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

#include <RNA_DeNovoProtocol.hh>

Inheritance diagram for protocols::rna::denovo::RNA_DeNovoProtocol:

[legend]

Public Member Functions
	RNA_DeNovoProtocol (core::import_pose::options::RNA_DeNovoProtocolOptionsCOP options=nullptr, core::import_pose::RNA_DeNovoParametersCOP params=nullptr)
	Construct the protocol object given the RNA fragment library to use. More...

	~RNA_DeNovoProtocol () override

protocols::moves::MoverOP	clone () const override
	Clone this object. More...

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

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

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

void	apply (core::pose::Pose &pose) override
	Apply the RNA denovo modeling protocol to the input pose. More...

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

void	output_to_silent_file (core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag, bool const score_only=false) const

void	align_and_output_to_silent_file (core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag) const

void	set_refine_pose_list (utility::vector1< core::pose::PoseOP > const &setting)

core::import_pose::options::RNA_DeNovoProtocolOptionsCOP	options () const

RNA_FragmentMonteCarloCOP	rna_fragment_monte_carlo () 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 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	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static void	register_options ()

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 Member Functions
void	initialize_lores_silent_file ()

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

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

void	initialize_tag_is_done ()

void	output_silent_struct (core::io::silent::SilentStruct &s, core::io::silent::SilentFileData &silent_file_data, std::string const &silent_file, core::pose::Pose &pose, std::string const &out_file_tag, bool const score_only=false) const

void	check_for_loop_modeling_case (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, core::pose::Pose const &pose) const

void	calc_rmsds (core::io::silent::SilentStruct &s, core::pose::Pose &pose, std::string const &out_file_tag) const

void	add_chem_shift_info (core::io::silent::SilentStruct &silent_struct, core::pose::Pose const &const_pose) const

Private Attributes
core::import_pose::options::RNA_DeNovoProtocolOptionsCOP	options_

core::import_pose::RNA_DeNovoParametersCOP	rna_params_

protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP	vdw_grid_

std::string	lores_silent_file_

RNA_FragmentMonteCarloOP	rna_fragment_monte_carlo_

std::map< std::string, bool >	tag_is_done_

core::scoring::ScoreFunctionOP	denovo_scorefxn_

core::scoring::ScoreFunctionOP	hires_scorefxn_

utility::vector1< core::pose::PoseOP >	refine_pose_list_

core::Size	refine_pose_id_ = 1

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

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

◆ RNA_DeNovoProtocol()

protocols::rna::denovo::RNA_DeNovoProtocol::RNA_DeNovoProtocol	(	core::import_pose::options::RNA_DeNovoProtocolOptionsCOP	options = `nullptr`,
		core::import_pose::RNA_DeNovoParametersCOP	params = `nullptr`
	)

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

References rna_params_.

◆ ~RNA_DeNovoProtocol()

protocols::rna::denovo::RNA_DeNovoProtocol::~RNA_DeNovoProtocol ( )

overridedefault

Member Function Documentation

◆ add_chem_shift_info()

void protocols::rna::denovo::RNA_DeNovoProtocol::add_chem_shift_info	(	core::io::silent::SilentStruct &	silent_struct,
		core::pose::Pose const &	const_pose
	)		const

private

References core::io::silent::SilentStruct::add_energy(), core::pose::Pose::energies(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_total_exp_chemical_shift_data_points(), core::io::silent::SilentStruct::has_energy(), options_, core::scoring::rna_chem_shift, and core::scoring::Energies::total_energies().

Referenced by output_to_silent_file().

◆ align_and_output_to_silent_file()

void protocols::rna::denovo::RNA_DeNovoProtocol::align_and_output_to_silent_file	(	core::pose::Pose &	pose,
		std::string const &	silent_file,
		std::string const &	out_file_tag
	)		const

References options_, output_to_silent_file(), rna_fragment_monte_carlo_, and rna_params_.

Referenced by apply().

◆ apply()

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

overridevirtual

Apply the RNA denovo modeling protocol to the input pose.

Apply the RNA de novo modeling protocol to a pose.

Implements protocols::moves::Mover.

References align_and_output_to_silent_file(), denovo_scorefxn_, core::io::pdb::dump_pdb(), core::pose::Pose::dump_pdb(), protocols::scoring::fill_vdw_cached_rep_screen_info_from_command_line(), protocols::moves::Mover::get_native_pose(), hires_scorefxn_, initialize_lores_silent_file(), initialize_scorefxn(), initialize_tag_is_done(), lores_silent_file_, options_, protocols::network::post_decoy(), protocols::network::post_file(), refine_pose_list_, core::io::silent::remove_silent_file_if_it_exists(), rna_fragment_monte_carlo_, rna_params_, tag_is_done_, vdw_grid_, and core::io::silent::SilentFileData::write_silent_struct().

◆ calc_rmsds()

void protocols::rna::denovo::RNA_DeNovoProtocol::calc_rmsds	(	core::io::silent::SilentStruct &	s,
		core::pose::Pose &	pose,
		std::string const &	out_file_tag
	)		const

private

References core::io::silent::SilentStruct::add_energy(), rna_fragment_monte_carlo_, and protocols::rna::denovo::TR().

Referenced by output_silent_struct().

◆ check_for_loop_modeling_case()

void protocols::rna::denovo::RNA_DeNovoProtocol::check_for_loop_modeling_case	(	std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map,
		core::pose::Pose const &	pose
	)		const

private

◆ clone()

protocols::moves::MoverOP protocols::rna::denovo::RNA_DeNovoProtocol::clone ( ) const

overridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

moves::MoverOP protocols::rna::denovo::RNA_DeNovoProtocol::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::rna::denovo::RNA_DeNovoProtocol::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ initialize_constraints()

void protocols::rna::denovo::RNA_DeNovoProtocol::initialize_constraints ( core::pose::Pose & pose )

private

References core::scoring::atom_pair_constraint, core::scoring::base_pair_constraint, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, denovo_scorefxn_, and options_.

Referenced by initialize_scorefxn().

◆ initialize_lores_silent_file()

void protocols::rna::denovo::RNA_DeNovoProtocol::initialize_lores_silent_file ( )

private

References core::io::silent::get_outfile_name_with_tag(), lores_silent_file_, and options_.

Referenced by apply().

◆ initialize_scorefxn()

void protocols::rna::denovo::RNA_DeNovoProtocol::initialize_scorefxn ( core::pose::Pose & pose )

private

References core::scoring::apply_set_weights(), core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), denovo_scorefxn_, core::scoring::elec_dens_fast, protocols::rna::denovo::get_rna_hires_scorefxn(), core::scoring::grid_vdw, hires_scorefxn_, initialize_constraints(), core::scoring::linear_chainbreak, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), options_, core::scoring::rna_chem_map_lores, and rna_params_.

Referenced by apply().

◆ initialize_tag_is_done()

void protocols::rna::denovo::RNA_DeNovoProtocol::initialize_tag_is_done ( )

private

References core::io::silent::initialize_tag_is_done(), options_, and tag_is_done_.

Referenced by apply().

◆ mover_name()

std::string protocols::rna::denovo::RNA_DeNovoProtocol::mover_name ( )

static

Referenced by get_name(), protocols::rna::denovo::RNA_DeNovoProtocolCreator::keyname(), and provide_xml_schema().

◆ options()

core::import_pose::options::RNA_DeNovoProtocolOptionsCOP protocols::rna::denovo::RNA_DeNovoProtocol::options ( ) const

inline

References options_.

◆ output_silent_struct()

void protocols::rna::denovo::RNA_DeNovoProtocol::output_silent_struct	(	core::io::silent::SilentStruct &	s,
		core::io::silent::SilentFileData &	silent_file_data,
		std::string const &	silent_file,
		core::pose::Pose &	pose,
		std::string const &	out_file_tag,
		bool const	score_only = `false`
	)		const

private

References core::io::silent::SilentStruct::add_energy(), core::pose::rna::add_number_base_pairs(), core::pose::rna::add_number_native_base_pairs(), calc_rmsds(), protocols::moves::Mover::get_native_pose(), options_, rna_fragment_monte_carlo_, protocols::rna::denovo::TR(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by output_to_silent_file().

◆ output_to_silent_file()

void protocols::rna::denovo::RNA_DeNovoProtocol::output_to_silent_file	(	core::pose::Pose &	pose,
		std::string const &	silent_file,
		std::string const &	out_file_tag,
		bool const	score_only = `false`
	)		const

References add_chem_shift_info(), core::chemical::FA_STANDARD, options_, output_silent_struct(), rna_params_, core::util::switch_to_residue_type_set(), and protocols::rna::denovo::TR().

Referenced by align_and_output_to_silent_file().

◆ parse_my_tag()

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

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.