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Rosetta 3.5
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Rosetta 3.5
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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 Types | |
| typedef std::pair < protocols::hotspot_hashing::HotspotStubSetOP, std::pair < protocols::hotspot_hashing::HotspotStubOP, core::Size > > | StubSetStubPos |
| typedef std::pair < protocols::simple_moves::DesignRepackMoverOP, core::Real > | MoverRealPair |
| typedef std::pair < simple_moves::DesignRepackMoverOP, bool > | DesignMoverFoldTreePair |
| typedef std::pair < simple_moves::DesignRepackMoverOP, core::Real > | DesignMoverRealPair |
| typedef std::pair < protocols::hotspot_hashing::HotspotStubSetOP, protocols::hotspot_hashing::HotspotStubOP > | StubsetStubPair |
| ResidueAuction is keyed by energy => we select the residue,stub,stubset combination with the best energy for each stubset,stub combination. More... | |
| typedef std::pair< core::Real, std::pair< core::Size, StubsetStubPair > > | ResidueAuctionItem |
| typedef std::multimap < core::Real, std::pair < core::Size, StubsetStubPair > > | ResidueAuction |
Public Member Functions | |
| PlaceSimultaneouslyMover () | |
| protocols::moves::MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| protocols::moves::MoverOP | fresh_instance () const |
| this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More... | |
| virtual void | apply (core::pose::Pose &pose) |
| a dummy apply so that instantiation of this baseclass would be possible. More... | |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. 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... | |
| virtual void | parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) |
| 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 &) |
| void | stub_sets (utility::vector1< StubSetStubPos > const sets) |
| void | host_chain (core::Size const host_chain) |
| virtual | ~PlaceSimultaneouslyMover () |
 Public Member Functions inherited from protocols::simple_moves::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 (utility::vector1< bool > const &min_sc) |
| utility::vector1< bool > const & | min_sc () const |
| bool | min_sc_set () const |
| void | min_bb (utility::vector1< bool > const &min_bb) |
| utility::vector1< bool > const & | min_bb () 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 |
| virtual | ~DesignRepackMover () |
| Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual | ~Mover () |
| virtual MoverSP | create () |
| virtual void | apply (core::io::serialization::PipeMap &pmap) |
| virtual void | parse_state (SerializableState const &state) |
| virtual void | parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) |
| virtual void | save_state (SerializableState &state) |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| Mover (Mover const &other) | |
| Mover & | operator= (Mover const &other) |
| assignment operator More... | |
| virtual core::Real | last_proposal_density_ratio () |
| std::string const & | type () const |
| 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... | |
| void | set_current_tag (std::string const &new_tag) |
| 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 |
| 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... | |
| void | type (const std::string &type_in) |
| std::string | get_type () const |
| 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... | |
| 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 bool | reinitialize_for_each_job () const |
| this function informs 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 |
| this function informs 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... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria.
Definition at line 49 of file PlaceSimultaneouslyMover.hh.
| typedef std::pair< simple_moves::DesignRepackMoverOP, bool > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::DesignMoverFoldTreePair |
Definition at line 58 of file PlaceSimultaneouslyMover.hh.
| typedef std::pair< simple_moves::DesignRepackMoverOP, core::Real > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::DesignMoverRealPair |
Definition at line 59 of file PlaceSimultaneouslyMover.hh.
| typedef std::pair< protocols::simple_moves::DesignRepackMoverOP, core::Real > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::MoverRealPair |
Definition at line 53 of file PlaceSimultaneouslyMover.hh.
| typedef std::multimap< core::Real, std::pair< core::Size, StubsetStubPair > > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::ResidueAuction |
Definition at line 63 of file PlaceSimultaneouslyMover.hh.
| typedef std::pair< core::Real, std::pair< core::Size, StubsetStubPair > > protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::ResidueAuctionItem |
Definition at line 62 of file PlaceSimultaneouslyMover.hh.
| 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.
Definition at line 61 of file PlaceSimultaneouslyMover.hh.
Definition at line 52 of file PlaceSimultaneouslyMover.hh.
| protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::PlaceSimultaneouslyMover | ( | ) |
Definition at line 669 of file PlaceSimultaneouslyMover.cc.
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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Definition at line 119 of file PlaceSimultaneouslyMover.cc.
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a dummy apply so that instantiation of this baseclass would be possible.
Reimplemented from protocols::simple_moves::DesignRepackMover.
Definition at line 449 of file PlaceSimultaneouslyMover.cc.
References core::scoring::backbone_stub_constraint, protocols::moves::FAIL_RETRY, protocols::moves::MS_SUCCESS, protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), and core::scoring::TR().
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clone has to be overridden only if clone invocation is expected.
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.
Implements protocols::simple_moves::DesignRepackMover.
Definition at line 123 of file PlaceSimultaneouslyMover.cc.
| 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
Definition at line 223 of file PlaceSimultaneouslyMover.cc.
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
Definition at line 393 of file PlaceSimultaneouslyMover.cc.
References core::pose::Pose::add_constraints(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, protocols::simple_moves::DesignRepackMover::prevent_repacking(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), protocols::simple_moves::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.
Definition at line 493 of file PlaceSimultaneouslyMover.cc.
References core::pose::Pose::clear(), and core::scoring::TR().
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this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
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.
Implements protocols::simple_moves::DesignRepackMover.
Definition at line 67 of file PlaceSimultaneouslyMover.hh.
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Each derived class must specify its name. The class name.
Reimplemented from protocols::simple_moves::DesignRepackMover.
Definition at line 487 of file PlaceSimultaneouslyMover.cc.
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Definition at line 96 of file PlaceSimultaneouslyMover.hh.
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.
Definition at line 150 of file PlaceSimultaneouslyMover.cc.
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::ScoreFunctionFactory::create_score_function(), protocols::protein_interface_design::movers::make_stub_scorefxn(), MinimizeInterface(), core::pose::Pose::num_jump(), protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, core::pose::Pose::total_residue(), 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
Definition at line 131 of file PlaceSimultaneouslyMover.cc.
References core::scoring::backbone_stub_constraint, protocols::simple_filters::ScoreTypeFilter::compute(), protocols::protein_interface_design::movers::make_stub_scorefxn(), MinimizeInterface(), core::pose::Pose::total_residue(), and core::scoring::TR().
| 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.
Definition at line 264 of file PlaceSimultaneouslyMover.cc.
References protocols::simple_filters::EnergyPerResidueFilter::apply(), core::io::serialization::clone(), core::scoring::ScoreFunctionFactory::create_score_function(), core::kinematics::distance(), core::conformation::Residue::is_protein(), protocols::protein_interface_design::movers::make_stub_scorefxn(), MinimizeInterface(), protocols::moves::modify_ResId_based_object(), protocols::moves::MS_SUCCESS, core::pack::pack_rotamers(), core::pose::Pose::residue(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, core::pose::Pose::total_residue(), core::scoring::total_score, core::scoring::TR(), 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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.
Reimplemented from protocols::simple_moves::DesignRepackMover.
Definition at line 509 of file PlaceSimultaneouslyMover.cc.
References core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, protocols::filters::TrueFilter::clone(), core::pack::task::TaskFactory::create_packer_task(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness(), protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), core::conformation::Residue::is_protein(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), core::pack::task::parse_resfile(), protocols::rosetta_scripts::parse_task_operations(), core::pose::Pose::residue(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, core::pose::Pose::total_residue(), 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
Definition at line 342 of file PlaceSimultaneouslyMover.cc.
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().
| 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.
Definition at line 371 of file PlaceSimultaneouslyMover.cc.
References core::pose::Pose::add_constraints(), core::scoring::constraints::add_coordinate_constraints(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), and core::scoring::TR().
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Definition at line 95 of file PlaceSimultaneouslyMover.hh.
References stub_sets_.
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Definition at line 116 of file PlaceSimultaneouslyMover.hh.
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Definition at line 125 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 117 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 118 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 116 of file PlaceSimultaneouslyMover.hh.
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where is the stub to be placed
Definition at line 101 of file PlaceSimultaneouslyMover.hh.
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
Definition at line 109 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 112 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 114 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 113 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 128 of file PlaceSimultaneouslyMover.hh.
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.
Definition at line 124 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 115 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 132 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 102 of file PlaceSimultaneouslyMover.hh.
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Definition at line 105 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Maximum per-residue energy the placed stub can have to be saved.
Definition at line 111 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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does the pose have any active constraints?
Definition at line 127 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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Definition at line 106 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover().
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stub sets and placed positions
Definition at line 104 of file PlaceSimultaneouslyMover.hh.
Referenced by PlaceSimultaneouslyMover(), and stub_sets().
1.8.4