Mercurial > repos > galaxy-australia > alphafold2
annotate docker/alphafold/alphafold/common/protein.py @ 1:6c92e000d684 draft
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
author | galaxy-australia |
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date | Tue, 01 Mar 2022 02:53:05 +0000 |
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6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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1 # Copyright 2021 DeepMind Technologies Limited |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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2 # |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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3 # Licensed under the Apache License, Version 2.0 (the "License"); |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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4 # you may not use this file except in compliance with the License. |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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5 # You may obtain a copy of the License at |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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6 # |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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7 # http://www.apache.org/licenses/LICENSE-2.0 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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8 # |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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9 # Unless required by applicable law or agreed to in writing, software |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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10 # distributed under the License is distributed on an "AS IS" BASIS, |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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11 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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12 # See the License for the specific language governing permissions and |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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13 # limitations under the License. |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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14 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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15 """Protein data type.""" |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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16 import dataclasses |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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17 import io |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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18 from typing import Any, Mapping, Optional |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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19 from alphafold.common import residue_constants |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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20 from Bio.PDB import PDBParser |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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21 import numpy as np |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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22 |
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23 FeatureDict = Mapping[str, np.ndarray] |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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24 ModelOutput = Mapping[str, Any] # Is a nested dict. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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25 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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26 # Complete sequence of chain IDs supported by the PDB format. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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27 PDB_CHAIN_IDS = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789' |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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28 PDB_MAX_CHAINS = len(PDB_CHAIN_IDS) # := 62. |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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29 |
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30 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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31 @dataclasses.dataclass(frozen=True) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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32 class Protein: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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33 """Protein structure representation.""" |
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34 |
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35 # Cartesian coordinates of atoms in angstroms. The atom types correspond to |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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36 # residue_constants.atom_types, i.e. the first three are N, CA, CB. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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37 atom_positions: np.ndarray # [num_res, num_atom_type, 3] |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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38 |
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39 # Amino-acid type for each residue represented as an integer between 0 and |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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40 # 20, where 20 is 'X'. |
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41 aatype: np.ndarray # [num_res] |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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42 |
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43 # Binary float mask to indicate presence of a particular atom. 1.0 if an atom |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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44 # is present and 0.0 if not. This should be used for loss masking. |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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45 atom_mask: np.ndarray # [num_res, num_atom_type] |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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46 |
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47 # Residue index as used in PDB. It is not necessarily continuous or 0-indexed. |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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48 residue_index: np.ndarray # [num_res] |
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49 |
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50 # 0-indexed number corresponding to the chain in the protein that this residue |
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51 # belongs to. |
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52 chain_index: np.ndarray # [num_res] |
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53 |
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54 # B-factors, or temperature factors, of each residue (in sq. angstroms units), |
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55 # representing the displacement of the residue from its ground truth mean |
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56 # value. |
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57 b_factors: np.ndarray # [num_res, num_atom_type] |
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58 |
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59 def __post_init__(self): |
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60 if len(np.unique(self.chain_index)) > PDB_MAX_CHAINS: |
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61 raise ValueError( |
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62 f'Cannot build an instance with more than {PDB_MAX_CHAINS} chains ' |
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63 'because these cannot be written to PDB format.') |
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64 |
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65 |
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66 def from_pdb_string(pdb_str: str, chain_id: Optional[str] = None) -> Protein: |
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67 """Takes a PDB string and constructs a Protein object. |
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68 |
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69 WARNING: All non-standard residue types will be converted into UNK. All |
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70 non-standard atoms will be ignored. |
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71 |
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72 Args: |
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73 pdb_str: The contents of the pdb file |
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74 chain_id: If chain_id is specified (e.g. A), then only that chain |
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75 is parsed. Otherwise all chains are parsed. |
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76 |
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77 Returns: |
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78 A new `Protein` parsed from the pdb contents. |
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79 """ |
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80 pdb_fh = io.StringIO(pdb_str) |
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81 parser = PDBParser(QUIET=True) |
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82 structure = parser.get_structure('none', pdb_fh) |
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83 models = list(structure.get_models()) |
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84 if len(models) != 1: |
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85 raise ValueError( |
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86 f'Only single model PDBs are supported. Found {len(models)} models.') |
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87 model = models[0] |
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88 |
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89 atom_positions = [] |
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90 aatype = [] |
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91 atom_mask = [] |
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92 residue_index = [] |
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93 chain_ids = [] |
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94 b_factors = [] |
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95 |
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96 for chain in model: |
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97 if chain_id is not None and chain.id != chain_id: |
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98 continue |
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99 for res in chain: |
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100 if res.id[2] != ' ': |
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101 raise ValueError( |
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102 f'PDB contains an insertion code at chain {chain.id} and residue ' |
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103 f'index {res.id[1]}. These are not supported.') |
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104 res_shortname = residue_constants.restype_3to1.get(res.resname, 'X') |
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105 restype_idx = residue_constants.restype_order.get( |
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106 res_shortname, residue_constants.restype_num) |
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107 pos = np.zeros((residue_constants.atom_type_num, 3)) |
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108 mask = np.zeros((residue_constants.atom_type_num,)) |
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109 res_b_factors = np.zeros((residue_constants.atom_type_num,)) |
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110 for atom in res: |
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111 if atom.name not in residue_constants.atom_types: |
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112 continue |
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113 pos[residue_constants.atom_order[atom.name]] = atom.coord |
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114 mask[residue_constants.atom_order[atom.name]] = 1. |
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115 res_b_factors[residue_constants.atom_order[atom.name]] = atom.bfactor |
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116 if np.sum(mask) < 0.5: |
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117 # If no known atom positions are reported for the residue then skip it. |
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118 continue |
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119 aatype.append(restype_idx) |
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120 atom_positions.append(pos) |
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121 atom_mask.append(mask) |
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122 residue_index.append(res.id[1]) |
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123 chain_ids.append(chain.id) |
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124 b_factors.append(res_b_factors) |
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125 |
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126 # Chain IDs are usually characters so map these to ints. |
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127 unique_chain_ids = np.unique(chain_ids) |
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128 chain_id_mapping = {cid: n for n, cid in enumerate(unique_chain_ids)} |
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129 chain_index = np.array([chain_id_mapping[cid] for cid in chain_ids]) |
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130 |
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131 return Protein( |
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132 atom_positions=np.array(atom_positions), |
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133 atom_mask=np.array(atom_mask), |
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134 aatype=np.array(aatype), |
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135 residue_index=np.array(residue_index), |
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136 chain_index=chain_index, |
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137 b_factors=np.array(b_factors)) |
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138 |
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139 |
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140 def _chain_end(atom_index, end_resname, chain_name, residue_index) -> str: |
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141 chain_end = 'TER' |
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142 return (f'{chain_end:<6}{atom_index:>5} {end_resname:>3} ' |
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143 f'{chain_name:>1}{residue_index:>4}') |
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144 |
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145 |
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146 def to_pdb(prot: Protein) -> str: |
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147 """Converts a `Protein` instance to a PDB string. |
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148 |
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149 Args: |
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150 prot: The protein to convert to PDB. |
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151 |
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152 Returns: |
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153 PDB string. |
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154 """ |
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155 restypes = residue_constants.restypes + ['X'] |
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156 res_1to3 = lambda r: residue_constants.restype_1to3.get(restypes[r], 'UNK') |
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157 atom_types = residue_constants.atom_types |
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158 |
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159 pdb_lines = [] |
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160 |
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161 atom_mask = prot.atom_mask |
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162 aatype = prot.aatype |
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163 atom_positions = prot.atom_positions |
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164 residue_index = prot.residue_index.astype(np.int32) |
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165 chain_index = prot.chain_index.astype(np.int32) |
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166 b_factors = prot.b_factors |
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167 |
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168 if np.any(aatype > residue_constants.restype_num): |
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169 raise ValueError('Invalid aatypes.') |
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170 |
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171 # Construct a mapping from chain integer indices to chain ID strings. |
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172 chain_ids = {} |
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173 for i in np.unique(chain_index): # np.unique gives sorted output. |
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174 if i >= PDB_MAX_CHAINS: |
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175 raise ValueError( |
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176 f'The PDB format supports at most {PDB_MAX_CHAINS} chains.') |
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177 chain_ids[i] = PDB_CHAIN_IDS[i] |
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178 |
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179 pdb_lines.append('MODEL 1') |
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180 atom_index = 1 |
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181 last_chain_index = chain_index[0] |
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182 # Add all atom sites. |
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183 for i in range(aatype.shape[0]): |
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184 # Close the previous chain if in a multichain PDB. |
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185 if last_chain_index != chain_index[i]: |
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186 pdb_lines.append(_chain_end( |
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187 atom_index, res_1to3(aatype[i - 1]), chain_ids[chain_index[i - 1]], |
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188 residue_index[i - 1])) |
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189 last_chain_index = chain_index[i] |
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190 atom_index += 1 # Atom index increases at the TER symbol. |
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191 |
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192 res_name_3 = res_1to3(aatype[i]) |
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193 for atom_name, pos, mask, b_factor in zip( |
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194 atom_types, atom_positions[i], atom_mask[i], b_factors[i]): |
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195 if mask < 0.5: |
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196 continue |
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197 |
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198 record_type = 'ATOM' |
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199 name = atom_name if len(atom_name) == 4 else f' {atom_name}' |
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200 alt_loc = '' |
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201 insertion_code = '' |
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202 occupancy = 1.00 |
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203 element = atom_name[0] # Protein supports only C, N, O, S, this works. |
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204 charge = '' |
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205 # PDB is a columnar format, every space matters here! |
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206 atom_line = (f'{record_type:<6}{atom_index:>5} {name:<4}{alt_loc:>1}' |
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207 f'{res_name_3:>3} {chain_ids[chain_index[i]]:>1}' |
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208 f'{residue_index[i]:>4}{insertion_code:>1} ' |
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209 f'{pos[0]:>8.3f}{pos[1]:>8.3f}{pos[2]:>8.3f}' |
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210 f'{occupancy:>6.2f}{b_factor:>6.2f} ' |
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211 f'{element:>2}{charge:>2}') |
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212 pdb_lines.append(atom_line) |
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213 atom_index += 1 |
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214 |
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215 # Close the final chain. |
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216 pdb_lines.append(_chain_end(atom_index, res_1to3(aatype[-1]), |
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217 chain_ids[chain_index[-1]], residue_index[-1])) |
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218 pdb_lines.append('ENDMDL') |
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219 pdb_lines.append('END') |
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220 |
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221 # Pad all lines to 80 characters. |
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222 pdb_lines = [line.ljust(80) for line in pdb_lines] |
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223 return '\n'.join(pdb_lines) + '\n' # Add terminating newline. |
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224 |
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225 |
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226 def ideal_atom_mask(prot: Protein) -> np.ndarray: |
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227 """Computes an ideal atom mask. |
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228 |
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229 `Protein.atom_mask` typically is defined according to the atoms that are |
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230 reported in the PDB. This function computes a mask according to heavy atoms |
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231 that should be present in the given sequence of amino acids. |
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232 |
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233 Args: |
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234 prot: `Protein` whose fields are `numpy.ndarray` objects. |
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235 |
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236 Returns: |
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237 An ideal atom mask. |
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238 """ |
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239 return residue_constants.STANDARD_ATOM_MASK[prot.aatype] |
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240 |
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241 |
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242 def from_prediction( |
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243 features: FeatureDict, |
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244 result: ModelOutput, |
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245 b_factors: Optional[np.ndarray] = None, |
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246 remove_leading_feature_dimension: bool = True) -> Protein: |
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247 """Assembles a protein from a prediction. |
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248 |
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249 Args: |
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250 features: Dictionary holding model inputs. |
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251 result: Dictionary holding model outputs. |
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252 b_factors: (Optional) B-factors to use for the protein. |
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253 remove_leading_feature_dimension: Whether to remove the leading dimension |
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254 of the `features` values. |
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255 |
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256 Returns: |
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257 A protein instance. |
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258 """ |
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259 fold_output = result['structure_module'] |
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260 |
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261 def _maybe_remove_leading_dim(arr: np.ndarray) -> np.ndarray: |
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262 return arr[0] if remove_leading_feature_dimension else arr |
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263 |
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264 if 'asym_id' in features: |
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265 chain_index = _maybe_remove_leading_dim(features['asym_id']) |
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266 else: |
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267 chain_index = np.zeros_like(_maybe_remove_leading_dim(features['aatype'])) |
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268 |
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269 if b_factors is None: |
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270 b_factors = np.zeros_like(fold_output['final_atom_mask']) |
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271 |
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272 return Protein( |
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273 aatype=_maybe_remove_leading_dim(features['aatype']), |
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274 atom_positions=fold_output['final_atom_positions'], |
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275 atom_mask=fold_output['final_atom_mask'], |
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276 residue_index=_maybe_remove_leading_dim(features['residue_index']) + 1, |
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277 chain_index=chain_index, |
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278 b_factors=b_factors) |