choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria. More...
#include <PlaceStubMover.hh>
Public Types | |
| typedef std::pair< calc_taskop_movers::DesignRepackMoverOP, bool > | DesignMoverFoldTreePair |
| typedef std::pair< calc_taskop_movers::DesignRepackMoverOP, core::Real > | DesignMoverRealPair |
 Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
Public Member Functions | |
| PlaceStubMover () | |
| PlaceStubMover (protocols::hotspot_hashing::HotspotStubSetOP stub_set, core::Real score_threshold, core::Size const host_chain, protocols::filters::FilterOP final_filter, bool const hurry=false, bool const triage_positions=true, core::Real stub_energy_threshold=1.0) | |
| ~PlaceStubMover () override | |
| 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 | stub_minimize_movers (utility::vector1< DesignMoverRealPair > const &dmrp) |
| utility::vector1< DesignMoverRealPair > const & | stub_minimize_movers () const |
| void | apply (core::pose::Pose &pose) override |
| 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... | |
| 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... | |
Private Member Functions | |
| void | place_stub (core::pose::Pose &pose, core::conformation::Residue const &res_stub, core::Size const res_num) |
| void | stub_based_atom_tree (core::pose::Pose &pose, core::conformation::Residue const &res_stub, core::Real const cst_sdev) |
| void | add_coordinate_constraints_for_res_stub (core::pose::Pose &pose, core::conformation::Residue const &res_stub, core::Real const cst_sdev) |
| add new coordinate constraints to the Pose based on the conformation of res_stub More... | |
| bool | SelectStubIteratively (protocols::hotspot_hashing::HotspotStubSet::Hs_vec::const_iterator stub_it) |
| bool | StubMinimize (core::pose::Pose &pose, protocols::hotspot_hashing::HotspotStubCOP=nullptr, core::Size const host_res=0, bool const hurry=false) |
| void | refresh_coordinate_constraints (core::pose::Pose &pose, core::Real const sdev) |
| void | refresh_coordinate_constraints (core::pose::Pose &pose, CoordinateConstraintStackOP csts, core::scoring::func::FuncOP newfunc) |
| recursively remove the constraints in csts from the input pose, and then reclone them as new constraints with a new func object. More... | |
| void | refresh_coordinate_constraints (core::pose::Pose &pose, utility::vector1< core::scoring::constraints::ConstraintCOP > &cst_vector, core::scoring::func::FuncOP newfunc) |
| void | cst_cleanup (core::pose::Pose &pose) |
| resets pose's constraints upon stub failure remove constraints if they exist. To be used on failure More... | |
| void | final_cleanup (core::pose::Pose &pose) |
| clean everything before exiting More... | |
| utility::vector1< core::Size > | disallowed_host_pos (core::pose::Pose const &pose) const |
Private Attributes | |
| core::Real | score_threshold_ |
| maximum bonus_value for accepting a stub More... | |
| core::Size | host_chain_ |
| where is the stub to be placed More... | |
| protocols::hotspot_hashing::HotspotStubSetOP | stub_set_ |
| stub set we're choosing from More... | |
| core::pose::PoseCOP | reference_pose_ |
| Reference Pose (usually the input) with which to initialize the stubset with. More... | |
| bool | add_constraints_ |
| or use fold tree rb jump. More... | |
| utility::vector1< core::Real > | coord_cst_std_ |
| what std to use for coordinate cst in each design mover More... | |
| core::select::residue_selector::ResidueSelectorCOP | allowed_host_pos_ |
The inverse of the disallowed_host_pos(). More... | |
| utility::vector1< DesignMoverRealPair > | stub_minimize_movers_ |
| utility::vector1< DesignMoverFoldTreePair > | design_movers_ |
| utility::vector1< core::Real > coord_cst_std_stub_minimize_; More... | |
| protocols::filters::FilterOP | after_placement_filter_ |
| immediately after placement + minimization More... | |
| protocols::filters::FilterOP | final_filter_ |
| a filter at the last stage of placement. Defaults to TrueFilter More... | |
| utility::vector1< std::pair< core::Size, bool > > | placed_stubs_ |
| core::kinematics::FoldTreeOP | default_fold_tree_ |
| core::scoring::constraints::ConstraintCOPs | curr_coordinate_constraints_ |
| CoordinateConstraintStackOP | coor_constraint_stack_ |
| CoordinateConstraintStackOP | residual_coordinate_constraints_ |
| store for the sake of updating the coordinate constraints of all the descendant PlaceStubMovers that successfully placed their Stubs and left their coordinate constraints in place; this object will not be a stack, but merely a vector of ConstraintOPs that are shared between mother and daughter PlaceStubMovers. More... | |
| bool | leave_coord_csts_after_placement_ |
| core::Real | post_placement_sdev_ |
| core::scoring::constraints::ConstraintCOPs | saved_bb_constraints_ |
| utility::vector1< core::Size > | saved_prevent_repacking_ |
| utility::vector1< std::pair< core::Size, bool > > | saved_placed_stubs_ |
| bool | place_scaffold_ |
| use inverse rotamers to place the scaffold More... | |
| core::Real | max_cb_cb_dist_ |
| the maximum distance for a stub to be considered a a neighbour to a host residue More... | |
| bool | hurry_ |
| Should we speed up StubMinimize at the expense of accuracy? More... | |
| bool | triage_positions_ |
| core::Real | stub_energy_threshold_ |
| Maximum per-residue energy the placed stub can have to be saved. More... | |
| core::pack::task::TaskFactoryOP | residue_level_tasks_for_placed_hotspots_ |
| utility::pointer::shared_ptr< basic::datacache::DataMapObj< utility::vector1< core::Size > > > | residue_numbers_ |
| std::string | user_defined_name_ |
| dflt NULL; a vector of residue numbers placed on the basic::datacache::DataMap which specifies all the placed residues. Useful to communicate between movers and filters, without the pesky NotifyMovers strategy More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
| Protected Attributes inherited from protocols::calc_taskop_movers::DesignRepackMover | |
| core::scoring::ScoreFunctionOP | scorefxn_repack_ |
| core::scoring::ScoreFunctionOP | scorefxn_minimize_ |
| bool | repack_partner1_ |
| bool | repack_partner2_ |
| bool | design_partner1_ |
| bool | design_partner2_ |
| utility::vector1< bool > | min_rb_ |
| utility::vector1< bool > | curr_min_sc_ |
| utility::vector1< bool > | curr_min_bb_ |
| utility::vector1< bool > | curr_min_rb_ |
| bool | min_rb_set_ |
| core::Real | interface_distance_cutoff_ |
| bool | repack_non_ala_ |
| bool | optimize_foldtree_ |
| bool | automatic_repacking_definition_ |
| core::pack::task::PackerTaskOP | task_ |
| bool | use_preset_task_ |
| utility::vector1< bool > | allowed_aas_ |
| utility::vector1< core::Size > | prevent_repacking_ |
| utility::vector1< core::Size > | restrict_to_repacking_ |
| core::pack::task::TaskFactoryOP | task_factory_ |
| bool | symmetry_ |
Detailed Description
choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria.
Member Typedef Documentation
◆ DesignMoverFoldTreePair
| typedef std::pair< calc_taskop_movers::DesignRepackMoverOP, bool > protocols::protein_interface_design::movers::PlaceStubMover::DesignMoverFoldTreePair |
◆ DesignMoverRealPair
| typedef std::pair< calc_taskop_movers::DesignRepackMoverOP, core::Real > protocols::protein_interface_design::movers::PlaceStubMover::DesignMoverRealPair |
Constructor & Destructor Documentation
◆ PlaceStubMover() [1/2]
| protocols::protein_interface_design::movers::PlaceStubMover::PlaceStubMover | ( | ) |
◆ PlaceStubMover() [2/2]
| protocols::protein_interface_design::movers::PlaceStubMover::PlaceStubMover | ( | protocols::hotspot_hashing::HotspotStubSetOP | stub_set, |
| core::Real | score_threshold, | ||
| core::Size const | host_chain, | ||
| protocols::filters::FilterOP | final_filter, | ||
| bool const | hurry = false, |
||
| bool const | triage_positions = true, |
||
| core::Real | stub_energy_threshold = 1.0 |
||
| ) |
References final_filter_, and stub_set_.
◆ ~PlaceStubMover()
|
overridedefault |
Member Function Documentation
◆ add_coordinate_constraints_for_res_stub()
|
private |
add new coordinate constraints to the Pose based on the conformation of res_stub
References protocols::protein_interface_design::movers::add_coordinate_constraints(), curr_coordinate_constraints_, host_chain_, placed_stubs_, and TR_debug().
Referenced by stub_based_atom_tree().
◆ apply()
|
overridevirtual |
Placing a stub in the context of a complex by putting a stub on top of the scaffold. The following steps are taken: 0. minimization of rb dofs in a bb_stub_constraint-dominated force field. Only the constraints implied by the stubset associated with this placestub mover will be applied.
- stub selection, by iterating over a randomly shuffled stubset.
- finding a residue on the host chain where the stub may be placed (distance cutoff).
- testing the stub's repulsive energy on that residue in the context of a poly-alanine host chain.
- repack/minimize the rb orientation of the pose (plus a little bb minimization around the stub, but no repacking of host_chain_).
- testing the stub's total_score in the context of the full pose.
- a vector of user-defined movers derived from DesignRepackMover. These may include further placestub movers. If this is the case, these movers can be constrained with coordinate constraints that are placed on the functional groups of the stub sidechain. These movers can also define the force constant of these harmonic constraints. Notice that this design should in principle be fully extensible to as many stub placement and design movers as the user chooses. If any of the user defined design movers (including subsequent stub placement) fail, another stub placement is attempted and the user defined movers are called again.
- user_defined final_filter_ is called. If the pose does not pass this, place stub return to iterate over another stub. If all stubs fail, the mover signals failure and exits.
Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.
References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, protocols::jd2::add_string_string_pair_to_current_job(), after_placement_filter_, protocols::protein_interface_design::movers::BuildAlaPose::apply(), core::scoring::backbone_stub_constraint, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), coor_constraint_stack_, coord_cst_std_, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), cst_cleanup(), curr_coordinate_constraints_, default_fold_tree_, design_movers_, disallowed_host_pos(), core::kinematics::distance(), core::sequence::end, core::scoring::fa_rep, protocols::moves::FAIL_RETRY, final_cleanup(), final_filter_, protocols::protein_interface_design::movers::finalize_stub_set(), core::pose::Pose::fold_tree(), core::scoring::get_score_function(), host_chain_, hurry_, core::chemical::ResidueType::is_disulfide_bonded(), max_cb_cb_dist_, protocols::moves::modify_ResId_based_object(), protocols::moves::MS_SUCCESS, core::conformation::Residue::name3(), place_scaffold_, place_stub(), placed_stubs_, protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking(), protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking_, reference_pose_, refresh_coordinate_constraints(), protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), residual_coordinate_constraints_, core::pose::Pose::residue(), residue_level_tasks_for_placed_hotspots_, residue_numbers_, protocols::rosetta_scripts::residue_packer_states(), core::scoring::rg, saved_bb_constraints_, saved_placed_stubs_, saved_prevent_repacking_, SelectStubIteratively(), protocols::moves::Mover::set_last_move_status(), core::scoring::SOFT_REP_DESIGN_WTS, stats_TR(), stub_energy_threshold_, stub_set_, StubMinimize(), protocols::calc_taskop_movers::DesignRepackMover::task_factory(), protocols::protein_interface_design::movers::test_res_res_aln(), core::scoring::total_score, protocols::protein_interface_design::movers::TR(), TR_debug(), triage_positions_, core::conformation::Residue::type(), user_defined_name_, and core::conformation::Residue::xyz().
◆ clone()
|
overridevirtual |
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.
◆ cst_cleanup()
|
private |
resets pose's constraints upon stub failure remove constraints if they exist. To be used on failure
reapply saved coord constraints and refresh placed_stubs and prevent_repacking Nov09 changed logic: curr_coordinate constraints are removed only
References curr_coordinate_constraints_, placed_stubs_, protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking_, core::pose::Pose::remove_constraints(), saved_placed_stubs_, saved_prevent_repacking_, protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().
Referenced by apply(), and final_cleanup().
◆ disallowed_host_pos()
|
private |
Locations where stubs are not allowed to be placed
- Note
- This is similar to DesignRepackMover::prevent_repacking() but we want to allow repacking at steps after stub placement.
References allowed_host_pos_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), host_chain_, and protocols::protein_interface_design::movers::TR().
Referenced by apply().
◆ final_cleanup()
|
private |
clean everything before exiting
This should be called before exiting placestub.
References core::pose::Pose::add_constraints(), cst_cleanup(), curr_coordinate_constraints_, protocols::moves::Mover::get_last_move_status(), leave_coord_csts_after_placement_, protocols::moves::MS_SUCCESS, placed_stubs_, post_placement_sdev_, protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking_, refresh_coordinate_constraints(), residual_coordinate_constraints_, protocols::calc_taskop_movers::DesignRepackMover::restrict_to_repacking_, saved_bb_constraints_, and protocols::protein_interface_design::movers::TR().
Referenced by apply().
◆ fresh_instance()
|
inlineoverridevirtual |
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.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.
References mover_name().
◆ mover_name()
|
static |
◆ parse_my_tag()
|
overridevirtual |
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 add_constraints_, after_placement_filter_, allowed_host_pos_, coord_cst_std_, design_movers_, final_filter_, protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness(), core::pose::get_resnum_selector(), host_chain_, hurry_, leave_coord_csts_after_placement_, protocols::rosetta_scripts::legacy_saved_pose_or_input(), max_cb_cb_dist_, protocols::calc_taskop_movers::DesignRepackMover::min_rb(), mover_name(), protocols::rosetta_scripts::parse_filter_or_null(), protocols::rosetta_scripts::parse_mover_or_null(), core::pack::task::parse_task_operations(), place_scaffold_, post_placement_sdev_, reference_pose_, residue_level_tasks_for_placed_hotspots_, residue_numbers_, score_threshold_, stub_energy_threshold_, stub_minimize_movers_, stub_set_, protocols::calc_taskop_movers::DesignRepackMover::task_factory(), protocols::protein_interface_design::movers::TR(), triage_positions_, and user_defined_name_.
◆ place_stub()
|
private |
utility function that places a stub at an acceptor position and cleans up the pose
References add_constraints_, core::kinematics::FoldTree::add_edge(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom_type(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), default_fold_tree_, core::kinematics::FoldTree::delete_self_edges(), core::chemical::AtomType::element(), core::pose::Pose::fold_tree(), host_chain_, core::pose::Pose::jump(), core::conformation::Residue::nbr_atom(), core::pose::Pose::num_jump(), core::kinematics::Edge::PEPTIDE, protocols::make_rot_lib::PEPTIDE, place_scaffold_, placed_stubs_, core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::set_jump(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::size(), core::pose::Pose::split_by_chain(), stub_based_atom_tree(), TR_debug(), core::conformation::Conformation::update_polymeric_connection(), and core::pose::Pose::update_residue_neighbors().
Referenced by apply().
◆ provide_xml_schema()
|
static |
References core::pose::attributes_for_get_resnum_selector(), 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::PlaceStub_DesignMovers_subelement_mangler(), protocols::protein_interface_design::movers::PlaceStub_NotifyMovers_subelement_mangler(), protocols::protein_interface_design::movers::PlaceStub_StubMinimize_subelement_mangler(), and protocols::protein_interface_design::movers::PlaceStub_subelement_mangler().
Referenced by protocols::protein_interface_design::movers::PlaceStubMoverCreator::provide_xml_schema().
◆ refresh_coordinate_constraints() [1/3]
|
private |
recursively remove the constraints in csts from the input pose, and then reclone them as new constraints with a new func object.
References refresh_coordinate_constraints().
◆ refresh_coordinate_constraints() [2/3]
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private |
remove all coordinate constraints from pose and then reapply them, changing the HarmonicFunc's sdev to a new value Nov09 Changing of previous logic. Now, only changing the sdev associated with the coordinate constraints. Jul15 NO! Constraints need to be constant after they are added to a Pose.
References coor_constraint_stack_, curr_coordinate_constraints_, core::pose::Pose::remove_constraints(), residual_coordinate_constraints_, and TR_debug().
Referenced by apply(), final_cleanup(), and refresh_coordinate_constraints().
◆ refresh_coordinate_constraints() [3/3]
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◆ SelectStubIteratively()
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selects stubs by iterating over the stub_set_. Returns the status of stub selection
References score_threshold_, stub_set_, and protocols::protein_interface_design::movers::TR().
Referenced by apply().
◆ stub_based_atom_tree()
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changes the pose's fold-tree to connect the nearest residue on the target to the stub on the scaffold. The foldtree connects the last carbon atom before the stub's functional group. That can be useful in minimization of the pose, b/c the stub's interaction with the target will not be lost due to minimization. Notice that the pose's fold tree changes in the process and so it is usually a good idea to save the old foldtree and reinstate it after minimization. Can work with multiple stubs. In that case, rb jumps are introduced between the target and each of the stubs and a cutpoint is introduced in the putative circle that has just been formed in the fold tree. Alternatively, if the current stub is to be added via a constraint, then a coordinate constraint is set up for this stub
References protocols::hybridization::add_constraints(), add_coordinate_constraints_for_res_stub(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), core::pose::Pose::fold_tree(), host_chain_, placed_stubs_, and protocols::protein_interface_design::movers::TR().
Referenced by place_stub().
◆ stub_minimize_movers() [1/2]
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References stub_minimize_movers_.
◆ stub_minimize_movers() [2/2]
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References stub_minimize_movers_.
◆ StubMinimize()
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minimize the rb orientation in the presence of a strong bb_stub_constraint potential, while reducing all other attractive scores. fa_sol is also reduced to avoid blowing up the structure. Returns false if current pose has no backbone_stub_constraint score. Removes stub constraints after minimization. If more than one stub has already been placed then the jumps are held rigid during minimization If a stub is specified, then a custom-made hotspot constraint is used
References core::pose::Pose::add_constraints(), core::conformation::Residue::atom_index(), core::scoring::backbone_stub_constraint, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::scoring::chainbreak, protocols::score_filters::ScoreTypeFilter::compute(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::kinematics::distance(), core::sequence::end, core::scoring::fa_atr, core::scoring::fa_dun, core::scoring::fa_pair, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::get_score_function(), core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, host_chain_, protocols::mean_field::max(), protocols::mean_field::min(), protocols::calc_taskop_movers::DesignRepackMover::min_rb(), protocols::protein_interface_design::MinimizeInterface(), protocols::antibody::design::no_min, core::pose::Pose::num_jump(), placed_stubs_, protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking(), protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking_, core::pose::Pose::remove_constraints(), protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), core::pose::Pose::residue(), core::conformation::Conformation::residue(), core::pose::Pose::size(), stats_TR(), stub_minimize_movers_, stub_set_, protocols::protein_interface_design::movers::test_res_res_aln(), protocols::protein_interface_design::movers::TR(), TR_debug(), and core::conformation::Residue::xyz().
Referenced by apply().
Member Data Documentation
◆ add_constraints_
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or use fold tree rb jump.
Referenced by parse_my_tag(), and place_stub().
◆ after_placement_filter_
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immediately after placement + minimization
Referenced by apply(), and parse_my_tag().
◆ allowed_host_pos_
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The inverse of the disallowed_host_pos().
Referenced by disallowed_host_pos(), and parse_my_tag().
◆ coor_constraint_stack_
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Referenced by apply(), and refresh_coordinate_constraints().
◆ coord_cst_std_
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what std to use for coordinate cst in each design mover
dflt false
Referenced by apply(), parse_my_tag(), and PlaceStubMover().
◆ curr_coordinate_constraints_
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saves the coordinate constraints that this mover has associated with the pose. At the end of the run, they should be removed
Referenced by add_coordinate_constraints_for_res_stub(), apply(), cst_cleanup(), final_cleanup(), PlaceStubMover(), and refresh_coordinate_constraints().
◆ default_fold_tree_
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this is the foldtree with which we come into the first PlaceStubMover. It will be passed between movers for the user to decide that it should be used.
Referenced by apply(), and place_stub().
◆ design_movers_
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utility::vector1< core::Real > coord_cst_std_stub_minimize_;
Referenced by apply(), parse_my_tag(), and PlaceStubMover().
◆ final_filter_
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a filter at the last stage of placement. Defaults to TrueFilter
Referenced by apply(), parse_my_tag(), and PlaceStubMover().
◆ host_chain_
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where is the stub to be placed
Referenced by add_coordinate_constraints_for_res_stub(), apply(), disallowed_host_pos(), parse_my_tag(), place_stub(), stub_based_atom_tree(), and StubMinimize().
◆ hurry_
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Should we speed up StubMinimize at the expense of accuracy?
Referenced by apply(), and parse_my_tag().
◆ leave_coord_csts_after_placement_
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Referenced by final_cleanup(), and parse_my_tag().
◆ max_cb_cb_dist_
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the maximum distance for a stub to be considered a a neighbour to a host residue
Referenced by apply(), and parse_my_tag().
◆ place_scaffold_
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use inverse rotamers to place the scaffold
Referenced by apply(), parse_my_tag(), and place_stub().
◆ placed_stubs_
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where stubs were placed and whether they use constraints. vector is necessary to maintain the order of the placed stubs
Referenced by add_coordinate_constraints_for_res_stub(), apply(), cst_cleanup(), final_cleanup(), place_stub(), PlaceStubMover(), stub_based_atom_tree(), and StubMinimize().
◆ post_placement_sdev_
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Referenced by final_cleanup(), and parse_my_tag().
◆ reference_pose_
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Reference Pose (usually the input) with which to initialize the stubset with.
Referenced by apply(), and parse_my_tag().
◆ residual_coordinate_constraints_
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store for the sake of updating the coordinate constraints of all the descendant PlaceStubMovers that successfully placed their Stubs and left their coordinate constraints in place; this object will not be a stack, but merely a vector of ConstraintOPs that are shared between mother and daughter PlaceStubMovers.
Referenced by apply(), final_cleanup(), and refresh_coordinate_constraints().
◆ residue_level_tasks_for_placed_hotspots_
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This task factory is used by placed stubs to add prevent repacking instructions to design movers that would be invoked after PlaceStub finishes successfully. It's a way to communicate the placements that should not be changed to design movers down stream. Note that this is a different implementation than the one used in PlaceSimultaneously.
Referenced by apply(), and parse_my_tag().
◆ residue_numbers_
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Referenced by apply(), and parse_my_tag().
◆ saved_bb_constraints_
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Referenced by apply(), final_cleanup(), and PlaceStubMover().
◆ saved_placed_stubs_
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Referenced by apply(), cst_cleanup(), and PlaceStubMover().
◆ saved_prevent_repacking_
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Referenced by apply(), and cst_cleanup().
◆ score_threshold_
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maximum bonus_value for accepting a stub
Referenced by parse_my_tag(), and SelectStubIteratively().
◆ stub_energy_threshold_
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Maximum per-residue energy the placed stub can have to be saved.
Referenced by apply(), and parse_my_tag().
◆ stub_minimize_movers_
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movers for stub minimization, vector of pairs of movers and whether or not to apply bb constraints during the mover
Referenced by parse_my_tag(), PlaceStubMover(), stub_minimize_movers(), and StubMinimize().
◆ stub_set_
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stub set we're choosing from
Referenced by apply(), parse_my_tag(), PlaceStubMover(), SelectStubIteratively(), and StubMinimize().
◆ triage_positions_
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Should we triage host positions based on smart criteria, such as current position? Leave false if partners have not already been docked.
Referenced by apply(), and parse_my_tag().
◆ user_defined_name_
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dflt NULL; a vector of residue numbers placed on the basic::datacache::DataMap which specifies all the placed residues. Useful to communicate between movers and filters, without the pesky NotifyMovers strategy
Referenced by apply(), and parse_my_tag().
The documentation for this class was generated from the following files:
- src/protocols/protein_interface_design/movers/PlaceStubMover.hh
- src/protocols/protein_interface_design/movers/PlaceStubMover.cc
