Thread a new sequence over a given RNA scaffold and do a little optimization. More...

#include <RNAThreadAndMinimizeMover.hh>

Inheritance diagram for protocols::rna::movers::RNAThreadAndMinimizeMover:

[legend]

Public Member Functions
	RNAThreadAndMinimizeMover (std::string const &seq, std::string const &template_sequence_from_alignment, bool long_strategy=false, std::string const &input_sequence_type="", std::string const &mutation_list="", std::string const &insertion_list="")

	RNAThreadAndMinimizeMover ()

	~RNAThreadAndMinimizeMover () override

void	accomodate_length_change (Pose &pose, core::Size const insertion_begin, core::Size const seqpos)

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

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

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

void	obtain_rtypes_for_target_sequence ()

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

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

core::kinematics::MoveMapOP	mm_from_residues (core::pose::Pose const &pose, utility::vector1< core::Size > const &changed_pos, bool add_nearby=false)

void	setup_alignment_map (std::map< core::Size, core::Size > &mapping, std::string const &sequence_from_alignment)

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

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

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

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 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...

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

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 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...

Static Public Member Functions
static std::string	class_name ()

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...

Private Attributes
std::string	seq_

std::string	template_sequence_from_alignment_

bool	long_strategy_

std::string	input_sequence_type_

core::scoring::ScoreFunctionOP	scorefxn_

std::string	target_sequence_

utility::vector1< core::Size >	working_res_

core::chemical::ResidueTypeCOPs	rtypes_

std::string	mutation_list_

std::string	insertion_list_

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

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

Thread a new sequence over a given RNA scaffold and do a little optimization.

Constructor & Destructor Documentation

◆ RNAThreadAndMinimizeMover() [1/2]

protocols::rna::movers::RNAThreadAndMinimizeMover::RNAThreadAndMinimizeMover	(	std::string const &	seq,
		std::string const &	template_sequence_from_alignment,
		bool	long_strategy = `false`,
		std::string const &	input_sequence_type = `""`,
		std::string const &	mutation_list = `""`,
		std::string const &	insertion_list = `""`
	)

◆ RNAThreadAndMinimizeMover() [2/2]

protocols::rna::movers::RNAThreadAndMinimizeMover::RNAThreadAndMinimizeMover ( )

inline

◆ ~RNAThreadAndMinimizeMover()

protocols::rna::movers::RNAThreadAndMinimizeMover::~RNAThreadAndMinimizeMover ( )

inlineoverride

Member Function Documentation

◆ accomodate_length_change()

void protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change	(	Pose &	pose,
		core::Size const	insertion_begin,
		core::Size const	seqpos
	)

References core::pose::Pose::add_constraint(), core::pose::addVirtualResAsRoot(), core::chemical::ResidueType::atom_index(), core::id::BB, core::scoring::cart_bonded, core::scoring::chainbreak, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::id::D, core::sequence::end, core::pose::Pose::fold_tree(), core::chemical::FULL_ATOM_t, core::chemical::ResidueType::has(), core::scoring::linear_chainbreak, core::pose::rna::mutate_position(), core::scoring::pro_close, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), core::scoring::rg, core::scoring::rna_torsion, protocols::hybridization::score, scorefxn_, core::pose::Pose::set_torsion(), core::scoring::suiteness_bonus, core::chemical::rings::THETA, core::pose::Pose::torsion(), core::pose::Pose::total_residue(), protocols::rna::movers::TR(), and core::conformation::Residue::xyz().

Referenced by process_deletions(), and process_insertions().

◆ apply()

void protocols::rna::movers::RNAThreadAndMinimizeMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::scoring::all_atom_rmsd(), core::pose::Pose::annotated_sequence(), core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), protocols::moves::Mover::info(), insertion_list_, long_mutate_strategy(), long_strategy_, mutate_all_at_once(), mutation_list_, obtain_rtypes_for_target_sequence(), core::pose::Pose::pdb_info(), core::pose::rna::remove_bracketed(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), seq_, set_up_target_sequence(), core::pose::setPoseExtraScore(), core::pose::Pose::size(), target_sequence_, protocols::rna::movers::TR(), and core::pose::virtual_type_for_pose().

◆ class_name()

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::class_name ( )

static

Referenced by get_name(), and protocols::rna::movers::RNAThreadAndMinimizeMoverCreator::keyname().

◆ clone()

protocols::moves::MoverOP protocols::rna::movers::RNAThreadAndMinimizeMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::rna::movers::RNAThreadAndMinimizeMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References class_name().

◆ long_mutate_strategy()

void protocols::rna::movers::RNAThreadAndMinimizeMover::long_mutate_strategy ( core::pose::Pose & pose )

References insertion_list_, mm_from_residues(), core::pose::rna::mutate_position(), process_deletions(), process_insertions(), core::scoring::rg, rtypes_, scorefxn_, core::pose::set_reasonable_fold_tree(), core::pose::Pose::total_residue(), and working_res_.

Referenced by apply().

◆ mm_from_residues()

core::kinematics::MoveMapOP protocols::rna::movers::RNAThreadAndMinimizeMover::mm_from_residues	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	changed_pos,
		bool	add_nearby = `false`
	)

References core::pose::Pose::total_residue().

Referenced by long_mutate_strategy(), and mutate_all_at_once().

◆ mutate_all_at_once()

void protocols::rna::movers::RNAThreadAndMinimizeMover::mutate_all_at_once ( core::pose::Pose & pose )

References mm_from_residues(), core::pose::rna::mutate_position(), rtypes_, scorefxn_, core::pose::set_reasonable_fold_tree(), core::pose::Pose::total_residue(), and working_res_.

Referenced by apply().

◆ obtain_rtypes_for_target_sequence()

void protocols::rna::movers::RNAThreadAndMinimizeMover::obtain_rtypes_for_target_sequence ( )

References core::chemical::FA_STANDARD, input_sequence_type_, mutation_list_, core::pose::residue_types_from_sequence(), rtypes_, and target_sequence_.

Referenced by apply().

◆ parse_my_tag()

void protocols::rna::movers::RNAThreadAndMinimizeMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

◆ process_deletions()

void protocols::rna::movers::RNAThreadAndMinimizeMover::process_deletions ( core::pose::Pose & pose )

References accomodate_length_change(), core::pose::Pose::delete_residue_slow(), and rtypes_.

Referenced by long_mutate_strategy().

◆ process_insertions()

void protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions ( core::pose::Pose & pose )

References accomodate_length_change(), core::pose::Pose::annotated_sequence(), core::io::NomenclatureManager::annotated_sequence_from_IUPAC_sequence(), core::io::NomenclatureManager::annotated_sequence_from_modomics_oneletter_sequence(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::pose::Pose::conformation(), core::chemical::FULL_ATOM_t, input_sequence_type_, insertion_list_, core::pose::Pose::residue_type_set_for_pose(), core::pose::residue_types_from_sequence(), and protocols::rna::movers::TR().

Referenced by long_mutate_strategy().

◆ set_up_target_sequence()

void protocols::rna::movers::RNAThreadAndMinimizeMover::set_up_target_sequence ( core::pose::Pose & pose )

References core::io::NomenclatureManager::annotated_sequence_from_IUPAC_sequence(), core::io::NomenclatureManager::annotated_sequence_from_modomics_oneletter_sequence(), input_sequence_type_, core::pose::rna::remove_bracketed(), seq_, target_sequence_, core::pose::Pose::total_residue(), and working_res_.

Referenced by apply().

◆ setup_alignment_map()

void protocols::rna::movers::RNAThreadAndMinimizeMover::setup_alignment_map	(	std::map< core::Size, core::Size > &	mapping,
		std::string const &	sequence_from_alignment
	)

inline

◆ show()

void protocols::rna::movers::RNAThreadAndMinimizeMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::rna::movers::operator<<().

Member Data Documentation

◆ input_sequence_type_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::input_sequence_type_

private

Referenced by obtain_rtypes_for_target_sequence(), process_insertions(), and set_up_target_sequence().

◆ insertion_list_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::insertion_list_

private

Referenced by apply(), long_mutate_strategy(), and process_insertions().

◆ long_strategy_

bool protocols::rna::movers::RNAThreadAndMinimizeMover::long_strategy_

private

Referenced by apply().

◆ mutation_list_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::mutation_list_

private

Referenced by apply(), and obtain_rtypes_for_target_sequence().

◆ rtypes_

core::chemical::ResidueTypeCOPs protocols::rna::movers::RNAThreadAndMinimizeMover::rtypes_

private

Referenced by long_mutate_strategy(), mutate_all_at_once(), obtain_rtypes_for_target_sequence(), and process_deletions().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::rna::movers::RNAThreadAndMinimizeMover::scorefxn_

private

Referenced by accomodate_length_change(), long_mutate_strategy(), and mutate_all_at_once().

◆ seq_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::seq_

private

Referenced by apply(), and set_up_target_sequence().

◆ target_sequence_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::target_sequence_

private

Referenced by apply(), obtain_rtypes_for_target_sequence(), and set_up_target_sequence().

◆ template_sequence_from_alignment_

std::string protocols::rna::movers::RNAThreadAndMinimizeMover::template_sequence_from_alignment_

private

◆ working_res_

utility::vector1< core::Size > protocols::rna::movers::RNAThreadAndMinimizeMover::working_res_

private

Referenced by long_mutate_strategy(), mutate_all_at_once(), and set_up_target_sequence().

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

src/protocols/rna/movers/RNAThreadAndMinimizeMover.hh
src/protocols/rna/movers/RNAThreadAndMinimizeMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RNAThreadAndMinimizeMover() [1/2]

◆ RNAThreadAndMinimizeMover() [2/2]

◆ ~RNAThreadAndMinimizeMover()

Member Function Documentation

◆ accomodate_length_change()

◆ apply()

◆ class_name()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ long_mutate_strategy()

◆ mm_from_residues()

◆ mutate_all_at_once()

◆ obtain_rtypes_for_target_sequence()

◆ parse_my_tag()

◆ process_deletions()

◆ process_insertions()

◆ set_up_target_sequence()

◆ setup_alignment_map()

◆ show()

Member Data Documentation

◆ input_sequence_type_

◆ insertion_list_

◆ long_strategy_

◆ mutation_list_

◆ rtypes_

◆ scorefxn_

◆ seq_

◆ target_sequence_

◆ template_sequence_from_alignment_

◆ working_res_