#include <CartesianHybridize.hh>

Inheritance diagram for protocols::hybridization::CartesianHybridize:

[legend]

Public Member Functions
	CartesianHybridize ()

	CartesianHybridize (utility::vector1< core::pose::PoseOP > const &templates_in, utility::vector1< core::Real > const &template_wts_in, utility::vector1< protocols::loops::Loops > const &template_chunks_in, utility::vector1< protocols::loops::Loops > const &template_contigs_in, core::fragment::FragSetOP fragments9_in)

void	init ()

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	set_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)

void	set_min_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)

void	set_pack_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)

void	set_increase_cycles (core::Real increase_cycles_in)

void	set_no_global_frame (bool no_global_frame_in)

void	set_linmin_only (bool linmin_only_in)

void	set_cartfrag_overlap (core::Size cartfrag_overlap_in)

void	set_seqfrags_only (bool seqfrags_only_in)

void	set_skip_long_min (bool skip_long_min_in)

void	set_cenrot (bool cenrot_in)

void	set_temperature (core::Real temp_in)

void	set_fragment_probs (core::Real prob, core::Real randprob)

void	set_max_insertion (int max_in)

void	set_per_residue_controls (utility::vector1< bool > const &residue_sample_template_in, utility::vector1< bool > const &residue_sample_abinitio_in)

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

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

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...

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...

Protected Member Functions
void	apply_frag (core::pose::Pose &pose, core::pose::Pose &templ, protocols::loops::Loop &frag, bool superpose=true)

void	apply_frame (core::pose::Pose &pose, core::fragment::Frame &frame)

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...

Private Attributes
bool	align_templates_to_pose_

core::Real	increase_cycles_

core::Size	ncycles_

core::Size	cartfrag_overlap_

bool	no_global_frame_

bool	linmin_only_

bool	seqfrags_only_

bool	skip_long_min_

bool	cenrot_

core::Real	temperature_

int	max_contig_insertion_

core::Real	fragprob_

core::Real	randfragprob_

utility::vector1< core::pose::PoseOP >	templates_

utility::vector1< core::Real >	template_wts_

utility::vector1< protocols::loops::Loops >	template_contigs_

core::fragment::FragSetOP	fragments9_

boost::unordered_map< core::Size, core::fragment::Frame >	library_

utility::vector1< bool >	residue_sample_template_

utility::vector1< bool >	residue_sample_abinitio_

core::scoring::ScoreFunctionOP	lowres_scorefxn_

core::scoring::ScoreFunctionOP	min_scorefxn_

core::scoring::ScoreFunctionOP	cenrot_repack_scorefxn_

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...

Constructor & Destructor Documentation

◆ CartesianHybridize() [1/2]

protocols::hybridization::CartesianHybridize::CartesianHybridize ( )

References init().

◆ CartesianHybridize() [2/2]

protocols::hybridization::CartesianHybridize::CartesianHybridize	(	utility::vector1< core::pose::PoseOP > const &	templates_in,
		utility::vector1< core::Real > const &	template_wts_in,
		utility::vector1< protocols::loops::Loops > const &	template_chunks_in,
		utility::vector1< protocols::loops::Loops > const &	template_contigs_in,
		core::fragment::FragSetOP	fragments9_in
	)

References fragments9_, init(), library_, template_contigs_, template_wts_, templates_, and protocols::hybridization::TR().

Member Function Documentation

◆ apply()

void protocols::hybridization::CartesianHybridize::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

Reimplemented in protocols::rbsegment_relax::ConfChangeMover.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, apply_frag(), apply_frame(), core::conformation::Residue::atom(), core::scoring::atom_pair_constraint, core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, cenrot_, cenrot_repack_scorefxn_, core::chemical::CENTROID, core::chemical::CENTROID_ROT, core::pose::Pose::conformation(), core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::data(), core::pose::Pose::fold_tree(), fragprob_, protocols::hybridization::get_num_residues_nonvirt(), increase_cycles_, core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_protein(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), library_, linmin_only_, lowres_scorefxn_, core::pose::symmetry::make_symmetric_movemap(), protocols::mean_field::max(), max_contig_insertion_, core::optimization::MinimizerOptions::max_iter(), protocols::mean_field::min(), min_scorefxn_, ncycles_, no_global_frame_, core::pack::pack_rotamers(), randfragprob_, core::pose::Pose::residue(), residue_sample_abinitio_, residue_sample_template_, core::pose::Pose::residue_type(), core::optimization::CartesianMinimizer::run(), seqfrags_only_, protocols::hybridization::TemplateHistory::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::size(), skip_long_min_, protocols::loops::start, protocols::loops::stop, temperature_, template_contigs_, templates_, protocols::hybridization::TR(), core::scoring::vdw, and core::conformation::Atom::xyz().

◆ apply_frag()

void protocols::hybridization::CartesianHybridize::apply_frag	(	core::pose::Pose &	pose,
		core::pose::Pose &	templ,
		protocols::loops::Loop &	frag,
		bool	superpose = `true`
	)

protected

References core::conformation::Residue::atom(), core::pose::Pose::batch_set_xyz(), protocols::simple_filters::coords(), protocols::mean_field::min(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::loops::Loop::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::conformation::Atom::xyz(), core::pose::Pose::xyz(), and core::conformation::Residue::xyz().

Referenced by apply(), and protocols::rbsegment_relax::ConfChangeMover::stage2().

◆ apply_frame()

void protocols::hybridization::CartesianHybridize::apply_frame	(	core::pose::Pose &	pose,
		core::fragment::Frame &	frame
	)

protected

◆ clone()

protocols::moves::MoverOP protocols::hybridization::CartesianHybridize::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::rbsegment_relax::ConfChangeMover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::hybridization::CartesianHybridize::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::hybridization::CartesianHybridize::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::rbsegment_relax::ConfChangeMover.

◆ init()

void protocols::hybridization::CartesianHybridize::init ( void )

References align_templates_to_pose_, cartfrag_overlap_, cenrot_, fragprob_, increase_cycles_, linmin_only_, max_contig_insertion_, no_global_frame_, randfragprob_, seqfrags_only_, skip_long_min_, and temperature_.

Referenced by CartesianHybridize().

◆ set_cartfrag_overlap()

void protocols::hybridization::CartesianHybridize::set_cartfrag_overlap ( core::Size cartfrag_overlap_in )

inline

References cartfrag_overlap_.

◆ set_cenrot()

void protocols::hybridization::CartesianHybridize::set_cenrot ( bool cenrot_in )

inline

References cenrot_.

◆ set_fragment_probs()

void protocols::hybridization::CartesianHybridize::set_fragment_probs	(	core::Real	prob,
		core::Real	randprob
	)

inline

References fragprob_, and randfragprob_.

◆ set_increase_cycles()

void protocols::hybridization::CartesianHybridize::set_increase_cycles ( core::Real increase_cycles_in )

inline

References increase_cycles_.

◆ set_linmin_only()

void protocols::hybridization::CartesianHybridize::set_linmin_only ( bool linmin_only_in )

inline

References linmin_only_.

◆ set_max_insertion()

void protocols::hybridization::CartesianHybridize::set_max_insertion ( int max_in )

inline

References max_contig_insertion_.

◆ set_min_scorefunction()

void protocols::hybridization::CartesianHybridize::set_min_scorefunction ( core::scoring::ScoreFunctionOP scorefxn_in )

References min_scorefxn_.

◆ set_no_global_frame()

void protocols::hybridization::CartesianHybridize::set_no_global_frame ( bool no_global_frame_in )

inline

References no_global_frame_.

◆ set_pack_scorefunction()

void protocols::hybridization::CartesianHybridize::set_pack_scorefunction ( core::scoring::ScoreFunctionOP scorefxn_in )

References cenrot_repack_scorefxn_.

◆ set_per_residue_controls()

void protocols::hybridization::CartesianHybridize::set_per_residue_controls	(	utility::vector1< bool > const &	residue_sample_template_in,
		utility::vector1< bool > const &	residue_sample_abinitio_in
	)