#include <RepeatPropagationMover.hh>

Inheritance diagram for protocols::simple_moves::RepeatPropagationMover:

[legend]

Public Member Functions
	RepeatPropagationMover ()

	RepeatPropagationMover (core::Size numb_repeats)

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

moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

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

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

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
void	initialize_repeat_pose (core::pose::Pose &pose, core::pose::Pose &repeat_pose)

void	duplicate_residues_by_type (core::pose::Pose &pose, core::pose::Pose &repeat_pose)

void	copy_phi_psi_omega (core::pose::Pose &pose, core::pose::Pose &repeat_pose)

void	add_cap_seq_and_structure (core::pose::Pose &pose, core::pose::Pose &repeat_pose)

void	add_cap_seq (core::pose::Pose &pose, core::pose::Pose &repeat_pose)

std::vector< core::Real >	get_center_of_mass (core::Real *coordinates, int number_of_atoms)

void	repeat_ligand (core::pose::Pose &pose, core::pose::Pose &repeat_pose)

utility::vector1< core::Size >	initial_constrained_residues (const core::pose::Pose &pose)

void	fix_ligand_residues (core::pose::Pose &pose, core::pose::Pose &repeat_pose)

core::id::SequenceMapping	setup_repeat_seqmap (core::Size repeat_number, core::Size ligand_in_pose, core::Size ligand_in_repeat)

void	repeat_ligand_constraints (core::pose::Pose &pose, core::pose::Pose &repeat_pose)

void	determine_overlap (const core::pose::Pose &pose, core::pose::Pose &parent_pose, core::Size overlap_max_length, core::Size overlap_range, std::string overlap_location_pose, core::Size &start_overlap_parent, core::Size &end_overlap_parent, core::Size &start_overlap_pose, core::Size &end_overlap_pose)

void	generate_overlap (core::pose::Pose &pose, core::pose::Pose &parent_pose, std::string overlap_location_pose, core::Size start_overlap_parent, core::Size end_overlap_parent, core::Size start_overlap_pose, core::Size end_overlap_pose)

void	extract_repeat_info_from_pose (const core::pose::Pose &pose)

void	trim_back_repeat_to_repair_scar (core::pose::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

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

◆ RepeatPropagationMover() [1/2]

protocols::simple_moves::RepeatPropagationMover::RepeatPropagationMover ( )

◆ RepeatPropagationMover() [2/2]

protocols::simple_moves::RepeatPropagationMover::RepeatPropagationMover ( core::Size numb_repeats )

References deal_with_length_change_scar_, extract_repeat_info_from_pose_, extract_repeat_template_repeat_, ideal_repeat_, maintain_cap_, maintain_cap_sequence_only_, maintain_ligand_, numb_repeats_, repeat_without_replacing_pose_, start_pose_duplicate_residues_, start_pose_length_, and start_pose_numb_repeats_.

Member Function Documentation

◆ add_cap_seq()

void protocols::simple_moves::RepeatPropagationMover::add_cap_seq	(	core::pose::Pose &	pose,
		core::pose::Pose &	repeat_pose
	)

private

References core::chemical::aa_from_oneletter_code(), core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::Pose::chi(), cTerm_cap_size_, core::pose::Pose::is_fullatom(), core::chemical::ResidueType::nchi(), nTerm_cap_size_, core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::Pose::residue_type(), core::pose::Pose::sequence(), core::pose::Pose::set_chi(), and core::pose::Pose::total_residue().

Referenced by apply().

◆ add_cap_seq_and_structure()

void protocols::simple_moves::RepeatPropagationMover::add_cap_seq_and_structure	(	core::pose::Pose &	pose,
		core::pose::Pose &	repeat_pose
	)

private

References core::pose::create_subpose(), cTerm_cap_size_, determine_overlap(), first_res_, generate_overlap(), last_res_, nTerm_cap_size_, and core::pose::Pose::size().

Referenced by apply().

◆ apply()

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

overridevirtual

◆ clone()

moves::MoverOP protocols::simple_moves::RepeatPropagationMover::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.

◆ copy_phi_psi_omega()

void protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega	(	core::pose::Pose &	pose,
		core::pose::Pose &	repeat_pose
	)

private

◆ determine_overlap()

void protocols::simple_moves::RepeatPropagationMover::determine_overlap	(	const core::pose::Pose &	pose,
		core::pose::Pose &	parent_pose,
		core::Size	overlap_max_length,
		core::Size	overlap_range,
		std::string	overlap_location_pose,
		core::Size &	start_overlap_parent,
		core::Size &	end_overlap_parent,
		core::Size &	start_overlap_pose,
		core::Size &	end_overlap_pose
	)

private

References core::scoring::CA_rmsd(), core::pose::pdbslice(), and core::pose::Pose::size().

Referenced by add_cap_seq_and_structure().

◆ duplicate_residues_by_type()

void protocols::simple_moves::RepeatPropagationMover::duplicate_residues_by_type	(	core::pose::Pose &	pose,
		core::pose::Pose &	repeat_pose
	)

private

References 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(), first_res_, last_res_, numb_repeats_, core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by initialize_repeat_pose().

◆ extract_repeat_info_from_pose()

void protocols::simple_moves::RepeatPropagationMover::extract_repeat_info_from_pose ( const core::pose::Pose & pose )

private

References cTerm_cap_size_, deal_with_length_change_scar_, extract_repeat_template_repeat_, first_res_, last_res_, maintain_cap_sequence_only_, nTerm_cap_size_, numb_repeats_, core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::size(), start_pose_duplicate_residues_, start_pose_length_, start_pose_numb_repeats_, and core::pose::Pose::total_residue().

Referenced by apply().

◆ fix_ligand_residues()

void protocols::simple_moves::RepeatPropagationMover::fix_ligand_residues	(	core::pose::Pose &	pose,
		core::pose::Pose &	repeat_pose
	)

private

References first_res_, initial_constrained_residues(), core::conformation::Residue::is_protein(), last_res_, numb_repeats_, core::pose::Pose::replace_residue(), and core::pose::Pose::residue().

Referenced by apply().

◆ generate_overlap()

void protocols::simple_moves::RepeatPropagationMover::generate_overlap	(	core::pose::Pose &	pose,
		core::pose::Pose &	parent_pose,
		std::string	overlap_location_pose,
		core::Size	start_overlap_parent,
		core::Size	end_overlap_parent,
		core::Size	start_overlap_pose,
		core::Size	end_overlap_pose
	)

private

References core::pose::append_pose_to_pose(), core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::pose::pdbslice(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::renumber_pdbinfo_based_on_conf_chains(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::scoring::superimpose_pose().

Referenced by add_cap_seq_and_structure().

◆ get_center_of_mass()

vector< Real > protocols::simple_moves::RepeatPropagationMover::get_center_of_mass	(	core::Real *	coordinates,
		int	number_of_atoms
	)

private

References core::conformation::membrane::center.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

◆ initial_constrained_residues()

vector1< core::Size > protocols::simple_moves::RepeatPropagationMover::initial_constrained_residues ( const core::pose::Pose & pose )

private

References core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by fix_ligand_residues().

◆ initialize_repeat_pose()

void protocols::simple_moves::RepeatPropagationMover::initialize_repeat_pose	(	core::pose::Pose &	pose,
		core::pose::Pose &	repeat_pose
	)

private

References duplicate_residues_by_type().

Referenced by apply().

◆ mover_name()

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

static

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

◆ parse_my_tag()

void protocols::simple_moves::RepeatPropagationMover::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 cTerm_cap_size_, deal_with_length_change_scar_, extract_repeat_info_from_pose_, extract_repeat_template_repeat_, first_res_, ideal_repeat_, last_res_, maintain_cap_, maintain_cap_sequence_only_, maintain_ligand_, nTerm_cap_size_, numb_repeats_, repeat_without_replacing_pose_, start_pose_duplicate_residues_, start_pose_length_, and start_pose_numb_repeats_.

◆ provide_xml_schema()

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

static

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

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

◆ repeat_ligand()

void protocols::simple_moves::RepeatPropagationMover::repeat_ligand	(	core::pose::Pose &	pose,
		core::pose::Pose &	repeat_pose
	)

private

References core::pose::motif::a(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::clone(), first_res_, core::conformation::Residue::is_protein(), last_res_, core::conformation::Residue::name3(), numb_repeats_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::simple_moves::TR(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ repeat_ligand_constraints()

void protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints	(	core::pose::Pose &	pose,
		core::pose::Pose &	repeat_pose
	)

private

References core::pose::Pose::add_constraint(), core::pose::Pose::constraint_set(), first_res_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::conformation::Residue::get_self_ptr(), core::id::SequenceMapping::insert_aligned_residue_safe(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_protein(), last_res_, core::conformation::Residue::name3(), numb_repeats_, core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), setup_repeat_seqmap(), core::pose::Pose::total_residue(), and protocols::simple_moves::TR().

Referenced by apply().

◆ setup_repeat_seqmap()

core::id::SequenceMapping protocols::simple_moves::RepeatPropagationMover::setup_repeat_seqmap	(	core::Size	repeat_number,
		core::Size	ligand_in_pose,
		core::Size	ligand_in_repeat
	)

private

References first_res_, core::id::SequenceMapping::insert_aligned_residue_safe(), and last_res_.

Referenced by repeat_ligand_constraints().

◆ trim_back_repeat_to_repair_scar()

void protocols::simple_moves::RepeatPropagationMover::trim_back_repeat_to_repair_scar ( core::pose::Pose & pose )

private

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_range_slow(), first_res_, last_res_, core::pose::renumber_pdbinfo_based_on_conf_chains(), and core::pose::Pose::total_residue().

Referenced by apply().

Member Data Documentation

◆ cTerm_cap_size_

core::Size protocols::simple_moves::RepeatPropagationMover::cTerm_cap_size_

private

Referenced by add_cap_seq(), add_cap_seq_and_structure(), extract_repeat_info_from_pose(), and parse_my_tag().

◆ deal_with_length_change_scar_

bool protocols::simple_moves::RepeatPropagationMover::deal_with_length_change_scar_

private

Referenced by apply(), extract_repeat_info_from_pose(), parse_my_tag(), and RepeatPropagationMover().

◆ extract_repeat_info_from_pose_

bool protocols::simple_moves::RepeatPropagationMover::extract_repeat_info_from_pose_

private

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

◆ extract_repeat_template_repeat_

core::Size protocols::simple_moves::RepeatPropagationMover::extract_repeat_template_repeat_

private

Referenced by extract_repeat_info_from_pose(), parse_my_tag(), and RepeatPropagationMover().

◆ first_res_

core::Size protocols::simple_moves::RepeatPropagationMover::first_res_

private

Referenced by add_cap_seq_and_structure(), copy_phi_psi_omega(), duplicate_residues_by_type(), extract_repeat_info_from_pose(), fix_ligand_residues(), parse_my_tag(), repeat_ligand(), repeat_ligand_constraints(), setup_repeat_seqmap(), and trim_back_repeat_to_repair_scar().

◆ ideal_repeat_

bool protocols::simple_moves::RepeatPropagationMover::ideal_repeat_

private

Referenced by copy_phi_psi_omega(), parse_my_tag(), and RepeatPropagationMover().

◆ last_res_

core::Size protocols::simple_moves::RepeatPropagationMover::last_res_

private

Referenced by add_cap_seq_and_structure(), apply(), copy_phi_psi_omega(), duplicate_residues_by_type(), extract_repeat_info_from_pose(), fix_ligand_residues(), parse_my_tag(), repeat_ligand(), repeat_ligand_constraints(), setup_repeat_seqmap(), and trim_back_repeat_to_repair_scar().

◆ maintain_cap_

bool protocols::simple_moves::RepeatPropagationMover::maintain_cap_

private

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

◆ maintain_cap_sequence_only_

bool protocols::simple_moves::RepeatPropagationMover::maintain_cap_sequence_only_

private

Referenced by apply(), extract_repeat_info_from_pose(), parse_my_tag(), and RepeatPropagationMover().

◆ maintain_ligand_

bool protocols::simple_moves::RepeatPropagationMover::maintain_ligand_

private

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

◆ nTerm_cap_size_

core::Size protocols::simple_moves::RepeatPropagationMover::nTerm_cap_size_

private

Referenced by add_cap_seq(), add_cap_seq_and_structure(), extract_repeat_info_from_pose(), and parse_my_tag().

◆ numb_repeats_

core::Size protocols::simple_moves::RepeatPropagationMover::numb_repeats_

private

Referenced by apply(), copy_phi_psi_omega(), duplicate_residues_by_type(), extract_repeat_info_from_pose(), fix_ligand_residues(), parse_my_tag(), repeat_ligand(), repeat_ligand_constraints(), and RepeatPropagationMover().

◆ repeat_without_replacing_pose_

bool protocols::simple_moves::RepeatPropagationMover::repeat_without_replacing_pose_

private

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

◆ start_pose_duplicate_residues_

core::Size protocols::simple_moves::RepeatPropagationMover::start_pose_duplicate_residues_

private

Referenced by extract_repeat_info_from_pose(), parse_my_tag(), and RepeatPropagationMover().

◆ start_pose_length_

core::Size protocols::simple_moves::RepeatPropagationMover::start_pose_length_

private

Referenced by extract_repeat_info_from_pose(), parse_my_tag(), and RepeatPropagationMover().

◆ start_pose_numb_repeats_

core::Size protocols::simple_moves::RepeatPropagationMover::start_pose_numb_repeats_

private

Referenced by extract_repeat_info_from_pose(), parse_my_tag(), and RepeatPropagationMover().

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

src/protocols/pose_creation/RepeatPropagationMover.hh
src/protocols/pose_creation/RepeatPropagationMover.cc

Private Attributes
core::Size	first_res_

core::Size	last_res_

core::Size	numb_repeats_

bool	ideal_repeat_

bool	repeat_without_replacing_pose_

bool	maintain_cap_

bool	maintain_cap_sequence_only_

bool	maintain_ligand_

core::Size	nTerm_cap_size_

core::Size	cTerm_cap_size_

bool	extract_repeat_info_from_pose_

core::Size	extract_repeat_template_repeat_

core::Size	start_pose_numb_repeats_

core::Size	start_pose_length_

core::Size	start_pose_duplicate_residues_

bool	deal_with_length_change_scar_

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ RepeatPropagationMover() [1/2]

◆ RepeatPropagationMover() [2/2]

Member Function Documentation

◆ add_cap_seq()

◆ add_cap_seq_and_structure()

◆ apply()

◆ clone()

◆ copy_phi_psi_omega()

◆ determine_overlap()

◆ duplicate_residues_by_type()

◆ extract_repeat_info_from_pose()

◆ fix_ligand_residues()

◆ generate_overlap()

◆ get_center_of_mass()

◆ get_name()

◆ initial_constrained_residues()

◆ initialize_repeat_pose()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ repeat_ligand()

◆ repeat_ligand_constraints()

◆ setup_repeat_seqmap()

◆ trim_back_repeat_to_repair_scar()

Member Data Documentation

◆ cTerm_cap_size_

◆ deal_with_length_change_scar_

◆ extract_repeat_info_from_pose_

◆ extract_repeat_template_repeat_

◆ first_res_

◆ ideal_repeat_

◆ last_res_

◆ maintain_cap_

◆ maintain_cap_sequence_only_

◆ maintain_ligand_

◆ nTerm_cap_size_

◆ numb_repeats_

◆ repeat_without_replacing_pose_

◆ start_pose_duplicate_residues_

◆ start_pose_length_

◆ start_pose_numb_repeats_