protocols::swa::rna::StepWiseRNA_JobParameters_Setup Class Reference

#include <StepWiseRNA_JobParameters_Setup.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_JobParameters_Setup:

Collaboration diagram for protocols::swa::rna::StepWiseRNA_JobParameters_Setup:

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_JobParametersOP &	job_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::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_
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
	)

References cutpoint_open_, figure_out_working_sequence_and_mapping(), is_cutpoint_, job_parameters_, moving_res_, moving_res_list_, protocols::swa::rna::Output_seq_num_list(), and protocols::swa::rna::Output_title_text().

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

virtual

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::apply ( )

virtual

References protocols::swa::rna::InternalWorkingResidueParameter::fake_working_moving_suite, 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_jump_partners(), figure_out_partition_definition(), figure_out_Prepend_Internal(), filter_user_alignment_res_, get_user_input_alignment_res_list(), job_parameters_, protocols::swa::rna::Output_title_text(), reroot_fold_tree(), reroot_fold_tree_simple(), setup_additional_cutpoint_closed(), setup_fold_tree(), and skip_complicated_stuff_.

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

References job_parameters_, protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), and core::kinematics::FoldTree::root().

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_chain_boundaries ( )

private

References is_cutpoint_, job_parameters_, and protocols::swa::rna::Output_title_text().

Referenced by apply().

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

References added_cutpoint_closed_, cutpoint_open_, and job_parameters_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Is_prepend_map ( )

private

References figure_out_Is_residue_prepend(), job_parameters_, protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), and simple_append_map_.

Referenced by apply().

bool protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Is_residue_prepend ( core::Size const  seq_num) const

private

References allow_chain_boundary_jump_partner_right_at_fixed_BP_, protocols::swa::rna::Contain_seq_num(), fixed_res_, is_cutpoint_, job_parameters_, jump_point_pair_list_, and protocols::swa::rna::Output_bool_list().

Referenced by figure_out_Is_prepend_map().

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_jump_partners ( )

private

References allow_chain_boundary_jump_partner_right_at_fixed_BP_, protocols::swa::rna::Contain_seq_num(), fixed_res_, job_parameters_, jump_partners_, jump_point_pair_list_, moving_res_, protocols::swa::rna::Output_boolean(), and protocols::swa::rna::Output_title_text().

Referenced by apply().

InternalWorkingResidueParameter protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_partition_definition ( )

private

References protocols::swa::rna::assert_can_append(), protocols::swa::rna::assert_can_prepend(), protocols::swa::rna::InternalWorkingResidueParameter::fake_working_moving_suite, input_struct_definition(), core::kinematics::FoldTree::is_cutpoint(), job_parameters_, protocols::swa::rna::make_cut_at_moving_suite(), protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_seq_num_list(), core::kinematics::FoldTree::partition_by_jump(), protocols::swa::rna::InternalWorkingResidueParameter::possible_working_res_1, protocols::swa::rna::InternalWorkingResidueParameter::possible_working_res_2, and skip_complicated_stuff_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Prepend_Internal ( core::Size const  root_res, InternalWorkingResidueParameter const &  internal_params  )

private

References protocols::swa::rna::assert_can_append(), protocols::swa::rna::assert_can_prepend(), protocols::swa::rna::InternalWorkingResidueParameter::fake_working_moving_suite, job_parameters_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), protocols::swa::rna::InternalWorkingResidueParameter::possible_working_res_1, protocols::swa::rna::InternalWorkingResidueParameter::possible_working_res_2, and skip_complicated_stuff_.

Referenced by apply().

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

References job_parameters_, moving_res_list_, and protocols::swa::rna::Output_title_text().

Referenced by StepWiseRNA_JobParameters_Setup().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_previously_closed_cutpoint_from_imported_silent_file ( ) const

private

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), protocols::swa::rna::import_pose_from_silent_file(), input_tags_, job_parameters_, protocols::swa::rna::Output_seq_num_list(), core::pose::Pose::residue(), silent_files_in_, and core::pose::Pose::total_residue().

Referenced by setup_additional_cutpoint_closed().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_user_input_alignment_res_list ( core::Size const  root_res)

private

References alignment_res_string_list_, protocols::swa::rna::apply_full_to_sub_mapping(), protocols::swa::rna::apply_sub_to_full_mapping(), protocols::swa::rna::Contain_seq_num(), filter_user_alignment_res_, fixed_res_, job_parameters_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), protocols::swa::rna::string_to_int(), and protocols::swa::rna::Tokenize().

Referenced by apply().

core::Size protocols::swa::rna::StepWiseRNA_JobParameters_Setup::input_struct_definition ( core::Size const  working_seq_num)

private

References protocols::swa::rna::Contain_seq_num(), and job_parameters_.

Referenced by figure_out_partition_definition().

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

References job_parameters_, protocols::swa::rna::Output_fold_tree_info(), protocols::swa::rna::Output_title_text(), protocols::swa::rna::possible_root(), core::kinematics::FoldTree::reorder(), and core::kinematics::FoldTree::root().

Referenced by apply().

core::Size protocols::swa::rna::StepWiseRNA_JobParameters_Setup::reroot_fold_tree_simple ( )

private

References job_parameters_, protocols::swa::rna::possible_root(), and core::kinematics::FoldTree::reorder().

Referenced by apply().

