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protocols::relax::LocalRelax Class Reference

#include <LocalRelax.hh>

Inheritance diagram for protocols::relax::LocalRelax:
Inheritance graph
[legend]

Public Member Functions

 LocalRelax ()
 
void optimization_loop (Pose &pose, core::pack::task::PackerTaskOP ptask, core::kinematics::MoveMapOP mm, core::Real, core::Real)
 one cycle of local optimization More...
 
utility::vector1
< utility::vector1< bool > > 
get_neighbor_graph (Pose const &pose)
 get matrix of interacting residues More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 RS integration. More...
 
protocols::moves::MoverOP clone () const override
 return a fresh instance of this class in an owning pointer More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void set_pack_sfxn (core::scoring::ScoreFunctionOP const &sf)
 
void set_min_sfxn (core::scoring::ScoreFunctionOP const &sf)
 
void set_sfxn (core::scoring::ScoreFunctionOP const &sf)
 
void set_K (core::Real const K)
 
void set_max_iter (core::Real const max_iter)
 
void set_ncyc (core::Size const ncyc)
 
void set_nexp (core::Size const nexp)
 
core::scoring::ScoreFunctionOP get_pack_sfxn () const
 
core::scoring::ScoreFunctionOP get_min_sfxn () const
 
core::Real get_K () const
 
core::Real get_max_iter () const
 
core::Size get_ncyc () const
 
core::Size get_nexp () const
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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

core::Size NCYC_
 
core::Size NEXP_
 
core::Real K_
 
core::Real max_iter_
 
bool ramp_cart_
 
bool verbose_
 
utility::vector1< core::Realramp_schedule_
 
core::scoring::ScoreFunctionOP pack_sfxn_
 
core::scoring::ScoreFunctionOP min_sfxn_
 

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...
 

Constructor & Destructor Documentation

protocols::relax::LocalRelax::LocalRelax ( )

Member Function Documentation

void protocols::relax::LocalRelax::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::relax::LocalRelax::clone ( ) const
inlineoverridevirtual

return a fresh instance of this class in an owning pointer

Reimplemented from protocols::moves::Mover.

core::Real protocols::relax::LocalRelax::get_K ( ) const
inline

References K_.

core::Real protocols::relax::LocalRelax::get_max_iter ( ) const
inline

References max_iter_.

core::scoring::ScoreFunctionOP protocols::relax::LocalRelax::get_min_sfxn ( ) const
inline

References min_sfxn_.

std::string protocols::relax::LocalRelax::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

core::Size protocols::relax::LocalRelax::get_ncyc ( ) const
inline

References NCYC_.

utility::vector1< utility::vector1< bool > > protocols::relax::LocalRelax::get_neighbor_graph ( Pose const &  pose)
core::Size protocols::relax::LocalRelax::get_nexp ( ) const
inline

References NEXP_.

core::scoring::ScoreFunctionOP protocols::relax::LocalRelax::get_pack_sfxn ( ) const
inline

References pack_sfxn_.

std::string protocols::relax::LocalRelax::mover_name ( )
static
void protocols::relax::LocalRelax::optimization_loop ( Pose pose,
core::pack::task::PackerTaskOP  ptask,
core::kinematics::MoveMapOP  mm,
core::Real  fa_rep_scale,
core::Real  min_tol 
)
void protocols::relax::LocalRelax::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

RS integration.

Reimplemented from protocols::moves::Mover.

void protocols::relax::LocalRelax::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::relax::LocalRelax::set_K ( core::Real const  K)
inline

References core::chemical::element::K, and K_.

void protocols::relax::LocalRelax::set_max_iter ( core::Real const  max_iter)
inline

References max_iter_.

void protocols::relax::LocalRelax::set_min_sfxn ( core::scoring::ScoreFunctionOP const &  sf)
inline

References min_sfxn_.

void protocols::relax::LocalRelax::set_ncyc ( core::Size const  ncyc)
inline

References NCYC_.

void protocols::relax::LocalRelax::set_nexp ( core::Size const  nexp)
inline

References NEXP_.

void protocols::relax::LocalRelax::set_pack_sfxn ( core::scoring::ScoreFunctionOP const &  sf)
inline

References pack_sfxn_.

void protocols::relax::LocalRelax::set_sfxn ( core::scoring::ScoreFunctionOP const &  sf)
inline

References min_sfxn_, and pack_sfxn_.

Member Data Documentation

core::Real protocols::relax::LocalRelax::K_
private

Referenced by get_K(), and set_K().

core::Real protocols::relax::LocalRelax::max_iter_
private

Referenced by get_max_iter(), and set_max_iter().

core::scoring::ScoreFunctionOP protocols::relax::LocalRelax::min_sfxn_
private
core::Size protocols::relax::LocalRelax::NCYC_
private

Referenced by get_ncyc(), and set_ncyc().

core::Size protocols::relax::LocalRelax::NEXP_
private

Referenced by get_nexp(), and set_nexp().

core::scoring::ScoreFunctionOP protocols::relax::LocalRelax::pack_sfxn_
private
bool protocols::relax::LocalRelax::ramp_cart_
private
utility::vector1< core::Real > protocols::relax::LocalRelax::ramp_schedule_
private
bool protocols::relax::LocalRelax::verbose_
private

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