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| # Copyright Generate Biomedicines, Inc. | |
| # | |
| # Licensed under the Apache License, Version 2.0 (the "License"); | |
| # you may not use this file except in compliance with the License. | |
| # You may obtain a copy of the License at | |
| # | |
| # http://www.apache.org/licenses/LICENSE-2.0 | |
| # | |
| # Unless required by applicable law or agreed to in writing, software | |
| # distributed under the License is distributed on an "AS IS" BASIS, | |
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| # See the License for the specific language governing permissions and | |
| # limitations under the License. | |
| """Constants used across protein representations. | |
| These constants standardize protein tokenization alphabets, ideal structure | |
| geometries and topologies, etc. | |
| """ | |
| from chroma.constants.geometry import AA_GEOMETRY | |
| # Standard tokenization for Omniprot and Omniprot-interacting models | |
| OMNIPROT_TOKENS = "ABCDEFGHIKLMNOPQRSTUVWYXZ*-#" | |
| POTTS_EXTENDED_TOKENS = "ACDEFGHIKLMNPQRSTVWY-*#" | |
| PAD = "-" | |
| START = "@" | |
| STOP = "*" | |
| MASK = "#" | |
| DNA_TOKENS = "ACGT" | |
| RNA_TOKENS = "AGCU" | |
| PROTEIN_TOKENS = "ACDEFGHIKLMNPQRSTVWY" | |
| # Minimal 20-letter alphabet and corresponding triplet codes | |
| AA20 = "ACDEFGHIKLMNPQRSTVWY" | |
| AA20_3_TO_1 = { | |
| "ALA": "A", | |
| "ARG": "R", | |
| "ASN": "N", | |
| "ASP": "D", | |
| "CYS": "C", | |
| "GLN": "Q", | |
| "GLU": "E", | |
| "GLY": "G", | |
| "HIS": "H", | |
| "ILE": "I", | |
| "LEU": "L", | |
| "LYS": "K", | |
| "MET": "M", | |
| "PHE": "F", | |
| "PRO": "P", | |
| "SER": "S", | |
| "THR": "T", | |
| "TRP": "W", | |
| "TYR": "Y", | |
| "VAL": "V", | |
| } | |
| AA20_1_TO_3 = { | |
| "A": "ALA", | |
| "R": "ARG", | |
| "N": "ASN", | |
| "D": "ASP", | |
| "C": "CYS", | |
| "Q": "GLN", | |
| "E": "GLU", | |
| "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", | |
| } | |
| AA20_3 = [AA20_1_TO_3[aa] for aa in AA20] | |
| # Adding noncanonical amino acids | |
| NONCANON_AA = [ | |
| "HSD", | |
| "HSE", | |
| "HSC", | |
| "HSP", | |
| "MSE", | |
| "CSO", | |
| "SEC", | |
| "CSX", | |
| "HIP", | |
| "SEP", | |
| "TPO", | |
| ] | |
| AA31_3 = AA20_3 + NONCANON_AA | |
| # Chain alphabet for PDB chain naming | |
| CHAIN_ALPHABET = "_ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789" | |
| # Standard atom indexing | |
| ATOMS_BB = ["N", "CA", "C", "O"] | |
| ATOM_SYMMETRIES = { | |
| "ARG": [("NH1", "NH2")], # Correct handling of NH1 and NH2 is relabeling | |
| "ASP": [("OD1", "OD2")], | |
| "GLU": [("OE1", "OE2")], | |
| "PHE": [("CD1", "CD2"), ("CE1", "CE2")], | |
| "TYR": [("CD1", "CD2"), ("CE1", "CE2")], | |
| } | |
| AA20_NUM_ATOMS = [4 + len(AA_GEOMETRY[aa]["atoms"]) for aa in AA20_3] | |
| AA20_NUM_CHI = [len(AA_GEOMETRY[aa]["chi_indices"]) for aa in AA20_3] | |