| """Minimal biological constants required by the local Boltz2 runtime. |
| |
| The upstream project contains additional training-time curation tables. They |
| are intentionally excluded here because FastPLMs neither trains Boltz2 nor |
| uses upstream data-processing code. Keeping only runtime inputs makes this |
| module auditable and prevents parity-oracle data from becoming a package |
| dependency. |
| """ |
|
|
| from __future__ import annotations |
|
|
|
|
| def _index(values: list[str]) -> dict[str, int]: |
| return {value: index for index, value in enumerate(values)} |
|
|
|
|
| chain_types = ["PROTEIN", "DNA", "RNA", "NONPOLYMER"] |
| chain_type_ids = _index(chain_types) |
|
|
|
|
| canonical_tokens = [ |
| "ALA", |
| "ARG", |
| "ASN", |
| "ASP", |
| "CYS", |
| "GLN", |
| "GLU", |
| "GLY", |
| "HIS", |
| "ILE", |
| "LEU", |
| "LYS", |
| "MET", |
| "PHE", |
| "PRO", |
| "SER", |
| "THR", |
| "TRP", |
| "TYR", |
| "VAL", |
| "UNK", |
| ] |
| tokens = [ |
| "<pad>", |
| "-", |
| *canonical_tokens, |
| "A", |
| "G", |
| "C", |
| "U", |
| "N", |
| "DA", |
| "DG", |
| "DC", |
| "DT", |
| "DN", |
| ] |
| token_ids = _index(tokens) |
| num_tokens = len(tokens) |
|
|
| prot_letter_to_token = dict( |
| zip( |
| "ARNDCEQGHILKMFPSTWYV", |
| [ |
| "ALA", |
| "ARG", |
| "ASN", |
| "ASP", |
| "CYS", |
| "GLU", |
| "GLN", |
| "GLY", |
| "HIS", |
| "ILE", |
| "LEU", |
| "LYS", |
| "MET", |
| "PHE", |
| "PRO", |
| "SER", |
| "THR", |
| "TRP", |
| "TYR", |
| "VAL", |
| ], |
| strict=True, |
| ) |
| ) |
| prot_letter_to_token.update({letter: "UNK" for letter in "XJBZOU"} | {"-": "-"}) |
|
|
|
|
| def _parse_atom_rows(rows: str) -> dict[str, list[str]]: |
| table: dict[str, list[str]] = {} |
| for row in rows.strip().splitlines(): |
| residue, *atom_names = row.split() |
| table[residue] = atom_names |
| return table |
|
|
|
|
| ref_atoms = {"PAD": [], "-": []} |
| ref_atoms.update( |
| _parse_atom_rows( |
| """ |
| UNK N CA C O CB |
| ALA N CA C O CB |
| ARG N CA C O CB CG CD NE CZ NH1 NH2 |
| ASN N CA C O CB CG OD1 ND2 |
| ASP N CA C O CB CG OD1 OD2 |
| CYS N CA C O CB SG |
| GLN N CA C O CB CG CD OE1 NE2 |
| GLU N CA C O CB CG CD OE1 OE2 |
| GLY N CA C O |
| HIS N CA C O CB CG ND1 CD2 CE1 NE2 |
| ILE N CA C O CB CG1 CG2 CD1 |
| LEU N CA C O CB CG CD1 CD2 |
| LYS N CA C O CB CG CD CE NZ |
| MET N CA C O CB CG SD CE |
| PHE N CA C O CB CG CD1 CD2 CE1 CE2 CZ |
| PRO N CA C O CB CG CD |
| SER N CA C O CB OG |
| THR N CA C O CB OG1 CG2 |
| TRP N CA C O CB CG CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 |
| TYR N CA C O CB CG CD1 CD2 CE1 CE2 CZ OH |
| VAL N CA C O CB CG1 CG2 |
| """ |
| ) |
| ) |
|
|
| protein_backbone_atom_names = ["N", "CA", "C", "O"] |
| nucleic_backbone_atom_names = [ |
| "P", |
| "OP1", |
| "OP2", |
| "O5'", |
| "C5'", |
| "C4'", |
| "O4'", |
| "C3'", |
| "O3'", |
| "C2'", |
| "O2'", |
| "C1'", |
| ] |
| protein_backbone_atom_index = _index(protein_backbone_atom_names) |
| nucleic_backbone_atom_index = _index(nucleic_backbone_atom_names) |
|
|
| _rna_backbone = nucleic_backbone_atom_names |
| _dna_backbone = [atom for atom in _rna_backbone if atom != "O2'"] |
| ref_atoms.update( |
| { |
| "A": [*_rna_backbone, "N9", "C8", "N7", "C5", "C6", "N6", "N1", "C2", "N3", "C4"], |
| "G": [*_rna_backbone, "N9", "C8", "N7", "C5", "C6", "O6", "N1", "C2", "N2", "N3", "C4"], |
| "C": [*_rna_backbone, "N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6"], |
| "U": [*_rna_backbone, "N1", "C2", "O2", "N3", "C4", "O4", "C5", "C6"], |
| "N": list(_rna_backbone), |
| "DA": [*_dna_backbone, "N9", "C8", "N7", "C5", "C6", "N6", "N1", "C2", "N3", "C4"], |
| "DG": [*_dna_backbone, "N9", "C8", "N7", "C5", "C6", "O6", "N1", "C2", "N2", "N3", "C4"], |
| "DC": [*_dna_backbone, "N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6"], |
| "DT": [*_dna_backbone, "N1", "C2", "O2", "N3", "C4", "O4", "C5", "C7", "C6"], |
| "DN": list(_dna_backbone), |
| } |
| ) |
|
|
| _protein_tokens = ["UNK", *canonical_tokens[:-1]] |
| _nucleic_tokens = ["A", "G", "C", "U", "N", "DA", "DG", "DC", "DT", "DN"] |
| res_to_center_atom = { |
| **dict.fromkeys(_protein_tokens, "CA"), |
| **dict.fromkeys(_nucleic_tokens, "C1'"), |
| } |
| res_to_disto_atom = { |
| **dict.fromkeys(_protein_tokens, "CB"), |
| "GLY": "CA", |
| "A": "C4", |
| "G": "C4", |
| "C": "C2", |
| "U": "C2", |
| "N": "C1'", |
| "DA": "C4", |
| "DG": "C4", |
| "DC": "C2", |
| "DT": "C2", |
| "DN": "C1'", |
| } |
|
|
|
|
| num_elements = 128 |
| bond_types = ["OTHER", "SINGLE", "DOUBLE", "TRIPLE", "AROMATIC", "COVALENT"] |
| contact_conditioning_info = { |
| "UNSPECIFIED": 0, |
| "UNSELECTED": 1, |
| "POCKET>BINDER": 2, |
| "BINDER>POCKET": 3, |
| "CONTACT": 4, |
| } |
| chunk_size_threshold = 384 |
|
|
| _method_groups = { |
| 0: ("MD",), |
| 1: ("X-RAY DIFFRACTION",), |
| 2: ("ELECTRON MICROSCOPY",), |
| 3: ("SOLUTION NMR",), |
| 4: ( |
| "SOLID-STATE NMR", |
| "NEUTRON DIFFRACTION", |
| "ELECTRON CRYSTALLOGRAPHY", |
| "FIBER DIFFRACTION", |
| "POWDER DIFFRACTION", |
| "INFRARED SPECTROSCOPY", |
| "FLUORESCENCE TRANSFER", |
| "EPR", |
| "THEORETICAL MODEL", |
| "SOLUTION SCATTERING", |
| "OTHER", |
| ), |
| 5: ("AFDB",), |
| 6: ("BOLTZ-1",), |
| 7: ("FUTURE1",), |
| 8: ("FUTURE2",), |
| 9: ("FUTURE3",), |
| 10: ("FUTURE4",), |
| 11: ("FUTURE5",), |
| } |
| method_types_ids = { |
| method.lower(): identifier |
| for identifier, methods in _method_groups.items() |
| for method in methods |
| } |
| num_method_types = len(_method_groups) |
|
|
| vdw_radii = [ |
| float(radius) |
| for radius in [ |
| "1.2", |
| "1.4", |
| "2.2", |
| "1.9", |
| "1.8", |
| "1.7", |
| "1.6", |
| "1.55", |
| "1.5", |
| "1.54", |
| "2.4", |
| "2.2", |
| "2.1", |
| "2.1", |
| "1.95", |
| "1.8", |
| "1.8", |
| "1.88", |
| "2.8", |
| "2.4", |
| "2.3", |
| "2.15", |
| "2.05", |
| "2.05", |
| "2.05", |
| "2.05", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.1", |
| "2.1", |
| "2.1", |
| "2.05", |
| "1.9", |
| "1.9", |
| "2.02", |
| "2.9", |
| "2.55", |
| "2.4", |
| "2.3", |
| "2.15", |
| "2.1", |
| "2.05", |
| "2.05", |
| "2.0", |
| "2.05", |
| "2.1", |
| "2.2", |
| "2.2", |
| "2.25", |
| "2.2", |
| "2.1", |
| "2.1", |
| "2.16", |
| "3.0", |
| "2.7", |
| "2.5", |
| "2.48", |
| "2.47", |
| "2.45", |
| "2.43", |
| "2.42", |
| "2.4", |
| "2.38", |
| "2.37", |
| "2.35", |
| "2.33", |
| "2.32", |
| "2.3", |
| "2.28", |
| "2.27", |
| "2.25", |
| "2.2", |
| "2.1", |
| "2.05", |
| "2.0", |
| "2.0", |
| "2.05", |
| "2.1", |
| "2.05", |
| "2.2", |
| "2.3", |
| "2.3", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.4", |
| "2.0", |
| "2.3", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| "2.0", |
| ] |
| ] |
|
|
