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Pulchra
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@bgruening
bgruening authored Jun 6, 2024
2 parents b90c5ab + bcfb727 commit 3c6707a
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16 changes: 16 additions & 0 deletions tools/buildtools/protein_structure_rebuilders/pulchra/.shed.yml
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name: pulchra
owner: chemteam
description: "Pulchra is a package used for rebuilding protein structures from reduced representations."
homepage_url: https://www.pirx.com/pulchra/
long_description: |
Pulchra (https://www.pirx.com/pulchra/) is a package used for rebuilding protein structures from reduced representations. Using a coarse grain model as input (alpha trace, with or without a sidechain bead), it can reconstruct the protein's missing heavy atoms.
remote_repository_url: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/
type: unrestricted
categories:
- Computational chemistry
auto_tool_repositories:
name_template: "{{ tool_id }}"
description_template: "Wrapper for the Pulchra package: {{ tool_name }}"
maintainers:
- thepineapplepirate

83 changes: 83 additions & 0 deletions tools/buildtools/protein_structure_rebuilders/pulchra/pulchra.xml
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<tool id="pulchra" name="PULCHRA recontruction of all atom proteins" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="22.05">
<description>from reduced representations</description>
<macros>
<token name="@TOOL_VERSION@">3.06</token>
<token name="@GALAXY_VERSION@">0</token>
</macros>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">pulchra</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
ln -s '$structure_input' ./structure_input.${structure_input.ext} &&
pulchra
##inputs
./structure_input.${structure_input.ext}
$skip_sidechain
-v
]]></command>
<inputs>
<param name="structure_input" type="data" format="pdb" label="Structure file" help="In PDB format. This input is usually an 'alpha trace' or other incomplete structure file."/>
<param argument="-s" name="skip_sidechain" type="boolean" truevalue="-s" falsevalue="" label="Skip sidechain reconstruction?" help="By default, both sidechains and backbone will be reconstructed otherwise."/>
</inputs>
<outputs>
<data name="output1" format="pdb" from_work_dir="*.rebuilt.pdb" label="PULCHRA rebuilt pdb file on ${on_string}"/>
</outputs>
<tests>
<test>
<param name="structure_input" value="model.pdb"/>
<output name="output1" ftype="pdb">
<assert_contents>
<has_text text="ATOM 1 N PHE 1 16.391 50.300 23.791"/>
<has_text text="ATOM 12 N LEU 2 14.039 47.806 25.433"/>
<has_text text="ATOM 20 N VAL 3 10.836 47.425 24.846"/>
</assert_contents>
</output>
</test>
<test>
<param name="structure_input" value="model.pdb"/>
<param name="skip_sidechain" value="true" />
<output name="output1" ftype="pdb">
<assert_contents>
<has_text text="ATOM 1 N PHE 1 16.391 50.300 23.791"/>
<has_text text="ATOM 12 O VAL 3 8.414 45.957 24.602"/>
<has_text text="ATOM 20 O MET 5 1.327 47.936 26.198"/>
</assert_contents>
</output>
</test>
</tests>
<help><![CDATA[
.. class:: infomark
