#include <GrowPeptides.hh>

Inheritance diagram for protocols::seeded_abinitio::GrowPeptides:

[legend]

Public Member Functions
	GrowPeptides ()

	~GrowPeptides () override

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

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...

bool	ddg ()

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
void	append_residues_nterminally (core::Size seq_register, core::Size res_pos, core::Size stop, std::string &nat_seq, core::pose::Pose &target_seeds)
	functions More...

void	append_residues_cterminally (core::Size seq_register, core::Size res_pos, core::Size stop, std::string &nat_seq, core::pose::Pose &target_seeds)

void	grow_from_seeds (core::pose::Pose curr_pose, std::string sequence, protocols::loops::Loops &seeds, utility::vector1< core::Size > cutpoints)

void	grow_from_vertices (core::pose::Pose &curr_pose, std::string sequence, protocols::loops::Loops &seeds, std::set< core::Size > vertex_set)

void	setup_cached_observers (core::pose::Pose &pose)

Private Attributes
core::Size	extend_nterm
	data More...

core::Size	extend_cterm

std::string	nsequence_

std::string	csequence_

std::string	seq_

bool	all_ala_N

bool	all_ala_C

bool	ddg_

core::pose::PoseOP	template_pdb_
	template pose to derrive a sequence from More...

bool	template_presence

bool	anchor_specified_

utility::vector1< core::Size >	anchors_

core::scoring::ScoreFunctionOP	scorefxn_

bool	output_centroid

utility::vector1< std::string >	sequence_chunks_
	vector of sequence pieces More...

utility::vector1< GrowPeptidesSegmentOP >	all_seeds_

bool	fetch_foldtree

core::kinematics::FoldTreeOP	seed_foldtree_
	foldtree after growing out peptide pieces More...

core::pose::PoseCOP	reference_pose_
	pointer for the reference pose for seeds More...

std::set< core::Size >	vertices_

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

◆ GrowPeptides()

protocols::seeded_abinitio::GrowPeptides::GrowPeptides ( )

default

◆ ~GrowPeptides()

protocols::seeded_abinitio::GrowPeptides::~GrowPeptides ( )

overridedefault

Member Function Documentation

◆ append_residues_cterminally()

void protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally	(	core::Size	seq_register,
		core::Size	res_pos,
		core::Size	stop,
		std::string &	nat_seq,
		core::pose::Pose &	target_seeds
	)

private

References protocols::cluster::calibur::aa, core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueTypeBase::mode(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::pose::Pose::set_omega(), protocols::loops::stop, and TR().

◆ append_residues_nterminally()

void protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally	(	core::Size	seq_register,
		core::Size	res_pos,
		core::Size	stop,
		std::string &	nat_seq,
		core::pose::Pose &	target_seeds
	)

private

functions

References protocols::cluster::calibur::aa, core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueTypeBase::mode(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), core::pose::Pose::set_omega(), protocols::loops::stop, and TR().

◆ apply()

void protocols::seeded_abinitio::GrowPeptides::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::loops::Loops::add_loop(), core::kinematics::FoldTree::cutpoints(), protocols::simple_filters::dssp(), core::sequence::end, core::pose::Pose::fold_tree(), core::chemical::FULL_ATOM_t, core::util::switch_to_residue_type_set(), TR(), and core::pose::Pose::update_residue_neighbors().

◆ clone()

protocols::moves::MoverOP protocols::seeded_abinitio::GrowPeptides::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.

◆ ddg()

bool protocols::seeded_abinitio::GrowPeptides::ddg ( )

◆ fresh_instance()

protocols::moves::MoverOP protocols::seeded_abinitio::GrowPeptides::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::seeded_abinitio::GrowPeptides::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ grow_from_seeds()

void protocols::seeded_abinitio::GrowPeptides::grow_from_seeds	(	core::pose::Pose	curr_pose,
		std::string	sequence,
		protocols::loops::Loops &	seeds,
		utility::vector1< core::Size >	cutpoints
	)

private

◆ grow_from_vertices()

void protocols::seeded_abinitio::GrowPeptides::grow_from_vertices	(	core::pose::Pose &	curr_pose,
		std::string	sequence,
		protocols::loops::Loops &	seeds,
		std::set< core::Size >	vertex_set
	)

private

References core::chemical::CENTROID_t, core::kinematics::FoldTree::clear(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::new_jump(), core::pose::Pose::size(), protocols::loops::start, protocols::loops::stop, core::util::switch_to_residue_type_set(), and TR().

◆ mover_name()

std::string protocols::seeded_abinitio::GrowPeptides::mover_name ( )

static

◆ parse_my_tag()

void protocols::seeded_abinitio::GrowPeptides::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 core::sequence::end, protocols::rosetta_scripts::legacy_saved_pose_or_input(), core::pose::parse_resnum(), core::scoring::parse_score_function(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and TR().

◆ provide_xml_schema()

void protocols::seeded_abinitio::GrowPeptides::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

◆ setup_cached_observers()

void protocols::seeded_abinitio::GrowPeptides::setup_cached_observers ( core::pose::Pose & pose )

private

putting a LengthEventCollector into the pose

References core::pose::datacache::LENGTH_EVENT_COLLECTOR, core::pose::Pose::observer_cache(), and core::pose::datacache::ObserverCache::set().

Member Data Documentation

◆ all_ala_C

bool protocols::seeded_abinitio::GrowPeptides::all_ala_C

private

◆ all_ala_N

bool protocols::seeded_abinitio::GrowPeptides::all_ala_N

private

◆ all_seeds_

utility::vector1< GrowPeptidesSegmentOP > protocols::seeded_abinitio::GrowPeptides::all_seeds_

private

◆ anchor_specified_

bool protocols::seeded_abinitio::GrowPeptides::anchor_specified_

private

◆ anchors_

utility::vector1< core::Size > protocols::seeded_abinitio::GrowPeptides::anchors_

private

◆ csequence_

std::string protocols::seeded_abinitio::GrowPeptides::csequence_

private

◆ ddg_

bool protocols::seeded_abinitio::GrowPeptides::ddg_

private

◆ extend_cterm

core::Size protocols::seeded_abinitio::GrowPeptides::extend_cterm

private

◆ extend_nterm

core::Size protocols::seeded_abinitio::GrowPeptides::extend_nterm

private

data

◆ fetch_foldtree

bool protocols::seeded_abinitio::GrowPeptides::fetch_foldtree

private

◆ nsequence_

std::string protocols::seeded_abinitio::GrowPeptides::nsequence_

private

◆ output_centroid

bool protocols::seeded_abinitio::GrowPeptides::output_centroid

private

◆ reference_pose_

core::pose::PoseCOP protocols::seeded_abinitio::GrowPeptides::reference_pose_

private

pointer for the reference pose for seeds

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::GrowPeptides::scorefxn_

private

◆ seed_foldtree_

core::kinematics::FoldTreeOP protocols::seeded_abinitio::GrowPeptides::seed_foldtree_

private

foldtree after growing out peptide pieces

◆ seq_

std::string protocols::seeded_abinitio::GrowPeptides::seq_

private

◆ sequence_chunks_

utility::vector1< std::string > protocols::seeded_abinitio::GrowPeptides::sequence_chunks_

private

vector of sequence pieces

◆ template_pdb_

core::pose::PoseOP protocols::seeded_abinitio::GrowPeptides::template_pdb_

private

template pose to derrive a sequence from

◆ template_presence

bool protocols::seeded_abinitio::GrowPeptides::template_presence

private

◆ vertices_

std::set< core::Size > protocols::seeded_abinitio::GrowPeptides::vertices_

private

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

src/protocols/seeded_abinitio/GrowPeptides.hh
src/protocols/seeded_abinitio/GrowPeptides.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ GrowPeptides()

◆ ~GrowPeptides()

Member Function Documentation

◆ append_residues_cterminally()

◆ append_residues_nterminally()

◆ apply()

◆ clone()

◆ ddg()

◆ fresh_instance()

◆ get_name()

◆ grow_from_seeds()

◆ grow_from_vertices()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ setup_cached_observers()

Member Data Documentation

◆ all_ala_C

◆ all_ala_N

◆ all_seeds_

◆ anchor_specified_

◆ anchors_

◆ csequence_

◆ ddg_

◆ extend_cterm

◆ extend_nterm

◆ fetch_foldtree

◆ nsequence_

◆ output_centroid

◆ reference_pose_

◆ scorefxn_

◆ seed_foldtree_

◆ seq_

◆ sequence_chunks_

◆ template_pdb_

◆ template_presence

◆ vertices_