Mover interface to BBDihedralSampler ( 1D ). Samples using BBDihedralSamplers randomly using residues set in the movemap. If multiple samplers are given, will randomly sample on them. More...

#include <BBDihedralSamplerMover.hh>

Inheritance diagram for protocols::simple_moves::BBDihedralSamplerMover:

[legend]

Public Member Functions
	BBDihedralSamplerMover ()

	BBDihedralSamplerMover (bb_sampler::BBDihedralSamplerOP sampler)

	BBDihedralSamplerMover (bb_sampler::BBDihedralSamplerOP sampler, core::select::residue_selector::ResidueSelectorCOP selector)

	BBDihedralSamplerMover (BBDihedralSamplerMover const &src)

	~BBDihedralSamplerMover () override

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

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Sets residues from a residue selector. More...

void	set_single_resnum (core::Size resnum)
	Set a single resnum instead of a movemap. More...

void	set_sampler (bb_sampler::BBDihedralSamplerOP sampler)
	Set a single sampler this mover will use. More...

void	add_sampler (bb_sampler::BBDihedralSamplerOP sampler)
	Add a sampler to this mover. More...

void	set_dihedral_mask (std::map< core::Size, utility::vector1< core::Size >> mask)
	Limit the torsions that are sampled using a mask. Mask is a vector of torsions we are allowed to sample at each residue. NOT every residue must be present - only the ones we need to mask. This helps for carbohydrates, since not every residue has all possible dihedrals, even if we have samplers to use. More...

void	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. More...

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

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...

bool	mover_provides_citation_info () const override
	Does this mover provide information about how to cite it? More...

utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const override
	Provide a list of authors and their e-mail addresses, as strings. More...

utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const override
	Although this mover has no citation info since it is unpublished, it can provide citation info for the residue selector that it calls. 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 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 bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

Private Member Functions
void	setup_samplers (core::pose::Pose const &pose)

void	setup_all_bb_residues (core::pose::Pose const &pose)
	Sets up bb_residues_ variable as all residues in the pose. More...

Private Attributes
std::map< core::Size, utility::vector1 < bb_sampler::BBDihedralSamplerOP > >	samplers_

utility::vector1< core::Size >	sampler_torsion_types_

core::select::residue_selector::ResidueSelectorOP	selector_ = nullptr

utility::vector1< core::Size >	bb_residues_

std::map< core::Size, utility::vector1< core::Size > >	sampler_torsions_

std::map< core::Size, utility::vector1< core::Size > >	dihedral_mask_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

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...

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 interface to BBDihedralSampler ( 1D ). Samples using BBDihedralSamplers randomly using residues set in the movemap. If multiple samplers are given, will randomly sample on them.

Constructor & Destructor Documentation

protocols::simple_moves::BBDihedralSamplerMover::BBDihedralSamplerMover ( )

protocols::simple_moves::BBDihedralSamplerMover::BBDihedralSamplerMover ( bb_sampler::BBDihedralSamplerOP sampler )

References set_sampler().

protocols::simple_moves::BBDihedralSamplerMover::BBDihedralSamplerMover	(	bb_sampler::BBDihedralSamplerOP	sampler,
		core::select::residue_selector::ResidueSelectorCOP	selector
	)

References set_residue_selector(), and set_sampler().

protocols::simple_moves::BBDihedralSamplerMover::BBDihedralSamplerMover ( BBDihedralSamplerMover const & src )

References samplers_, and selector_.

protocols::simple_moves::BBDihedralSamplerMover::~BBDihedralSamplerMover ( )

overridedefault

Member Function Documentation

void protocols::simple_moves::BBDihedralSamplerMover::add_sampler ( bb_sampler::BBDihedralSamplerOP sampler )

Add a sampler to this mover.

References sampler_torsion_types_, sampler_torsions_, and samplers_.

void protocols::simple_moves::BBDihedralSamplerMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References bb_residues_, protocols::moves::MS_FAIL, protocols::moves::MS_SUCCESS, core::scoring::rg, sampler_torsions_, samplers_, core::select::residue_selector::selection_positions(), selector_, protocols::moves::Mover::set_last_move_status(), setup_all_bb_residues(), setup_samplers(), core::id::to_string(), and protocols::simple_moves::TR().

protocols::moves::MoverOP protocols::simple_moves::BBDihedralSamplerMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

moves::MoverOP protocols::simple_moves::BBDihedralSamplerMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::simple_moves::BBDihedralSamplerMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

Referenced by provide_authorship_info_for_unpublished().

bool protocols::simple_moves::BBDihedralSamplerMover::mover_provides_citation_info ( ) const

overridevirtual

Does this mover provide information about how to cite it?

Reimplemented from protocols::moves::Mover.

void protocols::simple_moves::BBDihedralSamplerMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

overridevirtual

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

Reimplemented from protocols::moves::Mover.

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::simple_moves::BBDihedralSamplerMover::provide_authorship_info_for_unpublished ( ) const

overridevirtual

Provide a list of authors and their e-mail addresses, as strings.

Reimplemented from protocols::moves::Mover.

References get_name(), and selector_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::simple_moves::BBDihedralSamplerMover::provide_citation_info ( ) const

overridevirtual

Although this mover has no citation info since it is unpublished, it can provide citation info for the residue selector that it calls.

Reimplemented from protocols::moves::Mover.

References selector_.

void protocols::simple_moves::BBDihedralSamplerMover::set_dihedral_mask ( std::map< core::Size, utility::vector1< core::Size >> mask )

Limit the torsions that are sampled using a mask. Mask is a vector of torsions we are allowed to sample at each residue. NOT every residue must be present - only the ones we need to mask. This helps for carbohydrates, since not every residue has all possible dihedrals, even if we have samplers to use.

References dihedral_mask_, and sampler_torsions_.

void protocols::simple_moves::BBDihedralSamplerMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Sets residues from a residue selector.

References bb_residues_, sampler_torsions_, and selector_.

Referenced by BBDihedralSamplerMover().

void protocols::simple_moves::BBDihedralSamplerMover::set_sampler ( bb_sampler::BBDihedralSamplerOP sampler )

Set a single sampler this mover will use.

References sampler_torsion_types_, sampler_torsions_, and samplers_.

Referenced by BBDihedralSamplerMover().

void protocols::simple_moves::BBDihedralSamplerMover::set_single_resnum ( core::Size resnum )

Set a single resnum instead of a movemap.

References bb_residues_, and sampler_torsions_.

void protocols::simple_moves::BBDihedralSamplerMover::setup_all_bb_residues ( core::pose::Pose const & pose )

private

Sets up bb_residues_ variable as all residues in the pose.

References bb_residues_, core::select::residue_selector::selection_positions(), selector_, core::pose::Pose::total_residue(), and protocols::simple_moves::TR().

Referenced by apply().

void protocols::simple_moves::BBDihedralSamplerMover::setup_samplers ( core::pose::Pose const & pose )

private

References bb_residues_, protocols::sparta::contains(), dihedral_mask_, sampler_torsion_types_, sampler_torsions_, and protocols::simple_moves::TR().

Referenced by apply().

void protocols::simple_moves::BBDihedralSamplerMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

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

Referenced by protocols::simple_moves::operator<<().

Member Data Documentation

utility::vector1< core::Size > protocols::simple_moves::BBDihedralSamplerMover::bb_residues_

private

Referenced by apply(), set_residue_selector(), set_single_resnum(), setup_all_bb_residues(), and setup_samplers().

std::map< core::Size, utility::vector1< core::Size > > protocols::simple_moves::BBDihedralSamplerMover::dihedral_mask_

private

Referenced by set_dihedral_mask(), and setup_samplers().

utility::vector1< core::Size > protocols::simple_moves::BBDihedralSamplerMover::sampler_torsion_types_

private

Referenced by add_sampler(), set_sampler(), and setup_samplers().

std::map< core::Size, utility::vector1< core::Size > > protocols::simple_moves::BBDihedralSamplerMover::sampler_torsions_

private

Referenced by add_sampler(), apply(), set_dihedral_mask(), set_residue_selector(), set_sampler(), set_single_resnum(), and setup_samplers().

std::map< core::Size, utility::vector1< bb_sampler::BBDihedralSamplerOP > > protocols::simple_moves::BBDihedralSamplerMover::samplers_

private

Referenced by add_sampler(), apply(), BBDihedralSamplerMover(), and set_sampler().

core::select::residue_selector::ResidueSelectorOP protocols::simple_moves::BBDihedralSamplerMover::selector_ = nullptr

private

Referenced by apply(), BBDihedralSamplerMover(), provide_authorship_info_for_unpublished(), provide_citation_info(), set_residue_selector(), and setup_all_bb_residues().

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

src/protocols/simple_moves/BBDihedralSamplerMover.hh
src/protocols/simple_moves/BBDihedralSamplerMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation