Mover that builds and folds a structure via fragment insertion. More...

#include <FoldArchitectMover.hh>

Inheritance diagram for protocols::denovo_design::movers::FoldArchitectMover:

[legend]

Public Types
typedef core::Real	FoldScore

typedef utility::vector1< connection::ConnectionArchitectCOP >	ConnectionArchitectCOPs

typedef utility::vector1< protocols::moves::MoverOP >	MoverOPs

typedef utility::vector1< protocols::filters::FilterCOP >	FilterCOPs

typedef core::select::residue_selector::ResidueVector	ResidueVector

typedef protocols::constraint_generator::ConstraintGeneratorOP	ConstraintGeneratorOP

typedef protocols::constraint_generator::ConstraintGeneratorCOP	ConstraintGeneratorCOP

typedef protocols::constraint_generator::ConstraintGeneratorCOPs	ConstraintGeneratorCOPs

typedef components::RegisterShift	RegisterShift

typedef components::StrandOrientation	StrandOrientation

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
	FoldArchitectMover ()

	~FoldArchitectMover () override

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...

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

std::string const &	id () const

void	set_id (std::string const &id_value)
	Sets the ID of this mover. More...

void	set_architect (architects::DeNovoArchitect const &architect)
	Sets the architect that will be used to build blueprints dynamically. More...

void	set_folder (components::PoseFolder const &folder)
	Sets the pose folder that will be used to sample conformations. More...

void	set_folder (components::PoseFolderOP folder)
	Sets the pose folder that will be used to sample conformations. More...

void	set_builder (components::PoseBuilder const &builder)
	Sets the pose builder that will be used to create the extended-chain pose. More...

void	set_builder (components::PoseBuilderOP builder)
	Sets the pose builder that will be used to create the extended-chain pose. More...

void	set_perturber (components::StructureDataPerturber const &perturber)
	Sets the perturber that will be used to change the plans of the architects. More...

void	set_perturber (components::StructureDataPerturberOP perturber)
	Sets the perturber that will be used to change the plans of the architects. More...

void	set_start_segments (std::string const &segments_csv)
	sets names of segments to be included in the starting build phase More...

void	set_start_segments (SegmentNameSet const &segments)
	sets names of segments to be included in the starting build phase More...

void	set_stop_segments (std::string const &segments_csv)
	sets names of segments to be included in the final build phase More...

void	set_stop_segments (SegmentNameSet const &segments)
	sets names of segments to be included in the final build phase More...

void	set_build_overlap (core::Size const overlap_val)
	Sets the number of residues of overlap to use between build phases. More...

void	set_score_filter (protocols::filters::Filter const &filter)
	Sets the filter that will be used to evaluate the generated conformations. Used to return a score, not to evaluate true/false. More...

void	setup_from_xml_file (std::string const &xml_file, basic::datacache::DataMap &data)
	Reads/parses an XML file and uses it to set up the mover. More...

void	setup_from_xml_string (std::string const &xml_string, basic::datacache::DataMap &data)
	Reads/parses an XML string and uses it to set up the mover. More...

void	setup_from_xml_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Reads/parses a Tag object and uses it to set up the mover. More...

void	clear_prefold_movers ()
	Clears the list of prefold movers. More...

void	add_prefold_mover (protocols::moves::Mover const &mover)
	Adds a mover to the list of prefold movers. More...

void	clear_postfold_movers ()
	Clears the list of postfold movers. More...

void	add_postfold_mover (protocols::moves::Mover const &mover)
	Adds a mover to the list of postfold movers. More...

void	add_filter (protocols::filters::Filter const &filter)
	Adds a filter to the list of filters that indicate whether a given folding attempt is was successful or not. All filters must pass for a successful folding attempt. More...

void	clear_filters ()
	Clears the list of filters used to indicate whether a given folding attempt is successful. More...

void	set_dump_pdbs (bool const dump)
	If true, extra PDBs will be outputted for debugging purposes. Could be useful for figuring out why folding attempts are failing. If false, no extra files are outputted. More...

void	set_debug (bool const debug)
	The debug value of the poseBuilder will be set based on this. More...

void	set_iterations_per_phase (core::Size const niter)
	Sets the number of folding attempts for each build phase. 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...

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 void	provide_xml_schema_with_name (utility::tag::XMLSchemaDefinition &xsd, std::string const &mover_name)

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
FoldScore	folding_score (core::pose::Pose const &pose) const

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

void	check_pose (core::pose::Pose const &pose) const
	runs user-provided filters on the pose More...

void	check_and_accept (core::pose::Pose const &orig, core::pose::Pose &pose, FoldScore &bestscore) const

protocols::loops::Loops	create_loops (core::pose::Pose const &pose, ResidueVector &overlap_residues, SegmentNames &movable_segments) const

core::select::residue_selector::ResidueSubset	select_movable_residues (core::pose::Pose const &pose, SegmentNames const &movable_segments, ResidueVector const &overlap_residues) const

SegmentNames	segments_to_fold (components::StructureData const &sd) const

MoverOPs	prefold_movers (core::pose::Pose const &pose, protocols::loops::Loops const &loops, ConstraintGeneratorCOPs const &generators) const

MoverOPs	postfold_movers (core::pose::Pose const &pose, protocols::loops::Loops const &loops, ConstraintGeneratorCOPs const &generators) const

void	apply_movers (MoverOPs const &movers, core::pose::Pose &pose) const

SegmentNames	find_roots (core::pose::Pose const &pose, protocols::loops::Loops const &loops) const

ConstraintGeneratorCOPs	create_constraint_generators (ResidueVector const &residues) const

ConstraintGeneratorOP	create_overlap_constraint_generator (ResidueVector const &residues) const
	builds a constraint generator for residues that overlap between phases More...

void	remove_cutpoints (components::StructureData &sd, protocols::loops::Loops const &loops) const

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

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

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

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

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

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

MoverOPs	parse_movers (utility::tag::TagCOP tag, basic::datacache::DataMap &data) const

core::pose::PoseOP	build_in_phases (components::StructureData const &full_sd, components::BuildPhases const &phases, SegmentNameSet const &finished, core::Size const phase_num) const
	builds/folds pose in phases using recursive algorithm More...

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

Static Private Member Functions
static protocols::filters::FilterOP	default_score_filter ()

static std::string	build_denovo_backbone_ct_naming_func (std::string const &)

static std::string	prefold_ct_naming_func (std::string const &)

static std::string	postfold_ct_naming_func (std::string const &)

static std::string	filters_ct_naming_func (std::string const &)

static std::string	connections_ct_naming_func (std::string const &)

static std::string	folder_ct_namer (std::string const &)

static std::string	perturber_ct_namer (std::string const &)

static void	define_folder_group (utility::tag::XMLSchemaDefinition &)

static void	define_perturber_group (utility::tag::XMLSchemaDefinition &)

static void	define_filters_ct (utility::tag::XMLSchemaDefinition &)

static void	define_prefold_movers_ct (utility::tag::XMLSchemaDefinition &)

static void	define_postfold_movers_ct (utility::tag::XMLSchemaDefinition &)

static std::string	perturber_group_name ()

static std::string	folder_group_name ()

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...

Detailed Description

Mover that builds and folds a structure via fragment insertion.

Member Typedef Documentation

◆ ConnectionArchitectCOPs

typedef utility::vector1< connection::ConnectionArchitectCOP > protocols::denovo_design::movers::FoldArchitectMover::ConnectionArchitectCOPs

◆ ConstraintGeneratorCOP

typedef protocols::constraint_generator::ConstraintGeneratorCOP protocols::denovo_design::movers::FoldArchitectMover::ConstraintGeneratorCOP

◆ ConstraintGeneratorCOPs

typedef protocols::constraint_generator::ConstraintGeneratorCOPs protocols::denovo_design::movers::FoldArchitectMover::ConstraintGeneratorCOPs

◆ ConstraintGeneratorOP

typedef protocols::constraint_generator::ConstraintGeneratorOP protocols::denovo_design::movers::FoldArchitectMover::ConstraintGeneratorOP

◆ FilterCOPs

typedef utility::vector1< protocols::filters::FilterCOP > protocols::denovo_design::movers::FoldArchitectMover::FilterCOPs

◆ FoldScore

typedef core::Real protocols::denovo_design::movers::FoldArchitectMover::FoldScore

◆ MoverOPs

typedef utility::vector1< protocols::moves::MoverOP > protocols::denovo_design::movers::FoldArchitectMover::MoverOPs

◆ RegisterShift

typedef components::RegisterShift protocols::denovo_design::movers::FoldArchitectMover::RegisterShift

◆ ResidueVector

typedef core::select::residue_selector::ResidueVector protocols::denovo_design::movers::FoldArchitectMover::ResidueVector

◆ StrandOrientation

typedef components::StrandOrientation protocols::denovo_design::movers::FoldArchitectMover::StrandOrientation

Constructor & Destructor Documentation

◆ FoldArchitectMover()

protocols::denovo_design::movers::FoldArchitectMover::FoldArchitectMover ( )

References debug_, and set_debug().

◆ ~FoldArchitectMover()

protocols::denovo_design::movers::FoldArchitectMover::~FoldArchitectMover ( )

overridedefault

Member Function Documentation

◆ add_filter()

void protocols::denovo_design::movers::FoldArchitectMover::add_filter ( protocols::filters::Filter const & filter )

Adds a filter to the list of filters that indicate whether a given folding attempt is was successful or not. All filters must pass for a successful folding attempt.

References protocols::filters::Filter::clone(), and filters_.

Referenced by parse_filters().

◆ add_postfold_mover()

void protocols::denovo_design::movers::FoldArchitectMover::add_postfold_mover ( protocols::moves::Mover const & mover )

Adds a mover to the list of postfold movers.

References protocols::moves::Mover::clone(), and postfold_movers_.

Referenced by parse_postfold_movers().

◆ add_prefold_mover()

void protocols::denovo_design::movers::FoldArchitectMover::add_prefold_mover ( protocols::moves::Mover const & mover )

Adds a mover to the list of prefold movers.

References protocols::moves::Mover::clone(), and prefold_movers_.

Referenced by parse_prefold_movers().

◆ apply()

void protocols::denovo_design::movers::FoldArchitectMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References architect_, build_in_phases(), protocols::denovo_design::components::DivideAndConqueror::divide_and_conquer(), protocols::moves::FAIL_RETRY, get_name(), protocols::moves::Mover::set_last_move_status(), protocols::denovo_design::components::DivideAndConqueror::set_start_segments(), protocols::denovo_design::components::DivideAndConqueror::set_stop_segments(), start_segments_, stop_segments_, and protocols::TR().

Referenced by protocols::denovo_design::movers::BridgeChainsMover::apply(), and protocols::denovo_design::movers::ExtendChainMover::apply().

◆ apply_movers()

void protocols::denovo_design::movers::FoldArchitectMover::apply_movers	(	MoverOPs const &	movers,
		core::pose::Pose &	pose
	)		const

private

References protocols::TR().

Referenced by fold_attempt().

◆ build_denovo_backbone_ct_naming_func()

std::string protocols::denovo_design::movers::FoldArchitectMover::build_denovo_backbone_ct_naming_func ( std::string const & subelement_name )

staticprivate

Referenced by provide_xml_schema_with_name().

◆ build_in_phases()

core::pose::PoseOP protocols::denovo_design::movers::FoldArchitectMover::build_in_phases	(	components::StructureData const &	full_sd,
		components::BuildPhases const &	phases,
		SegmentNameSet const &	finished,
		core::Size const	phase_num
	)		const

private

builds/folds pose in phases using recursive algorithm

Exceptions

EXCN_Fold if we couldn't fold the pose

References builder_, dump_pdbs_, fold_attempt(), iterations_per_phase_, mover_name(), protocols::denovo_design::movers::pdb_filename(), perturber_, protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_begin(), protocols::denovo_design::components::StructureData::segments_end(), protocols::denovo_design::components::StructureData::set_template_pose(), protocols::denovo_design::components::StructureData::slice(), protocols::denovo_design::components::Segment::start(), protocols::denovo_design::components::Segment::stop(), and protocols::TR().

Referenced by apply().

◆ check_and_accept()

void protocols::denovo_design::movers::FoldArchitectMover::check_and_accept	(	core::pose::Pose const &	orig,
		core::pose::Pose &	pose,
		FoldScore &	bestscore
	)		const

private

◆ check_pose()

void protocols::denovo_design::movers::FoldArchitectMover::check_pose ( core::pose::Pose const & pose ) const

private

runs user-provided filters on the pose

checks the pose for whether it folded correctly, according to user's filters

Filters are called for each build phase, and for every folding attempt, in order. If a filter fails, an exception is thrown and no later filters are run.

Exceptions

EXCN_FilterFailed if any filter fails

References filters_.

Referenced by fold_attempt().

◆ clear_filters()

void protocols::denovo_design::movers::FoldArchitectMover::clear_filters ( )

Clears the list of filters used to indicate whether a given folding attempt is successful.

References filters_.

Referenced by parse_filters(), and setup_from_xml_tag().

◆ clear_postfold_movers()

void protocols::denovo_design::movers::FoldArchitectMover::clear_postfold_movers ( )

Clears the list of postfold movers.

References postfold_movers_.

Referenced by setup_from_xml_tag().

◆ clear_prefold_movers()

void protocols::denovo_design::movers::FoldArchitectMover::clear_prefold_movers ( )

Clears the list of prefold movers.

References prefold_movers_.

Referenced by setup_from_xml_tag().

◆ clone()

protocols::moves::MoverOP protocols::denovo_design::movers::FoldArchitectMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ connections_ct_naming_func()

static std::string protocols::denovo_design::movers::FoldArchitectMover::connections_ct_naming_func ( std::string const & )

staticprivate

◆ create_constraint_generators()

FoldArchitectMover::ConstraintGeneratorCOPs protocols::denovo_design::movers::FoldArchitectMover::create_constraint_generators ( ResidueVector const & residues ) const

private

References create_overlap_constraint_generator().

Referenced by fold_attempt().

◆ create_loops()

protocols::loops::Loops protocols::denovo_design::movers::FoldArchitectMover::create_loops	(	core::pose::Pose const &	pose,
		ResidueVector &	overlap_residues,
		SegmentNames &	movable_segments
	)		const

private

References protocols::denovo_design::movers::add_overlap_to_loops(), build_overlap_, protocols::denovo_design::components::FoldGraph::create_loops(), protocols::denovo_design::components::StructureDataFactory::get_from_const_pose(), segments_to_fold(), and protocols::moves::Mover::type().

Referenced by fold_attempt().

◆ create_overlap_constraint_generator()

FoldArchitectMover::ConstraintGeneratorOP protocols::denovo_design::movers::FoldArchitectMover::create_overlap_constraint_generator ( ResidueVector const & residues ) const

private

builds a constraint generator for residues that overlap between phases

Parameters

[in] residues Vector of resids corresponding to the overlap residues

References protocols::TR().

Referenced by create_constraint_generators().

◆ default_score_filter()

protocols::filters::FilterOP protocols::denovo_design::movers::FoldArchitectMover::default_score_filter ( )

staticprivate

◆ define_filters_ct()

void protocols::denovo_design::movers::FoldArchitectMover::define_filters_ct ( utility::tag::XMLSchemaDefinition & xsd )

staticprivate

References filters_ct_naming_func().

Referenced by provide_xml_schema_with_name().

◆ define_folder_group()

void protocols::denovo_design::movers::FoldArchitectMover::define_folder_group ( utility::tag::XMLSchemaDefinition & xsd )

staticprivate

References core::scoring::attributes_for_parse_score_function(), folder_ct_namer(), and folder_group_name().

Referenced by provide_xml_schema_with_name().

◆ define_perturber_group()

void protocols::denovo_design::movers::FoldArchitectMover::define_perturber_group ( utility::tag::XMLSchemaDefinition & xsd )

staticprivate

References perturber_ct_namer(), and perturber_group_name().

Referenced by provide_xml_schema_with_name().

◆ define_postfold_movers_ct()

void protocols::denovo_design::movers::FoldArchitectMover::define_postfold_movers_ct ( utility::tag::XMLSchemaDefinition & xsd )

staticprivate

References postfold_ct_naming_func(), and protocols::denovo_design::movers::pre_and_post_fold_mover_subelements().

Referenced by provide_xml_schema_with_name().

◆ define_prefold_movers_ct()

void protocols::denovo_design::movers::FoldArchitectMover::define_prefold_movers_ct ( utility::tag::XMLSchemaDefinition & xsd )

staticprivate

References protocols::denovo_design::movers::pre_and_post_fold_mover_subelements(), and prefold_ct_naming_func().

Referenced by provide_xml_schema_with_name().

◆ filters_ct_naming_func()

std::string protocols::denovo_design::movers::FoldArchitectMover::filters_ct_naming_func ( std::string const & subelement_name )

staticprivate

Referenced by define_filters_ct(), and provide_xml_schema_with_name().

◆ find_roots()

SegmentNames protocols::denovo_design::movers::FoldArchitectMover::find_roots	(	core::pose::Pose const &	pose,
		protocols::loops::Loops const &	loops
	)		const

private

References build_overlap_, id(), protocols::denovo_design::loop_start_without_overlap(), protocols::denovo_design::loop_stop_without_overlap(), protocols::denovo_design::components::Segment::lower_segment(), protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segment_name(), protocols::denovo_design::components::StructureData::segments_begin(), protocols::TR(), and protocols::denovo_design::components::Segment::upper_segment().

Referenced by prefold_movers().

◆ fold()

void protocols::denovo_design::movers::FoldArchitectMover::fold ( core::pose::Pose & pose ) const

private

◆ fold_attempt()

void protocols::denovo_design::movers::FoldArchitectMover::fold_attempt ( core::pose::Pose & pose ) const

private

References apply_movers(), check_pose(), protocols::denovo_design::components::StructureData::check_pose_consistency(), core::scoring::Energies::clear(), create_constraint_generators(), create_loops(), protocols::loops::Loops::empty(), core::pose::Pose::energies(), folder_, protocols::denovo_design::components::StructureDataFactory::get_from_pose(), protocols::denovo_design::movers::get_score_function(), protocols::denovo_design::components::StructureDataFactory::has_cached_data(), postfold_movers(), prefold_movers(), select_movable_residues(), and protocols::TR().

Referenced by build_in_phases().

◆ folder_ct_namer()

std::string protocols::denovo_design::movers::FoldArchitectMover::folder_ct_namer ( std::string const & folder_name )

staticprivate

Referenced by define_folder_group().

◆ folder_group_name()

std::string protocols::denovo_design::movers::FoldArchitectMover::folder_group_name ( )

staticprivate

Referenced by define_folder_group(), and provide_xml_schema_with_name().

◆ folding_score()

FoldArchitectMover::FoldScore protocols::denovo_design::movers::FoldArchitectMover::folding_score ( core::pose::Pose const & pose ) const

private

References protocols::hybridization::score, score_filter_, and protocols::TR().

◆ fresh_instance()

protocols::moves::MoverOP protocols::denovo_design::movers::FoldArchitectMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::denovo_design::movers::FoldArchitectMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::denovo_design::movers::BuildDeNovoBackboneMover.

References mover_name().

Referenced by apply(), and setup_from_xml_tag().

◆ id()

std::string const & protocols::denovo_design::movers::FoldArchitectMover::id ( ) const

References id_.

Referenced by find_roots().

◆ mover_name()

std::string protocols::denovo_design::movers::FoldArchitectMover::mover_name ( )

static

Referenced by build_in_phases(), get_name(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::get_name(), protocols::denovo_design::movers::FoldArchitectMoverCreator::keyname(), parse_movers(), provide_xml_schema(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::provide_xml_schema(), and provide_xml_schema_with_name().

◆ parse_architect()

void protocols::denovo_design::movers::FoldArchitectMover::parse_architect	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

private

References set_architect().

Referenced by setup_from_xml_tag().

◆ parse_filters()

void protocols::denovo_design::movers::FoldArchitectMover::parse_filters	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

private

References add_filter(), clear_filters(), protocols::rosetta_scripts::parse_filter_or_null(), protocols::TR(), and protocols::moves::Mover::type().

Referenced by setup_from_xml_tag().

◆ parse_folder()

void protocols::denovo_design::movers::FoldArchitectMover::parse_folder	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

private

References protocols::denovo_design::components::NullPoseFolder::class_name(), protocols::denovo_design::components::RandomTorsionPoseFolder::class_name(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::class_name(), and set_folder().

Referenced by setup_from_xml_tag().

◆ parse_movers()

FoldArchitectMover::MoverOPs protocols::denovo_design::movers::FoldArchitectMover::parse_movers	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)		const

private

References mover_name(), protocols::rosetta_scripts::parse_mover_or_null(), protocols::TR(), and protocols::moves::Mover::type().

Referenced by parse_postfold_movers(), and parse_prefold_movers().

◆ parse_my_tag()

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

overridevirtual

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

Reimplemented from protocols::moves::Mover.

References build_overlap_, debug_, dump_pdbs_, iterations_per_phase_, set_build_overlap(), set_debug(), set_dump_pdbs(), set_id(), set_iterations_per_phase(), set_start_segments(), set_stop_segments(), setup_from_xml_file(), and setup_from_xml_tag().

◆ parse_perturber()

void protocols::denovo_design::movers::FoldArchitectMover::parse_perturber	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

private

References protocols::denovo_design::components::StructureDataPerturber::create(), and set_perturber().

Referenced by setup_from_xml_tag().

◆ parse_postfold_movers()

void protocols::denovo_design::movers::FoldArchitectMover::parse_postfold_movers	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

private

References add_postfold_mover(), and parse_movers().

Referenced by setup_from_xml_tag().

◆ parse_prefold_movers()

void protocols::denovo_design::movers::FoldArchitectMover::parse_prefold_movers	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

private

References add_prefold_mover(), and parse_movers().

Referenced by setup_from_xml_tag().

◆ perturber_ct_namer()

std::string protocols::denovo_design::movers::FoldArchitectMover::perturber_ct_namer ( std::string const & perturber_name )

staticprivate

Referenced by define_perturber_group().

◆ perturber_group_name()

std::string protocols::denovo_design::movers::FoldArchitectMover::perturber_group_name ( )

staticprivate

Referenced by define_perturber_group(), and provide_xml_schema_with_name().

◆ postfold_ct_naming_func()

std::string protocols::denovo_design::movers::FoldArchitectMover::postfold_ct_naming_func ( std::string const & subelement_name )

staticprivate

Referenced by define_postfold_movers_ct(), and provide_xml_schema_with_name().

◆ postfold_movers()

FoldArchitectMover::MoverOPs protocols::denovo_design::movers::FoldArchitectMover::postfold_movers	(	core::pose::Pose const &	pose,
		protocols::loops::Loops const &	loops,
		ConstraintGeneratorCOPs const &	generators
	)		const

private

References postfold_movers_, and core::pose::Pose::size().

Referenced by fold_attempt().

◆ prefold_ct_naming_func()

std::string protocols::denovo_design::movers::FoldArchitectMover::prefold_ct_naming_func ( std::string const & subelement_name )

staticprivate

Referenced by define_prefold_movers_ct(), and provide_xml_schema_with_name().

◆ prefold_movers()

FoldArchitectMover::MoverOPs protocols::denovo_design::movers::FoldArchitectMover::prefold_movers	(	core::pose::Pose const &	pose,
		protocols::loops::Loops const &	loops,
		ConstraintGeneratorCOPs const &	generators
	)		const

private

References protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover::clone(), find_roots(), and prefold_movers_.

Referenced by fold_attempt().

◆ provide_xml_schema()

void protocols::denovo_design::movers::FoldArchitectMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and provide_xml_schema_with_name().

Referenced by protocols::denovo_design::movers::FoldArchitectMoverCreator::provide_xml_schema().

◆ provide_xml_schema_with_name()

void protocols::denovo_design::movers::FoldArchitectMover::provide_xml_schema_with_name	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	mover_name
	)

static

References protocols::denovo_design::architects::DeNovoArchitectFactory::architect_group_name(), build_denovo_backbone_ct_naming_func(), protocols::moves::complex_type_name_for_mover(), define_filters_ct(), define_folder_group(), define_perturber_group(), define_postfold_movers_ct(), define_prefold_movers_ct(), filters_ct_naming_func(), folder_group_name(), mover_name(), perturber_group_name(), postfold_ct_naming_func(), and prefold_ct_naming_func().

Referenced by provide_xml_schema(), and protocols::denovo_design::movers::BuildDeNovoBackboneMover::provide_xml_schema().

◆ remove_cutpoints()

void protocols::denovo_design::movers::FoldArchitectMover::remove_cutpoints	(	components::StructureData &	sd,
		protocols::loops::Loops const &	loops
	)		const

private

References protocols::denovo_design::components::StructureData::segment_name(), protocols::denovo_design::components::StructureData::set_cutpoint(), and protocols::TR().

◆ segments_to_fold()

SegmentNames protocols::denovo_design::movers::FoldArchitectMover::segments_to_fold ( components::StructureData const & sd ) const

private

References protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::StructureData::segments_begin(), protocols::denovo_design::components::StructureData::segments_end(), and protocols::denovo_design::components::Segment::template_pose().

Referenced by create_loops().

◆ select_movable_residues()

core::select::residue_selector::ResidueSubset protocols::denovo_design::movers::FoldArchitectMover::select_movable_residues	(	core::pose::Pose const &	pose,
		SegmentNames const &	movable_segments,
		ResidueVector const &	overlap_residues
	)		const

private

References protocols::denovo_design::components::Segment::lower(), protocols::denovo_design::components::StructureData::pose_length(), protocols::denovo_design::components::StructureData::segment(), core::pose::Pose::size(), and protocols::denovo_design::components::Segment::upper().

Referenced by fold_attempt().

◆ set_architect()

void protocols::denovo_design::movers::FoldArchitectMover::set_architect ( architects::DeNovoArchitect const & architect )

Sets the architect that will be used to build blueprints dynamically.

References architect_, and protocols::denovo_design::architects::DeNovoArchitect::clone().

Referenced by protocols::denovo_design::movers::BridgeChainsMover::apply(), protocols::denovo_design::movers::ExtendChainMover::apply(), and parse_architect().

◆ set_build_overlap()

void protocols::denovo_design::movers::FoldArchitectMover::set_build_overlap ( core::Size const overlap_val )

Sets the number of residues of overlap to use between build phases.

References build_overlap_.

Referenced by protocols::denovo_design::movers::BridgeChainsMover::apply(), protocols::denovo_design::movers::ExtendChainMover::apply(), and parse_my_tag().

◆ set_builder() [1/2]

void protocols::denovo_design::movers::FoldArchitectMover::set_builder ( components::PoseBuilder const & builder )

Sets the pose builder that will be used to create the extended-chain pose.

Clones the provided PoseBuilder

References protocols::denovo_design::components::PoseBuilder::clone().

◆ set_builder() [2/2]

void protocols::denovo_design::movers::FoldArchitectMover::set_builder ( components::PoseBuilderOP builder )

Sets the pose builder that will be used to create the extended-chain pose.

Uses/stores the provided PoseBuilder pointer directly

References builder_.

◆ set_debug()

void protocols::denovo_design::movers::FoldArchitectMover::set_debug ( bool const debug )

The debug value of the poseBuilder will be set based on this.

References builder_, core::pack::interaction_graph::debug, and debug_.

Referenced by FoldArchitectMover(), and parse_my_tag().

◆ set_dump_pdbs()

void protocols::denovo_design::movers::FoldArchitectMover::set_dump_pdbs ( bool const dump )

inline

If true, extra PDBs will be outputted for debugging purposes. Could be useful for figuring out why folding attempts are failing. If false, no extra files are outputted.

References dump_pdbs_.

Referenced by parse_my_tag().

◆ set_folder() [1/2]

void protocols::denovo_design::movers::FoldArchitectMover::set_folder ( components::PoseFolder const & folder )

Sets the pose folder that will be used to sample conformations.

Clones the PoseFolder

References protocols::denovo_design::components::PoseFolder::clone().

Referenced by protocols::denovo_design::movers::BridgeChainsMover::apply(), protocols::denovo_design::movers::ExtendChainMover::apply(), and parse_folder().

◆ set_folder() [2/2]

void protocols::denovo_design::movers::FoldArchitectMover::set_folder ( components::PoseFolderOP folder )

Sets the pose folder that will be used to sample conformations.

Uses the provided PoseFolder pointer directly

References folder_.

◆ set_id()

void protocols::denovo_design::movers::FoldArchitectMover::set_id ( std::string const & id_value )

Sets the ID of this mover.

References id_.

Referenced by parse_my_tag().

◆ set_iterations_per_phase()

void protocols::denovo_design::movers::FoldArchitectMover::set_iterations_per_phase ( core::Size const niter )

Sets the number of folding attempts for each build phase.

References iterations_per_phase_.

Referenced by protocols::denovo_design::movers::BridgeChainsMover::apply(), and parse_my_tag().

◆ set_perturber() [1/2]

void protocols::denovo_design::movers::FoldArchitectMover::set_perturber ( components::StructureDataPerturber const & perturber )

Sets the perturber that will be used to change the plans of the architects.

Clones the provided Perturber

References protocols::denovo_design::components::StructureDataPerturber::clone().

Referenced by parse_perturber().

◆ set_perturber() [2/2]

void protocols::denovo_design::movers::FoldArchitectMover::set_perturber ( components::StructureDataPerturberOP perturber )

Sets the perturber that will be used to change the plans of the architects.

Uses/stores the provided Perturber pointer directly

References perturber_.

◆ set_score_filter()

void protocols::denovo_design::movers::FoldArchitectMover::set_score_filter ( protocols::filters::Filter const & filter )

Sets the filter that will be used to evaluate the generated conformations. Used to return a score, not to evaluate true/false.

References protocols::filters::Filter::clone(), and score_filter_.

◆ set_start_segments() [1/2]

void protocols::denovo_design::movers::FoldArchitectMover::set_start_segments ( SegmentNameSet const & segments )

sets names of segments to be included in the starting build phase

Parameters

[in] segments Set of segment names

References start_segments_.

◆ set_start_segments() [2/2]

void protocols::denovo_design::movers::FoldArchitectMover::set_start_segments ( std::string const & segments_csv )

sets names of segments to be included in the starting build phase

Parameters

[in] segments_csv Comma-separated string containing segment names

Referenced by parse_my_tag().

◆ set_stop_segments() [1/2]

void protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments ( SegmentNameSet const & segments )

sets names of segments to be included in the final build phase

Parameters

[in] segments Set of segment names

References stop_segments_.

◆ set_stop_segments() [2/2]

void protocols::denovo_design::movers::FoldArchitectMover::set_stop_segments ( std::string const & segments_csv )

sets names of segments to be included in the final build phase

Parameters

[in] segments_csv Comma-separated string containing segment names

Referenced by parse_my_tag().

◆ setup_from_xml_file()

void protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_file	(	std::string const &	xml_file,
		basic::datacache::DataMap &	data
	)

Reads/parses an XML file and uses it to set up the mover.

References setup_from_xml_tag().

Referenced by parse_my_tag().

◆ setup_from_xml_string()

void protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_string	(	std::string const &	xml_string,
		basic::datacache::DataMap &	data
	)

Reads/parses an XML string and uses it to set up the mover.

References setup_from_xml_tag().

◆ setup_from_xml_tag()

void protocols::denovo_design::movers::FoldArchitectMover::setup_from_xml_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

Reads/parses a Tag object and uses it to set up the mover.

References clear_filters(), clear_postfold_movers(), clear_prefold_movers(), filters_, get_name(), parse_architect(), parse_filters(), parse_folder(), parse_perturber(), parse_postfold_movers(), parse_prefold_movers(), postfold_movers_, prefold_movers_, and protocols::TR().

Referenced by parse_my_tag(), setup_from_xml_file(), and setup_from_xml_string().

Member Data Documentation

◆ architect_

architects::DeNovoArchitectCOP protocols::denovo_design::movers::FoldArchitectMover::architect_

private

Referenced by apply(), and set_architect().

◆ build_overlap_

core::Size protocols::denovo_design::movers::FoldArchitectMover::build_overlap_

private

Referenced by create_loops(), find_roots(), parse_my_tag(), and set_build_overlap().

◆ builder_

components::PoseBuilderOP protocols::denovo_design::movers::FoldArchitectMover::builder_

private

Referenced by build_in_phases(), set_builder(), and set_debug().

◆ debug_

bool protocols::denovo_design::movers::FoldArchitectMover::debug_

private

Referenced by FoldArchitectMover(), parse_my_tag(), and set_debug().

◆ dry_run_

bool protocols::denovo_design::movers::FoldArchitectMover::dry_run_

private

◆ dump_pdbs_

bool protocols::denovo_design::movers::FoldArchitectMover::dump_pdbs_

private

Referenced by build_in_phases(), parse_my_tag(), and set_dump_pdbs().

◆ filters_

FilterCOPs protocols::denovo_design::movers::FoldArchitectMover::filters_

private

Referenced by add_filter(), check_pose(), clear_filters(), and setup_from_xml_tag().

◆ folder_

components::PoseFolderOP protocols::denovo_design::movers::FoldArchitectMover::folder_

private

Referenced by fold_attempt(), and set_folder().

◆ id_

std::string protocols::denovo_design::movers::FoldArchitectMover::id_

private

Referenced by id(), and set_id().

◆ iterations_per_phase_

core::Size protocols::denovo_design::movers::FoldArchitectMover::iterations_per_phase_

private

Referenced by build_in_phases(), parse_my_tag(), and set_iterations_per_phase().

◆ perturber_

components::StructureDataPerturberOP protocols::denovo_design::movers::FoldArchitectMover::perturber_

private

Referenced by build_in_phases(), and set_perturber().

◆ postfold_movers_

MoverOPs protocols::denovo_design::movers::FoldArchitectMover::postfold_movers_

private

Referenced by add_postfold_mover(), clear_postfold_movers(), postfold_movers(), and setup_from_xml_tag().

◆ prefold_movers_

MoverOPs protocols::denovo_design::movers::FoldArchitectMover::prefold_movers_

private

Referenced by add_prefold_mover(), clear_prefold_movers(), prefold_movers(), and setup_from_xml_tag().

◆ score_filter_

protocols::filters::FilterCOP protocols::denovo_design::movers::FoldArchitectMover::score_filter_

private

Referenced by folding_score(), and set_score_filter().

◆ start_segments_

SegmentNameSet protocols::denovo_design::movers::FoldArchitectMover::start_segments_

private

Referenced by apply(), and set_start_segments().

◆ stop_segments_

SegmentNameSet protocols::denovo_design::movers::FoldArchitectMover::stop_segments_

private

Referenced by apply(), and set_stop_segments().

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

src/protocols/denovo_design/movers/FoldArchitectMover.hh
src/protocols/denovo_design/movers/FoldArchitectMover.cc

Private Attributes
architects::DeNovoArchitectCOP	architect_

components::PoseBuilderOP	builder_

components::PoseFolderOP	folder_

components::StructureDataPerturberOP	perturber_

MoverOPs	prefold_movers_

MoverOPs	postfold_movers_

FilterCOPs	filters_

protocols::filters::FilterCOP	score_filter_

std::string	id_

bool	dry_run_

bool	dump_pdbs_

bool	debug_

core::Size	build_overlap_

core::Size	iterations_per_phase_

SegmentNameSet	start_segments_

SegmentNameSet	stop_segments_

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConnectionArchitectCOPs

◆ ConstraintGeneratorCOP

◆ ConstraintGeneratorCOPs

◆ ConstraintGeneratorOP

◆ FilterCOPs

◆ FoldScore

◆ MoverOPs

◆ RegisterShift

◆ ResidueVector

◆ StrandOrientation

Constructor & Destructor Documentation

◆ FoldArchitectMover()

◆ ~FoldArchitectMover()

Member Function Documentation

◆ add_filter()

◆ add_postfold_mover()

◆ add_prefold_mover()

◆ apply()

◆ apply_movers()

◆ build_denovo_backbone_ct_naming_func()

◆ build_in_phases()

◆ check_and_accept()

◆ check_pose()

◆ clear_filters()

◆ clear_postfold_movers()

◆ clear_prefold_movers()

◆ clone()

◆ connections_ct_naming_func()

◆ create_constraint_generators()

◆ create_loops()

◆ create_overlap_constraint_generator()

◆ default_score_filter()

◆ define_filters_ct()

◆ define_folder_group()

◆ define_perturber_group()

◆ define_postfold_movers_ct()

◆ define_prefold_movers_ct()

◆ filters_ct_naming_func()

◆ find_roots()

◆ fold()

◆ fold_attempt()

◆ folder_ct_namer()

◆ folder_group_name()

◆ folding_score()

◆ fresh_instance()

◆ get_name()

◆ id()

◆ mover_name()

◆ parse_architect()

◆ parse_filters()

◆ parse_folder()

◆ parse_movers()

◆ parse_my_tag()

◆ parse_perturber()

◆ parse_postfold_movers()

◆ parse_prefold_movers()

◆ perturber_ct_namer()

◆ perturber_group_name()

◆ postfold_ct_naming_func()

◆ postfold_movers()

◆ prefold_ct_naming_func()

◆ prefold_movers()

◆ provide_xml_schema()

◆ provide_xml_schema_with_name()

◆ remove_cutpoints()

◆ segments_to_fold()

◆ select_movable_residues()

◆ set_architect()

◆ set_build_overlap()

◆ set_builder() [1/2]

◆ set_builder() [2/2]