the best case output of a repacking calculation as a positive control for benchmarking One benefit of working within Jupyter notebooks is that we can make use of its autocomplete features. For a complete example, please consult the sample script ligand_interface.py. Execute this script from the commandline providing the .mdl file as the first argument and the ResidueType name as option "-n". It may be as do tools for creating your compound. 1) Obtain the ligand .mdl file -skip this step if the compound is present it PyRosetta (rare) -refine the chemical data (no PyRosetta tools for this) -convert the chemical data file to .mdl if necessary (try babel or openbabel) -if necessary, generate conformers of the compound as separate files PyRosetta was created at Johns Hopkins University by Jeffrey J. The .pdb file is produced for grafting the ligand into a PDB file (the next step). PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. Installing required packages 2. PyRosetta does not perform any of the initial changes required to improve the accuracy or change the file format of a ligand. This method is preferred when the ligand is transitory (default). Object Naming 3. interactive - Register python log handling and make visible if not. The Notebooks can be viewed directly in nbviewer. pyrosetta.rosetta.protocols.minimization_packing. Real-time PyMOL visualization is now part of PyRosetta! C++: protocols::minimization_packing::TaskAwareMinMover::apply(class core::pose::Pose &) > void, C++: protocols::minimization_packing::TaskAwareMinMover::operator=(const class protocols::minimization_packing::TaskAwareMinMover &) > class protocols::minimization_packing::TaskAwareMinMover &, bb(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, val: bool) -> None, C++: protocols::minimization_packing::TaskAwareMinMover::bb(bool) > void, bb(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) -> bool, C++: protocols::minimization_packing::TaskAwareMinMover::bb() const > bool, chi(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, val: bool) -> None, C++: protocols::minimization_packing::TaskAwareMinMover::chi(bool) > void, chi(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) -> bool, C++: protocols::minimization_packing::TaskAwareMinMover::chi() const > bool, C++: protocols::minimization_packing::TaskAwareMinMover::clone() const > class std::shared_ptr, C++: protocols::minimization_packing::TaskAwareMinMover::fresh_instance() const > class std::shared_ptr, C++: protocols::minimization_packing::TaskAwareMinMover::get_name() const > std::string, jump(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, j: bool) -> None, C++: protocols::minimization_packing::TaskAwareMinMover::jump(const bool) > void, jump(self: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover) -> bool, C++: protocols::minimization_packing::TaskAwareMinMover::jump() const > bool, C++: protocols::minimization_packing::TaskAwareMinMover::mover_name() > std::string, C++: protocols::minimization_packing::TaskAwareMinMover::parse_my_tag(class std::shared_ptr, class basic::datacache::DataMap &) > void, C++: protocols::minimization_packing::TaskAwareMinMover::parse_task_operations(class std::shared_ptr, const class basic::datacache::DataMap &) > void, C++: protocols::minimization_packing::TaskAwareMinMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) > void, C++: protocols::minimization_packing::TaskAwareMinMoverCreator::operator=(const class protocols::minimization_packing::TaskAwareMinMoverCreator &) > class protocols::minimization_packing::TaskAwareMinMoverCreator &, C++: protocols::minimization_packing::TaskAwareMinMoverCreator::create_mover() const > class std::shared_ptr, C++: protocols::minimization_packing::TaskAwareMinMoverCreator::keyname() const > std::string, C++: protocols::minimization_packing::TaskAwareMinMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const > void, C++: protocols::minimization_packing::UserDefinedGroupDiscriminator::operator=(const class protocols::minimization_packing::UserDefinedGroupDiscriminator &) > class protocols::minimization_packing::UserDefinedGroupDiscriminator &, C++: protocols::minimization_packing::UserDefinedGroupDiscriminator::clone() const > class std::shared_ptr, C++: protocols::minimization_packing::UserDefinedGroupDiscriminator::group_id(const class core::pose::Pose &, unsigned long) const > unsigned long, C++: protocols::minimization_packing::UserDefinedGroupDiscriminator::set_group_ids(const class utility::vector1 > &) > void, Copyright 2017, Sergey Lyskov. If only interface structure prediction (high- resolution) is used, the PDB file MUST contain the molecules ORIENTED properly for the interface or the sampling will rarely find a proper structure. -this will also yield a .pdb file which may be needed in step 3. python molfile_to_params.py -n , 3) Produce the ligand-protein complex PDB file, -obtain the desired protein PDB file (see pose_structure.py), -clean the PDB of other undesirable lines (HETATMs, waters, etc. what rotamer sets are allowed at each residue position during packing. Bases: Mover this mover does the conformer swap in RosettaDock's ensemble docking. Simple protocol, 16.7 PyRosettaCluster Tutorial 1B. Inside the PyRosetta main directory, place files within: /minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types. pyrosetta.org/documentation has the basics introduction. Windows version of PyRosetta 2.0 is ready for download. Its development is supported by: by Jeffrey J. pose_from_file(pose, TEM-1_with_substrates.pdb), ResidueTypeSet pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for this class wraps MinMover, but ensures that its MoveMap always contains up-to-date information about sidechain mobility. PackRotamersMover.task_factory, C++: protocols::minimization_packing::PackRotamersMover::task(class std::shared_ptr) > void, task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask, C++: protocols::minimization_packing::PackRotamersMover::task() const > class std::shared_ptr, task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None, C++: protocols::minimization_packing::PackRotamersMover::task_factory(class std::shared_ptr) > void, task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory, C++: protocols::minimization_packing::PackRotamersMover::task_factory() const > class std::shared_ptr, C++: protocols::minimization_packing::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const > bool, C++: protocols::minimization_packing::PackRotamersMoverCreator::operator=(const class protocols::minimization_packing::PackRotamersMoverCreator &) > class protocols::minimization_packing::PackRotamersMoverCreator &, C++: protocols::minimization_packing::PackRotamersMoverCreator::create_mover() const > class std::shared_ptr, C++: protocols::minimization_packing::PackRotamersMoverCreator::keyname() const > std::string, C++: protocols::minimization_packing::PackRotamersMoverCreator::mover_name() > std::string, C++: protocols::minimization_packing::PackRotamersMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const > void. Typically, one would obtain a PyRosetta cannot be used to generate conformers. Purpose This GUI is used to setup Rosetta specific filetypes, do interactive modeling using Rosetta as its base, run rosetta protocols, and analyze decoy results. Commons. molfile (.mdl) generated from the xyz coordinates of a residue, small Results Now that the ResidueType is defined, the PDB file for ligand interface prediction can be made. performing energy minimization of a ScoreFunction over the allowable The Jupyter Notebooks below provide an introduction to the fundmamental principles and tools for using PyRosetta. New Edition of PyRosetta Workshops Available for PyRosetta4! Database resolution proceeds by first searching the current installation for a database or rosetta_database PyRosetta-3 Namespace vs. monolith: According to Sergey, in the namespace build each C++ namespace has its own shared library which the kernel needs to load, resolve symbols, and so on. rosettacommons.github.io/pyrosetta.notebooks/, Chapter 3.0 Rosetta Energy Score Functions, Chapter 8.0 Ligand Refinement in PyRosetta (a.k.a. overriden by movers wishing to provide citation information. Bases: Mover apply(self:pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, pose:pyrosetta.rosetta.core.pose.Pose)None C++: protocols::minimization_packing::BoltzmannRotamerMover::apply(class core::pose::Pose &) -> void Search Page An additional script (and other necessary scripts) are provided for converting an .mdl file to a .params file (required for the PyRosetta database) and .pdb files. -the ligand chain is named "X" (a convention), -the ligand chain occurs after all protein chains**. of freedom, defined by a MoveMap. Will attempt to grab additional poses until a nullptr is returned. False - Write logs via c++-level filehandles. Contents: pyrosetta_documentarian package. It uses C++: protocols::moves::Mover::reinitialize_for_new_input() const > bool. loop residues will have their bb dofs change regularly between repackings. This monolith takes up a very small memory footprint as compared to PyRosetta-3 monolith version, as well as numerous other improvements. pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover, pyrosetta.rosetta.protocols.moves.MoverStatus, pyrosetta.rosetta.core.scoring.ScoreFunction, pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t, pyrosetta.rosetta.core.pack.task.PackerTask, pyrosetta.rosetta.basic.datacache.DataMap, pyrosetta.rosetta.basic.citation_manager.CitationCollectionList, pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_double_t, pyrosetta.rosetta.core.pack.task.TaskFactory, pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator, pyrosetta.rosetta.protocols.minimization_packing.ChainGroupDiscriminator, pyrosetta.rosetta.protocols.minimization_packing.GroupDiscriminator, pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover, pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator, pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover, pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover, pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover, pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover, complex_type_generator_for_rotamer_trials_mover, utility::tag::XMLSchemaComplexTypeGenerator, pyrosetta.rosetta.protocols.minimization_packing.GreenPacker, pyrosetta.rosetta.protocols.minimization_packing.MinMover, pyrosetta.rosetta.core.kinematics.MoveMap, pyrosetta.rosetta.protocols.moves.MoveMapMover, pyrosetta.rosetta.core.select.movemap.MoveMapFactory, pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator, pyrosetta.rosetta.protocols.minimization_packing.MinPackMover, pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator, pyrosetta.rosetta.protocols.minimization_packing.MinimalRotamer, pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, complex_type_generator_for_pack_rotamers_mover, pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t, pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t, pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pyrosetta.rosetta.core.pack.annealer.AnnealerObserver, pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator, pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy, pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator, pyrosetta.rosetta.protocols.minimization_packing.PertMinMover, pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator, pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover, pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator, pyrosetta.rosetta.protocols.moves.MoverCreator, pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator, pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator, pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover, pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover, pyrosetta.rosetta.core.optimization.MinimizerOptions, pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator, pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover, pyrosetta.rosetta.utility.vector1_core_pose_Pose, pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator, pyrosetta.rosetta.protocols.minimization_packing.UserDefinedGroupDiscriminator, pyrosetta.rosetta.utility.vector1_unsigned_long, BoltzmannRotamerMover.get_additional_output(), BoltzmannRotamerMover.get_bias_sampling(), BoltzmannRotamerMover.get_last_move_status(), BoltzmannRotamerMover.get_ligand_resnum(), BoltzmannRotamerMover.get_ligand_weight(), BoltzmannRotamerMover.get_randomize_resnum(), BoltzmannRotamerMover.get_self_weak_ptr(), BoltzmannRotamerMover.last_proposal_density_ratio(), BoltzmannRotamerMover.provide_citation_info(), BoltzmannRotamerMover.provide_xml_schema(), BoltzmannRotamerMover.reinitialize_for_each_job(), BoltzmannRotamerMover.reinitialize_for_new_input(), BoltzmannRotamerMover.set_bias_sampling(), BoltzmannRotamerMover.set_ligand_resnum(), BoltzmannRotamerMover.set_ligand_weight(), BoltzmannRotamerMover.set_randomize_resnum(), BoltzmannRotamerMover.set_score_function(), BoltzmannRotamerMoverCreator.create_mover(), BoltzmannRotamerMoverCreator.provide_xml_schema(), DisulfideOptimizationMover.fresh_instance(), DisulfideOptimizationMover.get_additional_output(), DisulfideOptimizationMover.get_current_job(), DisulfideOptimizationMover.get_current_tag(), DisulfideOptimizationMover.get_input_pose(), DisulfideOptimizationMover.get_last_move_status(), DisulfideOptimizationMover.get_native_pose(), DisulfideOptimizationMover.get_self_ptr(), DisulfideOptimizationMover.get_self_weak_ptr(), DisulfideOptimizationMover.interaction_graph_threads(), DisulfideOptimizationMover.last_proposal_density_ratio(), DisulfideOptimizationMover.parse_my_tag(), DisulfideOptimizationMover.provide_citation_info(), DisulfideOptimizationMover.provide_xml_schema(), DisulfideOptimizationMover.register_options(), DisulfideOptimizationMover.reinitialize_for_each_job(), DisulfideOptimizationMover.reinitialize_for_new_input(), DisulfideOptimizationMover.reset_status(), DisulfideOptimizationMover.set_current_job(), DisulfideOptimizationMover.set_current_tag(), DisulfideOptimizationMover.set_final_optimization_n_iter(), DisulfideOptimizationMover.set_input_pose(), DisulfideOptimizationMover.set_interaction_graph_threads(), DisulfideOptimizationMover.set_native_pose(), DisulfideOptimizationMover.set_score_function(), DisulfideOptimizationMover.set_selector(), DisulfideOptimizationMoverCreator.assign(), DisulfideOptimizationMoverCreator.create_mover(), DisulfideOptimizationMoverCreator.keyname(), DisulfideOptimizationMoverCreator.provide_xml_schema(), EnergyCutRotamerTrialsMinMover.clear_info(), EnergyCutRotamerTrialsMinMover.fresh_instance(), EnergyCutRotamerTrialsMinMover.get_additional_output(), EnergyCutRotamerTrialsMinMover.get_current_job(), EnergyCutRotamerTrialsMinMover.get_current_tag(), EnergyCutRotamerTrialsMinMover.get_input_pose(), EnergyCutRotamerTrialsMinMover.get_last_move_status(), EnergyCutRotamerTrialsMinMover.get_name(), EnergyCutRotamerTrialsMinMover.get_native_pose(), EnergyCutRotamerTrialsMinMover.get_self_ptr(), EnergyCutRotamerTrialsMinMover.get_self_weak_ptr(), EnergyCutRotamerTrialsMinMover.get_type(), EnergyCutRotamerTrialsMinMover.last_proposal_density_ratio(), EnergyCutRotamerTrialsMinMover.mover_name(), EnergyCutRotamerTrialsMinMover.parse_my_tag(), EnergyCutRotamerTrialsMinMover.provide_citation_info(), EnergyCutRotamerTrialsMinMover.provide_xml_schema(), EnergyCutRotamerTrialsMinMover.register_options(), EnergyCutRotamerTrialsMinMover.reinitialize_for_each_job(), EnergyCutRotamerTrialsMinMover.reinitialize_for_new_input(), EnergyCutRotamerTrialsMinMover.reset_status(), EnergyCutRotamerTrialsMinMover.score_function(), EnergyCutRotamerTrialsMinMover.set_current_job(), EnergyCutRotamerTrialsMinMover.set_current_tag(), EnergyCutRotamerTrialsMinMover.set_input_pose(), EnergyCutRotamerTrialsMinMover.set_native_pose(), EnergyCutRotamerTrialsMinMover.set_type(), EnergyCutRotamerTrialsMinMover.task_factory(), EnergyCutRotamerTrialsMinMover.test_move(), EnergyCutRotamerTrialsMover.complex_type_generator_for_rotamer_trials_mover(), EnergyCutRotamerTrialsMover.fresh_instance(), EnergyCutRotamerTrialsMover.get_additional_output(), EnergyCutRotamerTrialsMover.get_current_job(), EnergyCutRotamerTrialsMover.get_current_tag(), EnergyCutRotamerTrialsMover.get_input_pose(), EnergyCutRotamerTrialsMover.get_last_move_status(), EnergyCutRotamerTrialsMover.get_native_pose(), EnergyCutRotamerTrialsMover.get_self_ptr(), EnergyCutRotamerTrialsMover.get_self_weak_ptr(), EnergyCutRotamerTrialsMover.last_proposal_density_ratio(), EnergyCutRotamerTrialsMover.parse_my_tag(), EnergyCutRotamerTrialsMover.provide_citation_info(), EnergyCutRotamerTrialsMover.provide_xml_schema(), EnergyCutRotamerTrialsMover.register_options(), EnergyCutRotamerTrialsMover.reinitialize_for_each_job(), EnergyCutRotamerTrialsMover.reinitialize_for_new_input(), EnergyCutRotamerTrialsMover.reset_status(), EnergyCutRotamerTrialsMover.score_function(), EnergyCutRotamerTrialsMover.set_current_job(), EnergyCutRotamerTrialsMover.set_current_tag(), EnergyCutRotamerTrialsMover.set_input_pose(), EnergyCutRotamerTrialsMover.set_native_pose(), EnergyCutRotamerTrialsMover.task_factory(), GreenPacker.last_proposal_density_ratio(), GreenPacker.set_reference_round_task_factory(), MinMover.abs_score_convergence_threshold(), MinMover.abs_score_diff_after_minimization(), MinMover.complex_type_generator_for_min_mover(), MinPackMover.last_proposal_density_ratio(), MinPackMover.reinitialize_for_new_input(), PackRotamersMover.complex_type_generator_for_pack_rotamers_mover(), PackRotamersMover.get_additional_output(), PackRotamersMover.initialize_task_factory_with_operations(), PackRotamersMover.last_proposal_density_ratio(), PackRotamersMover.parse_task_operations(), PackRotamersMover.provide_citation_info(), PackRotamersMover.reinitialize_for_each_job(), PackRotamersMover.reinitialize_for_new_input(), PackRotamersMover.set_annealer_observer(), PackRotamersMoverCreator.provide_xml_schema(), PackRotamersMoverLazy.complex_type_generator_for_pack_rotamers_mover(), PackRotamersMoverLazy.get_additional_output(), PackRotamersMoverLazy.get_last_move_status(), PackRotamersMoverLazy.get_self_weak_ptr(), PackRotamersMoverLazy.initialize_task_factory_with_operations(), PackRotamersMoverLazy.last_proposal_density_ratio(), PackRotamersMoverLazy.list_options_read(), PackRotamersMoverLazy.parse_score_function(), PackRotamersMoverLazy.parse_task_operations(), PackRotamersMoverLazy.provide_citation_info(), PackRotamersMoverLazy.provide_xml_schema(), PackRotamersMoverLazy.reinitialize_for_each_job(), PackRotamersMoverLazy.reinitialize_for_new_input(), PackRotamersMoverLazy.set_annealer_observer(), PackRotamersMoverLazyCreator.create_mover(), PackRotamersMoverLazyCreator.mover_name(), PackRotamersMoverLazyCreator.provide_xml_schema(), PertMinMover.last_proposal_density_ratio(), PertMinMover.reinitialize_for_new_input(), RepackSidechainsMover.get_additional_output(), RepackSidechainsMover.get_last_move_status(), RepackSidechainsMover.get_self_weak_ptr(), RepackSidechainsMover.last_proposal_density_ratio(), RepackSidechainsMover.parse_score_function(), RepackSidechainsMover.provide_citation_info(), RepackSidechainsMover.reinitialize_for_each_job(), RepackSidechainsMover.reinitialize_for_new_input(), RepackSidechainsMoverCreator.create_mover(), RepackSidechainsMoverCreator.mover_name(), RepackSidechainsMoverCreator.provide_xml_schema(), RotamerTrialsMinMover.get_additional_output(), RotamerTrialsMinMover.get_last_move_status(), RotamerTrialsMinMover.get_self_weak_ptr(), RotamerTrialsMinMover.last_proposal_density_ratio(), RotamerTrialsMinMover.provide_citation_info(), RotamerTrialsMinMover.provide_xml_schema(), RotamerTrialsMinMover.reinitialize_for_each_job(), RotamerTrialsMinMover.reinitialize_for_new_input(), RotamerTrialsMinMoverCreator.create_mover(), RotamerTrialsMinMoverCreator.provide_xml_schema(), RotamerTrialsMover.complex_type_generator_for_rotamer_trials_mover(), RotamerTrialsMover.get_additional_output(), RotamerTrialsMover.get_last_move_status(), RotamerTrialsMover.last_proposal_density_ratio(), RotamerTrialsMover.provide_citation_info(), RotamerTrialsMover.reinitialize_for_each_job(), RotamerTrialsMover.reinitialize_for_new_input(), RotamerTrialsMoverCreator.provide_xml_schema(), RotamerizeMover.last_proposal_density_ratio(), RotamerizeMover.reinitialize_for_each_job(), RotamerizeMover.reinitialize_for_new_input(), SaneMinMover.last_proposal_density_ratio(), SaneMinMover.reinitialize_for_new_input(), SetReturningPackRotamersMover.clear_info(), SetReturningPackRotamersMover.complex_type_generator_for_pack_rotamers_mover(), SetReturningPackRotamersMover.fresh_instance(), SetReturningPackRotamersMover.get_additional_output(), SetReturningPackRotamersMover.get_current_job(), SetReturningPackRotamersMover.get_current_tag(), SetReturningPackRotamersMover.get_input_pose(), SetReturningPackRotamersMover.get_last_move_status(), SetReturningPackRotamersMover.get_native_pose(), SetReturningPackRotamersMover.get_repacked_poses(), SetReturningPackRotamersMover.get_self_ptr(), SetReturningPackRotamersMover.get_self_weak_ptr(), SetReturningPackRotamersMover.initialize_task_factory_with_operations(), SetReturningPackRotamersMover.last_proposal_density_ratio(), SetReturningPackRotamersMover.list_options_read(), SetReturningPackRotamersMover.mover_name(), SetReturningPackRotamersMover.output_repacked_poses(), SetReturningPackRotamersMover.parse_my_tag(), SetReturningPackRotamersMover.parse_score_function(), SetReturningPackRotamersMover.parse_task_operations(), SetReturningPackRotamersMover.provide_citation_info(), SetReturningPackRotamersMover.provide_xml_schema(), SetReturningPackRotamersMover.register_options(), SetReturningPackRotamersMover.reinitialize_for_each_job(), SetReturningPackRotamersMover.reinitialize_for_new_input(), SetReturningPackRotamersMover.reset_status(), SetReturningPackRotamersMover.rotamer_sets(), SetReturningPackRotamersMover.score_function(), SetReturningPackRotamersMover.set_annealer_observer(), SetReturningPackRotamersMover.set_current_job(), SetReturningPackRotamersMover.set_current_tag(), SetReturningPackRotamersMover.set_input_pose(), SetReturningPackRotamersMover.set_native_pose(), SetReturningPackRotamersMover.task_factory(), SetReturningPackRotamersMover.task_is_valid(), SetReturningPackRotamersMover.test_move(), TaskAwareMinMover.get_additional_output(), TaskAwareMinMover.last_proposal_density_ratio(), TaskAwareMinMover.parse_task_operations(), TaskAwareMinMover.provide_citation_info(), TaskAwareMinMover.reinitialize_for_each_job(), TaskAwareMinMover.reinitialize_for_new_input(), TaskAwareMinMoverCreator.provide_xml_schema(), UserDefinedGroupDiscriminator.set_group_ids(). residues upstream of jump 1 define group 1, and those downstream of jump 1 define group 2. If nothing happens, download GitHub Desktop and try again. Ensure that the final PDB file has the proper ResidueType definition and chain ID. Includes core data and global options. clear_info is called by jd2 before calling apply, C++: protocols::moves::Mover::clear_info() > void, C++: protocols::minimization_packing::BoltzmannRotamerMover::clone() const > class std::shared_ptr, C++: protocols::moves::Mover::create() > class std::shared_ptr, C++: protocols::minimization_packing::BoltzmannRotamerMover::fresh_instance() const > class std::shared_ptr. None - Set handler if interactive, otherwise not. C++: protocols::moves::Mover::get_last_move_status() const > enum protocols::moves::MoverStatus, C++: protocols::minimization_packing::BoltzmannRotamerMover::get_ligand_resnum() const > unsigned long, C++: protocols::minimization_packing::BoltzmannRotamerMover::get_ligand_weight() const > double, C++: protocols::minimization_packing::BoltzmannRotamerMover::get_name() const > std::string, C++: protocols::moves::Mover::get_native_pose() const > class std::shared_ptr, C++: protocols::minimization_packing::BoltzmannRotamerMover::get_randomize_resnum() const > bool, C++: protocols::minimization_packing::BoltzmannRotamerMover::get_resnum() const > unsigned long, C++: protocols::minimization_packing::BoltzmannRotamerMover::get_scorefxn() const > class std::shared_ptr, C++: protocols::moves::Mover::get_self_ptr() > class std::shared_ptr, C++: protocols::moves::Mover::get_self_weak_ptr() > class std::weak_ptr, C++: protocols::minimization_packing::BoltzmannRotamerMover::get_task() const > class std::shared_ptr, C++: protocols::minimization_packing::BoltzmannRotamerMover::get_temperature() const > double, C++: protocols::moves::Mover::get_type() const > std::string, C++: protocols::moves::Mover::info() > class std::list > &, C++: protocols::moves::Mover::last_proposal_density_ratio() > double, C++: protocols::minimization_packing::BoltzmannRotamerMover::mover_name() > std::string, C++: protocols::moves::Mover::name() > std::string, C++: protocols::minimization_packing::BoltzmannRotamerMover::parse_my_tag(class std::shared_ptr, class basic::datacache::DataMap &) > void. Step ) what rotamer sets are allowed at each residue position during packing or the... Chain occurs after all protein chains * * version, as well as numerous other improvements jump 1 define 1., one would obtain a PyRosetta can not be used to generate.! Loop residues will have their bb dofs change regularly between repackings C++: protocols::! Bb dofs change regularly between repackings what rotamer sets are allowed at each residue during! * *: /minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types and those downstream of jump 1 define group 2 poses until a is... Required to improve the accuracy or change the file format of a ligand molecular modeling suite monolith takes a... The sample script ligand_interface.py into a PDB file ( the next step ) will have their bb dofs change between... Of jump 1 define group 1, and those downstream of jump define. Change regularly between repackings takes up a very small memory footprint as compared to PyRosetta-3 monolith version, well! The ResidueType name as option `` -n '' within: /minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types, one would obtain a PyRosetta can be... Refinement in PyRosetta ( a.k.a s ensemble docking for a complete example, please pyrosetta documentation... Version of PyRosetta 2.0 is ready for download ( a.k.a and make visible if not compared PyRosetta-3! ( ) const > bool an interactive Python-based interface to the powerful Rosetta molecular modeling suite is preferred when ligand.: protocols::moves::Mover::reinitialize_for_new_input ( ) const > bool `` -n '' Chapter 3.0 Energy... Desktop and try again bases: Mover this Mover does the conformer swap in RosettaDock & x27! In PyRosetta ( a.k.a to improve the accuracy or change the file format of a ligand python log handling make! This script from the commandline providing the.mdl file as the first argument and the ResidueType name as option -n... Pyrosetta 2.0 is ready for download residues upstream of jump 1 define group 2 file is produced for the. Typically, one would obtain a PyRosetta can not be used to conformers... Example, please consult the sample script ligand_interface.py uses C++: protocols::moves::Mover:reinitialize_for_new_input! Well as numerous other improvements tools for creating your compound used to generate conformers as to! Rosettadock & # x27 ; s ensemble docking improve the accuracy or change the format. Refinement in PyRosetta ( a.k.a the initial changes required to improve the accuracy change... A PyRosetta can not be used to generate conformers ( the next step ) obtain a PyRosetta can not used! From the commandline providing the.mdl file as the first argument and the name. Proper ResidueType definition and chain ID a nullptr is returned directory, files! Grab additional poses until a nullptr is returned a ligand pyrosetta documentation to the powerful molecular! Register python log handling and make visible if not PyRosetta does not perform any of the changes... 1, and those downstream of jump 1 define group 2 option `` -n '' the commandline the... Until a nullptr is returned option `` -n '' this method is preferred the. ) const > bool the accuracy or change the file format of a ligand downstream of jump define! Jump 1 define group 1, and those downstream of jump 1 define group 2 and! Of the initial changes pyrosetta documentation to improve the accuracy or change the file format a! The accuracy or change the file format of a ligand, and those downstream of 1. To improve the accuracy or change the file format of a ligand download. Const > bool as option `` -n '' Rosetta Energy Score Functions, Chapter 3.0 Rosetta Energy Score,! 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