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protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup Class Reference

#include <StepWiseRNA_WorkingParametersSetup.hh>

Inheritance diagram for protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup:
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Public Member Functions

 StepWiseWorkingParametersSetup (utility::vector1< core::Size > const &moving_res_list, std::string const &full_sequence, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &input_res2, utility::vector1< core::Size > const &cutpoint_open, core::Size const cutpoint_closed)
 
 ~StepWiseWorkingParametersSetup () override
 
virtual void apply ()
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersOPworking_parameters ()
 
void set_fixed_res (utility::vector1< core::Size > const &fixed_res)
 
void set_terminal_res (utility::vector1< core::Size > const &terminal_res)
 
void set_cutpoint_closed_list (utility::vector1< core::Size > const &setting)
 
void set_jump_point_pair_list (utility::vector1< std::string > const &jump_point_pairs_string)
 
void set_assert_jump_point_in_fixed_res (bool const setting)
 
void set_calc_rms_res (utility::vector1< core::Size > const &setting)
 
void set_alignment_res (utility::vector1< std::string > const &setting)
 
void set_filter_user_alignment_res (bool const setting)
 
void set_native_alignment_res (utility::vector1< core::Size > const &native_alignment)
 
void set_global_sample_res_list (utility::vector1< core::Size > const &setting)
 
void set_force_syn_chi_res_list (utility::vector1< core::Size > const &setting)
 
void set_force_anti_chi_res_list (utility::vector1< core::Size > const &setting)
 
void set_force_north_sugar_list (utility::vector1< core::Size > const &setting)
 
void set_force_south_sugar_list (utility::vector1< core::Size > const &setting)
 
void set_protonated_H1_adenosine_list (utility::vector1< core::Size > const &setting)
 
void set_output_extra_RMSDs (bool const setting)
 
void set_add_virt_res_as_root (bool const setting)
 
void set_floating_base (bool const setting)
 
void set_floating_base_anchor_res (core::Size const setting)
 
void set_rebuild_bulge_mode (bool const setting)
 
void set_sample_both_sugar_base_rotamer (bool const setting)
 
void set_input_tags (utility::vector1< std::string > const &setting)
 
void set_silent_files_in (utility::vector1< std::string > const &setting)
 
void set_allow_chain_boundary_jump_partner_right_at_fixed_BP (bool const setting)
 
void set_allow_fixed_res_at_moving_res (bool const setting)
 
void set_simple_append_map (bool const setting)
 
void set_skip_complicated_stuff (bool const setting)
 
void set_force_user_defined_jumps (bool const setting)
 
void set_force_internal (bool const setting)
 
void force_fold_tree (core::kinematics::FoldTree const &fold_tree)
 

Private Member Functions

void check_moving_res_in_chain (core::Size const &start_chain, core::Size const &end_chain, core::Size const &num_chains, core::Size &which_chain_has_moving_res)
 
void figure_out_working_sequence_and_mapping ()
 
void setup_additional_cutpoint_closed ()
 
void figure_out_chain_boundaries ()
 
void figure_out_jump_partners ()
 
void figure_out_cuts ()
 
void setup_floating_base_jump_to_anchor ()
 
void setup_fold_tree ()
 
void figure_out_prepend_internal (core::Size const root_res, stepwise::modeler::rna::InternalWorkingResidueParameter const &internal_params)
 
void figure_out_working_moving_suite ()
 
void figure_out_is_prepend_map ()
 
bool figure_out_is_residue_prepend (core::Size const seq_num) const
 
core::Size input_struct_definition (core::Size const working_seq_num)
 
stepwise::modeler::rna::InternalWorkingResidueParameter figure_out_partition_definition ()
 
void figure_out_gap_size_and_five_prime_chain_break_res ()
 
core::Size reroot_fold_tree (core::Size const fake_working_moving_suite)
 
core::Size reroot_fold_tree_simple ()
 
void figure_out_working_alignment (core::Size const &root_res)
 
void figure_out_best_working_alignment ()
 
utility::vector1< core::Sizeget_user_input_alignment_res_list (core::Size const root_res)
 
utility::vector1< core::Sizeget_previously_closed_cutpoint_from_imported_silent_file () const
 

Private Attributes

core::Size const moving_res_
 
utility::vector1< core::Size >
const 
moving_res_list_
 
utility::vector1< core::Size >
const 
cutpoint_open_
 
utility::vector1< core::Sizeadded_cutpoint_closed_
 
utility::vector1< core::Sizefixed_res_
 
ObjexxFCL::FArray1D< boolis_cutpoint_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
jump_point_pair_list_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
jump_partners_
 
utility::vector1< core::Sizecuts_
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP working_parameters_
 
utility::vector1< std::string > alignment_res_string_list_
 
bool filter_user_alignment_res_
 
utility::vector1< std::string > input_tags_
 
utility::vector1< std::string > silent_files_in_
 
bool allow_chain_boundary_jump_partner_right_at_fixed_BP_
 
bool allow_fixed_res_at_moving_res_
 
bool simple_append_map_
 
bool skip_complicated_stuff_
 
bool force_fold_tree_
 
bool force_user_defined_jumps_
 
bool force_internal_
 
bool assert_jump_point_in_fixed_res_
 

Constructor & Destructor Documentation

protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::StepWiseWorkingParametersSetup ( utility::vector1< core::Size > const &  moving_res_list,
std::string const &  full_sequence,
utility::vector1< core::Size > const &  input_res,
utility::vector1< core::Size > const &  input_res2,
utility::vector1< core::Size > const &  cutpoint_open,
core::Size const  cutpoint_closed 
)
protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::~StepWiseWorkingParametersSetup ( )
overridedefault

Member Function Documentation

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::apply ( )
virtual
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::check_moving_res_in_chain ( core::Size const &  start_chain,
core::Size const &  end_chain,
core::Size const &  num_chains,
core::Size which_chain_has_moving_res 
)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_best_working_alignment ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_chain_boundaries ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_cuts ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_gap_size_and_five_prime_chain_break_res ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_prepend_map ( )
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_residue_prepend ( core::Size const  seq_num) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_jump_partners ( )
private
stepwise::modeler::rna::InternalWorkingResidueParameter protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_prepend_internal ( core::Size const  root_res,
stepwise::modeler::rna::InternalWorkingResidueParameter const &  internal_params 
)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_working_alignment ( core::Size const &  root_res)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_working_moving_suite ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_working_sequence_and_mapping ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::force_fold_tree ( core::kinematics::FoldTree const &  fold_tree)
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_previously_closed_cutpoint_from_imported_silent_file ( ) const
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_user_input_alignment_res_list ( core::Size const  root_res)
private
core::Size protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::input_struct_definition ( core::Size const  working_seq_num)
private
core::Size protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree ( core::Size const  fake_working_moving_suite)
private
core::Size protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree_simple ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_add_virt_res_as_root ( bool const  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_alignment_res ( utility::vector1< std::string > const &  setting)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_allow_chain_boundary_jump_partner_right_at_fixed_BP ( bool const  setting)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_allow_fixed_res_at_moving_res ( bool const  setting)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_assert_jump_point_in_fixed_res ( bool const  setting)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_calc_rms_res ( utility::vector1< core::Size > const &  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_cutpoint_closed_list ( utility::vector1< core::Size > const &  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_filter_user_alignment_res ( bool const  setting)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_fixed_res ( utility::vector1< core::Size > const &  fixed_res)
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_floating_base ( bool const  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_floating_base_anchor_res ( core::Size const  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_anti_chi_res_list ( utility::vector1< core::Size > const &  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_internal ( bool const  setting)
inline

References force_internal_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_north_sugar_list ( utility::vector1< core::Size > const &  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_south_sugar_list ( utility::vector1< core::Size > const &  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_syn_chi_res_list ( utility::vector1< core::Size > const &  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_force_user_defined_jumps ( bool const  setting)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_global_sample_res_list ( utility::vector1< core::Size > const &  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_input_tags ( utility::vector1< std::string > const &  setting)
inline

References input_tags_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_jump_point_pair_list ( utility::vector1< std::string > const &  jump_point_pairs_string)
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_native_alignment_res ( utility::vector1< core::Size > const &  native_alignment)
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_output_extra_RMSDs ( bool const  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_protonated_H1_adenosine_list ( utility::vector1< core::Size > const &  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_rebuild_bulge_mode ( bool const  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_sample_both_sugar_base_rotamer ( bool const  setting)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_silent_files_in ( utility::vector1< std::string > const &  setting)
inline

References silent_files_in_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_simple_append_map ( bool const  setting)
inline

References simple_append_map_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_skip_complicated_stuff ( bool const  setting)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_terminal_res ( utility::vector1< core::Size > const &  terminal_res)

References working_parameters_.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_additional_cutpoint_closed ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_floating_base_jump_to_anchor ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree ( )
private
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP & protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::working_parameters ( )

References working_parameters_.

Member Data Documentation

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::added_cutpoint_closed_
private
utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::alignment_res_string_list_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::allow_chain_boundary_jump_partner_right_at_fixed_BP_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::allow_fixed_res_at_moving_res_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::assert_jump_point_in_fixed_res_
private
utility::vector1< core::Size > const protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::cutpoint_open_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::cuts_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::filter_user_alignment_res_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::fixed_res_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::force_fold_tree_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::force_internal_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::force_user_defined_jumps_
private
utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::input_tags_
private
ObjexxFCL::FArray1D< bool > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::is_cutpoint_
private
utility::vector1< std::pair < core::Size, core::Size > > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::jump_partners_
private
utility::vector1< std::pair < core::Size, core::Size > > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::jump_point_pair_list_
private
core::Size const protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::moving_res_
private
utility::vector1< core::Size > const protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::moving_res_list_
private
utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::silent_files_in_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::simple_append_map_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::skip_complicated_stuff_
private
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::working_parameters_
private

The documentation for this class was generated from the following files: