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Rosetta
2021.16
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Rosetta
2021.16
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choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria. More...
#include <PlaceSimultaneouslyMover.hh>
Public Member Functions | |
| PlaceSimultaneouslyMover () | |
| protocols::moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| void | apply (core::pose::Pose &pose) override |
| a dummy apply so that instantiation of this baseclass would be possible. More... | |
| bool | minimize_no_bb (core::pose::Pose &pose) const |
| minimize towards clouds of stubs made up of all the stub sets More... | |
| void | minimize_all (core::pose::Pose &pose, core::Size const minimization_steps) const |
| minimize simultaneously towards the placed stubs from each of the stub sets returns false if one of the filters fails More... | |
| bool | pair_sets_with_positions (core::pose::Pose &pose) |
| pair each stub set with a position on the scaffold More... | |
| void | design (core::pose::Pose &pose) |
| conducts user-specified design movers. Returns true if the energy per residue filter passes for each of the placed hotspots More... | |
| bool | place_stubs (core::pose::Pose &pose) const |
| will be removed More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | final_cleanup (core::pose::Pose &pose) |
| void | refresh_coordinate_constraints (core::pose::Pose &pose, core::Real const coord_sdev) |
| removes and reinstates coordinate constraints for all placed hotspots according to coord_sdev More... | |
| core::pack::task::PackerTaskOP | create_task_for_hotspot_packing (core::pose::Pose const &) |
| core::pack::task::PackerTaskOP | create_task_for_allhotspot_packing (core::pose::Pose const &) |
| void | add_coordinatecst_for_hotspot_packing (core::pose::Pose &) |
| coordinate constraints to pose More... | |
| void | stub_sets (utility::vector1< StubSetStubPos > const sets) |
| void | host_chain (core::Size const host_chain) |
| ~PlaceSimultaneouslyMover () override | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
 Public Member Functions inherited from protocols::calc_taskop_movers::DesignRepackMover | |
| DesignRepackMover () | |
| DesignRepackMover (std::string const &name) | |
| void | setup_packer_and_movemap (core::pose::Pose const &pose) |
| void | min_rb (utility::vector1< bool > const &min_rb) |
| void | min_rb (bool const min_rb) |
| in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code. More... | |
| utility::vector1< bool > const & | min_rb () const |
| bool | min_rb_set () const |
| void | min_sc (core::select::residue_selector::ResidueSelectorOP min_sc) |
| utility::vector1< bool > | min_sc (core::pose::Pose const &pose) const |
| bool | min_sc_set () const |
| void | min_bb (core::select::residue_selector::ResidueSelectorOP min_bb) |
| utility::vector1< bool > | min_bb (core::pose::Pose const &pose) const |
| bool | min_bb_set () const |
| bool | optimize_foldtree () const |
| void | optimize_foldtree (bool const opt) |
| void | prevent_repacking (utility::vector1< core::Size > const &p) |
| utility::vector1< core::Size > const & | prevent_repacking () const |
| void | restrict_to_repacking (utility::vector1< core::Size > const &p) |
| utility::vector1< core::Size > const & | restrict_to_repacking () const |
| void | design (bool const des) |
| bool | design () const |
| void | set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn) |
| void | set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn) |
| core::scoring::ScoreFunctionOP | scorefxn_repack () const |
| core::scoring::ScoreFunctionOP | scorefxn_minimize () const |
| core::pack::task::PackerTaskCOP | task () const |
| core::pack::task::PackerTaskOP & | task () |
| void | clear_task () |
| after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered More... | |
| void | clear_task_factory () |
| void | use_preset_task (bool const bt) |
| bool | use_preset_task () const |
| void | task_factory (core::pack::task::TaskFactoryOP p) |
| core::pack::task::TaskFactoryOP & | task_factory () |
| core::pack::task::TaskFactoryOP | task_factory () const |
| ~DesignRepackMover () override | |
| void | target_residues (core::select::residue_selector::ResidueSelectorCOP setting) |
| Replace the current target_residue setting with the passed residue selector. More... | |
| core::select::residue_selector::ResidueSelectorCOP | target_residues () const |
| utility::vector1< core::Size > | target_residues (core::pose::Pose const &pose) const |
| Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| Static Public Member Functions inherited from protocols::calc_taskop_movers::DesignRepackMover | |
| static utility::tag::XMLSchemaComplexTypeGeneratorOP | get_xsd_complex_type () |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria.
| typedef std::pair< calc_taskop_movers::DesignRepackMoverOP, bool > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::DesignMoverFoldTreePair |
| typedef std::pair< calc_taskop_movers::DesignRepackMoverOP, core::Real > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::DesignMoverRealPair |
| typedef std::pair< protocols::calc_taskop_movers::DesignRepackMoverOP, core::Real > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::MoverRealPair |
| typedef std::multimap< core::Real, std::pair< core::Size, StubsetStubPair > > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::ResidueAuction |
| typedef std::pair< core::Real, std::pair< core::Size, StubsetStubPair > > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::ResidueAuctionItem |
| typedef std::pair< protocols::hotspot_hashing::HotspotStubSetOP, protocols::hotspot_hashing::HotspotStubOP > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::StubsetStubPair |
ResidueAuction is keyed by energy => we select the residue,stub,stubset combination with the best energy for each stubset,stub combination.
| protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::PlaceSimultaneouslyMover | ( | ) |
References auction_, design_movers_, explosion_, host_chain_, max_cb_cb_dist_, minimization_movers_, minimization_repeats_after_placement_, minimization_repeats_before_placement_, rbstub_minimization_, residue_level_tasks_for_placed_hotspots_, saved_bb_constraints_, saved_coord_constraints_, saved_stub_sets_, stub_energy_threshold_, stub_score_filter_, stub_set_filters_, and stub_sets_.
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| void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::add_coordinatecst_for_hotspot_packing | ( | core::pose::Pose & | pose | ) |
coordinate constraints to pose
References core::scoring::constraints::add_coordinate_constraints(), core::pose::Pose::residue(), and core::scoring::TR().
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a dummy apply so that instantiation of this baseclass would be possible.
Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.
References core::scoring::backbone_stub_constraint, protocols::moves::FAIL_RETRY, protocols::protein_interface_design::movers::finalize_stub_sets(), protocols::moves::MS_SUCCESS, protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), and core::scoring::TR().
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Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
| core::pack::task::PackerTaskOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::create_task_for_allhotspot_packing | ( | core::pose::Pose const & | pose | ) |
setup the residue level tasks for each of the paired positions in stub_sets_. Add all rotamers from the auction results
References core::pack::task::EX_THREE_THIRD_STEP_STDDEVS, core::chemical::num_canonical_aas, and core::scoring::TR().
| core::pack::task::PackerTaskOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::create_task_for_hotspot_packing | ( | core::pose::Pose const & | pose | ) |
setup the residue level tasks for each of the paired positions in stub_sets_. This sets the explosion level as well as the allowed identities at each position Note that two things happen in this function: 1) the task is modified to reflect the rotamer explosion operations. 2) residue_level_tasks_for_placed_hotspots_ is updated with these operations
References core::pack::task::EX_THREE_THIRD_STEP_STDDEVS, and core::chemical::num_canonical_aas.
| void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design | ( | core::pose::Pose & | pose | ) |
conducts user-specified design movers. Returns true if the energy per residue filter passes for each of the placed hotspots
wraps around the user-defined design movers. Applies coordinate constraints as specified by the user. Prevents repacking of placed hotspots
References core::pose::Pose::add_constraints(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), protocols::calc_taskop_movers::DesignRepackMover::task_factory(), and core::scoring::TR().
| void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::final_cleanup | ( | core::pose::Pose & | pose | ) |
This should be called before failing placesimultaneously.
References core::pose::Pose::clear(), and core::scoring::TR().
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Generates a new Mover object freshly created with the default ctor.
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
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Each derived class must specify its name. The class name.
Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.
References mover_name().
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References host_chain(), and host_chain_.
Referenced by host_chain().
| void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all | ( | core::pose::Pose & | pose, |
| core::Size const | minimization_steps | ||
| ) | const |
minimize simultaneously towards the placed stubs from each of the stub sets returns false if one of the filters fails
wraps around user-defined minimization movers. Note that setting up constraints should be done outside this method.
References core::scoring::backbone_stub_constraint, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::get_score_function(), protocols::protein_interface_design::movers::make_stub_scorefxn(), protocols::protein_interface_design::MinimizeInterface(), protocols::antibody::design::no_min, core::pose::Pose::num_jump(), protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), core::pose::Pose::size(), and core::scoring::TR().
| bool protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_no_bb | ( | core::pose::Pose & | pose | ) | const |
minimize towards clouds of stubs made up of all the stub sets
if bb_cst score is 0 return false, o/w true
preliminary rb minimization step in the presence of strong hotspot constraints. Reports failure if pre-minimization bb_cst score is 0. Note that setting up constraints should be done outside
References core::scoring::backbone_stub_constraint, protocols::score_filters::ScoreTypeFilter::compute(), protocols::protein_interface_design::movers::make_stub_scorefxn(), protocols::protein_interface_design::MinimizeInterface(), protocols::antibody::design::no_min, core::pose::Pose::size(), and core::scoring::TR().
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| bool protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions | ( | core::pose::Pose & | pose | ) |
pair each stub set with a position on the scaffold
if no mutually exclusive matches are found for all sets, return false
positions on the scaffold are auctioned to hotspot stub sets. The stubset that has a stub with the lowest constraint energy with respect to that position wins the auction. If the number of positions that are paired is less than the number of hotspot families, then failure is reported. If pairing succeeds, each of the paired positions is allowed to adopt an identity from its parent stubset that has below 0 constraint energy. Following which pack_rotamers is called with ex1, ex2, and rotamer explosion if directed by the user. Finally, each placed hotspot is tested for its total energy and for a user-defined filter. If one of these filters fails, failure is reported. Note that residues other than the lowest constraint energy identities might emerge from this process.
References protocols::simple_filters::EnergyPerResidueFilter::apply(), core::pose::Pose::clear(), core::scoring::coordinate_constraint, core::kinematics::distance(), core::scoring::get_score_function(), core::conformation::Residue::is_protein(), protocols::protein_interface_design::movers::make_stub_scorefxn(), protocols::protein_interface_design::MinimizeInterface(), protocols::moves::modify_ResId_based_object(), protocols::moves::MS_SUCCESS, protocols::antibody::design::no_min, core::pose::Pose::num_jump(), core::pack::pack_rotamers(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::total_score, core::scoring::TR(), core::pose::Pose::update_residue_neighbors(), and core::conformation::Residue::xyz().
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Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.
References protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness(), protocols::rosetta_scripts::legacy_saved_pose_or_input(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover_or_null(), core::pack::task::parse_task_operations(), and core::scoring::TR().
| bool protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs | ( | core::pose::Pose & | pose | ) | const |
will be removed
this will be removed in the future
References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::replace_residue(), core::conformation::Conformation::update_polymeric_connection(), and core::pose::Pose::update_residue_neighbors().
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References core::pack::task::attributes_for_parse_task_operations(), core::pose::attributes_for_saved_reference_pose_w_description(), protocols::moves::complex_type_name_for_mover(), mover_name(), protocols::protein_interface_design::movers::PlaceSimultaneously_DesignMovers_subelement_mangler(), protocols::protein_interface_design::movers::PlaceSimultaneously_NotifyMovers_subelement_mangler(), protocols::protein_interface_design::movers::PlaceSimultaneously_StubMinimize_subelement_mangler(), protocols::protein_interface_design::movers::PlaceSimultaneously_StubSets_subelement_mangler(), and protocols::protein_interface_design::movers::PlaceSimultaneously_subelement_mangler().
Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator::provide_xml_schema().
| void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints | ( | core::pose::Pose & | pose, |
| core::Real const | coord_sdev | ||
| ) |
removes and reinstates coordinate constraints for all placed hotspots according to coord_sdev
removes the coordinate constraints from the pose and reapplies them individually.
References core::pose::Pose::add_constraints(), core::scoring::constraints::add_coordinate_constraints(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), core::pose::Pose::residue(), and core::scoring::TR().
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References stub_sets_.
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Referenced by PlaceSimultaneouslyMover().
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Referenced by PlaceSimultaneouslyMover().
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Referenced by PlaceSimultaneouslyMover().
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where is the stub to be placed
Referenced by host_chain(), and PlaceSimultaneouslyMover().
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the maximum distance for a stub to be considered a a neighbour to a host residue
Referenced by PlaceSimultaneouslyMover().
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Referenced by PlaceSimultaneouslyMover().
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Referenced by PlaceSimultaneouslyMover().
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Referenced by PlaceSimultaneouslyMover().
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Referenced by PlaceSimultaneouslyMover().
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This task factory is used by placesimultaneously in two ways: 1) internally to create a packer task for hotspot placement and user-defined design movers. 2) For design movers downstream of PlaceSimultaneously so that they are aware of the choices made by PlaceSimultaneously. Note that item 1 is not implemented in PlaceStub. This means that PlaceSimultaneously always uses the task factory, whereas PlaceStub only uses it if the user specifies TaskAware design movers.
Referenced by PlaceSimultaneouslyMover().
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Referenced by PlaceSimultaneouslyMover().
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Referenced by PlaceSimultaneouslyMover().
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Referenced by PlaceSimultaneouslyMover().
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Maximum per-residue energy the placed stub can have to be saved.
Referenced by PlaceSimultaneouslyMover().
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does the pose have any active constraints?
Referenced by PlaceSimultaneouslyMover().
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Referenced by PlaceSimultaneouslyMover().
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stub sets and placed positions
Referenced by PlaceSimultaneouslyMover(), and stub_sets().
1.8.7