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protocols::recces::scratch::ThermalMinimizer Class Reference

Use a simulated tempering simulation to refine a pose. More...

#include <ThermalMinimizer.hh>

Inheritance diagram for protocols::recces::scratch::ThermalMinimizer:
Inheritance graph
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Public Member Functions

 ThermalMinimizer ()
 Constructors ///. More...
 
 ThermalMinimizer (ThermalMinimizer const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~ThermalMinimizer () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
 
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Get the name of the Mover. More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
void set_n_cycle (core::Size const setting)
 
void set_temp (Real const temp)
 
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
void set_mm (core::kinematics::MoveMapOP mm)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_kic_sampling (bool const &setting)
 
bool kic_sampling () const
 
void set_output_min_pose (bool const &setting)
 
bool output_min_pose () 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 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::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Types

typedef core::Size Size
 
typedef core::Real Real
 

Private Attributes

core::Size n_cycle_ = 100
 
Real angle_range_chi_ = 180
 
Real angle_range_bb_ = 60
 
Real temp_ = 0.5
 
core::scoring::ScoreFunctionOP score_fxn_
 
core::kinematics::MoveMapOP mm_
 
bool kic_sampling_ = true
 
bool output_min_pose_
 

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

Use a simulated tempering simulation to refine a pose.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::recces::scratch::ThermalMinimizer::ThermalMinimizer ( )

Constructors ///.

Default constructor

protocols::recces::scratch::ThermalMinimizer::ThermalMinimizer ( ThermalMinimizer const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::recces::scratch::ThermalMinimizer::~ThermalMinimizer ( )
overridedefault

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::recces::scratch::ThermalMinimizer::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::recces::scratch::ThermalMinimizer::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

moves::MoverOP protocols::recces::scratch::ThermalMinimizer::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::recces::scratch::ThermalMinimizer::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

bool protocols::recces::scratch::ThermalMinimizer::kic_sampling ( ) const
inline

References kic_sampling_.

std::string protocols::recces::scratch::ThermalMinimizer::mover_name ( )
static
bool protocols::recces::scratch::ThermalMinimizer::output_min_pose ( ) const
inline

References output_min_pose_.

void protocols::recces::scratch::ThermalMinimizer::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Get the name of the Mover.

Rosetta Scripts Support ///.

Rosetta Scripts Support /// parse XML tag (to use this Mover in Rosetta Scripts)

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

void protocols::recces::scratch::ThermalMinimizer::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::recces::scratch::ThermalMinimizer::set_kic_sampling ( bool const &  setting)
inline
void protocols::recces::scratch::ThermalMinimizer::set_mm ( core::kinematics::MoveMapOP  mm)
inline
void protocols::recces::scratch::ThermalMinimizer::set_n_cycle ( core::Size const  setting)
inline
void protocols::recces::scratch::ThermalMinimizer::set_output_min_pose ( bool const &  setting)
inline
void protocols::recces::scratch::ThermalMinimizer::set_scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)
inline
void protocols::recces::scratch::ThermalMinimizer::set_temp ( Real const  temp)
inline
void protocols::recces::scratch::ThermalMinimizer::show ( std::ostream &  output = std::cout) const
overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::recces::scratch::operator<<().

Member Data Documentation

Real protocols::recces::scratch::ThermalMinimizer::angle_range_bb_ = 60
private
Real protocols::recces::scratch::ThermalMinimizer::angle_range_chi_ = 180
private
bool protocols::recces::scratch::ThermalMinimizer::kic_sampling_ = true
private

Referenced by kic_sampling(), and set_kic_sampling().

core::kinematics::MoveMapOP protocols::recces::scratch::ThermalMinimizer::mm_
private

Referenced by set_mm().

core::Size protocols::recces::scratch::ThermalMinimizer::n_cycle_ = 100
private

Referenced by set_n_cycle().

bool protocols::recces::scratch::ThermalMinimizer::output_min_pose_
private
core::scoring::ScoreFunctionOP protocols::recces::scratch::ThermalMinimizer::score_fxn_
private

Referenced by set_scorefxn().

Real protocols::recces::scratch::ThermalMinimizer::temp_ = 0.5
private

Referenced by set_temp().


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