#include <StepWiseRNA_PoseSetup.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_PoseSetup:

Collaboration diagram for protocols::swa::rna::StepWiseRNA_PoseSetup:

Public Member Functions
	StepWiseRNA_PoseSetup (StepWiseRNA_JobParametersOP &job_parameters)

	~StepWiseRNA_PoseSetup ()

virtual void	apply (core::pose::Pose &pose)

virtual std::string	get_name () const
	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_rebuild_bulge_mode (bool const setting)

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)

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

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

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

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

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

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

void	correctly_copy_HO2star_positions (core::pose::Pose &full_pose, utility::vector1< core::pose::Pose > const &start_pose_list)

core::Real	get_nearest_dist_to_O2star (core::Size const O2star_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_

StepWiseRNA_JobParametersOP	job_parameters_

bool	copy_DOF_

bool	verbose_

utility::vector1< Size >	bulge_res_

utility::vector1< Size >	virtual_res_list_

utility::vector1< Size >	native_virtual_res_list_

bool	rebuild_bulge_mode_

bool	output_pdb_

bool	apply_virtual_res_variant_at_dinucleotide_

bool	align_to_native_

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

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...

Detailed Description

Definition at line 43 of file StepWiseRNA_PoseSetup.hh.

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_PoseSetup::StepWiseRNA_PoseSetup ( StepWiseRNA_JobParametersOP & job_parameters)

Definition at line 78 of file StepWiseRNA_PoseSetup.cc.

protocols::swa::rna::StepWiseRNA_PoseSetup::~StepWiseRNA_PoseSetup ( )

Definition at line 93 of file StepWiseRNA_PoseSetup.cc.

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root ( core::pose::Pose & pose)

private

Definition at line 990 of file StepWiseRNA_PoseSetup.cc.

References core::chemical::aa_vrt, core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), job_parameters_, core::chemical::ResidueTypeSet::name3_map(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::ResidueType::residue_type_set(), core::kinematics::FoldTree::root(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply(), and setup_native_pose().

void protocols::swa::rna::StepWiseRNA_PoseSetup::add_protonated_H1_adenosine_variants ( core::pose::Pose & pose) const

private

Definition at line 850 of file StepWiseRNA_PoseSetup.cc.

References protocols::swa::rna::apply_protonated_H1_adenosine_variant_type(), protocols::swa::rna::Contain_seq_num(), job_parameters_, and rebuild_bulge_mode_.

Referenced by apply(), and setup_native_pose().

void protocols::swa::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion ( core::pose::Pose & pose) const

private

Definition at line 768 of file StepWiseRNA_PoseSetup.cc.

References core::pose::Pose::constraint_set(), core::scoring::rna::first_base_atom_index(), core::pose::Pose::fold_tree(), job_parameters_, protocols::swa::rna::Output_seq_num_list(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_PoseSetup::apply ( core::pose::Pose & pose)

virtual

void protocols::swa::rna::StepWiseRNA_PoseSetup::apply_bulge_variants ( core::pose::Pose & pose) const

private

Definition at line 911 of file StepWiseRNA_PoseSetup.cc.

References core::pose::add_variant_type_to_pose_residue(), protocols::swa::rna::apply_sub_to_full_mapping(), bulge_res_, protocols::swa::rna::Contain_seq_num(), and job_parameters_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants	(	core::pose::Pose &	pose,
		core::pose::Pose &	pose_without_cutpoints
	)

private

Definition at line 650 of file StepWiseRNA_PoseSetup.cc.

References core::pose::add_variant_type_to_pose_residue(), core::id::BB, protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, job_parameters_, core::scoring::rna::NUM_RNA_MAINCHAIN_TORSIONS(), protocols::swa::rna::print_backbone_torsions(), core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and verbose_.

Referenced by apply(), and setup_native_pose().

void protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants ( core::pose::Pose & pose) const

private

Definition at line 733 of file StepWiseRNA_PoseSetup.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_UPPER, core::chemical::ResidueType::has_variant_type(), job_parameters_, core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant ( core::pose::Pose & pose) const

private

Definition at line 937 of file StepWiseRNA_PoseSetup.cc.

References protocols::swa::rna::apply_sub_to_full_mapping(), apply_virtual_res_variant_at_dinucleotide_, protocols::swa::rna::apply_virtual_rna_residue_variant_type(), protocols::swa::rna::Contain_seq_num(), job_parameters_, protocols::swa::rna::Output_boolean(), and virtual_res_list_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2star_positions	(	core::pose::Pose &	full_pose,
		utility::vector1< core::pose::Pose > const &	start_pose_list
	)

private

Definition at line 524 of file StepWiseRNA_PoseSetup.cc.

References core::id::CHI, protocols::swa::rna::Contain_seq_num(), protocols::swa::rna::create_full_to_input_res_map(), core::pose::Pose::dump_pdb(), get_nearest_dist_to_O2star(), job_parameters_, output_pdb_, protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), core::pose::Pose::set_torsion(), and verbose_.

Referenced by read_input_pose_and_copy_dofs().

std::string protocols::swa::rna::StepWiseRNA_PoseSetup::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 98 of file StepWiseRNA_PoseSetup.cc.

core::Real protocols::swa::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2star	(	core::Size const	O2star_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

Definition at line 608 of file StepWiseRNA_PoseSetup.cc.

References core::io::serialization::at(), protocols::swa::rna::Contain_seq_num(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by correctly_copy_HO2star_positions().

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

private

Definition at line 295 of file StepWiseRNA_PoseSetup.cc.

References copy_DOF_, protocols::swa::rna::import_pose_from_silent_file(), input_tags_, job_parameters_, protocols::rna::make_phosphate_nomenclature_matches_mini(), core::import_pose::pose_from_pdb(), rsd_set_, core::pose::Pose::sequence(), silent_files_in_, and core::pose::Pose::total_residue().

Referenced by read_input_pose_and_copy_dofs().

void protocols::swa::rna::StepWiseRNA_PoseSetup::make_pose ( core::pose::Pose & pose)

private

Definition at line 342 of file StepWiseRNA_PoseSetup.cc.

References core::pose::Pose::dump_pdb(), job_parameters_, core::pose::make_pose_from_sequence(), output_pdb_, and rsd_set_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs ( core::pose::Pose & pose)

private

Definition at line 362 of file StepWiseRNA_PoseSetup.cc.

References core::pose::add_variant_type_to_pose_residue(), protocols::swa::rna::apply_full_to_sub_mapping(), protocols::swa::rna::apply_protonated_H1_adenosine_variant_type(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), protocols::rna::assert_phosphate_nomenclature_matches_mini(), protocols::swa::rna::Contain_seq_num(), copy_DOF_, core::pose::copy_dofs_match_atom_names(), correctly_copy_HO2star_positions(), core::pose::Pose::dump_pdb(), core::pose::Pose::fold_tree(), protocols::swa::rna::has_virtual_rna_residue_variant_type(), Import_pose(), input_tags_, job_parameters_, core::chemical::na_rad, output_pdb_, protocols::swa::rna::Output_seq_num_list(), core::pose::remove_variant_type_from_pose_residue(), silent_files_in_, and core::io::serialization::size().

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_align_to_native ( bool const setting)

inline

Definition at line 92 of file StepWiseRNA_PoseSetup.hh.

References align_to_native_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_apply_virtual_res_variant_at_dinucleotide ( bool const setting)

inline

Definition at line 89 of file StepWiseRNA_PoseSetup.hh.

References apply_virtual_res_variant_at_dinucleotide_.

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

inline

Definition at line 65 of file StepWiseRNA_PoseSetup.hh.

References bulge_res_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_copy_DOF ( bool const setting)

inline

Definition at line 74 of file StepWiseRNA_PoseSetup.hh.

References copy_DOF_.

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

inline

Definition at line 59 of file StepWiseRNA_PoseSetup.hh.

References input_tags_.

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

inline

Definition at line 71 of file StepWiseRNA_PoseSetup.hh.

References native_virtual_res_list_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_output_pdb ( bool const setting)

inline

Definition at line 86 of file StepWiseRNA_PoseSetup.hh.

References output_pdb_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_rebuild_bulge_mode ( bool const setting)

inline

Definition at line 83 of file StepWiseRNA_PoseSetup.hh.

References rebuild_bulge_mode_.

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

inline

Definition at line 62 of file StepWiseRNA_PoseSetup.hh.

References silent_files_in_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_verbose ( bool const setting)

inline

Definition at line 77 of file StepWiseRNA_PoseSetup.hh.

References verbose_.

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

inline

Definition at line 68 of file StepWiseRNA_PoseSetup.hh.

References virtual_res_list_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose ( core::pose::Pose & pose)

void protocols::swa::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants ( core::pose::Pose & pose) const

private

Definition at line 871 of file StepWiseRNA_PoseSetup.cc.

References core::conformation::Residue::aa(), protocols::swa::rna::Contain_seq_num(), core::conformation::Residue::has_variant_type(), job_parameters_, core::chemical::na_rad, core::chemical::name_from_aa(), protocols::swa::rna::print_JobParameters_info(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by apply(), and setup_native_pose().

Member Data Documentation

bool protocols::swa::rna::StepWiseRNA_PoseSetup::align_to_native_

private

Definition at line 156 of file StepWiseRNA_PoseSetup.hh.

Referenced by set_align_to_native(), and setup_native_pose().

bool protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant_at_dinucleotide_

private

Definition at line 155 of file StepWiseRNA_PoseSetup.hh.

Referenced by apply_virtual_res_variant(), and set_apply_virtual_res_variant_at_dinucleotide().

utility::vector1< Size > protocols::swa::rna::StepWiseRNA_PoseSetup::bulge_res_

private

Definition at line 149 of file StepWiseRNA_PoseSetup.hh.

Referenced by apply_bulge_variants(), and set_bulge_res().

bool protocols::swa::rna::StepWiseRNA_PoseSetup::copy_DOF_

private

Definition at line 146 of file StepWiseRNA_PoseSetup.hh.

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

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

private

Definition at line 143 of file StepWiseRNA_PoseSetup.hh.

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

StepWiseRNA_JobParametersOP protocols::swa::rna::StepWiseRNA_PoseSetup::job_parameters_

private

Definition at line 145 of file StepWiseRNA_PoseSetup.hh.

Referenced by add_aa_virt_rsd_as_root(), add_protonated_H1_adenosine_variants(), add_terminal_res_repulsion(), apply(), apply_bulge_variants(), apply_cutpoint_variants(), apply_virtual_phosphate_variants(), apply_virtual_res_variant(), correctly_copy_HO2star_positions(), Import_pose(), make_pose(), read_input_pose_and_copy_dofs(), setup_native_pose(), and verify_protonated_H1_adenosine_variants().

utility::vector1< Size > protocols::swa::rna::StepWiseRNA_PoseSetup::native_virtual_res_list_

private

Definition at line 151 of file StepWiseRNA_PoseSetup.hh.

Referenced by set_native_virtual_res(), and setup_native_pose().

bool protocols::swa::rna::StepWiseRNA_PoseSetup::output_pdb_

private

Definition at line 154 of file StepWiseRNA_PoseSetup.hh.

Referenced by apply(), correctly_copy_HO2star_positions(), make_pose(), read_input_pose_and_copy_dofs(), set_output_pdb(), and setup_native_pose().

bool protocols::swa::rna::StepWiseRNA_PoseSetup::rebuild_bulge_mode_

private

Definition at line 153 of file StepWiseRNA_PoseSetup.hh.

Referenced by add_protonated_H1_adenosine_variants(), and set_rebuild_bulge_mode().

core::chemical::ResidueTypeSetCAP protocols::swa::rna::StepWiseRNA_PoseSetup::rsd_set_

private

Definition at line 142 of file StepWiseRNA_PoseSetup.hh.

Referenced by Import_pose(), and make_pose().

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

private

Definition at line 144 of file StepWiseRNA_PoseSetup.hh.

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

bool protocols::swa::rna::StepWiseRNA_PoseSetup::verbose_

private

Definition at line 147 of file StepWiseRNA_PoseSetup.hh.

Referenced by apply(), apply_cutpoint_variants(), correctly_copy_HO2star_positions(), set_verbose(), and setup_native_pose().

utility::vector1< Size > protocols::swa::rna::StepWiseRNA_PoseSetup::virtual_res_list_

private

Definition at line 150 of file StepWiseRNA_PoseSetup.hh.

Referenced by apply_virtual_res_variant(), and set_virtual_res().

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

src/protocols/swa/rna/StepWiseRNA_PoseSetup.hh
src/protocols/swa/rna/StepWiseRNA_PoseSetup.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation