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

#include <CoarseRNA_DeNovoProtocol.hh>

Public Member Functions
	CoarseRNA_DeNovoProtocol (Size const nstruct, Size const monte_carlo_cycles, std::string const silent_file)
	Construct the protocol object given the RNA fragment library to use. More...

	~CoarseRNA_DeNovoProtocol ()

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

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

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

void	set_dump_pdb (bool const setting)

void	set_force_ideal_chainbreak (bool const &setting)

void	set_check_pairing_dists (bool const &setting)

void	set_add_base_pair_constraints (bool const &setting)

void	set_jump_library_file (std::string const jump_library_file)

void	set_rna_params_file (std::string const file)

void	set_rna_data_file (std::string const file)

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

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

void	set_lores_scorefxn (std::string const &lores_scorefxn)

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	set_temperature (core::Real const &setting)

void	set_staged_constraints (bool const &setting)

void	set_sim_anneal (bool const &setting)

void	set_close_loops (bool const &setting)

void	set_choose_best_solution (bool const &setting)

void	set_freeze_domains (bool 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

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

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

void	initialize_tag_is_done ()

core::Real	get_temperature (Size const &r, Size const &rounds) const

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

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

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

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

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

Size	figure_out_constraint_separation_cutoff (Size const &r, Size const &rounds, Size const &max_dist)

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

void	update_domain_rot_trans_mag (Size const &r, Size const &rounds)

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

void	check_new_pairing_dists (core::pose::Pose &pose, Size const &frag_pos)

Private Attributes
Size const	nstruct_

Size const	monte_carlo_cycles_

Size const	rounds_

std::string const	silent_file_

bool	freeze_domains_

bool	dump_pdb_

core::Real	domain_move_frequency_

core::Real	m_Temperature_

bool	sim_anneal_

core::scoring::constraints::ConstraintSetOP	constraint_set_

bool	staged_constraints_

Size	frag_size_

protocols::moves::MonteCarloOP	monte_carlo_

std::string	rna_params_file_

std::string	rna_data_file_

std::string	all_rna_fragments_file_

std::string	jump_library_file_

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

std::string	lores_scorefxn_

core::scoring::ScoreFunctionOP	denovo_scorefxn_

protocols::farna::RNA_FragmentMoverOP	frag_mover_

protocols::farna::RNA_StructureParametersOP	rna_structure_parameters_

protocols::farna::RNA_DataReaderOP	rna_data_reader_

protocols::farna::RNA_ChunkLibraryOP	rna_chunk_library_

protocols::coarse_rna::CoarseRNA_LoopCloserOP	rna_loop_closer_

protocols::farna::MultipleDomainMoverOP	multiple_domain_mover_

utility::vector1< std::string >	chunk_silent_files_

utility::vector1< core::Size >	input_res_

bool	close_loops_

bool	choose_best_solution_

bool	force_ideal_chainbreak_

bool	add_base_pair_constraints_

bool	check_pairing_dists_

bool	view_monte_carlo_

utility::vector1< core::Real >	pairing_dists_

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::coarse_rna::CoarseRNA_DeNovoProtocol::CoarseRNA_DeNovoProtocol	(	Size const	nstruct,
		Size const	monte_carlo_cycles,
		std::string const	silent_file
	)

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

References database, and full_name().

Referenced by clone().

protocols::coarse_rna::CoarseRNA_DeNovoProtocol::~CoarseRNA_DeNovoProtocol ( )

Member Function Documentation

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::apply ( core::pose::Pose & pose )

virtual

Apply the loop-rebuild protocol to the input pose.

Apply the RNA de novo modeling protocol to a pose.

Implements protocols::moves::Mover.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::check_new_pairing_dists	(	core::pose::Pose &	pose,
		Size const &	frag_pos
	)

private

References core::pose::Pose::fold_tree(), j, length, pairing_dists_, rna_structure_parameters_, and core::pose::Pose::xyz().

Referenced by random_fragment_trial().

protocols::moves::MoverOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::clone ( ) const

virtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References CoarseRNA_DeNovoProtocol().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::do_random_fragment_insertions ( core::pose::Pose & pose )

private

Size protocols::coarse_rna::CoarseRNA_DeNovoProtocol::figure_out_constraint_separation_cutoff	(	Size const &	r,
		Size const &	rounds,
		Size const &	max_dist
	)

private

Referenced by update_pose_constraints().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::fill_pairing_dists ( core::pose::Pose & pose )

private

References j, length, pairing_dists_, rna_structure_parameters_, and core::pose::Pose::xyz().

Referenced by random_fragment_trial().

std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

core::Real protocols::coarse_rna::CoarseRNA_DeNovoProtocol::get_temperature	(	Size const &	r,
		Size const &	rounds
	)		const

private

References m_Temperature_, sim_anneal_, and temperature.

Referenced by apply().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::initialize_constraints ( core::pose::Pose & pose )

private

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

Referenced by apply().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::initialize_movers ( core::pose::Pose & pose )

private

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::initialize_tag_is_done ( )

private

References utility::file::file_exists(), core::io::silent::SilentFileData::read_tags_fast(), silent_file_, and tag_is_done_.

Referenced by apply().

void protocols::coarse_rna::CoarseRNA_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 all_atom_rmsd(), protocols::moves::Mover::get_native_pose(), rna_structure_parameters_, and s.

Referenced by apply().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::random_domain_move_trial ( core::pose::Pose & pose )

private

References protocols::moves::MonteCarlo::boltzmann(), freeze_domains_, monte_carlo_, multiple_domain_mover_, and rna_loop_closer_.

Referenced by RNA_move_trial().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::random_fragment_trial ( core::pose::Pose & pose )

private

References protocols::moves::MonteCarlo::boltzmann(), check_new_pairing_dists(), check_pairing_dists_, close_loops_, fill_pairing_dists(), frag_mover_, frag_size_, monte_carlo_, and rna_loop_closer_.

Referenced by RNA_move_trial().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::RNA_move_trial ( core::pose::Pose & pose )

private

References domain_move_frequency_, random_domain_move_trial(), random_fragment_trial(), and numeric::random::RandomGenerator::uniform().

Referenced by apply().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_add_base_pair_constraints ( bool const & setting )

inline

References add_base_pair_constraints_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_check_pairing_dists ( bool const & setting )

inline

References check_pairing_dists_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_choose_best_solution ( bool const & setting )

inline

References choose_best_solution_.

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

inline

References chunk_silent_files_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_close_loops ( bool const & setting )

inline

References close_loops_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_dump_pdb ( bool const setting )

inline

References dump_pdb_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_force_ideal_chainbreak ( bool const & setting )

inline

References force_ideal_chainbreak_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_freeze_domains ( bool const & setting )

inline

References freeze_domains_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_input_res ( utility::vector1< core::Size > const & setting )

inline

References input_res_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_jump_library_file ( std::string const jump_library_file )

inline

References jump_library_file_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_lores_scorefxn ( std::string const & lores_scorefxn )

inline

References lores_scorefxn_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_rna_data_file ( std::string const file )

inline

References rna_data_file_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_rna_params_file ( std::string const file )

inline

References rna_params_file_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_sim_anneal ( bool const & setting )

inline

References sim_anneal_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_staged_constraints ( bool const & setting )

inline

References staged_constraints_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_temperature ( core::Real const & setting )

inline

References m_Temperature_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::update_domain_rot_trans_mag	(	Size const &	r,
		Size const &	rounds
	)

private

References multiple_domain_mover_.

Referenced by apply().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::update_pose_constraints	(	Size const &	r,
		Size const &	rounds,
		core::pose::Pose &	pose
	)

private

References core::scoring::constraints::ConstraintSet::add_constraint(), 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, and staged_constraints_.

Referenced by apply().

Member Data Documentation

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::add_base_pair_constraints_

private

Referenced by apply(), and set_add_base_pair_constraints().

std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::all_rna_fragments_file_

private

Referenced by apply().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::check_pairing_dists_

private

Referenced by apply(), random_fragment_trial(), and set_check_pairing_dists().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::choose_best_solution_

private

Referenced by apply(), and set_choose_best_solution().

utility::vector1< std::string > protocols::coarse_rna::CoarseRNA_DeNovoProtocol::chunk_silent_files_

private

Referenced by apply(), and set_chunk_silent_files().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::close_loops_

private

Referenced by random_fragment_trial(), and set_close_loops().

core::scoring::constraints::ConstraintSetOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::constraint_set_

private

Referenced by initialize_constraints(), and update_pose_constraints().

core::scoring::ScoreFunctionOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::denovo_scorefxn_

private

Referenced by apply(), and initialize_constraints().

core::Real protocols::coarse_rna::CoarseRNA_DeNovoProtocol::domain_move_frequency_

private

Referenced by apply(), and RNA_move_trial().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::dump_pdb_

private

Referenced by apply(), and set_dump_pdb().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::force_ideal_chainbreak_

private

Referenced by apply(), and set_force_ideal_chainbreak().

protocols::farna::RNA_FragmentMoverOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::frag_mover_

private

Referenced by apply(), and random_fragment_trial().

Size protocols::coarse_rna::CoarseRNA_DeNovoProtocol::frag_size_

private

Referenced by apply(), and random_fragment_trial().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::freeze_domains_

private

Referenced by apply(), random_domain_move_trial(), and set_freeze_domains().

utility::vector1< core::Size > protocols::coarse_rna::CoarseRNA_DeNovoProtocol::input_res_

private

Referenced by apply(), and set_input_res().

std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::jump_library_file_

private

Referenced by apply(), and set_jump_library_file().

std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::lores_scorefxn_

private

Referenced by apply(), and set_lores_scorefxn().

core::Real protocols::coarse_rna::CoarseRNA_DeNovoProtocol::m_Temperature_

private

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

protocols::moves::MonteCarloOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::monte_carlo_

private

Referenced by apply(), random_domain_move_trial(), and random_fragment_trial().

Size const protocols::coarse_rna::CoarseRNA_DeNovoProtocol::monte_carlo_cycles_

private

Referenced by apply().

protocols::farna::MultipleDomainMoverOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::multiple_domain_mover_

private

Referenced by apply(), random_domain_move_trial(), and update_domain_rot_trans_mag().

Size const protocols::coarse_rna::CoarseRNA_DeNovoProtocol::nstruct_

private

Referenced by apply().

utility::vector1< core::Real > protocols::coarse_rna::CoarseRNA_DeNovoProtocol::pairing_dists_

private

Referenced by check_new_pairing_dists(), and fill_pairing_dists().

protocols::farna::RNA_ChunkLibraryOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_chunk_library_

private

Referenced by apply().

std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_data_file_

private

Referenced by apply(), and set_rna_data_file().

protocols::farna::RNA_DataReaderOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_data_reader_

private

Referenced by apply().

protocols::coarse_rna::CoarseRNA_LoopCloserOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_loop_closer_

private

Referenced by apply(), random_domain_move_trial(), and random_fragment_trial().

std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_params_file_

private

Referenced by apply(), and set_rna_params_file().

protocols::farna::RNA_StructureParametersOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_structure_parameters_

private

Referenced by apply(), check_new_pairing_dists(), fill_pairing_dists(), and output_to_silent_file().

Size const protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rounds_

private

Referenced by apply().

std::string const protocols::coarse_rna::CoarseRNA_DeNovoProtocol::silent_file_

private

Referenced by apply(), and initialize_tag_is_done().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::sim_anneal_

private

Referenced by get_temperature(), and set_sim_anneal().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::staged_constraints_

private

Referenced by set_staged_constraints(), and update_pose_constraints().

std::map< std::string, bool > protocols::coarse_rna::CoarseRNA_DeNovoProtocol::tag_is_done_

private

Referenced by apply(), and initialize_tag_is_done().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::view_monte_carlo_

private

Referenced by apply().

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

symlinks/rosetta/src/protocols/coarse_rna/CoarseRNA_DeNovoProtocol.hh
symlinks/rosetta/src/protocols/coarse_rna/CoarseRNA_DeNovoProtocol.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation