other: bool = ...,
model_id: str = ...,
) -> tuple[np.ndarray[int], mmcif_layout.MmcifLayout]: ...
def fix_residues(
layout: mmcif_layout.MmcifLayout,
comp_id: Sequence[str],
atom_id: Sequence[str],
atom_x: Sequence[float],
atom_y: Sequence[float],
atom_z: Sequence[float],
fix_arg: bool = ...,
) -> None: ...
def read_layout(
mmcif: cif_dict.CifDict, model_id: str = ...
) -> mmcif_layout.MmcifLayout: ...
def selected_ligand_residue_mask(
layout: mmcif_layout.MmcifLayout,
atom_site_label_asym_ids: list[str],
atom_site_label_seq_ids: list[str],
atom_site_auth_seq_ids: list[str],
atom_site_label_comp_ids: list[str],
atom_site_pdbx_pdb_ins_codes: list[str],
nonpoly_asym_ids: list[str],
nonpoly_auth_seq_ids: list[str],
nonpoly_pdb_ins_codes: list[str],
nonpoly_mon_ids: list[str],
branch_asym_ids: list[str],
branch_auth_seq_ids: list[str],
branch_pdb_ins_codes: list[str],
branch_mon_ids: list[str],
) -> tuple[list[bool], list[bool]]: ...
def selected_polymer_residue_mask(
layout: mmcif_layout.MmcifLayout,
atom_site_label_asym_ids: list[str],
atom_site_label_seq_ids: list[str],
atom_site_label_comp_ids: list[str],
poly_seq_asym_ids: list[str],
poly_seq_seq_ids: list[str],
poly_seq_mon_ids: list[str],
) -> list[bool]: ...
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