Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job. More...

#include <ERRASER2Protocol.hh>

Inheritance diagram for protocols::rna::movers::ERRASER2Protocol:

[legend]

Public Member Functions
	ERRASER2Protocol ()
	Constructors ///. More...

	ERRASER2Protocol (ERRASER2Protocol const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~ERRASER2Protocol () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

void	show (std::ostream &output=std::cout) const override
	Show the contents of the Mover. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Rosetta Scripts Support ///. 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...

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

void	score_function (core::scoring::ScoreFunctionOP const &scorefxn_in)

core::scoring::ScoreFunctionOP	score_function () const

void	n_rounds (core::Size const n_rounds)

core::Size	n_rounds () const

void	rebuild_residue_selector (core::select::residue_selector::ResidueSelectorCOP const &residue_selector)

core::select::residue_selector::ResidueSelectorCOP	rebuild_residue_selector () const

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
protocols::stepwise::monte_carlo::mover::StepWiseMasterMover	configure_master_mover (Pose const &start_pose)

void	resample_full_model (core::Size const resample_round, core::pose::Pose &start_pose, utility::vector1< core::Size > const &definite_residues, core::Size const nstruct)

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_ = nullptr

bool	minimize_protein_ = false

core::Size	n_rounds_ = 3

core::select::residue_selector::ResidueSelectorCOP	rebuild_residue_selector_ = nullptr

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...

Detailed Description

Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job.

Constructor & Destructor Documentation

◆ ERRASER2Protocol() [1/2]

protocols::rna::movers::ERRASER2Protocol::ERRASER2Protocol ( )

Constructors ///.

Default constructor

◆ ERRASER2Protocol() [2/2]

protocols::rna::movers::ERRASER2Protocol::ERRASER2Protocol ( ERRASER2Protocol const & src )

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References rebuild_residue_selector_, and scorefxn_.

◆ ~ERRASER2Protocol()

protocols::rna::movers::ERRASER2Protocol::~ERRASER2Protocol ( )

override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

◆ apply()

void protocols::rna::movers::ERRASER2Protocol::apply ( core::pose::Pose & start_pose )

overridevirtual

Mover Methods ///.

Apply the mover

Perform the erraser2 protocol in a working directory

This function also does pose readin (because it could be resuming from checkpoints). In MPI contexts, this function is run on every core. (We use a work-partition job distribution framework by default, where each core is just assigned a fixed set of nstruct.) As a result, it needs to take two ints, which represent its rank and the total number of processors. Since MPI libraries use signed ints, we follow their convention rather than contorting ourselves to make them Sizes.

Apply the mover

Implements protocols::moves::Mover.

References protocols::rna::movers::ErraserMinimizerMover::apply(), protocols::rna::movers::ErraserMinimizerMover::constrain_phosphate(), protocols::rna::movers::ErraserMinimizerMover::edens_scorefxn(), protocols::rna::movers::ErraserMinimizerMover::minimize_protein(), protocols::rna::movers::ErraserMinimizerMover::scorefxn(), protocols::rna::movers::show_accuracy_report(), core::pose::Pose::size(), protocols::rna::movers::TR(), and protocols::rna::movers::ErraserMinimizerMover::work_partition().

◆ clone()

protocols::moves::MoverOP protocols::rna::movers::ERRASER2Protocol::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ configure_master_mover()

mover::StepWiseMasterMover protocols::rna::movers::ERRASER2Protocol::configure_master_mover ( Pose const & start_pose )

private

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

◆ fresh_instance()

protocols::moves::MoverOP protocols::rna::movers::ERRASER2Protocol::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::rna::movers::ERRASER2Protocol::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ mover_name()

std::string protocols::rna::movers::ERRASER2Protocol::mover_name ( )

static

Referenced by protocols::rna::movers::ERRASER2ProtocolCreator::keyname().

◆ n_rounds() [1/2]

core::Size protocols::rna::movers::ERRASER2Protocol::n_rounds ( ) const

inline

References n_rounds_.

◆ n_rounds() [2/2]

void protocols::rna::movers::ERRASER2Protocol::n_rounds ( core::Size const n_rounds )

inline

References n_rounds(), and n_rounds_.

Referenced by n_rounds().

◆ parse_my_tag()

void protocols::rna::movers::ERRASER2Protocol::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Rosetta Scripts Support ///.

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References protocols::pack_daemon::error_message, core::select::residue_selector::get_residue_selector(), core::scoring::get_score_function(), core::scoring::parse_score_function(), and protocols::rna::movers::TR().

◆ provide_xml_schema()

void protocols::rna::movers::ERRASER2Protocol::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(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::rna::movers::ERRASER2ProtocolCreator::provide_xml_schema().

◆ rebuild_residue_selector() [1/2]

core::select::residue_selector::ResidueSelectorCOP protocols::rna::movers::ERRASER2Protocol::rebuild_residue_selector ( ) const

inline

References rebuild_residue_selector_.

◆ rebuild_residue_selector() [2/2]

void protocols::rna::movers::ERRASER2Protocol::rebuild_residue_selector ( core::select::residue_selector::ResidueSelectorCOP const & residue_selector )

inline

References rebuild_residue_selector_.

◆ resample_full_model()

void protocols::rna::movers::ERRASER2Protocol::resample_full_model	(	core::Size const	resample_round,
		core::pose::Pose &	start_pose,
		utility::vector1< core::Size > const &	definite_residues,
		core::Size const	nstruct
	)

private

References protocols::viewer::add_conformation_viewer(), protocols::viewer::clear_conformation_viewers(), core::pose::Pose::conformation(), protocols::rna::movers::determine_residues_to_rebuild(), core::chemical::ResidueTypeBase::name(), core::pose::Pose::pdb_info(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model(), core::pose::Pose::residue_type(), and protocols::rna::movers::TR().

◆ score_function() [1/2]

core::scoring::ScoreFunctionOP protocols::rna::movers::ERRASER2Protocol::score_function ( ) const

inline

References scorefxn_.

◆ score_function() [2/2]

void protocols::rna::movers::ERRASER2Protocol::score_function ( core::scoring::ScoreFunctionOP const & scorefxn_in )

inline

References scorefxn_.

◆ show()

void protocols::rna::movers::ERRASER2Protocol::show ( std::ostream & output = std::cout ) const

overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

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

Referenced by protocols::rna::movers::operator<<().

Member Data Documentation

◆ minimize_protein_

bool protocols::rna::movers::ERRASER2Protocol::minimize_protein_ = false

private

◆ n_rounds_

core::Size protocols::rna::movers::ERRASER2Protocol::n_rounds_ = 3

private

Referenced by n_rounds().

◆ rebuild_residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::rna::movers::ERRASER2Protocol::rebuild_residue_selector_ = nullptr

private

Referenced by ERRASER2Protocol(), and rebuild_residue_selector().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::rna::movers::ERRASER2Protocol::scorefxn_ = nullptr

private

Referenced by ERRASER2Protocol(), and score_function().

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

src/protocols/rna/movers/ERRASER2Protocol.hh
src/protocols/rna/movers/ERRASER2Protocol.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ERRASER2Protocol() [1/2]

◆ ERRASER2Protocol() [2/2]

◆ ~ERRASER2Protocol()

Member Function Documentation

◆ apply()

◆ clone()

◆ configure_master_mover()

◆ fresh_instance()

◆ get_name()

◆ mover_name()

◆ n_rounds() [1/2]

◆ n_rounds() [2/2]

◆ parse_my_tag()

◆ provide_xml_schema()

◆ rebuild_residue_selector() [1/2]

◆ rebuild_residue_selector() [2/2]

◆ resample_full_model()

◆ score_function() [1/2]

◆ score_function() [2/2]

◆ show()

Member Data Documentation

◆ minimize_protein_

◆ n_rounds_

◆ rebuild_residue_selector_

◆ scorefxn_