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

References alignment_res_string_list_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::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::swa::rna::StepWiseRNA_JobParameters_Setup::set_allow_fixed_res_at_moving_res ( bool const  setting)

inline

References allow_fixed_res_at_moving_res_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_filter_user_alignment_res ( bool const  setting)

inline

References filter_user_alignment_res_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_fixed_res

(

utility::vector1< core::Size > const &

fixed_res)

References allow_fixed_res_at_moving_res_, protocols::swa::rna::apply_full_to_sub_mapping(), protocols::swa::rna::Contain_seq_num(), fixed_res_, job_parameters_, moving_res_list_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_seq_num_list(), and protocols::swa::rna::Output_title_text().

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)

References protocols::swa::rna::Contain_seq_num(), fixed_res_, jump_point_pair_list_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::output_pair_size(), protocols::swa::rna::output_pair_size_vector(), protocols::swa::rna::Sort_pair_list(), protocols::swa::rna::string_to_int(), and protocols::swa::rna::Tokenize().

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_native_alignment_res

(

utility::vector1< Size > const &

native_alignment)

References protocols::swa::rna::apply_full_to_sub_mapping(), job_parameters_, protocols::swa::rna::Output_seq_num_list(), and protocols::swa::rna::Output_title_text().

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

References skip_complicated_stuff_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_terminal_res

(

utility::vector1< core::Size > const &

terminal_res)

References protocols::swa::rna::apply_full_to_sub_mapping(), and job_parameters_.

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_additional_cutpoint_closed ( )

private

References added_cutpoint_closed_, protocols::swa::rna::Contain_seq_num(), fixed_res_, get_previously_closed_cutpoint_from_imported_silent_file(), is_cutpoint_, job_parameters_, jump_point_pair_list_, moving_res_, protocols::swa::rna::Output_bool_list(), protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_size_list(), and protocols::swa::rna::Output_title_text().

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_fold_tree ( )

private

References cuts_, core::kinematics::FoldTree::downstream_jump_residue(), job_parameters_, jump_partners_, moving_res_, core::kinematics::FoldTree::num_cutpoint(), protocols::swa::rna::Output_fold_tree_info(), protocols::swa::rna::Output_title_text(), core::kinematics::FoldTree::set_jump_atoms(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by apply().

Member Data Documentation

utility::vector1< Size > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::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::swa::rna::StepWiseRNA_JobParameters_Setup::alignment_res_string_list_

private

Referenced by get_user_input_alignment_res_list(), and set_alignment_res().

bool protocols::swa::rna::StepWiseRNA_JobParameters_Setup::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::swa::rna::StepWiseRNA_JobParameters_Setup::allow_fixed_res_at_moving_res_

private

Referenced by set_allow_fixed_res_at_moving_res(), and set_fixed_res().

utility::vector1< Size > const protocols::swa::rna::StepWiseRNA_JobParameters_Setup::cutpoint_open_

private

Referenced by figure_out_gap_size_and_five_prime_chain_break_res(), and StepWiseRNA_JobParameters_Setup().

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

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

utility::vector1< Size > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::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().

utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::input_tags_

private

Referenced by get_previously_closed_cutpoint_from_imported_silent_file(), and set_input_tags().

ObjexxFCL::FArray1D< bool > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::is_cutpoint_

private

Referenced by figure_out_chain_boundaries(), figure_out_Is_residue_prepend(), setup_additional_cutpoint_closed(), and StepWiseRNA_JobParameters_Setup().

StepWiseRNA_JobParametersOP protocols::swa::rna::StepWiseRNA_JobParameters_Setup::job_parameters_

private

Referenced by apply(), 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_sequence_and_mapping(), get_previously_closed_cutpoint_from_imported_silent_file(), get_user_input_alignment_res_list(), input_struct_definition(), job_parameters(), reroot_fold_tree(), reroot_fold_tree_simple(), set_add_virt_res_as_root(), set_fixed_res(), set_force_north_ribose_list(), set_force_south_ribose_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_rmsd_res_list(), set_terminal_res(), setup_additional_cutpoint_closed(), setup_fold_tree(), and StepWiseRNA_JobParameters_Setup().

utility::vector1< std::pair< core::Size, core::Size > > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::jump_partners_

private

Referenced by figure_out_jump_partners(), and setup_fold_tree().

utility::vector1< std::pair< core::Size, core::Size > > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::jump_point_pair_list_

private

Referenced by figure_out_Is_residue_prepend(), figure_out_jump_partners(), set_jump_point_pair_list(), and setup_additional_cutpoint_closed().

Size const protocols::swa::rna::StepWiseRNA_JobParameters_Setup::moving_res_

private

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

utility::vector1< core::Size > const protocols::swa::rna::StepWiseRNA_JobParameters_Setup::moving_res_list_

private

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

utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_JobParameters_Setup::silent_files_in_

private

Referenced by get_previously_closed_cutpoint_from_imported_silent_file(), and set_silent_files_in().

bool protocols::swa::rna::StepWiseRNA_JobParameters_Setup::simple_append_map_

private

Referenced by figure_out_Is_prepend_map(), and set_simple_append_map().

bool protocols::swa::rna::StepWiseRNA_JobParameters_Setup::skip_complicated_stuff_

private

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

---

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

• src/protocols/swa/rna/StepWiseRNA_JobParameters_Setup.hh
• src/protocols/swa/rna/StepWiseRNA_JobParameters_Setup.cc