#################################################################################################### # CHAINS #################################################################################################### chain_types = [ "PROTEIN", "DNA", "RNA", "NONPOLYMER", ] chain_type_ids = {chain: i for i, chain in enumerate(chain_types)} out_types = [ "dna_protein", "rna_protein", "ligand_protein", "dna_ligand", "rna_ligand", "intra_ligand", "intra_dna", "intra_rna", "intra_protein", "protein_protein", "modified", ] out_types_weights_af3 = { "dna_protein": 10.0, "rna_protein": 10.0, "ligand_protein": 10.0, "dna_ligand": 5.0, "rna_ligand": 5.0, "intra_ligand": 20.0, "intra_dna": 4.0, "intra_rna": 16.0, "intra_protein": 20.0, "protein_protein": 20.0, "modified": 0.0, } out_types_weights = { "dna_protein": 5.0, "rna_protein": 5.0, "ligand_protein": 20.0, "dna_ligand": 2.0, "rna_ligand": 2.0, "intra_ligand": 20.0, "intra_dna": 2.0, "intra_rna": 8.0, "intra_protein": 20.0, "protein_protein": 20.0, "modified": 0.0, } out_single_types = ["protein", "ligand", "dna", "rna"] clash_types = [ "dna_protein", "rna_protein", "ligand_protein", "protein_protein", "dna_ligand", "rna_ligand", "ligand_ligand", "rna_dna", "dna_dna", "rna_rna", ] chain_types_to_clash_type = { frozenset(("PROTEIN", "DNA")): "dna_protein", frozenset(("PROTEIN", "RNA")): "rna_protein", frozenset(("PROTEIN", "NONPOLYMER")): "ligand_protein", frozenset(("PROTEIN",)): "protein_protein", frozenset(("NONPOLYMER", "DNA")): "dna_ligand", frozenset(("NONPOLYMER", "RNA")): "rna_ligand", frozenset(("NONPOLYMER",)): "ligand_ligand", frozenset(("DNA", "RNA")): "rna_dna", frozenset(("DNA",)): "dna_dna", frozenset(("RNA",)): "rna_rna", } chain_type_to_out_single_type = { "PROTEIN": "protein", "DNA": "dna", "RNA": "rna", "NONPOLYMER": "ligand", } #################################################################################################### # RESIDUES & TOKENS #################################################################################################### canonical_tokens = [ "ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "GLY", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL", "UNK", # unknown protein token ] tokens = [ "", "-", *canonical_tokens, "A", "G", "C", "U", "N", # unknown rna token "DA", "DG", "DC", "DT", "DN", # unknown dna token ] token_ids = {token: i for i, token in enumerate(tokens)} num_tokens = len(tokens) unk_token = {"PROTEIN": "UNK", "DNA": "DN", "RNA": "N"} unk_token_ids = {m: token_ids[t] for m, t in unk_token.items()} prot_letter_to_token = { "A": "ALA", "R": "ARG", "N": "ASN", "D": "ASP", "C": "CYS", "E": "GLU", "Q": "GLN", "G": "GLY", "H": "HIS", "I": "ILE", "L": "LEU", "K": "LYS", "M": "MET", "F": "PHE", "P": "PRO", "S": "SER", "T": "THR", "W": "TRP", "Y": "TYR", "V": "VAL", "X": "UNK", "J": "UNK", "B": "UNK", "Z": "UNK", "O": "UNK", "U": "UNK", "-": "-", } prot_token_to_letter = {v: k for k, v in prot_letter_to_token.items()} prot_token_to_letter["UNK"] = "X" rna_letter_to_token = { "A": "A", "G": "G", "C": "C", "U": "U", "N": "N", } rna_token_to_letter = {v: k for k, v in rna_letter_to_token.items()} dna_letter_to_token = { "A": "DA", "G": "DG", "C": "DC", "T": "DT", "N": "DN", } dna_token_to_letter = {v: k for k, v in dna_letter_to_token.items()} #################################################################################################### # ATOMS #################################################################################################### num_elements = 128 chirality_types = [ "CHI_UNSPECIFIED", "CHI_TETRAHEDRAL_CW", "CHI_TETRAHEDRAL_CCW", "CHI_SQUAREPLANAR", "CHI_OCTAHEDRAL", "CHI_TRIGONALBIPYRAMIDAL", "CHI_OTHER", ] chirality_type_ids = {chirality: i for i, chirality in enumerate(chirality_types)} unk_chirality_type = "CHI_OTHER" hybridization_map = [ "S", "SP", "SP2", "SP2D", "SP3", "SP3D", "SP3D2", "OTHER", "UNSPECIFIED", ] hybridization_type_ids = {hybrid: i for i, hybrid in enumerate(hybridization_map)} unk_hybridization_type = "UNSPECIFIED" # fmt: off ref_atoms = { "PAD": [], "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"], # noqa: E501 "TYR": ["N", "CA", "C", "O", "CB", "CG", "CD1", "CD2", "CE1", "CE2", "CZ", "OH"], "VAL": ["N", "CA", "C", "O", "CB", "CG1", "CG2"], "A": ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "O2'", "C1'", "N9", "C8", "N7", "C5", "C6", "N6", "N1", "C2", "N3", "C4"], # noqa: E501 "G": ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "O2'", "C1'", "N9", "C8", "N7", "C5", "C6", "O6", "N1", "C2", "N2", "N3", "C4"], # noqa: E501 "C": ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "O2'", "C1'", "N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6"], # noqa: E501 "U": ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "O2'", "C1'", "N1", "C2", "O2", "N3", "C4", "O4", "C5", "C6"], # noqa: E501 "N": ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "O2'", "C1'"], # noqa: E501 "DA": ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "C1'", "N9", "C8", "N7", "C5", "C6", "N6", "N1", "C2", "N3", "C4"], # noqa: E501 "DG": ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "C1'", "N9", "C8", "N7", "C5", "C6", "O6", "N1", "C2", "N2", "N3", "C4"], # noqa: E501 "DC": ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "C1'", "N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6"], # noqa: E501 "DT": ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "C1'", "N1", "C2", "O2", "N3", "C4", "O4", "C5", "C7", "C6"], # noqa: E501 "DN": ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "C1'"] } 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 = {name: i for i, name in enumerate(protein_backbone_atom_names)} nucleic_backbone_atom_index = {name: i for i, name in enumerate(nucleic_backbone_atom_names)} ref_symmetries = { "PAD": [], "ALA": [], "ARG": [], "ASN": [], "ASP": [[(6, 7), (7, 6)]], "CYS": [], "GLN": [], "GLU": [[(7, 8), (8, 7)]], "GLY": [], "HIS": [], "ILE": [], "LEU": [], "LYS": [], "MET": [], "PHE": [[(6, 7), (7, 6), (8, 9), (9, 8)]], "PRO": [], "SER": [], "THR": [], "TRP": [], "TYR": [[(6, 7), (7, 6), (8, 9), (9, 8)]], "VAL": [], "A": [[(1, 2), (2, 1)]], "G": [[(1, 2), (2, 1)]], "C": [[(1, 2), (2, 1)]], "U": [[(1, 2), (2, 1)]], #"N": [[(1, 2), (2, 1)]], "DA": [[(1, 2), (2, 1)]], "DG": [[(1, 2), (2, 1)]], "DC": [[(1, 2), (2, 1)]], "DT": [[(1, 2), (2, 1)]], #"DN": [[(1, 2), (2, 1)]] } res_to_center_atom = { "UNK": "CA", "ALA": "CA", "ARG": "CA", "ASN": "CA", "ASP": "CA", "CYS": "CA", "GLN": "CA", "GLU": "CA", "GLY": "CA", "HIS": "CA", "ILE": "CA", "LEU": "CA", "LYS": "CA", "MET": "CA", "PHE": "CA", "PRO": "CA", "SER": "CA", "THR": "CA", "TRP": "CA", "TYR": "CA", "VAL": "CA", "A": "C1'", "G": "C1'", "C": "C1'", "U": "C1'", "N": "C1'", "DA": "C1'", "DG": "C1'", "DC": "C1'", "DT": "C1'", "DN": "C1'" } res_to_disto_atom = { "UNK": "CB", "ALA": "CB", "ARG": "CB", "ASN": "CB", "ASP": "CB", "CYS": "CB", "GLN": "CB", "GLU": "CB", "GLY": "CA", "HIS": "CB", "ILE": "CB", "LEU": "CB", "LYS": "CB", "MET": "CB", "PHE": "CB", "PRO": "CB", "SER": "CB", "THR": "CB", "TRP": "CB", "TYR": "CB", "VAL": "CB", "A": "C4", "G": "C4", "C": "C2", "U": "C2", "N": "C1'", "DA": "C4", "DG": "C4", "DC": "C2", "DT": "C2", "DN": "C1'" } res_to_center_atom_id = { res: ref_atoms[res].index(atom) for res, atom in res_to_center_atom.items() } res_to_disto_atom_id = { res: ref_atoms[res].index(atom) for res, atom in res_to_disto_atom.items() } # fmt: on #################################################################################################### # BONDS #################################################################################################### atom_interface_cutoff = 5.0 interface_cutoff = 15.0 bond_types = [ "OTHER", "SINGLE", "DOUBLE", "TRIPLE", "AROMATIC", "COVALENT", ] bond_type_ids = {bond: i for i, bond in enumerate(bond_types)} unk_bond_type = "OTHER" #################################################################################################### # Contacts #################################################################################################### pocket_contact_info = { "UNSPECIFIED": 0, "UNSELECTED": 1, "POCKET": 2, "BINDER": 3, } contact_conditioning_info = { "UNSPECIFIED": 0, "UNSELECTED": 1, "POCKET>BINDER": 2, "BINDER>POCKET": 3, "CONTACT": 4, } #################################################################################################### # MSA #################################################################################################### max_msa_seqs = 16384 max_paired_seqs = 8192 #################################################################################################### # CHUNKING #################################################################################################### chunk_size_threshold = 384 #################################################################################################### # Method conditioning #################################################################################################### # Methods method_types_ids = { "MD": 0, "X-RAY DIFFRACTION": 1, "ELECTRON MICROSCOPY": 2, "SOLUTION NMR": 3, "SOLID-STATE NMR": 4, "NEUTRON DIFFRACTION": 4, "ELECTRON CRYSTALLOGRAPHY": 4, "FIBER DIFFRACTION": 4, "POWDER DIFFRACTION": 4, "INFRARED SPECTROSCOPY": 4, "FLUORESCENCE TRANSFER": 4, "EPR": 4, "THEORETICAL MODEL": 4, "SOLUTION SCATTERING": 4, "OTHER": 4, "AFDB": 5, "BOLTZ-1": 6, "FUTURE1": 7, # Placeholder for future supervision sources "FUTURE2": 8, "FUTURE3": 9, "FUTURE4": 10, "FUTURE5": 11, } method_types_ids = {k.lower(): v for k, v in method_types_ids.items()} num_method_types = len(set(method_types_ids.values())) # Temperature temperature_bins = [(265, 280), (280, 295), (295, 310)] temperature_bins_ids = {temp: i for i, temp in enumerate(temperature_bins)} temperature_bins_ids["other"] = len(temperature_bins) num_temp_bins = len(temperature_bins_ids) # pH ph_bins = [(0, 6), (6, 8), (8, 14)] ph_bins_ids = {ph: i for i, ph in enumerate(ph_bins)} ph_bins_ids["other"] = len(ph_bins) num_ph_bins = len(ph_bins_ids) #################################################################################################### # VDW_RADII #################################################################################################### # fmt: off vdw_radii = [ 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 ] # fmt: on #################################################################################################### # Excluded ligands #################################################################################################### ligand_exclusion = { "144", "15P", "1PE", "2F2", "2JC", "3HR", "3SY", "7N5", "7PE", "9JE", "AAE", "ABA", "ACE", "ACN", "ACT", "ACY", "AZI", "BAM", "BCN", "BCT", "BDN", "BEN", "BME", "BO3", "BTB", "BTC", "BU1", "C8E", "CAD", "CAQ", "CBM", "CCN", "CIT", "CL", "CLR", "CM", "CMO", "CO3", "CPT", "CXS", "D10", "DEP", "DIO", "DMS", "DN", "DOD", "DOX", "EDO", "EEE", "EGL", "EOH", "EOX", "EPE", "ETF", "FCY", "FJO", "FLC", "FMT", "FW5", "GOL", "GSH", "GTT", "GYF", "HED", "IHP", "IHS", "IMD", "IOD", "IPA", "IPH", "LDA", "MB3", "MEG", "MES", "MLA", "MLI", "MOH", "MPD", "MRD", "MSE", "MYR", "N", "NA", "NH2", "NH4", "NHE", "NO3", "O4B", "OHE", "OLA", "OLC", "OMB", "OME", "OXA", "P6G", "PE3", "PE4", "PEG", "PEO", "PEP", "PG0", "PG4", "PGE", "PGR", "PLM", "PO4", "POL", "POP", "PVO", "SAR", "SCN", "SEO", "SEP", "SIN", "SO4", "SPD", "SPM", "SR", "STE", "STO", "STU", "TAR", "TBU", "TME", "TPO", "TRS", "UNK", "UNL", "UNX", "UPL", "URE", } #################################################################################################### # TEMPLATES #################################################################################################### min_coverage_residues = 10 min_coverage_fraction = 0.1 #################################################################################################### # Ambiguous atoms #################################################################################################### ambiguous_atoms = { "CA": { "*": "C", "OEX": "CA", "OEC": "CA", "543": "CA", "OC6": "CA", "OC1": "CA", "OC7": "CA", "OEY": "CA", "OC4": "CA", "OC3": "CA", "ICA": "CA", "CA": "CA", "OC2": "CA", "OC5": "CA", }, "CD": {"*": "C", "CD": "CD", "CD3": "CD", "CD5": "CD", "CD1": "CD"}, "BR": "BR", "CL": { "*": "CL", "C8P": "C", "L3T": "C", "TLC": "C", "TZ0": "C", "471": "C", "NLK": "C", "PGM": "C", "PNE": "C", "RCY": "C", "11F": "C", "PII": "C", "C1Q": "C", "4MD": "C", "R5A": "C", "KW2": "C", "I7M": "C", "R48": "C", "FC3": "C", "55V": "C", "KPF": "C", "SPZ": "C", "0TT": "C", "R9A": "C", "5NA": "C", "C55": "C", "NIX": "C", "5PM": "C", "PP8": "C", "544": "C", "812": "C", "NPM": "C", "KU8": "C", "A1AMM": "C", "4S0": "C", "AQC": "C", "2JK": "C", "WJR": "C", "A1AAW": "C", "85E": "C", "MB0": "C", "ZAB": "C", "85K": "C", "GBP": "C", "A1H80": "C", "A1AFR": "C", "L9M": "C", "MYK": "C", "MB9": "C", "38R": "C", "EKB": "C", "NKF": "C", "UMQ": "C", "T4K": "C", "3PT": "C", "A1A7S": "C", "1Q9": "C", "11R": "C", "D2V": "C", "SM8": "C", "IFC": "C", "DB5": "C", "L2T": "C", "GNB": "C", "PP7": "C", "072": "C", "P88": "C", "DRL": "C", "C9W": "C", "NTP": "C", "4HJ": "C", "7NA": "C", "LPC": "C", "T8W": "C", "63R": "C", "570": "C", "R4A": "C", "3BG": "C", "4RB": "C", "GSO": "C", "BQ6": "C", "R4P": "C", "5CP": "C", "TTR": "C", "6UZ": "C", "SPJ": "C", "0SA": "C", "ZL1": "C", "BYG": "C", "F0E": "C", "PC0": "C", "B2Q": "C", "KV6": "C", "NTO": "C", "CLG": "C", "R7U": "C", "SMQ": "C", "GM2": "C", "Z7P": "C", "NXF": "C", "C6Q": "C", "A1G": "C", "433": "C", "L9N": "C", "7OX": "C", "A1H84": "C", "97L": "C", "HDV": "C", "LUO": "C", "R6A": "C", "1PC": "C", "4PT": "C", "SBZ": "C", "EAB": "C", "FL4": "C", "OPS": "C", "C2X": "C", "SLL": "C", "BFC": "C", "GIP": "C", "7CP": "C", "CLH": "C", "34E": "C", "5NE": "C", "PBF": "C", "ABD": "C", "ABC": "C", "LPF": "C", "TIZ": "C", "4HH": "C", "AFC": "C", "WQH": "C", "9JL": "C", "CS3": "C", "NL0": "C", "KPY": "C", "DNA": "C", "B3C": "C", "TKL": "C", "KVS": "C", "HO6": "C", "NLH": "C", "1PB": "C", "CYF": "C", "G4M": "C", "R5B": "C", "N4S": "C", "N11": "C", "C8F": "C", "PIJ": "C", "WIN": "C", "NT1": "C", "WJW": "C", "HF7": "C", "TY1": "C", "VM1": "C", }, "OS": {"*": "O", "DWC": "OS", "OHX": "OS", "OS": "OS", "8WV": "OS", "OS4": "OS"}, "PB": {"*": "P", "ZN9": "PB", "ZN7": "PB", "PBM": "PB", "PB": "PB", "CSB": "PB"}, "CE": {"*": "C", "CE": "CE"}, "FE": {"*": "FE", "TFR": "F", "PF5": "F", "IFC": "F", "F5C": "F"}, "NA": {"*": "N", "CGO": "NA", "R2K": "NA", "LVQ": "NA", "NA": "NA"}, "ND": {"*": "N", "ND": "ND"}, "CF": {"*": "C", "CF": "CF"}, "RU": "RU", "BRAF": "BR", "EU": "EU", "CLAA": "CL", "CLBQ": "CL", "CM": {"*": "C", "ZCM": "CM"}, "SN": {"*": "SN", "TAP": "S", "SND": "S", "TAD": "S", "XPT": "S"}, "AG": "AG", "CLN": "CL", "CLM": "CL", "CLA": {"*": "CL", "PII": "C", "TDL": "C", "D0J": "C", "GM2": "C", "PIJ": "C"}, "CLB": { "*": "CL", "TD5": "C", "PII": "C", "TDL": "C", "GM2": "C", "TD7": "C", "TD6": "C", "PIJ": "C", }, "CR": { "*": "C", "BW9": "CR", "CQ4": "CR", "AC9": "CR", "TIL": "CR", "J7U": "CR", "CR": "CR", }, "CLAY": "CL", "CLBC": "CL", "PD": { "*": "P", "F6Q": "PD", "SVP": "PD", "SXC": "PD", "U5U": "PD", "PD": "PD", "PLL": "PD", }, "CO": { "*": "C", "J1S": "CO", "OCN": "CO", "OL3": "CO", "OL4": "CO", "B12": "CO", "XCO": "CO", "UFU": "CO", "CON": "CO", "OL5": "CO", "B13": "CO", "7KI": "CO", "PL1": "CO", "OCO": "CO", "J1R": "CO", "COH": "CO", "SIR": "CO", "6KI": "CO", "NCO": "CO", "9CO": "CO", "PC3": "CO", "BWU": "CO", "B1Z": "CO", "J83": "CO", "CO": "CO", "COY": "CO", "CNC": "CO", "3CO": "CO", "OCL": "CO", "R5Q": "CO", "X5Z": "CO", "CBY": "CO", "OLS": "CO", "F0X": "CO", "I2A": "CO", "OCM": "CO", }, "CU": { "*": "C", "8ZR": "CU", "K7E": "CU", "CU3": "CU", "SI9": "CU", "35N": "CU", "C2O": "CU", "SI7": "CU", "B15": "CU", "SI0": "CU", "CUP": "CU", "SQ1": "CU", "CUK": "CU", "CUL": "CU", "SI8": "CU", "IC4": "CU", "CUM": "CU", "MM2": "CU", 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