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asford/180104_barrel_closure_generation.ipynb

Created January 6, 2018 07:04
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topology_mining/closure_generation/180104_barrel_closure_generation.ipynb
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180104_barrel_closure_generation.ipynb
{
"cells": [
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "import logging\nlogging.basicConfig(\n level=logging.INFO,\n format=\"%(asctime)s.%(msecs).03d %(name)s %(message)s\",\n datefmt='%Y-%m-%dT%H:%M:%S'\n)\n\nlogging.getLogger(\"rosetta\").setLevel(logging.WARNING)",
"execution_count": 2,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "import faulthandler\nfaulthandler.enable()\n\nimport os\n\nimport pyrosetta\nimport pyrosetta.distributed\nimport pyrosetta.distributed.packed_pose as packed_pose\nimport pyrosetta.distributed.tasks.rosetta_scripts as rosetta_scripts\n\nimport datetime\n\nimport dask\nimport dask.callbacks\nimport dask.bag\nimport dask.dataframe\nimport dask.delayed\nimport dask.diagnostics\nimport dask.distributed\n\nimport pandas",
"execution_count": 95,
"outputs": []
},
{
"metadata": {
"scrolled": false,
"trusted": true
},
"cell_type": "code",
"source": "client = dask.distributed.Client(\"salish:8786\")",
"execution_count": 4,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "import toolz\nfrom toolz.curried import valmap, first, take, valfilter, keyfilter, get, reduce, compose\n\n@toolz.curry\ndef gets(keys, d, factory=dict):\n return keyvilter(lambda k: k in keys, d, factory=factory)",
"execution_count": 5,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "from dask_support import (\n persist_walk, compute_walk, WorkStream, enable_gcsfs_cloud_access, WorkStream)\nenable_gcsfs_cloud_access()",
"execution_count": 6,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "input_decoys = pandas.read_pickle(\"/home/fordas/180101_loop_rebuild/180102_av9_scaffolds.pickle\")",
"execution_count": 7,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "segment_lookup_xml = open(\"closure_segment_lookup.xml\").read()\nsegment_refinement_xml = open(\"closure_segment_refinement.xml\").read()",
"execution_count": 8,
"outputs": []
},
{
"metadata": {
"scrolled": true,
"trusted": true
},
"cell_type": "code",
"source": "input_decoys",
"execution_count": 99,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 99,
"data": {
"text/plain": " ... x 23 columns]",
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<th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th rowspan=\"3\" valign=\"top\">loop1</th>\n <th>loop_1A.pdb</th>\n <td>0.427981</td>\n <td>-605.976303</td>\n <td>-262.891933</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>623.470600</td>\n <td>370.760305</td>\n <td>-22.457388</td>\n <td>0.592360</td>\n <td>27.66355</td>\n <td>...</td>\n <td>-61.953966</td>\n <td>-20.815381</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-81.772791</td>\n <td>0.871678</td>\n <td>-177.461089</td>\n <td>15.202064</td>\n <td>-39.132055</td>\n <td>19.293436</td>\n <td>10.906382</td>\n </tr>\n <tr>\n <th>loop_1B.pdb</th>\n <td>-0.550940</td>\n <td>-598.485416</td>\n <td>-254.320925</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>621.493431</td>\n <td>362.473770</td>\n <td>-22.015594</td>\n <td>0.592360</td>\n <td>29.11450</td>\n <td>...</td>\n <td>-61.613406</td>\n <td>-20.815381</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-79.670707</td>\n <td>0.871678</td>\n <td>-169.582506</td>\n <td>15.074372</td>\n <td>-37.832893</td>\n <td>18.983185</td>\n <td>10.811182</td>\n </tr>\n <tr>\n <th>loop_1C.pdb</th>\n <td>-0.790311</td>\n <td>-590.716545</td>\n <td>-249.786929</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>619.629560</td>\n <td>356.905338</td>\n <td>-20.494898</td>\n <td>0.592360</td>\n <td>27.96275</td>\n <td>...</td>\n <td>-61.302003</td>\n <td>-20.815381</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.073495</td>\n <td>0.871678</td>\n <td>-159.627644</td>\n <td>15.107859</td>\n <td>-35.413731</td>\n <td>18.933559</td>\n <td>10.671736</td>\n </tr>\n <tr>\n <th rowspan=\"27\" valign=\"top\">loop13</th>\n <th>loop_1A_3A.pdb</th>\n <td>0.521399</td>\n <td>-592.508183</td>\n <td>-254.563644</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>619.120770</td>\n <td>358.770438</td>\n <td>-20.494898</td>\n <td>0.592360</td>\n <td>29.30082</td>\n <td>...</td>\n <td>-57.893993</td>\n <td>-17.279610</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-81.809269</td>\n <td>0.871678</td>\n <td>-160.219676</td>\n <td>12.033803</td>\n <td>-37.832893</td>\n <td>19.223833</td>\n <td>11.273045</td>\n </tr>\n <tr>\n <th>loop_1A_3B.pdb</th>\n <td>-0.101111</td>\n <td>-583.517849</td>\n <td>-249.270822</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>615.810275</td>\n <td>352.451832</td>\n <td>-19.255723</td>\n <td>1.021082</td>\n <td>29.39556</td>\n <td>...</td>\n <td>-56.497931</td>\n <td>-17.279610</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-80.669545</td>\n <td>0.871678</td>\n <td>-154.037035</td>\n <td>12.717758</td>\n <td>-37.832893</td>\n <td>18.701686</td>\n <td>12.507425</td>\n </tr>\n <tr>\n <th>loop_1A_3C.pdb</th>\n <td>0.088271</td>\n <td>-578.918702</td>\n <td>-250.065673</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>615.341905</td>\n <td>350.977102</td>\n <td>-19.255723</td>\n <td>0.479743</td>\n <td>31.03877</td>\n <td>...</td>\n <td>-55.209486</td>\n <td>-17.279610</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-80.652393</td>\n <td>0.871678</td>\n <td>-149.975857</td>\n <td>13.693157</td>\n <td>-37.832893</td>\n <td>18.694548</td>\n <td>9.956815</td>\n </tr>\n <tr>\n <th>loop_1A_3D.pdb</th>\n <td>0.016544</td>\n <td>-574.750127</td>\n <td>-250.440884</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>612.342751</td>\n <td>351.245406</td>\n <td>-19.255723</td>\n <td>1.021082</td>\n <td>27.09182</td>\n <td>...</td>\n <td>-56.370072</td>\n <td>-17.279610</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-80.669545</td>\n <td>0.871678</td>\n <td>-154.604768</td>\n <td>12.415455</td>\n <td>-37.832893</td>\n <td>18.454402</td>\n <td>12.520862</td>\n </tr>\n <tr>\n <th>loop_1A_3E.pdb</th>\n <td>0.210270</td>\n <td>-570.325795</td>\n <td>-250.813399</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>611.874380</td>\n <td>349.900989</td>\n <td>-19.255723</td>\n <td>0.479743</td>\n <td>28.73503</td>\n <td>...</td>\n <td>-55.081628</td>\n <td>-17.279610</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-80.652393</td>\n <td>0.871678</td>\n <td>-150.161413</td>\n <td>13.390854</td>\n <td>-37.832893</td>\n <td>18.447264</td>\n <td>9.970252</td>\n </tr>\n <tr>\n <th>loop_1A_3F.pdb</th>\n <td>-0.448273</td>\n <td>-607.401244</td>\n <td>-257.298830</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>187.595020</td>\n <td>381.462721</td>\n <td>-17.240688</td>\n <td>0.412579</td>\n <td>27.98825</td>\n <td>...</td>\n <td>-59.115526</td>\n <td>-18.445242</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-83.838991</td>\n <td>0.004762</td>\n <td>-365.075957</td>\n <td>15.200993</td>\n <td>-33.568555</td>\n <td>21.344730</td>\n <td>11.072534</td>\n </tr>\n <tr>\n <th>loop_1A_3G.pdb</th>\n <td>0.571688</td>\n <td>-598.779473</td>\n <td>-254.215769</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>186.718730</td>\n <td>374.013345</td>\n <td>-15.726783</td>\n <td>0.412579</td>\n <td>28.53035</td>\n <td>...</td>\n <td>-56.521674</td>\n <td>-18.445242</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-82.430703</td>\n <td>0.004762</td>\n <td>-356.139812</td>\n <td>18.905274</td>\n <td>-33.568555</td>\n <td>21.024869</td>\n <td>11.326025</td>\n </tr>\n <tr>\n <th>loop_1A_3H.pdb</th>\n <td>1.695791</td>\n <td>-603.989633</td>\n <td>-263.734414</td>\n <td>-0.933767</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>717.181635</td>\n <td>381.332831</td>\n <td>-21.991998</td>\n <td>0.519413</td>\n <td>23.29555</td>\n <td>...</td>\n <td>-55.131337</td>\n <td>-17.602364</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-85.514202</td>\n <td>0.605638</td>\n <td>-106.818819</td>\n <td>17.291149</td>\n <td>-40.690320</td>\n <td>20.374454</td>\n <td>13.016483</td>\n </tr>\n <tr>\n <th>loop_1A_3I.pdb</th>\n <td>-0.479444</td>\n <td>-593.911496</td>\n <td>-251.079925</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>186.071090</td>\n <td>371.243396</td>\n <td>-15.726783</td>\n <td>0.412579</td>\n <td>27.20567</td>\n <td>...</td>\n <td>-56.558067</td>\n <td>-18.445242</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-81.018535</td>\n <td>0.004762</td>\n <td>-352.036319</td>\n <td>19.075430</td>\n <td>-33.568555</td>\n <td>21.066347</td>\n <td>11.438556</td>\n </tr>\n <tr>\n <th>loop_1A_3J.pdb</th>\n <td>1.583147</td>\n <td>-598.428659</td>\n <td>-262.248310</td>\n <td>-0.933767</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>716.216153</td>\n <td>377.758857</td>\n <td>-21.991998</td>\n <td>0.519413</td>\n <td>22.14380</td>\n <td>...</td>\n <td>-55.196019</td>\n <td>-17.602364</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-83.977161</td>\n <td>0.605638</td>\n <td>-103.403925</td>\n <td>17.696756</td>\n <td>-40.690320</td>\n <td>20.666487</td>\n <td>12.738688</td>\n </tr>\n <tr>\n <th>loop_1A_3K.pdb</th>\n <td>0.383381</td>\n <td>-595.452923</td>\n <td>-262.720240</td>\n <td>-0.962284</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>337.355151</td>\n <td>370.708394</td>\n <td>-21.949849</td>\n <td>0.526784</td>\n <td>26.06090</td>\n <td>...</td>\n <td>-58.647574</td>\n <td>-17.652317</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-82.610431</td>\n <td>0.004241</td>\n <td>-316.906056</td>\n <td>18.670808</td>\n <td>-38.264223</td>\n <td>18.827019</td>\n <td>14.620069</td>\n </tr>\n <tr>\n <th>loop_1A_3L.pdb</th>\n <td>-1.312678</td>\n <td>-581.334877</td>\n <td>-248.265871</td>\n <td>-0.956218</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>237.753637</td>\n <td>355.962917</td>\n <td>-15.788587</td>\n <td>0.441025</td>\n <td>30.54229</td>\n <td>...</td>\n <td>-57.286482</td>\n <td>-18.382021</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-84.155259</td>\n <td>0.026246</td>\n <td>-332.268063</td>\n <td>10.487782</td>\n <td>-27.713510</td>\n <td>19.226782</td>\n <td>15.050501</td>\n </tr>\n <tr>\n <th>loop_1A_3M.pdb</th>\n <td>-0.296429</td>\n <td>-582.702013</td>\n <td>-242.280478</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>183.930235</td>\n <td>357.720234</td>\n <td>-15.726783</td>\n <td>0.412579</td>\n <td>31.15526</td>\n <td>...</td>\n <td>-56.290641</td>\n <td>-18.445242</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-79.904241</td>\n <td>0.004762</td>\n <td>-348.141557</td>\n <td>10.533591</td>\n <td>-29.037535</td>\n <td>20.028875</td>\n <td>10.922606</td>\n </tr>\n <tr>\n <th>loop_1A_3N.pdb</th>\n <td>-1.342802</td>\n <td>-577.844870</td>\n <td>-239.146820</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>183.282595</td>\n <td>354.887287</td>\n <td>-15.726783</td>\n <td>0.412579</td>\n <td>29.83058</td>\n <td>...</td>\n <td>-56.327034</td>\n <td>-18.445242</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.492073</td>\n <td>0.004762</td>\n <td>-344.109325</td>\n <td>10.703747</td>\n <td>-29.037535</td>\n <td>20.070353</td>\n <td>11.035137</td>\n </tr>\n <tr>\n <th>loop_1B_3A.pdb</th>\n <td>-0.186486</td>\n <td>-586.662698</td>\n <td>-248.933277</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>617.883115</td>\n <td>353.118093</td>\n <td>-20.494898</td>\n <td>0.592360</td>\n <td>30.75177</td>\n <td>...</td>\n <td>-57.553433</td>\n <td>-17.279610</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-79.707185</td>\n <td>0.871678</td>\n <td>-155.356135</td>\n <td>11.906110</td>\n <td>-37.832893</td>\n <td>18.913583</td>\n <td>11.177845</td>\n </tr>\n <tr>\n <th>loop_1B_3B.pdb</th>\n <td>-0.808995</td>\n <td>-577.672366</td>\n <td>-243.640456</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>614.572620</td>\n <td>346.799487</td>\n <td>-19.255723</td>\n <td>1.021082</td>\n <td>30.84651</td>\n <td>...</td>\n <td>-56.157371</td>\n <td>-17.279610</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.567460</td>\n <td>0.871678</td>\n <td>-149.173495</td>\n <td>12.590066</td>\n <td>-37.832893</td>\n <td>18.391435</td>\n <td>12.412225</td>\n </tr>\n <tr>\n <th>loop_1B_3C.pdb</th>\n <td>-0.619613</td>\n <td>-573.073219</td>\n <td>-244.435307</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>614.104250</td>\n <td>345.324757</td>\n <td>-19.255723</td>\n <td>0.479743</td>\n <td>32.48972</td>\n <td>...</td>\n <td>-54.868926</td>\n <td>-17.279610</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.550308</td>\n <td>0.871678</td>\n <td>-145.112318</td>\n <td>13.565465</td>\n <td>-37.832893</td>\n <td>18.384297</td>\n <td>9.861614</td>\n </tr>\n <tr>\n <th>loop_1B_3D.pdb</th>\n <td>-0.727621</td>\n <td>-569.832140</td>\n <td>-244.850472</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>611.379914</td>\n <td>345.140518</td>\n <td>-19.255723</td>\n <td>1.021082</td>\n <td>28.54277</td>\n <td>...</td>\n <td>-56.029512</td>\n <td>-17.279610</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.567460</td>\n <td>0.871678</td>\n <td>-151.046352</td>\n <td>12.287763</td>\n <td>-37.832893</td>\n <td>18.144152</td>\n <td>12.425662</td>\n </tr>\n <tr>\n <th>loop_1B_3E.pdb</th>\n <td>-0.533895</td>\n <td>-565.407809</td>\n <td>-245.222987</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>610.911544</td>\n <td>343.796101</td>\n <td>-19.255723</td>\n <td>0.479743</td>\n <td>30.18598</td>\n <td>...</td>\n <td>-54.741068</td>\n <td>-17.279610</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.550308</td>\n <td>0.871678</td>\n <td>-146.602997</td>\n <td>13.263162</td>\n <td>-37.832893</td>\n <td>18.137013</td>\n <td>9.875052</td>\n </tr>\n <tr>\n <th>loop_1B_3F.pdb</th>\n <td>-0.801441</td>\n <td>-597.689660</td>\n <td>-252.086153</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>184.164420</td>\n <td>373.202431</td>\n <td>-17.240688</td>\n <td>0.412579</td>\n <td>29.43920</td>\n <td>...</td>\n <td>-58.624095</td>\n <td>-18.445242</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-82.690396</td>\n <td>0.004762</td>\n <td>-361.857522</td>\n <td>15.831030</td>\n <td>-32.215263</td>\n <td>20.889205</td>\n <td>11.131266</td>\n </tr>\n <tr>\n <th>loop_1B_3G.pdb</th>\n <td>0.218520</td>\n <td>-589.068576</td>\n <td>-249.003092</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>183.288130</td>\n <td>365.753055</td>\n <td>-15.726783</td>\n <td>0.412579</td>\n <td>29.98130</td>\n <td>...</td>\n <td>-56.030243</td>\n <td>-18.445242</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-81.282109</td>\n <td>0.004762</td>\n <td>-352.922065</td>\n <td>19.535311</td>\n <td>-32.215263</td>\n <td>20.569344</td>\n <td>11.384757</td>\n </tr>\n <tr>\n <th>loop_1B_3H.pdb</th>\n <td>1.486190</td>\n <td>-596.434917</td>\n <td>-258.801441</td>\n <td>-0.933767</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>715.613300</td>\n <td>373.803127</td>\n <td>-21.991998</td>\n <td>0.519413</td>\n <td>24.74650</td>\n <td>...</td>\n <td>-54.754017</td>\n <td>-17.602364</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-82.657385</td>\n <td>0.605638</td>\n <td>-103.424996</td>\n <td>17.096448</td>\n <td>-40.690320</td>\n <td>19.553933</td>\n <td>12.899527</td>\n </tr>\n <tr>\n <th>loop_1B_3I.pdb</th>\n <td>-0.832612</td>\n <td>-584.200599</td>\n <td>-245.867249</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>182.640490</td>\n <td>362.983107</td>\n <td>-15.726783</td>\n <td>0.412579</td>\n <td>28.65662</td>\n <td>...</td>\n <td>-56.066637</td>\n <td>-18.445242</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-79.869940</td>\n <td>0.004762</td>\n <td>-348.818573</td>\n <td>19.705467</td>\n <td>-32.215263</td>\n <td>20.610822</td>\n <td>11.497288</td>\n </tr>\n <tr>\n <th>loop_1B_3J.pdb</th>\n <td>1.373545</td>\n <td>-590.873942</td>\n <td>-257.315337</td>\n <td>-0.933767</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>714.647818</td>\n <td>370.229153</td>\n <td>-21.991998</td>\n <td>0.519413</td>\n <td>23.59475</td>\n <td>...</td>\n <td>-54.818699</td>\n <td>-17.602364</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-81.120344</td>\n <td>0.605638</td>\n <td>-100.010102</td>\n <td>17.502056</td>\n <td>-40.690320</td>\n <td>19.845966</td>\n <td>12.621732</td>\n </tr>\n <tr>\n <th>loop_1B_3K.pdb</th>\n <td>0.424920</td>\n <td>-587.790616</td>\n <td>-257.148094</td>\n <td>-0.962284</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>335.900858</td>\n <td>363.065825</td>\n <td>-21.949849</td>\n <td>0.526784</td>\n <td>27.51185</td>\n <td>...</td>\n <td>-58.269361</td>\n <td>-17.652317</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-79.911496</td>\n <td>0.004241</td>\n <td>-311.259403</td>\n <td>18.466418</td>\n <td>-38.264223</td>\n <td>18.489694</td>\n <td>14.409994</td>\n </tr>\n <tr>\n <th>loop_1B_3L.pdb</th>\n <td>-0.867992</td>\n <td>-572.415757</td>\n <td>-244.662952</td>\n <td>-0.956218</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>236.340487</td>\n <td>348.415674</td>\n <td>-15.788587</td>\n <td>0.441025</td>\n <td>31.99324</td>\n <td>...</td>\n <td>-56.396332</td>\n <td>-18.382021</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-82.762609</td>\n <td>0.026246</td>\n <td>-329.505766</td>\n <td>11.401726</td>\n <td>-27.713510</td>\n <td>18.784556</td>\n <td>14.964063</td>\n </tr>\n <tr>\n <th>loop_1B_3M.pdb</th>\n <td>-0.722697</td>\n <td>-576.794376</td>\n <td>-238.658991</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>182.751493</td>\n <td>351.591836</td>\n <td>-15.726783</td>\n <td>0.412579</td>\n <td>32.60621</td>\n <td>...</td>\n <td>-55.799210</td>\n <td>-18.445242</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.837536</td>\n <td>0.004762</td>\n <td>-348.456129</td>\n <td>11.163628</td>\n <td>-29.037535</td>\n <td>19.573351</td>\n <td>10.981338</td>\n </tr>\n <tr>\n <th>...</th>\n <th>...</th>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n </tr>\n <tr>\n <th rowspan=\"5\" valign=\"top\">loop35</th>\n <th>loop_3M_5E.pdb</th>\n <td>-0.215914</td>\n <td>-576.231562</td>\n <td>-248.040739</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>181.097740</td>\n <td>363.352826</td>\n <td>-17.103376</td>\n <td>0.412579</td>\n <td>25.71137</td>\n <td>...</td>\n <td>-56.122316</td>\n <td>-20.330856</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-79.838828</td>\n <td>0.004762</td>\n <td>-347.473800</td>\n <td>16.240633</td>\n <td>-29.037535</td>\n <td>19.939435</td>\n <td>11.454939</td>\n </tr>\n <tr>\n <th>loop_3N_5A.pdb</th>\n <td>-0.669145</td>\n <td>-557.705168</td>\n <td>-240.179708</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>176.374920</td>\n <td>350.971757</td>\n <td>-17.103376</td>\n <td>0.365199</td>\n <td>26.57200</td>\n <td>...</td>\n <td>-54.227543</td>\n <td>-20.330856</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-76.435942</td>\n <td>0.004762</td>\n <td>-331.528546</td>\n <td>18.628428</td>\n <td>-29.037535</td>\n <td>19.652264</td>\n <td>11.265637</td>\n </tr>\n <tr>\n <th>loop_3N_5B.pdb</th>\n <td>-0.811751</td>\n <td>-547.888672</td>\n <td>-235.514330</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>170.845333</td>\n <td>344.759964</td>\n <td>-17.175330</td>\n <td>0.365199</td>\n <td>24.91465</td>\n <td>...</td>\n <td>-54.690251</td>\n <td>-20.330856</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-75.018750</td>\n <td>0.004762</td>\n <td>-328.617641</td>\n <td>18.582039</td>\n <td>-29.037535</td>\n <td>19.574523</td>\n <td>11.361671</td>\n </tr>\n <tr>\n <th>loop_3N_5C.pdb</th>\n <td>-1.302248</td>\n <td>-538.265630</td>\n <td>-223.711057</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>168.339416</td>\n <td>333.148731</td>\n <td>-15.557610</td>\n <td>0.365199</td>\n <td>25.62923</td>\n <td>...</td>\n <td>-53.711454</td>\n <td>-20.330856</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-73.816424</td>\n <td>0.004762</td>\n <td>-317.281769</td>\n <td>19.010809</td>\n <td>-27.646128</td>\n <td>19.378838</td>\n <td>11.197360</td>\n </tr>\n <tr>\n <th>loop_3N_5E.pdb</th>\n <td>-1.219428</td>\n <td>-571.593187</td>\n <td>-245.173269</td>\n <td>-0.785559</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>180.450100</td>\n <td>360.191119</td>\n <td>-17.103376</td>\n <td>0.412579</td>\n <td>24.38669</td>\n <td>...</td>\n <td>-56.158709</td>\n <td>-20.330856</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.426660</td>\n <td>0.004762</td>\n <td>-344.212424</td>\n <td>16.410789</td>\n <td>-29.037535</td>\n <td>19.980913</td>\n <td>11.567470</td>\n </tr>\n <tr>\n <th rowspan=\"5\" valign=\"top\">loop5</th>\n <th>loop_5A.pdb</th>\n <td>1.187429</td>\n <td>-583.614182</td>\n <td>-263.941161</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>617.880765</td>\n <td>365.239642</td>\n <td>-23.644610</td>\n <td>0.545919</td>\n <td>24.40497</td>\n <td>...</td>\n <td>-60.122051</td>\n <td>-22.940598</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.846426</td>\n <td>0.871678</td>\n <td>-161.063454</td>\n <td>20.279623</td>\n <td>-39.132055</td>\n <td>18.889458</td>\n <td>10.878454</td>\n </tr>\n <tr>\n <th>loop_5B.pdb</th>\n <td>1.100593</td>\n <td>-572.729804</td>\n <td>-258.801959</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>610.901227</td>\n <td>358.638877</td>\n <td>-23.644219</td>\n <td>0.545919</td>\n <td>22.74762</td>\n <td>...</td>\n <td>-60.638893</td>\n <td>-22.940598</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-77.178787</td>\n <td>0.871678</td>\n <td>-157.625146</td>\n <td>20.066192</td>\n <td>-39.132055</td>\n <td>18.807489</td>\n <td>10.878177</td>\n </tr>\n <tr>\n <th>loop_5C.pdb</th>\n <td>0.669895</td>\n <td>-563.689435</td>\n <td>-246.888954</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>608.968468</td>\n <td>347.327873</td>\n <td>-21.552936</td>\n <td>0.545919</td>\n <td>23.46220</td>\n <td>...</td>\n <td>-59.563071</td>\n <td>-22.940598</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-76.227524</td>\n <td>0.871678</td>\n <td>-145.217692</td>\n <td>20.557862</td>\n <td>-37.621672</td>\n <td>18.589586</td>\n <td>11.111255</td>\n </tr>\n <tr>\n <th>loop_5D.pdb</th>\n <td>-1.385064</td>\n <td>-577.584922</td>\n <td>-249.491326</td>\n <td>-0.954132</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>630.180791</td>\n <td>367.413935</td>\n <td>-25.183996</td>\n <td>0.695641</td>\n <td>22.72914</td>\n <td>...</td>\n <td>-60.531247</td>\n <td>-21.125742</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-76.806353</td>\n <td>0.417203</td>\n <td>-116.582986</td>\n <td>11.838985</td>\n <td>-30.924892</td>\n <td>19.834835</td>\n <td>26.905132</td>\n </tr>\n <tr>\n <th>loop_5E.pdb</th>\n <td>0.619011</td>\n <td>-597.635675</td>\n <td>-267.995296</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>621.661519</td>\n <td>375.210991</td>\n <td>-23.644610</td>\n <td>0.592360</td>\n <td>22.21966</td>\n <td>...</td>\n <td>-61.894800</td>\n <td>-22.940598</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-80.690265</td>\n <td>0.871678</td>\n <td>-171.997096</td>\n <td>17.964725</td>\n <td>-39.132055</td>\n <td>19.221867</td>\n <td>11.457418</td>\n </tr>\n <tr>\n <th rowspan=\"16\" valign=\"top\">loop57</th>\n <th>loop_7A_5A.pdb</th>\n <td>1.660496</td>\n <td>-573.253056</td>\n <td>-258.583037</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>615.363473</td>\n <td>356.555268</td>\n <td>-21.552936</td>\n <td>0.545919</td>\n <td>26.04224</td>\n <td>...</td>\n <td>-55.909379</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-79.190906</td>\n <td>0.871678</td>\n <td>-148.049358</td>\n <td>18.665225</td>\n <td>-39.132055</td>\n <td>18.600627</td>\n <td>11.313952</td>\n </tr>\n <tr>\n <th>loop_7A_5B.pdb</th>\n <td>1.088464</td>\n <td>-563.369338</td>\n <td>-254.110248</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>608.435321</td>\n <td>350.273875</td>\n <td>-21.552936</td>\n <td>0.545919</td>\n <td>24.38489</td>\n <td>...</td>\n <td>-56.426221</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-77.523267</td>\n <td>0.871678</td>\n <td>-146.416074</td>\n <td>18.451794</td>\n <td>-39.132055</td>\n <td>18.518659</td>\n <td>11.313675</td>\n </tr>\n <tr>\n <th>loop_7A_5C.pdb</th>\n <td>1.082178</td>\n <td>-556.185329</td>\n <td>-247.722720</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>606.840310</td>\n <td>341.466929</td>\n <td>-21.552936</td>\n <td>0.545919</td>\n <td>25.09947</td>\n <td>...</td>\n <td>-55.350398</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-77.515373</td>\n <td>0.871678</td>\n <td>-141.310880</td>\n <td>18.943464</td>\n <td>-37.621672</td>\n <td>18.300756</td>\n <td>11.546752</td>\n </tr>\n <tr>\n <th>loop_7A_5E.pdb</th>\n <td>1.080582</td>\n <td>-587.265177</td>\n <td>-262.821223</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>619.144227</td>\n <td>366.481152</td>\n <td>-21.552936</td>\n <td>0.592360</td>\n <td>23.85693</td>\n <td>...</td>\n <td>-57.682127</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-81.034745</td>\n <td>0.871678</td>\n <td>-159.214641</td>\n <td>16.350327</td>\n <td>-39.132055</td>\n <td>18.933037</td>\n <td>11.892916</td>\n </tr>\n <tr>\n <th>loop_7B_5A.pdb</th>\n <td>1.255204</td>\n <td>-566.249800</td>\n <td>-252.837511</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>615.061890</td>\n <td>348.611371</td>\n <td>-20.438285</td>\n <td>0.545919</td>\n <td>26.33193</td>\n <td>...</td>\n <td>-56.074248</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-77.903057</td>\n <td>0.871678</td>\n <td>-140.026638</td>\n <td>18.926184</td>\n <td>-37.340823</td>\n <td>18.545264</td>\n <td>11.097749</td>\n </tr>\n <tr>\n <th>loop_7B_5B.pdb</th>\n <td>0.683173</td>\n <td>-556.366082</td>\n <td>-248.364722</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>608.133737</td>\n <td>342.329978</td>\n <td>-20.438285</td>\n <td>0.545919</td>\n <td>24.67458</td>\n <td>...</td>\n <td>-56.591090</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-76.235418</td>\n <td>0.871678</td>\n <td>-138.393355</td>\n <td>18.712753</td>\n <td>-37.340823</td>\n <td>18.463295</td>\n <td>11.097472</td>\n </tr>\n <tr>\n <th>loop_7B_5C.pdb</th>\n <td>0.676887</td>\n <td>-549.182073</td>\n <td>-241.977194</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>606.538727</td>\n <td>333.523032</td>\n <td>-20.438285</td>\n <td>0.545919</td>\n <td>25.38916</td>\n <td>...</td>\n <td>-55.515268</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-76.227524</td>\n <td>0.871678</td>\n <td>-133.288161</td>\n <td>19.204424</td>\n <td>-35.830440</td>\n <td>18.245393</td>\n <td>11.330549</td>\n </tr>\n <tr>\n <th>loop_7B_5E.pdb</th>\n <td>0.675291</td>\n <td>-580.261922</td>\n <td>-257.075697</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>618.842644</td>\n <td>358.537255</td>\n <td>-20.438285</td>\n <td>0.592360</td>\n <td>24.14662</td>\n <td>...</td>\n <td>-57.846997</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-79.746896</td>\n <td>0.871678</td>\n <td>-151.191922</td>\n <td>16.611286</td>\n <td>-37.340823</td>\n <td>18.877674</td>\n <td>11.676713</td>\n </tr>\n <tr>\n <th>loop_7C_5A.pdb</th>\n <td>0.438562</td>\n <td>-557.341038</td>\n <td>-238.651946</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>613.153185</td>\n <td>337.093863</td>\n <td>-19.493335</td>\n <td>0.545919</td>\n <td>27.04651</td>\n <td>...</td>\n <td>-55.812689</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-76.844600</td>\n <td>0.871678</td>\n <td>-128.717674</td>\n <td>18.339766</td>\n <td>-35.808319</td>\n <td>18.426568</td>\n <td>10.893522</td>\n </tr>\n <tr>\n <th>loop_7C_5B.pdb</th>\n <td>-0.133470</td>\n <td>-547.457320</td>\n <td>-234.179157</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>606.225033</td>\n <td>330.812469</td>\n <td>-19.493335</td>\n <td>0.545919</td>\n <td>25.38916</td>\n <td>...</td>\n <td>-56.329531</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-75.176960</td>\n <td>0.871678</td>\n <td>-127.084391</td>\n <td>18.126335</td>\n <td>-35.808319</td>\n <td>18.344600</td>\n <td>10.893245</td>\n </tr>\n <tr>\n <th>loop_7C_5C.pdb</th>\n <td>-0.139756</td>\n <td>-540.273311</td>\n <td>-227.791630</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>604.630022</td>\n <td>322.005523</td>\n <td>-19.493335</td>\n <td>0.545919</td>\n <td>26.10374</td>\n <td>...</td>\n <td>-55.253709</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-75.169067</td>\n <td>0.871678</td>\n <td>-121.979197</td>\n <td>18.618005</td>\n <td>-34.297936</td>\n <td>18.126697</td>\n <td>11.126322</td>\n </tr>\n <tr>\n <th>loop_7C_5E.pdb</th>\n <td>-0.141352</td>\n <td>-571.353160</td>\n <td>-242.890133</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>616.933939</td>\n <td>347.019746</td>\n <td>-19.493335</td>\n <td>0.592360</td>\n <td>24.86120</td>\n <td>...</td>\n <td>-57.585438</td>\n <td>-19.179380</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.688438</td>\n <td>0.871678</td>\n <td>-139.882958</td>\n <td>16.024868</td>\n <td>-35.808319</td>\n <td>18.758978</td>\n <td>11.472486</td>\n </tr>\n <tr>\n <th>loop_7D_5A.pdb</th>\n <td>0.652506</td>\n <td>-582.831819</td>\n <td>-256.696897</td>\n <td>-0.960594</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>572.533083</td>\n <td>361.896245</td>\n <td>-22.388870</td>\n <td>0.790544</td>\n <td>26.09307</td>\n <td>...</td>\n <td>-56.536068</td>\n <td>-18.936168</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-82.416527</td>\n <td>0.845762</td>\n <td>-167.605163</td>\n <td>18.471743</td>\n <td>-38.520539</td>\n <td>19.017233</td>\n <td>18.146724</td>\n </tr>\n <tr>\n <th>loop_7D_5B.pdb</th>\n <td>0.363684</td>\n <td>-572.901511</td>\n <td>-252.417547</td>\n <td>-0.960594</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>566.091242</td>\n <td>355.710003</td>\n <td>-22.388870</td>\n <td>0.790544</td>\n <td>24.43572</td>\n <td>...</td>\n <td>-56.998376</td>\n <td>-18.936168</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-81.033439</td>\n <td>0.845762</td>\n <td>-165.602157</td>\n <td>18.366955</td>\n <td>-38.520539</td>\n <td>18.933465</td>\n <td>18.174656</td>\n </tr>\n <tr>\n <th>loop_7D_5C.pdb</th>\n <td>-0.244013</td>\n <td>-563.440934</td>\n <td>-239.483529</td>\n <td>-0.960594</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>564.170107</td>\n <td>344.121480</td>\n <td>-22.388870</td>\n <td>0.790544</td>\n <td>25.15030</td>\n <td>...</td>\n <td>-56.195917</td>\n <td>-18.936168</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.834448</td>\n <td>0.845762</td>\n <td>-153.686708</td>\n <td>18.644928</td>\n <td>-37.053212</td>\n <td>18.728098</td>\n <td>17.968875</td>\n </tr>\n <tr>\n <th>loop_7D_5E.pdb</th>\n <td>0.006896</td>\n <td>-596.660985</td>\n <td>-261.375255</td>\n <td>-0.960594</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>576.123672</td>\n <td>371.162245</td>\n <td>-22.388870</td>\n <td>0.817205</td>\n <td>23.90776</td>\n <td>...</td>\n <td>-58.416146</td>\n <td>-18.936168</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-84.402576</td>\n <td>0.845762</td>\n <td>-180.011525</td>\n <td>16.438733</td>\n <td>-38.520539</td>\n <td>19.342830</td>\n <td>18.820410</td>\n </tr>\n <tr>\n <th rowspan=\"4\" valign=\"top\">loop7</th>\n <th>loop_7A.pdb</th>\n <td>0.488278</td>\n <td>-609.650988</td>\n <td>-264.488945</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>623.499468</td>\n <td>375.479621</td>\n <td>-24.655289</td>\n <td>0.592360</td>\n <td>25.22871</td>\n <td>...</td>\n <td>-60.752253</td>\n <td>-20.921207</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-81.154763</td>\n <td>0.871678</td>\n <td>-178.287852</td>\n <td>15.572039</td>\n <td>-39.132055</td>\n <td>19.014853</td>\n <td>11.107272</td>\n </tr>\n <tr>\n <th>loop_7B.pdb</th>\n <td>0.082987</td>\n <td>-602.647732</td>\n <td>-258.743419</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>623.197885</td>\n <td>367.535724</td>\n <td>-23.540638</td>\n <td>0.592360</td>\n <td>25.51840</td>\n <td>...</td>\n <td>-60.917122</td>\n <td>-20.921207</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-79.866915</td>\n <td>0.871678</td>\n <td>-170.265132</td>\n <td>15.832998</td>\n <td>-37.340823</td>\n <td>18.959489</td>\n <td>10.891068</td>\n </tr>\n <tr>\n <th>loop_7C.pdb</th>\n <td>-0.733656</td>\n <td>-593.738970</td>\n <td>-244.557854</td>\n <td>-0.959038</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>621.289180</td>\n <td>356.018216</td>\n <td>-22.595688</td>\n <td>0.592360</td>\n <td>26.23298</td>\n <td>...</td>\n <td>-60.655563</td>\n <td>-20.921207</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-78.808457</td>\n <td>0.871678</td>\n <td>-158.956169</td>\n <td>15.246580</td>\n <td>-35.808319</td>\n <td>18.840794</td>\n <td>10.686841</td>\n </tr>\n <tr>\n <th>loop_7D.pdb</th>\n <td>-0.787984</td>\n <td>-616.995915</td>\n <td>-261.105225</td>\n <td>-0.960594</td>\n <td>2017.48.post.dev+92.fordas.dev.17260dd14b0</td>\n <td>580.830213</td>\n <td>378.765998</td>\n <td>-24.236830</td>\n <td>0.817205</td>\n <td>25.27954</td>\n <td>...</td>\n <td>-61.595987</td>\n <td>-20.711738</td>\n <td>gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2...</td>\n <td>-84.609973</td>\n <td>0.845762</td>\n <td>-195.578016</td>\n <td>15.452874</td>\n <td>-38.520539</td>\n <td>19.426485</td>\n <td>17.927649</td>\n </tr>\n </tbody>\n</table>\n<p>133 rows × 23 columns</p>\n</div>"
},
"metadata": {}
}
]
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "input_poses = packed_pose.to_packed(input_decoys.reset_index(\"group\", drop=True))",
"execution_count": 176,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "def zip_pack(kvps):\n from io import BytesIO\n from zipfile import ZipFile, ZIP_DEFLATED\n from collections.abc import Mapping\n\n if isinstance(kvps,Mapping):\n kvps = kvps.items()\n\n iob = BytesIO()\n\n with ZipFile(iob, \"w\", compression=ZIP_DEFLATED) as archive:\n for k, v in kvps:\n archive.writestr(k, v)\n\n return iob.getvalue()\n\ndef write_records_and_pdbs(pose_bag, output_prefix, output_partitions = 8):\n \n def stripped_output_record(p):\n from pyrosetta.distributed.io import to_output_record\n p = to_output_record(p)\n del p[\"pickled_pose\"]\n \n return p\n \n output_records = pose_bag.map(stripped_output_record).repartition(output_partitions)\n \n @dask.delayed\n def zip_bytes(index_key, records):\n return zip_pack((index_key(i), r) for i, r in enumerate(records))\n\n @toolz.curry\n def format_name(i, j):\n return \"%i_%i.pdb\" % (i, j)\n \n zip_contents = [\n zip_bytes(format_name(i), pdbs)\n for i, pdbs in enumerate(output_records.map(get(\"pdb_pose\")).to_delayed())\n ]\n\n write_pdb, pdb_output_path = dask.bytes.core.write_bytes(\n zip_contents,\n output_prefix + \"*.decoy_pdbs.zip\",\n compression=None,\n )\n \n json_contents = output_records.map(json.dumps).to_delayed()\n\n write_json, json_output_path = dask.bytes.core.write_bytes(\n json_contents,\n output_prefix + \"*.decoy_records.json.gz\",\n compression=\"gzip\", encoding=\"utf-8\"\n )\n\n return {\n \"write_pdb\" : write_pdb,\n \"write_json\" : write_json,\n \"pdb_output_paths\" : pdb_output_path, \n \"json_output_paths\" : json_output_path, \n }\n\n return result ",
"execution_count": 189,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "client.restart()",
"execution_count": 185,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 185,
"data": {
"text/plain": "<Client: sche...ses=0 cores=0>",
"text/html": "<table style=\"border: 2px solid white;\">\n<tr>\n<td style=\"vertical-align: top; border: 0px solid white\">\n<h3>Client</h3>\n<ul>\n <li><b>Scheduler: </b>tcp://salish:8786\n <li><b>Dashboard: </b><a href='http://salish:8787' target='_blank'>http://salish:8787</a>\n</ul>\n</td>\n<td style=\"vertical-align: top; border: 0px solid white\">\n<h3>Cluster</h3>\n<ul>\n <li><b>Workers: </b>4</li>\n <li><b>Cores: </b>60</li>\n <li><b>Memory: </b>237.73 GB</li>\n</ul>\n</td>\n</tr>\n</table>"
},
"metadata": {}
}
]
},
{
"metadata": {
"trusted": true,
"code_folding": []
},
"cell_type": "code",
"source": "import json\nimport pyrosetta.distributed.io as io\nimport pyrosetta.distributed.tasks.score as score\n\nimport topology_closure\nimport importlib\ntopology_closure = importlib.reload(topology_closure)\n\nclosure_manager = topology_closure.TopologyClosureManager(\n segment_lookup_xml,\n segment_refinement_xml,\n max_refinement_tasks = 64 * 32,\n candidates_per_closure_length = 8,\n candidates_per_closure = 64,\n decoys_per_closure_path = 64 * 64,\n)\n\noutput_prefix=\"gs://protein-design-ipd-public/190104_barrel_closure_generation\"\n\ndef initial_analysis(name, input_structure):\n logger = logging.getLogger(\"close_and_refine\")\n\n input_chains = list(packed_pose.to_pose(input_structure).split_by_chain())\n logger.info(\"loaded input chains: %s\", len(input_chains))\n \n assert input_chains[-1].annotated_sequence() == \"Z[pdb_HBI]\"\n input_chains = input_chains[:-1]\n \n closure_result = closure_manager.initialize(input_chains)\n closure_manager.closure_analysis(closure_result, \"source_order\")\n \n closure_manager.refine_closure_analysis(closure_result)\n closure_manager.connectivity_analysis(closure_result)\n \n result = closure_result._trait_values\n result[\"name\"] = name\n \n @dask.delayed\n def flatten(decoys):\n results = []\n for k, v in decoys.items():\n results.extend(v)\n return results\n \n decoys =(\n dask.bag.from_delayed(flatten(result[\"closed_decoys\"]))\n .repartition(64)\n .map(score.ScorePoseTask())\n )\n \n\n result.update(\n write_records_and_pdbs(\n decoys, \n \"gs://protein-design-ipd-public/190104_barrel_closure_generation/%s/\" % os.path.splitext(name)[0],\n 1\n )\n )\n \n return result",
"execution_count": 192,
"outputs": []
},
{
"metadata": {
"scrolled": true,
"trusted": true
},
"cell_type": "code",
"source": "task_keys = [\"name\", \"write_pdb\", \"write_json\", \"pdb_output_paths\", \"json_output_paths\", \"initial_lookup_counts\"]\ntest_tasks = [\n get(task_keys,initial_analysis(n, p)) for n, p in list(input_poses.items())\n]",
"execution_count": 193,
"outputs": [
{
"output_type": "stream",
"text": "2018-01-06T06:46:19.316 close_and_refine loaded input chains: 4\n2018-01-06T06:46:19.347 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:19.548 close_and_refine loaded input chains: 4\n2018-01-06T06:46:19.580 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:19.768 close_and_refine loaded input chains: 4\n2018-01-06T06:46:19.799 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:19.984 close_and_refine loaded input chains: 4\n2018-01-06T06:46:20.014 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:20.193 close_and_refine loaded input chains: 4\n2018-01-06T06:46:20.224 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:20.415 close_and_refine loaded input chains: 3\n2018-01-06T06:46:20.440 topology_closure.TopologyClosureManager Expanding closure 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Expanding closure pairs:\nsource_order\n2018-01-06T06:46:22.258 close_and_refine loaded input chains: 3\n2018-01-06T06:46:22.283 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:22.422 close_and_refine loaded input chains: 4\n2018-01-06T06:46:22.454 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:22.649 close_and_refine loaded input chains: 4\n2018-01-06T06:46:22.680 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:22.877 close_and_refine loaded input chains: 4\n2018-01-06T06:46:22.912 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:23.109 close_and_refine loaded input chains: 4\n2018-01-06T06:46:23.139 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:23.318 close_and_refine loaded input chains: 4\n2018-01-06T06:46:23.349 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:23.544 close_and_refine loaded input chains: 3\n2018-01-06T06:46:23.571 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:23.711 close_and_refine loaded input chains: 4\n2018-01-06T06:46:23.740 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:23.922 close_and_refine loaded input chains: 4\n2018-01-06T06:46:23.954 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:24.150 close_and_refine loaded input chains: 4\n2018-01-06T06:46:24.182 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:24.382 close_and_refine loaded input chains: 4\n2018-01-06T06:46:24.417 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:24.618 close_and_refine loaded input chains: 4\n2018-01-06T06:46:24.650 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:24.840 close_and_refine loaded input chains: 4\n2018-01-06T06:46:24.872 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:25.067 close_and_refine loaded input chains: 4\n2018-01-06T06:46:25.098 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:25.292 close_and_refine loaded input chains: 4\n2018-01-06T06:46:25.324 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:25.520 close_and_refine loaded input chains: 4\n2018-01-06T06:46:25.553 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:25.741 close_and_refine loaded input chains: 4\n2018-01-06T06:46:25.770 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:25.963 close_and_refine loaded input chains: 4\n2018-01-06T06:46:25.995 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:26.187 close_and_refine loaded input chains: 4\n2018-01-06T06:46:26.219 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:26.417 close_and_refine loaded input chains: 4\n2018-01-06T06:46:26.451 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:26.648 close_and_refine loaded input chains: 4\n2018-01-06T06:46:26.679 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:26.872 close_and_refine loaded input chains: 4\n2018-01-06T06:46:26.904 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:27.106 close_and_refine loaded input chains: 4\n2018-01-06T06:46:27.139 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:27.331 close_and_refine loaded input chains: 3\n2018-01-06T06:46:27.356 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:27.495 close_and_refine loaded input chains: 4\n2018-01-06T06:46:27.527 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:27.716 close_and_refine loaded input chains: 4\n2018-01-06T06:46:27.748 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:27.945 close_and_refine loaded input chains: 3\n2018-01-06T06:46:27.973 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:28.121 close_and_refine loaded input chains: 4\n2018-01-06T06:46:28.154 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:28.353 close_and_refine loaded input chains: 4\n2018-01-06T06:46:28.383 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:28.573 close_and_refine loaded input chains: 4\n2018-01-06T06:46:28.605 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:28.802 close_and_refine loaded input chains: 4\n2018-01-06T06:46:28.837 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:29.037 close_and_refine loaded input chains: 4\n2018-01-06T06:46:29.069 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:29.269 close_and_refine loaded input chains: 4\n2018-01-06T06:46:29.305 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:29.507 close_and_refine loaded input chains: 3\n2018-01-06T06:46:29.531 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:29.679 close_and_refine loaded input chains: 4\n2018-01-06T06:46:29.711 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:29.906 close_and_refine loaded input chains: 4\n2018-01-06T06:46:29.939 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:30.137 close_and_refine loaded input chains: 3\n2018-01-06T06:46:30.161 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:30.293 close_and_refine loaded input chains: 4\n",
"name": "stderr"
},
{
"output_type": "stream",
"text": "2018-01-06T06:46:30.324 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:30.528 close_and_refine loaded input chains: 4\n2018-01-06T06:46:30.559 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:30.755 close_and_refine loaded input chains: 4\n2018-01-06T06:46:30.787 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:30.981 close_and_refine loaded input chains: 3\n2018-01-06T06:46:31.008 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:31.150 close_and_refine loaded input chains: 4\n2018-01-06T06:46:31.183 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:31.748 close_and_refine loaded input chains: 4\n2018-01-06T06:46:31.779 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:31.973 close_and_refine loaded input chains: 4\n2018-01-06T06:46:32.004 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:32.196 close_and_refine loaded input chains: 4\n2018-01-06T06:46:32.226 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:32.414 close_and_refine loaded input chains: 4\n2018-01-06T06:46:32.447 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:32.650 close_and_refine loaded input chains: 4\n2018-01-06T06:46:32.683 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:32.883 close_and_refine loaded input chains: 4\n2018-01-06T06:46:32.913 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:33.102 close_and_refine loaded input chains: 3\n2018-01-06T06:46:33.127 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:33.267 close_and_refine loaded input chains: 4\n2018-01-06T06:46:33.298 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:33.497 close_and_refine loaded input chains: 4\n2018-01-06T06:46:33.531 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:33.728 close_and_refine loaded input chains: 4\n2018-01-06T06:46:33.759 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:33.954 close_and_refine loaded input chains: 4\n2018-01-06T06:46:33.987 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:34.171 close_and_refine loaded input chains: 3\n2018-01-06T06:46:34.197 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:34.340 close_and_refine loaded input chains: 4\n2018-01-06T06:46:34.370 topology_closure.TopologyClosureManager Expanding closure 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Expanding closure pairs:\nsource_order\n2018-01-06T06:46:35.760 close_and_refine loaded input chains: 4\n2018-01-06T06:46:35.792 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:35.992 close_and_refine loaded input chains: 4\n2018-01-06T06:46:36.024 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:36.220 close_and_refine loaded input chains: 4\n2018-01-06T06:46:36.251 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:36.456 close_and_refine loaded input chains: 4\n2018-01-06T06:46:36.489 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:36.689 close_and_refine loaded input chains: 3\n2018-01-06T06:46:36.715 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:36.850 close_and_refine loaded input chains: 3\n2018-01-06T06:46:36.877 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:37.018 close_and_refine loaded input chains: 4\n2018-01-06T06:46:37.049 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:37.235 close_and_refine loaded input chains: 3\n2018-01-06T06:46:37.262 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:37.404 close_and_refine loaded input chains: 4\n2018-01-06T06:46:37.437 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:37.629 close_and_refine loaded input chains: 4\n2018-01-06T06:46:37.659 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:37.858 close_and_refine loaded input chains: 4\n2018-01-06T06:46:37.892 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:38.098 close_and_refine loaded input chains: 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close_and_refine loaded input chains: 4\n2018-01-06T06:46:40.840 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:41.039 close_and_refine loaded input chains: 4\n2018-01-06T06:46:41.072 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:41.270 close_and_refine loaded input chains: 4\n2018-01-06T06:46:41.300 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n",
"name": "stderr"
},
{
"output_type": "stream",
"text": "2018-01-06T06:46:41.498 close_and_refine loaded input chains: 4\n2018-01-06T06:46:41.529 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:41.727 close_and_refine loaded input chains: 4\n2018-01-06T06:46:41.758 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:41.947 close_and_refine loaded input chains: 4\n2018-01-06T06:46:41.978 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:42.174 close_and_refine loaded input chains: 4\n2018-01-06T06:46:42.207 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:42.402 close_and_refine loaded input chains: 4\n2018-01-06T06:46:42.434 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:42.631 close_and_refine loaded input chains: 4\n2018-01-06T06:46:42.663 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:42.859 close_and_refine loaded input chains: 4\n2018-01-06T06:46:42.891 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:43.090 close_and_refine loaded input chains: 3\n2018-01-06T06:46:43.116 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:43.258 close_and_refine loaded input chains: 4\n2018-01-06T06:46:43.291 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:43.489 close_and_refine loaded input chains: 3\n2018-01-06T06:46:43.515 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:43.659 close_and_refine loaded input chains: 4\n2018-01-06T06:46:43.689 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:44.323 close_and_refine loaded input chains: 3\n2018-01-06T06:46:44.348 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:44.490 close_and_refine loaded input chains: 3\n2018-01-06T06:46:44.517 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:44.668 close_and_refine loaded input chains: 4\n2018-01-06T06:46:44.701 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:44.900 close_and_refine loaded input chains: 4\n2018-01-06T06:46:44.932 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:45.132 close_and_refine loaded input chains: 4\n2018-01-06T06:46:45.164 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:45.356 close_and_refine loaded input chains: 4\n2018-01-06T06:46:45.388 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:45.593 close_and_refine loaded input chains: 3\n2018-01-06T06:46:45.617 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:45.761 close_and_refine loaded input chains: 3\n2018-01-06T06:46:45.787 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:45.935 close_and_refine loaded input chains: 4\n2018-01-06T06:46:45.968 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:46.176 close_and_refine loaded input chains: 4\n2018-01-06T06:46:46.209 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:46.414 close_and_refine loaded input chains: 4\n2018-01-06T06:46:46.448 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:46.647 close_and_refine loaded input chains: 3\n2018-01-06T06:46:46.673 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:46.821 close_and_refine loaded input chains: 4\n2018-01-06T06:46:46.854 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:47.060 close_and_refine loaded input chains: 4\n2018-01-06T06:46:47.092 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:47.291 close_and_refine loaded input chains: 4\n2018-01-06T06:46:47.321 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:47.520 close_and_refine loaded input chains: 4\n2018-01-06T06:46:47.552 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:47.758 close_and_refine loaded input chains: 4\n2018-01-06T06:46:47.791 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:47.996 close_and_refine loaded input chains: 4\n2018-01-06T06:46:48.031 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:48.235 close_and_refine loaded input chains: 4\n2018-01-06T06:46:48.267 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:48.473 close_and_refine loaded input chains: 4\n2018-01-06T06:46:48.507 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:48.712 close_and_refine loaded input chains: 4\n2018-01-06T06:46:48.746 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:48.950 close_and_refine loaded input chains: 3\n2018-01-06T06:46:48.979 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n2018-01-06T06:46:49.123 close_and_refine loaded input chains: 3\n2018-01-06T06:46:49.152 topology_closure.TopologyClosureManager Expanding closure pairs:\nsource_order\n",
"name": "stderr"
}
]
},
{
"metadata": {
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"cell_type": "code",
"source": "source_closure_results = WorkStream(test_tasks)",
"execution_count": 198,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "source_closure_results.max_working = 10",
"execution_count": 199,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "results = source_closure_results.runloop()",
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"text": "2018-01-06T07:04:49.437 work_stream stream status: {'input_queue': 122, 'error_results': 0, 'results': 1, 'working': 10}\n2018-01-06T07:04:49.438 work_stream store\n2018-01-06T07:04:49.440 work_stream num_unfinished: {0: 4, 1: 4, 2: 4, 3: 4, 4: 2, 5: 3, 6: 4, 7: 4, 8: 3, 9: 4}\n",
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}
]
}
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