Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup Class Reference

#include <StepWiseRNA_WorkingParametersSetup.hh>

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, Size const &cutpoint_closed)
 
virtual ~StepWiseWorkingParametersSetup ()
 
virtual void apply ()
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP & working_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< 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_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 (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 (Size const &start_chain, Size const &end_chain, Size const &num_chains, 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 (Size const &root_res)
 
void figure_out_best_working_alignment ()
 
utility::vector1< core::Size > get_user_input_alignment_res_list (core::Size const root_res)
 
utility::vector1< core::Size > get_previously_closed_cutpoint_from_imported_silent_file () const
 

Private Attributes

Size const moving_res_
 
utility::vector1< core::Size >
const 		moving_res_list_
 
utility::vector1< Size > const cutpoint_open_
 
utility::vector1< Size > added_cutpoint_closed_
 
utility::vector1< Size > fixed_res_
 
ObjexxFCL::FArray1D< bool > is_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::Size > cuts_
 
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,
Size const &  cutpoint_closed 
)

References cutpoint_open_, figure_out_working_sequence_and_mapping(), is_cutpoint_, moving_res_, moving_res_list_, protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), size(), stepwise, protocols::TR, utility_exit_with_message, and working_parameters_.

protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::~StepWiseWorkingParametersSetup ( )
virtual

Member Function Documentation

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::apply ( )
virtual

References protocols::stepwise::modeler::rna::InternalWorkingResidueParameter::fake_working_moving_suite, figure_out_chain_boundaries(), figure_out_cuts(), figure_out_gap_size_and_five_prime_chain_break_res(), figure_out_is_prepend_map(), figure_out_jump_partners(), figure_out_partition_definition(), figure_out_prepend_internal(), figure_out_working_alignment(), filter_user_alignment_res_, force_fold_tree_, protocols::stepwise::modeler::rna::output_title_text(), reroot_fold_tree(), reroot_fold_tree_simple(), root_res, setup_additional_cutpoint_closed(), setup_floating_base_jump_to_anchor(), setup_fold_tree(), skip_complicated_stuff_, and protocols::TR.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::check_moving_res_in_chain ( Size const &  start_chain,
Size const &  end_chain,
Size const &  num_chains,
Size &  which_chain_has_moving_res 
)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_best_working_alignment ( )
private

References fold_tree, full_to_sub(), protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), core::kinematics::FoldTree::root(), protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by figure_out_working_alignment().

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_chain_boundaries ( )
private

References is_cutpoint_, nres, protocols::stepwise::modeler::rna::output_title_text(), protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_cuts ( )
private

References cuts_, full_to_sub(), and working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_gap_size_and_five_prime_chain_break_res ( )
private

References added_cutpoint_closed_, cutpoint_open_, full_to_sub(), GAP_SIZE_DUMMY, protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_prepend_map ( )
private

References calc_rms_res, figure_out_is_residue_prepend(), protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), simple_append_map_, protocols::TR, and working_parameters_.

Referenced by apply().

bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_residue_prepend ( core::Size const  seq_num) const
private

References allow_chain_boundary_jump_partner_right_at_fixed_BP_, exit, fixed_res_, fold_tree, full_to_sub(), utility::vector1< T, class >::has_value(), is_cutpoint_, jump_point_pair_list_, protocols::stepwise::legacy::modeler::rna::output_bool_list(), protocols::stepwise::modeler::rna::output_title_text(), protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by figure_out_is_prepend_map().

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_jump_partners ( )
private

References allow_chain_boundary_jump_partner_right_at_fixed_BP_, fixed_res_, force_user_defined_jumps_, full_to_sub(), utility::vector1< T, class >::has_value(), jump_partners_, jump_point_pair_list_, moving_res_, output_boolean(), protocols::stepwise::modeler::rna::output_title_text(), runtime_assert, protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by apply().

stepwise::modeler::rna::InternalWorkingResidueParameter protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition ( )
private

References protocols::stepwise::legacy::modeler::rna::check_can_append(), protocols::stepwise::legacy::modeler::rna::check_can_prepend(), protocols::stepwise::modeler::rna::InternalWorkingResidueParameter::fake_working_moving_suite, fold_tree, force_internal_, input_struct_definition(), core::kinematics::FoldTree::is_cutpoint(), nres, output_boolean(), protocols::stepwise::modeler::rna::output_seq_num_list(), core::kinematics::FoldTree::partition_by_residue(), protocols::stepwise::modeler::rna::InternalWorkingResidueParameter::possible_working_res_1, protocols::stepwise::modeler::rna::InternalWorkingResidueParameter::possible_working_res_2, skip_complicated_stuff_, protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_prepend_internal ( core::Size const  root_res,
stepwise::modeler::rna::InternalWorkingResidueParameter const &  internal_params 
)
private

References protocols::stepwise::legacy::modeler::rna::check_can_append(), protocols::stepwise::legacy::modeler::rna::check_can_prepend(), protocols::stepwise::modeler::rna::InternalWorkingResidueParameter::fake_working_moving_suite, fold_tree, force_internal_, nres, output_boolean(), protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), protocols::stepwise::modeler::rna::InternalWorkingResidueParameter::possible_working_res_1, protocols::stepwise::modeler::rna::InternalWorkingResidueParameter::possible_working_res_2, skip_complicated_stuff_, sub_to_full(), protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_working_alignment ( Size const &  root_res)
private

References figure_out_best_working_alignment(), get_user_input_alignment_res_list(), and working_parameters_.

Referenced by apply().

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

References full_to_sub(), MOVING_RES, moving_res_list_, nres, protocols::stepwise::modeler::rna::output_title_text(), protocols::TR, and working_parameters_.

Referenced by StepWiseWorkingParametersSetup().

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::force_fold_tree ( core::kinematics::FoldTree const &  fold_tree)

References force_fold_tree_, and working_parameters_.

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_previously_closed_cutpoint_from_imported_silent_file ( ) const
private

References core::conformation::Residue::has_variant_type(), protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file(), input_tags_, protocols::stepwise::modeler::rna::output_seq_num_list(), core::pose::Pose::residue(), silent_files_in_, core::pose::Pose::total_residue(), protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by setup_additional_cutpoint_closed().

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_user_input_alignment_res_list ( core::Size const  root_res)
private

References alignment_res, alignment_res_string_list_, protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(), protocols::stepwise::modeler::rna::apply_sub_to_full_mapping(), filter_user_alignment_res_, fixed_res_, utility::vector1< T, class >::has_value(), output_boolean(), protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), string_to_int(), protocols::stepwise::modeler::rna::tokenize(), protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by figure_out_working_alignment().

core::Size protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::input_struct_definition ( core::Size const  working_seq_num)
private

References has_value(), sub_to_full(), protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by figure_out_partition_definition().

core::Size protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree ( core::Size const  fake_working_moving_suite)
private

References fold_tree, force_fold_tree_, nres, protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(), protocols::stepwise::modeler::rna::output_title_text(), core::kinematics::FoldTree::possible_root(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::root(), root_res, runtime_assert, sub_to_full(), protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by apply().

core::Size protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree_simple ( )
private

References fold_tree, core::kinematics::FoldTree::possible_root(), core::kinematics::FoldTree::reorder(), and working_parameters_.

Referenced by apply().

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

References alignment_res_string_list_.

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

References allow_chain_boundary_jump_partner_right_at_fixed_BP_.

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

References allow_fixed_res_at_moving_res_.

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

References assert_jump_point_in_fixed_res_.

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

References filter_user_alignment_res_.

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

References allow_fixed_res_at_moving_res_, protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(), fixed_res_, utility::vector1< T, class >::has_value(), moving_res_list_, output_boolean(), protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), protocols::TR, and working_parameters_.

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 ( 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 force_north_sugar_list, and working_parameters_.

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

References force_south_sugar_list, and working_parameters_.

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

References force_syn_chi_res_list, and working_parameters_.

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

References force_user_defined_jumps_.

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

References global_sample_res_list, and 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)

References assert_jump_point_in_fixed_res_, fixed_res_, utility::vector1< T, class >::has_value(), jump_point_pair_list_, output_boolean(), protocols::stepwise::legacy::modeler::rna::output_pair_size(), runtime_assert, protocols::stepwise::legacy::modeler::rna::sort_pair_list(), string_to_int(), protocols::stepwise::modeler::rna::tokenize(), protocols::TR, and utility_exit_with_message.

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_native_alignment_res ( utility::vector1< Size > const &  native_alignment)

References protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(), protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), protocols::TR, and working_parameters_.

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 protonated_H1_adenosine_list, and 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

References skip_complicated_stuff_.

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

References added_cutpoint_closed_, fixed_res_, get_previously_closed_cutpoint_from_imported_silent_file(), utility::vector1< T, class >::has_value(), is_cutpoint_, jump_point_pair_list_, moving_res_, nres, protocols::stepwise::legacy::modeler::rna::output_bool_list(), protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::legacy::modeler::rna::output_size_list(), protocols::stepwise::modeler::rna::output_title_text(), protocols::TR, utility_exit_with_message, and working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_floating_base_jump_to_anchor ( )
private

References cuts_, full_to_sub(), is_cutpoint_, jump_partners_, jump_point_pair_list_, runtime_assert, protocols::TR, and working_parameters_.

Referenced by apply().

void protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree ( )
private

References cuts_, core::kinematics::FoldTree::downstream_jump_residue(), fold_tree, full_to_sub(), jump_partners_, moving_res_, nres, core::kinematics::FoldTree::num_cutpoint(), protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(), protocols::stepwise::modeler::rna::output_title_text(), root_res, runtime_assert, core::kinematics::FoldTree::set_jump_atoms(), protocols::TR, core::kinematics::FoldTree::tree_from_jumps_and_cuts(), core::kinematics::FoldTree::upstream_jump_residue(), utility_exit_with_message, and working_parameters_.

Referenced by apply().

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP & protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::working_parameters ( )

References working_parameters_.

Member Data Documentation

utility::vector1< Size > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::added_cutpoint_closed_
private

Referenced by figure_out_gap_size_and_five_prime_chain_break_res(), and setup_additional_cutpoint_closed().

utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::alignment_res_string_list_
private

Referenced by get_user_input_alignment_res_list(), and set_alignment_res().

bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::allow_chain_boundary_jump_partner_right_at_fixed_BP_
private

Referenced by figure_out_is_residue_prepend(), figure_out_jump_partners(), and set_allow_chain_boundary_jump_partner_right_at_fixed_BP().

bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::allow_fixed_res_at_moving_res_
private

Referenced by set_allow_fixed_res_at_moving_res(), and set_fixed_res().

bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::assert_jump_point_in_fixed_res_
private

Referenced by set_assert_jump_point_in_fixed_res(), and set_jump_point_pair_list().

utility::vector1< Size > const protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::cutpoint_open_
private

Referenced by figure_out_gap_size_and_five_prime_chain_break_res(), and StepWiseWorkingParametersSetup().

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::cuts_
private

Referenced by figure_out_cuts(), setup_floating_base_jump_to_anchor(), and setup_fold_tree().

bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::filter_user_alignment_res_
private

Referenced by apply(), get_user_input_alignment_res_list(), and set_filter_user_alignment_res().

utility::vector1< Size > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::fixed_res_
private

Referenced by figure_out_is_residue_prepend(), figure_out_jump_partners(), get_user_input_alignment_res_list(), set_fixed_res(), set_jump_point_pair_list(), and setup_additional_cutpoint_closed().

bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::force_fold_tree_
private

Referenced by apply(), force_fold_tree(), and reroot_fold_tree().

bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::force_internal_
private

Referenced by figure_out_partition_definition(), figure_out_prepend_internal(), and set_force_internal().

bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::force_user_defined_jumps_
private

Referenced by figure_out_jump_partners(), and set_force_user_defined_jumps().

utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::input_tags_
private

Referenced by get_previously_closed_cutpoint_from_imported_silent_file(), and set_input_tags().

ObjexxFCL::FArray1D< bool > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::is_cutpoint_
private

Referenced by figure_out_chain_boundaries(), figure_out_is_residue_prepend(), setup_additional_cutpoint_closed(), setup_floating_base_jump_to_anchor(), and StepWiseWorkingParametersSetup().

utility::vector1< std::pair < core::Size, core::Size > > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::jump_partners_
private

Referenced by figure_out_jump_partners(), setup_floating_base_jump_to_anchor(), and setup_fold_tree().

utility::vector1< std::pair < core::Size, core::Size > > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::jump_point_pair_list_
private

Referenced by figure_out_is_residue_prepend(), figure_out_jump_partners(), set_jump_point_pair_list(), setup_additional_cutpoint_closed(), and setup_floating_base_jump_to_anchor().

Size const protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::moving_res_
private

Referenced by figure_out_jump_partners(), setup_additional_cutpoint_closed(), setup_fold_tree(), and StepWiseWorkingParametersSetup().

utility::vector1< core::Size > const protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::moving_res_list_
private

Referenced by figure_out_working_sequence_and_mapping(), set_fixed_res(), and StepWiseWorkingParametersSetup().

utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::silent_files_in_
private

Referenced by get_previously_closed_cutpoint_from_imported_silent_file(), and set_silent_files_in().

bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::simple_append_map_
private

Referenced by figure_out_is_prepend_map(), and set_simple_append_map().

bool protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::skip_complicated_stuff_
private

Referenced by apply(), figure_out_partition_definition(), figure_out_prepend_internal(), and set_skip_complicated_stuff().

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::working_parameters_
private

Referenced by figure_out_best_working_alignment(), figure_out_chain_boundaries(), figure_out_cuts(), figure_out_gap_size_and_five_prime_chain_break_res(), figure_out_is_prepend_map(), figure_out_is_residue_prepend(), figure_out_jump_partners(), figure_out_partition_definition(), figure_out_prepend_internal(), figure_out_working_alignment(), figure_out_working_sequence_and_mapping(), force_fold_tree(), get_previously_closed_cutpoint_from_imported_silent_file(), get_user_input_alignment_res_list(), input_struct_definition(), reroot_fold_tree(), reroot_fold_tree_simple(), set_add_virt_res_as_root(), set_calc_rms_res(), set_cutpoint_closed_list(), set_fixed_res(), set_floating_base(), set_floating_base_anchor_res(), set_force_north_sugar_list(), set_force_south_sugar_list(), set_force_syn_chi_res_list(), set_global_sample_res_list(), set_native_alignment_res(), set_output_extra_RMSDs(), set_protonated_H1_adenosine_list(), set_rebuild_bulge_mode(), set_sample_both_sugar_base_rotamer(), set_terminal_res(), setup_additional_cutpoint_closed(), setup_floating_base_jump_to_anchor(), setup_fold_tree(), StepWiseWorkingParametersSetup(), and working_parameters().

The documentation for this class was generated from the following files:
Generated on Wed Sep 10 2014 11:46:31 for Rosetta Protocols by   doxygen 1.8.7