#include <RemodelMover.hh>
Classes | |
| struct | instruction_flags |
Public Member Functions | |
| RemodelMover () | |
| default constructor More... | |
| RemodelMover (RemodelMover const &rval) | |
| copy constructor More... | |
| ~RemodelMover () override | |
| default destructor More... | |
| MoverOP | clone () const override |
| clone this object, for parser More... | |
| MoverOP | fresh_instance () const override |
| create this type of object, for parser More... | |
| virtual MoverOP | clone () |
| clone this object More... | |
| virtual MoverOP | fresh_instance () |
| create this type of object More... | |
| ScoreFunction const & | centroid_scorefunction () const |
| the centroid level score function, default "remodel_cen" More... | |
| ScoreFunction const & | fullatom_scorefunction () const |
| the full-atom level score function More... | |
| void | max_linear_chainbreak (Real const threshold) |
| add instruction to the manager of this RemodelMover (no copy) More... | |
| void | centroid_loop_mover_str (String const &loop_mover_str) |
| the loop mover string to use during centroid build More... | |
| void | redesign_loop_neighborhood (bool const flag) |
| redesign the neighborhood around the loop? if false, then just repacks during the design phase More... | |
| void | dr_cycles (core::Size const cycles) |
| set the number of design-refine cycles to perform More... | |
| void | centroid_scorefunction (ScoreFunction const &sfx) |
| set the centroid level score function More... | |
| void | centroid_scorefunction (ScoreFunctionOP const &sfx) |
| set the centroid level score function More... | |
| void | fullatom_scorefunction (ScoreFunction const &sfx) |
| set the full-atom level score function More... | |
| void | fullatom_scorefunction (ScoreFunctionOP const &sfx) |
| set the full-atom level score function More... | |
| void | apply (Pose &pose) override |
| apply defined moves to given Pose More... | |
| bool | confirm_sequence (core::pose::Pose &pose) |
| As best as I can tell, does some loop closure and calculates RMSD to native. Returns true. NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of rmsd value, because this stage is not being used as a filter Checks the value of -remodel::swap_refine_confirm_protocols. More... | |
| void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const override |
| Provide the citation. More... | |
| void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override |
| parse xml More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
 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... | |
Static Public Member Functions | |
| static String | neighborhood_calc_name () |
| the name for the loops' neighborhood calculator More... | |
| static String | loops_buns_polar_calc_name () |
| the name for the loops' buried unsatisfied polars calculator More... | |
| static String | neighborhood_buns_polar_calc_name () |
| the name for the loops' neighborhood buried unsatisfied polars calculator More... | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| 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 Types | |
| typedef protocols::moves::Mover | Super |
Private Member Functions | |
| RemodelMover & | operator= (RemodelMover const &rval) |
| copy assignment More... | |
| forge::remodel::RemodelData | setup_remodel_data_for_loop_btw_parametric_components (core::pose::Pose &pose) |
| sets up remodel data for combining blueprint with parametric mode More... | |
| bool | SamePose (Pose const &pose1, Pose const &pose2) |
| Apply method for Mover. Checks the values of the following options -remodel::checkpoint -remodel::domainFusion::insert_segment_from_pdb -remodel::bypass_fragments, -remodel::num_trajectory, -remodel::repeat_structure -remodel::build_disulf -remodel::quick_and_dirty -remodel::use_pose_relax -remodel::run_confirmation -enzdes::cstfile -symmetry::symmetry_definition -run::show_simulation_in_pymol. More... | |
| void | register_user_options () |
| Checks for presence of any score term weight override options and calls set_weight on the centroid scorefunction. Note: options only get applied to centroid scorefunction - fullatom scorefunction left as is. More... | |
| bool | centroid_build (Pose &pose, protocols::forge::build::BuildManager &manager) |
| get_name function for JobDistributor More... | |
| bool | centroid_build (Pose &pose) |
| run the centroid level build stage More... | |
| bool | design_refine_seq_relax (Pose &pose, RemodelDesignMover &designMover) |
| Sets up constraints and a modified scorefunction and run design/relax cycles. Checks the value of -remodel:repeat_structure. More... | |
| bool | design_refine_cart_relax (Pose &pose, RemodelDesignMover &designMover) |
| bool | design_refine (Pose &pose, RemodelDesignMover &designMover) |
| run the design-refine stage More... | |
| TaskFactoryOP | generic_taskfactory () |
| return a TaskFactory useable as a starting point for either design or refinement More... | |
| void | process_continuous_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf) |
| process a continuous design string, adding appropriate operations to the TaskFactory More... | |
| void | process_insert_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf) |
| process a design string containing an insert, adding appropriate operations to the TaskFactory More... | |
| void | set_param_from_options () |
Static Private Member Functions | |
| static utility::vector1< bool > const & | allowed_surface_aa () |
| return a boolean vector specifying allowed a.a. when designing on the surface 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... | |
Member Typedef Documentation
◆ BuildInstructionOP
| typedef protocols::forge::build::BuildInstructionOP protocols::forge::remodel::RemodelMover::BuildInstructionOP |
◆ BuildManager
◆ DataMap
◆ DesignInfo
| typedef utility::vector1< OriginalInterval2DesignString > protocols::forge::remodel::RemodelMover::DesignInfo |
◆ Interval
◆ MoverOP
◆ Original2Modified
| typedef protocols::forge::build::BuildManager::Original2Modified protocols::forge::remodel::RemodelMover::Original2Modified |
◆ OriginalInterval2DesignString
| typedef std::pair< Interval, String > protocols::forge::remodel::RemodelMover::OriginalInterval2DesignString |
A pair storing a instruction's original interval and a string denoting the sequence during design.
- Remarks
- This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.
◆ Pose
◆ Real
◆ RemodelData
◆ RemodelWorkingSet
| typedef protocols::forge::remodel::RemodelWorkingSet protocols::forge::remodel::RemodelMover::RemodelWorkingSet |
◆ ScoreFunction
◆ ScoreFunctionOP
◆ Size
◆ String
| typedef std::string protocols::forge::remodel::RemodelMover::String |
◆ Super
◆ TagCOP
| typedef utility::tag::TagCOP protocols::forge::remodel::RemodelMover::TagCOP |
◆ TaskFactoryOP
◆ VarLengthBuild
| typedef protocols::forge::components::VarLengthBuild protocols::forge::remodel::RemodelMover::VarLengthBuild |
◆ VarLengthBuildOP
| typedef protocols::forge::components::VarLengthBuildOP protocols::forge::remodel::RemodelMover::VarLengthBuildOP |
Constructor & Destructor Documentation
◆ RemodelMover() [1/2]
| protocols::forge::remodel::RemodelMover::RemodelMover | ( | ) |
default constructor
Default constructor. Checks values of options packing::soft_rep_design, and remodel::dr_cycles Creates and sets the centroid and fullatom score functions.
References blueprint_, centroid_loop_mover_str_, centroid_sfx_, core::scoring::ScoreFunctionFactory::create_score_function(), disulf_fa_max_, dr_cycles_, fullatom_sfx_, core::scoring::get_score_function(), last_input_pose_, max_linear_chainbreak_, redesign_loop_neighborhood_, register_user_options(), relax_bb_for_disulf_, rosetta_scripts_, rosetta_scripts_build_disulfide_, rosetta_scripts_bypass_fragments_, rosetta_scripts_fast_disulfide_, rosetta_scripts_include_current_ds_, rosetta_scripts_keep_current_ds_, rosetta_scripts_match_rt_limit_, rosetta_scripts_max_disulfides_, rosetta_scripts_min_disulfides_, rosetta_scripts_min_loop_, rosetta_scripts_quick_and_dirty_, core::scoring::SOFT_REP_DESIGN_WTS, protocols::forge::remodel::TR(), use_disulf_fa_score_, and use_match_rt_.
◆ RemodelMover() [2/2]
| protocols::forge::remodel::RemodelMover::RemodelMover | ( | RemodelMover const & | rval | ) |
◆ ~RemodelMover()
|
overridedefault |
default destructor
Default destructor. Does this need to free the VarLengthBuild memory?
Member Function Documentation
◆ allowed_surface_aa()
|
staticprivate |
return a boolean vector specifying allowed a.a. when designing on the surface
References core::chemical::aa_from_oneletter_code().
Referenced by process_continuous_design_string(), and process_insert_design_string().
◆ apply()
|
overridevirtual |
apply defined moves to given Pose
Implements protocols::moves::Mover.
References core::chemical::aa_from_oneletter_code(), accumulator_, protocols::viewer::add_conformation_viewer(), protocols::symmetry::SetupNCSMover::add_group(), core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_score_line_string(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), core::pose::Pose::append_residue_by_bond(), protocols::symmetry::SetupForSymmetryMover::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::score_filters::ScoreTypeFilter::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), protocols::forge::remodel::RemodelGlobalFrame::apply(), core::scoring::atom_pair_constraint, protocols::forge::remodel::RemodelData::blueprint, blueprint_, core::scoring::CA_rmsd(), core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, core::scoring::cen_hb, centroid_build(), centroid_sfx_, core::chemical::CENTROID_t, protocols::forge::remodel::RemodelAccumulator::clear(), protocols::forge::remodel::RemodelAccumulator::cluster_switch(), protocols::forge::remodel::RemodelAccumulator::clustered_best_poses(), protocols::forge::remodel::RemodelData::collectInsertionPose(), protocols::score_filters::ScoreTypeFilter::compute(), confirm_sequence(), core::pose::Pose::conformation(), protocols::forge::remodel::RemodelAccumulator::contents_in_pose_store(), core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), core::id::D, core::pose::Pose::delete_residue_range_slow(), core::conformation::Conformation::delete_residue_slow(), design_refine(), design_refine_cart_relax(), design_refine_seq_relax(), core::scoring::dihedral_constraint, disulf_fa_max_, protocols::simple_filters::dssp(), protocols::forge::build::BuildManager::dummy_modify(), core::pose::Pose::dump_pdb(), core::sequence::end, core::pose::datacache::ENZDES_OBSERVER, protocols::moves::FAIL_DO_NOT_RETRY, core::chemical::modifications::FAIL_RETRY, protocols::moves::FAIL_RETRY, protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), core::pose::Pose::fold_tree(), core::chemical::FULL_ATOM_t, fullatom_sfx_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::pose::get_restype_for_pose(), core::scoring::get_score_function(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), last_input_pose_, loops_buns_polar_calc_name(), protocols::forge::remodel::RemodelDesignMover::make_disulfide(), protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast(), protocols::forge::remodel::RemodelWorkingSet::manager, manager_, core::pose::Pose::metric(), protocols::forge::remodel::RemodelLigandHandler::minimize(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::BuildManager::movemap(), protocols::moves::MS_SUCCESS, core::chemical::name_from_aa(), native_pose_, protocols::forge::remodel::RemodelData::natro_movemap_, neighborhood_buns_polar_calc_name(), neighborhood_calc_name(), core::pose::Pose::observer_cache(), protocols::forge::remodel::RemodelGlobalFrame::omega(), core::pose::Pose::omega(), core::scoring::omega, core::pose::Pose::pdb_info(), core::pose::Pose::phi(), protocols::forge::remodel::RemodelAccumulator::pop(), core::pose::Pose::psi(), protocols::forge::remodel::RemodelGlobalFrame::radius(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::forge::remodel::recursive_multiple_disulfide_former(), relax_bb_for_disulf_, remodel_data_, core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::renumber_pdbinfo_based_on_conf_chains(), core::kinematics::FoldTree::reorder(), core::pose::replace_pose_residue_copying_existing_coordinates(), core::scoring::res_type_constraint, core::scoring::res_type_linking_constraint, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), protocols::forge::remodel::RemodelGlobalFrame::rise(), rosetta_scripts_, rosetta_scripts_build_disulfide_, rosetta_scripts_bypass_fragments_, rosetta_scripts_fast_disulfide_, rosetta_scripts_include_current_ds_, rosetta_scripts_keep_current_ds_, rosetta_scripts_match_rt_limit_, rosetta_scripts_max_disulfides_, rosetta_scripts_min_disulfides_, rosetta_scripts_min_loop_, rosetta_scripts_quick_and_dirty_, protocols::forge::remodel::RemodelWorkingSet::safe_root_, core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), SamePose(), protocols::hybridization::score, protocols::forge::remodel::RemodelDesignMover::scorefunction(), core::pose::Pose::secstruct(), protocols::forge::remodel::RemodelData::sequence, core::pose::datacache::ObserverCache::set(), protocols::moves::Mover::set_last_move_status(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), protocols::forge::remodel::RemodelDesignMover::set_state(), setup_remodel_data_for_loop_btw_parametric_components(), protocols::forge::remodel::RemodelAccumulator::size(), core::pose::Pose::size(), protocols::forge::build::BuildManager::size(), core::pose::Pose::split_by_chain(), core::util::switch_to_residue_type_set(), core::id::THETA, core::id::to_string(), core::pose::Pose::total_residue(), core::scoring::total_score, protocols::forge::remodel::TR(), protocols::forge::build::BuildManager::union_of_intervals_containing_undefined_positions(), protocols::forge::remodel::RemodelData::updateWithDsspAssignment(), use_disulf_fa_score_, use_match_rt_, core::io::RemarkInfo::value, working_model_, protocols::forge::remodel::RemodelWorkingSet::workingSetGen(), and protocols::forge::remodel::RemodelAccumulator::write_checkpoint().
◆ centroid_build() [1/2]
|
private |
run the centroid level build stage
Runs the centroid level build state. Returns true if loop was closed, false if not. Also checks the value of options -remodel:use_same_length_fragments, -remodel:use_blueprint_sequence and -remodel:repeat_structure.
- Returns
- true if loop closed, false otherwise
References protocols::forge::remodel::RemodelWorkingSet::abego, protocols::symmetry::SetupForSymmetryMover::apply(), protocols::forge::remodel::RemodelData::blueprint, centroid_loop_mover_str_, centroid_sfx_, core::scoring::Energies::clear(), core::pose::Pose::conformation(), core::pose::Pose::energies(), core::chemical::FULL_ATOM_t, protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), manager_, max_linear_chainbreak_, protocols::moves::MS_SUCCESS, core::pose::Pose::pdb_info(), remodel_data_, protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), core::conformation::Conformation::residue_typeset_mode(), protocols::forge::methods::restore_residues(), protocols::forge::remodel::RemodelData::sequence, protocols::forge::remodel::RemodelLoopMover::set_repeat_tail_length(), protocols::forge::remodel::RemodelWorkingSet::ss, core::util::switch_to_residue_type_set(), protocols::forge::remodel::TR(), vlb_, and working_model_.
◆ centroid_build() [2/2]
|
private |
get_name function for JobDistributor
Does the same as function below, but takes in a BuildManager object. Also checks the value of the option -remodel::bypass_fragments.
References protocols::symmetry::SetupForSymmetryMover::apply(), protocols::forge::remodel::RemodelData::blueprint, protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), manager_, core::pose::Pose::pdb_info(), remodel_data_, protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), rosetta_scripts_bypass_fragments_, rosetta_scripts_fast_disulfide_, protocols::forge::remodel::RemodelData::sequence, protocols::forge::remodel::RemodelLoopMover::set_repeat_tail_length(), and protocols::forge::remodel::TR().
Referenced by apply().
◆ centroid_loop_mover_str()
|
inline |
the loop mover string to use during centroid build
- Remarks
- set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"
References centroid_loop_mover_str_.
◆ centroid_scorefunction() [1/3]
| ScoreFunction const & protocols::forge::remodel::RemodelMover::centroid_scorefunction | ( | ) | const |
the centroid level score function, default "remodel_cen"
References centroid_sfx_.
◆ centroid_scorefunction() [2/3]
| void protocols::forge::remodel::RemodelMover::centroid_scorefunction | ( | ScoreFunction const & | sfx | ) |
set the centroid level score function
References centroid_sfx_, and core::scoring::ScoreFunction::clone().
◆ centroid_scorefunction() [3/3]
| void protocols::forge::remodel::RemodelMover::centroid_scorefunction | ( | ScoreFunctionOP const & | sfx | ) |
set the centroid level score function
References centroid_sfx_.
◆ clone() [1/2]
|
virtual |
clone this object
◆ clone() [2/2]
|
overridevirtual |
◆ confirm_sequence()
| bool protocols::forge::remodel::RemodelMover::confirm_sequence | ( | core::pose::Pose & | pose | ) |
As best as I can tell, does some loop closure and calculates RMSD to native. Returns true. NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of rmsd value, because this stage is not being used as a filter Checks the value of -remodel::swap_refine_confirm_protocols.
References protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), core::sequence::end, protocols::loops::loop_mover::LoopMover::false_movemap(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), fullatom_sfx_, generic_taskfactory(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_confirmation_loops(), core::chemical::ResidueTypeBase::is_DNA(), protocols::loops::loop_mover::KIC(), manager_, protocols::forge::build::BuildManager::movemap(), native_pose_, protocols::forge::remodel::RemodelData::natro_movemap_, neighborhood_calc_name(), core::pose::Pose::pdb_info(), remodel_data_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory(), core::pose::Pose::size(), protocols::loops::stop, core::id::to_string(), protocols::forge::remodel::TR(), core::io::RemarkInfo::value, and core::conformation::Residue::xyz().
Referenced by apply().
◆ design_refine()
|
private |
run the design-refine stage
Run the design-refine stage. Checks the value of -remodel:repeat_structure and -remodel:swap_refine_confirm_protocols NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of if chain breaks test passes or fails.
- Returns
- currently always true
References protocols::forge::remodel::RemodelDesignMover::apply(), core::scoring::atom_pair_constraint, core::scoring::Energies::clear(), core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, dr_cycles_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), generic_taskfactory(), core::kinematics::MoveMap::get_chi(), core::scoring::get_score_function(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), core::conformation::Residue::is_DNA(), protocols::loops::loop_mover::KIC(), protocols::forge::methods::linear_chainbreak(), manager_, max_linear_chainbreak_, protocols::forge::build::BuildManager::movemap(), protocols::forge::remodel::RemodelData::natro_movemap_, neighborhood_calc_name(), protocols::forge::build::BuildManager::original2modified_interval_endpoints(), remodel_data_, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::forge::remodel::RemodelDesignMover::set_state(), core::pose::Pose::size(), and protocols::forge::remodel::TR().
Referenced by apply().
◆ design_refine_cart_relax()
|
private |
References protocols::symmetry::SetupNCSMover::add_group(), core::scoring::angle_constraint, core::pose::annotated_to_oneletter_sequence(), protocols::symmetry::SetupNCSMover::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), core::scoring::atom_pair_constraint, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, core::scoring::Energies::clear(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, protocols::relax::cyclize_pose(), core::scoring::dihedral_constraint, dr_cycles_, core::pose::Pose::energies(), protocols::forge::methods::fill_non_loop_cst_set(), core::pose::Pose::fold_tree(), core::scoring::get_score_function(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), core::conformation::symmetry::is_symmetric(), protocols::forge::methods::linear_chainbreak(), manager_, protocols::forge::build::BuildManager::movemap(), protocols::forge::remodel::RemodelData::natro_movemap_, protocols::forge::build::BuildManager::original2modified_interval_endpoints(), remodel_data_, protocols::loops::remove_cutpoint_variants(), core::scoring::res_type_constraint, core::scoring::res_type_linking_constraint, core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::symmetry::SetupNCSMover::set_bb(), protocols::forge::remodel::RemodelDesignMover::set_state(), core::kinematics::FoldTree::simple_tree(), core::pose::Pose::size(), core::pose::symmetry::symmetry_info(), and protocols::forge::remodel::TR().
Referenced by apply().
◆ design_refine_seq_relax()
|
private |
Sets up constraints and a modified scorefunction and run design/relax cycles. Checks the value of -remodel:repeat_structure.
References protocols::symmetry::SetupNCSMover::add_group(), core::scoring::angle_constraint, protocols::relax::FastRelax::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), core::scoring::atom_pair_constraint, core::scoring::Energies::clear(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, protocols::relax::cyclize_pose(), core::scoring::dihedral_constraint, dr_cycles_, core::pose::Pose::energies(), protocols::forge::methods::fill_non_loop_cst_set(), core::scoring::get_score_function(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), core::conformation::symmetry::is_symmetric(), manager_, protocols::forge::build::BuildManager::original2modified_interval_endpoints(), core::scoring::res_type_constraint, core::scoring::res_type_linking_constraint, protocols::forge::remodel::RemodelDesignMover::set_state(), core::pose::Pose::size(), core::pose::symmetry::symmetry_info(), and protocols::forge::remodel::TR().
Referenced by apply().
◆ dr_cycles()
|
inline |
set the number of design-refine cycles to perform
- Remarks
- set this to 0 to skip design-refine
References dr_cycles_.
◆ fresh_instance() [1/2]
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virtual |
create this type of object
◆ fresh_instance() [2/2]
|
overridevirtual |
create this type of object, for parser
fresh instance for parser
Reimplemented from protocols::moves::Mover.
◆ fullatom_scorefunction() [1/3]
| ScoreFunction const & protocols::forge::remodel::RemodelMover::fullatom_scorefunction | ( | ) | const |
the full-atom level score function
References fullatom_sfx_.
◆ fullatom_scorefunction() [2/3]
| void protocols::forge::remodel::RemodelMover::fullatom_scorefunction | ( | ScoreFunction const & | sfx | ) |
set the full-atom level score function
References core::scoring::ScoreFunction::clone(), and fullatom_sfx_.
◆ fullatom_scorefunction() [3/3]
| void protocols::forge::remodel::RemodelMover::fullatom_scorefunction | ( | ScoreFunctionOP const & | sfx | ) |
set the full-atom level score function
References fullatom_sfx_.
◆ generic_taskfactory()
|
private |
return a TaskFactory useable as a starting point for either design or refinement
Returns a TaskFactory useable as a starting point for either design or refinement. Only adds the NoRepackDisulfides, IncludeCurrent, and Init from command line ops. ReadResfile is not included.
Referenced by confirm_sequence(), and design_refine().
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ loops_buns_polar_calc_name()
|
inlinestatic |
the name for the loops' buried unsatisfied polars calculator
Referenced by apply().
◆ max_linear_chainbreak()
|
inline |
add instruction to the manager of this RemodelMover (no copy)
- Parameters
-
[in] bi BuildInstruction [in] aa_during_design_refine The allowed amino acid sequence during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly, and remember to use any special characters, e.g. the insertion character for SegmentInsert
the maximum allowed linear chainbreak
References max_linear_chainbreak_.
◆ mover_name()
|
static |
Referenced by get_name(), protocols::forge::remodel::RemodelMoverCreator::keyname(), and provide_xml_schema().
◆ neighborhood_buns_polar_calc_name()
|
inlinestatic |
the name for the loops' neighborhood buried unsatisfied polars calculator
Referenced by apply().
◆ neighborhood_calc_name()
|
inlinestatic |
the name for the loops' neighborhood calculator
Referenced by apply(), confirm_sequence(), and design_refine().
◆ operator=()
|
private |
copy assignment
- Remarks
- Mover base class prevents this from working properly...
◆ parse_my_tag()
|
overridevirtual |
parse xml
Reimplemented from protocols::moves::Mover.
References blueprint_, disulf_fa_max_, relax_bb_for_disulf_, rosetta_scripts_, rosetta_scripts_build_disulfide_, rosetta_scripts_bypass_fragments_, rosetta_scripts_fast_disulfide_, rosetta_scripts_include_current_ds_, rosetta_scripts_keep_current_ds_, rosetta_scripts_match_rt_limit_, rosetta_scripts_max_disulfides_, rosetta_scripts_min_disulfides_, rosetta_scripts_min_loop_, rosetta_scripts_quick_and_dirty_, protocols::forge::remodel::TR(), use_disulf_fa_score_, and use_match_rt_.
◆ process_continuous_design_string()
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private |
process a continuous design string, adding appropriate operations to the TaskFactory
References core::chemical::aa_from_oneletter_code(), allowed_surface_aa(), and protocols::forge::build::Interval::left.
◆ process_insert_design_string()
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private |
process a design string containing an insert, adding appropriate operations to the TaskFactory
References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), allowed_surface_aa(), protocols::forge::build::SegmentInsert::insertion_char(), protocols::forge::build::Interval::left, protocols::forge::build::Interval::length(), and protocols::forge::build::Interval::right.
◆ provide_citation_info()
|
overridevirtual |
Provide the citation.
Reimplemented from protocols::moves::Mover.
References centroid_sfx_, and fullatom_sfx_.
◆ provide_xml_schema()
|
static |
References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::forge::remodel::RemodelMoverCreator::provide_xml_schema().
◆ redesign_loop_neighborhood()
|
inline |
redesign the neighborhood around the loop? if false, then just repacks during the design phase
References redesign_loop_neighborhood_.
◆ register_user_options()
|
private |
Checks for presence of any score term weight override options and calls set_weight on the centroid scorefunction. Note: options only get applied to centroid scorefunction - fullatom scorefunction left as is.
References core::scoring::cbeta, core::scoring::cenpack, centroid_sfx_, core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::rama, core::scoring::rg, core::scoring::rg_local, core::scoring::rsigma, core::scoring::ss_pair, protocols::forge::remodel::TR(), and core::scoring::vdw.
Referenced by RemodelMover().
◆ SamePose()
|
private |
Apply method for Mover. Checks the values of the following options -remodel::checkpoint -remodel::domainFusion::insert_segment_from_pdb -remodel::bypass_fragments, -remodel::num_trajectory, -remodel::repeat_structure -remodel::build_disulf -remodel::quick_and_dirty -remodel::use_pose_relax -remodel::run_confirmation -enzdes::cstfile -symmetry::symmetry_definition -run::show_simulation_in_pymol.
References core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), and core::pose::Pose::size().
Referenced by apply().
◆ set_param_from_options()
|
private |
◆ setup_remodel_data_for_loop_btw_parametric_components()
|
private |
sets up remodel data for combining blueprint with parametric mode
References blueprint_, protocols::simple_filters::dssp(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint(), core::pose::Pose::split_by_chain(), and protocols::forge::remodel::TR().
Referenced by apply().
Member Data Documentation
◆ accumulator_
|
private |
Referenced by apply().
◆ blueprint_
|
private |
Referenced by apply(), parse_my_tag(), RemodelMover(), and setup_remodel_data_for_loop_btw_parametric_components().
◆ centroid_loop_mover_str_
|
private |
the loop mover string to use during centroid build (default "RemodelLoopMover")
- Remarks
- set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"
Referenced by centroid_build(), centroid_loop_mover_str(), and RemodelMover().
◆ centroid_sfx_
|
private |
the centroid scorefunction to use, default "remodel_cen"
Referenced by apply(), centroid_build(), centroid_scorefunction(), provide_citation_info(), register_user_options(), and RemodelMover().
◆ design_info_
|
private |
Stores instructions' original interval and a string denoting the sequence during design.
- Remarks
- This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.
◆ disulf_fa_max_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ dr_cycles_
|
private |
name of the resfile to use during design-refine; empty string implies no resfile String resfile_;
the number of design-refine cycles to perform, default 3
Referenced by design_refine(), design_refine_cart_relax(), design_refine_seq_relax(), dr_cycles(), and RemodelMover().
◆ fullatom_sfx_
|
private |
the full-atom scorefunction to use
Referenced by apply(), confirm_sequence(), fullatom_scorefunction(), provide_citation_info(), and RemodelMover().
◆ last_input_pose_
|
private |
Referenced by apply(), and RemodelMover().
◆ manager_
|
private |
the BuildManager
Referenced by apply(), centroid_build(), confirm_sequence(), design_refine(), design_refine_cart_relax(), and design_refine_seq_relax().
◆ max_linear_chainbreak_
|
private |
use sequence biased fragments when building the loop? (default false) bool use_sequence_bias_;
the maximum allowed linear chainbreak (default 0.07)
Referenced by centroid_build(), design_refine(), max_linear_chainbreak(), and RemodelMover().
◆ native_pose_
|
private |
Referenced by apply(), and confirm_sequence().
◆ redesign_loop_neighborhood_
|
private |
redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true)
Referenced by redesign_loop_neighborhood(), and RemodelMover().
◆ relax_bb_for_disulf_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ remodel_data_
|
private |
holds all the blueprint info, contains build manager
Referenced by apply(), centroid_build(), confirm_sequence(), design_refine(), and design_refine_cart_relax().
◆ rosetta_scripts_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ rosetta_scripts_build_disulfide_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ rosetta_scripts_bypass_fragments_
|
private |
Referenced by apply(), centroid_build(), parse_my_tag(), and RemodelMover().
◆ rosetta_scripts_fast_disulfide_
|
private |
Referenced by apply(), centroid_build(), parse_my_tag(), and RemodelMover().
◆ rosetta_scripts_include_current_ds_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ rosetta_scripts_keep_current_ds_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ rosetta_scripts_match_rt_limit_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ rosetta_scripts_max_disulfides_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ rosetta_scripts_min_disulfides_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ rosetta_scripts_min_loop_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ rosetta_scripts_quick_and_dirty_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ use_disulf_fa_score_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ use_match_rt_
|
private |
Referenced by apply(), parse_my_tag(), and RemodelMover().
◆ vlb_
|
private |
VLB for centroid_build.
- Remarks
- Store it here instead of re-instantiation each centroid_build() call so fragment caching works.
- Warning
- Remember to set this to null if the BuildManager changes.
Referenced by centroid_build(), and RemodelMover().
◆ working_model_
|
private |
working set holds all the modified index that is required for the remodeling task
Referenced by apply(), and centroid_build().
The documentation for this class was generated from the following files:
- src/protocols/forge/remodel/RemodelMover.hh
- src/protocols/forge/remodel/RemodelMover.cc
