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

#include <RNA_Minimizer.hh>

Inheritance diagram for protocols::rna::denovo::movers::RNA_Minimizer:

[legend]

Public Member Functions
	RNA_Minimizer (core::import_pose::options::RNA_MinimizerOptionsCOP options=nullptr)
	Construct the protocol object given the RNA fragment library to use. More...

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

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

void	set_perform_minimizer_run (bool const setting)

void	set_options (core::import_pose::options::RNA_MinimizerOptionsCOP setting)

void	set_include_default_linear_chainbreak (bool const setting)

void	set_atom_level_domain_map (core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map)

void	set_score_function (core::scoring::ScoreFunctionCOP scorefxn)

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

core::scoring::ScoreFunctionOP	clone_scorefxn () const

void	set_skip_chi_min (bool const &setting)

bool	skip_chi_min () const

void	set_min_tol (float const &setting)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

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...

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

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

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

void	packing_trials (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP const &packer_scorefxn) const

void	packing_trials (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP const &packer_scorefxn, utility::vector1< core::Size > residues_to_pack) const

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

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

void	update_atom_level_domain_map_to_move_rosetta_library_chunks ()

Private Attributes
core::import_pose::options::RNA_MinimizerOptionsCOP	options_

core::Real const	coord_sdev_

core::Real const	coord_cst_weight_

bool	perform_minimizer_run_

bool	include_default_linear_chainbreak_

bool	close_loops_

core::pose::toolbox::AtomLevelDomainMapCOP	atom_level_domain_map_input_

core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map_

core::scoring::ScoreFunctionOP	scorefxn_

bool	skip_chi_min_

float	min_tol_

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...

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

◆ RNA_Minimizer()

protocols::rna::denovo::movers::RNA_Minimizer::RNA_Minimizer ( core::import_pose::options::RNA_MinimizerOptionsCOP options = nullptr )

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

Member Function Documentation

◆ apply()

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

overridevirtual

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(), core::pose::rna::add_syn_anti_chi_constraints(), protocols::rna::movers::RNA_LoopCloser::apply(), atom_level_domain_map_, atom_level_domain_map_input_, core::scoring::atom_pair_constraint, core::scoring::base_pair_constraint, core::scoring::cart_bonded, close_loops_, core::pose::Pose::constraint_set(), protocols::stepwise::modeler::protein::contains_protein(), coord_cst_weight_, coord_sdev_, core::scoring::coordinate_constraint, core::scoring::fa_rep, protocols::stepwise::modeler::figure_out_moving_chain_break_res(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), protocols::rna::denovo::get_rna_hires_scorefxn(), include_default_linear_chainbreak_, core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::scoring::linear_chainbreak, core::optimization::MinimizerOptions::max_iter(), min_tol_, core::optimization::MinimizerOptions::nblist_auto_update(), options_, packing_trials(), perform_minimizer_run_, core::pose::Pose::residue(), core::optimization::AtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), scorefxn_, setup_movemap(), core::pose::Pose::size(), protocols::rna::denovo::TR(), update_atom_level_domain_map_to_move_rosetta_library_chunks(), and update_atom_level_domain_map_with_extra_minimize_res().

◆ clone()

protocols::moves::MoverOP protocols::rna::denovo::movers::RNA_Minimizer::clone ( ) const

inlineoverridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

◆ clone_scorefxn()

core::scoring::ScoreFunctionOP protocols::rna::denovo::movers::RNA_Minimizer::clone_scorefxn ( ) const

inline

References scorefxn_.

◆ get_name()

std::string protocols::rna::denovo::movers::RNA_Minimizer::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ o2prime_trials()

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

private

References core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), core::pack::rotamer_trials(), core::pose::Pose::size(), and protocols::rna::denovo::TR().

◆ packing_trials() [1/2]

void protocols::rna::denovo::movers::RNA_Minimizer::packing_trials	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP const &	packer_scorefxn
	)		const

private

References core::pose::Pose::size().

Referenced by apply().

◆ packing_trials() [2/2]

void protocols::rna::denovo::movers::RNA_Minimizer::packing_trials	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP const &	packer_scorefxn,
		utility::vector1< core::Size >	residues_to_pack
	)		const

private

References core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::pack::rotamer_trials(), core::pose::Pose::size(), and protocols::rna::denovo::TR().

◆ score_function()

core::scoring::ScoreFunctionOP const& protocols::rna::denovo::movers::RNA_Minimizer::score_function ( ) const

inline

References scorefxn_.

◆ set_atom_level_domain_map()

void protocols::rna::denovo::movers::RNA_Minimizer::set_atom_level_domain_map ( core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map )

inline

References atom_level_domain_map_input_.

◆ set_include_default_linear_chainbreak()

void protocols::rna::denovo::movers::RNA_Minimizer::set_include_default_linear_chainbreak ( bool const setting )

inline

References include_default_linear_chainbreak_.

◆ set_min_tol()

void protocols::rna::denovo::movers::RNA_Minimizer::set_min_tol ( float const & setting )

inline

References min_tol_.

◆ set_options()

void protocols::rna::denovo::movers::RNA_Minimizer::set_options ( core::import_pose::options::RNA_MinimizerOptionsCOP setting )

inline

References options_.

◆ set_perform_minimizer_run()

void protocols::rna::denovo::movers::RNA_Minimizer::set_perform_minimizer_run ( bool const setting )

inline

References perform_minimizer_run_.

◆ set_score_function()

void protocols::rna::denovo::movers::RNA_Minimizer::set_score_function ( core::scoring::ScoreFunctionCOP scorefxn )

References scorefxn_.

◆ set_skip_chi_min()

void protocols::rna::denovo::movers::RNA_Minimizer::set_skip_chi_min ( bool const & setting )

inline

References skip_chi_min_.

◆ setup_movemap()

void protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose &	pose
	)

private

References atom_level_domain_map_, core::id::BB, core::chemical::rna::CHI, core::pose::Pose::conformation(), core::id::D, core::kinematics::FoldTree::downstream_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::chemical::FIVEPRIME_CAP, core::pose::Pose::fold_tree(), core::pose::rna::get_rigid_body_jumps(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_polymer(), core::conformation::Residue::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), protocols::rna::denovo::let_rigid_body_jumps_move(), core::pose::rna::moveable_jump(), core::conformation::named_atom_id_to_atom_id(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), options_, core::chemical::rings::PHI, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::size(), skip_chi_min_, core::chemical::rings::THETA, protocols::moves::Mover::type(), core::kinematics::FoldTree::upstream_atom(), core::kinematics::FoldTree::upstream_jump_residue(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by apply().

◆ show()

void protocols::rna::denovo::movers::RNA_Minimizer::show ( std::ostream & output = std::cout ) 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 include_default_linear_chainbreak_, options_, perform_minimizer_run_, and scorefxn_.

Referenced by protocols::rna::denovo::movers::operator<<().

◆ skip_chi_min()

bool protocols::rna::denovo::movers::RNA_Minimizer::skip_chi_min ( ) const

inline

References skip_chi_min_.

◆ update_atom_level_domain_map_to_move_rosetta_library_chunks()

void protocols::rna::denovo::movers::RNA_Minimizer::update_atom_level_domain_map_to_move_rosetta_library_chunks ( )

private

References atom_level_domain_map_, and core::import_pose::libraries::ROSETTA_LIBRARY_DOMAIN.

Referenced by apply().

◆ update_atom_level_domain_map_with_extra_minimize_res()

void protocols::rna::denovo::movers::RNA_Minimizer::update_atom_level_domain_map_with_extra_minimize_res ( core::pose::Pose const & pose )

private

References atom_level_domain_map_, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_RNA(), core::chemical::ResidueType::is_virtual(), core::conformation::named_atom_id_to_atom_id(), options_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by apply().

Member Data Documentation

◆ atom_level_domain_map_

core::pose::toolbox::AtomLevelDomainMapOP protocols::rna::denovo::movers::RNA_Minimizer::atom_level_domain_map_

private

Referenced by apply(), setup_movemap(), update_atom_level_domain_map_to_move_rosetta_library_chunks(), and update_atom_level_domain_map_with_extra_minimize_res().

◆ atom_level_domain_map_input_

core::pose::toolbox::AtomLevelDomainMapCOP protocols::rna::denovo::movers::RNA_Minimizer::atom_level_domain_map_input_

private

Referenced by apply(), and set_atom_level_domain_map().

◆ close_loops_

bool protocols::rna::denovo::movers::RNA_Minimizer::close_loops_

private

Referenced by apply().

◆ coord_cst_weight_

core::Real const protocols::rna::denovo::movers::RNA_Minimizer::coord_cst_weight_

private

Referenced by apply().

◆ coord_sdev_

core::Real const protocols::rna::denovo::movers::RNA_Minimizer::coord_sdev_

private

Referenced by apply().

◆ include_default_linear_chainbreak_

bool protocols::rna::denovo::movers::RNA_Minimizer::include_default_linear_chainbreak_

private

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

◆ min_tol_

float protocols::rna::denovo::movers::RNA_Minimizer::min_tol_

private

Referenced by apply(), and set_min_tol().

◆ options_

core::import_pose::options::RNA_MinimizerOptionsCOP protocols::rna::denovo::movers::RNA_Minimizer::options_

private

Referenced by apply(), set_options(), setup_movemap(), show(), and update_atom_level_domain_map_with_extra_minimize_res().

◆ perform_minimizer_run_

bool protocols::rna::denovo::movers::RNA_Minimizer::perform_minimizer_run_

private

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

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::rna::denovo::movers::RNA_Minimizer::scorefxn_

private

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

◆ skip_chi_min_

bool protocols::rna::denovo::movers::RNA_Minimizer::skip_chi_min_

private

Referenced by set_skip_chi_min(), setup_movemap(), and skip_chi_min().

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

src/protocols/rna/denovo/movers/RNA_Minimizer.hh
src/protocols/rna/denovo/movers/RNA_Minimizer.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RNA_Minimizer()

Member Function Documentation

◆ apply()

◆ clone()

◆ clone_scorefxn()

◆ get_name()

◆ o2prime_trials()

◆ packing_trials() [1/2]

◆ packing_trials() [2/2]

◆ score_function()

◆ set_atom_level_domain_map()

◆ set_include_default_linear_chainbreak()

◆ set_min_tol()

◆ set_options()

◆ set_perform_minimizer_run()

◆ set_score_function()

◆ set_skip_chi_min()

◆ setup_movemap()

◆ show()

◆ skip_chi_min()

◆ update_atom_level_domain_map_to_move_rosetta_library_chunks()

◆ update_atom_level_domain_map_with_extra_minimize_res()

Member Data Documentation

◆ atom_level_domain_map_

◆ atom_level_domain_map_input_

◆ close_loops_

◆ coord_cst_weight_

◆ coord_sdev_

◆ include_default_linear_chainbreak_

◆ min_tol_

◆ options_

◆ perform_minimizer_run_

◆ scorefxn_

◆ skip_chi_min_