A mover that makes independent random perturbations of the phi and psi torsion angles of residue i. It selects residue i at random among movable residues (set by its MoveMap), and the final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified. More...
#include <BackboneMover.hh>
Public Member Functions | |
| SmallMover () | |
| SmallMover (core::kinematics::MoveMapOP movemap_in, core::Real temperature_in, core::Size nmoves_in) | |
| Constructs a SmallMover smallmover = SmallMover( movemap , kT , n_moves ) More... | |
| ~SmallMover () override | |
| protocols::moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| void | setup_list (core::pose::Pose &pose) override |
| void | set_angles (core::Real angle_in) override |
| utility::vector1< core::id::TorsionID_Range > | torsion_id_ranges (core::pose::Pose &pose) override |
| get the TorsionIDs perturbed by the mover during moves, along with their ranges More... | |
| utility::vector1< core::id::DOF_ID_Range > | dof_id_ranges (core::pose::Pose &pose) override |
| get the DOF_IDs perturbed by the mover during moves, along with their ranges More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
 Public Member Functions inherited from protocols::simple_moves::BackboneMover | |
| BackboneMover () | |
| BackboneMover (core::kinematics::MoveMapOP movemap_in, core::Real temperature_in, core::Size nmoves_in) | |
| BackboneMover (BackboneMover const &src) | |
| Copy constructor. More... | |
| ~BackboneMover () override | |
| void | apply (core::pose::Pose &) override |
| Main Method. More... | |
| void | show (std::ostream &output=std::cout) const override |
| Outputs details about the Mover, including current settings. More... | |
| bool | make_move (core::pose::Pose &) |
| void | test_move (core::pose::Pose &) override |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| void | clear () |
| bool | check_rama () |
| void | temperature (core::Real const temperature_in) |
| core::Real | temperature () const |
| void | nmoves (core::Size const nmoves_in) |
| core::Size | nmoves () const |
| void | movemap (core::kinematics::MoveMapOP new_movemap) |
| void | movemap_factory (core::select::movemap::MoveMapFactoryCOP new_movemap_factory) |
| core::kinematics::MoveMapCOP | movemap (core::pose::Pose const &pose) |
| Get the movemap for this pose. More... | |
| core::select::residue_selector::ResidueSelectorCOP | selector () const |
| Return the residue selector that can be used to dynamically select residues to perturb at runtime. More... | |
| void | selector (core::select::residue_selector::ResidueSelectorCOP selector) |
| core::scoring::ScoreFunctionOP | scorefxn () const |
| If set, this scorefunction will be used instead of the original rama method (default = not set). More... | |
| void | scorefxn (core::scoring::ScoreFunctionOP sfxn) |
| void | angle_max (core::Real const angle) |
| Set the maximum angle of perturbation, independent of secondary structure. new_angle = old_angle +/- ( angle_max/2 ) More... | |
| void | angle_max (char const type, core::Real const angle) |
| Sets the max angle of perturbation for residues with <type> secondary structure. (<type> must be 'H', 'E', or 'L'.) new_angle = old_angle +/- ( angle_max/2 ) More... | |
| void | angle_max (std::map< char, core::Real > angle_max_in) |
| Sets the max angle of perturbation, for secondary structures 'H', 'E', and 'L'. new_angle = old_angle +/- ( angle_max/2 ) More... | |
| core::Real | get_angle_max (char const type) const |
| Gets the max angle of perturbation for residues with <type> secondary structure. (<type> must be 'H', 'E', or 'L'.) More... | |
| void | set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector) |
| Set the ResidueSelector that this mover will use. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| bool | preserve_detailed_balance () const override |
| get whether detailed balance is preserved (i.e. no Ramachandran biasing) More... | |
| void | set_preserve_detailed_balance (bool preserve_detailed_balance) override |
| set whether detailed balance is preserved (i.e. no Ramachandran biasing) More... | |
| void | set_warn_empty_list (bool warn_empty) |
| Set to warn of an empty setup list. Default true. More... | |
| Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover | |
| ThermodynamicMover () | |
| Default constructor. More... | |
| ~ThermodynamicMover () override | |
| Default destructor. More... | |
| virtual void | initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle) |
| Callback executed before any Monte Carlo trials are attempted. More... | |
| virtual void | observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover) |
| Callback executed after the Metropolis criterion is evaluated. More... | |
| core::Real | last_proposal_density_ratio () override |
| Return the proposal density ratio for last apply method. More... | |
| virtual void | finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover) |
| Callback executed after all Monte Carlo trials are completed. More... | |
| virtual bool | is_multi_trial () |
| Return true if the move performs multiple trials on each apply. More... | |
| virtual core::Real | last_inner_score_delta_over_temperature () |
| If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More... | |
| virtual protocols::canonical_sampling::MetropolisHastingsMoverAP | metropolis_hastings_mover () |
| If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More... | |
| virtual void | set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover) |
| If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. 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 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 | 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::simple_moves::BackboneMover | |
| static utility::tag::XMLSchemaComplexTypeGeneratorOP | complex_type_generator_for_backbone_mover (utility::tag::XMLSchemaDefinition &xsd) |
| static std::string | backbone_mover_complex_type_namer (std::string tag_name) |
| 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 Member Functions | |
| bool | move_with_scorefxn (core::pose::Pose &pose) override |
| bool | move_with_rama (core::pose::Pose &pose) override |
Additional Inherited Members | |
| Public Types inherited from protocols::simple_moves::BackboneMover | |
| typedef core::Real | Real |
| 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::simple_moves::BackboneMover | |
| core::select::residue_selector::ResidueSubset | compute_selected_residues (core::pose::Pose const &pose) const |
| Set the ResidueSelector that this mover will use. More... | |
| utility::vector1< core::id::TorsionID > | get_mainchain_TorsionIDs (core::conformation::Conformation const &conf, core::uint const seqpos) const |
| Return a list of TorsionIDs for the standard main-chain torsions of this residue. More... | |
| bool | are_torsions_allowed (utility::vector1< core::id::TorsionID > torsions, core::kinematics::MoveMapCOP mm) const |
| Is this set of torsions allowed to move by the MoveMap? More... | |
| 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... | |
| Protected Attributes inherited from protocols::simple_moves::BackboneMover | |
| std::map< char, core::Real > | angle_max_ |
| core::uint | resnum_ |
| core::Real | big_angle_ |
| core::Real | small_angle_ |
| utility::vector1< core::id::TorsionID > | moving_torsions_ |
| utility::vector1< std::tuple< core::uint, utility::vector1< core::id::TorsionID >, core::Real > > | move_pos_list_ |
| core::Real | old_rama_score_ |
| core::Real | new_rama_score_ |
Detailed Description
A mover that makes independent random perturbations of the phi and psi torsion angles of residue i. It selects residue i at random among movable residues (set by its MoveMap), and the final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified.
Common Methods: SmallMover.apply SmallMover.angle_max
Constructor & Destructor Documentation
◆ SmallMover() [1/2]
| protocols::simple_moves::SmallMover::SmallMover | ( | ) |
References protocols::moves::Mover::type().
◆ SmallMover() [2/2]
| protocols::simple_moves::SmallMover::SmallMover | ( | core::kinematics::MoveMapOP | movemap_in, |
| core::Real | temperature_in, | ||
| core::Size | nmoves_in | ||
| ) |
Constructs a SmallMover smallmover = SmallMover( movemap , kT , n_moves )
MoveMap movemap /object storing BB torsion movability Real (float) kT /used in rama Metropolis Criterion core::Size (int) n_moves /the number of perturbations for one move
References protocols::moves::Mover::type().
◆ ~SmallMover()
|
overridedefault |
Member Function Documentation
◆ clone()
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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.
◆ dof_id_ranges()
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overridevirtual |
get the DOF_IDs perturbed by the mover during moves, along with their ranges
Implements protocols::simple_moves::BackboneMover.
References core::id::BB, protocols::simple_moves::BackboneMover::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::dof_id_from_torsion_id(), protocols::simple_moves::BackboneMover::move_pos_list_, core::id::phi_torsion(), core::id::psi_torsion(), setup_list(), and core::id::DOF_ID::valid().
◆ fresh_instance()
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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.
◆ get_name()
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overridevirtual |
Each derived class must specify its name. The class name.
Reimplemented from protocols::simple_moves::BackboneMover.
References mover_name().
◆ move_with_rama()
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overrideprivatevirtual |
Implements protocols::simple_moves::BackboneMover.
References core::conformation::Residue::aa(), core::chemical::aa_unk, protocols::simple_moves::BackboneMover::big_angle_, protocols::simple_moves::BackboneMover::check_rama(), core::chemical::ResidueType::is_oligourea(), core::conformation::Residue::is_protein(), protocols::simple_moves::BackboneMover::moving_torsions_, protocols::simple_moves::BackboneMover::new_rama_score_, protocols::simple_moves::BackboneMover::old_rama_score_, core::id::phi_torsion(), core::id::psi_torsion(), core::scoring::rama, core::pose::Pose::residue(), protocols::simple_moves::BackboneMover::resnum_, core::scoring::rg, core::pose::Pose::set_torsion(), protocols::simple_moves::BackboneMover::small_angle_, core::pose::Pose::torsion(), and core::conformation::Residue::type().
◆ move_with_scorefxn()
|
overrideprivatevirtual |
Implements protocols::simple_moves::BackboneMover.
References protocols::simple_moves::BackboneMover::big_angle_, protocols::simple_moves::BackboneMover::check_rama(), protocols::simple_moves::BackboneMover::moving_torsions_, protocols::simple_moves::BackboneMover::new_rama_score_, protocols::simple_moves::BackboneMover::old_rama_score_, core::scoring::rg, protocols::simple_moves::BackboneMover::scorefxn(), core::pose::Pose::set_torsion(), protocols::simple_moves::BackboneMover::small_angle_, protocols::simple_moves::BackboneMover::temperature(), core::pose::Pose::torsion(), and protocols::simple_moves::TR().
◆ mover_name()
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static |
Referenced by get_name(), protocols::simple_moves::SmallMoverCreator::keyname(), and provide_xml_schema().
◆ provide_xml_schema()
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static |
◆ set_angles()
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overridevirtual |
◆ setup_list()
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overridevirtual |
Implements protocols::simple_moves::BackboneMover.
References protocols::simple_moves::BackboneMover::angle_max_, protocols::simple_moves::BackboneMover::are_torsions_allowed(), protocols::simple_moves::BackboneMover::compute_selected_residues(), core::pose::Pose::conformation(), protocols::simple_moves::BackboneMover::get_mainchain_TorsionIDs(), protocols::simple_moves::BackboneMover::move_pos_list_, protocols::simple_moves::BackboneMover::movemap(), core::pose::Pose::secstruct(), and core::pose::Pose::size().
Referenced by dof_id_ranges().
◆ torsion_id_ranges()
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overridevirtual |
get the TorsionIDs perturbed by the mover during moves, along with their ranges
Implements protocols::canonical_sampling::ThermodynamicMover.
The documentation for this class was generated from the following files:
- src/protocols/simple_moves/BackboneMover.hh
- src/protocols/simple_moves/BackboneMover.cc
