Superimpose pose onto reference pose. Default CA only. All residues. Optionally set to superimpose regions or backbone only (N, C, CA, O) More...

#include <SuperimposeMover.hh>

Inheritance diagram for protocols::simple_moves::SuperimposeMover:

[legend]

Public Member Functions
	SuperimposeMover ()
	empty constructor More...

	SuperimposeMover (core::pose::Pose const &ref_pose)

	SuperimposeMover (core::pose::Pose const &ref_pose, core::Size ref_start, core::Size ref_end, core::Size target_start, core::Size target_end, bool CA_only)

	~SuperimposeMover () override

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

void	set_reference_pose (core::pose::Pose const &pose, core::Size start=1, core::Size end=0)

void	set_target_range (core::Size start, core::Size end)

void	set_ca_only (bool setting)

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data_map) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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...

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

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
core::Real	superimpose (core::pose::Pose &mod_pose, core::pose::Pose const &ref_pose, core::Size ref_start, core::Size ref_end, core::Size target_start, core::Size target_end)

core::Real	superimposebb (core::pose::Pose &mod_pose, core::pose::Pose const &ref_pose, core::Size ref_start, core::Size ref_end, core::Size target_start, core::Size target_end)

Private Attributes
core::pose::PoseOP	ref_pose_

core::Size	ref_start_

core::Size	ref_end_

core::Size	target_start_

core::Size	target_end_

bool	CA_only_

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...

Detailed Description

Superimpose pose onto reference pose. Default CA only. All residues. Optionally set to superimpose regions or backbone only (N, C, CA, O)

Constructor & Destructor Documentation

◆ SuperimposeMover() [1/3]

protocols::simple_moves::SuperimposeMover::SuperimposeMover ( )

empty constructor

◆ SuperimposeMover() [2/3]

protocols::simple_moves::SuperimposeMover::SuperimposeMover ( core::pose::Pose const & ref_pose )

◆ SuperimposeMover() [3/3]

protocols::simple_moves::SuperimposeMover::SuperimposeMover	(	core::pose::Pose const &	ref_pose,
		core::Size	ref_start,
		core::Size	ref_end,
		core::Size	target_start,
		core::Size	target_end,
		bool	CA_only
	)

◆ ~SuperimposeMover()

protocols::simple_moves::SuperimposeMover::~SuperimposeMover ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References CA_only_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), ref_end_, ref_pose_, ref_start_, core::scoring::rms, core::pose::Pose::size(), superimpose(), superimposebb(), target_end_, target_start_, and protocols::simple_moves::TR().

Referenced by protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys().

◆ clone()

protocols::moves::MoverOP protocols::simple_moves::SuperimposeMover::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.

◆ fresh_instance()

protocols::moves::MoverOP protocols::simple_moves::SuperimposeMover::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::simple_moves::SuperimposeMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::simple_moves::SuperimposeMover::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::SuperimposeMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::simple_moves::SuperimposeMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References CA_only_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), ref_end_, ref_pose_, ref_start_, protocols::rosetta_scripts::saved_reference_pose(), target_end_, and target_start_.

◆ provide_xml_schema()

void protocols::simple_moves::SuperimposeMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::attributes_for_saved_reference_pose(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::simple_moves::SuperimposeMoverCreator::provide_xml_schema().

◆ set_ca_only()

void protocols::simple_moves::SuperimposeMover::set_ca_only ( bool setting )

References CA_only_.

◆ set_reference_pose()

void protocols::simple_moves::SuperimposeMover::set_reference_pose	(	core::pose::Pose const &	pose,
		core::Size	start = `1`,
		core::Size	end = `0`
	)

References core::sequence::end, ref_end_, ref_pose_, ref_start_, core::pose::Pose::size(), and protocols::loops::start.

Referenced by protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys().

◆ set_target_range()

void protocols::simple_moves::SuperimposeMover::set_target_range	(	core::Size	start,
		core::Size	end
	)

References core::sequence::end, protocols::loops::start, target_end_, and target_start_.

◆ superimpose()

core::Real protocols::simple_moves::SuperimposeMover::superimpose	(	core::pose::Pose &	mod_pose,
		core::pose::Pose const &	ref_pose,
		core::Size	ref_start,
		core::Size	ref_end,
		core::Size	target_start,
		core::Size	target_end
	)

private

copied and modified from calpha_superimpose_pose

References core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), and core::scoring::superimpose_pose().

Referenced by apply().

◆ superimposebb()

core::Real protocols::simple_moves::SuperimposeMover::superimposebb	(	core::pose::Pose &	mod_pose,
		core::pose::Pose const &	ref_pose,
		core::Size	ref_start,
		core::Size	ref_end,
		core::Size	target_start,
		core::Size	target_end
	)

private

copied and modified from calpha_superimpose_pose

References core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), and core::scoring::superimpose_pose().

Referenced by apply().

Member Data Documentation

◆ CA_only_

bool protocols::simple_moves::SuperimposeMover::CA_only_

private

Referenced by apply(), parse_my_tag(), and set_ca_only().

◆ ref_end_

core::Size protocols::simple_moves::SuperimposeMover::ref_end_

private

Referenced by apply(), parse_my_tag(), and set_reference_pose().

◆ ref_pose_

core::pose::PoseOP protocols::simple_moves::SuperimposeMover::ref_pose_

private

Referenced by apply(), parse_my_tag(), and set_reference_pose().

◆ ref_start_

core::Size protocols::simple_moves::SuperimposeMover::ref_start_

private

Referenced by apply(), parse_my_tag(), and set_reference_pose().

◆ target_end_

core::Size protocols::simple_moves::SuperimposeMover::target_end_

private

Referenced by apply(), parse_my_tag(), and set_target_range().

◆ target_start_

core::Size protocols::simple_moves::SuperimposeMover::target_start_

private

Referenced by apply(), parse_my_tag(), and set_target_range().

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

src/protocols/simple_moves/SuperimposeMover.hh
src/protocols/simple_moves/SuperimposeMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SuperimposeMover() [1/3]

◆ SuperimposeMover() [2/3]

◆ SuperimposeMover() [3/3]

◆ ~SuperimposeMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_ca_only()

◆ set_reference_pose()

◆ set_target_range()

◆ superimpose()

◆ superimposebb()

Member Data Documentation

◆ CA_only_

◆ ref_end_

◆ ref_pose_

◆ ref_start_

◆ target_end_

◆ target_start_