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Rosetta
2016.11
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#include <StepWiseProteinBackboneSampler.hh>
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StepWiseProteinBackboneSampler (protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters) | |
~StepWiseProteinBackboneSampler () | |
virtual void | apply (core::pose::Pose &pose_to_visualize) |
Apply the minimizer to one pose. More... | |
virtual std::string | get_name () const |
Each derived class must specify its name. The class name. More... | |
void | set_silent_file (std::string const &setting) |
void | set_rmsd_cutoff (core::Real const &setting) |
void | set_n_sample (core::Size const &setting) |
void | set_nstruct_centroid (core::Size const &setting) |
void | set_filter_native_big_bins (bool const &setting) |
void | set_centroid_screen (bool const &setting) |
void | set_ghost_loops (bool const &setting) |
void | set_apply_vdw_cut (bool const &setting) |
void | set_centroid_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn) |
void | set_centroid_score_diff_cut (core::Real const &setting) |
utility::vector1 < MainChainTorsionSetList > const & | main_chain_torsion_set_lists () const |
utility::vector1 < utility::vector1< core::Real > > | main_chain_torsion_set_lists_real () const |
utility::vector1 < core::id::TorsionID > | which_torsions () |
void | setup_centroid_screen (core::Real const ¢roid_score_diff_cut, std::string const ¢roid_weights, core::Size const nstruct_centroid, bool const ghost_loops) |
core::Size | get_big_bin (core::Real const phi, core::Real const psi) const |
void | set_moving_residues (utility::vector1< core::Size > const &moving_res) |
void | set_fixed_residues (utility::vector1< core::Size > const &fixed_res) |
void | set_expand_loop_takeoff (bool const setting) |
bool | expand_loop_takeoff () const |
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Mover () | |
virtual | ~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... | |
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... | |
virtual 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 | |
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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 |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
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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::modeler::protein::StepWiseProteinBackboneSampler::StepWiseProteinBackboneSampler | ( | protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP | working_parameters | ) |
References initialize_is_fixed_res().
protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::~StepWiseProteinBackboneSampler | ( | ) |
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Apply the minimizer to one pose.
Implements protocols::moves::Mover.
References centroid_scores_, centroid_screen_, convert_to_centroid(), define_moving_res(), filter_main_chain_torsion_sets(), ghost_loops_, nstruct_centroid_, prepare_ghost_pose(), sample_residues_recursively(), setup_torsion_sets(), and protocols::TR().
Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().
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References core::pose::add_variant_type_to_pose_residue(), core::chemical::C_METHYLAMIDATION, core::chemical::CENTROID, core::scoring::dssp::Dssp::insert_ss_into_pose(), core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::pose::remove_variant_type_from_pose_residue(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), and core::chemical::UPPER_TERMINUS_VARIANT.
Referenced by apply(), and prepare_ghost_pose().
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References core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_name(), core::sequence::end, core::chemical::ResidueType::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), protocols::TR(), and core::pose::Pose::xyz().
Referenced by filter_and_save(), and initialize_ghost_pose().
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References expand_loop_takeoff_.
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References core::sequence::end, core::kinematics::FoldTree::new_jump(), and protocols::TR().
Referenced by prepare_ghost_pose().
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References apply_vdw_cut_, centroid_score_diff_cut_, centroid_score_ref_, centroid_scores_, centroid_screen_, centroid_vdw_ref_, copy_coords(), protocols::moves::Mover::get_native_pose(), ghost_loops_, ghost_map_, ghost_pose_, core::scoring::is_protein_backbone_including_O(), main_chain_torsion_set_for_moving_residues_, main_chain_torsion_sets_for_moving_residues_, rmsd_cutoff_, core::scoring::rmsd_with_super(), protocols::TR(), and core::scoring::vdw.
Referenced by sample_residues_recursively().
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References filter_big_bin().
Referenced by get_main_chain_torsion_set_list().
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References get_big_bin().
Referenced by filter_based_on_desired_secstruct(), and filter_native_BIG_BINS().
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References centroid_scores_, main_chain_torsion_sets_for_moving_residues_, and nstruct_centroid_.
Referenced by apply().
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Size protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_big_bin | ( | core::Real const | phi, |
core::Real const | psi | ||
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Referenced by filter_big_bin(), and filter_native_BIG_BINS().
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References core::chemical::C_METHYLAMIDATION, expand_loop_takeoff_, filter_based_on_desired_secstruct(), filter_native_BIG_BINS(), filter_native_big_bins_, core::pose::full_model_info::get_fixed_domain_from_full_model_info_const(), get_main_chain_torsion_set_list_c_terminus(), get_main_chain_torsion_set_list_coarse(), get_main_chain_torsion_set_list_full(), get_main_chain_torsion_set_list_n_terminus(), get_main_chain_torsion_set_list_sample_phi_only(), get_main_chain_torsion_set_list_sample_psi_only(), core::conformation::Residue::has_variant_type(), is_fixed_res_, is_pre_proline_, moving_residues_, core::chemical::N_ACETYLATION, core::pose::Pose::residue(), sample_cis_omega(), core::pose::Pose::secstruct(), core::pose::Pose::total_residue(), protocols::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.
Referenced by sample_residues_recursively().
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References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), get_rotamer_angle(), n_sample_, and ramachandran_.
Referenced by get_main_chain_torsion_set_list().
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References core::pose::Pose::aa(), core::chemical::aa_gly, and core::chemical::aa_pro.
Referenced by get_main_chain_torsion_set_list().
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References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), get_rotamer_angle(), n_sample_, and ramachandran_.
Referenced by get_main_chain_torsion_set_list().
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References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), get_rotamer_angle(), n_sample_, and ramachandran_.
Referenced by get_main_chain_torsion_set_list().
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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References core::chemical::CENTROID, copy_coords(), and core::pose::make_pose_from_sequence().
Referenced by prepare_ghost_pose().
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References set_fixed_residues(), and working_parameters_.
Referenced by StepWiseProteinBackboneSampler().
utility::vector1< MainChainTorsionSetList > const & protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists | ( | ) | const |
References main_chain_torsion_sets_for_moving_residues_.
utility::vector1< utility::vector1< core::Real > > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists_real | ( | ) | const |
References main_chain_torsion_sets_for_moving_residues_, and core::scoring::omega.
Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().
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References centroid_score_ref_, centroid_scorefxn_, centroid_vdw_ref_, convert_to_centroid(), figure_out_fold_tree(), protocols::moves::Mover::get_native_pose(), ghost_map_, ghost_native_pose_, ghost_pose_, initialize_ghost_pose(), moving_residues_, core::pose::Pose::sequence(), core::kinematics::Jump::set_translation(), protocols::TR(), and core::scoring::vdw.
Referenced by apply().
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Referenced by get_main_chain_torsion_set_list().
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References filter_and_save(), get_main_chain_torsion_set_list(), main_chain_torsion_set_for_moving_residues_, moving_residues_, protocols::stepwise::modeler::protein::MainChainTorsionSet::omega(), protocols::stepwise::modeler::protein::MainChainTorsionSet::phi(), protocols::stepwise::modeler::protein::MainChainTorsionSet::psi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().
Referenced by apply().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_apply_vdw_cut | ( | bool const & | setting | ) |
References apply_vdw_cut_.
Referenced by setup_centroid_screen().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_centroid_score_diff_cut | ( | core::Real const & | setting | ) |
References centroid_score_diff_cut_.
Referenced by setup_centroid_screen().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_centroid_scorefxn | ( | core::scoring::ScoreFunctionOP const & | scorefxn | ) |
References centroid_scorefxn_.
Referenced by setup_centroid_screen().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_centroid_screen | ( | bool const & | setting | ) |
References centroid_screen_.
Referenced by setup_centroid_screen().
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References expand_loop_takeoff_.
Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_filter_native_big_bins | ( | bool const & | setting | ) |
References filter_native_big_bins_.
Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_fixed_residues | ( | utility::vector1< core::Size > const & | fixed_res | ) |
References is_fixed_res_input_, and working_parameters_.
Referenced by initialize_is_fixed_res().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_ghost_loops | ( | bool const & | setting | ) |
References ghost_loops_.
Referenced by setup_centroid_screen().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_moving_residues | ( | utility::vector1< core::Size > const & | moving_res | ) |
References moving_residues_.
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_n_sample | ( | core::Size const & | setting | ) |
References n_sample_.
Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_nstruct_centroid | ( | core::Size const & | setting | ) |
References nstruct_centroid_.
Referenced by setup_centroid_screen().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_rmsd_cutoff | ( | core::Real const & | setting | ) |
References rmsd_cutoff_.
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_silent_file | ( | std::string const & | setting | ) |
References silent_file_.
Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::setup_centroid_screen | ( | core::Real const & | centroid_score_diff_cut, |
std::string const & | centroid_weights, | ||
core::Size const | nstruct_centroid, | ||
bool const | ghost_loops | ||
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References main_chain_torsion_set_for_moving_residues_, main_chain_torsion_sets_for_moving_residues_, and moving_residues_.
Referenced by apply().
utility::vector1< id::TorsionID > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::which_torsions | ( | ) |
References core::id::BB, and moving_residues_.
Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().
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Referenced by filter_and_save(), and set_apply_vdw_cut().
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Referenced by filter_and_save(), and set_centroid_score_diff_cut().
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Referenced by filter_and_save(), and prepare_ghost_pose().
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Referenced by prepare_ghost_pose(), and set_centroid_scorefxn().
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Referenced by apply(), filter_and_save(), and filter_main_chain_torsion_sets().
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Referenced by apply(), filter_and_save(), and set_centroid_screen().
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Referenced by filter_and_save(), and prepare_ghost_pose().
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Referenced by define_moving_res(), expand_loop_takeoff(), get_main_chain_torsion_set_list(), and set_expand_loop_takeoff().
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Referenced by get_main_chain_torsion_set_list(), and set_filter_native_big_bins().
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Referenced by apply(), filter_and_save(), and set_ghost_loops().
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Referenced by filter_and_save(), and prepare_ghost_pose().
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Referenced by prepare_ghost_pose().
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Referenced by filter_and_save(), and prepare_ghost_pose().
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Referenced by define_moving_res(), and get_main_chain_torsion_set_list().
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Referenced by define_moving_res(), and set_fixed_residues().
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Referenced by get_main_chain_torsion_set_list().
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Referenced by filter_and_save(), sample_residues_recursively(), and setup_torsion_sets().
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Referenced by define_moving_res().
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Referenced by apply(), filter_main_chain_torsion_sets(), and set_nstruct_centroid().
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Referenced by filter_and_save(), and set_rmsd_cutoff().
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Referenced by set_silent_file().
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Referenced by initialize_is_fixed_res(), and set_fixed_residues().