**What it does**
This tool rebuilds a protein structure from reduced representations (alpha carbon trace), producing an all-heavy atom PDB file.
_____
.. class:: infomark
**Input**
- Alpha carbon trace PDB file
_____
.. class:: infomark
**Output**
- Rebuilt all-heavy atom PDB file
]]></help>
<citations>
<citation type="doi">10.1002/jcc.20906</citation>
</citations>
</tool>

209 changes: 209 additions & 0 deletions tools/buildtools/protein_structure_rebuilders/pulchra/test-data/model.pdb
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ATOM 2 CA PHE A 1 15.513 49.774 25.062
ATOM 13 CA LEU A 2 13.229 46.739 25.121
ATOM 21 CA VAL A 3 9.685 47.820 25.820
ATOM 28 CA ALA A 4 6.727 45.678 26.933
ATOM 33 CA MET A 5 3.258 46.604 25.633
ATOM 41 CA LYS A 6 1.754 47.436 29.050
ATOM 50 CA GLU A 7 -1.796 46.206 28.577
ATOM 59 CA ASP A 8 -4.356 45.140 25.963
ATOM 67 CA SER A 9 -6.347 48.340 26.542
ATOM 73 CA ILE A 10 -6.479 51.896 25.155
ATOM 81 CA GLU A 11 -5.024 53.056 28.465
ATOM 90 CA GLY A 12 -2.092 50.587 28.253
ATOM 94 CA ILE A 13 -1.524 51.170 24.528
ATOM 102 CA TYR A 14 -1.360 54.936 25.069
ATOM 114 CA ASP A 15 0.880 54.606 28.142
ATOM 122 CA THR A 16 3.271 52.449 26.116
ATOM 129 CA LEU A 17 3.152 55.037 23.308
ATOM 137 CA LYS A 18 4.073 57.812 25.696
ATOM 146 CA GLU A 19 6.918 55.660 27.044
ATOM 155 CA CYS A 20 8.265 55.087 23.534
ATOM 161 CA ALA A 21 8.000 58.836 22.878
ATOM 166 CA LEU A 22 9.916 59.614 26.054
ATOM 174 CA ILE A 23 12.642 57.053 25.216
ATOM 182 CA SER A 24 12.843 58.202 21.563
ATOM 188 CA LYS A 25 13.339 61.844 22.744
ATOM 197 CA THR A 26 16.769 61.089 24.174
ATOM 204 CA ALA A 27 18.165 58.874 21.425
ATOM 209 CA GLY A 28 18.068 55.045 21.367
ATOM 213 CA GLY A 29 16.332 52.353 19.371
ATOM 217 CA ILE A 30 13.358 50.441 20.677
ATOM 225 CA GLY A 31 12.347 46.829 20.481
ATOM 229 CA LEU A 32 8.668 46.673 21.426
ATOM 237 CA HIS A 33 6.716 43.433 21.921
ATOM 247 CA ILE A 34 3.033 43.450 21.056
ATOM 255 CA HIS A 35 1.885 39.824 21.507
ATOM 265 CA ASN A 36 -0.832 40.699 24.018
ATOM 273 CA ILE A 37 -2.855 42.979 21.704
ATOM 281 CA ARG A 38 -6.141 41.342 20.658
ATOM 292 CA SER A 39 -6.447 40.798 16.932
ATOM 298 CA THR A 40 -8.871 42.000 14.268
ATOM 305 CA GLY A 41 -12.512 41.252 14.849
ATOM 309 CA SER A 42 -12.039 40.546 18.540
ATOM 315 CA TYR A 43 -14.811 41.687 20.821
ATOM 327 CA ILE A 44 -14.547 44.860 22.909
ATOM 335 CA ALA A 45 -16.725 44.603 26.031
ATOM 340 CA GLY A 46 -16.657 48.201 27.322
ATOM 344 CA THR A 47 -18.433 49.470 24.180
ATOM 351 CA ASN A 48 -19.897 46.329 22.557
ATOM 359 CA GLY A 49 -17.563 46.982 19.630
ATOM 363 CA THR A 50 -15.001 45.215 17.479
ATOM 370 CA SER A 51 -11.226 45.592 17.205
ATOM 376 CA ASN A 52 -9.416 46.541 13.983
ATOM 384 CA GLY A 53 -6.314 44.746 15.242
ATOM 388 CA LEU A 54 -2.585 45.438 15.118
ATOM 396 CA ILE A 55 -2.175 47.559 11.968
ATOM 404 CA PRO A 56 -4.111 50.731 12.974
ATOM 411 CA MET A 57 -2.238 50.528 16.289
ATOM 419 CA ILE A 58 1.127 50.044 14.489
ATOM 427 CA ARG A 59 0.314 53.199 12.474
ATOM 438 CA VAL A 60 0.003 55.268 15.656
ATOM 445 CA PHE A 61 3.465 54.048 16.786
ATOM 456 CA ASN A 62 4.780 54.684 13.244
ATOM 464 CA ASN A 63 3.673 58.290 13.426
ATOM 472 CA THR A 64 5.257 58.637 16.799
ATOM 479 CA ALA A 65 8.571 57.349 15.416
ATOM 484 CA ARG A 66 8.374 60.002 12.684
ATOM 495 CA TYR A 67 7.404 62.790 15.135
ATOM 507 CA VAL A 68 9.845 62.259 17.934
ATOM 514 CA ASP A 69 13.137 62.476 16.016
ATOM 522 CA GLN A 70 15.687 61.786 18.768
ATOM 531 CA GLY A 71 15.737 65.222 20.429
ATOM 535 CA GLY A 72 14.445 67.695 17.872
ATOM 539 CA ASN A 73 15.773 67.386 14.334
ATOM 547 CA LYS A 74 18.343 64.716 15.095
ATOM 556 CA ARG A 75 17.327 61.270 13.835
ATOM 567 CA PRO A 76 13.870 59.798 13.113
ATOM 574 CA GLY A 77 12.677 57.366 15.823
ATOM 578 CA ALA A 78 13.703 53.747 15.230
ATOM 583 CA PHE A 79 11.388 50.967 16.501
ATOM 594 CA ALA A 80 11.394 47.248 15.853
ATOM 599 CA LEU A 81 8.157 45.412 16.713
ATOM 607 CA TYR A 82 8.195 41.792 17.871
ATOM 619 CA LEU A 83 5.305 39.378 17.239
ATOM 627 CA GLU A 84 4.951 35.609 17.580
ATOM 636 CA PRO A 85 3.752 34.000 14.333
ATOM 643 CA TRP A 86 0.601 32.494 15.986
ATOM 657 CA HIS A 87 -0.903 36.043 16.345
ATOM 667 CA ALA A 88 -3.986 36.372 14.058
ATOM 672 CA ASP A 89 -2.785 39.638 12.491
ATOM 680 CA ILE A 90 0.520 38.111 11.424
ATOM 688 CA PHE A 91 0.091 38.278 7.616
ATOM 699 CA ASP A 92 -0.359 42.044 7.622
ATOM 707 CA PHE A 93 2.349 42.459 10.252
ATOM 718 CA ILE A 94 5.148 40.830 8.190
ATOM 726 CA ASP A 95 4.295 43.157 5.231
ATOM 734 CA ILE A 96 4.434 46.431 7.145
ATOM 742 CA ARG A 97 7.450 47.544 5.045
ATOM 753 CA LYS A 98 6.243 46.469 1.584
ATOM 762 CA ASN A 99 6.495 49.063 -1.146
ATOM 770 CA HIS A 100 3.217 48.441 -2.945
ATOM 780 CA GLY A 101 -0.379 49.589 -2.579
ATOM 784 CA LYS A 102 -2.799 49.597 0.358
ATOM 793 CA GLU A 103 -1.222 52.562 2.129
ATOM 802 CA GLU A 104 -3.556 52.501 5.174
ATOM 811 CA ILE A 105 -2.242 48.964 5.938
ATOM 819 CA ARG A 106 1.526 49.688 5.860
ATOM 830 CA ALA A 107 3.866 51.161 8.487
ATOM 835 CA ARG A 108 6.981 51.978 6.597
ATOM 846 CA ASP A 109 9.019 53.717 9.344
ATOM 854 CA LEU A 110 8.963 50.573 11.581
ATOM 862 CA PHE A 111 10.741 47.219 11.481
ATOM 873 CA PRO A 112 8.927 43.899 11.888
ATOM 880 CA ALA A 113 10.646 41.064 13.698
ATOM 885 CA LEU A 114 9.415 37.548 14.271
ATOM 893 CA TRP A 115 9.639 36.030 17.736
ATOM 907 CA ILE A 116 9.575 32.420 16.431
ATOM 915 CA PRO A 117 8.814 29.424 18.694
ATOM 922 CA ASP A 118 10.334 26.056 17.651
ATOM 930 CA LEU A 119 6.863 24.580 17.071
ATOM 938 CA PHE A 120 6.394 26.919 14.122
ATOM 949 CA MET A 121 9.559 25.623 12.574
ATOM 957 CA LYS A 122 8.585 21.986 13.168
ATOM 966 CA ARG A 123 5.130 22.537 11.599
ATOM 977 CA VAL A 124 6.763 24.243 8.611
ATOM 984 CA GLU A 125 9.226 21.371 7.955
ATOM 993 CA GLU A 126 6.589 18.683 8.672
ATOM 1002 CA ASN A 127 4.268 20.387 6.136
ATOM 1010 CA GLY A 128 1.724 20.525 8.990
ATOM 1014 CA THR A 129 -0.938 22.978 10.158
ATOM 1021 CA TRP A 130 -0.556 26.273 12.035
ATOM 1035 CA THR A 131 -3.172 27.967 14.180
ATOM 1042 CA LEU A 132 -3.671 31.713 14.460
ATOM 1050 CA PHE A 133 -5.048 33.014 17.769
ATOM 1061 CA SER A 134 -6.103 36.321 19.160
ATOM 1067 CA PRO A 135 -4.264 36.449 22.521
ATOM 1074 CA THR A 136 -7.668 36.933 24.213
ATOM 1081 CA SER A 137 -8.883 33.500 22.957
ATOM 1087 CA ALA A 138 -5.591 31.820 23.824
ATOM 1092 CA PRO A 139 -3.908 33.546 26.799
ATOM 1099 CA GLY A 140 -0.348 32.973 28.087
ATOM 1103 CA LEU A 141 1.377 31.807 24.904
ATOM 1111 CA SER A 142 4.042 34.520 25.106
ATOM 1117 CA ASP A 143 4.576 33.941 28.849
ATOM 1125 CA CYS A 144 5.947 30.378 28.375
ATOM 1131 CA TYR A 145 8.362 28.713 25.905
ATOM 1143 CA GLY A 146 9.640 25.205 24.880
ATOM 1147 CA ASP A 147 7.540 22.107 25.749
ATOM 1155 CA GLU A 148 5.383 24.125 28.120
ATOM 1164 CA PHE A 149 4.454 26.370 25.166
ATOM 1175 CA GLU A 150 3.898 23.372 22.884
ATOM 1184 CA ALA A 151 1.581 21.753 25.430
ATOM 1189 CA LEU A 152 -0.496 24.977 25.847
ATOM 1197 CA TYR A 153 -0.477 25.843 22.149
ATOM 1209 CA THR A 154 -1.580 22.248 21.266
ATOM 1216 CA ARG A 155 -4.450 22.335 23.818
ATOM 1227 CA TYR A 156 -5.751 25.738 22.595
ATOM 1239 CA GLU A 157 -5.465 24.329 19.074
ATOM 1248 CA LYS A 158 -7.586 21.226 19.866
ATOM 1257 CA GLU A 159 -10.100 23.284 21.849
ATOM 1266 CA GLY A 160 -10.833 25.114 18.567
ATOM 1270 CA ARG A 161 -9.779 28.511 19.907
ATOM 1281 CA GLY A 162 -8.104 29.739 16.742
ATOM 1285 CA LYS A 163 -8.034 29.584 12.963
ATOM 1294 CA THR A 164 -6.061 26.793 11.311
ATOM 1301 CA ILE A 165 -4.141 27.113 8.050
ATOM 1309 CA LYS A 166 -1.246 25.368 6.295
ATOM 1318 CA ALA A 167 2.014 26.352 8.025
ATOM 1323 CA GLN A 168 3.864 26.633 4.708
ATOM 1332 CA LYS A 169 1.354 29.273 3.672
ATOM 1341 CA LEU A 170 2.678 31.558 6.432
ATOM 1349 CA TRP A 171 6.222 30.443 5.637
ATOM 1363 CA TYR A 172 5.981 31.420 1.952
ATOM 1375 CA SER A 173 4.572 34.803 2.968
ATOM 1381 CA ILE A 174 7.454 35.307 5.487
ATOM 1389 CA LEU A 175 9.940 34.412 2.725
ATOM 1397 CA GLU A 176 8.234 36.795 0.286
ATOM 1406 CA ALA A 177 8.465 39.814 2.611
ATOM 1411 CA GLN A 178 12.166 39.108 3.325
ATOM 1420 CA THR A 179 13.006 38.936 -0.410
ATOM 1427 CA GLU A 180 11.279 42.279 -0.959
ATOM 1436 CA THR A 181 12.009 44.363 2.152
ATOM 1443 CA GLY A 182 14.875 42.664 4.010
ATOM 1447 CA THR A 183 12.367 42.104 6.853
ATOM 1454 CA PRO A 184 11.033 40.662 9.047
ATOM 1461 CA PHE A 185 13.964 39.725 11.238
ATOM 1472 CA VAL A 186 13.985 36.297 12.823
ATOM 1479 CA VAL A 187 14.852 35.579 16.411
ATOM 1486 CA TYR A 188 14.121 32.196 17.939
ATOM 1498 CA LYS A 189 12.207 32.578 21.210
ATOM 1507 CA ASP A 190 13.041 29.157 22.609
ATOM 1515 CA ALA A 191 16.833 29.437 22.020
ATOM 1520 CA CYS A 192 16.777 32.950 23.576
ATOM 1526 CA ASN A 193 14.876 31.768 26.586
ATOM 1534 CA ARG A 194 16.560 28.403 27.140
ATOM 1545 CA LYS A 195 20.093 29.813 26.800
ATOM 1554 CA SER A 196 19.758 33.077 28.799
ATOM 1560 CA ASN A 197 21.312 33.966 32.130
ATOM 1568 CA GLN A 198 18.220 36.153 32.709
ATOM 1577 CA LYS A 199 15.911 33.091 32.744
ATOM 1586 CA ASN A 200 15.228 33.387 36.482
ATOM 1594 CA LEU A 201 13.475 36.720 35.733
ATOM 1602 CA GLY A 202 10.621 35.377 33.641
ATOM 1606 CA VAL A 203 10.036 34.749 29.971
ATOM 1613 CA ILE A 204 11.853 37.018 27.504
ATOM 1621 CA LYS A 205 9.390 38.402 25.004
ATOM 1630 CA SER A 206 11.494 40.301 22.472
ATOM 1636 CA SER A 207 14.873 41.246 21.190
ATOM 1642 CA ASN A 208 15.753 44.844 20.229
ATOM 1650 CA LEU A 209 16.097 47.102 17.196
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