The RNA de novo structure modeling protocol. More...

#include <RNP_HighResMover.hh>

Inheritance diagram for protocols::rna::denovo::movers::RNP_HighResMover:

[legend]

Public Member Functions
	RNP_HighResMover (RNA_FragmentMoverOP rna_fragment_mover, protocols::rna::movers::RNA_LoopCloserOP rna_loop_closer, core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP options)
	Construct the protocol object given the RNA fragment library to use. More...

	~RNP_HighResMover () override

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

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

std::string	get_name () const override
	Each derived class must specify its name. The class name. 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 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	protein_sidechain_packing (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP const &packer_scorefxn) const

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

Private Attributes
RNA_FragmentMoverOP	rna_fragment_mover_

protocols::rna::movers::RNA_LoopCloserOP	rna_loop_closer_

core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP	options_

core::Size const	fragment_cycles_

core::Size const	frag_size_

core::Real	protein_sc_pack_cutoff_

bool	is_init_

core::kinematics::FoldTree	rnp_docking_ft_

protocols::rigid::RigidBodyPerturbMoverOP	rnp_docking_mover_

bool	docking_

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...

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

◆ RNP_HighResMover()

protocols::rna::denovo::movers::RNP_HighResMover::RNP_HighResMover	(	RNA_FragmentMoverOP	rna_fragment_mover,
		protocols::rna::movers::RNA_LoopCloserOP	rna_loop_closer,
		core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP	options
	)

Construct the protocol object given the RNA fragment library to use.

References protein_sc_pack_cutoff_.

◆ ~RNP_HighResMover()

protocols::rna::denovo::movers::RNP_HighResMover::~RNP_HighResMover ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Apply the RNP high-res mover

Implements protocols::moves::Mover.

References core::scoring::atom_pair_constraint, core::scoring::base_pair_constraint, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), docking_, core::scoring::elec_dens_fast, core::scoring::fa_rep, frag_size_, fragment_cycles_, core::scoring::get_score_function(), is_init_, options_, protein_sidechain_packing(), rna_fragment_mover_, rna_loop_closer_, rnp_docking(), and protocols::rna::denovo::TR().

◆ get_name()

std::string protocols::rna::denovo::movers::RNP_HighResMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ initialize()

void protocols::rna::denovo::movers::RNP_HighResMover::initialize ( core::pose::Pose const & pose )

References docking_, is_init_, protocols::rna::denovo::let_rigid_body_jumps_move(), options_, protocols::rigid::partner_upstream, rnp_docking_mover_, and core::kinematics::MoveMap::set_jump().

◆ protein_sidechain_packing()

void protocols::rna::denovo::movers::RNP_HighResMover::protein_sidechain_packing	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP const &	packer_scorefxn
	)		const

private

References protocols::rna::denovo::get_residues_within_dist_of_RNA(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), protein_sc_pack_cutoff_, core::pose::Pose::residue(), core::pack::rotamer_trials(), core::pose::Pose::size(), and protocols::rna::denovo::TR().

Referenced by apply().

◆ rnp_docking()

void protocols::rna::denovo::movers::RNP_HighResMover::rnp_docking ( core::pose::Pose & pose ) const

private

References rnp_docking_mover_.

Referenced by apply().

Member Data Documentation

◆ docking_

bool protocols::rna::denovo::movers::RNP_HighResMover::docking_

private

Referenced by apply(), and initialize().

◆ frag_size_

core::Size const protocols::rna::denovo::movers::RNP_HighResMover::frag_size_

private

Referenced by apply().

◆ fragment_cycles_

core::Size const protocols::rna::denovo::movers::RNP_HighResMover::fragment_cycles_

private

Referenced by apply().

◆ is_init_

bool protocols::rna::denovo::movers::RNP_HighResMover::is_init_

private

Referenced by apply(), and initialize().

◆ options_

core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP protocols::rna::denovo::movers::RNP_HighResMover::options_

private

Referenced by apply(), and initialize().

◆ protein_sc_pack_cutoff_

core::Real protocols::rna::denovo::movers::RNP_HighResMover::protein_sc_pack_cutoff_

private

Referenced by protein_sidechain_packing(), and RNP_HighResMover().

◆ rna_fragment_mover_

RNA_FragmentMoverOP protocols::rna::denovo::movers::RNP_HighResMover::rna_fragment_mover_

private

Referenced by apply().

◆ rna_loop_closer_

protocols::rna::movers::RNA_LoopCloserOP protocols::rna::denovo::movers::RNP_HighResMover::rna_loop_closer_

private

Referenced by apply().

◆ rnp_docking_ft_

core::kinematics::FoldTree protocols::rna::denovo::movers::RNP_HighResMover::rnp_docking_ft_

private

◆ rnp_docking_mover_

protocols::rigid::RigidBodyPerturbMoverOP protocols::rna::denovo::movers::RNP_HighResMover::rnp_docking_mover_

private

Referenced by initialize(), and rnp_docking().

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

src/protocols/rna/denovo/movers/RNP_HighResMover.hh
src/protocols/rna/denovo/movers/RNP_HighResMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RNP_HighResMover()

◆ ~RNP_HighResMover()

Member Function Documentation

◆ apply()

◆ get_name()

◆ initialize()

◆ protein_sidechain_packing()

◆ rnp_docking()

Member Data Documentation

◆ docking_

◆ frag_size_

◆ fragment_cycles_

◆ is_init_

◆ options_

◆ protein_sc_pack_cutoff_

◆ rna_fragment_mover_

◆ rna_loop_closer_

◆ rnp_docking_ft_

◆ rnp_docking_mover_