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

#include <RNA_KinematicCloser.hh>

Public Member Functions
	RNA_KinematicCloser (core::pose::PoseOP const &ref_pose, core::Size const moving_suite, core::Size const chainbreak_suite)

	~RNA_KinematicCloser ()

std::string	get_name () const
	Class name. More...

virtual RotamerType	type () const
	Type of class (see enum in RotamerTypes.hh) More...

void	init ()
	Initialization. More...

virtual void	apply (core::pose::Pose &pose, core::Size const id)
	Apply the i-th rotamer to pose. More...

core::Size	size () const
	Get the total number of rotamers in sampler. More...

void	set_verbose (bool const setting)
	Set verbose. More...

Public Member Functions inherited from protocols::rotamer_sampler::RotamerSized
	RotamerSized ()

virtual	~RotamerSized ()

virtual void	reset ()
	Reset to the first (or random if random()) rotamer. More...

virtual void	operator++ ()
	Move to next rotamer. More...

virtual bool	not_end () const
	Check if reach the end of rotamer list. More...

void	apply (core::pose::Pose &pose)
	Apply the current rotamer to pose. More...

Size const &	id () const

virtual void	fast_forward ()

virtual void	set_id (Size const setting)

Public Member Functions inherited from protocols::rotamer_sampler::RotamerBase
	RotamerBase ()

virtual	~RotamerBase ()

virtual bool	random () const
	Check if is random sampling. More...

virtual void	set_random (bool const setting)
	Set the random sampling state. More...

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 MoverOP	clone () const
	Return a clone of the Mover object. More...

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	figure_out_dof_ids_and_offsets ()

void	figure_out_offset (core::id::DOF_ID const &dof_id, core::Real const original_torsion_value)

void	fill_chainTORS ()

void	output_chainTORS () const

	RNA_KinematicCloser (const RNA_KinematicCloser &)

void	operator= (const RNA_KinematicCloser &)

Private Attributes
core::pose::PoseOP	ref_pose_

core::Size const	moving_suite_

core::Size const	chainbreak_suite_

bool	verbose_

core::Size	nsol_

utility::vector1 < core::id::NamedAtomID >	atom_ids_

utility::vector1< core::Real >	offset_save_

utility::vector1 < core::id::DOF_ID >	dof_ids_

utility::vector1 < utility::vector1< core::Real > >	t_ang_

utility::vector1 < utility::vector1< core::Real > >	b_ang_

utility::vector1 < utility::vector1< core::Real > >	b_len_

utility::vector1 < utility::vector1< core::Real > >	atoms_

utility::vector1< core::Real >	dt_ang_

utility::vector1< core::Real >	db_len_

utility::vector1< core::Real >	db_ang_

Additional Inherited Members
Public Types inherited from protocols::rotamer_sampler::RotamerBase
typedef utility::vector1 < core::Real >	TorsionList

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::rotamer_sampler::RotamerBase
bool	is_init () const
	Check if the sampler has been initialized. More...

void	set_init (bool const setting)
	Set the initialization state. More...

template<class T >
void	set_and_reinit (T &params, T const &setting)
	Set value of a parameter, return to pre-init state. 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...

Protected Attributes inherited from protocols::rotamer_sampler::RotamerSized
core::Size	id_

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::rotamer_sampler::rna::RNA_KinematicCloser::RNA_KinematicCloser	(	core::pose::PoseOP const &	ref_pose,
		core::Size const	moving_suite,
		core::Size const	chainbreak_suite
	)

protocols::rotamer_sampler::rna::RNA_KinematicCloser::~RNA_KinematicCloser ( )

protocols::rotamer_sampler::rna::RNA_KinematicCloser::RNA_KinematicCloser ( const RNA_KinematicCloser & )

private

Member Function Documentation

void protocols::rotamer_sampler::rna::RNA_KinematicCloser::apply	(	core::pose::Pose &	pose,
		core::Size const	id
	)

virtual

Apply the i-th rotamer to pose.

Implements protocols::rotamer_sampler::RotamerSized.

References dof_ids_, protocols::rotamer_sampler::RotamerBase::is_init(), nsol_, offset_save_, principal_angle(), radians(), runtime_assert, core::pose::Pose::set_dof(), and t_ang_.

void protocols::rotamer_sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets ( )

private

References core::conformation::Residue::atom_index(), core::pose::Pose::atom_tree(), chainbreak_suite_, dt_ang_, figure_out_offset(), moving_suite_, ref_pose_, core::pose::Pose::residue(), and core::kinematics::AtomTree::torsion_angle_dof_id().

Referenced by init().

void protocols::rotamer_sampler::rna::RNA_KinematicCloser::figure_out_offset	(	core::id::DOF_ID const &	dof_id,
		core::Real const	original_torsion_value
	)

private

References BOGUS_DOF_ID, core::pose::Pose::dof(), dof_ids_, offset_save_, radians(), ref_pose_, protocols::rotamer_sampler::rna::TR, utility_exit_with_message, and verbose_.

Referenced by figure_out_dof_ids_and_offsets().

void protocols::rotamer_sampler::rna::RNA_KinematicCloser::fill_chainTORS ( )

private

References atom_ids_, atoms_, chainTORS(), db_ang_, db_len_, dt_ang_, ref_pose_, and core::pose::Pose::xyz().

Referenced by init().

std::string protocols::rotamer_sampler::rna::RNA_KinematicCloser::get_name ( ) const

inlinevirtual

Class name.

Reimplemented from protocols::rotamer_sampler::RotamerSized.

void protocols::rotamer_sampler::rna::RNA_KinematicCloser::init ( void )

virtual

void protocols::rotamer_sampler::rna::RNA_KinematicCloser::operator= ( const RNA_KinematicCloser & )

private

void protocols::rotamer_sampler::rna::RNA_KinematicCloser::output_chainTORS ( ) const

private

References db_ang_, db_len_, dt_ang_, protocols::abinitio::abscript::I, and protocols::rotamer_sampler::rna::TR.

Referenced by init().

void protocols::rotamer_sampler::rna::RNA_KinematicCloser::set_verbose ( bool const setting )

inline

Set verbose.

References verbose_.

core::Size protocols::rotamer_sampler::rna::RNA_KinematicCloser::size ( ) const

inlinevirtual

Get the total number of rotamers in sampler.

Implements protocols::rotamer_sampler::RotamerSized.

References nsol_.

virtual RotamerType protocols::rotamer_sampler::rna::RNA_KinematicCloser::type ( ) const

inlinevirtual

Type of class (see enum in RotamerTypes.hh)

Reimplemented from protocols::rotamer_sampler::RotamerSized.

References protocols::rotamer_sampler::RNA_KINEMATIC_CLOSER.

Member Data Documentation

utility::vector1< core::id::NamedAtomID > protocols::rotamer_sampler::rna::RNA_KinematicCloser::atom_ids_

private

Referenced by fill_chainTORS(), and init().

utility::vector1< utility::vector1< core::Real > > protocols::rotamer_sampler::rna::RNA_KinematicCloser::atoms_

private

Referenced by fill_chainTORS(), and init().

utility::vector1< utility::vector1< core::Real > > protocols::rotamer_sampler::rna::RNA_KinematicCloser::b_ang_

private

Referenced by init().

utility::vector1< utility::vector1< core::Real > > protocols::rotamer_sampler::rna::RNA_KinematicCloser::b_len_

private

Referenced by init().

core::Size const protocols::rotamer_sampler::rna::RNA_KinematicCloser::chainbreak_suite_

private

Referenced by figure_out_dof_ids_and_offsets(), and init().

utility::vector1< core::Real > protocols::rotamer_sampler::rna::RNA_KinematicCloser::db_ang_

private

Referenced by fill_chainTORS(), init(), and output_chainTORS().

utility::vector1< core::Real > protocols::rotamer_sampler::rna::RNA_KinematicCloser::db_len_

private

Referenced by fill_chainTORS(), init(), and output_chainTORS().

utility::vector1< core::id::DOF_ID > protocols::rotamer_sampler::rna::RNA_KinematicCloser::dof_ids_

private

Referenced by apply(), figure_out_offset(), and init().

utility::vector1< core::Real > protocols::rotamer_sampler::rna::RNA_KinematicCloser::dt_ang_

private

Referenced by figure_out_dof_ids_and_offsets(), fill_chainTORS(), init(), and output_chainTORS().

core::Size const protocols::rotamer_sampler::rna::RNA_KinematicCloser::moving_suite_

private

Referenced by figure_out_dof_ids_and_offsets(), and init().

core::Size protocols::rotamer_sampler::rna::RNA_KinematicCloser::nsol_

private

Referenced by apply(), init(), and size().

utility::vector1< core::Real > protocols::rotamer_sampler::rna::RNA_KinematicCloser::offset_save_

private

Referenced by apply(), figure_out_offset(), and init().

core::pose::PoseOP protocols::rotamer_sampler::rna::RNA_KinematicCloser::ref_pose_

private

Referenced by figure_out_dof_ids_and_offsets(), figure_out_offset(), fill_chainTORS(), and init().

utility::vector1< utility::vector1< core::Real > > protocols::rotamer_sampler::rna::RNA_KinematicCloser::t_ang_

private

Referenced by apply(), and init().

bool protocols::rotamer_sampler::rna::RNA_KinematicCloser::verbose_

private

Referenced by figure_out_offset(), init(), and set_verbose().

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

symlinks/rosetta/src/protocols/rotamer_sampler/rna/RNA_KinematicCloser.hh
symlinks/rosetta/src/protocols/rotamer_sampler/rna/RNA_KinematicCloser.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation