a RemodelConstraintGenerator that creates AmbiguousConstraints for all positions in a remodeled region towards a list of inverse rotamers. For every remodel position/inverse rotamer pair, there will be one MultiConstraint consisting of three CoordinateConstraints. the three coordinate constraints will be between: 1) remodel res N - invrot N coords 2) remodel res Ca - invrot Ca coords 3) remodel res Cb - invrot Cb coords All of these MultiConstraints are combined to form one AmbiguousConstraint. In effect, this RCG should bias the remodel trajectory such that one remodel residue backbone overlays with one inverse rotamer backbone More...

#include <InverseRotamersRCG.hh>

Inheritance diagram for protocols::forge::constraints::InverseRotamersRCG:

[legend]

Public Member Functions
	InverseRotamersRCG ()

	InverseRotamersRCG (InverseRotamersRCG const &rval)
	copy constructor More...

	InverseRotamersRCG (core::Size const lstart, core::Size const lstop, std::list< core::conformation::ResidueCOP > const &inverse_rotamers)
	value constructor which initializes and then calls init() More...

	~InverseRotamersRCG () override

void	parse_my_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
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

void	generate_remodel_constraints (core::pose::Pose const &pose) override

void	set_constraint_func (core::scoring::func::FuncOP constraint_func)

void	clear_inverse_rotamers ()

void	init (core::Size const lstart, core::Size const lstop, std::list< core::conformation::ResidueCOP > const &inverse_rotamers)
	initialize with given lstart, lstop, and inverse rotamer residue list More...

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

Public Member Functions inherited from protocols::forge::remodel::RemodelConstraintGenerator
	~RemodelConstraintGenerator () override
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

void	apply (core::pose::Pose &pose) override
	generates constraints and adds them to the pose More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override
	This is called if this mover is instantiated from XML. More...

	RemodelConstraintGenerator ()

	RemodelConstraintGenerator (RemodelConstraintGenerator const &rval)

void	add_remodel_constraints_to_pose (core::pose::Pose &pose)

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

virtual void	init (core::pose::Pose const &)
	Pose-specific setup routines go here. More...

VarLengthBuildAP	vlb () const

void	set_vlb (VarLengthBuildAP vlb)

std::string	id () const

void	set_id (std::string const &id)

void	set_seqmap (core::id::SequenceMappingCOP seqmap)

core::id::SequenceMappingCOP	seqmap () const

core::scoring::constraints::ConstraintCOPs const &	constraints () const

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

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

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. 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...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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::forge::remodel::RemodelConstraintGenerator
static core::scoring::constraints::ConstraintCOPs const	lookup_stored_constraints (std::string const &id)

static void	attributes_for_remodel_constraint_generator (utility::tag::AttributeList &)

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 Attributes
utility::vector1 < forge::build::Interval >	intervals_

std::list < core::conformation::ResidueCOP >	inverse_rotamers_

core::scoring::func::FuncOP	constraint_func_

core::Real	func_sd_

Additional Inherited Members
Public Types inherited from protocols::forge::remodel::RemodelConstraintGenerator
typedef protocols::forge::components::VarLengthBuildAP	VarLengthBuildAP

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

Protected Member Functions inherited from protocols::forge::remodel::RemodelConstraintGenerator
void	add_constraint (core::scoring::constraints::ConstraintCOP cst)

void	add_constraints (core::scoring::constraints::ConstraintCOPs csts)

void	clear_constraints ()

void	clear_stored_constraints ()

void	store_constraints ()

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

a RemodelConstraintGenerator that creates AmbiguousConstraints for all positions in a remodeled region towards a list of inverse rotamers. For every remodel position/inverse rotamer pair, there will be one MultiConstraint consisting of three CoordinateConstraints. the three coordinate constraints will be between: 1) remodel res N - invrot N coords 2) remodel res Ca - invrot Ca coords 3) remodel res Cb - invrot Cb coords All of these MultiConstraints are combined to form one AmbiguousConstraint. In effect, this RCG should bias the remodel trajectory such that one remodel residue backbone overlays with one inverse rotamer backbone

Constructor & Destructor Documentation

protocols::forge::constraints::InverseRotamersRCG::InverseRotamersRCG ( )

protocols::forge::constraints::InverseRotamersRCG::InverseRotamersRCG ( InverseRotamersRCG const & rval )

copy constructor

protocols::forge::constraints::InverseRotamersRCG::InverseRotamersRCG	(	core::Size const	lstart,
		core::Size const	lstop,
		std::list< core::conformation::ResidueCOP > const &	inverse_rotamers
	)

value constructor which initializes and then calls init()

References init().

protocols::forge::constraints::InverseRotamersRCG::~InverseRotamersRCG ( )

overridedefault

Member Function Documentation

void protocols::forge::constraints::InverseRotamersRCG::clear_inverse_rotamers ( )

References inverse_rotamers_.

Referenced by generate_remodel_constraints().

protocols::moves::MoverOP protocols::forge::constraints::InverseRotamersRCG::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::forge::constraints::InverseRotamersRCG::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

void protocols::forge::constraints::InverseRotamersRCG::generate_remodel_constraints ( core::pose::Pose const & pose )

overridevirtual

Implements protocols::forge::remodel::RemodelConstraintGenerator.

References protocols::forge::remodel::RemodelConstraintGenerator::add_constraints(), clear_inverse_rotamers(), protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(), constraint_func_, func_sd_, intervals_, inverse_rotamers_, core::sequence::left, and protocols::forge::remodel::RemodelConstraintGenerator::seqmap().

std::string protocols::forge::constraints::InverseRotamersRCG::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::forge::constraints::InverseRotamersRCG::init	(	core::Size const	lstart,
		core::Size const	lstop,
		std::list< core::conformation::ResidueCOP > const &	inverse_rotamers
	)

initialize with given lstart, lstop, and inverse rotamer residue list

References intervals_, and inverse_rotamers_.

Referenced by InverseRotamersRCG().

std::string protocols::forge::constraints::InverseRotamersRCG::mover_name ( )

static

Referenced by get_name(), protocols::forge::constraints::InverseRotamersCstGeneratorCreator::keyname(), and provide_xml_schema().

void protocols::forge::constraints::InverseRotamersRCG::parse_my_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

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

void protocols::forge::constraints::InverseRotamersRCG::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::forge::constraints::InverseRotamersCstGeneratorCreator::provide_xml_schema().

void protocols::forge::constraints::InverseRotamersRCG::set_constraint_func ( core::scoring::func::FuncOP constraint_func )

References constraint_func_.

Member Data Documentation

core::scoring::func::FuncOP protocols::forge::constraints::InverseRotamersRCG::constraint_func_

private

Referenced by generate_remodel_constraints(), and set_constraint_func().

core::Real protocols::forge::constraints::InverseRotamersRCG::func_sd_

private

Referenced by generate_remodel_constraints().

utility::vector1< forge::build::Interval > protocols::forge::constraints::InverseRotamersRCG::intervals_

private

Referenced by generate_remodel_constraints(), and init().

std::list< core::conformation::ResidueCOP > protocols::forge::constraints::InverseRotamersRCG::inverse_rotamers_

private

Referenced by clear_inverse_rotamers(), generate_remodel_constraints(), and init().

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

src/protocols/forge/constraints/InverseRotamersRCG.hh
src/protocols/forge/constraints/InverseRotamersRCG.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation