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protocols::forge::constraints::InverseRotamersRCG Class Reference

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:
Inheritance graph
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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) 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 VirtualBase. 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 &) 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 Stringsinfo ()
 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 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 ( )
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
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
void protocols::forge::constraints::InverseRotamersRCG::parse_my_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.

void protocols::forge::constraints::InverseRotamersRCG::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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
core::Real protocols::forge::constraints::InverseRotamersRCG::func_sd_
private
utility::vector1< forge::build::Interval > protocols::forge::constraints::InverseRotamersRCG::intervals_
private
std::list< core::conformation::ResidueCOP > protocols::forge::constraints::InverseRotamersRCG::inverse_rotamers_
private

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