Use a simulated tempering simulation to refine a pose. More...
#include <ThermalSamplingMover.hh>
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::Size > | residues () const |
| void | set_free_rsd (utility::vector1< core::Size > const &free_rsd) |
| utility::vector1< core::Size > | free_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 Strings & | info () |
| 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::Size > | residues_ |
| core::Size | total_sampled_ |
| utility::vector1< core::Size > | free_rsd_ |
| utility::vector1< core::Size > | loop_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< Real > | temps_ |
| utility::vector1< Real > | st_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
|
private |
◆ Size
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private |
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()
|
overridedefault |
Destructor (important for properly forward-declaring smart-pointer members)
Member Function Documentation
◆ apply()
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overridevirtual |
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()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ free_rsd()
|
inline |
References free_rsd_.
Referenced by set_free_rsd().
◆ fresh_instance()
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overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ get_name()
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ mover_name()
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static |
◆ parse_my_tag()
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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.
◆ provide_xml_schema()
|
static |
◆ residues()
|
inline |
References residues_.
Referenced by set_residues().
◆ set_dump_pdb()
|
inline |
References dump_silent_.
◆ set_dump_silent()
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inline |
References dump_pdb_.
◆ set_dumping_app()
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inline |
References dumping_app_.
◆ set_free_rsd()
|
inline |
References free_rsd(), and free_rsd_.
◆ set_n_cycle()
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inline |
References n_cycle_.
◆ set_recces_turner_mode()
|
inline |
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 | ||
| ) |
Sets thermal sampling level given a MoveMap.
References core::id::BB, core::chemical::rna::BETA, core::chemical::rna::DELTA, core::chemical::rna::EPSILON, free_rsd_, core::chemical::rna::GAMMA, core::kinematics::MoveMap::get(), mm_, residues_, core::pose::Pose::size(), total_sampled_, and protocols::TR().
◆ set_residues()
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inline |
References residues(), and residues_.
◆ set_temps()
|
inline |
References temps_.
◆ set_weights()
|
inline |
References st_weights_.
◆ show()
|
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
◆ angle_range_bb_
|
private |
Referenced by apply().
◆ angle_range_chi_
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private |
Referenced by apply().
◆ angle_range_loop_bb_
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private |
Referenced by apply().
◆ dump_pdb_
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private |
Referenced by apply(), and set_dump_silent().
◆ dump_silent_
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private |
Referenced by apply(), and set_dump_pdb().
◆ dumping_app_
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private |
Referenced by apply(), and set_dumping_app().
◆ free_rsd_
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private |
Referenced by apply(), free_rsd(), set_free_rsd(), and set_residue_sampling_from_pose_and_movemap().
◆ loop_rsd_
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private |
Referenced by apply().
◆ mm_
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private |
Referenced by apply(), and set_residue_sampling_from_pose_and_movemap().
◆ n_cycle_
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private |
Referenced by apply(), and set_n_cycle().
◆ recces_turner_mode_
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private |
Referenced by apply(), and set_recces_turner_mode().
◆ residues_
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private |
Referenced by apply(), residues(), set_residue_sampling_from_pose_and_movemap(), set_residues(), and ThermalSamplingMover().
◆ st_weights_
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private |
Referenced by apply(), set_weights(), and ThermalSamplingMover().
◆ temps_
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private |
Referenced by apply(), set_temps(), and ThermalSamplingMover().
◆ total_sampled_
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private |
Referenced by apply(), set_residue_sampling_from_pose_and_movemap(), and ThermalSamplingMover().
The documentation for this class was generated from the following files:
- src/protocols/recces/scratch/ThermalSamplingMover.hh
- src/protocols/recces/scratch/ThermalSamplingMover.cc
