Aligns one residue onto another. More...

#include <AlignResiduesMover.hh>

Inheritance diagram for protocols::denovo_design::movers::AlignResiduesMover:

[legend]

Public Types
typedef utility::vector1< core::select::residue_selector::ResidueSelectorCOP >	ResidueSelectorCOPs

typedef utility::vector1< core::select::residue_selector::ResidueVector >	ResidueVectors

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

Public Member Functions
	AlignResiduesMover ()

	~AlignResiduesMover () override

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

void	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

void	set_id (std::string const &id)
	Sets the ID of this mover. More...

void	add_template_selector (core::select::residue_selector::ResidueSelector const &selector)
	Adds residue selector that selects the template (i.e. the reference residues that we are aligning to) More...

void	add_target_selector (core::select::residue_selector::ResidueSelector const &selector)
	Adds residue selector that selects the target (i.e. the residues that we are moving to align with the template) More...

void	add_template_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Adds residue selector that selects the template (i.e. the reference residues that we are aligning to) More...

void	add_target_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Adds residue selector that selects the target (i.e. the residues that we are moving to align with the template) More...

void	clear_template_selectors ()
	clears the list of template residue selectors More...

void	clear_target_selectors ()
	clears the list of target residue selectors 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 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::Size	align_residues (core::pose::Pose &pose, core::Size const align_count, core::select::residue_selector::ResidueVector const &template_subset, core::select::residue_selector::ResidueVector const &target_subset) const
	aligns residues from template and target subsets More...

void	align_residues (core::pose::Pose &pose, core::Size const align_count, core::Size const template_resid, core::Size const target_resid) const

void	align_residues (core::pose::Pose &pose, core::Size const jump_idx, core::Size const template_resid, core::Size const target_resid, core::Size const res_with_torsions) const
	aligns two residues so their backbones are completely superimposed More...

void	copy_residue (core::pose::Pose &pose, core::Size const resid_has_info, core::Size const resid_wants_info) const

void	add_metadata (components::StructureData &sd, core::Size const align_count, std::string const &template_segment, std::string const &target_segment, core::Size const target_resid) const

ResidueVectors	compute_target_residues (core::pose::Pose const &pose) const

ResidueVectors	compute_template_residues (core::pose::Pose const &pose) const

void	delete_residues (core::pose::Pose &pose, core::select::residue_selector::ResidueVector const &resids) const

Private Attributes
std::string	id_

ResidueSelectorCOPs	template_selectors_

ResidueSelectorCOPs	target_selectors_

Additional Inherited Members
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

Aligns one residue onto another.

Member Typedef Documentation

◆ ResidueSelectorCOPs

typedef utility::vector1< core::select::residue_selector::ResidueSelectorCOP > protocols::denovo_design::movers::AlignResiduesMover::ResidueSelectorCOPs

◆ ResidueVectors

typedef utility::vector1< core::select::residue_selector::ResidueVector > protocols::denovo_design::movers::AlignResiduesMover::ResidueVectors

Constructor & Destructor Documentation

◆ AlignResiduesMover()

protocols::denovo_design::movers::AlignResiduesMover::AlignResiduesMover ( )

◆ ~AlignResiduesMover()

protocols::denovo_design::movers::AlignResiduesMover::~AlignResiduesMover ( )

overridedefault

Member Function Documentation

◆ add_metadata()

void protocols::denovo_design::movers::AlignResiduesMover::add_metadata	(	components::StructureData &	sd,
		core::Size const	align_count,
		std::string const &	template_segment,
		std::string const &	target_segment,
		core::Size const	target_resid
	)		const

private

References id_, protocols::denovo_design::components::Segment::movable_group(), protocols::denovo_design::PARENT_DELIMETER, protocols::denovo_design::components::StructureData::renumber_movable_group(), protocols::denovo_design::components::StructureData::segment(), and protocols::denovo_design::components::StructureData::set_alias().

Referenced by align_residues().

◆ add_target_selector() [1/2]

void protocols::denovo_design::movers::AlignResiduesMover::add_target_selector ( core::select::residue_selector::ResidueSelector const & selector )

Adds residue selector that selects the target (i.e. the residues that we are moving to align with the template)

Clones the residue selector

References core::select::residue_selector::ResidueSelector::clone().

Referenced by parse_my_tag().

◆ add_target_selector() [2/2]

void protocols::denovo_design::movers::AlignResiduesMover::add_target_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Adds residue selector that selects the target (i.e. the residues that we are moving to align with the template)

Directly stores the ResidueSelectorCOP

References target_selectors_.

◆ add_template_selector() [1/2]

void protocols::denovo_design::movers::AlignResiduesMover::add_template_selector ( core::select::residue_selector::ResidueSelector const & selector )

Adds residue selector that selects the template (i.e. the reference residues that we are aligning to)

Clones the residue selector

References core::select::residue_selector::ResidueSelector::clone().

Referenced by parse_my_tag().

◆ add_template_selector() [2/2]

void protocols::denovo_design::movers::AlignResiduesMover::add_template_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Adds residue selector that selects the template (i.e. the reference residues that we are aligning to)

Directly stores the ResidueSelectorCOP

References template_selectors_.

◆ align_residues() [1/3]

core::Size protocols::denovo_design::movers::AlignResiduesMover::align_residues	(	core::pose::Pose &	pose,
		core::Size const	align_count,
		core::select::residue_selector::ResidueVector const &	template_subset,
		core::select::residue_selector::ResidueVector const &	target_subset
	)		const

private

aligns residues from template and target subsets

Returns: template resid that was aligned

References mover_name(), and core::scoring::rg.

Referenced by align_residues(), and apply().

◆ align_residues() [2/3]

void protocols::denovo_design::movers::AlignResiduesMover::align_residues	(	core::pose::Pose &	pose,
		core::Size const	align_count,
		core::Size const	template_resid,
		core::Size const	target_resid
	)		const

private

References add_metadata(), align_residues(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), copy_residue(), protocols::denovo_design::find_jump_rec(), core::pose::Pose::fold_tree(), protocols::denovo_design::components::StructureDataFactory::get_from_pose(), protocols::denovo_design::components::Segment::safe(), protocols::denovo_design::components::StructureDataFactory::save_into_pose(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segment_name(), and protocols::TR().

◆ align_residues() [3/3]

void protocols::denovo_design::movers::AlignResiduesMover::align_residues	(	core::pose::Pose &	pose,
		core::Size const	jump_idx,
		core::Size const	template_resid,
		core::Size const	target_resid,
		core::Size const	res_with_torsions
	)		const

private

aligns two residues so their backbones are completely superimposed

References core::chemical::ResidueType::atom_index(), core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::conformation::Conformation::set_stub_transform(), protocols::denovo_design::slide_jump(), and core::conformation::Residue::type().

◆ apply()

void protocols::denovo_design::movers::AlignResiduesMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References align_residues(), protocols::denovo_design::components::StructureDataFactory::attach_observer(), compute_target_residues(), compute_template_residues(), delete_residues(), target_selectors_, and template_selectors_.

◆ clear_target_selectors()

void protocols::denovo_design::movers::AlignResiduesMover::clear_target_selectors ( )

inline

clears the list of target residue selectors

References target_selectors_.

◆ clear_template_selectors()

void protocols::denovo_design::movers::AlignResiduesMover::clear_template_selectors ( )

inline

clears the list of template residue selectors

References template_selectors_.

◆ clone()

protocols::moves::MoverOP protocols::denovo_design::movers::AlignResiduesMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ compute_target_residues()

AlignResiduesMover::ResidueVectors protocols::denovo_design::movers::AlignResiduesMover::compute_target_residues ( core::pose::Pose const & pose ) const

private

References protocols::denovo_design::movers::compute_residues_from_selectors(), and target_selectors_.

Referenced by apply().

◆ compute_template_residues()

AlignResiduesMover::ResidueVectors protocols::denovo_design::movers::AlignResiduesMover::compute_template_residues ( core::pose::Pose const & pose ) const

private

References protocols::denovo_design::movers::compute_residues_from_selectors(), and template_selectors_.

Referenced by apply().

◆ copy_residue()

void protocols::denovo_design::movers::AlignResiduesMover::copy_residue	(	core::pose::Pose &	pose,
		core::Size const	resid_has_info,
		core::Size const	resid_wants_info
	)		const

private

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), and protocols::TR().

Referenced by align_residues().

◆ delete_residues()

void protocols::denovo_design::movers::AlignResiduesMover::delete_residues	(	core::pose::Pose &	pose,
		core::select::residue_selector::ResidueVector const &	resids
	)		const