Public Member Functions | Static Public Member Functions | Private Types | Private Attributes | List of all members
protocols::recces::scratch::ThermalSamplingMover Class Reference

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

#include <ThermalSamplingMover.hh>

Inheritance diagram for protocols::recces::scratch::ThermalSamplingMover:
Inheritance graph

Public Member Functions

 ThermalSamplingMover ()
 Constructors ///. More...
 ThermalSamplingMover (ThermalSamplingMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 ~ThermalSamplingMover () 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_residues (utility::vector1< core::Size > const &residues)
utility::vector1< core::Sizeresidues () const
void set_free_rsd (utility::vector1< core::Size > const &free_rsd)
utility::vector1< core::Sizefree_rsd () const
void set_recces_turner_mode (bool const setting)
void set_dumping_app (bool const setting)
void set_n_cycle (core::Size const setting)
void set_dump_silent (bool const setting)
void set_dump_pdb (bool const setting)
void set_temps (utility::vector1< core::Size > const &temps)
void set_weights (utility::vector1< core::Size > const &weights)
void set_residue_sampling_from_pose_and_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap const &mm)
 Sets thermal sampling level given a MoveMap. More...
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...
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 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 Types

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

Private Attributes

utility::vector1< core::Sizeresidues_
core::Size total_sampled_
utility::vector1< core::Sizefree_rsd_
utility::vector1< core::Sizeloop_rsd_
bool recces_turner_mode_ = false
bool dumping_app_ = false
core::Size n_cycle_
bool dump_pdb_ = false
bool dump_silent_ = false
Real angle_range_chi_ = 180
Real angle_range_bb_ = 60
Real angle_range_loop_bb_ = 180
utility::vector1< Realtemps_
utility::vector1< Realst_weights_
core::kinematics::MoveMapOP mm_

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

◆ Real

◆ Size

Constructor & Destructor Documentation

◆ ThermalSamplingMover() [1/2]

protocols::recces::scratch::ThermalSamplingMover::ThermalSamplingMover ( )

Constructors ///.

Default constructor

References residues_, st_weights_, temps_, and total_sampled_.

◆ ThermalSamplingMover() [2/2]

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

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~ThermalSamplingMover()

protocols::recces::scratch::ThermalSamplingMover::~ThermalSamplingMover ( )

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

Member Function Documentation

◆ apply()

void protocols::recces::scratch::ThermalSamplingMover::apply ( core::pose::Pose pose)

Mover Methods ///.

Apply the mover

Implements protocols::moves::Mover.

References protocols::recces::sampler::rna::MC_RNA_MultiSuite::add_rotamer(), core::chemical::rna::ALPHA, angle_range_bb_, angle_range_chi_, angle_range_loop_bb_, protocols::recces::sampler::MC_Comb::apply(), core::id::BB, core::chemical::rna::BETA, protocols::moves::SimulatedTempering::check_boltzmann(), core::chemical::rna::CHI, core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::dump_pdb(), dump_pdb_, dump_silent_, dumping_app_, core::chemical::rna::EPSILON, protocols::recces::fill_data(), protocols::recces::scratch::find_likely_first_chain_ending(), free_rsd_, core::chemical::rna::GAMMA, core::scoring::get_score_function(), protocols::recces::get_scoretypes(), protocols::recces::scratch::get_torsions(), protocols::recces::sampler::MC_Comb::init(), loop_rsd_, protocols::mean_field::max(), protocols::mean_field::min(), mm_, n_cycle_, protocols::moves::Mover::name(), recces_turner_mode_, residues_, core::scoring::rg, core::scoring::RNA_HIRES_WTS, protocols::recces::sampler::rna::MC_RNA_MultiSuite::set_angle(), protocols::recces::scratch::set_gaussian_stdevs(), core::pose::Pose::size(), st_weights_, protocols::kinmatch::str(), protocols::moves::SimulatedTempering::t_jump(), protocols::moves::SimulatedTempering::temp_id(), temps_, core::id::TorsionID::torsion(), total_sampled_, protocols::TR(), protocols::recces::sampler::MC_Comb::update(), protocols::recces::update_scores(), protocols::recces::vector2disk_in1d(), protocols::recces::vector2disk_in2d(), core::io::silent::SilentFileData::write_silent_struct(), and core::chemical::rna::ZETA.

◆ clone()

protocols::moves::MoverOP protocols::recces::scratch::ThermalSamplingMover::clone ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ free_rsd()

utility::vector1< core::Size > protocols::recces::scratch::ThermalSamplingMover::free_rsd ( ) const

References free_rsd_.

Referenced by set_free_rsd().

