protocols::generalized_kinematic_closure::GeneralizedKIC Member List

This is the complete list of members for protocols::generalized_kinematic_closure::GeneralizedKIC, including all inherited members.

add_atomset_to_perturber_atomset_list(core::Size const perturber_index, utility::vector1< core::id::NamedAtomID > const &atomset)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_atomset_to_perturber_atomset_list(utility::vector1< core::id::NamedAtomID > const &atomset)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter()	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter(filter::filter_type const &filtertype)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter(std::string const &filtertypename)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter_parameter(core::Size const filter_index, std::string const &param_name, core::Real const &value)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter_parameter(core::Size const filter_index, std::string const &param_name, core::Size const value)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter_parameter(core::Size const filter_index, std::string const &param_name, bool const value)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter_parameter(core::Size const filter_index, std::string const &param_name, std::string const &value)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter_parameter(std::string const &param_name, core::Real const &value)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter_parameter(std::string const &param_name, core::Size const value)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter_parameter(std::string const &param_name, bool const value)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_filter_parameter(std::string const &param_name, std::string const &value)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_loop_residue(core::Size const residue_index)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_perturber()	protocols::generalized_kinematic_closure::GeneralizedKIC
add_perturber(perturber::perturber_effect const &effect)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_perturber(std::string const &effectname)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_residue_to_perturber_residue_list(core::Size const perturber_index, core::Size const residue_index)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_residue_to_perturber_residue_list(core::Size const residue_index)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_solution(core::pose::PoseOP pose_in)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
add_tail_residue(core::Size const residue_index)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_value_to_perturber_value_list(core::Size const perturber_index, core::Real const &val)	protocols::generalized_kinematic_closure::GeneralizedKIC
add_value_to_perturber_value_list(core::Real const &val)	protocols::generalized_kinematic_closure::GeneralizedKIC
addloopgeometry(core::pose::Pose &perturbedloop_pose, core::pose::Pose const &pose, bool const build_ideal, utility::vector1< std::pair< core::Size, core::Size > > &residue_map)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
addloweranchor(core::pose::Pose &perturbedloop_pose, core::pose::Pose const &pose)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
addtailgeometry(core::pose::Pose &perturbedloop_pose, core::pose::Pose const &pose, bool const build_ideal, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > &tail_residue_map)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
addupperanchor(core::pose::Pose &perturbedloop_pose, core::pose::Pose const &pose)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
apply(core::pose::Pose &pose) override	protocols::generalized_kinematic_closure::GeneralizedKIC	virtual
apply_perturbations(core::pose::Pose const &loop_pose, core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bondangles, utility::vector1< core::Real > &bondlengths) const	protocols::generalized_kinematic_closure::GeneralizedKIC	private
atomlist_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
attach_boinc_ghost_observer() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
attach_boinc_ghost_observer_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
bondangle_solutions_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
bondlength_solutions_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
build_ideal_geometry_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
check_loop_residues_sensible(core::pose::Pose const &pose)	protocols::generalized_kinematic_closure::GeneralizedKIC
check_tail_residues_sensible(core::pose::Pose const &pose)	protocols::generalized_kinematic_closure::GeneralizedKIC
clear_info()	protocols::moves::Mover	inlinevirtual
clear_loop_residues()	protocols::generalized_kinematic_closure::GeneralizedKIC
clear_perturber_residue_list(core::Size const perturber_idx)	protocols::generalized_kinematic_closure::GeneralizedKIC
clear_perturber_residue_lists()	protocols::generalized_kinematic_closure::GeneralizedKIC
clear_stored_solutions()	protocols::generalized_kinematic_closure::GeneralizedKIC
clone() const override	protocols::generalized_kinematic_closure::GeneralizedKIC	virtual
close_bond(core::Size const rsd1, std::string const &at1, core::Size const rsd2, std::string const &at2, core::Size const rsd1_before, std::string const &at1_before, core::Size const rsd2_after, std::string const &at2_after, core::Real const &bondlength, core::Real const &bondangle1, core::Real const &bondangle2, core::Real const &torsion, bool const randomize_this_torsion, bool const randomize_flanking_torsions)	protocols::generalized_kinematic_closure::GeneralizedKIC
correct_polymer_dependent_atoms() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
correct_polymer_dependent_atoms_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
create()	protocols::moves::Mover	virtual
doKIC(core::pose::Pose const &pose, core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, core::Size &solution_index, utility::vector1< core::Real > &selected_torsions, utility::vector1< core::Real > &selected_bondangles, utility::vector1< core::Real > &selected_bondlengths)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
dont_fail_if_no_solution_found() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
dont_fail_if_no_solution_found_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
filter_solutions(core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< utility::vector1< core::Real > > &torsions, utility::vector1< utility::vector1< core::Real > > &bondangles, utility::vector1< utility::vector1< core::Real > > &bondlengths, int &nsol) const	protocols::generalized_kinematic_closure::GeneralizedKIC	private
filterlist_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
fresh_instance() const override	protocols::generalized_kinematic_closure::GeneralizedKIC	virtual
GeneralizedKIC()	protocols::generalized_kinematic_closure::GeneralizedKIC
GeneralizedKIC(GeneralizedKIC const &src)	protocols::generalized_kinematic_closure::GeneralizedKIC
generate_atomlist(core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
generate_bridgeobjects_data_from_atomlist(utility::vector1< utility::fixedsizearray1< core::Real, 3 > > &atoms, utility::vector1< core::Real > &dt, utility::vector1< core::Real > &da, utility::vector1< core::Real > &db, utility::vector1< core::Size > &order)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
get_additional_output()	protocols::moves::Mover	virtual
get_build_ideal_geometry()	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
get_closure_attempts() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
get_connection(core::Size const res_with_connection, core::Size const other_res, core::pose::Pose const &pose)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
get_current_job() const	protocols::moves::Mover
get_current_tag() const	protocols::moves::Mover	inline
get_input_pose() const	protocols::moves::Mover
get_last_move_status() const	protocols::moves::Mover
get_name() const override	protocols::generalized_kinematic_closure::GeneralizedKIC	virtual
get_native_pose() const	protocols::moves::Mover
get_ntries_before_giving_up() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
get_path(core::Size const first_atom, core::Size const second_atom, core::conformation::Residue const &rsd, utility::vector1< core::Size > &path_indices)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
get_perturbedloop_rsd(core::Size const original_pose_rsd, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
get_selector_type() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
get_selector_type_name() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
get_self_ptr() const	protocols::moves::Mover	inline
get_self_ptr()	protocols::moves::Mover	inline
get_self_weak_ptr() const	protocols::moves::Mover	inline
get_self_weak_ptr()	protocols::moves::Mover	inline
get_type() const	protocols::moves::Mover	inline
has_geometric_connection(core::Size const residue1, core::Size const residue2, core::pose::Pose const &pose)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
infer_anchor_connIDs(core::pose::Pose const &pose)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
info()	protocols::moves::Mover	inlinevirtual
info() const	protocols::moves::Mover	inlinevirtual
last_proposal_density_ratio()	protocols::moves::Mover	inlinevirtual
last_run_successful()	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
last_run_successful_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
load_filter_bin_params(core::Size const filter_index, std::string const &bin_params_file)	protocols::generalized_kinematic_closure::GeneralizedKIC
load_filter_bin_params(std::string const &bin_params_file)	protocols::generalized_kinematic_closure::GeneralizedKIC
load_perturber_bin_params(core::Size const perturber_index, std::string const &bin_params_file)	protocols::generalized_kinematic_closure::GeneralizedKIC
load_perturber_bin_params(std::string const &bin_params_file)	protocols::generalized_kinematic_closure::GeneralizedKIC
loopresidues_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
low_memory_mode() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
low_memory_mode_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
lower_anchor_connID_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
min_solution_count() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
min_solution_count_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
Mover()	protocols::moves::Mover
Mover(std::string const &type_name)	protocols::moves::Mover
mover_name()	protocols::generalized_kinematic_closure::GeneralizedKIC	static
n_closure_attempts_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
name()	protocols::moves::Mover	inlinestatic
ntries_before_giving_up_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data) override	protocols::generalized_kinematic_closure::GeneralizedKIC	virtual
perturberlist_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
pick_pivots(core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< core::Size > &pivots)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
pivot_1_atmname_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
pivot_1_rsd_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
pivot_2_atmname_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
pivot_2_rsd_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
pivot_3_atmname_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
pivot_3_rsd_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
Pose typedef	protocols::moves::Mover
PoseCOP typedef	protocols::moves::Mover
pre_selection_mover_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
pre_selection_mover_exists_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
preselection_mover_exists() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inlineprivate
provide_citation_info(basic::citation_manager::CitationCollectionList &) const override	protocols::generalized_kinematic_closure::GeneralizedKIC	virtual
provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd)	protocols::generalized_kinematic_closure::GeneralizedKIC	static
prune_extra_atoms(utility::vector1< core::Size > &pivots)	protocols::generalized_kinematic_closure::GeneralizedKIC	private
register_options()	protocols::moves::Mover	inlinestatic
reinitialize_for_each_job() const	protocols::moves::Mover	virtual
reinitialize_for_new_input() const	protocols::moves::Mover	virtual
reset_status()	protocols::moves::Mover
rosettascripts_filter_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
rosettascripts_filter_exists_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
select_solution(core::pose::Pose const &pose, core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &torsions, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &bondangles, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &bondlengths, utility::vector1< core::Size > const &nsol_for_attempt, core::Size const total_solutions, utility::vector1< core::Real > const &energies_for_solution) const	protocols::generalized_kinematic_closure::GeneralizedKIC	private
selector_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
set_attach_boinc_ghost_observer(bool const setting)	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
set_build_ideal_geometry(bool const buildideal)	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
set_closure_attempts(core::Size const attempts)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_correct_polymer_dependent_atoms(bool const setting)	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
set_current_job(protocols::jobdist::BasicJobCOP job)	protocols::moves::Mover
set_current_tag(std::string const &new_tag)	protocols::moves::Mover	inlinevirtual
set_dont_fail_if_no_solution_found(bool const setting)	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
set_filter_attach_boinc_ghost_observer(core::Size const filter_index, bool const setting)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_filter_attach_boinc_ghost_observer(bool const setting)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_filter_bin(core::Size const filter_index, std::string const &name_in)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_filter_bin(std::string const &name_in)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_filter_rama_cutoff_energy(core::Size const filter_index, core::Real const &cutoff_energy)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_filter_rama_cutoff_energy(core::Real const &cutoff_energy)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_filter_resnum(core::Size const filter_index, core::Size const value)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_filter_resnum(core::Size const value)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_final_solution(core::pose::Pose &output_pose, core::Size const solution_index) const	protocols::generalized_kinematic_closure::GeneralizedKIC	private
set_final_solution(core::pose::Pose &pose, core::pose::Pose &looppose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &bondangles, utility::vector1< core::Real > const &bondlengths) const	protocols::generalized_kinematic_closure::GeneralizedKIC	private
set_input_pose(PoseCOP pose)	protocols::moves::Mover	virtual
set_last_move_status(MoverStatus status)	protocols::moves::Mover	protected
set_low_memory_mode(bool const setting)	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
set_min_solution_count(core::Size const count_in)	protocols::generalized_kinematic_closure::GeneralizedKIC	inline
set_native_pose(PoseCOP pose)	protocols::moves::Mover	virtual
set_ntries_before_giving_up(core::Size const ntries)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_attach_boinc_ghost_observer(core::Size const perturber_index, bool const setting)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_attach_boinc_ghost_observer(bool const setting)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_bin(core::Size const perturber_index, std::string const &bin)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_bin(std::string const &bin)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_custom_rama_table(core::Size const perturber_index, std::string const &table_name)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_custom_rama_table(core::Size const perturber_index, core::scoring::Rama_Table_Type const table_type)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_custom_rama_table(std::string const &table_name)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_custom_rama_table(core::scoring::Rama_Table_Type const table_type)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_effect(core::Size const perturber_index, perturber::perturber_effect const &effect)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_iterations(core::Size const perturber_index, core::Size const val)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_iterations(core::Size const val)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_must_switch_bins(core::Size const perturber_index, bool const val)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_perturber_must_switch_bins(bool const val)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_pivot_atoms(core::Size const rsd1, std::string const &at1, core::Size const rsd2, std::string const &at2, core::Size const rsd3, std::string const &at3)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_preselection_mover(protocols::moves::MoverOP mover)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_selector_kbt(core::Real const &kbt)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_selector_scorefunction(core::scoring::ScoreFunctionOP sfxn)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_selector_type(selector::selector_type const &stype)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_selector_type(std::string const &stypename)	protocols::generalized_kinematic_closure::GeneralizedKIC
set_type(std::string const &setting)	protocols::moves::Mover	inline
show(std::ostream &output=std::cout) const	protocols::moves::Mover	virtual
solutions_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
Strings typedef	protocols::moves::Mover
TagCOP typedef	protocols::moves::Mover
tailresidues_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
test_move(Pose &pose)	protocols::moves::Mover	inlinevirtual
total_stored_solutions() const	protocols::generalized_kinematic_closure::GeneralizedKIC	inlineprivate
type(const std::string &type_in)	protocols::moves::Mover	inline
type() const	protocols::moves::Mover	inline
upper_anchor_connID_	protocols::generalized_kinematic_closure::GeneralizedKIC	private
~GeneralizedKIC() override	protocols::generalized_kinematic_closure::GeneralizedKIC