#include <BundleGridSampler.hh>

Inheritance diagram for protocols::helical_bundle::BundleGridSampler:

[legend]

Public Types
typedef core::conformation::parametric::Parameters	Parameters

typedef core::conformation::parametric::ParametersOP	ParametersOP

typedef core::conformation::parametric::ParametersSet	ParametersSet

typedef core::conformation::parametric::ParametersSetOP	ParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParameters	BundleParameters

typedef protocols::helical_bundle::parameters::BundleParametersOP	BundleParametersOP

typedef protocols::helical_bundle::parameters::BundleParametersCOP	BundleParametersCOP

typedef protocols::helical_bundle::parameters::BundleParametersSet	BundleParametersSet

typedef protocols::helical_bundle::parameters::BundleParametersSetOP	BundleParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParametersSetCOP	BundleParametersSetCOP

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
	BundleGridSampler ()
	Creator for BundleGridSampler mover. More...

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

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

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

protocols::moves::MoverOP	fresh_instance () const override
	Fresh_instance operator to create a pointer to a fresh BundleGridSampler 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
	parse XML (specifically in the context of the parser/Rosetta_scripting scheme) More...

void	set_reset_mode (bool const val)
	Set the reset mode. More...

bool	reset_mode () const
	Get the reset mode. More...

void	set_use_degrees (bool const use_degrees)
	Set whether we're using degrees (true) or radians (false) More...

bool	use_degrees () const
	Get whether we're using degrees (true) or radians (false) More...

MakeBundleHelixOP	helix (core::Size const helix_index)
	Access the mover that makes one of the helices (non-const): More...

MakeBundleHelixCOP	helix_cop (core::Size const helix_index) const
	Access the mover that makes one of the helices (const): More...

core::Size	add_helix ()
	Add options for a new helix. 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	increment_helix_count ()
	Increments the number of helices that have been defined. More...

core::Size	n_helices () const
	Returns the number of helices that have been defined. 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_preselection_mover (protocols::moves::MoverOP mover)
	Sets the mover that will be applied to all helical bundles generated prior to energy evaluation. More...

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

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

bool	preselection_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_default_crick_params_file (std::string const &default_crick_file)
	Set the default Crick params file. 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...

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	reset_mode_
	Should the pose be reset before applying the GridSampler? Default true. More...

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 Crick parameters 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	n_helices_
	The number of helices that have been defined. More...

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

MakeBundleOP	make_bundle_
	A MakeBundle mover that this mover will call. More...

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

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

protocols::filters::FilterOP	pre_selection_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_selection_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...

BundleParametrizationCalculatorOP	default_calculator_
	A calculator object for the Crick parameterization. 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

◆ BundleParameters

typedef protocols::helical_bundle::parameters::BundleParameters protocols::helical_bundle::BundleGridSampler::BundleParameters

◆ BundleParametersCOP

typedef protocols::helical_bundle::parameters::BundleParametersCOP protocols::helical_bundle::BundleGridSampler::BundleParametersCOP

◆ BundleParametersOP

typedef protocols::helical_bundle::parameters::BundleParametersOP protocols::helical_bundle::BundleGridSampler::BundleParametersOP

◆ BundleParametersSet

typedef protocols::helical_bundle::parameters::BundleParametersSet protocols::helical_bundle::BundleGridSampler::BundleParametersSet

◆ BundleParametersSetCOP

typedef protocols::helical_bundle::parameters::BundleParametersSetCOP protocols::helical_bundle::BundleGridSampler::BundleParametersSetCOP

◆ BundleParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParametersSetOP protocols::helical_bundle::BundleGridSampler::BundleParametersSetOP

◆ Parameters

typedef core::conformation::parametric::Parameters protocols::helical_bundle::BundleGridSampler::Parameters

◆ ParametersOP

typedef core::conformation::parametric::ParametersOP protocols::helical_bundle::BundleGridSampler::ParametersOP

◆ ParametersSet

typedef core::conformation::parametric::ParametersSet protocols::helical_bundle::BundleGridSampler::ParametersSet

◆ ParametersSetOP

typedef core::conformation::parametric::ParametersSetOP protocols::helical_bundle::BundleGridSampler::ParametersSetOP

Constructor & Destructor Documentation

◆ BundleGridSampler() [1/2]

protocols::helical_bundle::BundleGridSampler::BundleGridSampler ( )

Creator for BundleGridSampler mover.

References default_calculator_, and make_bundle_.

◆ BundleGridSampler() [2/2]

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

Copy constructor for BundleGridSampler mover.

References default_calculator_, and make_bundle_.

◆ ~BundleGridSampler()

protocols::helical_bundle::BundleGridSampler::~BundleGridSampler ( )

overridedefault

Destructor for BundleGridSampler mover.

Member Function Documentation

◆ add_helix()

core::Size protocols::helical_bundle::BundleGridSampler::add_helix ( )

Add options for a new helix.

Return value is the current total number of helices after the addition.

References increment_helix_count(), make_bundle_, and n_helices().

Referenced by parse_my_tag().

◆ apply()

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

overridevirtual

Actually apply the mover to the pose.

Implements protocols::moves::Mover.

References protocols::helical_bundle::BPC_last_parameter_to_be_sampled, calculate_total_samples(), protocols::jd2::current_nstruct_index(), core::pose::Pose::dump_scored_pdb(), core::pose::Pose::energies(), protocols::moves::FAIL_RETRY, protocols::jd2::jd2_used(), make_bundle_, protocols::jd2::max_nstruct_index(), max_samples(), protocols::moves::MS_SUCCESS, n_helices(), nstruct_mode(), nstruct_repeats(), protocols::helical_bundle::BundleParametrizationCalculator::parameter_name_from_enum(), pdb_output(), pdb_prefix(), pre_selection_filter_, pre_selection_mover_, preselection_filter_exists(), preselection_mover_exists(), reset_mode(), selection_low(), protocols::moves::Mover::set_last_move_status(), sfxn_, sfxn_set(), core::scoring::Energies::total_energy(), and protocols::helical_bundle::TR().

◆ calculate_total_samples()

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

private

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

References protocols::helical_bundle::BPC_last_parameter_to_be_sampled, make_bundle_, and n_helices().

Referenced by apply().

◆ clone()

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

overridevirtual

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

Reimplemented from protocols::moves::Mover.

Referenced by parse_my_tag().

◆ fresh_instance()

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

overridevirtual

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

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ helix()

MakeBundleHelixOP protocols::helical_bundle::BundleGridSampler::helix ( core::Size const helix_index )

inline

Access the mover that makes one of the helices (non-const):

References make_bundle_.

◆ helix_cop()

MakeBundleHelixCOP protocols::helical_bundle::BundleGridSampler::helix_cop ( core::Size const helix_index ) const

inline

Access the mover that makes one of the helices (const):

References make_bundle_.

◆ increment_helix_count()

void protocols::helical_bundle::BundleGridSampler::increment_helix_count ( )

inline

Increments the number of helices that have been defined.

References n_helices_.

Referenced by add_helix().

◆ is_in_list()

bool protocols::helical_bundle::BundleGridSampler::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::BundleGridSampler::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::BundleGridSampler::mover_name ( )

static

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

◆ n_helices()

core::Size protocols::helical_bundle::BundleGridSampler::n_helices ( ) const

inline

Returns the number of helices that have been defined.

References n_helices_.

Referenced by add_helix(), apply(), calculate_total_samples(), and parse_my_tag().

◆ nstruct_mode()

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

inline

Get the nstruct mode.

If true, each job samples one set of Crick parameters. If false, every job samples every set of Crick parameters. False by default.

References nstruct_mode_.

Referenced by apply().

◆ nstruct_repeats()

core::Size protocols::helical_bundle::BundleGridSampler::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 Crick parameters. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same Crick parameters. 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::BundleGridSampler::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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

Reimplemented from protocols::moves::Mover.

References add_helix(), protocols::helical_bundle::BPC_end_of_list, clone(), default_calculator_, make_bundle_, n_helices(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), protocols::helical_bundle::parse_resnames(), core::scoring::parse_score_function(), reset_mode(), set_default_crick_params_file(), set_max_samples(), set_nstruct_mode(), set_nstruct_repeats(), set_pdb_output(), set_pdb_prefix(), set_preselection_filter(), set_preselection_mover(), set_reset_mode(), set_selection_low(), set_sfxn(), protocols::helical_bundle::TR(), use_degrees(), and protocols::hybridization::val.

◆ pdb_output()

bool protocols::helical_bundle::BundleGridSampler::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::BundleGridSampler::pdb_prefix ( )

inline

Access the filename prefix for PDB output.

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

References pdb_prefix_.

Referenced by apply().

◆ preselection_filter_exists()

bool protocols::helical_bundle::BundleGridSampler::preselection_filter_exists ( ) const

inline

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

References pre_selection_filter_exists_.

Referenced by apply().

◆ preselection_mover_exists()

bool protocols::helical_bundle::BundleGridSampler::preselection_mover_exists ( ) const

inline

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

References pre_selection_mover_exists_.

Referenced by apply().

◆ provide_citation_info()

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

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References pre_selection_filter_, and pre_selection_mover_.

◆ provide_xml_schema()

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

static

References protocols::helical_bundle::add_attributes_for_helix_params(), protocols::helical_bundle::add_attributes_for_make_bundle_minorhelix_defaults(), protocols::helical_bundle::add_attributes_for_make_bundle_other_defaults(), protocols::helical_bundle::add_attributes_for_make_bundle_symmetry(), protocols::helical_bundle::add_attributes_for_minor_helix_params(), protocols::helical_bundle::add_attributes_for_other_helix_params(), core::scoring::attributes_for_parse_score_function(), protocols::helical_bundle::BPC_end_of_list, mover_name(), protocols::helical_bundle::subtag_for_bundgrid(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

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

◆ reset_mode()

bool protocols::helical_bundle::BundleGridSampler::reset_mode ( ) const

inline

Get the reset mode.

If true (default), the pose is reset before generating bundles. If false, it is not.

References reset_mode_.

Referenced by apply(), and parse_my_tag().

◆ selection_low()

bool protocols::helical_bundle::BundleGridSampler::selection_low ( )

inline

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

References select_low_.

Referenced by apply().

◆ set_default_crick_params_file()

void protocols::helical_bundle::BundleGridSampler::set_default_crick_params_file ( std::string const & default_crick_file )

Set the default Crick params file.

This is used unless overridden on a helix-by-helix basis.

Note: Triggers a read from disk!

References default_calculator_, and make_bundle_.

Referenced by parse_my_tag().

◆ set_max_samples()

void protocols::helical_bundle::BundleGridSampler::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_nstruct_mode()

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

inline

Set the nstruct mode.

If true, each job samples one set of Crick parameters. If false, every job samples every set of Crick parameters. False by default.

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

Referenced by parse_my_tag().

◆ set_nstruct_repeats()

void protocols::helical_bundle::BundleGridSampler::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 Crick parameters. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same Crick parameters. 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::BundleGridSampler::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::BundleGridSampler::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_preselection_filter()

void protocols::helical_bundle::BundleGridSampler::set_preselection_filter ( protocols::filters::FilterOP filter )

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

See the pre_selection_filter_ private member variable for details.

References pre_selection_filter_, and pre_selection_filter_exists_.

Referenced by parse_my_tag().

◆ set_preselection_mover()

void protocols::helical_bundle::BundleGridSampler::set_preselection_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_selection_mover_, and pre_selection_mover_exists_.

Referenced by parse_my_tag().

◆ set_reset_mode()

void protocols::helical_bundle::BundleGridSampler::set_reset_mode ( bool const val )

inline

Set the reset mode.

If true (default), the pose is reset before generating bundles. If false, it is not.

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

Referenced by parse_my_tag().

◆ set_selection_low()

void protocols::helical_bundle::BundleGridSampler::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::BundleGridSampler::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_use_degrees()

void protocols::helical_bundle::BundleGridSampler::set_use_degrees ( bool const use_degrees )

Set whether we're using degrees (true) or radians (false)

References make_bundle_, and use_degrees().

◆ sfxn_set()

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

inline

Returns whether the scorefunction has been set.

References sfxn_set_.

Referenced by apply().

◆ use_degrees()

bool protocols::helical_bundle::BundleGridSampler::use_degrees ( ) const

Get whether we're using degrees (true) or radians (false)

References make_bundle_.

Referenced by parse_my_tag(), and set_use_degrees().

Member Data Documentation

◆ default_calculator_

BundleParametrizationCalculatorOP protocols::helical_bundle::BundleGridSampler::default_calculator_

private

A calculator object for the Crick parameterization.

This one will be used for default properties. Individual calculators for individual helices will be cloned from this one before being independently configured.

Referenced by BundleGridSampler(), parse_my_tag(), and set_default_crick_params_file().

◆ dump_pdbs_

bool protocols::helical_bundle::BundleGridSampler::dump_pdbs_

private

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

Referenced by pdb_output(), and set_pdb_output().

◆ make_bundle_

MakeBundleOP protocols::helical_bundle::BundleGridSampler::make_bundle_

private

A MakeBundle mover that this mover will call.

Referenced by add_helix(), apply(), BundleGridSampler(), calculate_total_samples(), helix(), helix_cop(), parse_my_tag(), set_default_crick_params_file(), set_use_degrees(), and use_degrees().

◆ max_samples_

core::Size protocols::helical_bundle::BundleGridSampler::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().

◆ n_helices_

core::Size protocols::helical_bundle::BundleGridSampler::n_helices_

private

The number of helices that have been defined.

Referenced by increment_helix_count(), and n_helices().

◆ nstruct_mode_

bool protocols::helical_bundle::BundleGridSampler::nstruct_mode_

private

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

If true, each job samples one set of Crick parameters. If false, every job samples every set of Crick parameters. False by default.

Referenced by nstruct_mode(), and set_nstruct_mode().

◆ nstruct_mode_repeats_

core::Size protocols::helical_bundle::BundleGridSampler::nstruct_mode_repeats_

private

If nstruct_mode_ is true, how many times should each set of Crick parameters be repeated?

This is set to 1 by default, which means that each nstruct number correspnds to a different set of Crick parameters. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same Crick parameters. 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::BundleGridSampler::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().

◆ pre_selection_filter_

protocols::filters::FilterOP protocols::helical_bundle::BundleGridSampler::pre_selection_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_preselection_filter().

◆ pre_selection_filter_exists_

bool protocols::helical_bundle::BundleGridSampler::pre_selection_filter_exists_

private

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

Referenced by preselection_filter_exists(), and set_preselection_filter().

◆ pre_selection_mover_

protocols::moves::MoverOP protocols::helical_bundle::BundleGridSampler::pre_selection_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_preselection_mover().

◆ pre_selection_mover_exists_

bool protocols::helical_bundle::BundleGridSampler::pre_selection_mover_exists_

private

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

Referenced by preselection_mover_exists(), and set_preselection_mover().

◆ reset_mode_

bool protocols::helical_bundle::BundleGridSampler::reset_mode_

private

Should the pose be reset before applying the GridSampler? Default true.

Referenced by reset_mode(), and set_reset_mode().

◆ select_low_

bool protocols::helical_bundle::BundleGridSampler::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 selection_low(), and set_selection_low().

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::helical_bundle::BundleGridSampler::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::BundleGridSampler::sfxn_set_

private

Has the scorefunction been set?

False by default.

Referenced by set_sfxn(), and sfxn_set().

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

src/protocols/helical_bundle/BundleGridSampler.hh
src/protocols/helical_bundle/BundleGridSampler.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BundleParameters

◆ BundleParametersCOP

◆ BundleParametersOP

◆ BundleParametersSet

◆ BundleParametersSetCOP

◆ BundleParametersSetOP

◆ Parameters

◆ ParametersOP

◆ ParametersSet

◆ ParametersSetOP

Constructor & Destructor Documentation

◆ BundleGridSampler() [1/2]

◆ BundleGridSampler() [2/2]

◆ ~BundleGridSampler()

Member Function Documentation

◆ add_helix()

◆ apply()

◆ calculate_total_samples()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ helix()

◆ helix_cop()

◆ increment_helix_count()

◆ is_in_list()

◆ max_samples()

◆ mover_name()

◆ n_helices()

◆ nstruct_mode()

◆ nstruct_repeats()

◆ parse_my_tag()

◆ pdb_output()

◆ pdb_prefix()

◆ preselection_filter_exists()

◆ preselection_mover_exists()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ reset_mode()

◆ selection_low()

◆ set_default_crick_params_file()

◆ set_max_samples()

◆ set_nstruct_mode()

◆ set_nstruct_repeats()

◆ set_pdb_output()

◆ set_pdb_prefix()

◆ set_preselection_filter()

◆ set_preselection_mover()

◆ set_reset_mode()

◆ set_selection_low()

◆ set_sfxn()

◆ set_use_degrees()

◆ sfxn_set()

◆ use_degrees()

Member Data Documentation

◆ default_calculator_

◆ dump_pdbs_

◆ make_bundle_

◆ max_samples_

◆ n_helices_

◆ nstruct_mode_

◆ nstruct_mode_repeats_

◆ pdb_prefix_

◆ pre_selection_filter_

◆ pre_selection_filter_exists_

◆ pre_selection_mover_

◆ pre_selection_mover_exists_

◆ reset_mode_

◆ select_low_

◆ sfxn_

◆ sfxn_set_