 |
Rosetta Protocols
2014.35
|
|
Rosetta Protocols
2014.35
|
#include <StepWiseRNA_PoseSetup.hh>
Public Member Functions | |
| StepWiseRNA_PoseSetup (stepwise::modeler::working_parameters::StepWiseWorkingParametersOP &working_parameters) | |
| ~StepWiseRNA_PoseSetup () | |
| virtual void | apply (pose::Pose &pose) |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| void | set_input_tags (utility::vector1< std::string > const &setting) |
| void | set_silent_files_in (utility::vector1< std::string > const &setting) |
| void | set_bulge_res (utility::vector1< Size > const &bulge_res) |
| void | set_virtual_res (utility::vector1< Size > const &virtual_res_list) |
| void | set_native_virtual_res (utility::vector1< Size > const &native_virtual_res_list) |
| void | set_copy_DOF (bool const setting) |
| void | set_verbose (bool const setting) |
| void | setup_native_pose (pose::Pose &pose) |
| void | set_output_pdb (bool const setting) |
| void | set_apply_virtual_res_variant_at_dinucleotide (bool const setting) |
| void | set_align_to_native (bool const setting) |
| void | set_use_phenix_geo (bool const setting) |
| void | update_fold_tree_at_virtual_sugars (pose::Pose &pose) |
 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 |
| void | set_type (std::string const &setting) |
| 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) |
| virtual MoverOP | clone () const |
| Return a clone of the Mover object. More... | |
| virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| 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 |
| 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... | |
| virtual MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef protocols::filters::Filters_map | Filters_map |
| typedef std::list< std::string > | Strings |
| 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... | |
| 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... | |
| protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::StepWiseRNA_PoseSetup | ( | stepwise::modeler::working_parameters::StepWiseWorkingParametersOP & | working_parameters | ) |
References chemical, FA_RNA, and residue_type_set.
| protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::~StepWiseRNA_PoseSetup | ( | ) |
|
private |
References core::chemical::aa_vrt, core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeSet::name3_map(), nres, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::ResidueType::residue_type_set(), core::kinematics::FoldTree::root(), core::pose::Pose::total_residue(), protocols::TR, and working_parameters_.
Referenced by apply(), and setup_native_pose().
|
private |
|
private |
References core::pose::Pose::constraint_set(), first_base_atom_index(), core::pose::Pose::fold_tree(), length, nres, protocols::stepwise::modeler::rna::output_seq_num_list(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::total_residue(), protocols::TR, working_parameters_, and core::pose::Pose::xyz().
Referenced by apply().
|
private |
References protocols::stepwise::legacy::modeler::rna::setup_chain_break_jump_point(), virtualize_sugar_and_backbone_at_moving_res(), and working_parameters_.
Referenced by apply().
|
virtual |
Implements protocols::moves::Mover.
References add_aa_virt_rsd_as_root(), add_protonated_H1_adenosine_variants(), add_terminal_res_repulsion(), additional_setup_for_floating_base(), apply_bulge_variants(), apply_cutpoint_variants(), apply_virtual_phosphate_variants(), apply_virtual_res_variant(), create_starting_pose(), core::pose::Pose::dump_pdb(), instantiate_residue_if_rebuilding_bulge(), output_pdb_, protocols::stepwise::modeler::rna::output_title_text(), setup_full_model_info(), protocols::TR, update_fold_tree_at_virtual_sugars(), use_phenix_geo_, verbose_, verify_protonated_H1_adenosine_variants(), and working_parameters_.
|
private |
References protocols::stepwise::modeler::rna::apply_sub_to_full_mapping(), bulge_res_, full_to_sub(), runtime_assert, terminal_res, and working_parameters_.
Referenced by apply().
|
private |
References core::pose::correctly_add_cutpoint_variants(), cutpoint_closed, full_to_sub(), protocols::stepwise::legacy::modeler::rna::print_backbone_torsions(), core::pose::Pose::set_torsion(), protocols::antibody::simple_fold_tree(), core::id::TorsionID::torsion(), core::pose::Pose::total_residue(), protocols::TR, utility_exit_with_message, verbose_, and working_parameters_.
Referenced by apply(), and setup_native_pose().
|
private |
References cutpoint_closed, core::chemical::CUTPOINT_UPPER, full_to_sub(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::type(), utility_exit_with_message, and working_parameters_.
Referenced by apply().
|
private |
References protocols::stepwise::modeler::rna::apply_sub_to_full_mapping(), apply_virtual_res_variant_at_dinucleotide_, core::pose::rna::apply_virtual_rna_residue_variant_type(), full_to_sub(), output_boolean(), terminal_res, protocols::TR, utility_exit_with_message, virtual_res_list_, and working_parameters_.
Referenced by apply().
|
private |
References protocols::stepwise::modeler::rna::create_full_to_input_res_map(), core::pose::Pose::dump_pdb(), full_to_sub(), get_nearest_dist_to_O2prime(), has_value(), output_pdb_, protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), core::pose::Pose::set_torsion(), torsion(), protocols::TR, verbose_, and working_parameters_.
Referenced by read_input_pose_and_copy_dofs().
|
private |
References core::pose::Pose::fold_tree(), make_extended_pose(), read_input_pose_and_copy_dofs(), protocols::TR, and working_parameters_.
Referenced by create_starting_pose().
|
private |
References copy_DOF_, create_pose_from_input_poses(), core::pose::Pose::fold_tree(), and working_parameters_.
Referenced by apply().
|
private |
References core::conformation::Residue::aa(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), has_value(), core::conformation::Residue::has_variant_type(), core::chemical::na_rad, core::pose::Pose::residue(), runtime_assert, silent_files_in_, and working_parameters_.
Referenced by read_input_pose_and_copy_dofs().
|
virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
|
private |
|
private |
References copy_DOF_, protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file(), input_res, input_tags_, protocols::farna::make_phosphate_nomenclature_matches_mini(), rsd_set_, runtime_assert, core::pose::Pose::sequence(), silent_files_in_, core::pose::Pose::total_residue(), protocols::TR, utility_exit_with_message, and working_parameters_.
Referenced by read_input_pose_and_copy_dofs().
|
private |
References core::pose::rna::remove_virtual_rna_residue_variant_type(), and working_parameters_.
Referenced by apply().
|
private |
References core::pose::Pose::dump_pdb(), make_pose_from_sequence(), output_pdb_, rsd_set_, protocols::TR, and working_parameters_.
Referenced by create_pose_from_input_poses().
|
private |
References add_variant_type_to_pose_residue(), protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(), apply_virtual_rna_residue_variant_type(), protocols::farna::assert_phosphate_nomenclature_matches_mini(), copy_DOF_, core::pose::copydofs::copy_dofs_match_atom_names(), correctly_copy_HO2prime_positions(), do_checks_and_apply_protonated_H1_adenosine_variant(), core::pose::Pose::dump_pdb(), core::pose::Pose::fold_tree(), full_to_sub(), has_virtual_rna_residue_variant_type(), Import_pose(), input_res, input_tags_, output_pdb_, remove_variant_type_from_pose_residue(), runtime_assert, size(), protocols::TR, utility_exit_with_message, and working_parameters_.
Referenced by create_pose_from_input_poses().
|
inline |
|
inline |
|
inline |
|
inline |
|
inline |
|
inline |
|
inline |
|
inline |
|
inline |
|
inline |
|
inline |
|
private |
References CALC_RMS, EXTRA_MINIMIZE, FIXED_DOMAIN, fixed_res, MOVING_RES, RNA_NORTH_SUGAR, RNA_SOUTH_SUGAR, RNA_SYN_CHI, RNA_TERMINAL, set_full_model_info(), working_parameters_, and working_res.
Referenced by apply(), and setup_native_pose().
| void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose | ( | pose::Pose & | pose | ) |
References add_aa_virt_rsd_as_root(), add_protonated_H1_adenosine_variants(), protocols::stepwise::modeler::rna::align_poses(), align_to_native_, apply_cutpoint_variants(), protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(), core::pose::rna::apply_virtual_rna_residue_variant_type(), core::pose::Pose::dump_pdb(), core::pose::Pose::fold_tree(), protocols::moves::Mover::get_native_pose(), protocols::farna::make_phosphate_nomenclature_matches_mini(), native_virtual_res_list_, output_pdb_, protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), setup_full_model_info(), protocols::TR, utility_exit_with_message, verbose_, verify_protonated_H1_adenosine_variants(), and working_parameters_.
| void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::update_fold_tree_at_virtual_sugars | ( | pose::Pose & | pose | ) |
References core::pose::Pose::fold_tree(), protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_without_fold_tree(), core::kinematics::FoldTree::jump_exists(), protocols::stepwise::legacy::modeler::rna::setup_chain_break_jump_point(), protocols::TR, virtual_sugar_res, and working_parameters_.
Referenced by apply().
|
private |
References core::conformation::Residue::aa(), core::conformation::Residue::has_variant_type(), core::chemical::na_rad, name_from_aa(), protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::TR, utility_exit_with_message, and working_parameters_.
Referenced by apply(), and setup_native_pose().
|
private |
References working_parameters_.
Referenced by additional_setup_for_floating_base().
|
private |
Referenced by setup_native_pose().
|
private |
Referenced by apply_virtual_res_variant().
|
private |
Referenced by apply_bulge_variants().
|
private |
Referenced by create_starting_pose(), Import_pose(), and read_input_pose_and_copy_dofs().
|
private |
Referenced by Import_pose(), and read_input_pose_and_copy_dofs().
|
private |
Referenced by setup_native_pose().
|
private |
|
private |
Referenced by Import_pose(), and make_extended_pose().
|
private |
Referenced by do_checks_and_apply_protonated_H1_adenosine_variant(), and Import_pose().
|
private |
Referenced by apply().
|
private |
Referenced by apply(), apply_cutpoint_variants(), correctly_copy_HO2prime_positions(), and setup_native_pose().
|
private |
Referenced by apply_virtual_res_variant().
|
private |
Referenced by add_aa_virt_rsd_as_root(), add_protonated_H1_adenosine_variants(), add_terminal_res_repulsion(), additional_setup_for_floating_base(), apply(), apply_bulge_variants(), apply_cutpoint_variants(), apply_virtual_phosphate_variants(), apply_virtual_res_variant(), correctly_copy_HO2prime_positions(), create_pose_from_input_poses(), create_starting_pose(), do_checks_and_apply_protonated_H1_adenosine_variant(), Import_pose(), instantiate_residue_if_rebuilding_bulge(), make_extended_pose(), read_input_pose_and_copy_dofs(), setup_full_model_info(), setup_native_pose(), update_fold_tree_at_virtual_sugars(), verify_protonated_H1_adenosine_variants(), and virtualize_sugar_and_backbone_at_moving_res().
1.8.7