◆ fresh_instance()

moves::MoverOP protocols::recces::scratch::ThermalSamplingMover::fresh_instance ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::recces::scratch::ThermalSamplingMover::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::recces::scratch::ThermalSamplingMover::mover_name ( )

◆ parse_my_tag()

void protocols::recces::scratch::ThermalSamplingMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

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.

◆ provide_xml_schema()

void protocols::recces::scratch::ThermalSamplingMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ residues()

utility::vector1< core::Size > protocols::recces::scratch::ThermalSamplingMover::residues ( ) const

References residues_.

Referenced by set_residues().

◆ set_dump_pdb()

void protocols::recces::scratch::ThermalSamplingMover::set_dump_pdb ( bool const  setting)

References dump_silent_.

◆ set_dump_silent()

void protocols::recces::scratch::ThermalSamplingMover::set_dump_silent ( bool const  setting)

References dump_pdb_.

◆ set_dumping_app()

void protocols::recces::scratch::ThermalSamplingMover::set_dumping_app ( bool const  setting)

References dumping_app_.

◆ set_free_rsd()

void protocols::recces::scratch::ThermalSamplingMover::set_free_rsd ( utility::vector1< core::Size > const &  free_rsd)

References free_rsd(), and free_rsd_.

◆ set_n_cycle()

void protocols::recces::scratch::ThermalSamplingMover::set_n_cycle ( core::Size const  setting)

References n_cycle_.

◆ set_recces_turner_mode()

void protocols::recces::scratch::ThermalSamplingMover::set_recces_turner_mode ( bool const  setting)

References recces_turner_mode_.

◆ set_residue_sampling_from_pose_and_movemap()

void protocols::recces::scratch::ThermalSamplingMover::set_residue_sampling_from_pose_and_movemap ( core::pose::Pose const &  pose,
core::kinematics::MoveMap const &  mm 

◆ set_residues()

void protocols::recces::scratch::ThermalSamplingMover::set_residues ( utility::vector1< core::Size > const &  residues)

References residues(), and residues_.

◆ set_temps()

void protocols::recces::scratch::ThermalSamplingMover::set_temps ( utility::vector1< core::Size > const &  temps)

References temps_.

◆ set_weights()

void protocols::recces::scratch::ThermalSamplingMover::set_weights ( utility::vector1< core::Size > const &  weights)

References st_weights_.

◆ show()

void protocols::recces::scratch::ThermalSamplingMover::show ( std::ostream &  output = std::cout) const

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

◆ angle_range_bb_

Real protocols::recces::scratch::ThermalSamplingMover::angle_range_bb_ = 60

Referenced by apply().

◆ angle_range_chi_

Real protocols::recces::scratch::ThermalSamplingMover::angle_range_chi_ = 180

Referenced by apply().

◆ angle_range_loop_bb_

Real protocols::recces::scratch::ThermalSamplingMover::angle_range_loop_bb_ = 180

Referenced by apply().

◆ dump_pdb_

bool protocols::recces::scratch::ThermalSamplingMover::dump_pdb_ = false

Referenced by apply(), and set_dump_silent().

◆ dump_silent_

bool protocols::recces::scratch::ThermalSamplingMover::dump_silent_ = false

Referenced by apply(), and set_dump_pdb().

◆ dumping_app_

bool protocols::recces::scratch::ThermalSamplingMover::dumping_app_ = false

Referenced by apply(), and set_dumping_app().

◆ free_rsd_

utility::vector1< core::Size > protocols::recces::scratch::ThermalSamplingMover::free_rsd_

◆ loop_rsd_

utility::vector1< core::Size > protocols::recces::scratch::ThermalSamplingMover::loop_rsd_

Referenced by apply().

◆ mm_

core::kinematics::MoveMapOP protocols::recces::scratch::ThermalSamplingMover::mm_

◆ n_cycle_

core::Size protocols::recces::scratch::ThermalSamplingMover::n_cycle_

Referenced by apply(), and set_n_cycle().

◆ recces_turner_mode_

bool protocols::recces::scratch::ThermalSamplingMover::recces_turner_mode_ = false

Referenced by apply(), and set_recces_turner_mode().

◆ residues_

utility::vector1< core::Size > protocols::recces::scratch::ThermalSamplingMover::residues_

◆ st_weights_

utility::vector1< Real > protocols::recces::scratch::ThermalSamplingMover::st_weights_

◆ temps_

utility::vector1< Real > protocols::recces::scratch::ThermalSamplingMover::temps_

◆ total_sampled_

core::Size protocols::recces::scratch::ThermalSamplingMover::total_sampled_

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