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

#include <RNA_DeNovoProtocol.hh>

Public Member Functions
	RNA_DeNovoProtocol (Size const nstruct, std::string const silent_file, bool const heat_structure=true, bool const minimize_structure=false, bool const relax_structure=false, bool const allow_bulge=false)
	Construct the protocol object given the RNA fragment library to use. More...

	~RNA_DeNovoProtocol ()

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

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

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

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

void	set_dump_pdb (bool const setting)

void	set_temperature (core::Real const setting)

void	set_jump_library_file (std::string const jump_library_file)

void	set_all_rna_fragments_file (std::string const file)

void	set_vall_torsions_file (std::string const file)

void	set_rna_params_file (std::string const file)

void	set_rna_data_file (std::string const file)

void	set_chunk_pdb_files (utility::vector1< std::string > const &chunk_pdb_files)

void	set_chunk_silent_files (utility::vector1< std::string > const &chunk_silent_files)

void	set_input_res (utility::vector1< Size > const &input_res)

void	ignore_secstruct (bool const setting)

void	jump_change_frequency (core::Real const value)

void	set_close_loops (bool const setting)

void	set_close_loops_after_each_move (bool const setting)

void	simple_rmsd_cutoff_relax (bool const setting)

void	output_lores_silent_file (bool const setting)

void	set_filter_lores_base_pairs (bool const setting)

void	set_filter_lores_base_pairs_early (bool const setting)

void	set_filter_chain_closure (bool const setting)

void	set_filter_chain_closure_distance (core::Real const setting)

void	set_filter_chain_closure_halfway (bool const setting)

void	set_binary_rna_output (bool const setting)

void	set_suppress_bp_constraint (core::Real const setting)

void	set_lores_scorefxn (std::string const &lores_scorefxn)

void	set_vary_bond_geometry (bool const setting)

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_staged_constraints (bool const setting)

void	set_allow_consecutive_bulges (bool const setting)

void	set_chainbreak_weight (core::Real setting)

void	set_linear_chainbreak_weight (core::Real setting)

void	set_allowed_bulge_res (utility::vector1< core::Size > const &setting)

void	set_move_first_rigid_body (bool const setting)

void	set_root_at_first_rigid_body (bool const setting)

void	set_output_filters (bool const setting)

void	set_autofilter (bool const setting)

void	set_monte_carlo_cycles (Size const setting)

void	set_rounds (Size const setting)

void	set_extra_minimize_res (utility::vector1< core::Size > setting)

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

void	set_refine_pose (Size const setting)

void	set_bps_moves (Size const setting)

void	set_minimizer_use_coordinate_constraints (Size 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 void	parse_my_tag (TagCOP tag, basic::datacache::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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	initialize_movers (core::pose::Pose &pose)

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

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

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	setup_rigid_body_mover (core::pose::Pose const &pose, core::Size const r)

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	do_random_moves (core::pose::Pose &pose)

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

void	update_denovo_scorefxn_weights (Size const r)

Size	figure_out_constraint_separation_cutoff (Size const r, Size const max_dist)

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

void	update_frag_size (Size const r)

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

bool	random_chunk_trial (core::pose::Pose &pose)

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

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

void	add_number_base_pairs (core::pose::Pose const &pose_input, core::io::silent::SilentStruct &s) const

void	add_number_native_base_pairs (core::pose::Pose &pose, core::io::silent::SilentStruct &s) const

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

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

Private Attributes
Size const	nstruct_

Size	rounds_

Size	monte_carlo_cycles_

Size const	monte_carlo_cycles_max_default_

bool	user_defined_cycles_

std::string	all_rna_fragments_file_

std::string const	silent_file_

std::string	lores_silent_file_

bool const	heat_structure_

bool	dump_pdb_

bool const	minimize_structure_

bool const	relax_structure_

bool	ignore_secstruct_

bool	do_close_loops_

bool	close_loops_at_end_

bool	close_loops_in_last_round_

bool	close_loops_after_each_move_

bool	simple_rmsd_cutoff_relax_

bool	allow_bulge_

bool	allow_consecutive_bulges_

bool const	use_chem_shift_data_

core::Real	m_Temperature_

Size	frag_size_

protocols::moves::MonteCarloOP	monte_carlo_

protocols::farna::RNA_FragmentsOP	all_rna_fragments_

protocols::farna::RNA_FragmentMoverOP	rna_fragment_mover_

protocols::farna::RNA_LoopCloserOP	rna_loop_closer_

protocols::farna::RNA_ChunkLibraryOP	rna_chunk_library_

protocols::farna::RNA_MinimizerOP	rna_minimizer_

protocols::farna::RNA_RelaxerOP	rna_relaxer_

protocols::rigid::RigidBodyPerturbMoverOP	rigid_body_mover_

std::string	rna_params_file_

std::string	rna_data_file_

std::string	jump_library_file_

RNA_StructureParametersOP	rna_structure_parameters_

RNA_DataReaderOP	rna_data_reader_

bool	output_lores_silent_file_

bool	filter_lores_base_pairs_

bool	filter_lores_base_pairs_early_

bool	filter_chain_closure_

core::Real	filter_chain_closure_distance_

bool	filter_chain_closure_halfway_

bool	vary_bond_geometry_

bool	binary_rna_output_

core::scoring::constraints::ConstraintSetOP	constraint_set_

core::Real	jump_change_frequency_

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

std::string	lores_scorefxn_

core::scoring::ScoreFunctionOP	denovo_scorefxn_

core::scoring::ScoreFunctionOP	hires_scorefxn_

core::scoring::ScoreFunctionOP	chem_shift_scorefxn_

core::scoring::ScoreFunctionOP	initial_denovo_scorefxn_

core::scoring::rna::RNA_LowResolutionPotential	local_rna_low_resolution_potential_

utility::vector1< std::string >	chunk_pdb_files_

utility::vector1< std::string >	chunk_silent_files_

utility::vector1< core::Size >	input_res_

utility::vector1< core::Size >	allowed_bulge_res_

utility::vector1< core::Size >	extra_minimize_res_

core::Real	chunk_coverage_

bool	staged_constraints_

core::Real	chainbreak_weight_

core::Real	linear_chainbreak_weight_

bool	titrate_stack_bonus_

bool	move_first_rigid_body_

bool	root_at_first_rigid_body_

core::Real	suppress_bp_constraint_

bool	output_filters_

core::Real	lores_score_early_

core::Real	lores_score_final_

bool	autofilter_

core::Real	autofilter_score_quantile_

std::list< core::Real >	all_lores_score_final_

bool	refine_from_silent_

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

bool	refine_pose_

bool	bps_moves_

bool	minimizer_use_coordinate_constraints_

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 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. 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

protocols::farna::RNA_DeNovoProtocol::RNA_DeNovoProtocol	(	Size const	nstruct,
		std::string const	silent_file,
		bool const	heat_structure = `true`,
		bool const	minimize_structure = `false`,
		bool const	relax_structure = `false`,
		bool const	allow_bulge = `false`
	)

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

References database, full_name(), local_rna_low_resolution_potential_, core::scoring::rna::RNA_LowResolutionPotential::more_precise_base_pair_classification(), option, options, rna_chemical_shift_exp_data, rna_loop_closer_, score, and user.

Referenced by clone().

protocols::farna::RNA_DeNovoProtocol::~RNA_DeNovoProtocol ( )

Member Function Documentation

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

private

References core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_total_exp_chemical_shift_data_points(), use_chem_shift_data_, and utility_exit_with_message.

Referenced by output_to_silent_file().

void protocols::farna::RNA_DeNovoProtocol::add_number_base_pairs	(	core::pose::Pose const &	pose_input,
		core::io::silent::SilentStruct &	s
	)		const

private

References protocols::farna::classify_base_pairs(), protocols::farna::get_number_base_stacks(), protocols::abinitio::abscript::I, j, core::chemical::rna::possibly_canonical(), core::pose::Pose::residue(), and core::chemical::rna::WATSON_CRICK.

Referenced by output_silent_struct().

void protocols::farna::RNA_DeNovoProtocol::add_number_native_base_pairs	(	core::pose::Pose &	pose,
		core::io::silent::SilentStruct &	s
	)		const

private

References protocols::farna::check_in_base_pair_list(), protocols::farna::classify_base_pairs(), core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, get_edge_from_num(), protocols::moves::Mover::get_native_pose(), j, core::conformation::Residue::name1(), core::scoring::rna::Base_pair::orientation, possibly_canonical(), core::scoring::rna::Base_pair::res1, core::scoring::rna::Base_pair::res2, core::pose::Pose::residue(), and core::chemical::rna::WATSON_CRICK.

Referenced by output_silent_struct().

void protocols::farna::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 protocols::stepwise::create_alignment_id_map(), get_moving_res(), protocols::moves::Mover::get_native_pose(), input_res_, output_to_silent_file(), rna_chunk_library_, core::scoring::superimpose_pose(), protocols::farna::RNA_ChunkLibrary::superimpose_to_first_chunk(), core::pose::Pose::total_residue(), and protocols::farna::TR.

Referenced by apply().

void protocols::farna::RNA_DeNovoProtocol::apply ( core::pose::Pose & pose )

virtual

Apply the RNA denovo modeling protocol to the input pose.

Apply the RNA de novo modeling protocol to a pose.

Implements protocols::moves::Mover.

void protocols::farna::RNA_DeNovoProtocol::apply_chem_shift_data	(	core::pose::Pose &	pose,
		std::string const	out_file_tag
	)

private

References protocols::farna::RNA_Minimizer::apply(), protocols::farna::RNA_LoopCloser::apply(), chem_shift_scorefxn_, close_loops_at_end_, protocols::farna::RNA_StructureParameters::connections(), hires_scorefxn_, minimize_structure_, rna_loop_closer_, rna_minimizer_, rna_structure_parameters_, protocols::farna::RNA_Minimizer::set_score_function(), use_chem_shift_data_, and utility_exit_with_message.

