#include <CombinePoseMover.hh>

Inheritance diagram for protocols::simple_moves::CombinePoseMover:

[legend]

Public Member Functions
	CombinePoseMover (core::scoring::ScoreFunctionCOP sfxn, core::pose::Pose const &pose_ref)

	~CombinePoseMover () override

void	apply (core::pose::Pose &pose2) override
	Main Method. More...

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

void	set_default ()

void	set_max_struct (core::Size const n)

void	set_max_try (core::Size const n)

void	set_minfrac_crossover (core::Real const value)

void	set_maxfrac_crossover (core::Real const value)

void	set_nonideal (bool const setting)

void	set_minimize (bool const setting)

void	set_cartesian (bool const setting)

void	set_rmsdcut (core::Real const setting)

core::Size	max_struct () const

core::Size	max_struct_try () const

core::pose::Pose const	pose_ref () const

std::string	pose_tag () const

void	set_pose_tag (std::string const value)

void	set_store_silents (bool const value)

std::vector< core::io::silent::SilentStructOP >	return_silent () const

void	clear_combine_history ()

void	append_combine_history (std::vector< core::Size > const v)

std::vector< std::vector< core::Size > >	return_combine_history () const

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 Attributes
core::pose::Pose	pose_ref_

core::Size	max_struct_

core::Size	max_struct_try_

core::Real	minfrac_crossover_

core::Real	maxfrac_crossover_

bool	cartesian_crossover_

bool	nonideal_

bool	store_silents_

bool	do_minimize_

std::string	pose_tag_

core::scoring::ScoreFunctionCOP	sfxn_

core::scoring::ScoreFunctionCOP	sfxn0_

core::Real	vdwcut_

core::Real	rmsdcut_

std::vector< std::vector< core::Size > >	combine_history_

std::vector< core::io::silent::SilentStructOP >	sampled_structures_

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

◆ CombinePoseMover()

protocols::simple_moves::CombinePoseMover::CombinePoseMover	(	core::scoring::ScoreFunctionCOP	sfxn,
		core::pose::Pose const &	pose_ref
	)

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

◆ ~CombinePoseMover()

protocols::simple_moves::CombinePoseMover::~CombinePoseMover ( )

overridedefault

Member Function Documentation

◆ append_combine_history()

void protocols::simple_moves::CombinePoseMover::append_combine_history ( std::vector< core::Size > const v )

inline

References combine_history_.

◆ apply()

void protocols::simple_moves::CombinePoseMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::scoring::CA_rmsd(), core::scoring::calpha_superimpose_pose(), core::chemical::CENTROID, core::pose::Pose::chi(), core::sequence::end, core::pose::Pose::is_centroid(), core::optimization::MinimizerOptions::max_iter(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rg, core::optimization::AtomTreeMinimizer::run(), protocols::hybridization::score, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::pose::Pose::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), protocols::loops::start, core::id::to_string(), protocols::simple_moves::TR(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run().

◆ clear_combine_history()

void protocols::simple_moves::CombinePoseMover::clear_combine_history ( )

inline

References combine_history_.

◆ get_name()

std::string protocols::simple_moves::CombinePoseMover::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ max_struct()

core::Size protocols::simple_moves::CombinePoseMover::max_struct ( ) const

inline

References max_struct_.

◆ max_struct_try()

core::Size protocols::simple_moves::CombinePoseMover::max_struct_try ( ) const

inline

References max_struct_try_.

◆ pose_ref()

core::pose::Pose const protocols::simple_moves::CombinePoseMover::pose_ref ( ) const

inline

References pose_ref_.

◆ pose_tag()

std::string protocols::simple_moves::CombinePoseMover::pose_tag ( ) const

inline

References pose_tag_.

◆ return_combine_history()

std::vector< std::vector< core::Size > > protocols::simple_moves::CombinePoseMover::return_combine_history ( ) const

inline

References combine_history_.

◆ return_silent()

std::vector< core::io::silent::SilentStructOP > protocols::simple_moves::CombinePoseMover::return_silent ( ) const

inline

References sampled_structures_.

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run().

◆ set_cartesian()

void protocols::simple_moves::CombinePoseMover::set_cartesian ( bool const setting )

inline

References cartesian_crossover_.

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run().

◆ set_default()

void protocols::simple_moves::CombinePoseMover::set_default ( )

References core::scoring::ScoreFunctionFactory::create_score_function().

◆ set_max_struct()

void protocols::simple_moves::CombinePoseMover::set_max_struct ( core::Size const n )

inline

References max_struct_.

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run().

◆ set_max_try()

void protocols::simple_moves::CombinePoseMover::set_max_try ( core::Size const n )

inline

References max_struct_try_.

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run().

◆ set_maxfrac_crossover()

void protocols::simple_moves::CombinePoseMover::set_maxfrac_crossover ( core::Real const value )

inline

References maxfrac_crossover_.

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run().

◆ set_minfrac_crossover()

void protocols::simple_moves::CombinePoseMover::set_minfrac_crossover ( core::Real const value )

inline

References minfrac_crossover_.

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run().

◆ set_minimize()

void protocols::simple_moves::CombinePoseMover::set_minimize ( bool const setting )

inline

References do_minimize_.

◆ set_nonideal()

void protocols::simple_moves::CombinePoseMover::set_nonideal ( bool const setting )

inline

References nonideal_.

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run().

◆ set_pose_tag()

void protocols::simple_moves::CombinePoseMover::set_pose_tag ( std::string const value )

inline

References pose_tag_.

◆ set_rmsdcut()

void protocols::simple_moves::CombinePoseMover::set_rmsdcut ( core::Real const setting )

inline

References rmsdcut_.

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run().

◆ set_store_silents()

void protocols::simple_moves::CombinePoseMover::set_store_silents ( bool const value )

inline

References store_silents_.

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run().

Member Data Documentation

◆ cartesian_crossover_

bool protocols::simple_moves::CombinePoseMover::cartesian_crossover_

private

Referenced by set_cartesian().

◆ combine_history_

std::vector< std::vector< core::Size > > protocols::simple_moves::CombinePoseMover::combine_history_

private

Referenced by append_combine_history(), clear_combine_history(), and return_combine_history().

◆ do_minimize_

bool protocols::simple_moves::CombinePoseMover::do_minimize_

private

Referenced by set_minimize().

◆ max_struct_

core::Size protocols::simple_moves::CombinePoseMover::max_struct_

private

Referenced by max_struct(), and set_max_struct().

◆ max_struct_try_

core::Size protocols::simple_moves::CombinePoseMover::max_struct_try_

private

Referenced by max_struct_try(), and set_max_try().

◆ maxfrac_crossover_

core::Real protocols::simple_moves::CombinePoseMover::maxfrac_crossover_

private

Referenced by set_maxfrac_crossover().

◆ minfrac_crossover_

core::Real protocols::simple_moves::CombinePoseMover::minfrac_crossover_

private

Referenced by set_minfrac_crossover().

◆ nonideal_

bool protocols::simple_moves::CombinePoseMover::nonideal_

private

Referenced by set_nonideal().

◆ pose_ref_

core::pose::Pose protocols::simple_moves::CombinePoseMover::pose_ref_

private

Referenced by pose_ref().

◆ pose_tag_

std::string protocols::simple_moves::CombinePoseMover::pose_tag_

private

Referenced by pose_tag(), and set_pose_tag().

◆ rmsdcut_

core::Real protocols::simple_moves::CombinePoseMover::rmsdcut_

private

Referenced by set_rmsdcut().

◆ sampled_structures_

std::vector< core::io::silent::SilentStructOP > protocols::simple_moves::CombinePoseMover::sampled_structures_

private

Referenced by return_silent().

◆ sfxn0_

core::scoring::ScoreFunctionCOP protocols::simple_moves::CombinePoseMover::sfxn0_

private

◆ sfxn_

core::scoring::ScoreFunctionCOP protocols::simple_moves::CombinePoseMover::sfxn_

private

◆ store_silents_

bool protocols::simple_moves::CombinePoseMover::store_silents_

private

Referenced by set_store_silents().

◆ vdwcut_

core::Real protocols::simple_moves::CombinePoseMover::vdwcut_

private

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

src/protocols/simple_moves/CombinePoseMover.hh
src/protocols/simple_moves/CombinePoseMover.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CombinePoseMover()

◆ ~CombinePoseMover()

Member Function Documentation

◆ append_combine_history()

◆ apply()

◆ clear_combine_history()

◆ get_name()

◆ max_struct()

◆ max_struct_try()

◆ pose_ref()

◆ pose_tag()

◆ return_combine_history()

◆ return_silent()

◆ set_cartesian()

◆ set_default()

◆ set_max_struct()

◆ set_max_try()

◆ set_maxfrac_crossover()

◆ set_minfrac_crossover()

◆ set_minimize()

◆ set_nonideal()

◆ set_pose_tag()

◆ set_rmsdcut()

◆ set_store_silents()

Member Data Documentation

◆ cartesian_crossover_

◆ combine_history_

◆ do_minimize_

◆ max_struct_

◆ max_struct_try_

◆ maxfrac_crossover_

◆ minfrac_crossover_

◆ nonideal_

◆ pose_ref_

◆ pose_tag_

◆ rmsdcut_

◆ sampled_structures_

◆ sfxn0_

◆ sfxn_

◆ store_silents_

◆ vdwcut_