#include <AddResidueCouplingConstraint.hh>

Inheritance diagram for protocols::simple_moves::AddResidueCouplingConstraint:

Public Member Functions
	AddResidueCouplingConstraint ()

	AddResidueCouplingConstraint (std::string const &tensor_file, std::string const &index_file, core::Real strength, std::string const &alphabet)

	AddResidueCouplingConstraint (AddResidueCouplingConstraint const &)=default

	~AddResidueCouplingConstraint () override

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

void	apply (core::pose::Pose &pose) override
	Main Method. 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) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

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

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

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

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

std::string	get_type () const

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

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

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

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

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

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

jobdist::BasicJobCOP	get_current_job () const

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

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

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

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static 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
std::string	tensor_file_

std::string	index_file_

std::string	alphabet_

core::Real	strength_

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 std::list< std::string >	Strings

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

The mover is designed to improve the design process by using information from co-evolutionary correlation matrices. These matrices can be created by different methods, e.g. GREMLIN or plmDCA. The matrices get input as tensor of the shape [N, A, N, A] where N is the length of the protein and A is the length of the alphabet (typically 21 amino acids + 1 for gaps).

GRELIN alphabet order: ARNDCQEGHILKMFPSTWYV- plmDCA alphabet order: ACDEFGHIKLMNPQRSTVWY-

The order of the alphabet used can be defined by the user. To access the measure of co-evolution between, e.g., residue 1 (ALA) and residue 2 (ARG) the tensor lookup would be [1, 0, 2, 1] (using the GREMLIN alphabet order). The co-evolution strength is multiplied by a user defined strength factor (default=1) and then added as new term to the scoring function.

Constructor & Destructor Documentation

protocols::simple_moves::AddResidueCouplingConstraint::AddResidueCouplingConstraint ( )

protocols::simple_moves::AddResidueCouplingConstraint::AddResidueCouplingConstraint	(	std::string const &	tensor_file,
		std::string const &	index_file,
		core::Real	strength,
		std::string const &	alphabet
	)

protocols::simple_moves::AddResidueCouplingConstraint::AddResidueCouplingConstraint ( AddResidueCouplingConstraint const & )

default

protocols::simple_moves::AddResidueCouplingConstraint::~AddResidueCouplingConstraint ( )

inlineoverride

Member Function Documentation

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References alphabet_, index_file_, strength_, tensor_file_, and protocols::simple_moves::TR().

protocols::moves::MoverOP protocols::simple_moves::AddResidueCouplingConstraint::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.

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::simple_moves::AddResidueCouplingConstraint::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::AddResidueCouplingConstraintCreator::keyname(), and provide_xml_schema().

void protocols::simple_moves::AddResidueCouplingConstraint::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References alphabet_, index_file_, strength_, and tensor_file_.

void protocols::simple_moves::AddResidueCouplingConstraint::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::simple_moves::AddResidueCouplingConstraintCreator::provide_xml_schema().