GALigandDock
Protocol with pyrosetta.distributed
Using the beta_cart.wts
Scorefunction¶Warning: This notebook uses pyrosetta.distributed.viewer
code, which runs in jupyter notebook
and might not run if you're using jupyterlab
.
Note: This Jupyter notebook requires the PyRosetta distributed layer. Please make sure to activate the PyRosetta.notebooks
conda environment before running this notebook. The kernel is set to use this environment.
import logging
logging.basicConfig(level=logging.INFO)
import matplotlib
%matplotlib inline
import os
import pandas as pd
import pyrosetta
import pyrosetta.distributed
import pyrosetta.distributed.io as io
import pyrosetta.distributed.viewer as viewer
import pyrosetta.distributed.packed_pose as packed_pose
import pyrosetta.distributed.tasks.rosetta_scripts as rosetta_scripts
import seaborn
seaborn.set()
import sys
!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta
Load the TPA.am1-bcc.gp.params
file when using the -beta_cart
flag, which has gen_potential
atom typing and AM1-BCC partial charges:
pdb_filename = "inputs/test_lig.pdb"
ligand_params = "inputs/TPA.am1-bcc.gp.params"
flags = f"""
-ignore_unrecognized_res 1
-extra_res_fa {ligand_params}
-beta_cart
-out:level 200
"""
pyrosetta.distributed.init(flags)
pose_obj = io.pose_from_file(filename=pdb_filename)
INFO:pyrosetta.distributed:maybe_init performing pyrosetta initialization: {'extra_options': '-ignore_unrecognized_res 1 -extra_res_fa inputs/TPA.am1-bcc.gp.params -beta_cart -out:level 200', 'silent': True} INFO:pyrosetta.rosetta:Found rosetta database at: /mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database; using it.... INFO:pyrosetta.rosetta:PyRosetta-4 2019 [Rosetta PyRosetta4.conda.linux.CentOS.python36.Release 2019.39+release.93456a567a8125cafdf7f8cb44400bc20b570d81 2019-09-26T14:24:44] retrieved from: http://www.pyrosetta.org (C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team. INFO:rosetta:core.init.score_function_corrections: {0} [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file! INFO:rosetta:core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] TPA337 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.
Now we change the scorefunction in our RosettaScripts script to beta_cart.wts
, the weights of which were optimized on protein-ligand complexes using ligands with AM1-BCC partial charges generated with Amber's antechamber
.
GALigandDock
within RosettaScripts normally outputs multiple .pdb
files to disk if run by the command line. However, when using the MultioutputRosettaScriptsTask
function in pyrosetta.distributed
, the outputs will be captured in memory within this Jupyter session!
xml = f"""
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="fa_standard" weights="beta_cart.wts"/>
</SCOREFXNS>
<MOVERS>
<GALigandDock name="dock"
scorefxn="fa_standard"
scorefxn_relax="fa_standard"
grid_step="0.25"
padding="5.0"
hashsize="8.0"
subhash="3"
nativepdb="{pdb_filename}"
final_exact_minimize="sc"
random_oversample="10"
rotprob="0.9"
rotEcut="100"
sidechains="auto"
initial_pool="{pdb_filename}">
<Stage repeats="10" npool="50" pmut="0.2" smoothing="0.375" rmsdthreshold="2.5" maxiter="50" pack_cycles="100" ramp_schedule="0.1,1.0"/>
<Stage repeats="10" npool="50" pmut="0.2" smoothing="0.375" rmsdthreshold="1.5" maxiter="50" pack_cycles="100" ramp_schedule="0.1,1.0"/>
</GALigandDock>
</MOVERS>
<PROTOCOLS>
<Add mover="dock"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
"""
xml_obj = rosetta_scripts.MultioutputRosettaScriptsTask(xml)
xml_obj.setup()
INFO:rosetta:core.io.pose_from_sfr.PoseFromSFRBuilder: {0} [ WARNING ] TPA337 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.
MultioutputRosettaScriptsTask
is a python generator object. Therefore, we need to call list()
or set()
on it to run it.
Warning, the following cell runs for ~45 minutes CPU time.
if not os.getenv("DEBUG"):
%time results = list(xml_obj(pose_obj))
GALigandDock
trajectories:¶if not os.getenv("DEBUG"):
df = pd.DataFrame.from_records(packed_pose.to_dict(results))
df
cart_bonded | dslf_fa13 | fa_atr | fa_dun_dev | fa_dun_rot | fa_dun_semi | fa_elec | fa_intra_atr_xover4 | fa_intra_elec | fa_intra_rep_xover4 | ... | lk_ball | lk_ball_bridge | lk_ball_bridge_uncpl | lk_ball_iso | omega | p_aa_pp | pickled_pose | rama_prepro | ref | total_score | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | 1123.712502 | 0.0 | -2151.762324 | 2073.947599 | 351.670653 | 526.462836 | -608.942522 | -152.925958 | -91.709467 | 484.474982 | ... | 914.974515 | 8.028863 | 56.938398 | 2237.073939 | 3.205810 | -84.787860 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 338.665837 | -83.04488 | 2146.657901 |
1 | 1126.994362 | 0.0 | -2153.494398 | 2074.354803 | 350.045712 | 527.638427 | -598.326113 | -155.611156 | -95.374631 | 487.259466 | ... | 912.676585 | 8.185741 | 57.137773 | 2236.078391 | 2.616802 | -84.905751 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 338.066308 | -83.04488 | 2154.465790 |
2 | 1122.218749 | 0.0 | -2152.061341 | 2074.616276 | 352.358914 | 528.828818 | -592.915774 | -152.872453 | -94.779139 | 484.857347 | ... | 911.937969 | 8.482099 | 59.081443 | 2234.873025 | 2.785344 | -84.712778 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 338.017765 | -83.04488 | 2160.068530 |
3 | 1124.089966 | 0.0 | -2152.510428 | 2074.255528 | 352.854664 | 526.668672 | -594.728864 | -154.667979 | -91.274751 | 484.674904 | ... | 911.669956 | 8.161121 | 56.862517 | 2235.493136 | 2.689288 | -84.570622 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 338.948903 | -83.04488 | 2168.046714 |
4 | 1127.329477 | 0.0 | -2144.634818 | 2074.065162 | 353.115713 | 528.590003 | -591.697767 | -157.057321 | -99.639525 | 488.113252 | ... | 911.687657 | 8.390250 | 59.421205 | 2230.112093 | 3.098268 | -84.642988 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 339.732965 | -83.04488 | 2171.305626 |
5 | 1119.868142 | 0.0 | -2135.739776 | 2073.996665 | 353.098796 | 528.725083 | -585.912100 | -153.333212 | -95.675236 | 484.059834 | ... | 904.758285 | 8.352889 | 59.583429 | 2222.677958 | 2.782730 | -84.397516 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 339.262489 | -83.04488 | 2174.354305 |
6 | 1119.054847 | 0.0 | -2128.180817 | 2074.125675 | 354.267620 | 527.658626 | -600.190559 | -152.753968 | -93.492140 | 484.075625 | ... | 910.301829 | 8.267338 | 58.256741 | 2225.289996 | 2.463544 | -83.967544 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.339600 | -83.04488 | 2175.892215 |
7 | 1118.147392 | 0.0 | -2120.681500 | 2073.846102 | 354.157516 | 527.871629 | -589.804841 | -153.593008 | -94.975244 | 485.339630 | ... | 901.078625 | 8.301181 | 57.906715 | 2210.271834 | 2.188813 | -84.127671 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.763695 | -83.04488 | 2176.467254 |
8 | 1117.748559 | 0.0 | -2123.042805 | 2074.240598 | 354.436350 | 528.611581 | -590.876958 | -153.665083 | -94.331011 | 485.674473 | ... | 902.906292 | 8.220858 | 58.551026 | 2216.794578 | 2.357257 | -84.155674 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 339.664206 | -83.04488 | 2176.841510 |
9 | 1122.056963 | 0.0 | -2148.039319 | 2074.745640 | 352.344596 | 529.868373 | -594.182910 | -153.210177 | -92.399237 | 484.908058 | ... | 914.566198 | 7.920984 | 55.527792 | 2237.359424 | 2.137919 | -84.688511 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 339.407441 | -83.04488 | 2176.972496 |
10 | 1117.741151 | 0.0 | -2121.369976 | 2074.302515 | 354.174154 | 527.791725 | -590.241078 | -153.597633 | -95.827353 | 484.667353 | ... | 902.542067 | 8.345890 | 58.585494 | 2213.451888 | 2.415969 | -83.917844 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.436524 | -83.04488 | 2177.730121 |
11 | 1119.795446 | 0.0 | -2117.973995 | 2074.530476 | 354.559199 | 527.338329 | -589.618991 | -152.679052 | -94.486570 | 483.735919 | ... | 900.964799 | 8.310695 | 59.028378 | 2209.505589 | 2.363121 | -83.626671 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 341.958594 | -83.04488 | 2178.204123 |
12 | 1118.312826 | 0.0 | -2114.047445 | 2073.902282 | 354.175136 | 527.752024 | -582.787032 | -155.366733 | -95.968917 | 484.953600 | ... | 897.209214 | 8.592110 | 60.281273 | 2205.347438 | 2.395891 | -83.962223 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.457713 | -83.04488 | 2178.866416 |
13 | 1118.317051 | 0.0 | -2117.307557 | 2074.313993 | 354.138775 | 527.433465 | -590.049904 | -153.449984 | -93.513722 | 484.159308 | ... | 901.034141 | 8.282241 | 58.387106 | 2209.445302 | 2.383612 | -83.789749 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.885252 | -83.04488 | 2179.058794 |
14 | 1118.256140 | 0.0 | -2123.629410 | 2074.260297 | 354.132779 | 527.720437 | -592.217546 | -152.449089 | -94.956140 | 484.107818 | ... | 904.939033 | 8.292054 | 58.087667 | 2215.458503 | 2.156304 | -83.943825 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.712217 | -83.04488 | 2180.117049 |
15 | 1117.752265 | 0.0 | -2114.376414 | 2074.038976 | 354.257153 | 527.919548 | -589.463209 | -154.153409 | -96.869409 | 485.552224 | ... | 900.635260 | 8.353362 | 58.863490 | 2208.448162 | 2.554803 | -84.106625 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.456327 | -83.04488 | 2180.583104 |
16 | 1119.663802 | 0.0 | -2115.773970 | 2074.093793 | 354.151646 | 527.533400 | -588.314086 | -153.611090 | -95.320298 | 485.147909 | ... | 900.851984 | 8.401965 | 58.705711 | 2208.861342 | 2.298621 | -83.990494 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.444064 | -83.04488 | 2180.631216 |
17 | 1118.929507 | 0.0 | -2116.099773 | 2073.909466 | 353.177818 | 527.268960 | -582.793771 | -152.797945 | -94.676084 | 484.698239 | ... | 899.264890 | 8.385106 | 58.834187 | 2207.193408 | 2.493420 | -84.059707 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.345752 | -83.04488 | 2180.725153 |
18 | 1118.692345 | 0.0 | -2121.193398 | 2074.323205 | 354.166226 | 527.657215 | -588.721658 | -153.256935 | -95.684619 | 484.856754 | ... | 902.384370 | 8.368650 | 58.995883 | 2213.820288 | 2.424769 | -83.954573 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.770906 | -83.04488 | 2180.847581 |
19 | 1121.517245 | 0.0 | -2132.859286 | 2073.740747 | 354.283261 | 527.735912 | -598.362623 | -153.919304 | -92.398482 | 483.048769 | ... | 908.434224 | 8.123019 | 56.443615 | 2226.746092 | 2.195113 | -84.087127 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.751774 | -83.04488 | 2180.751217 |
20 | 1120.747776 | 0.0 | -2127.375634 | 2073.896934 | 356.547817 | 527.681799 | -600.943325 | -153.540042 | -92.812196 | 485.343720 | ... | 908.716709 | 8.092196 | 56.262864 | 2225.237135 | 1.934896 | -84.138227 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.643492 | -83.04488 | 2180.879864 |
21 | 1116.839196 | 0.0 | -2118.482689 | 2073.891207 | 354.155908 | 526.806919 | -586.305973 | -154.254092 | -91.845749 | 485.066702 | ... | 899.245585 | 8.394896 | 59.021236 | 2208.290013 | 2.226094 | -83.855202 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.857928 | -83.04488 | 2181.324150 |
22 | 1117.941693 | 0.0 | -2115.636826 | 2074.302958 | 354.146873 | 527.749761 | -587.750200 | -153.653116 | -95.974025 | 484.157755 | ... | 900.967950 | 8.426505 | 59.073716 | 2211.663744 | 2.362630 | -83.991207 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.408618 | -83.04488 | 2181.401864 |
23 | 1116.500637 | 0.0 | -2114.357782 | 2074.051987 | 354.119153 | 527.691554 | -588.315750 | -153.221795 | -92.867507 | 483.416645 | ... | 899.084521 | 8.246251 | 57.568979 | 2207.411666 | 2.362959 | -83.992033 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.335161 | -83.04488 | 2181.440088 |
24 | 1120.434458 | 0.0 | -2122.899390 | 2073.935206 | 354.080054 | 527.643448 | -598.458861 | -152.784966 | -94.281443 | 484.558852 | ... | 907.877157 | 8.220266 | 57.625948 | 2221.312457 | 2.273240 | -84.084665 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.841184 | -83.04488 | 2181.525400 |
25 | 1119.431342 | 0.0 | -2120.640287 | 2074.014195 | 354.108787 | 527.879213 | -583.333339 | -153.362764 | -94.510391 | 484.397750 | ... | 899.917327 | 8.269664 | 58.201673 | 2209.080229 | 2.580138 | -83.971134 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.407423 | -83.04488 | 2181.759201 |
26 | 1120.266241 | 0.0 | -2118.909596 | 2074.762505 | 353.521146 | 527.725522 | -583.715146 | -153.625307 | -92.616395 | 484.624171 | ... | 899.566101 | 8.234914 | 57.339780 | 2205.439602 | 2.335625 | -83.754730 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 341.944039 | -83.04488 | 2181.829008 |
27 | 1117.264440 | 0.0 | -2117.967615 | 2073.920889 | 352.837101 | 527.984058 | -583.429823 | -153.081684 | -96.927710 | 484.420431 | ... | 900.899472 | 8.364630 | 59.048445 | 2209.367978 | 2.274618 | -83.939094 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.668094 | -83.04488 | 2181.989318 |
28 | 1117.192046 | 0.0 | -2116.088396 | 2074.109505 | 354.226898 | 527.758834 | -587.301089 | -153.499639 | -94.926420 | 484.217262 | ... | 900.514420 | 8.324491 | 58.216448 | 2209.462522 | 2.235938 | -84.040372 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.500974 | -83.04488 | 2181.941843 |
29 | 1115.740407 | 0.0 | -2121.220723 | 2073.950516 | 354.180802 | 527.823457 | -584.729707 | -153.132527 | -92.970132 | 484.788703 | ... | 901.835244 | 8.304383 | 58.752266 | 2213.783240 | 2.400138 | -84.022702 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.452932 | -83.04488 | 2181.977075 |
30 | 1118.176537 | 0.0 | -2118.976859 | 2074.091208 | 354.235640 | 527.771483 | -591.733103 | -153.193661 | -94.015077 | 484.421670 | ... | 905.297959 | 8.225279 | 57.791513 | 2214.322574 | 2.560843 | -83.994720 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.584211 | -83.04488 | 2182.044673 |
31 | 1117.720868 | 0.0 | -2117.913073 | 2073.964761 | 354.143081 | 527.906426 | -589.163726 | -152.904905 | -94.489469 | 484.573393 | ... | 901.256252 | 8.229592 | 56.822766 | 2210.611495 | 2.201650 | -84.126880 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.613090 | -83.04488 | 2182.105762 |
32 | 1120.610165 | 0.0 | -2120.058676 | 2074.137857 | 354.221243 | 526.489176 | -589.280668 | -153.848764 | -91.706236 | 484.522268 | ... | 902.329492 | 8.334486 | 58.820247 | 2210.819610 | 2.267812 | -84.308570 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.590574 | -83.04488 | 2182.142107 |
33 | 1116.528835 | 0.0 | -2114.868437 | 2073.857444 | 354.169507 | 527.771740 | -587.077078 | -153.825286 | -93.215278 | 484.916617 | ... | 899.883852 | 8.286588 | 57.875725 | 2207.725086 | 2.314438 | -84.073244 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.429989 | -83.04488 | 2182.435992 |
34 | 1118.887136 | 0.0 | -2119.543055 | 2074.126521 | 353.328521 | 528.791448 | -584.198246 | -153.874909 | -96.050302 | 484.634286 | ... | 899.690522 | 8.214202 | 57.495022 | 2208.838554 | 2.626603 | -84.212765 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 339.517557 | -83.04488 | 2182.829516 |
35 | 1117.173583 | 0.0 | -2116.769462 | 2074.056933 | 354.164934 | 527.351801 | -584.333500 | -153.785952 | -92.757097 | 483.602991 | ... | 899.034577 | 8.332849 | 58.410754 | 2206.737206 | 2.301316 | -83.816302 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.539722 | -83.04488 | 2182.715754 |
36 | 1118.897286 | 0.0 | -2123.904734 | 2073.872455 | 354.384303 | 527.646746 | -590.495957 | -154.263097 | -95.314800 | 484.645354 | ... | 906.082402 | 8.268748 | 56.961587 | 2218.768584 | 2.820835 | -84.201293 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.705109 | -83.04488 | 2183.402096 |
37 | 1126.205813 | 0.0 | -2152.142984 | 2074.917354 | 353.307715 | 528.107170 | -582.578905 | -154.116226 | -95.336262 | 487.068420 | ... | 909.171597 | 8.781040 | 62.662417 | 2237.343204 | 3.504083 | -84.192562 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 337.419080 | -83.04488 | 2182.847308 |
38 | 1116.328492 | 0.0 | -2117.094750 | 2073.901394 | 354.204171 | 527.850793 | -590.565227 | -152.014204 | -94.162300 | 483.845064 | ... | 903.492147 | 8.190625 | 56.990750 | 2212.085955 | 2.336527 | -84.112099 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.552713 | -83.04488 | 2183.796557 |
39 | 1118.472471 | 0.0 | -2118.173586 | 2073.906513 | 354.093842 | 527.694559 | -579.597896 | -153.772378 | -94.421606 | 484.157218 | ... | 899.414054 | 8.320370 | 58.245026 | 2209.080366 | 2.185829 | -84.037889 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.548692 | -83.04488 | 2183.988985 |
40 | 1122.074279 | 0.0 | -2120.153906 | 2074.046413 | 354.141093 | 527.769415 | -586.209890 | -155.410559 | -94.022582 | 485.814683 | ... | 901.952444 | 8.477702 | 58.843519 | 2213.276321 | 2.649365 | -83.926852 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.441443 | -83.04488 | 2184.389649 |
41 | 1120.563660 | 0.0 | -2122.478336 | 2074.408840 | 354.076905 | 527.893912 | -589.536028 | -153.098357 | -94.206318 | 484.609542 | ... | 905.121053 | 8.361940 | 59.220623 | 2216.119579 | 2.268016 | -83.997958 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.609626 | -83.04488 | 2184.355960 |
42 | 1122.183065 | 0.0 | -2134.140192 | 2074.061703 | 354.273227 | 527.587301 | -594.595432 | -153.088345 | -94.107961 | 483.686954 | ... | 910.903751 | 8.118174 | 56.584244 | 2230.277951 | 2.311996 | -84.196198 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 341.194660 | -83.04488 | 2184.470170 |
43 | 1121.896046 | 0.0 | -2122.725356 | 2073.888454 | 354.339331 | 528.732720 | -582.161860 | -153.748085 | -93.864669 | 485.063471 | ... | 900.362161 | 8.190309 | 56.311753 | 2211.958350 | 2.368035 | -84.045210 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 339.576207 | -83.04488 | 2185.656786 |
44 | 1120.136109 | 0.0 | -2129.790646 | 2074.069462 | 354.917341 | 527.542480 | -586.778335 | -153.076268 | -95.400060 | 484.850197 | ... | 906.779590 | 8.362696 | 57.329232 | 2225.100940 | 3.163210 | -84.006384 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.155735 | -83.04488 | 2186.132616 |
45 | 1119.679063 | 0.0 | -2134.665902 | 2073.996940 | 355.192983 | 527.415419 | -593.001728 | -153.120848 | -94.091495 | 484.763015 | ... | 910.660655 | 8.068935 | 56.222138 | 2229.244793 | 2.515460 | -84.164875 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.078616 | -83.04488 | 2185.720084 |
46 | 1118.074433 | 0.0 | -2113.160467 | 2074.074668 | 353.120830 | 526.287474 | -586.075877 | -153.679664 | -93.415569 | 483.843130 | ... | 900.288128 | 8.436855 | 59.436842 | 2207.194812 | 2.567297 | -83.991158 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 340.728354 | -83.04488 | 2186.292344 |
47 | 1117.514275 | 0.0 | -2115.978997 | 2074.329427 | 353.768894 | 526.949539 | -575.206892 | -153.425757 | -96.710046 | 486.046957 | ... | 896.743939 | 8.183895 | 56.891607 | 2205.048713 | 2.446659 | -83.981252 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 341.310476 | -83.04488 | 2186.556645 |
48 | 1116.978234 | 0.0 | -2125.072550 | 2074.670339 | 353.297882 | 528.306793 | -587.755445 | -152.715260 | -95.858052 | 483.961905 | ... | 905.459894 | 8.162587 | 56.287570 | 2220.501922 | 2.741407 | -84.342385 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 338.792190 | -83.04488 | 2186.276192 |
49 | 1122.186473 | 0.0 | -2141.044482 | 2074.397811 | 354.212538 | 527.553732 | -589.354853 | -154.016633 | -94.162834 | 485.014271 | ... | 911.224885 | 8.216895 | 57.795436 | 2234.960243 | 2.454796 | -84.284048 | gANjcHlyb3NldHRhLnJvc2V0dGEuY29yZS5wb3NlClBvc2... | 341.233187 | -83.04488 | 2189.951239 |
50 rows × 30 columns
GALigandDock
, we can plot the ligand binding energy landscape:¶if not os.getenv("DEBUG"):
matplotlib.rcParams["figure.figsize"] = [12.0, 8.0]
seaborn.scatterplot(x="lig_rms", y="total_score", data=df)
<matplotlib.axes._subplots.AxesSubplot at 0x7fffec3d07b8>
Let's look at the ligand dock with the lowest total_score
score!
if not os.getenv("DEBUG"):
ppose_lowest_total_score = results[df.sort_values(by="total_score").index[0]]
view = viewer.init(ppose_lowest_total_score)
view.add(viewer.setStyle())
view.add(viewer.setStyle(command=({"hetflag": True}, {"stick": {"colorscheme": "brownCarbon", "radius": 0.2}})))
view.add(viewer.setSurface(residue_selector=pyrosetta.rosetta.core.select.residue_selector.ChainSelector("E"), opacity=0.7, color='white'))
view.add(viewer.setHydrogenBonds())
view()
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol