Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::simple_moves::AddResidueCouplingConstraint Class Reference

#include <AddResidueCouplingConstraint.hh>

Inheritance diagram for protocols::simple_moves::AddResidueCouplingConstraint:
Inheritance graph

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 Stringsinfo ()
 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).


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

◆ AddResidueCouplingConstraint() [1/3]

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

◆ AddResidueCouplingConstraint() [2/3]

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

◆ AddResidueCouplingConstraint() [3/3]

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

◆ ~AddResidueCouplingConstraint()

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

Member Function Documentation

◆ apply()

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

◆ clone()

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

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.

◆ get_name()

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

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

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

◆ parse_my_tag()

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

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_.

◆ provide_xml_schema()

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

Member Data Documentation

◆ alphabet_

std::string protocols::simple_moves::AddResidueCouplingConstraint::alphabet_

Referenced by apply(), and parse_my_tag().

◆ index_file_

std::string protocols::simple_moves::AddResidueCouplingConstraint::index_file_

Referenced by apply(), and parse_my_tag().

◆ strength_

core::Real protocols::simple_moves::AddResidueCouplingConstraint::strength_

Referenced by apply(), and parse_my_tag().

◆ tensor_file_

std::string protocols::simple_moves::AddResidueCouplingConstraint::tensor_file_

Referenced by apply(), and parse_my_tag().

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