#include <SliceToMiniProteinMover.hh>

Inheritance diagram for protocols::pose_creation::SliceToMiniProteinMover:

[legend]

Classes
struct	Chunk

struct	SSElement

Public Types
typedef core::select::residue_selector::ResidueSelectorOP	ResidueSelectorOP

typedef core::select::residue_selector::ResidueSelectorCOP	ResidueSelectorCOP

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
utility::vector1< SliceToMiniProteinMover::SSElement >	parse_ss (core::pose::Pose const &pose) const
	parse pdb into ssecondary structure elements based on input selector More...

utility::vector1< SliceToMiniProteinMover::Chunk >	parse_chunks (core::pose::Pose const &pose, utility::vector1< SliceToMiniProteinMover::SSElement > ss_elements)
	parse pdb into initial chunks More...

utility::vector1< SliceToMiniProteinMover::Chunk >	filter_chunks (utility::vector1< SliceToMiniProteinMover::Chunk > chunks)
	filter chunks based on ddg More...

utility::vector1< SliceToMiniProteinMover::Chunk >	trim_chunks (utility::vector1< SliceToMiniProteinMover::Chunk > chunks)
	trim any overhanging helices and helices that are slightly too long More...

void	setup_chunks_for_output (utility::vector1< SliceToMiniProteinMover::Chunk > &chunks)
	setups chunks for output. all, longest or best_ddg More...

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) 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...

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
core::scoring::ScoreFunctionOP	scorefxn_

protocols::moves::MoverOP	relax_mover_

core::Size	max_length_

core::Size	min_sse_count_

core::Size	min_sse_length_

core::Real	ddg_ala_slice_score_

core::select::residue_selector::ResidueSelectorCOP	selector_

utility::vector1< SliceToMiniProteinMover::Chunk >	final_chunks_

std::string	output_mode_

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...

Member Typedef Documentation

◆ ResidueSelectorCOP

typedef core::select::residue_selector::ResidueSelectorCOP protocols::pose_creation::SliceToMiniProteinMover::ResidueSelectorCOP

◆ ResidueSelectorOP

typedef core::select::residue_selector::ResidueSelectorOP protocols::pose_creation::SliceToMiniProteinMover::ResidueSelectorOP

Constructor & Destructor Documentation

◆ SliceToMiniProteinMover()

protocols::pose_creation::SliceToMiniProteinMover::SliceToMiniProteinMover ( )

Constructor.

Member Function Documentation

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References filter_chunks(), final_chunks_, get_additional_output(), parse_chunks(), parse_ss(), core::pose::Pose::pdb_info(), selector_, setup_chunks_for_output(), core::pose::Pose::size(), core::pose::Pose::total_residue(), and trim_chunks().

◆ clone()

moves::MoverOP protocols::pose_creation::SliceToMiniProteinMover::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.

◆ filter_chunks()

utility::vector1< SliceToMiniProteinMover::Chunk > protocols::pose_creation::SliceToMiniProteinMover::filter_chunks ( utility::vector1< SliceToMiniProteinMover::Chunk > chunks )

filter chunks based on ddg

References ddg_ala_slice_score_, relax_mover_, scorefxn_, and protocols::pose_creation::TR().

Referenced by apply().

◆ fresh_instance()

moves::MoverOP protocols::pose_creation::SliceToMiniProteinMover::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_additional_output()

core::pose::PoseOP protocols::pose_creation::SliceToMiniProteinMover::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 protocols::moves::FAIL_DO_NOT_RETRY, final_chunks_, protocols::moves::MS_SUCCESS, protocols::moves::Mover::set_last_move_status(), and protocols::pose_creation::TR().

Referenced by apply().

◆ get_name()

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

static

Referenced by get_name(), protocols::pose_creation::SliceToMiniProteinMoverCreator::keyname(), and provide_xml_schema().

◆ parse_chunks()

utility::vector1< SliceToMiniProteinMover::Chunk > protocols::pose_creation::SliceToMiniProteinMover::parse_chunks	(	core::pose::Pose const &	pose,
		utility::vector1< SliceToMiniProteinMover::SSElement >	ss_elements
	)

parse pdb into initial chunks

References max_length_, min_sse_count_, core::pose::pdbslice(), and protocols::moves::Mover::type().

Referenced by apply().

◆ parse_my_tag()

void protocols::pose_creation::SliceToMiniProteinMover::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 ddg_ala_slice_score_, max_length_, min_sse_count_, min_sse_length_, output_mode_, protocols::rosetta_scripts::parse_mover(), core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), relax_mover_, scorefxn_, and selector_.

◆ parse_ss()

utility::vector1< SliceToMiniProteinMover::SSElement > protocols::pose_creation::SliceToMiniProteinMover::parse_ss ( core::pose::Pose const & pose ) const

parse pdb into ssecondary structure elements based on input selector

References protocols::simple_filters::dssp(), core::pose::Pose::total_residue(), protocols::pose_creation::TR(), and protocols::moves::Mover::type().

Referenced by apply(), and trim_chunks().

◆ provide_xml_schema()

void protocols::pose_creation::SliceToMiniProteinMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::scoring::attributes_for_parse_score_function(), protocols::moves::complex_type_name_for_mover(), and mover_name().

Referenced by protocols::pose_creation::SliceToMiniProteinMoverCreator::provide_xml_schema().

◆ setup_chunks_for_output()

void protocols::pose_creation::SliceToMiniProteinMover::setup_chunks_for_output ( utility::vector1< SliceToMiniProteinMover::Chunk > & chunks )

setups chunks for output. all, longest or best_ddg

References output_mode_.

Referenced by apply().

◆ trim_chunks()

utility::vector1< SliceToMiniProteinMover::Chunk > protocols::pose_creation::SliceToMiniProteinMover::trim_chunks ( utility::vector1< SliceToMiniProteinMover::Chunk > chunks )

trim any overhanging helices and helices that are slightly too long

References max_length_, min_sse_length_, parse_ss(), and core::pose::pdbslice().

Referenced by apply().

Member Data Documentation

◆ ddg_ala_slice_score_

core::Real protocols::pose_creation::SliceToMiniProteinMover::ddg_ala_slice_score_

private

Referenced by filter_chunks(), and parse_my_tag().

◆ final_chunks_

utility::vector1<SliceToMiniProteinMover::Chunk> protocols::pose_creation::SliceToMiniProteinMover::final_chunks_

private

Referenced by apply(), and get_additional_output().

◆ max_length_

core::Size protocols::pose_creation::SliceToMiniProteinMover::max_length_

private

Referenced by parse_chunks(), parse_my_tag(), and trim_chunks().

◆ min_sse_count_

core::Size protocols::pose_creation::SliceToMiniProteinMover::min_sse_count_

private

Referenced by parse_chunks(), and parse_my_tag().

◆ min_sse_length_

core::Size protocols::pose_creation::SliceToMiniProteinMover::min_sse_length_

private

Referenced by parse_my_tag(), and trim_chunks().

◆ output_mode_

std::string protocols::pose_creation::SliceToMiniProteinMover::output_mode_

private

Referenced by parse_my_tag(), and setup_chunks_for_output().

◆ relax_mover_

protocols::moves::MoverOP protocols::pose_creation::SliceToMiniProteinMover::relax_mover_

private

Referenced by filter_chunks(), and parse_my_tag().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::pose_creation::SliceToMiniProteinMover::scorefxn_

private

Referenced by filter_chunks(), and parse_my_tag().

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::pose_creation::SliceToMiniProteinMover::selector_

private

Referenced by apply(), and parse_my_tag().

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

src/protocols/pose_creation/SliceToMiniProteinMover.hh
src/protocols/pose_creation/SliceToMiniProteinMover.cc

Classes

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ ResidueSelectorCOP

◆ ResidueSelectorOP

Constructor & Destructor Documentation

◆ SliceToMiniProteinMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ filter_chunks()

◆ fresh_instance()

◆ get_additional_output()

◆ get_name()

◆ mover_name()

◆ parse_chunks()

◆ parse_my_tag()

◆ parse_ss()

◆ provide_xml_schema()

◆ setup_chunks_for_output()

◆ trim_chunks()

Member Data Documentation

◆ ddg_ala_slice_score_

◆ final_chunks_

◆ max_length_

◆ min_sse_count_

◆ min_sse_length_

◆ output_mode_

◆ relax_mover_

◆ scorefxn_

◆ selector_