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

#include <RNA_Minimizer.hh>

Public Member Functions
	RNA_Minimizer ()
	Construct the protocol object given the RNA fragment library to use. More...

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...

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

void	deriv_check (bool const setting)

void	use_coordinate_constraints (bool const setting)

void	skip_o2prime_trials (bool const setting)

void	set_perform_minimizer_run (bool const setting)

void	vary_bond_geometry (bool const setting)

void	set_include_default_linear_chainbreak (bool const setting)

void	set_verbose (bool const setting)

void	set_do_dump_pdb (bool const setting)

void	set_move_first_rigid_body (bool const setting)

void	set_min_type (std::string const setting)

void	set_allow_insert (toolbox::AllowInsertOP allow_insert)

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

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

void	set_score_function (core::scoring::ScoreFunctionOP const &scorefxn)

core::scoring::ScoreFunctionOP const &	score_function () const

core::scoring::ScoreFunctionOP	clone_scorefxn () const

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

void	set_type (std::string const &setting)

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	o2prime_trials (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP const &scorefxn) const

void	setup_movemap (core::kinematics::MoveMap &mm, core::pose::Pose &pose)

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

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_Minimizer::RNA_Minimizer ( )

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

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::get_score_function(), minimize_rounds, option, basic::options::option, options, rna, core::scoring::RNA_HIRES_WTS, scorefxn_, user, and basic::options::OptionKeys::score::weights.

Referenced by clone().

Member Function Documentation

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

virtual

Apply the loop-rebuild protocol to the input pose.

Apply the RNA full atom minimizer.

Implements protocols::moves::Mover.

References core::scoring::constraints::add_coordinate_constraints(), allow_insert_, atom_pair_constraint, core::scoring::ScoreFunction::clone(), close_loops_, core::pose::Pose::constraint_set(), coord_cst_weight_, coord_sdev_, coordinate_constraint, deriv_check_, fa_rep, protocols::stepwise::modeler::figure_out_moving_chain_break_res(), include_default_linear_chainbreak_, linear_chainbreak, min_type_, core::optimization::MinimizerOptions::nblist_auto_update(), o2prime_trials(), options, perform_minimizer_run_, rna_bond_geometry, rounds_, scorefxn_, setup_movemap(), skip_o2prime_trials_, protocols::farna::TR, update_allow_insert_with_extra_minimize_res(), use_coordinate_constraints_, and vary_bond_geometry_.

Referenced by protocols::farna::RNA_Relaxer::apply(), protocols::farna::RNA_DeNovoProtocol::apply(), and protocols::farna::RNA_DeNovoProtocol::apply_chem_shift_data().

virtual protocols::moves::MoverOP protocols::farna::RNA_Minimizer::clone ( ) const

inlinevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References RNA_Minimizer().

core::scoring::ScoreFunctionOP protocols::farna::RNA_Minimizer::clone_scorefxn ( ) const

inline

References core::scoring::ScoreFunction::clone(), and scorefxn_.

Referenced by protocols::farna::RNA_DeNovoProtocol::initialize_scorefxn().

void protocols::farna::RNA_Minimizer::deriv_check ( bool const setting )

inline

References deriv_check_.

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

virtual

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

Implements protocols::moves::Mover.

void protocols::farna::RNA_Minimizer::o2prime_trials	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP const &	scorefxn
	)		const

private

References core::pack::task::ResidueLevelTask::and_extrachi_cutoff(), core::conformation::Residue::is_RNA(), core::pack::task::PackerTask::nonconst_residue_task(), core::pack::task::ResidueLevelTask::or_include_current(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::farna::TR.

Referenced by apply().

core::scoring::ScoreFunctionOP const& protocols::farna::RNA_Minimizer::score_function ( ) const

inline

References scorefxn_.

void protocols::farna::RNA_Minimizer::set_allow_insert ( toolbox::AllowInsertOP allow_insert )

References allow_insert_.

Referenced by protocols::farna::RNA_DeNovoProtocol::apply().

void protocols::farna::RNA_Minimizer::set_do_dump_pdb ( bool const setting )

inline

References do_dump_pdb_.

void protocols::farna::RNA_Minimizer::set_extra_minimize_chi_res ( utility::vector1< core::Size > setting )

References extra_minimize_chi_res_.

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

References extra_minimize_res_.

void protocols::farna::RNA_Minimizer::set_include_default_linear_chainbreak ( bool const setting )

inline

References include_default_linear_chainbreak_.

void protocols::farna::RNA_Minimizer::set_min_type ( std::string const setting )

inline

References min_type_.

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

inline

References move_first_rigid_body_.

void protocols::farna::RNA_Minimizer::set_perform_minimizer_run ( bool const setting )

inline

References perform_minimizer_run_.

void protocols::farna::RNA_Minimizer::set_score_function ( core::scoring::ScoreFunctionOP const & scorefxn )

References core::scoring::ScoreFunction::clone(), and scorefxn_.

Referenced by protocols::farna::RNA_DeNovoProtocol::apply_chem_shift_data().

void protocols::farna::RNA_Minimizer::set_verbose ( bool const setting )

inline

References verbose_.

void protocols::farna::RNA_Minimizer::setup_movemap	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose &	pose
	)

private

Referenced by apply().

void protocols::farna::RNA_Minimizer::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 deriv_check_, do_dump_pdb_, include_default_linear_chainbreak_, min_type_, move_first_rigid_body_, perform_minimizer_run_, scorefxn_, skip_o2prime_trials_, use_coordinate_constraints_, and vary_bond_geometry_.

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

void protocols::farna::RNA_Minimizer::skip_o2prime_trials ( bool const setting )

inline

References skip_o2prime_trials_.

void protocols::farna::RNA_Minimizer::update_allow_insert_with_extra_minimize_res ( core::pose::Pose const & pose )

private

References allow_insert_, extra_minimize_res_, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_RNA(), core::conformation::Residue::is_virtual(), named_atom_id_to_atom_id(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::farna::RNA_Minimizer::use_coordinate_constraints ( bool const setting )

inline

References use_coordinate_constraints_.

void protocols::farna::RNA_Minimizer::vary_bond_geometry ( bool const setting )

inline

References vary_bond_geometry_.

Member Data Documentation

toolbox::AllowInsertOP protocols::farna::RNA_Minimizer::allow_insert_

private

Referenced by apply(), set_allow_insert(), setup_movemap(), and update_allow_insert_with_extra_minimize_res().

bool protocols::farna::RNA_Minimizer::close_loops_

private

Referenced by apply().

core::Real const protocols::farna::RNA_Minimizer::coord_cst_weight_

private

Referenced by apply().

core::Real const protocols::farna::RNA_Minimizer::coord_sdev_

private

Referenced by apply().

bool protocols::farna::RNA_Minimizer::deriv_check_

private

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

bool protocols::farna::RNA_Minimizer::do_dump_pdb_

private

Referenced by set_do_dump_pdb(), and show().

utility::vector1< core::Size > protocols::farna::RNA_Minimizer::extra_minimize_chi_res_

private

Referenced by set_extra_minimize_chi_res(), and setup_movemap().

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

private

Referenced by set_extra_minimize_res(), and update_allow_insert_with_extra_minimize_res().

bool protocols::farna::RNA_Minimizer::include_default_linear_chainbreak_

private

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

std::string protocols::farna::RNA_Minimizer::min_type_

private

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

bool protocols::farna::RNA_Minimizer::move_first_rigid_body_

private

Referenced by set_move_first_rigid_body(), setup_movemap(), and show().

bool protocols::farna::RNA_Minimizer::perform_minimizer_run_

private

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

core::Size const protocols::farna::RNA_Minimizer::rounds_

private

Referenced by apply().

core::scoring::ScoreFunctionOP protocols::farna::RNA_Minimizer::scorefxn_

private

Referenced by apply(), clone_scorefxn(), RNA_Minimizer(), score_function(), set_score_function(), and show().

bool protocols::farna::RNA_Minimizer::skip_o2prime_trials_

private

Referenced by apply(), show(), and skip_o2prime_trials().

bool protocols::farna::RNA_Minimizer::use_coordinate_constraints_

private

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

bool protocols::farna::RNA_Minimizer::vary_bond_geometry_

private

Referenced by apply(), setup_movemap(), show(), and vary_bond_geometry().

bool protocols::farna::RNA_Minimizer::verbose_

private

Referenced by set_verbose().

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

src/protocols/farna/RNA_Minimizer.hh
src/protocols/farna/RNA_Minimizer.cc

Private Attributes
bool	deriv_check_

bool	use_coordinate_constraints_

core::Real const	coord_sdev_

core::Real const	coord_cst_weight_

core::Size const	rounds_

bool	skip_o2prime_trials_

bool	perform_minimizer_run_

bool	vary_bond_geometry_

bool	include_default_linear_chainbreak_

bool	verbose_

bool	do_dump_pdb_

bool	move_first_rigid_body_

bool	close_loops_

std::string	min_type_

toolbox::AllowInsertOP	allow_insert_

utility::vector1< core::Size >	extra_minimize_res_

utility::vector1< core::Size >	extra_minimize_chi_res_

core::scoring::ScoreFunctionOP	scorefxn_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation