#include <StepWiseRNA_PoseSetup.hh>

Inheritance diagram for protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup:

[legend]

Public Member Functions
	StepWiseRNA_PoseSetup (stepwise::modeler::working_parameters::StepWiseWorkingParametersOP &working_parameters)

	~StepWiseRNA_PoseSetup () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	set_input_tags (utility::vector1< std::string > const &setting)

void	set_silent_files_in (utility::vector1< std::string > const &setting)

void	set_bulge_res (utility::vector1< core::Size > const &bulge_res)

void	set_virtual_res (utility::vector1< core::Size > const &virtual_res_list)

void	set_native_virtual_res (utility::vector1< core::Size > const &native_virtual_res_list)

void	set_copy_DOF (bool const setting)

void	set_verbose (bool const setting)

void	setup_native_pose (core::pose::Pose &pose)

void	set_output_pdb (bool const setting)

void	set_apply_virtual_res_variant_at_dinucleotide (bool const setting)

void	set_align_to_native (bool const setting)

void	set_use_phenix_geo (bool const setting)

void	update_fold_tree_at_virtual_sugars (core::pose::Pose &pose)

void	setup_full_model_info (core::pose::Pose &pose) const

void	setup_vdw_cached_rep_screen_info (core::pose::Pose &pose) const

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	Import_pose (core::Size const &i, core::pose::Pose &import_pose) const

void	make_extended_pose (core::pose::Pose &pose)

void	create_starting_pose (core::pose::Pose &pose)

void	create_pose_from_input_poses (core::pose::Pose &pose)

void	read_input_pose_and_copy_dofs (core::pose::Pose &pose)

void	apply_cutpoint_variants (core::pose::Pose &pose)

void	apply_bulge_variants (core::pose::Pose &pose) const

void	apply_virtual_phosphate_variants (core::pose::Pose &pose) const

void	add_terminal_res_repulsion (core::pose::Pose &pose) const

void	additional_setup_for_floating_base (core::pose::Pose &pose) const

void	instantiate_residue_if_rebuilding_bulge (core::pose::Pose &pose)

void	virtualize_sugar_and_backbone_at_moving_res (core::pose::Pose &pose) const

void	apply_virtual_res_variant (core::pose::Pose &pose) const

void	do_checks_and_apply_protonated_H1_adenosine_variant (core::pose::Pose &pose, core::pose::Pose const &start_pose_with_variant, core::Size const &n, core::Size const &i, utility::vector1< core::Size > const &input_res, std::map< core::Size, core::Size > &full_to_sub)

void	correctly_copy_HO2prime_positions (core::pose::Pose &full_pose, utility::vector1< core::pose::Pose > const &start_pose_list)

core::Real	get_nearest_dist_to_O2prime (core::Size const O2prime_seq_num, core::pose::Pose const &input_pose, utility::vector1< core::Size > const &input_res_list, utility::vector1< core::Size > const &common_res_list)

void	add_protonated_H1_adenosine_variants (core::pose::Pose &pose) const

void	verify_protonated_H1_adenosine_variants (core::pose::Pose &pose) const

void	add_aa_virt_rsd_as_root (core::pose::Pose &pose)

Private Attributes
core::chemical::ResidueTypeSetCAP	rsd_set_

utility::vector1< std::string >	input_tags_

utility::vector1< std::string >	silent_files_in_

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP	working_parameters_

bool	copy_DOF_

bool	verbose_

utility::vector1< core::Size >	bulge_res_

utility::vector1< core::Size >	virtual_res_list_

utility::vector1< core::Size >	native_virtual_res_list_

bool	output_pdb_

bool	apply_virtual_res_variant_at_dinucleotide_

bool	align_to_native_

bool	use_phenix_geo_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

◆ StepWiseRNA_PoseSetup()

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

◆ ~StepWiseRNA_PoseSetup()

protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::~StepWiseRNA_PoseSetup ( )

overridedefault

Member Function Documentation

◆ add_aa_virt_rsd_as_root()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root ( core::pose::Pose & pose )

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), protocols::TR(), core::pose::virtual_type_for_pose(), and working_parameters_.

Referenced by apply(), and setup_native_pose().

◆ add_protonated_H1_adenosine_variants()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_protonated_H1_adenosine_variants ( core::pose::Pose & pose ) const

private

References protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), protocols::TR(), and working_parameters_.

Referenced by apply(), and setup_native_pose().

◆ add_terminal_res_repulsion()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion ( core::pose::Pose & pose ) const

private

References core::pose::Pose::constraint_set(), core::chemical::rna::first_base_atom_index(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), protocols::stepwise::modeler::rna::output_seq_num_list(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), protocols::TR(), core::chemical::VIRTUAL_RNA_RESIDUE, working_parameters_, and core::pose::Pose::xyz().

Referenced by apply().

◆ additional_setup_for_floating_base()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::additional_setup_for_floating_base ( core::pose::Pose & pose ) const

private

References protocols::stepwise::legacy::modeler::rna::setup_chain_break_jump_point(), virtualize_sugar_and_backbone_at_moving_res(), and working_parameters_.

Referenced by apply().

◆ apply()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply ( core::pose::Pose & )

overridevirtual

◆ apply_bulge_variants()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_bulge_variants ( core::pose::Pose & pose ) const

private

References core::pose::add_variant_type_to_pose_residue(), protocols::stepwise::modeler::rna::apply_sub_to_full_mapping(), core::chemical::BULGE, bulge_res_, core::pose::full_model_info::full_to_sub(), and working_parameters_.

Referenced by apply().

◆ apply_cutpoint_variants()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants ( core::pose::Pose & pose )

private

References core::id::BB, core::pose::correctly_add_cutpoint_variants(), core::pose::Pose::fold_tree(), core::pose::full_model_info::full_to_sub(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), protocols::stepwise::legacy::modeler::rna::print_backbone_torsions(), core::pose::Pose::set_torsion(), protocols::antibody::simple_fold_tree(), core::pose::Pose::size(), core::pose::Pose::torsion(), protocols::TR(), verbose_, and working_parameters_.

Referenced by apply(), and setup_native_pose().

◆ apply_virtual_phosphate_variants()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants ( core::pose::Pose & pose ) const

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_UPPER, core::pose::full_model_info::full_to_sub(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::type(), core::chemical::VIRTUAL_PHOSPHATE, and working_parameters_.

Referenced by apply().

◆ apply_virtual_res_variant()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant ( core::pose::Pose & pose ) const

private

References protocols::stepwise::modeler::rna::apply_sub_to_full_mapping(), apply_virtual_res_variant_at_dinucleotide_, core::pose::rna::apply_virtual_rna_residue_variant_type(), core::pose::full_model_info::full_to_sub(), core::pose::rna::output_boolean(), protocols::TR(), virtual_res_list_, and working_parameters_.

Referenced by apply().

◆ correctly_copy_HO2prime_positions()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2prime_positions	(	core::pose::Pose &	full_pose,
		utility::vector1< core::pose::Pose > const &	start_pose_list
	)

private

References core::chemical::rna::CHI, protocols::stepwise::modeler::rna::create_full_to_input_res_map(), core::pose::Pose::dump_pdb(), core::pose::full_model_info::full_to_sub(), get_nearest_dist_to_O2prime(), output_pdb_, protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), core::pose::Pose::set_torsion(), protocols::TR(), verbose_, and working_parameters_.

Referenced by read_input_pose_and_copy_dofs().

◆ create_pose_from_input_poses()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::create_pose_from_input_poses ( core::pose::Pose & pose )

private

References core::pose::Pose::fold_tree(), make_extended_pose(), read_input_pose_and_copy_dofs(), protocols::TR(), and working_parameters_.

Referenced by create_starting_pose().

◆ create_starting_pose()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::create_starting_pose ( core::pose::Pose & pose )

private

References copy_DOF_, create_pose_from_input_poses(), core::pose::Pose::fold_tree(), and working_parameters_.

Referenced by apply().

◆ do_checks_and_apply_protonated_H1_adenosine_variant()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant	(	core::pose::Pose &	pose,
		core::pose::Pose const &	start_pose_with_variant,
		core::Size const &	n,
		core::Size const &	i,
		utility::vector1< core::Size > const &	input_res,
		std::map< core::Size, core::Size > &	full_to_sub
	)

private

References core::conformation::Residue::aa(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::pose::full_model_info::full_to_sub(), core::conformation::Residue::has_variant_type(), core::chemical::na_rad, core::chemical::PROTONATED_N1, core::pose::Pose::residue(), silent_files_in_, and working_parameters_.

Referenced by read_input_pose_and_copy_dofs().

◆ get_name()

std::string protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

◆ get_nearest_dist_to_O2prime()

core::Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2prime	(	core::Size const	O2prime_seq_num,
		core::pose::Pose const &	input_pose,
		utility::vector1< core::Size > const &	input_res_list,
		utility::vector1< core::Size > const &	common_res_list
	)

private

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by correctly_copy_HO2prime_positions().

◆ Import_pose()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::Import_pose	(	core::Size const &	i,
		core::pose::Pose &	import_pose
	)		const

private

References copy_DOF_, protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file(), input_tags_, core::pose::rna::make_phosphate_nomenclature_matches_mini(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::pose::rna::remove_bracketed(), rsd_set_, core::pose::Pose::sequence(), silent_files_in_, core::pose::Pose::size(), protocols::TR(), and working_parameters_.

Referenced by read_input_pose_and_copy_dofs().

◆ instantiate_residue_if_rebuilding_bulge()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::instantiate_residue_if_rebuilding_bulge ( core::pose::Pose & pose )

private

References core::pose::rna::remove_virtual_rna_residue_variant_type(), and working_parameters_.

Referenced by apply().

◆ make_extended_pose()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::make_extended_pose ( core::pose::Pose & pose )

private

References core::pose::Pose::dump_pdb(), core::pose::make_pose_from_sequence(), output_pdb_, rsd_set_, protocols::TR(), and working_parameters_.

Referenced by create_pose_from_input_poses().

◆ read_input_pose_and_copy_dofs()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs ( core::pose::Pose & pose )

private

References core::pose::add_variant_type_to_pose_residue(), protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(), core::pose::rna::apply_virtual_rna_residue_variant_type(), core::pose::rna::assert_phosphate_nomenclature_matches_mini(), core::chemical::BULGE, copy_DOF_, core::pose::copydofs::copy_dofs_match_atom_names(), correctly_copy_HO2prime_positions(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, do_checks_and_apply_protonated_H1_adenosine_variant(), core::pose::Pose::dump_pdb(), core::chemical::FIVE_PRIME_END_OH, core::chemical::FIVE_PRIME_END_PHOSPHATE, core::pose::Pose::fold_tree(), core::pose::full_model_info::full_to_sub(), core::conformation::Residue::has_variant_type(), core::pose::rna::has_virtual_rna_residue_variant_type(), Import_pose(), input_tags_, output_pdb_, core::chemical::PROTONATED_N1, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), core::chemical::THREE_PRIME_END_OH, protocols::TR(), core::chemical::VIRTUAL_O2PRIME_HYDROGEN, core::chemical::VIRTUAL_PHOSPHATE, core::chemical::VIRTUAL_RIBOSE, core::chemical::VIRTUAL_RNA_RESIDUE, and working_parameters_.

Referenced by create_pose_from_input_poses().

◆ set_align_to_native()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_align_to_native ( bool const setting )

inline

References align_to_native_.

◆ set_apply_virtual_res_variant_at_dinucleotide()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_apply_virtual_res_variant_at_dinucleotide ( bool const setting )

inline

References apply_virtual_res_variant_at_dinucleotide_.

◆ set_bulge_res()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_bulge_res ( utility::vector1< core::Size > const & bulge_res )

inline

References bulge_res_.

◆ set_copy_DOF()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_copy_DOF ( bool const setting )

inline

References copy_DOF_.

◆ set_input_tags()

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

inline

References input_tags_.

◆ set_native_virtual_res()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_native_virtual_res ( utility::vector1< core::Size > const & native_virtual_res_list )

inline

References native_virtual_res_list_.

◆ set_output_pdb()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_output_pdb ( bool const setting )

inline

References output_pdb_.

◆ set_silent_files_in()

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

inline

References silent_files_in_.

◆ set_use_phenix_geo()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_use_phenix_geo ( bool const setting )

inline

References use_phenix_geo_.

◆ set_verbose()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_verbose ( bool const setting )

inline

References verbose_.

◆ set_virtual_res()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_virtual_res ( utility::vector1< core::Size > const & virtual_res_list )

inline

References virtual_res_list_.

◆ setup_full_model_info()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_full_model_info ( core::pose::Pose & pose ) const

Referenced by apply(), and setup_native_pose().

◆ setup_native_pose()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose ( core::pose::Pose & pose )

References add_aa_virt_rsd_as_root(), add_protonated_H1_adenosine_variants(), protocols::stepwise::modeler::rna::align_poses(), align_to_native_, apply_cutpoint_variants(), protocols::stepwise::modeler::rna::apply_full_to_sub_mapping(), core::pose::rna::apply_virtual_rna_residue_variant_type(), core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::pose::Pose::dump_pdb(), core::pose::Pose::fold_tree(), protocols::moves::Mover::get_native_pose(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), native_virtual_res_list_, output_pdb_, protocols::stepwise::modeler::rna::output_seq_num_list(), protocols::stepwise::modeler::rna::output_title_text(), core::pose::rna::remove_bracketed(), core::pose::Pose::sequence(), setup_full_model_info(), core::pose::Pose::size(), protocols::TR(), verbose_, verify_protonated_H1_adenosine_variants(), and working_parameters_.

◆ setup_vdw_cached_rep_screen_info()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_vdw_cached_rep_screen_info ( core::pose::Pose & pose ) const

References protocols::scoring::fill_vdw_cached_rep_screen_info_from_command_line().

Referenced by apply().

◆ update_fold_tree_at_virtual_sugars()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::update_fold_tree_at_virtual_sugars ( core::pose::Pose & pose )

References core::pose::Pose::fold_tree(), protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_without_fold_tree(), core::kinematics::FoldTree::jump_exists(), protocols::stepwise::legacy::modeler::rna::setup_chain_break_jump_point(), protocols::TR(), and working_parameters_.

Referenced by apply().

◆ verify_protonated_H1_adenosine_variants()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants ( core::pose::Pose & pose ) const

private

References core::chemical::ResidueTypeBase::aa(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::na_rad, core::chemical::name_from_aa(), protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info(), core::chemical::PROTONATED_N1, core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::TR(), core::chemical::VIRTUAL_RNA_RESIDUE, and working_parameters_.

Referenced by apply(), and setup_native_pose().

◆ virtualize_sugar_and_backbone_at_moving_res()

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::virtualize_sugar_and_backbone_at_moving_res ( core::pose::Pose & pose ) const

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::VIRTUAL_PHOSPHATE, core::chemical::VIRTUAL_RIBOSE, and working_parameters_.

Referenced by additional_setup_for_floating_base().

Member Data Documentation

◆ align_to_native_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::align_to_native_

private

Referenced by set_align_to_native(), and setup_native_pose().

◆ apply_virtual_res_variant_at_dinucleotide_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant_at_dinucleotide_

private

Referenced by apply_virtual_res_variant(), and set_apply_virtual_res_variant_at_dinucleotide().

◆ bulge_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::bulge_res_

private

Referenced by apply_bulge_variants(), and set_bulge_res().

◆ copy_DOF_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::copy_DOF_

private

Referenced by create_starting_pose(), Import_pose(), read_input_pose_and_copy_dofs(), and set_copy_DOF().

◆ input_tags_

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

private

Referenced by Import_pose(), read_input_pose_and_copy_dofs(), and set_input_tags().

◆ native_virtual_res_list_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::native_virtual_res_list_

private

Referenced by set_native_virtual_res(), and setup_native_pose().

◆ output_pdb_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::output_pdb_

private

Referenced by apply(), correctly_copy_HO2prime_positions(), make_extended_pose(), read_input_pose_and_copy_dofs(), set_output_pdb(), and setup_native_pose().

◆ rsd_set_

core::chemical::ResidueTypeSetCAP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::rsd_set_

private

Referenced by Import_pose(), and make_extended_pose().

◆ silent_files_in_

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

private

Referenced by do_checks_and_apply_protonated_H1_adenosine_variant(), Import_pose(), and set_silent_files_in().

◆ use_phenix_geo_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::use_phenix_geo_

private

Referenced by apply(), and set_use_phenix_geo().

◆ verbose_

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verbose_

private

Referenced by apply(), apply_cutpoint_variants(), correctly_copy_HO2prime_positions(), set_verbose(), and setup_native_pose().

◆ virtual_res_list_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::virtual_res_list_

private

Referenced by apply_virtual_res_variant(), and set_virtual_res().

◆ working_parameters_

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::working_parameters_

private

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

src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetup.hh
src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetup.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StepWiseRNA_PoseSetup()

◆ ~StepWiseRNA_PoseSetup()

Member Function Documentation

◆ add_aa_virt_rsd_as_root()

◆ add_protonated_H1_adenosine_variants()

◆ add_terminal_res_repulsion()

◆ additional_setup_for_floating_base()

◆ apply()

◆ apply_bulge_variants()

◆ apply_cutpoint_variants()

◆ apply_virtual_phosphate_variants()

◆ apply_virtual_res_variant()

◆ correctly_copy_HO2prime_positions()

◆ create_pose_from_input_poses()

◆ create_starting_pose()

◆ do_checks_and_apply_protonated_H1_adenosine_variant()

◆ get_name()

◆ get_nearest_dist_to_O2prime()

◆ Import_pose()

◆ instantiate_residue_if_rebuilding_bulge()

◆ make_extended_pose()

◆ read_input_pose_and_copy_dofs()

◆ set_align_to_native()

◆ set_apply_virtual_res_variant_at_dinucleotide()

◆ set_bulge_res()

◆ set_copy_DOF()

◆ set_input_tags()

◆ set_native_virtual_res()

◆ set_output_pdb()

◆ set_silent_files_in()

◆ set_use_phenix_geo()

◆ set_verbose()

◆ set_virtual_res()

◆ setup_full_model_info()

◆ setup_native_pose()

◆ setup_vdw_cached_rep_screen_info()

◆ update_fold_tree_at_virtual_sugars()

◆ verify_protonated_H1_adenosine_variants()

◆ virtualize_sugar_and_backbone_at_moving_res()

Member Data Documentation

◆ align_to_native_

◆ apply_virtual_res_variant_at_dinucleotide_

◆ bulge_res_

◆ copy_DOF_

◆ input_tags_

◆ native_virtual_res_list_

◆ output_pdb_

◆ rsd_set_

◆ silent_files_in_

◆ use_phenix_geo_

◆ verbose_

◆ virtual_res_list_

◆ working_parameters_