#include <MakeJunctionsMover.hh>

Inheritance diagram for protocols::pose_creation::MakeJunctionsMover:

[legend]

Classes
struct	Design

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

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

moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

	MakeJunctionsMover ()

Design	line_to_design (std::string line)

std::queue< Design >	read_in_designs ()

void	parse_attach_description (std::string attach_description, std::string &pdb_location, char &chain, core::Size &n_term_trim, core::Size &c_term_trim, core::Size &n_repeats, core::Size &n_term_attach_length, core::Size &c_term_attach_length, std::string &n_term_seq, std::string &c_term_seq)

void	generate_start_pose (core::pose::Pose &pose, core::pose::Pose &background_pose, std::string attach_description)

bool	attach_next_part (core::pose::Pose &pose, std::string attach_termini, std::string attach_description)

void	trim_pose (core::pose::Pose &pose, core::Size n_term_trim, core::Size c_term_trim)

void	assign_seq (core::pose::Pose &pose, std::string n_term_seq, std::string c_term_seq)

core::pose::Pose	get_and_cache_pdb (std::string pdb_location)

bool	check_all_junctions_good (MakeJunctionsMover::Design design)

bool	make_pose_from_design (MakeJunctionsMover::Design design, core::pose::PoseOP &return_pose)

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

core::pose::PoseOP	get_additional_output () override
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

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

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 Attributes
std::map< std::string, core::pose::Pose >	pdb_cache_

core::scoring::ScoreFunctionOP	sfxn_

std::string	designs_fn_

std::queue< Design >	design_q_

bool	pdb_cache_bool_

core::Size	pdb_cache_max_size_

core::Real	junction_rmsd_thresh_

std::multiset< std::string >	junction_failure_set_

char	chain_

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

◆ MakeJunctionsMover()

protocols::pose_creation::MakeJunctionsMover::MakeJunctionsMover ( )

Member Function Documentation

◆ apply()

void protocols::pose_creation::MakeJunctionsMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References design_q_, get_additional_output(), and read_in_designs().

◆ assign_seq()

void protocols::pose_creation::MakeJunctionsMover::assign_seq	(	core::pose::Pose &	pose,
		std::string	n_term_seq,
		std::string	c_term_seq
	)

References core::chemical::aa_from_oneletter_code(), core::select::fill_neighbor_residues(), core::optimization::MinimizerOptions::max_iter(), core::optimization::AtomTreeMinimizer::run(), core::pose::Pose::sequence(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), sfxn_, core::pose::Pose::size(), and protocols::pose_creation::TR().

Referenced by attach_next_part(), and generate_start_pose().

◆ attach_next_part()

bool protocols::pose_creation::MakeJunctionsMover::attach_next_part	(	core::pose::Pose &	pose,
		std::string	attach_termini,
		std::string	attach_description
	)

References assign_seq(), get_and_cache_pdb(), core::pose::Pose::is_fullatom(), junction_failure_set_, junction_rmsd_thresh_, parse_attach_description(), sfxn_, and trim_pose().

Referenced by make_pose_from_design().

◆ check_all_junctions_good()

bool protocols::pose_creation::MakeJunctionsMover::check_all_junctions_good ( MakeJunctionsMover::Design design )

References protocols::pose_creation::MakeJunctionsMover::Design::c_term_stack, junction_failure_set_, and protocols::pose_creation::MakeJunctionsMover::Design::n_term_stack.

Referenced by make_pose_from_design().

◆ clone()

moves::MoverOP protocols::pose_creation::MakeJunctionsMover::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()

moves::MoverOP protocols::pose_creation::MakeJunctionsMover::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.

◆ generate_start_pose()

void protocols::pose_creation::MakeJunctionsMover::generate_start_pose	(	core::pose::Pose &	pose,
		core::pose::Pose &	background_pose,
		std::string	attach_description
	)

References assign_seq(), chain_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_range_slow(), get_and_cache_pdb(), core::pose::get_chain_id_from_chain(), core::pose::has_chain(), parse_attach_description(), sfxn_, core::pose::Pose::size(), core::pose::Pose::split_by_chain(), and trim_pose().

Referenced by make_pose_from_design().

◆ get_additional_output()

core::pose::PoseOP protocols::pose_creation::MakeJunctionsMover::get_additional_output ( )

overridevirtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References design_q_, protocols::moves::FAIL_DO_NOT_RETRY, make_pose_from_design(), protocols::moves::Mover::set_last_move_status(), and sfxn_.

Referenced by apply().

◆ get_and_cache_pdb()

core::pose::Pose protocols::pose_creation::MakeJunctionsMover::get_and_cache_pdb ( std::string pdb_location )

References core::chemical::FA_STANDARD, pdb_cache_, pdb_cache_bool_, pdb_cache_max_size_, core::import_pose::PDB_file, and core::import_pose::pose_from_file().

Referenced by attach_next_part(), and generate_start_pose().

◆ get_name()

std::string protocols::pose_creation::MakeJunctionsMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ line_to_design()

MakeJunctionsMover::Design protocols::pose_creation::MakeJunctionsMover::line_to_design ( std::string line )

References protocols::moves::Mover::name().

Referenced by read_in_designs().

◆ make_pose_from_design()

bool protocols::pose_creation::MakeJunctionsMover::make_pose_from_design	(	MakeJunctionsMover::Design	design,
		core::pose::PoseOP &	return_pose
	)

References core::pose::append_pose_to_pose(), attach_next_part(), protocols::pose_creation::MakeJunctionsMover::Design::c_term_stack, check_all_junctions_good(), generate_start_pose(), protocols::jd2::JobDistributor::get_instance(), protocols::pose_creation::MakeJunctionsMover::Design::n_term_stack, protocols::pose_creation::MakeJunctionsMover::Design::name, core::pose::renumber_pdbinfo_based_on_conf_chains(), core::pose::Pose::size(), and protocols::pose_creation::MakeJunctionsMover::Design::start_struct.

Referenced by get_additional_output().

◆ mover_name()

std::string protocols::pose_creation::MakeJunctionsMover::mover_name ( )

static

Referenced by get_name(), and provide_xml_schema().

◆ parse_attach_description()

void protocols::pose_creation::MakeJunctionsMover::parse_attach_description	(	std::string	attach_description,
		std::string &	pdb_location,
		char &	chain,
		core::Size &	n_term_trim,
		core::Size &	c_term_trim,
		core::Size &	n_repeats,
		core::Size &	n_term_attach_length,
		core::Size &	c_term_attach_length,
		std::string &	n_term_seq,
		std::string &	c_term_seq
	)

Referenced by attach_next_part(), and generate_start_pose().

◆ parse_my_tag()

void protocols::pose_creation::MakeJunctionsMover::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 designs_fn_, junction_rmsd_thresh_, pdb_cache_bool_, pdb_cache_max_size_, and sfxn_.