XMLObjects
Using the ref2015.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.viewer as viewer
import seaborn
seaborn.set()
import sys
!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()
Now we change the scorefunction to ref2015.wts
, the weights of which were optimized on ligands with AM1-BCC partial charges generated with Amber's antechamber
. Therefore, the Rosetta .params
file should ideally also have AM1-BCC partial charges generated with antechamber
.
ligand_params = "inputs/TPA.am1-bcc.fa.params"
flags = f"""
-ignore_unrecognized_res 1
-extra_res_fa {ligand_params}
"""
pyrosetta.distributed.init(flags)
pose = pyrosetta.io.pose_from_file(filename="inputs/test_lig.pdb")
scorefxn = pyrosetta.create_score_function("ref2015")
INFO:pyrosetta.distributed:maybe_init performing pyrosetta initialization: {'extra_options': '-ignore_unrecognized_res 1 -extra_res_fa inputs/TPA.am1-bcc.fa.params', '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: {0} Checking for fconfig files in pwd and ./rosetta/flags INFO:rosetta:core.init: {0} Rosetta version: PyRosetta4.conda.linux.CentOS.python36.Release r233 2019.39+release.93456a5 93456a567a8125cafdf7f8cb44400bc20b570d81 http://www.pyrosetta.org 2019-09-26T14:24:44 INFO:rosetta:core.init: {0} command: PyRosetta -ex1 -ex2aro -ignore_unrecognized_res 1 -extra_res_fa inputs/TPA.am1-bcc.fa.params -database /mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database INFO:rosetta:basic.random.init_random_generator: {0} 'RNG device' seed mode, using '/dev/urandom', seed=-2105863589 seed_offset=0 real_seed=-2105863589 thread_index=0 INFO:rosetta:basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-2105863589 RG_type=mt19937 INFO:rosetta:core.chemical.GlobalResidueTypeSet: {0} Finished initializing fa_standard residue type set. Created 981 residue types INFO:rosetta:core.chemical.GlobalResidueTypeSet: {0} Total time to initialize 1.97866 seconds. INFO:rosetta:core.import_pose.import_pose: {0} File 'inputs/test_lig.pdb' automatically determined to be of type PDB INFO:rosetta:core.scoring.etable: {0} Starting energy table calculation INFO:rosetta:core.scoring.etable: {0} smooth_etable: changing atr/rep split to bottom of energy well INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing lj etables (maxdis = 6) INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing solvation etables (max_dis = 6) INFO:rosetta:core.scoring.etable: {0} Finished calculating energy tables. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/all.ramaProb INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA_n INFO:rosetta:core.scoring.P_AA: {0} shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
Ligand docking using XmlObjects
:
xml = pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects.create_from_string("""
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="fa_standard" weights="ref2015.wts"/>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Chain name="chX" chains="X"/>
</RESIDUE_SELECTORS>
<SIMPLE_METRICS>
<RMSDMetric name="rmsd_chX" residue_selector="chX" reference_name="store_native" residue_selector_ref="chX" robust="true" rmsd_type="rmsd_all" />
</SIMPLE_METRICS>
<SCORINGGRIDS ligand_chain="X" width="25">
<ClassicGrid grid_name="vdw" weight="1.0"/>
</SCORINGGRIDS>
<LIGAND_AREAS>
<LigandArea name="docking_sidechain_X" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<LigandArea name="final_sidechain_X" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<LigandArea name="final_backbone_X" chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
</LIGAND_AREAS>
<INTERFACE_BUILDERS>
<InterfaceBuilder name="side_chain_for_docking" ligand_areas="docking_sidechain_X"/>
<InterfaceBuilder name="side_chain_for_final" ligand_areas="final_sidechain_X"/>
<InterfaceBuilder name="backbone" ligand_areas="final_backbone_X" extension_window="3"/>
</INTERFACE_BUILDERS>
<MOVEMAP_BUILDERS>
<MoveMapBuilder name="docking" sc_interface="side_chain_for_docking" minimize_water="true"/>
<MoveMapBuilder name="final" sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
</MOVEMAP_BUILDERS>
<MOVERS>
<SavePoseMover name="spm" restore_pose="0" reference_name="store_native"/>
<Transform name="transform" chain="X" box_size="20.0" move_distance="10" angle="360" initial_perturb="2" cycles="500" repeats="5" temperature="1000"/>
<HighResDocker name="high_res_docker" cycles="9" repack_every_Nth="3" scorefxn="fa_standard" movemap_builder="docking"/>
<FinalMinimizer name="final" scorefxn="fa_standard" movemap_builder="final"/>
</MOVERS>
<FILTERS>
<LigInterfaceEnergy name="interfE" scorefxn="fa_standard" energy_cutoff="0.0" confidence="0"/>
<SimpleMetricFilter name="rmsd_chX" metric="rmsd_chX" cutoff="999999." comparison_type="lt" confidence="0"/>
</FILTERS>
<PROTOCOLS>
<Add mover="spm"/>
<Add mover="transform"/>
<Add mover="high_res_docker"/>
<Add mover="final"/>
<Add filter="interfE"/>
<Add filter="rmsd_chX"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
""").get_mover("ParsedProtocol")
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts... INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator... INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script... INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script: <ROSETTASCRIPTS> <SCOREFXNS> <ScoreFunction name="fa_standard" weights="ref2015.wts"/> </SCOREFXNS> <RESIDUE_SELECTORS> <Chain chains="X" name="chX"/> </RESIDUE_SELECTORS> <SIMPLE_METRICS> <RMSDMetric name="rmsd_chX" reference_name="store_native" residue_selector="chX" residue_selector_ref="chX" rmsd_type="rmsd_all" robust="true"/> </SIMPLE_METRICS> <SCORINGGRIDS ligand_chain="X" width="25"> <ClassicGrid grid_name="vdw" weight="1.0"/> </SCORINGGRIDS> <LIGAND_AREAS> <LigandArea add_nbr_radius="true" all_atom_mode="true" chain="X" cutoff="6.0" minimize_ligand="10" name="docking_sidechain_X"/> <LigandArea add_nbr_radius="true" all_atom_mode="true" chain="X" cutoff="6.0" name="final_sidechain_X"/> <LigandArea Calpha_restraints="0.3" add_nbr_radius="false" all_atom_mode="true" chain="X" cutoff="7.0" name="final_backbone_X"/> </LIGAND_AREAS> <INTERFACE_BUILDERS> <InterfaceBuilder ligand_areas="docking_sidechain_X" name="side_chain_for_docking"/> <InterfaceBuilder ligand_areas="final_sidechain_X" name="side_chain_for_final"/> <InterfaceBuilder extension_window="3" ligand_areas="final_backbone_X" name="backbone"/> </INTERFACE_BUILDERS> <MOVEMAP_BUILDERS> <MoveMapBuilder minimize_water="true" name="docking" sc_interface="side_chain_for_docking"/> <MoveMapBuilder bb_interface="backbone" minimize_water="true" name="final" sc_interface="side_chain_for_final"/> </MOVEMAP_BUILDERS> <MOVERS> <SavePoseMover name="spm" reference_name="store_native" restore_pose="0"/> <Transform angle="360" box_size="20.0" chain="X" cycles="500" initial_perturb="2" move_distance="10" name="transform" repeats="5" temperature="1000"/> <HighResDocker cycles="9" movemap_builder="docking" name="high_res_docker" repack_every_Nth="3" scorefxn="fa_standard"/> <FinalMinimizer movemap_builder="final" name="final" scorefxn="fa_standard"/> </MOVERS> <FILTERS> <LigInterfaceEnergy confidence="0" energy_cutoff="0.0" name="interfE" scorefxn="fa_standard"/> <SimpleMetricFilter comparison_type="lt" confidence="0" cutoff="999999." metric="rmsd_chX" name="rmsd_chX"/> </FILTERS> <PROTOCOLS> <Add mover="spm"/> <Add mover="transform"/> <Add mover="high_res_docker"/> <Add mover="final"/> <Add filter="interfE"/> <Add filter="rmsd_chX"/> </PROTOCOLS> </ROSETTASCRIPTS> INFO:rosetta:core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015 INFO:rosetta:core.scoring.etable: {0} Starting energy table calculation INFO:rosetta:core.scoring.etable: {0} smooth_etable: changing atr/rep split to bottom of energy well INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing lj etables (maxdis = 6) INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing solvation etables (max_dis = 6) INFO:rosetta:core.scoring.etable: {0} Finished calculating energy tables. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt INFO:rosetta:core.scoring.ramachandran: {0} shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/avg_L_rama.dat INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama.dat. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_all_rama.dat INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama.dat. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_G_rama.dat INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama.dat. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_P_rama.dat INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama.dat. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/avg_L_rama_str.dat INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama_str.dat. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_all_rama_str.dat INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama_str.dat. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_G_rama_str.dat INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama_str.dat. INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_P_rama_str.dat INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama_str.dat. INFO:rosetta:protocols.jd2.parser.ScoreFunctionLoader: {0} defined score function "fa_standard" with weights "ref2015.wts" INFO:rosetta:core.select.residue_selector.util: {0} Found residue selector chX INFO:rosetta:core.select.residue_selector.util: {0} Found residue selector chX INFO:rosetta:core.pose.ref_pose: {0} Loading PDB: store_native INFO:rosetta:core.simple_metrics.metrics.RMSDMetric: {0} Loaded reference pose: store_native with 0 residues INFO:rosetta:core.pose.ref_pose: {0} Loading PDB: store_native INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named "spm" of type SavePoseMover INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named "transform" of type Transform INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named "high_res_docker" of type HighResDocker INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named "final" of type FinalMinimizer INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined filter named "interfE" of type LigInterfaceEnergy INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined filter named "rmsd_chX" of type SimpleMetricFilter INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following movers and filters INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "spm" with filter "true_filter" INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "transform" with filter "true_filter" INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "high_res_docker" with filter "true_filter" INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "final" with filter "true_filter" INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "NULL_MOVER" with filter "interfE" INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "NULL_MOVER" with filter "rmsd_chX"
Produce 5 global ligand docking trajectories using PyJobDistributor
:
if not os.getenv("DEBUG"):
working_dir = os.getcwd()
output_dir = "outputs"
if not os.path.exists(output_dir):
os.mkdir(output_dir)
os.chdir(output_dir)
jd = pyrosetta.toolbox.py_jobdistributor.PyJobDistributor(pdb_name="test_lig_XMLObjects",
nstruct=5,
scorefxn=scorefxn)
jd.native_pose = pose
df = pd.DataFrame()
while not jd.job_complete:
test_pose = pose.clone()
xml.apply(test_pose)
test_df = pd.DataFrame.from_records(dict(test_pose.scores), index=[jd.current_name])
df = df.append(test_df)
jd.output_decoy(test_pose)
os.chdir(working_dir)
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform======================= INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} [ WARNING ] option -qsar:grid_dir is not set. Use this flag to specify a directory to store scoring grids. This will save you a huge amount of time INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} No conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Updating grid and adding it to the cache
Working on decoy: test_lig_XMLObjects_1.pdb
INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1433 0.5732 1067 INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1063 0.4252 INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] A large number of moves were rejected for being outside the grid. You likely want to reexamine your settings. INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] For the current settings, a grid size of at least 259.2 and a box size of at least 243.2 are recommended. INFO:rosetta:protocols.evaluation.ChiWellRmsdEvaluatorCreator: {0} Evaluation Creator active ... INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -34 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker======================= INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/elec_cp_reps.dat INFO:rosetta:core.scoring.elec.util: {0} Read 40 countpair representative atoms INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib_fixes_enable option is true. INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} Binary rotamer library selected: /mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} Using Dunbrack library binary file '/mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} Dunbrack 2010 library took 0.442342 seconds to load from binary INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 2057 rotamers at 69 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 1986 rotamers at 66 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 1987 rotamers at 66 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1600.31 1600.31 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final======================= INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1600.31 INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1456.97 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-28.1887 INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -28.2764 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} chain res AA total contact fa_atr fa_rep hb_bb_sc hb_sc fa_sol fa_dun fa_pair E 48 THR -2.417 -3.119 -6.763 1.021 -0.993 -0.583 4.200 0.450 0.000 E 49 LEU -6.543 -7.144 -9.186 0.803 0.000 0.000 1.238 0.075 0.000 E 50 GLY -2.059 -0.700 -4.684 0.811 0.000 0.000 3.173 0.000 0.000 E 51 THR -1.979 -1.965 -4.199 0.355 0.000 0.000 1.879 0.099 0.000 E 52 GLY -0.176 0.969 -2.910 0.272 0.000 0.000 3.608 0.000 0.000 E 53 SER -2.735 0.784 -3.306 0.162 -0.931 -0.328 5.188 0.270 0.000 E 54 PHE 0.876 -1.600 -6.411 0.658 -0.411 0.000 4.564 2.876 0.000 E 55 GLY -1.377 0.007 -2.945 0.151 -0.511 0.000 3.312 0.000 0.000 E 56 ARG -1.088 -1.522 -6.706 0.518 0.000 -0.357 5.024 2.218 0.000 E 57 VAL -6.165 -4.674 -9.023 1.013 0.000 0.000 3.336 0.060 0.000 E 58 MET -2.147 -3.447 -9.067 1.359 0.000 0.000 4.260 1.512 0.000 E 59 LEU -5.857 -5.463 -8.600 1.494 0.000 0.000 1.643 0.422 0.000 E 69 TYR -0.690 -4.729 -9.958 1.822 0.000 -0.419 3.827 2.872 0.000 E 70 ALA -2.410 -3.401 -6.353 0.516 0.000 0.000 2.437 0.000 0.000 E 71 MET -2.666 -6.202 -9.279 1.245 0.000 0.000 1.832 1.710 0.000 E 72 LYS -4.477 0.903 -7.895 0.904 0.000 -0.646 8.540 1.037 0.000 E 74 LEU -1.722 -2.492 -6.620 1.523 0.000 0.000 2.605 0.910 0.000 E 78 LYS -3.043 -0.299 -6.728 0.818 -0.861 0.000 6.473 1.565 0.000 E 82 LEU -0.419 -2.208 -5.790 0.787 -0.503 0.000 3.298 1.863 0.000 E 84 GLN -4.641 -2.305 -7.459 0.571 -0.503 -0.725 5.810 2.196 0.000 E 87 HIS -0.886 -1.113 -7.215 0.802 0.000 -0.725 6.025 2.189 0.000 E 91 GLU -3.591 0.525 -8.598 0.855 0.000 -0.646 8.914 2.849 0.000 E 104 VAL -2.234 -4.151 -6.001 0.510 0.000 0.000 1.340 0.567 0.000 E 105 LYS -0.037 0.469 -4.287 0.256 0.000 0.000 4.501 1.138 0.000 E 106 LEU -4.116 -5.203 -7.960 1.520 0.000 0.000 1.237 0.385 0.000 E 118 MET -1.417 -4.497 -8.675 1.533 0.000 0.000 2.646 1.986 0.000 E 119 VAL -4.636 -4.850 -8.706 2.116 0.000 0.000 1.741 0.110 0.000 E 120 MET -3.844 -4.911 -9.727 0.778 0.000 0.000 4.038 1.848 0.000 E 121 GLU -1.310 -0.462 -4.028 0.206 0.000 0.000 3.360 2.373 0.000 E 122 TYR -4.442 -6.152 -8.669 0.525 -0.330 0.000 2.322 2.406 0.000 E 123 VAL -2.182 -4.170 -6.584 0.877 0.000 0.000 1.537 0.017 0.000 E 124 ALA -2.617 -2.974 -3.698 0.205 -0.799 0.000 1.318 0.000 0.000 E 125 GLY -1.329 -0.985 -4.236 0.734 -0.556 0.000 3.073 0.000 0.000 E 126 GLY -3.437 -0.662 -4.172 0.426 0.000 0.000 3.085 0.000 0.000 E 127 GLU -2.925 1.039 -6.871 1.447 0.000 -0.564 7.027 2.748 0.000 E 129 PHE -0.241 -1.619 -8.049 1.213 0.000 0.000 5.216 1.387 0.000 E 130 SER -0.329 0.469 -3.921 0.233 0.000 0.000 4.157 1.080 0.000 E 165 ARG -0.333 -2.149 -8.747 1.746 -1.333 -0.520 6.705 3.113 0.000 E 166 ASP 0.543 1.140 -5.401 0.991 -0.482 -0.630 6.663 2.948 0.000 E 168 LYS -3.030 1.904 -9.478 2.652 0.000 -0.673 9.403 1.179 0.000 E 169 PRO -3.490 -1.704 -7.718 2.992 0.000 0.000 3.023 0.065 0.000 E 170 GLU -1.311 0.098 -6.086 0.567 0.000 0.000 5.616 2.716 0.000 E 171 ASN -4.392 -0.202 -7.832 0.790 -0.482 -0.245 7.566 1.695 0.000 E 172 LEU -5.886 -6.302 -8.858 1.341 0.000 0.000 1.215 0.637 0.000 E 173 LEU -5.721 -5.168 -9.243 1.134 0.000 0.000 2.941 0.551 0.000 E 181 GLN -1.309 -2.677 -7.989 0.498 -0.630 0.000 5.444 4.290 0.000 E 182 VAL -4.450 -4.501 -6.797 0.742 0.000 0.000 1.553 0.074 0.000 E 183 THR -3.797 -3.976 -6.762 0.572 -0.795 -0.657 3.666 2.388 0.000 E 184 ASP 4.753 2.582 -5.326 0.990 -0.699 -0.245 7.861 2.374 0.000 E 185 PHE -0.523 -6.075 -8.430 1.314 0.000 0.000 1.042 3.227 0.000 E 186 GLY 1.335 0.780 -3.222 0.783 -0.148 0.000 3.367 0.000 0.000 E 187 PHE -2.917 -3.863 -7.082 0.523 -0.834 0.000 3.529 1.619 0.000 E 200 GLY -2.562 -1.246 -2.623 0.242 0.000 0.000 1.135 0.000 0.000 E 201 THR 3.537 1.468 -6.014 3.466 0.000 -0.914 4.930 0.030 0.000 E 204 TYR -2.788 -4.504 -9.457 1.975 0.000 -0.471 3.449 2.682 0.000 E 324 THR -1.583 -0.856 -4.823 1.003 0.000 -0.765 3.730 0.002 0.000 E 327 PHE -3.412 -4.721 -8.228 0.931 0.000 0.000 2.576 1.602 0.000 E 328 ASP -0.300 0.147 -2.732 0.306 -0.583 0.000 3.155 2.607 0.000 E 330 TYR -1.936 -2.871 -6.672 0.840 0.000 0.000 2.960 1.343 0.000 X 1 TPA -8.279 1.922 -19.728 1.307 -1.854 -1.938 24.135 0.000 0.000 ============End report for interfE================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform======================= INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1353 0.5412 1147 INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1144 0.4576 INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] A large number of moves were rejected for being outside the grid. You likely want to reexamine your settings. INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] For the current settings, a grid size of at least 252.4 and a box size of at least 236.4 are recommended. INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -20 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================
Working on decoy: test_lig_XMLObjects_2.pdb
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 1285 rotamers at 47 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 700 rotamers at 25 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 749 rotamers at 28 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1700.33 1699.91 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final======================= INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1699.91 INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1642.36 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-9.16448 INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -9.16449 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} chain res AA total contact fa_atr fa_rep hb_bb_sc hb_sc fa_sol fa_dun fa_pair E 50 GLY -2.296 -0.757 -3.364 0.450 0.000 0.000 2.158 0.000 0.000 E 51 THR -1.745 -2.048 -3.708 0.328 0.000 0.000 1.332 0.201 0.000 E 52 GLY -0.743 0.562 -2.039 0.177 0.000 0.000 2.424 0.000 0.000 E 53 SER -2.328 0.986 -2.794 0.138 -0.642 -0.323 4.606 0.459 0.000 E 54 PHE 1.582 -2.847 -4.806 0.484 0.000 0.000 1.476 3.029 0.000 E 55 GLY 2.725 -0.245 -2.547 0.231 0.000 0.000 2.070 0.000 0.000 E 56 ARG -0.269 -0.805 -5.369 0.636 0.000 0.000 3.929 2.112 0.000 E 78 LYS 20.730 0.029 -6.578 0.992 -1.154 0.000 6.769 25.465 0.000 E 129 PHE -0.876 -1.288 -8.575 1.275 0.000 0.000 6.012 1.430 0.000 E 165 ARG -0.079 -2.045 -8.668 1.792 -1.201 -0.529 6.560 2.703 0.000 E 166 ASP 1.767 1.464 -5.566 1.647 -0.551 -0.792 6.725 3.451 0.000 E 168 LYS 1.055 2.719 -10.010 2.216 0.000 0.000 10.513 3.967 0.000 E 170 GLU 1.793 1.101 -6.604 0.571 0.000 0.000 7.135 3.642 0.000 E 171 ASN -2.146 1.006 -7.524 1.171 -0.551 -0.170 8.080 2.803 0.000 E 184 ASP 2.815 1.050 -4.320 0.764 -0.801 0.000 5.407 2.996 0.000 E 187 PHE -0.381 -3.856 -7.494 1.055 -0.702 0.000 3.285 3.732 0.000 E 200 GLY -0.160 0.327 -2.553 1.984 0.000 0.000 0.896 0.000 0.000 E 201 THR 0.282 0.738 -5.717 2.727 0.000 -0.622 4.349 0.045 0.000 E 202 PRO -2.553 -1.789 -5.301 1.953 0.000 0.000 1.559 1.056 0.000 E 203 GLU -1.442 -1.872 -5.333 0.519 0.000 0.000 2.943 3.079 0.000 E 204 TYR -3.817 -5.068 -9.444 1.464 0.000 -0.772 3.684 2.401 0.000 E 243 PRO -1.520 -0.674 -5.010 1.704 0.000 0.000 2.632 0.092 0.000 E 328 ASP -1.224 0.218 -2.808 0.180 -0.812 0.000 3.658 2.781 0.000 E 330 TYR -2.065 -3.112 -6.174 0.461 0.000 0.000 2.601 1.424 0.000 E 331 GLU -0.535 0.167 -1.627 0.081 0.000 0.000 1.713 2.598 0.000 E 333 GLU 1.144 1.728 -3.952 0.965 -0.181 0.000 4.897 3.221 0.000 X 1 TPA 2.588 2.692 -2.422 0.013 -0.350 -0.323 5.773 0.000 0.000 ============End report for interfE================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform======================= INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1374 0.5496 1126 INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1125 0.45 INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] A large number of moves were rejected for being outside the grid. You likely want to reexamine your settings. INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] For the current settings, a grid size of at least 254.1 and a box size of at least 238.1 are recommended. INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -20 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================
Working on decoy: test_lig_XMLObjects_3.pdb
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 1342 rotamers at 48 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 1163 rotamers at 42 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 1167 rotamers at 43 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1686.12 1686.12 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final======================= INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1686.12 INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1591.67 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:2.79191 INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is 2.54229 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} chain res AA total contact fa_atr fa_rep hb_bb_sc hb_sc fa_sol fa_dun fa_pair E 48 THR -2.568 -2.644 -6.709 1.086 -0.720 -0.458 4.157 0.516 0.000 E 49 LEU -5.507 -6.602 -7.780 0.585 0.000 0.000 0.593 0.203 0.000 E 50 GLY -2.529 -0.930 -4.443 0.883 0.000 0.000 2.630 0.000 0.000 E 51 THR 0.706 -1.417 -4.608 0.553 0.000 0.000 2.638 0.461 0.000 E 52 GLY 0.587 0.625 -1.602 0.166 0.000 0.000 2.060 0.000 0.000 E 53 SER -0.679 -0.364 -2.358 0.195 -0.261 0.000 2.060 1.040 0.000 E 54 PHE 2.458 -2.900 -5.225 0.622 0.000 0.000 1.703 3.540 0.000 E 55 GLY 9.392 -0.410 -2.625 0.249 0.000 0.000 1.967 0.000 0.000 E 56 ARG -1.234 -1.626 -6.936 0.600 0.000 -0.322 5.031 2.663 0.000 E 57 VAL -4.318 -3.181 -6.370 0.670 0.000 0.000 2.519 0.027 0.000 E 72 LYS -3.991 -0.900 -7.739 1.305 0.000 -0.642 6.177 1.612 0.000 E 126 GLY -3.003 -0.605 -4.369 0.381 0.000 0.000 3.383 0.000 0.000 E 127 GLU -0.249 -0.078 -7.265 1.183 0.000 -0.388 6.391 4.655 0.000 E 128 MET -4.301 -5.412 -9.602 0.969 0.000 0.000 3.221 1.982 0.000 E 129 PHE -0.264 -0.947 -9.168 1.249 0.000 0.000 6.972 1.906 0.000 E 130 SER -0.959 0.198 -4.887 0.318 0.000 -0.388 5.155 0.650 0.000 E 133 ARG -0.063 -0.981 -5.668 0.330 0.000 -0.987 5.343 3.519 0.000 E 134 ARG 3.262 0.797 -3.061 0.638 0.000 0.000 3.220 2.070 0.000 E 168 LYS 3.329 4.262 -9.570 4.595 0.000 -0.171 9.408 3.034 0.000 E 169 PRO -0.923 -0.402 -7.917 4.430 0.000 0.000 3.085 0.402 0.000 E 170 GLU 4.451 1.155 -7.463 1.622 -0.296 0.000 7.292 6.067 0.000 E 171 ASN -3.417 -0.606 -7.327 0.614 -0.584 0.000 6.690 1.525 0.000 E 172 LEU -6.024 -6.343 -8.757 1.260 0.000 0.000 1.154 0.693 0.000 E 173 LEU -4.450 -4.174 -8.186 1.308 0.000 0.000 2.704 0.778 0.000 E 183 THR -1.365 -2.833 -5.282 0.387 -0.365 0.000 2.426 1.430 0.000 E 184 ASP 2.686 0.881 -4.167 0.374 -0.792 0.000 5.465 3.613 0.000 E 201 THR 0.998 0.304 -4.625 1.925 0.000 -0.539 3.543 0.074 0.000 E 202 PRO -0.038 -1.535 -4.797 1.704 0.000 0.000 1.557 1.410 0.000 E 203 GLU 0.951 -1.048 -5.555 0.460 0.000 0.000 4.046 2.504 0.000 E 204 TYR 1.143 -3.667 -10.113 2.033 0.000 0.000 4.413 2.503 0.000 E 235 TYR 0.109 -1.418 -6.762 2.623 0.000 0.000 2.721 1.597 0.000 E 236 PRO 7.370 -0.861 -6.286 2.169 0.000 0.000 3.256 3.299 0.000 E 239 PHE -0.312 -2.086 -4.550 0.764 0.000 0.000 1.700 1.078 0.000 E 241 ASP -0.399 -0.142 -1.859 0.136 0.000 0.000 1.582 1.900 0.000 E 243 PRO -1.533 -0.702 -5.038 1.698 0.000 0.000 2.638 0.096 0.000 E 327 PHE -3.273 -4.278 -7.562 0.650 0.000 0.000 2.634 1.460 0.000 E 328 ASP -0.363 -0.146 -2.248 0.086 -0.839 0.000 2.856 3.043 0.000 E 329 ASP -2.612 0.083 -2.195 0.067 -0.839 -0.297 3.347 2.636 0.000 E 330 TYR -1.929 -2.696 -7.460 0.824 0.000 -0.276 4.215 1.429 0.000 X 1 TPA 7.066 4.327 -8.387 1.313 -0.296 -0.447 12.144 0.000 0.000 ============End report for interfE================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform======================= INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1349 0.5396 1151 INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1150 0.46 INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] A large number of moves were rejected for being outside the grid. You likely want to reexamine your settings. INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] For the current settings, a grid size of at least 251.5 and a box size of at least 235.5 are recommended. INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -21 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================
Working on decoy: test_lig_XMLObjects_0.pdb
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 1219 rotamers at 44 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 933 rotamers at 38 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 952 rotamers at 40 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1611.25 1611.25 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final======================= INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1611.25 INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1519.85 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-11.7332 INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -11.7982 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} chain res AA total contact fa_atr fa_rep hb_bb_sc hb_sc fa_sol fa_dun fa_pair E 51 THR -1.563 -1.798 -2.919 0.245 0.000 0.000 0.876 0.153 0.000 E 52 GLY 5.776 0.711 -2.165 0.054 0.000 0.000 2.822 0.000 0.000 E 53 SER 7.427 0.446 -3.310 0.661 -0.525 -0.368 3.988 1.607 0.000 E 54 PHE 6.186 -2.451 -5.163 0.674 0.000 0.000 2.038 3.284 0.000 E 55 GLY -2.106 -0.347 -2.810 0.143 0.000 0.000 2.320 0.000 0.000 E 56 ARG -1.271 -1.790 -6.885 0.415 0.000 -0.382 5.061 3.036 0.000 E 78 LYS -1.823 -0.573 -6.139 0.645 -0.861 0.000 5.782 2.390 0.000 E 82 LEU -2.364 -2.190 -5.796 0.810 -0.495 0.000 3.292 0.042 0.000 E 165 ARG -2.459 -3.163 -8.056 0.915 -1.849 -0.595 6.421 2.208 0.000 E 166 ASP -2.087 0.447 -4.710 0.538 -0.340 -0.944 5.903 2.476 0.000 E 168 LYS -2.531 1.567 -9.979 2.888 0.000 -0.928 9.586 0.926 0.000 E 170 GLU -1.701 0.172 -5.437 0.554 0.000 -0.258 5.313 2.644 0.000 E 171 ASN -3.745 -0.489 -6.885 0.438 -0.340 -0.224 6.522 1.908 0.000 E 184 ASP -0.614 0.819 -3.444 0.766 -0.357 -0.285 4.138 2.651 0.000 E 187 PHE -0.373 -4.362 -7.258 0.696 -0.749 0.000 2.950 3.700 0.000 E 198 LEU 1.834 -1.331 -2.905 0.752 0.000 0.000 0.823 0.576 0.000 E 199 CYS 5.081 -3.481 -6.217 0.919 0.000 0.000 1.817 2.442 0.000 E 200 GLY -2.235 -1.423 -2.525 0.108 0.000 0.000 0.995 0.000 0.000 E 201 THR -2.011 -0.071 -5.331 1.734 0.000 -1.390 4.915 0.051 0.000 E 202 PRO -3.321 -1.984 -5.694 1.727 0.000 0.000 1.982 1.019 0.000 E 203 GLU -1.351 -1.740 -5.010 0.541 0.000 0.000 2.729 3.089 0.000 E 204 TYR -3.569 -4.762 -8.961 1.374 0.000 -0.733 3.557 2.658 0.000 E 205 LEU -2.973 -4.662 -6.935 0.899 0.000 0.000 1.374 0.956 0.000 E 210 ILE 46.181 -3.743 -5.688 1.091 0.000 0.000 0.854 47.349 0.000 E 242 GLN 0.549 0.380 -4.327 1.292 -0.244 0.000 3.659 2.465 0.000 E 243 PRO -3.732 -1.299 -5.921 1.289 0.000 0.000 3.333 0.134 0.000 E 244 ILE 1.292 -0.636 -4.342 0.600 0.000 0.000 3.106 0.133 0.000 E 246 ILE -4.078 -3.923 -9.900 1.563 0.000 0.000 4.414 0.116 0.000 E 247 TYR -1.044 -4.043 -10.503 2.098 0.000 0.000 4.362 3.693 0.000 X 1 TPA 1.273 1.190 -4.233 0.213 -0.525 -0.368 6.102 0.000 0.000 ============End report for interfE================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform======================= INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1363 0.5452 1137 INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1136 0.4544 INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] A large number of moves were rejected for being outside the grid. You likely want to reexamine your settings. INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] For the current settings, a grid size of at least 253.2 and a box size of at least 237.2 are recommended. INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -20 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================
Working on decoy: test_lig_XMLObjects_4.pdb
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 1013 rotamers at 35 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 959 rotamers at 33 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.pack_rotamers: {0} built 990 rotamers at 36 positions. INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line() INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1697.63 1697.63 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final======================= INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1697.63 INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1628.15 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX======================= INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-14.9022 INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -15.1627 INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} chain res AA total contact fa_atr fa_rep hb_bb_sc hb_sc fa_sol fa_dun fa_pair E 50 GLY -2.600 -0.787 -3.367 0.435 0.000 0.000 2.145 0.000 0.000 E 51 THR 7.583 -1.229 -2.633 0.172 0.000 0.000 1.232 0.037 0.000 E 52 GLY 0.178 0.809 -2.585 0.425 0.000 0.000 2.969 0.000 0.000 E 53 SER -3.224 0.460 -2.928 0.168 -1.012 -0.299 4.531 0.298 0.000 E 54 PHE 2.350 -2.057 -4.940 0.813 0.000 0.000 2.070 3.101 0.000 E 55 GLY -1.168 -0.190 -2.719 0.251 0.000 0.000 2.278 0.000 0.000 E 56 ARG 0.113 -1.410 -6.148 0.773 0.000 -0.411 4.376 3.603 0.000 E 127 GLU 5.674 0.265 -6.455 1.188 0.000 0.000 5.532 5.527 0.000 E 129 PHE -2.187 -2.254 -9.665 1.325 0.000 0.000 6.085 1.411 0.000 E 130 SER -0.490 0.509 -4.664 0.405 0.000 0.000 4.769 0.469 0.000 E 133 ARG 1.166 -0.886 -5.718 0.435 0.000 -0.982 5.379 4.010 0.000 E 134 ARG 3.354 1.267 -4.227 1.445 0.000 0.000 4.049 2.042 0.000 E 165 ARG 0.630 -1.073 -8.797 2.914 -1.167 -0.506 6.483 2.654 0.000 E 166 ASP 3.562 3.175 -4.858 3.206 -0.654 0.000 5.482 2.057 0.000 E 168 LYS -0.694 2.273 -10.086 2.547 0.000 -1.344 11.157 2.410 0.000 E 169 PRO -3.279 -2.341 -7.808 1.650 0.000 0.000 3.817 0.765 0.000 E 170 GLU -0.540 1.225 -6.618 0.772 0.000 -0.226 7.296 4.054 0.000 E 171 ASN -3.534 -0.548 -6.847 0.680 -0.654 0.000 6.273 1.839 0.000 E 184 ASP 2.870 0.655 -4.090 0.497 -0.882 0.000 5.131 2.941 0.000 E 187 PHE -0.138 -3.956 -7.393 0.944 -0.667 0.000 3.161 4.153 0.000 E 199 CYS 6.887 -3.734 -6.109 0.820 0.000 0.000 1.555 1.717 0.000 E 200 GLY -1.379 -0.992 -2.480 0.181 0.000 0.000 1.308 0.000 0.000 E 201 THR -0.477 1.709 -6.176 2.025 0.000 -0.856 6.715 0.233 0.000 E 202 PRO -3.121 -1.733 -6.090 2.213 0.000 0.000 2.143 0.972 0.000 E 203 GLU -1.709 -1.867 -5.405 0.573 0.000 0.000 2.965 3.113 0.000 E 204 TYR -3.322 -4.715 -9.141 1.386 0.000 -0.746 3.786 2.709 0.000 E 205 LEU -2.956 -4.722 -7.322 1.400 0.000 0.000 1.200 0.956 0.000 E 235 TYR 0.122 -1.408 -6.782 2.630 0.000 0.000 2.743 1.616 0.000 E 236 PRO 7.327 -0.974 -6.149 2.112 0.000 0.000 3.064 3.290 0.000 E 239 PHE -0.307 -2.076 -4.537 0.748 0.000 0.000 1.713 1.082 0.000 E 243 PRO -1.686 -0.869 -5.261 1.702 0.000 0.000 2.690 0.096 0.000 E 327 PHE -2.893 -4.383 -8.065 0.694 0.000 0.000 2.989 1.670 0.000 E 328 ASP -1.274 -0.065 -3.252 0.186 -1.244 0.000 4.244 2.773 0.000 E 329 ASP -0.818 -0.140 -2.374 0.113 -0.738 0.000 2.859 2.979 0.000 E 330 TYR -1.763 -2.681 -6.591 0.659 0.000 0.000 3.251 1.362 0.000 X 1 TPA -1.690 3.484 -7.017 0.166 -0.759 -1.336 12.431 0.000 0.000 ============End report for interfE================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX================== INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================
Now that we have sampled some global ligand docking trajectories, let's plot the ligand binding energy landscape:
#Skip for tests (as DF is not present)
if not os.getenv("DEBUG"):
matplotlib.rcParams['figure.figsize'] = [12.0, 8.0]
seaborn.scatterplot(x="rmsd_chX", y="interfE", data=df)
<matplotlib.axes._subplots.AxesSubplot at 0x7ffff5de1278>
We can check which .pdb
file has the lowest interfE
score:
#Skip for tests
if not os.getenv("DEBUG"):
df.sort_values(by="interfE")
dslf_fa13 | fa_atr | fa_dun | fa_elec | fa_intra_rep | fa_intra_sol_xover4 | fa_rep | fa_sol | hbond_bb_sc | hbond_lr_bb | ... | interfE | lk_ball_wtd | omega | p_aa_pp | pro_close | rama_prepro | ref | rmsd_chX | total_score | yhh_planarity | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
test_lig_XMLObjects_1.pdb | 0.0 | -2141.790247 | 2839.589602 | -505.303161 | 1549.888068 | 90.394684 | 1355.538397 | 1338.970707 | -52.121705 | -49.476625 | ... | -28.276440 | -50.974895 | 16.443889 | -84.493475 | 91.445419 | 117.822680 | 81.74634 | 0.631487 | 1456.971339 | 1.100056 |
test_lig_XMLObjects_4.pdb | 0.0 | -2117.511239 | 3002.017883 | -484.395373 | 1575.126871 | 91.668637 | 1434.239151 | 1329.615403 | -48.468502 | -47.234071 | ... | -15.162686 | -49.593810 | -1.135463 | -85.518547 | 68.279343 | 118.636338 | 81.74634 | 11.435035 | 1628.146163 | 0.366937 |
test_lig_XMLObjects_0.pdb | 0.0 | -2101.634782 | 2881.724947 | -484.021972 | 1552.937939 | 90.957571 | 1395.967000 | 1307.276630 | -48.113076 | -47.985689 | ... | -11.798166 | -48.713822 | -0.016234 | -86.665216 | 73.794018 | 111.035818 | 81.74634 | 18.723389 | 1519.846938 | 0.360842 |
test_lig_XMLObjects_2.pdb | 0.0 | -2108.199196 | 2995.956828 | -483.697206 | 1572.754514 | 91.583322 | 1441.994818 | 1317.274987 | -47.207246 | -47.496493 | ... | -9.164489 | -48.398568 | 3.595816 | -82.205583 | 73.140703 | 122.270933 | 81.74634 | 13.237048 | 1642.356614 | 0.294935 |
test_lig_XMLObjects_3.pdb | 0.0 | -2114.363249 | 2941.806947 | -471.461845 | 1563.092110 | 90.772894 | 1426.594993 | 1318.093586 | -47.347564 | -48.064493 | ... | 2.542285 | -49.704318 | 4.201275 | -83.261999 | 68.786798 | 117.522522 | 81.74634 | 9.790556 | 1591.672471 | 0.122519 |
5 rows × 22 columns
Let's take a look at the pose with the lowest interfE
value that was generated:
#Skip for tests
if not os.getenv("DEBUG"):
lowest_energy_pdb_filename = os.path.join("expected_outputs", df.sort_values(by="interfE").head(1).index[0])
test_pose = pyrosetta.io.pose_from_file(filename=lowest_energy_pdb_filename)
chE = pyrosetta.rosetta.core.select.residue_selector.ChainSelector("E")
view = viewer.init(test_pose)
view.add(viewer.setStyle())
view.add(viewer.setStyle(command=({"hetflag": True}, {"stick": {"colorscheme": "brownCarbon", "radius": 0.2}})))
view.add(viewer.setSurface(residue_selector=chE, 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
Exercise:
Re-run the above example with more sampling. Pretend that you have done enough sampling (i.e. ~2,000-10,000 global ligand docking trajectories depending on the surface area of the protein) and that the decoy with the lowest interfE
score is the "native" ligand binding mode. Re-plot the ligand binding energy landscape fixing that decoy to rmsd_chX
=0.0
Hint: You have all of the decoys saved as .pdb
files, so you need to re-score them using the command line flag -in:file:native
specifying the .pdb
file with the lowest interfE
score, that way all rmsd_chX
values correspond to the RMSD from that decoy, not the binding mode we started with above. Use the following cell to get started! The code below does not save the new scores to a scorefile, but if you would like to, make use of the pyrosetta.toolbox.py_jobdistributor.output_scorefile()
function.
Restart Jupyter Notebook kernel to properly re-initialize PyRosetta
import glob
import logging
logging.basicConfig(level=logging.INFO)
import matplotlib
%matplotlib inline
import os
import pandas as pd
import pyrosetta
import pyrosetta.distributed.viewer as viewer
import seaborn
seaborn.set()
import sys
!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()
if not os.getenv("DEBUG"):
pdb_filenames = glob.glob("expected_outputs/test_lig_XMLObjects*.pdb")
ligand_params = "inputs/TPA.am1-bcc.fa.params"
native_pdb_filename = "expected_outputs/test_lig_XMLObjects_1.pdb"
flags = f"""
-extra_res_fa {ligand_params}
-in:file:native {native_pdb_filename}
-ignore_unrecognized_res 1
-mute all
"""
pyrosetta.distributed.init(flags)
scorefxn = pyrosetta.create_score_function("ref2015")
xml = pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects.create_from_string("""
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="fa_standard" weights="ref2015.wts"/>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Chain name="chX" chains="X"/>
</RESIDUE_SELECTORS>
<SIMPLE_METRICS>
<RMSDMetric name="rmsd_chX" use_native="true" residue_selector="chX" residue_selector_ref="chX" robust="true" rmsd_type="rmsd_all" />
</SIMPLE_METRICS>
<FILTERS>
<LigInterfaceEnergy name="interfE" scorefxn="fa_standard" energy_cutoff="0.0" confidence="0"/>
<SimpleMetricFilter name="rmsd_chX" metric="rmsd_chX" cutoff="999999." comparison_type="lt" confidence="0"/>
</FILTERS>
<PROTOCOLS>
<Add filter="interfE"/>
<Add filter="rmsd_chX"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
""").get_mover("ParsedProtocol")
df = pd.DataFrame()
for pdb_filename in pdb_filenames:
test_pose = pyrosetta.io.pose_from_file(filename=pdb_filename)
xml.apply(test_pose)
test_df = pd.DataFrame.from_records(dict(test_pose.scores), index=[pdb_filename.split("/")[-1]])
df = df.append(test_df)
matplotlib.rcParams['figure.figsize'] = [12.0, 8.0]
seaborn.scatterplot(x="rmsd_chX", y="interfE", data=df)
INFO:pyrosetta.distributed:maybe_init performing pyrosetta initialization: {'extra_options': '-extra_res_fa inputs/TPA.am1-bcc.fa.params -in:file:native expected_outputs/test_lig_XMLObjects_1.pdb -ignore_unrecognized_res 1 -mute all', '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.