#include <BackboneGridSampler.hh>

Inheritance diagram for protocols::helical_bundle::BackboneGridSampler:

[legend]

Public Types
typedef protocols::cyclic_peptide::PeptideStubMover	PeptideStubMover

typedef protocols::cyclic_peptide::PeptideStubMoverOP	PeptideStubMoverOP

typedef protocols::cyclic_peptide::PeptideStubMoverCOP	PeptideStubMoverCOP

typedef protocols::helical_bundle::BackboneGridSamplerHelper	BackboneGridSamplerHelper

typedef protocols::helical_bundle::BackboneGridSamplerHelperOP	BackboneGridSamplerHelperOP

typedef protocols::helical_bundle::BackboneGridSamplerHelperCOP	BackboneGridSamplerHelperCOP

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
	BackboneGridSampler ()
	Creator for BackboneGridSampler mover. More...

	BackboneGridSampler (BackboneGridSampler const &src)
	Copy constructor for BackboneGridSampler mover. More...

	~BackboneGridSampler () override
	Destructor for BackboneGridSampler mover. More...

protocols::moves::MoverOP	clone () const override
	Clone operator to create a pointer to a fresh BackboneGridSampler object that copies this one. More...

protocols::moves::MoverOP	fresh_instance () const override
	Fresh_instance operator to create a pointer to a fresh BackboneGridSampler object that does NOT copy this one. More...

void	apply (core::pose::Pose &pose) override
	Actually apply the mover to the pose. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Returns the name of this mover ("BackboneGridSampler"). More...

void	set_max_samples (core::Size const val)
	Set the maximum number of samples for the mover. More...

core::Size	max_samples () const
	Get the maximum number of samples for the mover. More...

void	set_selection_low (bool const val)
	Sets whether the selection should be for the lowest score value (true) or highest (false). More...

bool	selection_low ()
	Returns whether the selection should be for the lowest score value (true) or highest (false). More...

void	set_prescoring_mover (protocols::moves::MoverOP mover)
	Sets the mover that will be applied to all helical bundles generated prior to energy evaluation. More...

void	set_prescoring_filter (protocols::filters::FilterOP filter)
	Sets the filter that will be applied to all helical bundles generated prior to energy evaluation. More...

bool	prescoring_mover_exists () const
	Returns "true" if and only if a preselection mover has been assigned. More...

bool	prescoring_filter_exists () const
	Returns "true" if and only if a preselection filter has been assigned. More...

void	set_pdb_output (bool const val)
	Set whether the mover dumps pdbs or not. More...

bool	pdb_output () const
	Returns whether the mover dumps pdbs or not. More...

void	set_pdb_prefix (std::string const &prefix)
	Sets the filename prefix for PDB output. More...

std::string	pdb_prefix ()
	Access the filename prefix for PDB output. More...

void	set_sfxn (core::scoring::ScoreFunctionOP sfxn_in)
	Sets the scorefunction for this mover. More...

bool	sfxn_set () const
	Returns whether the scorefunction has been set. More...

void	set_nstruct_mode (bool const &val)
	Set the nstruct mode. More...

bool	nstruct_mode () const
	Get the nstruct mode. More...

void	set_nstruct_repeats (core::Size const val)
	Set the nstruct repeats. More...

core::Size	nstruct_repeats () const
	Get the nstruct repeats. More...

void	add_torsion_to_sample (core::Size const residue_index, core::Size const torsion_index, core::Real const &start_of_range, core::Real const &end_of_range, core::Size const samples)
	Add a mainchain torsion to sample, the range of values that will be sampled, and the number of samples. More...

void	add_torsion_to_fix (core::Size const residue_index, core::Size const torsion_index, core::Real const &torsion_value)
	Add a mainchain torsion to fix, and that torsion's value. More...

void	set_nres (core::Size const nres_in)
	Set the number of residues in the pose to build. More...

core::Size	nres () const
	Get the number of residues in the pose to build. More...

void	set_resname (core::Size const res_index, std::string const &resname_in)
	Set the residue type. More...

std::string	resname (core::Size const res_index) const
	Get the residue type. More...

void	set_cap_ends (bool cap)
	Set whether then ends should be capped (N-acetyl, C-methylamide). More...

bool	cap_ends () const
	Return whether the ends should be capped (N-acetyl, C-methylamide). More...

void	set_up_peptide_stub_mover ()
	Set up the PeptideStubMover object that will be used to build geometry. More...

bool	peptide_stub_mover_initialized () const
	Has the PeptideStubMover been initialized? More...

void	reset_and_initialize_data ()
	Reset the torsions_to_sample_, torsions_to_fix_, and resname_ vectors, and initialize them based on the value of residues_per_repeat_. More...

void	set_residues_per_repeat (core::Size const val)
	Set the number of residues per repeat. More...

core::Size	residues_per_repeat () const
	Get the number of residues per repeat. More...

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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...

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
bool	is_in_list (core::Size const val, utility::vector1< core::Size > const &list) const
	Is a value in a list? More...

core::Size	calculate_total_samples () const
	Calculate the number of grid points that will be sampled, based on the options set by the user. More...

Private Attributes
bool	nstruct_mode_
	Should the parallel sampling be done based on the job (nstruct number)? More...

core::Size	nstruct_mode_repeats_
	If nstruct_mode_ is true, how many times should each set of mainchain torsion values be repeated? More...

bool	select_low_
	The selection type. @default If false, the pose with the highest score value is selected. If true, the pose with the lowest score value is selected. True by default. More...

core::Size	max_samples_
	The maximum number of gridpoints allowed. More...

protocols::moves::MoverOP	pre_scoring_mover_
	Owning pointer for an (optional) pre-selection mover applied to all helical bundles before energy evaluation. More...

bool	pre_scoring_mover_exists_
	Bool determining whether there exists a pre-selection mover that wlil be applied. More...

protocols::filters::FilterOP	pre_scoring_filter_
	Owning pointer for an (optional) pre-selection filter applied to all helical bundles after the pre-selection mover but before picking the lowest-energy solution. If PDBs are dumped, only those passing filters are dumped. More...

bool	pre_scoring_filter_exists_
	Bool determining whether a pre-selection filter has been set. More...

bool	dump_pdbs_
	Dump a PDB file for each bundle generated? False by default. More...

std::string	pdb_prefix_
	PDB filename prefix. Filename will be of the form <prefix>_#####.pdb. More...

bool	sfxn_set_
	Has the scorefunction been set? More...

core::scoring::ScoreFunctionOP	sfxn_
	The scorefunction that this mover will use to pick the lowest-energy bundle. More...

core::Size	residues_per_repeat_
	The number of residues in the repeating unit. More...

utility::vector1< utility::vector1< std::pair< core::Size, std::pair< std::pair< core::Real, core::Real >, core::Size > > > >	torsions_to_sample_
	The list of mainchain torsions to sample, and the range of values. More...

utility::vector1< utility::vector1< std::pair< core::Size, core::Real > > >	torsions_to_fix_
	The list of mainchain torsions to fix, and the values at which to fix them. More...

core::Size	nres_
	The number of residues in the pose to build. More...

utility::vector1< std::string >	resname_
	The residue type (full name) for the pose to build. More...

bool	cap_ends_
	Should we add terminal caps (N-acetyl, C-methylamidation) to the polymer? More...

PeptideStubMoverOP	peptide_stub_mover_
	A PeptideStubMover used to build the new pose. More...

bool	peptide_stub_mover_initialized_
	Has the PeptideStubMover been initialized? More...

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

◆ BackboneGridSamplerHelper

typedef protocols::helical_bundle::BackboneGridSamplerHelper protocols::helical_bundle::BackboneGridSampler::BackboneGridSamplerHelper

◆ BackboneGridSamplerHelperCOP

typedef protocols::helical_bundle::BackboneGridSamplerHelperCOP protocols::helical_bundle::BackboneGridSampler::BackboneGridSamplerHelperCOP

◆ BackboneGridSamplerHelperOP

typedef protocols::helical_bundle::BackboneGridSamplerHelperOP protocols::helical_bundle::BackboneGridSampler::BackboneGridSamplerHelperOP

◆ PeptideStubMover

typedef protocols::cyclic_peptide::PeptideStubMover protocols::helical_bundle::BackboneGridSampler::PeptideStubMover

◆ PeptideStubMoverCOP

typedef protocols::cyclic_peptide::PeptideStubMoverCOP protocols::helical_bundle::BackboneGridSampler::PeptideStubMoverCOP

◆ PeptideStubMoverOP

typedef protocols::cyclic_peptide::PeptideStubMoverOP protocols::helical_bundle::BackboneGridSampler::PeptideStubMoverOP

Constructor & Destructor Documentation

◆ BackboneGridSampler() [1/2]

protocols::helical_bundle::BackboneGridSampler::BackboneGridSampler ( )

Creator for BackboneGridSampler mover.

References resname_, torsions_to_fix_, and torsions_to_sample_.

◆ BackboneGridSampler() [2/2]

protocols::helical_bundle::BackboneGridSampler::BackboneGridSampler ( BackboneGridSampler const & src )

Copy constructor for BackboneGridSampler mover.

◆ ~BackboneGridSampler()

protocols::helical_bundle::BackboneGridSampler::~BackboneGridSampler ( )

overridedefault

Destructor for BackboneGridSampler mover.

Member Function Documentation

◆ add_torsion_to_fix()

void protocols::helical_bundle::BackboneGridSampler::add_torsion_to_fix	(	core::Size const	residue_index,
		core::Size const	torsion_index,
		core::Real const &	torsion_value
	)

Add a mainchain torsion to fix, and that torsion's value.

The residue_index is the index of the residue in the repeating unit (1st, 2nd, 3rd, etc.). The torsion_index is the mainchain torsion index in this residue, and the torsion_value is the value at which to fix this residue.

References residues_per_repeat(), torsions_to_fix_, and torsions_to_sample_.

Referenced by parse_my_tag().

◆ add_torsion_to_sample()

void protocols::helical_bundle::BackboneGridSampler::add_torsion_to_sample	(	core::Size const	residue_index,
		core::Size const	torsion_index,
		core::Real const &	start_of_range,
		core::Real const &	end_of_range,
		core::Size const	samples
	)

Add a mainchain torsion to sample, the range of values that will be sampled, and the number of samples.

The residue_index is the index in the repeating unit (1st residue, 2nd residue, etc.). The torsion_index is the mainchain torsion index in this residue. Sampled values will go from start_of_range to end_of_range, with the total number of samples given by the samples parameter. If the range is -180 to 180, the samples are adjusted so that 180 is not sampled twice.

References protocols::sic_dock::range(), residues_per_repeat(), torsions_to_fix_, and torsions_to_sample_.

Referenced by parse_my_tag().

◆ apply()

void protocols::helical_bundle::BackboneGridSampler::apply ( core::pose::Pose & pose )

overridevirtual

Actually apply the mover to the pose.

Implements protocols::moves::Mover.

References core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::pose::add_variant_type_to_pose_residue(), core::id::BB, calculate_total_samples(), cap_ends(), protocols::jd2::current_nstruct_index(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, protocols::moves::FAIL_DO_NOT_RETRY, protocols::jd2::jd2_used(), core::chemical::LOWER_TERMINUS_VARIANT, protocols::jd2::max_nstruct_index(), max_samples(), core::chemical::METHYLATED_CTERMINUS_VARIANT, protocols::moves::MS_SUCCESS, nres(), nstruct_mode(), nstruct_repeats(), pdb_output(), pdb_prefix(), peptide_stub_mover_, peptide_stub_mover_initialized(), pre_scoring_filter_, pre_scoring_mover_, prescoring_filter_exists(), prescoring_mover_exists(), core::pose::remove_variant_type_from_pose_residue(), residues_per_repeat(), resname(), select_low_, protocols::moves::Mover::set_last_move_status(), set_up_peptide_stub_mover(), sfxn_, torsions_to_fix_, torsions_to_sample_, protocols::helical_bundle::TR(), protocols::helical_bundle::TR_Results(), and core::chemical::UPPER_TERMINUS_VARIANT.

◆ calculate_total_samples()

core::Size protocols::helical_bundle::BackboneGridSampler::calculate_total_samples ( ) const

private

Calculate the number of grid points that will be sampled, based on the options set by the user.

References torsions_to_sample_.

Referenced by apply().

◆ cap_ends()

bool protocols::helical_bundle::BackboneGridSampler::cap_ends ( ) const

inline

Return whether the ends should be capped (N-acetyl, C-methylamide).

References cap_ends_.

Referenced by apply(), and parse_my_tag().

◆ clone()

protocols::moves::MoverOP protocols::helical_bundle::BackboneGridSampler::clone ( ) const

overridevirtual

Clone operator to create a pointer to a fresh BackboneGridSampler object that copies this one.

Reimplemented from protocols::moves::Mover.

Referenced by parse_my_tag().

◆ fresh_instance()

protocols::moves::MoverOP protocols::helical_bundle::BackboneGridSampler::fresh_instance ( ) const

overridevirtual

Fresh_instance operator to create a pointer to a fresh BackboneGridSampler object that does NOT copy this one.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::helical_bundle::BackboneGridSampler::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ is_in_list()

bool protocols::helical_bundle::BackboneGridSampler::is_in_list	(	core::Size const	val,
		utility::vector1< core::Size > const &	list
	)		const

private

Is a value in a list?

References protocols::hybridization::val.

◆ max_samples()

core::Size protocols::helical_bundle::BackboneGridSampler::max_samples ( ) const

inline

Get the maximum number of samples for the mover.

If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted.

References max_samples_.

Referenced by apply().

◆ mover_name()

std::string protocols::helical_bundle::BackboneGridSampler::mover_name ( )

static

Referenced by get_name(), protocols::helical_bundle::BackboneGridSamplerCreator::keyname(), and provide_xml_schema().

◆ nres()

core::Size protocols::helical_bundle::BackboneGridSampler::nres ( ) const

inline

Get the number of residues in the pose to build.

This is actually the number of REPEATS. If there are two residues per repeat, you'd have twice this number of resiudes.

References nres_.

Referenced by apply(), parse_my_tag(), and set_up_peptide_stub_mover().

◆ nstruct_mode()

bool protocols::helical_bundle::BackboneGridSampler::nstruct_mode ( ) const

inline

Get the nstruct mode.

If true, each job samples one set of mainchain torsion values. If false, every job samples every set of mainchain torsion values. False by default.

References nstruct_mode_.

Referenced by apply().

◆ nstruct_repeats()

core::Size protocols::helical_bundle::BackboneGridSampler::nstruct_repeats ( ) const

inline

Get the nstruct repeats.

This is set to 1 by default, which means that each nstruct number correspnds to a different set of mainchain torsion values. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same mainchain torsion values. This allows combinatorially combining this mover's sampling with another, similar mover's sampling.

References nstruct_mode_repeats_.

Referenced by apply().

◆ parse_my_tag()

void protocols::helical_bundle::BackboneGridSampler::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data_map
	)

overridevirtual

Returns the name of this mover ("BackboneGridSampler").

parse XML (specifically in the context of the parser/Rosetta_scripting scheme)

Reimplemented from protocols::moves::Mover.

References add_torsion_to_fix(), add_torsion_to_sample(), cap_ends(), clone(), core::sequence::end, nres(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), residues_per_repeat(), resname(), set_cap_ends(), set_max_samples(), set_nres(), set_nstruct_mode(), set_nstruct_repeats(), set_pdb_output(), set_pdb_prefix(), set_prescoring_filter(), set_prescoring_mover(), set_residues_per_repeat(), set_resname(), set_selection_low(), set_sfxn(), protocols::loops::start, protocols::helical_bundle::TR(), and protocols::hybridization::val.

◆ pdb_output()

bool protocols::helical_bundle::BackboneGridSampler::pdb_output ( ) const

inline

Returns whether the mover dumps pdbs or not.

References dump_pdbs_.

Referenced by apply().

◆ pdb_prefix()

std::string protocols::helical_bundle::BackboneGridSampler::pdb_prefix ( )

inline

Access the filename prefix for PDB output.

PDB files are of the form <prefix>_#####.pdb.

References pdb_prefix_.

Referenced by apply().

◆ peptide_stub_mover_initialized()

bool protocols::helical_bundle::BackboneGridSampler::peptide_stub_mover_initialized ( ) const

inline

Has the PeptideStubMover been initialized?

References peptide_stub_mover_initialized_.

Referenced by apply().

◆ prescoring_filter_exists()

bool protocols::helical_bundle::BackboneGridSampler::prescoring_filter_exists ( ) const

inline

Returns "true" if and only if a preselection filter has been assigned.

References pre_scoring_filter_exists_.

Referenced by apply().

◆ prescoring_mover_exists()

bool protocols::helical_bundle::BackboneGridSampler::prescoring_mover_exists ( ) const

inline

Returns "true" if and only if a preselection mover has been assigned.

References pre_scoring_mover_exists_.

Referenced by apply().

◆ provide_citation_info()

void protocols::helical_bundle::BackboneGridSampler::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References pre_scoring_filter_, and pre_scoring_mover_.

◆ provide_xml_schema()

void protocols::helical_bundle::BackboneGridSampler::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), protocols::helical_bundle::subtag_for_bbgrid(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::helical_bundle::BackboneGridSamplerCreator::provide_xml_schema().

◆ reset_and_initialize_data()

void protocols::helical_bundle::BackboneGridSampler::reset_and_initialize_data ( )

Reset the torsions_to_sample_, torsions_to_fix_, and resname_ vectors, and initialize them based on the value of residues_per_repeat_.

References residues_per_repeat(), resname_, torsions_to_fix_, and torsions_to_sample_.

Referenced by set_residues_per_repeat().

◆ residues_per_repeat()

core::Size protocols::helical_bundle::BackboneGridSampler::residues_per_repeat ( ) const

inline

Get the number of residues per repeat.

References residues_per_repeat_.

Referenced by add_torsion_to_fix(), add_torsion_to_sample(), apply(), parse_my_tag(), reset_and_initialize_data(), and set_up_peptide_stub_mover().

◆ resname()

std::string protocols::helical_bundle::BackboneGridSampler::resname ( core::Size const res_index ) const

inline

Get the residue type.

Returns the residue type (full name string) for the nth residue in the list of residues defining the repeating unit.

References resname_.

Referenced by apply(), parse_my_tag(), and set_up_peptide_stub_mover().

◆ selection_low()

bool protocols::helical_bundle::BackboneGridSampler::selection_low ( )

inline

Returns whether the selection should be for the lowest score value (true) or highest (false).

References select_low_.

◆ set_cap_ends()

void protocols::helical_bundle::BackboneGridSampler::set_cap_ends ( bool cap )

inline

Set whether then ends should be capped (N-acetyl, C-methylamide).

References cap_ends_.

Referenced by parse_my_tag().

◆ set_max_samples()

void protocols::helical_bundle::BackboneGridSampler::set_max_samples ( core::Size const val )

inline

Set the maximum number of samples for the mover.

If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted.

References max_samples_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_nres()

void protocols::helical_bundle::BackboneGridSampler::set_nres ( core::Size const nres_in )

inline

Set the number of residues in the pose to build.

This is actually the number of REPEATS. If there are two residues per repeat, you'd have twice this number of resiudes.

References nres_.

Referenced by parse_my_tag().

◆ set_nstruct_mode()

void protocols::helical_bundle::BackboneGridSampler::set_nstruct_mode ( bool const & val )

inline

Set the nstruct mode.

If true, each job samples one set of mainchain torsion values. If false, every job samples every set of mainchain torsion values. False by default.

References nstruct_mode_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_nstruct_repeats()

void protocols::helical_bundle::BackboneGridSampler::set_nstruct_repeats ( core::Size const val )

inline

Set the nstruct repeats.

This is set to 1 by default, which means that each nstruct number correspnds to a different set of mainchain torsion values. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same mainchain torsion values. This allows combinatorially combining this mover's sampling with another, similar mover's sampling.

References nstruct_mode_repeats_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_pdb_output()

void protocols::helical_bundle::BackboneGridSampler::set_pdb_output ( bool const val )

inline

Set whether the mover dumps pdbs or not.

References dump_pdbs_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_pdb_prefix()

void protocols::helical_bundle::BackboneGridSampler::set_pdb_prefix ( std::string const & prefix )

inline

Sets the filename prefix for PDB output.

PDB files are of the form <prefix>_#####.pdb.

References pdb_prefix_.

Referenced by parse_my_tag().

◆ set_prescoring_filter()

void protocols::helical_bundle::BackboneGridSampler::set_prescoring_filter ( protocols::filters::FilterOP filter )

Sets the filter that will be applied to all helical bundles generated prior to energy evaluation.

See the pre_scoring_filter_ private member variable for details.

References pre_scoring_filter_, and pre_scoring_filter_exists_.

Referenced by parse_my_tag().

◆ set_prescoring_mover()

void protocols::helical_bundle::BackboneGridSampler::set_prescoring_mover ( protocols::moves::MoverOP mover )

Sets the mover that will be applied to all helical bundles generated prior to energy evaluation.

Note: if this is used, there is no guarantee that the resulting geometry will still lie within the parameter space. (That is, this mover could move the backbone.)

References pre_scoring_mover_, and pre_scoring_mover_exists_.

Referenced by parse_my_tag().

◆ set_residues_per_repeat()

void protocols::helical_bundle::BackboneGridSampler::set_residues_per_repeat ( core::Size const val )

Set the number of residues per repeat.

This resets the torsions_to_sample_, torsions_to_fix_, and resname_ vectors, and must therefore be called BEFORE setting up the torsions to sample, torsions to fix, or residue types.

References reset_and_initialize_data(), residues_per_repeat_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_resname()

void protocols::helical_bundle::BackboneGridSampler::set_resname	(	core::Size const	res_index,
		std::string const &	resname_in
	)

inline

Set the residue type.

Sets the residue type for the nth residue in the list of residues defining the repeating unit.

References resname_.

Referenced by parse_my_tag().

◆ set_selection_low()

void protocols::helical_bundle::BackboneGridSampler::set_selection_low ( bool const val )

inline

Sets whether the selection should be for the lowest score value (true) or highest (false).

References select_low_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_sfxn()

void protocols::helical_bundle::BackboneGridSampler::set_sfxn ( core::scoring::ScoreFunctionOP sfxn_in )

inline

Sets the scorefunction for this mover.

This must be done before calling the apply() function.

References sfxn_, and sfxn_set_.

Referenced by parse_my_tag().

◆ set_up_peptide_stub_mover()

void protocols::helical_bundle::BackboneGridSampler::set_up_peptide_stub_mover ( )

Set up the PeptideStubMover object that will be used to build geometry.

References nres(), peptide_stub_mover_, peptide_stub_mover_initialized_, residues_per_repeat(), and resname().

Referenced by apply().

◆ sfxn_set()

bool protocols::helical_bundle::BackboneGridSampler::sfxn_set ( ) const

inline

Returns whether the scorefunction has been set.

References sfxn_set_.

Member Data Documentation

◆ cap_ends_

bool protocols::helical_bundle::BackboneGridSampler::cap_ends_

private

Should we add terminal caps (N-acetyl, C-methylamidation) to the polymer?

If false, the ends are just the regular terminal types (NH3+, COO-). False by default.

Referenced by cap_ends(), and set_cap_ends().

◆ dump_pdbs_

bool protocols::helical_bundle::BackboneGridSampler::dump_pdbs_

private

Dump a PDB file for each bundle generated? False by default.

Referenced by pdb_output(), and set_pdb_output().

◆ max_samples_

core::Size protocols::helical_bundle::BackboneGridSampler::max_samples_

private

The maximum number of gridpoints allowed.

If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted. Default value is ten thousand (10,000).

Referenced by max_samples(), and set_max_samples().

◆ nres_

core::Size protocols::helical_bundle::BackboneGridSampler::nres_

private

The number of residues in the pose to build.

This is actually the number of REPEATS. If there are two residues per repeat, you'd have twice this number of resiudes.

Referenced by nres(), and set_nres().

◆ nstruct_mode_

bool protocols::helical_bundle::BackboneGridSampler::nstruct_mode_

private

Should the parallel sampling be done based on the job (nstruct number)?

If true, each job samples one set of mainchain torsion values. If false, every job samples every set of mainchain torsion values. False by default.

Referenced by nstruct_mode(), and set_nstruct_mode().

◆ nstruct_mode_repeats_

core::Size protocols::helical_bundle::BackboneGridSampler::nstruct_mode_repeats_

private

If nstruct_mode_ is true, how many times should each set of mainchain torsion values be repeated?

This is set to 1 by default, which means that each nstruct number correspnds to a different set of mainchain torsion values. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same mainchain torsion values. This allows combinatorially combining this mover's sampling with another, similar mover's sampling.

Referenced by nstruct_repeats(), and set_nstruct_repeats().

◆ pdb_prefix_

std::string protocols::helical_bundle::BackboneGridSampler::pdb_prefix_

private

PDB filename prefix. Filename will be of the form <prefix>_#####.pdb.

Defaults to "bgs_out".

Referenced by pdb_prefix(), and set_pdb_prefix().

◆ peptide_stub_mover_

PeptideStubMoverOP protocols::helical_bundle::BackboneGridSampler::peptide_stub_mover_

private

A PeptideStubMover used to build the new pose.

Referenced by apply(), and set_up_peptide_stub_mover().

◆ peptide_stub_mover_initialized_

bool protocols::helical_bundle::BackboneGridSampler::peptide_stub_mover_initialized_

private

Has the PeptideStubMover been initialized?

Referenced by peptide_stub_mover_initialized(), and set_up_peptide_stub_mover().

◆ pre_scoring_filter_

protocols::filters::FilterOP protocols::helical_bundle::BackboneGridSampler::pre_scoring_filter_

private

Owning pointer for an (optional) pre-selection filter applied to all helical bundles after the pre-selection mover but before picking the lowest-energy solution. If PDBs are dumped, only those passing filters are dumped.

Referenced by apply(), provide_citation_info(), and set_prescoring_filter().

◆ pre_scoring_filter_exists_

bool protocols::helical_bundle::BackboneGridSampler::pre_scoring_filter_exists_

private

Bool determining whether a pre-selection filter has been set.

Referenced by prescoring_filter_exists(), and set_prescoring_filter().

◆ pre_scoring_mover_

protocols::moves::MoverOP protocols::helical_bundle::BackboneGridSampler::pre_scoring_mover_

private

Owning pointer for an (optional) pre-selection mover applied to all helical bundles before energy evaluation.

Referenced by apply(), provide_citation_info(), and set_prescoring_mover().

◆ pre_scoring_mover_exists_

bool protocols::helical_bundle::BackboneGridSampler::pre_scoring_mover_exists_

private

Bool determining whether there exists a pre-selection mover that wlil be applied.

Referenced by prescoring_mover_exists(), and set_prescoring_mover().

◆ residues_per_repeat_

core::Size protocols::helical_bundle::BackboneGridSampler::residues_per_repeat_

private

The number of residues in the repeating unit.

The repeating unit in the helix need not be a single residue, particularly if the helix is composed of residues of an alternating type.

Referenced by residues_per_repeat(), and set_residues_per_repeat().

◆ resname_

utility::vector1<std::string> protocols::helical_bundle::BackboneGridSampler::resname_

private

The residue type (full name) for the pose to build.

This is a vector of strings, with one entry for each residue in the repeating unit.

Referenced by BackboneGridSampler(), reset_and_initialize_data(), resname(), and set_resname().

◆ select_low_

bool protocols::helical_bundle::BackboneGridSampler::select_low_

private

The selection type. @default If false, the pose with the highest score value is selected. If true, the pose with the lowest score value is selected. True by default.

Referenced by apply(), selection_low(), and set_selection_low().

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::helical_bundle::BackboneGridSampler::sfxn_

private

The scorefunction that this mover will use to pick the lowest-energy bundle.

Must be set prior to calling apply() function.

Referenced by apply(), and set_sfxn().

◆ sfxn_set_

bool protocols::helical_bundle::BackboneGridSampler::sfxn_set_

private

Has the scorefunction been set?

False by default.

Referenced by set_sfxn(), and sfxn_set().

◆ torsions_to_fix_

utility::vector1< utility::vector1 < std::pair <core::Size , core::Real > > > protocols::helical_bundle::BackboneGridSampler::torsions_to_fix_

private

The list of mainchain torsions to fix, and the values at which to fix them.

The outer vecotr corresponds to the list of residues in the repeating unit.

Referenced by add_torsion_to_fix(), add_torsion_to_sample(), apply(), BackboneGridSampler(), and reset_and_initialize_data().

◆ torsions_to_sample_

utility::vector1< utility::vector1 < std::pair <core::Size , std::pair < std::pair < core::Real , core::Real >, core::Size > > > > protocols::helical_bundle::BackboneGridSampler::torsions_to_sample_

private

The list of mainchain torsions to sample, and the range of values.

The outer vector corresponds to the list of residues in the repeating unit.

Referenced by add_torsion_to_fix(), add_torsion_to_sample(), apply(), BackboneGridSampler(), calculate_total_samples(), and reset_and_initialize_data().

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

src/protocols/helical_bundle/BackboneGridSampler.hh
src/protocols/helical_bundle/BackboneGridSampler.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BackboneGridSamplerHelper

◆ BackboneGridSamplerHelperCOP

◆ BackboneGridSamplerHelperOP

◆ PeptideStubMover

◆ PeptideStubMoverCOP

◆ PeptideStubMoverOP

Constructor & Destructor Documentation

◆ BackboneGridSampler() [1/2]

◆ BackboneGridSampler() [2/2]

◆ ~BackboneGridSampler()

Member Function Documentation

◆ add_torsion_to_fix()

◆ add_torsion_to_sample()

◆ apply()

◆ calculate_total_samples()

◆ cap_ends()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ is_in_list()

◆ max_samples()

◆ mover_name()

◆ nres()

◆ nstruct_mode()

◆ nstruct_repeats()

◆ parse_my_tag()

◆ pdb_output()

◆ pdb_prefix()

◆ peptide_stub_mover_initialized()

◆ prescoring_filter_exists()

◆ prescoring_mover_exists()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ reset_and_initialize_data()

◆ residues_per_repeat()

◆ resname()

◆ selection_low()

◆ set_cap_ends()

◆ set_max_samples()

◆ set_nres()

◆ set_nstruct_mode()

◆ set_nstruct_repeats()

◆ set_pdb_output()

◆ set_pdb_prefix()

◆ set_prescoring_filter()

◆ set_prescoring_mover()

◆ set_residues_per_repeat()

◆ set_resname()

◆ set_selection_low()

◆ set_sfxn()

◆ set_up_peptide_stub_mover()

◆ sfxn_set()

Member Data Documentation

◆ cap_ends_

◆ dump_pdbs_

◆ max_samples_

◆ nres_

◆ nstruct_mode_

◆ nstruct_mode_repeats_

◆ pdb_prefix_

◆ peptide_stub_mover_

◆ peptide_stub_mover_initialized_

◆ pre_scoring_filter_

◆ pre_scoring_filter_exists_

◆ pre_scoring_mover_

◆ pre_scoring_mover_exists_

◆ residues_per_repeat_

◆ resname_

◆ select_low_

◆ sfxn_

◆ sfxn_set_

◆ torsions_to_fix_

◆ torsions_to_sample_