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

#include <RNA_KinematicCloser.hh>

Inheritance diagram for protocols::stepwise::sampler::rna::RNA_KinematicCloser:

[legend]

Public Member Functions
	RNA_KinematicCloser (core::pose::Pose const &init_pose, core::Size const moving_suite, core::Size const chainbreak_suite, bool const is_TNA_=false)

	~RNA_KinematicCloser () override

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

toolbox::SamplerPlusPlusType	type () const override
	Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh) More...

void	init () override
	Initialization. More...

void	init (const Pose &pose_current, const Pose &pose_closed, bool use_pose_closed=true)

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

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

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

void	set_calculate_jacobians (bool const &setting)

bool	calculate_jacobians () const

core::Real	get_jacobian (Pose &pose) const
	Calculate the jacobian. More...

utility::vector1< core::Real >	get_all_jacobians () const

virtual void	apply (core::pose::Pose &, core::Size const)=0
	Apply the i-th rotamer to pose. More...

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

Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSized
	StepWiseSamplerSized ()

	~StepWiseSamplerSized () override

void	init () override
	Initialization. More...

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

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

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

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

std::string	get_name () const override
	Name of the class. More...

toolbox::SamplerPlusPlusType	type () const override
	Type of class (see enum in SamplerPlusPlusTypes.hh) More...

core::Size const &	id () const

virtual void	fast_forward ()

virtual void	set_id (core::Size const setting)

void	show (std::ostream &out, core::Size const indent=0) const override
	output summary of class More...

Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSampler
	StepWiseSampler ()

	~StepWiseSampler () override

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

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

Public Member Functions inherited from protocols::toolbox::SamplerPlusPlus
	SamplerPlusPlus ()

	~SamplerPlusPlus () override

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 MoverOP	clone () const
	Return a clone of the Mover object. 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 void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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	figure_out_dof_ids_and_offsets (core::pose::Pose const &pose)

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

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

void	output_chainTORS () const

	RNA_KinematicCloser (const RNA_KinematicCloser &)

void	operator= (const RNA_KinematicCloser &)

Private Attributes
core::pose::Pose const &	init_pose_

core::Size const	moving_suite_

core::Size const	chainbreak_suite_

bool	verbose_ = false

core::Size	nsol_ = 0

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

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

utility::vector1< core::Real >	offset_save_

utility::vector1< core::Real >	all_jacobians_

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::fixedsizearray1< core::Real, 3 > >	atoms_

utility::vector1< core::Real >	dt_ang_

utility::vector1< core::Real >	db_len_

utility::vector1< core::Real >	db_ang_

bool	calculate_jacobians_ = false

bool	is_TNA_ = false

Additional Inherited Members
Public Types inherited from protocols::toolbox::SamplerPlusPlus
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 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::toolbox::SamplerPlusPlus
bool	is_init () const
	return OP to the subsampler that controls exactly this torsion_id (assume only one). This is worked out in recces/sampler/MC_Sampler & derived classes – wouldn't be too hard to generalize to stepwise/sampler/ classes, too. 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::stepwise::sampler::StepWiseSamplerSized
core::Size	id_

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

◆ RNA_KinematicCloser() [1/2]

protocols::stepwise::sampler::rna::RNA_KinematicCloser::RNA_KinematicCloser	(	core::pose::Pose const &	init_pose,
		core::Size const	moving_suite,
		core::Size const	chainbreak_suite,
		bool const	is_TNA_ = `false`
	)

◆ ~RNA_KinematicCloser()

protocols::stepwise::sampler::rna::RNA_KinematicCloser::~RNA_KinematicCloser ( )

overridedefault

◆ RNA_KinematicCloser() [2/2]

protocols::stepwise::sampler::rna::RNA_KinematicCloser::RNA_KinematicCloser ( const RNA_KinematicCloser & )

private

Member Function Documentation

◆ apply() [1/3]

virtual void protocols::stepwise::sampler::StepWiseSamplerSized::apply

Apply the i-th rotamer to pose.

Referenced by init().

◆ apply() [2/3]

void protocols::stepwise::sampler::StepWiseSamplerSized::apply

inlineoverride

Apply the current rotamer to pose.

◆ apply() [3/3]

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

overridevirtual

Apply the i-th rotamer to pose.

Implements protocols::stepwise::sampler::StepWiseSamplerSized.

References dof_ids_, protocols::toolbox::SamplerPlusPlus::is_init(), nsol_, offset_save_, core::pose::Pose::set_dof(), and t_ang_.

◆ calculate_jacobians()

bool protocols::stepwise::sampler::rna::RNA_KinematicCloser::calculate_jacobians ( ) const

inline

References calculate_jacobians_.

◆ figure_out_dof_ids_and_offsets()

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets ( core::pose::Pose const & pose )

private

References core::chemical::ResidueType::atom_index(), core::pose::Pose::atom_tree(), core::chemical::rna::RNA_Info::c2prime_atom_index(), core::chemical::rna::RNA_Info::c3prime_atom_index(), core::chemical::rna::RNA_Info::c4prime_atom_index(), core::chemical::rna::RNA_Info::c5prime_atom_index(), chainbreak_suite_, dt_ang_, figure_out_offset(), is_TNA_, moving_suite_, core::chemical::rna::RNA_Info::o2prime_index(), core::chemical::rna::RNA_Info::o3prime_atom_index(), core::chemical::rna::RNA_Info::o5prime_atom_index(), core::chemical::rna::RNA_Info::p_atom_index(), core::pose::Pose::residue_type(), core::chemical::ResidueType::RNA_info(), and core::kinematics::AtomTree::torsion_angle_dof_id().

Referenced by init().

◆ figure_out_offset()

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_offset	(	core::id::DOF_ID const &	dof_id,
		core::Real const	original_torsion_value,
		core::pose::Pose const &	pose
	)

private

References core::id::DOF_ID::BOGUS_DOF_ID(), core::pose::Pose::dof(), dof_ids_, offset_save_, protocols::stepwise::sampler::rna::TR(), and verbose_.

Referenced by figure_out_dof_ids_and_offsets().

◆ fill_chainTORS()

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::fill_chainTORS ( core::pose::Pose const & pose )

private

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

Referenced by init().

◆ get_all_jacobians()

utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_all_jacobians ( ) const

inline

References all_jacobians_.

◆ get_jacobian()

Real protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_jacobian ( Pose & pose ) const

Calculate the jacobian.

References protocols::mean_field::max(), pivot_ids_, protocols::hybridization::r1, protocols::hybridization::r2, and core::pose::Pose::xyz().

Referenced by init().

◆ get_name()

std::string protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_name ( ) const

inlineoverridevirtual

Class name.

Implements protocols::toolbox::SamplerPlusPlus.

◆ init() [1/2]

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::init ( void )

overridevirtual

Initialization.

Implements protocols::toolbox::SamplerPlusPlus.

References init_pose_.

◆ init() [2/2]

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::init	(	const Pose &	pose_current,
		const Pose &	pose_closed,
		bool	use_pose_closed = `true`
	)

◆ operator=()

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::operator= ( const RNA_KinematicCloser & )

private

◆ output_chainTORS()

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::output_chainTORS ( ) const

private

References db_ang_, db_len_, dt_ang_, core::chemical::element::F, core::chemical::element::I, and protocols::stepwise::sampler::rna::TR().

Referenced by init().

◆ set_calculate_jacobians()

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::set_calculate_jacobians ( bool const & setting )

inline

References calculate_jacobians_.

◆ set_verbose()

void protocols::stepwise::sampler::rna::RNA_KinematicCloser::set_verbose ( bool const setting )

inline

Set verbose.

References verbose_.

◆ size()

core::Size protocols::stepwise::sampler::rna::RNA_KinematicCloser::size ( ) const

inlineoverridevirtual

Get the total number of rotamers in sampler.

Implements protocols::stepwise::sampler::StepWiseSamplerSized.

References nsol_.

◆ type()

toolbox::SamplerPlusPlusType protocols::stepwise::sampler::rna::RNA_KinematicCloser::type ( ) const

inlineoverridevirtual

Type of class (see enum in toolbox::SamplerPlusPlusTypes.hh)

Implements protocols::toolbox::SamplerPlusPlus.

