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protocols::simple_moves::ShearMover Class Reference

A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a 'shearing' effect, minimizing the downstream consequences of this torsional perturbation. 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>

Inheritance diagram for protocols::simple_moves::ShearMover:
Inheritance graph
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Public Member Functions

 ShearMover ()
 
 ShearMover (core::kinematics::MoveMapOP movemap_in, core::Real temperature_in, core::Size nmoves_in)
 Constructs a ShearMover shearmover = ShearMover( movemap , kT , n_moves ) More...
 
 ~ShearMover () 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...
 
- 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 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::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
 
std::pair< utility::vector1
< core::id::TorsionID >
, utility::vector1
< core::id::TorsionID > > 
setup_list_for_saccharide_residue (core::pose::Pose &pose, core::uint seq_pos)
 

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::Realangle_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 perturbs the phi of residue i and the psi of residue i-1 such that they create a 'shearing' effect, minimizing the downstream consequences of this torsional perturbation. 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: ShearMover.apply

Constructor & Destructor Documentation

protocols::simple_moves::ShearMover::ShearMover ( )
protocols::simple_moves::ShearMover::ShearMover ( core::kinematics::MoveMapOP  movemap_in,
core::Real  temperature_in,
core::Size  nmoves_in 
)

Constructs a ShearMover shearmover = ShearMover( 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().

protocols::simple_moves::ShearMover::~ShearMover ( )
overridedefault

Member Function Documentation

protocols::moves::MoverOP protocols::simple_moves::ShearMover::clone ( ) const
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.

utility::vector1< core::id::DOF_ID_Range > protocols::simple_moves::ShearMover::dof_id_ranges ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::simple_moves::ShearMover::fresh_instance ( ) const
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.

std::string protocols::simple_moves::ShearMover::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::simple_moves::BackboneMover.

References mover_name().

bool protocols::simple_moves::ShearMover::move_with_rama ( core::pose::Pose pose)
overrideprivatevirtual
bool protocols::simple_moves::ShearMover::move_with_scorefxn ( core::pose::Pose pose)
overrideprivatevirtual
std::string protocols::simple_moves::ShearMover::mover_name ( )
static
void protocols::simple_moves::ShearMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_moves::ShearMover::set_angles ( core::Real  angle_in)
overridevirtual
void protocols::simple_moves::ShearMover::setup_list ( core::pose::Pose pose)
overridevirtual
std::pair< utility::vector1< core::id::TorsionID >, utility::vector1< core::id::TorsionID > > protocols::simple_moves::ShearMover::setup_list_for_saccharide_residue ( core::pose::Pose pose,
core::uint  seq_pos 
)
private
utility::vector1< core::id::TorsionID_Range > protocols::simple_moves::ShearMover::torsion_id_ranges ( core::pose::Pose pose)
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: