#include <FlipChiralityMover.hh>

Inheritance diagram for protocols::cyclic_peptide::FlipChiralityMover:

Public Member Functions
	FlipChiralityMover ()
	Constructor for FlipChirality mover. More...

	~FlipChiralityMover () override
	destructor for GeneralizedKIC mover. More...

	FlipChiralityMover (FlipChiralityMover const &src)
	Copy constructor for FlipChiralityMover mover. More...

void	apply (core::pose::Pose &) override
	Actually apply the mover to the pose. More...

moves::MoverOP	clone () const override
	Clone operator to create a pointer to a fresh GeneralizedKIC object that copies this one. More...

moves::MoverOP	fresh_instance () const override
	Fresh_instance operator to create a pointer to a fresh GeneralizedKIC object that does NOT copy this one. More...

void	parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
	Returns the name of this mover ("FlipChiralityMover"). More...

numeric::xyzVector< core::Real > const &	get_normal ()
	sets the normal vector either from tags or calculates it. More...

numeric::xyzVector< core::Real > const &	get_center (core::select::residue_selector::ResidueSubset, core::pose::Pose const &)
	sets the normal vector either from tags or calculates it. More...

virtual void	set_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	sets the selector More...

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

void	set_center (core::Real const &, core::Real const &, core::Real const &)

void	set_normal (core::Real const &, core::Real const &, core::Real 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 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

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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Member Functions
numeric::xyzVector< core::Real > const	calculate_reflect (core::pose::Pose const &, core::Size, core::Size)
	does the actual calculation fo the reflection More...

numeric::xyzVector< core::Real >	center_mass (core::select::residue_selector::ResidueSubset, core::pose::Pose const &)

Private Attributes
numeric::xyzVector< core::Real >	normal_

numeric::xyzVector< core::Real >	center_

core::select::residue_selector::ResidueSelectorCOP	selector_

bool	normal_assigned_

bool	center_assigned_

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

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

protocols::cyclic_peptide::FlipChiralityMover::FlipChiralityMover ( )

Constructor for FlipChirality mover.

References center_, center_assigned_, normal_, and normal_assigned_.

protocols::cyclic_peptide::FlipChiralityMover::~FlipChiralityMover ( )

overridedefault

destructor for GeneralizedKIC mover.

protocols::cyclic_peptide::FlipChiralityMover::FlipChiralityMover ( FlipChiralityMover const & src )

Copy constructor for FlipChiralityMover mover.

References center_, center_assigned_, normal_, and normal_assigned_.

Member Function Documentation

void protocols::cyclic_peptide::FlipChiralityMover::apply ( core::pose::Pose & pose )

overridevirtual

Actually apply the mover to the pose.

Implements protocols::moves::Mover.

References calculate_reflect(), get_center(), get_normal(), core::chemical::ResidueTypeBase::mode(), core::conformation::Residue::natoms(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), selector_, core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::conformation::Residue::type().

numeric::xyzVector< core::Real > const protocols::cyclic_peptide::FlipChiralityMover::calculate_reflect	(	core::pose::Pose const &	pose,
		core::Size	ia,
		core::Size	ir
	)

private

does the actual calculation fo the reflection

References center_, normal_, and core::pose::Pose::xyz().

Referenced by apply().

numeric::xyzVector< core::Real > protocols::cyclic_peptide::FlipChiralityMover::center_mass	(	core::select::residue_selector::ResidueSubset	subset,
		core::pose::Pose const &	pose
	)

private

References core::chemical::aa_vrt, core::pose::Pose::residue(), core::pose::Pose::size(), protocols::cyclic_peptide::TR(), and core::conformation::Atom::xyz().

Referenced by get_center().

protocols::moves::MoverOP protocols::cyclic_peptide::FlipChiralityMover::clone ( ) const

overridevirtual

Clone operator to create a pointer to a fresh GeneralizedKIC object that copies this one.

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::cyclic_peptide::FlipChiralityMover::fresh_instance ( ) const

overridevirtual

Fresh_instance operator to create a pointer to a fresh GeneralizedKIC object that does NOT copy this one.

Reimplemented from protocols::moves::Mover.

numeric::xyzVector< core::Real > const & protocols::cyclic_peptide::FlipChiralityMover::get_center	(	core::select::residue_selector::ResidueSubset	subset,
		core::pose::Pose const &	pose
	)