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| # Copyright 2021 AlQuraishi Laboratory | |
| # Copyright 2021 DeepMind Technologies Limited | |
| # | |
| # 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. | |
| # This mapping is used when we need to store atom data in a format that requires | |
| # fixed atom data size for every residue (e.g. a numpy array). | |
| atom_types = [ | |
| "N", | |
| "CA", | |
| "C", | |
| "CB", | |
| "O", | |
| "CG", | |
| "CG1", | |
| "CG2", | |
| "OG", | |
| "OG1", | |
| "SG", | |
| "CD", | |
| "CD1", | |
| "CD2", | |
| "ND1", | |
| "ND2", | |
| "OD1", | |
| "OD2", | |
| "SD", | |
| "CE", | |
| "CE1", | |
| "CE2", | |
| "CE3", | |
| "NE", | |
| "NE1", | |
| "NE2", | |
| "OE1", | |
| "OE2", | |
| "CH2", | |
| "NH1", | |
| "NH2", | |
| "OH", | |
| "CZ", | |
| "CZ2", | |
| "CZ3", | |
| "NZ", | |
| "OXT", | |
| ] | |
| atom_order = {atom_type: i for i, atom_type in enumerate(atom_types)} | |
| atom_type_num = len(atom_types) # := 37. | |
| restype_1to3 = { | |
| "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", | |
| } | |