#include <MRMover.hh>

Inheritance diagram for protocols::hybridization::MRMover:

[legend]

Public Member Functions
	MRMover ()

void	init ()

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

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...

void	set_centroid_density_weight (core::Real newval)

void	set_fullatom_density_weight (core::Real newval, bool fast)

void	set_max_gaplength_to_model (core::Size newval)

void	set_symmdef_file (std::string newval)

void	set_censcale (core::Real newval)

void	set_cen_cst_weight (core::Real newval)

void	set_fa_cst_weight (core::Real newval)

void	set_disulf (utility::vector1< std::string > newval)

void	set_big_fragments (core::fragment::FragSetOP newval)

void	set_small_fragments (core::fragment::FragSetOP newval)

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...

Private Member Functions
void	trim_target_pose (Pose &query_pose, protocols::loops::Loops &loops, core::Size max_gaplength)

void	pack_missing_sidechains (Pose &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 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...

Constructor & Destructor Documentation

◆ MRMover()

protocols::hybridization::MRMover::MRMover ( )

References init().

Member Function Documentation

◆ apply()

void protocols::hybridization::MRMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

◆ clone()

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

inlineoverridevirtual

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.

◆ fresh_instance()

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

inlineoverridevirtual

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::MRMover::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ init()

void protocols::hybridization::MRMover::init ( void )

References core::scoring::atom_pair_constraint, cen1_scorefxn_, cen2_scorefxn_, censcale_, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::elec_dens_fast, core::scoring::elec_dens_window, fa_scorefxn_, core::scoring::get_score_function(), core::scoring::electron_density::getDensityMap(), max_gaplength_to_model_, relax_cycles_, relax_max_iter_, and core::scoring::electron_density::ElectronDensity::setWindow().

Referenced by MRMover().

◆ pack_missing_sidechains()

void protocols::hybridization::MRMover::pack_missing_sidechains ( Pose & pose )

private

References protocols::minimization_packing::PackRotamersMover::apply(), core::conformation::Residue::atom(), core::pack::task::TaskFactory::create_packer_task(), fa_scorefxn_, core::conformation::Residue::first_sidechain_atom(), core::chemical::ResidueType::has(), core::chemical::ResidueTypeBase::is_protein(), core::pose::symmetry::make_residue_mask_symmetric(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

◆ set_big_fragments()

void protocols::hybridization::MRMover::set_big_fragments ( core::fragment::FragSetOP newval )

inline

References fragments_big_, and fragments_big_trim_.

◆ set_cen_cst_weight()

void protocols::hybridization::MRMover::set_cen_cst_weight ( core::Real newval )

inline

References core::scoring::atom_pair_constraint, cen1_scorefxn_, and cen2_scorefxn_.

◆ set_censcale()

void protocols::hybridization::MRMover::set_censcale ( core::Real newval )

inline

References censcale_.

◆ set_centroid_density_weight()

void protocols::hybridization::MRMover::set_centroid_density_weight ( core::Real newval )

inline

References cen1_scorefxn_, cen2_scorefxn_, and core::scoring::elec_dens_fast.

◆ set_disulf()

void protocols::hybridization::MRMover::set_disulf ( utility::vector1< std::string > newval )

inline

References disulfs_.

◆ set_fa_cst_weight()

void protocols::hybridization::MRMover::set_fa_cst_weight ( core::Real newval )

inline

References core::scoring::atom_pair_constraint, and fa_scorefxn_.

◆ set_fullatom_density_weight()

void protocols::hybridization::MRMover::set_fullatom_density_weight	(	core::Real	newval,
		bool	fast
	)

inline

References core::scoring::elec_dens_fast, core::scoring::elec_dens_window, and fa_scorefxn_.

◆ set_max_gaplength_to_model()

void protocols::hybridization::MRMover::set_max_gaplength_to_model ( core::Size newval )

inline

References max_gaplength_to_model_.

◆ set_small_fragments()

void protocols::hybridization::MRMover::set_small_fragments ( core::fragment::FragSetOP newval )

inline

References fragments_small_, and fragments_small_trim_.

◆ set_symmdef_file()

void protocols::hybridization::MRMover::set_symmdef_file ( std::string newval )

inline

References symm_def_file_.

◆ trim_target_pose()

void protocols::hybridization::MRMover::trim_target_pose	(	Pose &	query_pose,
		protocols::loops::Loops &	loops,
		core::Size	max_gaplength
	)

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom(), core::kinematics::FoldTree::end(), core::pose::Pose::fold_tree(), fragments_big_, fragments_big_trim_, fragments_small_, fragments_small_trim_, core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), protocols::loops::Loops::push_back(), core::kinematics::FoldTree::renumber_jumps(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), protocols::loops::Loops::size(), core::kinematics::FoldTree::slide_jump(), protocols::loops::start, protocols::loops::stop, core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by apply().

Member Data Documentation

◆ cen1_scorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::MRMover::cen1_scorefxn_

private

Referenced by apply(), init(), set_cen_cst_weight(), and set_centroid_density_weight().

◆ cen2_scorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::MRMover::cen2_scorefxn_

private

Referenced by apply(), init(), set_cen_cst_weight(), and set_centroid_density_weight().

◆ censcale_

core::Real protocols::hybridization::MRMover::censcale_

private

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

◆ disulfs_

utility::vector1<std::string> protocols::hybridization::MRMover::disulfs_

private

Referenced by apply(), and set_disulf().

◆ fa_scorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::MRMover::fa_scorefxn_

private

Referenced by apply(), init(), pack_missing_sidechains(), set_fa_cst_weight(), and set_fullatom_density_weight().

◆ fragments_big_

core::fragment::FragSetOP protocols::hybridization::MRMover::fragments_big_

private

Referenced by set_big_fragments(), and trim_target_pose().

◆ fragments_big_trim_

core::fragment::FragSetOP protocols::hybridization::MRMover::fragments_big_trim_

private

Referenced by apply(), set_big_fragments(), and trim_target_pose().

◆ fragments_small_

core::fragment::FragSetOP protocols::hybridization::MRMover::fragments_small_

private

Referenced by set_small_fragments(), and trim_target_pose().

◆ fragments_small_trim_

core::fragment::FragSetOP protocols::hybridization::MRMover::fragments_small_trim_

private

Referenced by apply(), set_small_fragments(), and trim_target_pose().

◆ max_gaplength_to_model_

core::Size protocols::hybridization::MRMover::max_gaplength_to_model_

private

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

◆ relax_cycles_

core::Size protocols::hybridization::MRMover::relax_cycles_

private

Referenced by apply(), and init().

◆ relax_max_iter_

core::Size protocols::hybridization::MRMover::relax_max_iter_

private

Referenced by apply(), and init().

◆ symm_def_file_

std::string protocols::hybridization::MRMover::symm_def_file_

private

Referenced by apply(), and set_symmdef_file().

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

src/protocols/hybridization/MRMover.hh
src/protocols/hybridization/MRMover.cc

Private Attributes
std::string	symm_def_file_

core::fragment::FragSetOP	fragments_big_

core::fragment::FragSetOP	fragments_small_

core::fragment::FragSetOP	fragments_big_trim_

core::fragment::FragSetOP	fragments_small_trim_

core::scoring::ScoreFunctionOP	cen1_scorefxn_

core::scoring::ScoreFunctionOP	cen2_scorefxn_

core::scoring::ScoreFunctionOP	fa_scorefxn_

utility::vector1< std::string >	disulfs_

core::Size	max_gaplength_to_model_

core::Size	relax_max_iter_

core::Size	relax_cycles_

core::Real	censcale_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MRMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ init()

◆ pack_missing_sidechains()

◆ set_big_fragments()

◆ set_cen_cst_weight()

◆ set_censcale()

◆ set_centroid_density_weight()

◆ set_disulf()

◆ set_fa_cst_weight()

◆ set_fullatom_density_weight()

◆ set_max_gaplength_to_model()

◆ set_small_fragments()

◆ set_symmdef_file()

◆ trim_target_pose()

Member Data Documentation

◆ cen1_scorefxn_

◆ cen2_scorefxn_

◆ censcale_

◆ disulfs_

◆ fa_scorefxn_

◆ fragments_big_

◆ fragments_big_trim_

◆ fragments_small_

◆ fragments_small_trim_

◆ max_gaplength_to_model_

◆ relax_cycles_

◆ relax_max_iter_

◆ symm_def_file_