#include <RNA_FragmentMonteCarlo.hh>

Inheritance diagram for protocols::rna::denovo::RNA_FragmentMonteCarlo:

[legend]

Public Member Functions
	RNA_FragmentMonteCarlo (core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP=nullptr)

	~RNA_FragmentMonteCarlo () override

void	apply (core::pose::Pose &pose) override
	Apply the loop-rebuild protocol to the input pose. More...

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

void	set_refine_pose (bool const setting)

void	set_all_lores_score_final (std::list< core::Real > const &setting)

void	set_denovo_scorefxn (core::scoring::ScoreFunctionCOP setting)

void	set_hires_scorefxn (core::scoring::ScoreFunctionCOP setting)

void	set_vdw_grid (protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP setting)

void	set_is_rna_and_protein (bool const &setting)

void	set_out_file_tag (std::string const &setting)

std::list< core::Real > const &	all_lores_score_final () const

core::pose::PoseOP	lores_pose ()

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

core::Real	lores_score_early () const

core::Real	lores_score_final () const

void	set_rna_base_pair_handler (core::import_pose::RNA_BasePairHandlerCOP setting)

core::import_pose::RNA_BasePairHandlerCOP	rna_base_pair_handler () const

void	set_rna_de_novo_pose_initializer (protocols::rna::denovo::RNA_DeNovoPoseInitializerCOP setting)

void	set_user_input_chunk_library (core::import_pose::libraries::RNA_ChunkLibraryCOP setting)

void	set_user_input_chunk_initialization_library (core::import_pose::libraries::RNA_ChunkLibraryCOP setting)

core::import_pose::libraries::RNA_ChunkLibraryCOP	rna_chunk_library () const

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

void	align_pose (core::pose::Pose &pose, bool const verbose=false) const

core::Real	get_rmsd_no_superimpose (core::pose::Pose const &pose) const

core::Real	get_rmsd_stems_no_superimpose (core::pose::Pose const &pose) const

core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map () const

protocols::rna::movers::RNA_LoopCloserCOP	rna_loop_closer () const

bool	loop_modeling () const

void	set_outputter (output::RNA_FragmentMonteCarloOutputterOP const &setting)

output::RNA_FragmentMonteCarloOutputterOP	outputter () 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...

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

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

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

void	initialize_score_functions ()

void	initialize_parameters ()

void	update_denovo_scorefxn_weights (core::Size const r)

core::Size	figure_out_constraint_separation_cutoff (core::Size const r, core::Size const max_dist)

void	update_pose_constraints (core::Size const r, core::pose::Pose &pose)

void	update_rna_denovo_master_mover (core::Size const &r, core::pose::Pose const &pose)
	moves should get finer as simulation progresses through rounds More...

core::Size	update_frag_size (core::Size const &r) const

void	get_rigid_body_move_mags (core::Size const &r, core::Real &rot_mag, core::Real &trans_mag, core::Real const &rot_mag_init, core::Real const &trans_mag_init, core::Real const &rot_mag_final, core::Real const &trans_mag_final) const

bool	check_score_filter (core::Real const lores_score_, std::list< core::Real > &all_lores_score_)

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

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

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

utility::vector1< core::Size >	reroot_pose_before_align_and_return_moving_res (core::pose::Pose &pose) const

core::Real	get_rmsd (core::pose::Pose const &const_pose) const

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

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

core::Real	randomize_and_close_all_chains (core::pose::Pose &pose, bool const &close_chains) const

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

void	copy_structure_keep_fold_tree (core::pose::Pose &pose, core::pose::Pose const &pose_to_copy) const

Private Attributes
core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP	options_

std::string	out_file_tag_

core::import_pose::RNA_BasePairHandlerCOP	rna_base_pair_handler_

core::import_pose::libraries::RNA_ChunkLibraryCOP	user_input_rna_chunk_library_

core::import_pose::libraries::RNA_ChunkLibraryCOP	user_input_rna_chunk_initialization_library_

core::import_pose::libraries::RNA_ChunkLibraryOP	rna_chunk_library_

core::import_pose::libraries::RNA_ChunkLibraryOP	rna_chunk_initialization_library_

protocols::rna::denovo::RNA_DeNovoPoseInitializerCOP	rna_de_novo_pose_initializer_

protocols::rna::movers::RNA_LoopCloserOP	rna_loop_closer_

protocols::rna::movers::RNA_LoopCloserOP	rna_loop_closer_init_

movers::RNA_DeNovoMasterMoverOP	rna_denovo_master_mover_

movers::RNA_DeNovoMasterMoverOP	rna_denovo_master_mover_init_

movers::RNA_HelixMoverOP	rna_helix_mover_

movers::RNA_MinimizerOP	rna_minimizer_

movers::RNA_RelaxerOP	rna_relaxer_

movers::RNP_HighResMoverOP	rnp_high_res_mover_

core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map_

core::scoring::ScoreFunctionCOP	denovo_scorefxn_

core::scoring::ScoreFunctionCOP	hires_scorefxn_

core::scoring::ScoreFunctionCOP	chem_shift_scorefxn_

core::scoring::ScoreFunctionOP	chainbreak_sfxn_

core::scoring::ScoreFunctionCOP	final_scorefxn_

core::scoring::ScoreFunctionOP	working_denovo_scorefxn_

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

core::Size const	monte_carlo_cycles_max_default_

core::Size	monte_carlo_cycles_

core::Size	rounds_

bool	refine_pose_

core::Real	lores_score_early_

core::Real	lores_score_final_

std::list< core::Real >	all_lores_score_final_

core::scoring::constraints::ConstraintSetOP	constraint_set_

core::pose::PoseCOP	align_pose_

core::pose::PoseOP	lores_pose_

bool	is_rna_and_protein_

output::RNA_FragmentMonteCarloOutputterOP	outputter_

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

◆ RNA_FragmentMonteCarlo()

protocols::rna::denovo::RNA_FragmentMonteCarlo::RNA_FragmentMonteCarlo ( core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP options = nullptr )

Holds the main loop for Fragment assembly of RNA (FARNA).

Two major modes: in classic mode, assumes pose is unfolded, and tries to fold from scratch; several stages gradually turn on chain closure, apply filters, etc.

in refine_pose mode, carries out the last stage of classic modeling, with all score terms on, all constraints on, and loop closing active.

Can be called by two wrapper classes – RNA_DeNovoProtocol (setup through .params file or command lines in 'classic' rna_denovo application) RNA_DeNovoOptimizer (better encapsulation, used inside stepwise)

TODO

simulated tempering as an alternative to gradual turn on of score terms
factor out alignment stuff, unify with stepwise. [Move StepWisePoseAligner to toolbox?]
encapsulate filters into function outside of main loop.

◆ ~RNA_FragmentMonteCarlo()

protocols::rna::denovo::RNA_FragmentMonteCarlo::~RNA_FragmentMonteCarlo ( )

overridedefault

Member Function Documentation

◆ align_pose()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::align_pose	(	core::pose::Pose &	pose,
		bool const	verbose = `false`
	)		const

References protocols::stepwise::modeler::align::create_alignment_id_map_legacy(), protocols::moves::Mover::get_native_pose(), options_, rna_chunk_library_, core::pose::Pose::size(), core::scoring::superimpose_pose(), and protocols::rna::denovo::TR().

Referenced by apply(), and get_rmsd().

◆ all_lores_score_final()

std::list< core::Real > const& protocols::rna::denovo::RNA_FragmentMonteCarlo::all_lores_score_final ( ) const

inline

References all_lores_score_final_.

◆ apply()

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

overridevirtual

Apply the loop-rebuild protocol to the input pose.

Implements protocols::moves::Mover.

◆ apply_chem_shift_data()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::apply_chem_shift_data ( core::pose::Pose & pose )

private

References chem_shift_scorefxn_, final_scorefxn_, hires_scorefxn_, options_, rna_base_pair_handler_, rna_loop_closer_, and rna_minimizer_.

Referenced by apply().

◆ atom_level_domain_map()

core::pose::toolbox::AtomLevelDomainMapCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::atom_level_domain_map ( ) const

inline

References atom_level_domain_map_.

◆ check_fold_tree_cutpoints_ok()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::check_fold_tree_cutpoints_ok ( core::pose::Pose const & pose ) const

private

References core::chemical::CUTPOINT_LOWER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by apply().

◆ check_for_loop_modeling_case()

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

private

References loop_modeling(), rna_chunk_library_, core::import_pose::libraries::ROSETTA_LIBRARY_DOMAIN, and protocols::rna::denovo::TR().

Referenced by get_rmsd_no_superimpose().

◆ check_score_filter()

bool protocols::rna::denovo::RNA_FragmentMonteCarlo::check_score_filter	(	core::Real const	lores_score_,
		std::list< core::Real > &	all_lores_score_
	)

private

References core::sequence::end, options_, and protocols::rna::denovo::TR().

Referenced by apply().

◆ copy_structure_keep_fold_tree()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::copy_structure_keep_fold_tree	(	core::pose::Pose &	pose,
		core::pose::Pose const &	pose_to_copy
	)		const

private

References atom_level_domain_map_, core::pose::Pose::fold_tree(), and rna_de_novo_pose_initializer_.

Referenced by apply().

◆ figure_out_constraint_separation_cutoff()

Size protocols::rna::denovo::RNA_FragmentMonteCarlo::figure_out_constraint_separation_cutoff	(	core::Size const	r,
		core::Size const	max_dist
	)

private

Used in staged_constraints only.

References rounds_.

Referenced by update_pose_constraints().

◆ final_score()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::final_score ( core::pose::Pose & pose )

private

Having this final_score function allows slow terms to not be applied during Monte Carlo but only as an extra score at end.

References final_scorefxn_, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), options_, and core::scoring::rna_chem_map.

Referenced by apply().

◆ get_additional_output()

PoseOP protocols::rna::denovo::RNA_FragmentMonteCarlo::get_additional_output ( )

overridevirtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References lores_pose_, and options_.

◆ get_name()

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

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ get_rigid_body_move_mags()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rigid_body_move_mags	(	core::Size const &	r,
		core::Real &	rot_mag,
		core::Real &	trans_mag,
		core::Real const &	rot_mag_init,
		core::Real const &	trans_mag_init,
		core::Real const &	rot_mag_final,
		core::Real const &	trans_mag_final
	)		const

private

References options_, and rounds_.

Referenced by update_rna_denovo_master_mover().

◆ get_rmsd()

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd ( core::pose::Pose const & const_pose ) const

private

References align_pose(), and get_rmsd_no_superimpose().

Referenced by apply().

◆ get_rmsd_no_superimpose()

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_no_superimpose ( core::pose::Pose const & pose ) const

References check_for_loop_modeling_case(), protocols::moves::Mover::get_native_pose(), core::scoring::rms_at_corresponding_atoms_no_super(), and core::scoring::setup_matching_heavy_atoms().

Referenced by apply(), and get_rmsd().

◆ get_rmsd_stems_no_superimpose()

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_stems_no_superimpose ( core::pose::Pose const & pose ) const

References protocols::moves::Mover::get_native_pose(), core::scoring::rms_at_corresponding_atoms_no_super(), rna_base_pair_handler(), and core::scoring::setup_matching_heavy_atoms().

Referenced by apply().

◆ initialize()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize ( core::pose::Pose & pose )

private

References initialize_libraries(), initialize_movers(), initialize_parameters(), and initialize_score_functions().

Referenced by apply().

◆ initialize_libraries()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_libraries ( core::pose::Pose & pose )

private

References atom_level_domain_map_, options_, rna_base_pair_handler_, rna_chunk_initialization_library_, rna_chunk_library_, user_input_rna_chunk_initialization_library_, and user_input_rna_chunk_library_.

Referenced by initialize().

◆ initialize_movers()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_movers ( core::pose::Pose const & pose )

private

References align_pose_, atom_level_domain_map_, denovo_scorefxn_, hires_scorefxn_, is_rna_and_protein_, options_, outputter_, rna_base_pair_handler_, rna_chunk_initialization_library_, rna_chunk_library_, rna_denovo_master_mover_, rna_denovo_master_mover_init_, rna_helix_mover_, rna_loop_closer_, rna_loop_closer_init_, rna_minimizer_, rna_relaxer_, and rnp_high_res_mover_.

Referenced by initialize().

◆ initialize_parameters()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_parameters ( )

private

References align_pose_, core::chemical::FA_STANDARD, protocols::moves::Mover::get_native_pose(), core::import_pose::get_pdb_with_full_model_info(), options_, refine_pose_, and rounds_.

Referenced by initialize().

◆ initialize_score_functions()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_score_functions ( )

private

References chainbreak_sfxn_, chem_shift_scorefxn_, core::scoring::ScoreFunctionFactory::create_score_function(), denovo_scorefxn_, hires_scorefxn_, core::scoring::linear_chainbreak, options_, core::scoring::rna_chem_shift, and working_denovo_scorefxn_.

Referenced by initialize().

◆ loop_modeling()

bool protocols::rna::denovo::RNA_FragmentMonteCarlo::loop_modeling ( ) const

References rna_chunk_library_.

Referenced by check_for_loop_modeling_case().

◆ lores_pose()

core::pose::PoseOP protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_pose ( )

inline

References lores_pose_.

◆ lores_score_early()

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_score_early ( ) const

inline

References lores_score_early_.

Referenced by apply().

◆ lores_score_final()

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_score_final ( ) const

inline

References lores_score_final_.

Referenced by apply().

◆ outputter()

output::RNA_FragmentMonteCarloOutputterOP protocols::rna::denovo::RNA_FragmentMonteCarlo::outputter ( ) const

inline

References outputter_.

◆ randomize_and_close_all_chains()

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::randomize_and_close_all_chains	(	core::pose::Pose &	pose,
		bool const &	close_chains
	)		const

private

References protocols::moves::MonteCarlo::boltzmann(), chainbreak_sfxn_, is_rna_and_protein_, protocols::moves::MonteCarlo::last_accepted_score(), protocols::moves::MonteCarlo::lowest_score_pose(), monte_carlo_cycles_, options_, rna_chunk_initialization_library_, rna_denovo_master_mover_init_, rna_loop_closer_init_, protocols::hybridization::score, and protocols::moves::MonteCarlo::score_function().

Referenced by setup_full_initial_structure().

◆ reroot_pose_before_align_and_return_moving_res()

vector1< core::Size > protocols::rna::denovo::RNA_FragmentMonteCarlo::reroot_pose_before_align_and_return_moving_res ( core::pose::Pose & pose ) const

private

References atom_level_domain_map_, core::pose::Pose::fold_tree(), protocols::rna::denovo::get_moving_res(), core::kinematics::FoldTree::get_parent_residue(), core::kinematics::FoldTree::jump_nr(), and protocols::stepwise::modeler::revise_root_and_moving_res().

Referenced by apply().

◆ rna_base_pair_handler()

core::import_pose::RNA_BasePairHandlerCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_base_pair_handler ( ) const

inline

References rna_base_pair_handler_.

Referenced by get_rmsd_stems_no_superimpose().

◆ rna_chunk_library()

core::import_pose::libraries::RNA_ChunkLibraryCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_chunk_library ( ) const

inline

References rna_chunk_library_.

◆ rna_loop_closer()

protocols::rna::movers::RNA_LoopCloserCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_loop_closer ( ) const

inline

References rna_loop_closer_.

◆ set_all_lores_score_final()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_all_lores_score_final ( std::list< core::Real > const & setting )

inline

References all_lores_score_final_.

◆ set_denovo_scorefxn()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_denovo_scorefxn ( core::scoring::ScoreFunctionCOP setting )

inline

References denovo_scorefxn_.

◆ set_hires_scorefxn()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_hires_scorefxn ( core::scoring::ScoreFunctionCOP setting )

inline

References hires_scorefxn_.

◆ set_is_rna_and_protein()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_is_rna_and_protein ( bool const & setting )

inline

References is_rna_and_protein_.

◆ set_out_file_tag()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_out_file_tag ( std::string const & setting )

inline

References out_file_tag_.

◆ set_outputter()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_outputter ( output::RNA_FragmentMonteCarloOutputterOP const & setting )

inline

References outputter_.

◆ set_refine_pose()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_refine_pose ( bool const setting )

inline

References refine_pose_.

◆ set_rna_base_pair_handler()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_rna_base_pair_handler ( core::import_pose::RNA_BasePairHandlerCOP setting )

inline

References rna_base_pair_handler_.

◆ set_rna_de_novo_pose_initializer()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_rna_de_novo_pose_initializer ( protocols::rna::denovo::RNA_DeNovoPoseInitializerCOP setting )

inline

References rna_de_novo_pose_initializer_.

◆ set_user_input_chunk_initialization_library()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_user_input_chunk_initialization_library ( core::import_pose::libraries::RNA_ChunkLibraryCOP setting )

inline

References user_input_rna_chunk_initialization_library_.

◆ set_user_input_chunk_library()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_user_input_chunk_library ( core::import_pose::libraries::RNA_ChunkLibraryCOP setting )

inline

References user_input_rna_chunk_library_.

◆ set_vdw_grid()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_vdw_grid ( protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP setting )

inline

References vdw_grid_.

◆ setup_full_initial_structure()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::setup_full_initial_structure ( core::pose::Pose & pose ) const

private

References options_, randomize_and_close_all_chains(), rna_chunk_initialization_library_, rna_de_novo_pose_initializer_, rna_denovo_master_mover_init_, and protocols::hybridization::score.

Referenced by apply().

◆ setup_monte_carlo_cycles()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::setup_monte_carlo_cycles ( core::pose::Pose const & pose )

private

References atom_level_domain_map_, protocols::rna::denovo::get_moving_res(), core::pose::rna::get_rigid_body_jumps(), monte_carlo_cycles_, monte_carlo_cycles_max_default_, options_, rna_chunk_library_, and protocols::rna::denovo::TR().

Referenced by apply().

◆ show()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::show ( std::ostream & output ) 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 lores_score_early_, lores_score_final_, monte_carlo_cycles_, monte_carlo_cycles_max_default_, and rounds_.

◆ update_denovo_scorefxn_weights()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::update_denovo_scorefxn_weights ( core::Size const r )

private

Progressive upweighting of 'fine-scale' RNA modeling terms. Stack geometry, chainbreak, and constraint terms are zero for first of 10 rna_denovo rounds, then titrated up to final weight. Analogous to abinitio protocol for proteins, where strand geometry terms are turned on late.

References core::scoring::atom_pair_constraint, core::scoring::base_pair_constraint, core::scoring::chainbreak, core::scoring::coordinate_constraint, denovo_scorefxn_, core::scoring::linear_chainbreak, options_, core::scoring::rna_base_axis, core::scoring::rna_base_stack_axis, core::scoring::rna_base_stagger, core::scoring::rna_chem_map_lores, core::scoring::rnp_vdw, rounds_, and working_denovo_scorefxn_.

Referenced by apply().

◆ update_frag_size()

Size protocols::rna::denovo::RNA_FragmentMonteCarlo::update_frag_size ( core::Size const & r ) const

private

Classic 3->2->1 RNA fragment size reduction, set by round r.

References options_, and rounds_.

Referenced by update_rna_denovo_master_mover().

◆ update_pose_constraints()

void protocols::rna::denovo::RNA_FragmentMonteCarlo::update_pose_constraints	(	core::Size const	r,
		core::pose::Pose &	pose
	)

private

Only does something if -staged_constraints flag is on. Progressively introduces constraints, with shortest range first (as determined by distance in fold-tree). Inspired by classic fold_constraints protocol for proteins.

References core::pose::Pose::constraint_set(), constraint_set_, core::kinematics::ShortestPathInFoldTree::dist(), figure_out_constraint_separation_cutoff(), core::pose::Pose::fold_tree(), core::kinematics::ShortestPathInFoldTree::max_dist(), options_, rounds_, and protocols::rna::denovo::TR().

Referenced by apply().