References protocols::toolbox::RNA_KINEMATIC_CLOSER.

Member Data Documentation

◆ all_jacobians_

utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::all_jacobians_

private

Referenced by get_all_jacobians(), and init().

◆ atom_ids_

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

private

Referenced by fill_chainTORS(), and init().

◆ atoms_

utility::vector1< utility::fixedsizearray1< core::Real, 3 > > protocols::stepwise::sampler::rna::RNA_KinematicCloser::atoms_

private

Referenced by fill_chainTORS(), and init().

◆ b_ang_

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::sampler::rna::RNA_KinematicCloser::b_ang_

private

Referenced by init().

◆ b_len_

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::sampler::rna::RNA_KinematicCloser::b_len_

private

Referenced by init().

◆ calculate_jacobians_

bool protocols::stepwise::sampler::rna::RNA_KinematicCloser::calculate_jacobians_ = false

private

Referenced by calculate_jacobians(), init(), and set_calculate_jacobians().

◆ chainbreak_suite_

core::Size const protocols::stepwise::sampler::rna::RNA_KinematicCloser::chainbreak_suite_

private

Referenced by figure_out_dof_ids_and_offsets(), and init().

◆ db_ang_

utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::db_ang_

private

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

◆ db_len_

utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::db_len_

private

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

◆ dof_ids_

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

private

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

◆ dt_ang_

utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::dt_ang_

private

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

◆ init_pose_

core::pose::Pose const& protocols::stepwise::sampler::rna::RNA_KinematicCloser::init_pose_

private

Referenced by init().

◆ is_TNA_

bool protocols::stepwise::sampler::rna::RNA_KinematicCloser::is_TNA_ = false

private

Referenced by figure_out_dof_ids_and_offsets(), and init().

◆ moving_suite_

core::Size const protocols::stepwise::sampler::rna::RNA_KinematicCloser::moving_suite_

private

Referenced by figure_out_dof_ids_and_offsets(), and init().

◆ nsol_

core::Size protocols::stepwise::sampler::rna::RNA_KinematicCloser::nsol_ = 0

private

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

◆ offset_save_

utility::vector1< core::Real > protocols::stepwise::sampler::rna::RNA_KinematicCloser::offset_save_

private

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

◆ pivot_ids_

utility::vector1< core::id::NamedAtomID > protocols::stepwise::sampler::rna::RNA_KinematicCloser::pivot_ids_

private

Referenced by get_jacobian(), and init().

◆ t_ang_

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::sampler::rna::RNA_KinematicCloser::t_ang_

private

Referenced by apply(), and init().

◆ verbose_

bool protocols::stepwise::sampler::rna::RNA_KinematicCloser::verbose_ = false

private

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

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

src/protocols/stepwise/sampler/rna/RNA_KinematicCloser.hh
src/protocols/stepwise/sampler/rna/RNA_KinematicCloser.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RNA_KinematicCloser() [1/2]

◆ ~RNA_KinematicCloser()

◆ RNA_KinematicCloser() [2/2]

Member Function Documentation

◆ apply() [1/3]

◆ apply() [2/3]

◆ apply() [3/3]

◆ calculate_jacobians()

◆ figure_out_dof_ids_and_offsets()

◆ figure_out_offset()

◆ fill_chainTORS()

◆ get_all_jacobians()

◆ get_jacobian()

◆ get_name()

◆ init() [1/2]

◆ init() [2/2]

◆ operator=()

◆ output_chainTORS()

◆ set_calculate_jacobians()

◆ set_verbose()

◆ size()

◆ type()

Member Data Documentation

◆ all_jacobians_

◆ atom_ids_

◆ atoms_

◆ b_ang_

◆ b_len_

◆ calculate_jacobians_

◆ chainbreak_suite_

◆ db_ang_

◆ db_len_

◆ dof_ids_

◆ dt_ang_

◆ init_pose_

◆ is_TNA_

◆ moving_suite_

◆ nsol_

◆ offset_save_

◆ pivot_ids_

◆ t_ang_

◆ verbose_