Referenced by apply().

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

private

References all_atom_rmsd(), protocols::moves::Mover::get_native_pose(), protocols::farna::RNA_StructureParameters::get_stem_residues(), rmsd, rna_structure_parameters_, and protocols::farna::TR.

Referenced by output_silent_struct().

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

private

References autofilter_score_quantile_, and protocols::farna::TR.

Referenced by apply().

protocols::moves::MoverOP protocols::farna::RNA_DeNovoProtocol::clone ( ) const

virtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References RNA_DeNovoProtocol().

void protocols::farna::RNA_DeNovoProtocol::do_random_moves ( core::pose::Pose & pose )

private

References protocols::farna::RNA_ChunkLibrary::check_fold_tree_OK(), core::pose::Pose::dump_pdb(), dump_pdb_, protocols::farna::RNA_ChunkLibrary::initialize_random_chunks(), protocols::farna::RNA_FragmentMover::random_fragment_insertion(), randomize_rigid_body_orientations(), rna_chunk_library_, rna_fragment_mover_, core::pose::Pose::total_residue(), protocols::farna::TR, and protocols::farna::translate_virtual_anchor_to_first_rigid_body().

Referenced by apply().

Size protocols::farna::RNA_DeNovoProtocol::figure_out_constraint_separation_cutoff	(	Size const	r,
		Size const	max_dist
	)

private

References rounds_.

Referenced by update_pose_constraints().

utility::vector1< Size > protocols::farna::RNA_DeNovoProtocol::get_moving_res ( core::pose::Pose const & pose ) const

private

References protocols::farna::RNA_StructureParameters::allow_insert(), utility::pointer::owning_ptr< T >::get(), rna_structure_parameters_, and core::pose::Pose::total_residue().

Referenced by align_and_output_to_silent_file(), and setup_monte_carlo_cycles().

std::string protocols::farna::RNA_DeNovoProtocol::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::farna::RNA_DeNovoProtocol::ignore_secstruct ( bool const setting )

inline

References ignore_secstruct_.

void protocols::farna::RNA_DeNovoProtocol::initialize_constraints ( core::pose::Pose & pose )

private

References atom_pair_constraint, core::pose::Pose::constraint_set(), constraint_set_, coordinate_constraint, and denovo_scorefxn_.

Referenced by apply(), and initialize_scorefxn().

void protocols::farna::RNA_DeNovoProtocol::initialize_lores_silent_file ( )

private

References lores_silent_file_, output_lores_silent_file_, silent_file_, and utility_exit_with_message.

Referenced by apply().

void protocols::farna::RNA_DeNovoProtocol::initialize_movers ( core::pose::Pose & pose )

private

Referenced by apply().

void protocols::farna::RNA_DeNovoProtocol::initialize_scorefxn ( core::pose::Pose & pose )

private

References chainbreak, chainbreak_weight_, chem_shift_scorefxn_, core::scoring::ScoreFunction::clone(), protocols::farna::RNA_Minimizer::clone_scorefxn(), denovo_scorefxn_, hires_scorefxn_, initial_denovo_scorefxn_, initialize_constraints(), linear_chainbreak, linear_chainbreak_weight_, lores_scorefxn_, rna_chem_shift, rna_minimizer_, and use_chem_shift_data_.

Referenced by apply().

void protocols::farna::RNA_DeNovoProtocol::initialize_tag_is_done ( )

private

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

Referenced by apply().

void protocols::farna::RNA_DeNovoProtocol::jump_change_frequency ( core::Real const value )

inline

References jump_change_frequency_.

void protocols::farna::RNA_DeNovoProtocol::output_lores_silent_file ( bool const setting )

inline

References output_lores_silent_file_.

void protocols::farna::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 add_number_base_pairs(), add_number_native_base_pairs(), calc_rmsds(), protocols::moves::Mover::get_native_pose(), lores_score_early_, lores_score_final_, minimize_structure_, output_filters_, protocols::farna::TR, and core::io::silent::SilentFileData::write_silent_struct().

Referenced by output_to_silent_file().

void protocols::farna::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(), binary_rna_output_, output_silent_struct(), s, protocols::farna::TR, and use_chem_shift_data_.

Referenced by align_and_output_to_silent_file().

bool protocols::farna::RNA_DeNovoProtocol::random_chunk_trial ( core::pose::Pose & pose )

private

References protocols::farna::RNA_LoopCloser::apply(), protocols::moves::MonteCarlo::boltzmann(), do_close_loops_, monte_carlo_, protocols::farna::RNA_ChunkLibrary::random_chunk_insertion(), rna_chunk_library_, and rna_loop_closer_.

Referenced by RNA_move_trial().

void protocols::farna::RNA_DeNovoProtocol::random_fragment_trial ( core::pose::Pose & pose )

private

References protocols::farna::RNA_LoopCloser::apply(), protocols::moves::MonteCarlo::boltzmann(), do_close_loops_, frag_size_, monte_carlo_, protocols::farna::RNA_FragmentMover::random_fragment_insertion(), rna_fragment_mover_, and rna_loop_closer_.

Referenced by RNA_move_trial().

void protocols::farna::RNA_DeNovoProtocol::random_jump_trial ( core::pose::Pose & pose )

private

References protocols::farna::RNA_LoopCloser::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::moves::MonteCarlo::boltzmann(), do_close_loops_, monte_carlo_, protocols::farna::RNA_StructureParameters::random_jump_change(), protocols::farna::RG, rigid_body_mover_, rna_loop_closer_, rna_structure_parameters_, and numeric::random::RandomGenerator::uniform().

Referenced by RNA_move_trial().

void protocols::farna::RNA_DeNovoProtocol::randomize_rigid_body_orientations ( core::pose::Pose & pose )

private

References protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::farna::get_rigid_body_jumps(), core::kinematics::Jump::get_translation(), core::pose::Pose::jump(), protocols::rigid::partner_upstream, core::pose::Pose::set_jump(), and core::kinematics::Jump::set_translation().

Referenced by do_random_moves().

void protocols::farna::RNA_DeNovoProtocol::RNA_move_trial ( core::pose::Pose & pose )

private

References chunk_coverage_, jump_change_frequency_, random_chunk_trial(), random_fragment_trial(), random_jump_trial(), protocols::farna::RG, and numeric::random::RandomGenerator::uniform().

Referenced by apply().

void protocols::farna::RNA_DeNovoProtocol::set_all_rna_fragments_file ( std::string const file )

inline

References all_rna_fragments_file_.

void protocols::farna::RNA_DeNovoProtocol::set_allow_consecutive_bulges ( bool const setting )

inline

References allow_consecutive_bulges_.

void protocols::farna::RNA_DeNovoProtocol::set_allowed_bulge_res ( utility::vector1< core::Size > const & setting )

inline

References allowed_bulge_res_.

void protocols::farna::RNA_DeNovoProtocol::set_autofilter ( bool const setting )

inline

References autofilter_.

void protocols::farna::RNA_DeNovoProtocol::set_binary_rna_output ( bool const setting )

inline

References binary_rna_output_.

void protocols::farna::RNA_DeNovoProtocol::set_bps_moves ( Size const setting )

inline

References bps_moves_.

void protocols::farna::RNA_DeNovoProtocol::set_chainbreak_weight ( core::Real setting )

inline

References chainbreak_weight_.

void protocols::farna::RNA_DeNovoProtocol::set_chunk_pdb_files ( utility::vector1< std::string > const & chunk_pdb_files )

inline

References chunk_pdb_files_.

void protocols::farna::RNA_DeNovoProtocol::set_chunk_silent_files ( utility::vector1< std::string > const & chunk_silent_files )

inline

References chunk_silent_files_.

void protocols::farna::RNA_DeNovoProtocol::set_close_loops ( bool const setting )

inline

References binary_rna_output_, and close_loops_at_end_.

void protocols::farna::RNA_DeNovoProtocol::set_close_loops_after_each_move ( bool const setting )

inline

References close_loops_after_each_move_.

void protocols::farna::RNA_DeNovoProtocol::set_dump_pdb ( bool const setting )

inline

References dump_pdb_.

void protocols::farna::RNA_DeNovoProtocol::set_extra_minimize_res ( utility::vector1< core::Size > setting )

References extra_minimize_res_.

void protocols::farna::RNA_DeNovoProtocol::set_filter_chain_closure ( bool const setting )

inline

References filter_chain_closure_.

void protocols::farna::RNA_DeNovoProtocol::set_filter_chain_closure_distance ( core::Real const setting )

inline

References filter_chain_closure_distance_.

void protocols::farna::RNA_DeNovoProtocol::set_filter_chain_closure_halfway ( bool const setting )

inline

References filter_chain_closure_halfway_.

void protocols::farna::RNA_DeNovoProtocol::set_filter_lores_base_pairs ( bool const setting )

inline

References filter_lores_base_pairs_.

void protocols::farna::RNA_DeNovoProtocol::set_filter_lores_base_pairs_early ( bool const setting )

inline

References filter_lores_base_pairs_, and filter_lores_base_pairs_early_.

void protocols::farna::RNA_DeNovoProtocol::set_input_res ( utility::vector1< Size > const & input_res )

inline

References input_res_.

void protocols::farna::RNA_DeNovoProtocol::set_jump_library_file ( std::string const jump_library_file )

inline

References jump_library_file_.

void protocols::farna::RNA_DeNovoProtocol::set_linear_chainbreak_weight ( core::Real setting )

inline

References linear_chainbreak_weight_.

void protocols::farna::RNA_DeNovoProtocol::set_lores_scorefxn ( std::string const & lores_scorefxn )

inline

References lores_scorefxn_.

void protocols::farna::RNA_DeNovoProtocol::set_minimizer_use_coordinate_constraints ( Size const setting )

inline

References minimizer_use_coordinate_constraints_.

void protocols::farna::RNA_DeNovoProtocol::set_monte_carlo_cycles ( Size const setting )

inline

References monte_carlo_cycles_, and user_defined_cycles_.

void protocols::farna::RNA_DeNovoProtocol::set_move_first_rigid_body ( bool const setting )

inline

References move_first_rigid_body_.

void protocols::farna::RNA_DeNovoProtocol::set_output_filters ( bool const setting )

inline

References output_filters_.

void protocols::farna::RNA_DeNovoProtocol::set_refine_pose ( Size const setting )

inline

References refine_pose_.

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

References refine_from_silent_, refine_pose_list_, and rounds_.

void protocols::farna::RNA_DeNovoProtocol::set_rna_data_file ( std::string const file )

inline

References rna_data_file_.

void protocols::farna::RNA_DeNovoProtocol::set_rna_params_file ( std::string const file )

inline

References rna_params_file_.

void protocols::farna::RNA_DeNovoProtocol::set_root_at_first_rigid_body ( bool const setting )

inline

References root_at_first_rigid_body_.

void protocols::farna::RNA_DeNovoProtocol::set_rounds ( Size const setting )

inline

References rounds_.

void protocols::farna::RNA_DeNovoProtocol::set_staged_constraints ( bool const setting )

inline

References staged_constraints_.

void protocols::farna::RNA_DeNovoProtocol::set_suppress_bp_constraint ( core::Real const setting )

inline

References suppress_bp_constraint_.

void protocols::farna::RNA_DeNovoProtocol::set_temperature ( core::Real const setting )

inline

References m_Temperature_.

void protocols::farna::RNA_DeNovoProtocol::set_vall_torsions_file ( std::string const file )

inline

References all_rna_fragments_file_.

void protocols::farna::RNA_DeNovoProtocol::set_vary_bond_geometry ( bool const setting )

inline

References binary_rna_output_, and vary_bond_geometry_.

void protocols::farna::RNA_DeNovoProtocol::setup_monte_carlo_cycles ( core::pose::Pose const & pose )

private

References get_moving_res(), protocols::farna::get_rigid_body_jumps(), monte_carlo_cycles_, monte_carlo_cycles_max_default_, protocols::farna::RNA_ChunkLibrary::num_moving_chunks(), rna_chunk_library_, protocols::farna::TR, and user_defined_cycles_.

Referenced by apply().

void protocols::farna::RNA_DeNovoProtocol::setup_rigid_body_mover	(	core::pose::Pose const &	pose,
		core::Size const	r
	)

private

References binary_rna_output_, jump_change_frequency_, protocols::farna::let_rigid_body_jumps_move(), move_first_rigid_body_, movemap, protocols::rigid::partner_upstream, rigid_body_mover_, rounds_, core::kinematics::MoveMap::set_jump(), protocols::farna::TR, and utility_exit_with_message.

Referenced by apply().

void protocols::farna::RNA_DeNovoProtocol::show ( std::ostream & output = std::cout ) const

virtual

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 all_rna_fragments_file_, allow_bulge_, allow_consecutive_bulges_, autofilter_, autofilter_score_quantile_, binary_rna_output_, chunk_coverage_, close_loops_after_each_move_, close_loops_at_end_, close_loops_in_last_round_, do_close_loops_, dump_pdb_, filter_chain_closure_, filter_chain_closure_distance_, filter_chain_closure_halfway_, filter_lores_base_pairs_, filter_lores_base_pairs_early_, frag_size_, heat_structure_, ignore_secstruct_, jump_change_frequency_, jump_library_file_, lores_score_early_, lores_score_final_, m_Temperature_, minimize_structure_, monte_carlo_cycles_, monte_carlo_cycles_max_default_, move_first_rigid_body_, nstruct_, output_filters_, output_lores_silent_file_, relax_structure_, rna_data_file_, rna_params_file_, root_at_first_rigid_body_, rounds_, simple_rmsd_cutoff_relax_, staged_constraints_, titrate_stack_bonus_, use_chem_shift_data_, user_defined_cycles_, and vary_bond_geometry_.

Referenced by protocols::farna::operator<<().

void protocols::farna::RNA_DeNovoProtocol::simple_rmsd_cutoff_relax ( bool const setting )

inline

References simple_rmsd_cutoff_relax_.

void protocols::farna::RNA_DeNovoProtocol::update_denovo_scorefxn_weights ( Size const r )

private

References atom_pair_constraint, chainbreak, coordinate_constraint, denovo_scorefxn_, initial_denovo_scorefxn_, linear_chainbreak, rna_base_axis, rna_base_stack_axis, rna_base_stagger, rounds_, and titrate_stack_bonus_.

Referenced by apply().

void protocols::farna::RNA_DeNovoProtocol::update_frag_size ( Size const r )

private

References frag_size_, rounds_, and protocols::farna::TR.

Referenced by apply().

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

private

References core::pose::Pose::constraint_set(), constraint_set_, cst, figure_out_constraint_separation_cutoff(), core::pose::Pose::fold_tree(), core::scoring::constraints::ConstraintSet::get_all_constraints(), j, rounds_, staged_constraints_, and protocols::farna::TR.

Referenced by apply().

Member Data Documentation

std::list< core::Real > protocols::farna::RNA_DeNovoProtocol::all_lores_score_final_

private

Referenced by apply().

protocols::farna::RNA_FragmentsOP protocols::farna::RNA_DeNovoProtocol::all_rna_fragments_

private

Referenced by initialize_movers().

std::string protocols::farna::RNA_DeNovoProtocol::all_rna_fragments_file_

private

Referenced by initialize_movers(), set_all_rna_fragments_file(), set_vall_torsions_file(), and show().

bool protocols::farna::RNA_DeNovoProtocol::allow_bulge_

private

Referenced by apply(), and show().

bool protocols::farna::RNA_DeNovoProtocol::allow_consecutive_bulges_

private

Referenced by apply(), set_allow_consecutive_bulges(), and show().

utility::vector1< core::Size > protocols::farna::RNA_DeNovoProtocol::allowed_bulge_res_

private

Referenced by apply(), and set_allowed_bulge_res().

bool protocols::farna::RNA_DeNovoProtocol::autofilter_

private

Referenced by apply(), set_autofilter(), and show().

core::Real protocols::farna::RNA_DeNovoProtocol::autofilter_score_quantile_

private

Referenced by check_score_filter(), and show().

bool protocols::farna::RNA_DeNovoProtocol::binary_rna_output_

private

Referenced by output_to_silent_file(), set_binary_rna_output(), set_close_loops(), set_vary_bond_geometry(), setup_rigid_body_mover(), and show().

bool protocols::farna::RNA_DeNovoProtocol::bps_moves_

private

Referenced by initialize_movers(), and set_bps_moves().

core::Real protocols::farna::RNA_DeNovoProtocol::chainbreak_weight_

private

Referenced by initialize_scorefxn(), and set_chainbreak_weight().

core::scoring::ScoreFunctionOP protocols::farna::RNA_DeNovoProtocol::chem_shift_scorefxn_

private

Referenced by apply(), apply_chem_shift_data(), and initialize_scorefxn().

core::Real protocols::farna::RNA_DeNovoProtocol::chunk_coverage_

private

Referenced by initialize_movers(), RNA_move_trial(), and show().

utility::vector1< std::string > protocols::farna::RNA_DeNovoProtocol::chunk_pdb_files_

private

Referenced by initialize_movers(), and set_chunk_pdb_files().

utility::vector1< std::string > protocols::farna::RNA_DeNovoProtocol::chunk_silent_files_

private

Referenced by initialize_movers(), and set_chunk_silent_files().

bool protocols::farna::RNA_DeNovoProtocol::close_loops_after_each_move_

private

Referenced by apply(), set_close_loops_after_each_move(), and show().

bool protocols::farna::RNA_DeNovoProtocol::close_loops_at_end_

private

Referenced by apply(), apply_chem_shift_data(), set_close_loops(), and show().

bool protocols::farna::RNA_DeNovoProtocol::close_loops_in_last_round_

private

Referenced by apply(), and show().

core::scoring::constraints::ConstraintSetOP protocols::farna::RNA_DeNovoProtocol::constraint_set_

private

Referenced by initialize_constraints(), and update_pose_constraints().

core::scoring::ScoreFunctionOP protocols::farna::RNA_DeNovoProtocol::denovo_scorefxn_

private

Referenced by apply(), initialize_constraints(), initialize_scorefxn(), and update_denovo_scorefxn_weights().

bool protocols::farna::RNA_DeNovoProtocol::do_close_loops_

private

Referenced by apply(), random_chunk_trial(), random_fragment_trial(), random_jump_trial(), and show().

bool protocols::farna::RNA_DeNovoProtocol::dump_pdb_

private

Referenced by apply(), do_random_moves(), set_dump_pdb(), and show().

utility::vector1< core::Size > protocols::farna::RNA_DeNovoProtocol::extra_minimize_res_

private

Referenced by initialize_movers(), and set_extra_minimize_res().

bool protocols::farna::RNA_DeNovoProtocol::filter_chain_closure_

private

Referenced by apply(), set_filter_chain_closure(), and show().

core::Real protocols::farna::RNA_DeNovoProtocol::filter_chain_closure_distance_

private

Referenced by apply(), set_filter_chain_closure_distance(), and show().

bool protocols::farna::RNA_DeNovoProtocol::filter_chain_closure_halfway_

private

Referenced by apply(), set_filter_chain_closure_halfway(), and show().

bool protocols::farna::RNA_DeNovoProtocol::filter_lores_base_pairs_

private

Referenced by apply(), set_filter_lores_base_pairs(), set_filter_lores_base_pairs_early(), and show().

bool protocols::farna::RNA_DeNovoProtocol::filter_lores_base_pairs_early_

private

Referenced by apply(), set_filter_lores_base_pairs_early(), and show().

Size protocols::farna::RNA_DeNovoProtocol::frag_size_

private

Referenced by apply(), random_fragment_trial(), show(), and update_frag_size().

bool const protocols::farna::RNA_DeNovoProtocol::heat_structure_

private

Referenced by apply(), and show().

core::scoring::ScoreFunctionOP protocols::farna::RNA_DeNovoProtocol::hires_scorefxn_

private

Referenced by apply(), apply_chem_shift_data(), and initialize_scorefxn().

bool protocols::farna::RNA_DeNovoProtocol::ignore_secstruct_

private

Referenced by ignore_secstruct(), initialize_movers(), and show().

core::scoring::ScoreFunctionOP protocols::farna::RNA_DeNovoProtocol::initial_denovo_scorefxn_

private

Referenced by initialize_scorefxn(), and update_denovo_scorefxn_weights().

utility::vector1< core::Size > protocols::farna::RNA_DeNovoProtocol::input_res_

private

Referenced by align_and_output_to_silent_file(), initialize_movers(), and set_input_res().

core::Real protocols::farna::RNA_DeNovoProtocol::jump_change_frequency_

private

Referenced by jump_change_frequency(), RNA_move_trial(), setup_rigid_body_mover(), and show().

std::string protocols::farna::RNA_DeNovoProtocol::jump_library_file_

private

Referenced by initialize_movers(), set_jump_library_file(), and show().

core::Real protocols::farna::RNA_DeNovoProtocol::linear_chainbreak_weight_

private

Referenced by initialize_scorefxn(), and set_linear_chainbreak_weight().

core::scoring::rna::RNA_LowResolutionPotential protocols::farna::RNA_DeNovoProtocol::local_rna_low_resolution_potential_

private

Referenced by RNA_DeNovoProtocol().

core::Real protocols::farna::RNA_DeNovoProtocol::lores_score_early_

private

Referenced by apply(), output_silent_struct(), and show().

core::Real protocols::farna::RNA_DeNovoProtocol::lores_score_final_

private

Referenced by apply(), output_silent_struct(), and show().

std::string protocols::farna::RNA_DeNovoProtocol::lores_scorefxn_

private

Referenced by initialize_scorefxn(), and set_lores_scorefxn().

std::string protocols::farna::RNA_DeNovoProtocol::lores_silent_file_

private

Referenced by apply(), and initialize_lores_silent_file().

core::Real protocols::farna::RNA_DeNovoProtocol::m_Temperature_

private

Referenced by apply(), set_temperature(), and show().

bool const protocols::farna::RNA_DeNovoProtocol::minimize_structure_

private

Referenced by apply(), apply_chem_shift_data(), output_silent_struct(), and show().

bool protocols::farna::RNA_DeNovoProtocol::minimizer_use_coordinate_constraints_

private

Referenced by initialize_movers(), and set_minimizer_use_coordinate_constraints().

protocols::moves::MonteCarloOP protocols::farna::RNA_DeNovoProtocol::monte_carlo_

private

Referenced by apply(), random_chunk_trial(), random_fragment_trial(), and random_jump_trial().

Size protocols::farna::RNA_DeNovoProtocol::monte_carlo_cycles_

private

Referenced by apply(), set_monte_carlo_cycles(), setup_monte_carlo_cycles(), and show().

Size const protocols::farna::RNA_DeNovoProtocol::monte_carlo_cycles_max_default_

private

Referenced by setup_monte_carlo_cycles(), and show().

bool protocols::farna::RNA_DeNovoProtocol::move_first_rigid_body_

private

Referenced by initialize_movers(), set_move_first_rigid_body(), setup_rigid_body_mover(), and show().

Size const protocols::farna::RNA_DeNovoProtocol::nstruct_

private

Referenced by apply(), and show().

bool protocols::farna::RNA_DeNovoProtocol::output_filters_

private

Referenced by output_silent_struct(), set_output_filters(), and show().

bool protocols::farna::RNA_DeNovoProtocol::output_lores_silent_file_

private

Referenced by apply(), initialize_lores_silent_file(), output_lores_silent_file(), and show().

bool protocols::farna::RNA_DeNovoProtocol::refine_from_silent_

private

Referenced by apply(), and set_refine_pose_list().

bool protocols::farna::RNA_DeNovoProtocol::refine_pose_

private

Referenced by apply(), and set_refine_pose().

utility::vector1<core::pose::PoseOP> protocols::farna::RNA_DeNovoProtocol::refine_pose_list_

private

Referenced by apply(), and set_refine_pose_list().

bool const protocols::farna::RNA_DeNovoProtocol::relax_structure_

private

Referenced by apply(), and show().

protocols::rigid::RigidBodyPerturbMoverOP protocols::farna::RNA_DeNovoProtocol::rigid_body_mover_

private

Referenced by random_jump_trial(), and setup_rigid_body_mover().

protocols::farna::RNA_ChunkLibraryOP protocols::farna::RNA_DeNovoProtocol::rna_chunk_library_

private

Referenced by align_and_output_to_silent_file(), apply(), do_random_moves(), initialize_movers(), random_chunk_trial(), and setup_monte_carlo_cycles().

std::string protocols::farna::RNA_DeNovoProtocol::rna_data_file_

private

Referenced by initialize_movers(), set_rna_data_file(), and show().

RNA_DataReaderOP protocols::farna::RNA_DeNovoProtocol::rna_data_reader_

private

Referenced by initialize_movers().

protocols::farna::RNA_FragmentMoverOP protocols::farna::RNA_DeNovoProtocol::rna_fragment_mover_

private

Referenced by do_random_moves(), initialize_movers(), and random_fragment_trial().

protocols::farna::RNA_LoopCloserOP protocols::farna::RNA_DeNovoProtocol::rna_loop_closer_

private

Referenced by apply(), apply_chem_shift_data(), random_chunk_trial(), random_fragment_trial(), random_jump_trial(), and RNA_DeNovoProtocol().

protocols::farna::RNA_MinimizerOP protocols::farna::RNA_DeNovoProtocol::rna_minimizer_

private

Referenced by apply(), apply_chem_shift_data(), initialize_movers(), and initialize_scorefxn().

std::string protocols::farna::RNA_DeNovoProtocol::rna_params_file_

private

Referenced by initialize_movers(), set_rna_params_file(), and show().

protocols::farna::RNA_RelaxerOP protocols::farna::RNA_DeNovoProtocol::rna_relaxer_

private

Referenced by apply(), and initialize_movers().

RNA_StructureParametersOP protocols::farna::RNA_DeNovoProtocol::rna_structure_parameters_

private

Referenced by apply(), apply_chem_shift_data(), calc_rmsds(), get_moving_res(), initialize_movers(), and random_jump_trial().

bool protocols::farna::RNA_DeNovoProtocol::root_at_first_rigid_body_

private

Referenced by initialize_movers(), set_root_at_first_rigid_body(), and show().

Size protocols::farna::RNA_DeNovoProtocol::rounds_

private

Referenced by apply(), figure_out_constraint_separation_cutoff(), set_refine_pose_list(), set_rounds(), setup_rigid_body_mover(), show(), update_denovo_scorefxn_weights(), update_frag_size(), and update_pose_constraints().

std::string const protocols::farna::RNA_DeNovoProtocol::silent_file_

private

Referenced by apply(), initialize_lores_silent_file(), and initialize_tag_is_done().

bool protocols::farna::RNA_DeNovoProtocol::simple_rmsd_cutoff_relax_

private

Referenced by initialize_movers(), show(), and simple_rmsd_cutoff_relax().

bool protocols::farna::RNA_DeNovoProtocol::staged_constraints_

private

Referenced by set_staged_constraints(), show(), and update_pose_constraints().

core::Real protocols::farna::RNA_DeNovoProtocol::suppress_bp_constraint_

private

Referenced by initialize_movers(), and set_suppress_bp_constraint().

std::map< std::string, bool > protocols::farna::RNA_DeNovoProtocol::tag_is_done_

private

Referenced by apply(), and initialize_tag_is_done().

bool protocols::farna::RNA_DeNovoProtocol::titrate_stack_bonus_

private

Referenced by show(), and update_denovo_scorefxn_weights().

bool const protocols::farna::RNA_DeNovoProtocol::use_chem_shift_data_

private

Referenced by add_chem_shift_info(), apply(), apply_chem_shift_data(), initialize_scorefxn(), output_to_silent_file(), and show().

bool protocols::farna::RNA_DeNovoProtocol::user_defined_cycles_

private

Referenced by set_monte_carlo_cycles(), setup_monte_carlo_cycles(), and show().

bool protocols::farna::RNA_DeNovoProtocol::vary_bond_geometry_

private

Referenced by initialize_movers(), set_vary_bond_geometry(), and show().

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

symlinks/rosetta/src/protocols/farna/RNA_DeNovoProtocol.hh
symlinks/rosetta/src/protocols/farna/RNA_DeNovoProtocol.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation