Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::swa::rna::StepWiseRNA_JobParameters_Setup Class Reference

#include <StepWiseRNA_JobParameters_Setup.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_JobParameters_Setup:
Inheritance graph
[legend]
Collaboration diagram for protocols::swa::rna::StepWiseRNA_JobParameters_Setup:
Collaboration graph
[legend]

Public Member Functions

 StepWiseRNA_JobParameters_Setup (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 ~StepWiseRNA_JobParameters_Setup ()
 
virtual void apply ()
 
StepWiseRNA_JobParametersOPjob_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_jump_point_pair_list (utility::vector1< std::string > const &jump_point_pairs_string)
 
void set_rmsd_res_list (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_ribose_list (utility::vector1< core::Size > const &setting)
 
void set_force_south_ribose_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_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)
 

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_fold_tree ()
 
void figure_out_Prepend_Internal (core::Size const root_res, 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)
 
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_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

Size const moving_res_
 
utility::vector1< core::Size >
const 
moving_res_list_
 
utility::vector1< Size > const cutpoint_open_
 
utility::vector1< Sizeadded_cutpoint_closed_
 
utility::vector1< 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_
 
StepWiseRNA_JobParametersOP job_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_
 

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_JobParameters_Setup::StepWiseRNA_JobParameters_Setup ( 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 
)
protocols::swa::rna::StepWiseRNA_JobParameters_Setup::~StepWiseRNA_JobParameters_Setup ( )
virtual

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::apply ( )
virtual
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::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::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_best_working_alignment ( )
private
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_chain_boundaries ( )
private
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_cuts ( )
private

References cuts_, and job_parameters_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_gap_size_and_five_prime_chain_break_res ( )
private
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Is_prepend_map ( )
private
bool protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Is_residue_prepend ( core::Size const  seq_num) const
private
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_jump_partners ( )
private
InternalWorkingResidueParameter protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_partition_definition ( )
private
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Prepend_Internal ( core::Size const  root_res,
InternalWorkingResidueParameter const &  internal_params 
)
private
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_working_moving_suite ( )
private
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_working_sequence_and_mapping ( )
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_previously_closed_cutpoint_from_imported_silent_file ( ) const
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_user_input_alignment_res_list ( core::Size const  root_res)
private
core::Size protocols::swa::rna::StepWiseRNA_JobParameters_Setup::input_struct_definition ( core::Size const  working_seq_num)
private
StepWiseRNA_JobParametersOP & protocols::swa::rna::StepWiseRNA_JobParameters_Setup::job_parameters ( )

References job_parameters_.

core::Size protocols::swa::rna::StepWiseRNA_JobParameters_Setup::reroot_fold_tree ( core::Size const  fake_working_moving_suite)
private
core::Size protocols::swa::rna::StepWiseRNA_JobParameters_Setup::reroot_fold_tree_simple ( )
private
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_add_virt_res_as_root ( bool const  setting)

References job_parameters_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_alignment_res ( utility::vector1< std::string > const &  setting)
inline
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_allow_chain_boundary_jump_partner_right_at_fixed_BP ( bool const  setting)
inline
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_allow_fixed_res_at_moving_res ( bool const  setting)
inline
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_filter_user_alignment_res ( bool const  setting)
inline
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_fixed_res ( utility::vector1< core::Size > const &  fixed_res)
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_force_north_ribose_list ( utility::vector1< core::Size > const &  setting)

References job_parameters_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_force_south_ribose_list ( utility::vector1< core::Size > const &  setting)

References job_parameters_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_force_syn_chi_res_list ( utility::vector1< core::Size > const &  setting)

References job_parameters_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_global_sample_res_list ( utility::vector1< core::Size > const &  setting)

References job_parameters_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_input_tags ( utility::vector1< std::string > const &  setting)
inline

References input_tags_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_jump_point_pair_list ( utility::vector1< std::string > const &  jump_point_pairs_string)
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_native_alignment_res ( utility::vector1< Size > const &  native_alignment)
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_output_extra_RMSDs ( bool const  setting)

References job_parameters_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_protonated_H1_adenosine_list ( utility::vector1< core::Size > const &  setting)

References job_parameters_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_rmsd_res_list ( utility::vector1< core::Size > const &  setting)

References job_parameters_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_silent_files_in ( utility::vector1< std::string > const &  setting)
inline

References silent_files_in_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_simple_append_map ( bool const  setting)
inline

References simple_append_map_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_skip_complicated_stuff ( bool const  setting)
inline
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_terminal_res ( utility::vector1< core::Size > const &  terminal_res)
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_additional_cutpoint_closed ( )
private
void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_fold_tree ( )
private

Member Data Documentation

utility::vector1< Size > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::added_cutpoint_closed_
private
utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::alignment_res_string_list_
private
bool protocols::swa::rna::StepWiseRNA_JobParameters_Setup::allow_chain_boundary_jump_partner_right_at_fixed_BP_
private
bool protocols::swa::rna::StepWiseRNA_JobParameters_Setup::allow_fixed_res_at_moving_res_
private
utility::vector1< Size > const protocols::swa::rna::StepWiseRNA_JobParameters_Setup::cutpoint_open_
private
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::cuts_
private

Referenced by figure_out_cuts(), and setup_fold_tree().

bool protocols::swa::rna::StepWiseRNA_JobParameters_Setup::filter_user_alignment_res_
private
utility::vector1< Size > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::fixed_res_
private
utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::input_tags_
private
ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::is_cutpoint_
private
StepWiseRNA_JobParametersOP protocols::swa::rna::StepWiseRNA_JobParameters_Setup::job_parameters_
private
utility::vector1< std::pair< core::Size, core::Size > > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::jump_partners_
private
utility::vector1< std::pair< core::Size, core::Size > > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::jump_point_pair_list_
private
Size const protocols::swa::rna::StepWiseRNA_JobParameters_Setup::moving_res_
private
utility::vector1< core::Size > const protocols::swa::rna::StepWiseRNA_JobParameters_Setup::moving_res_list_
private
utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::silent_files_in_
private
bool protocols::swa::rna::StepWiseRNA_JobParameters_Setup::simple_append_map_
private
bool protocols::swa::rna::StepWiseRNA_JobParameters_Setup::skip_complicated_stuff_
private

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