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protocols::rigid::RigidBodyPerturbMover Class Reference

This Mover does a perturbation defined by the rotational and translational magnitudes. More...

#include <RigidBodyMover.hh>

Inheritance diagram for protocols::rigid::RigidBodyPerturbMover:
Inheritance graph
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Public Types

typedef RigidBodyMover parent
 
- Public Types inherited from protocols::rigid::RigidBodyMover
typedef ThermodynamicMover parent
 
- 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
 

Public Member Functions

 RigidBodyPerturbMover ()
 
 RigidBodyPerturbMover (int const rb_jump_in, core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in=partner_downstream, bool interface_in=false)
 
 RigidBodyPerturbMover (int const rb_jump_in, core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in, utility::vector1< bool > const &ok_for_centroid_calculation)
 
 RigidBodyPerturbMover (core::pose::Pose const &pose_in, core::kinematics::MoveMap const &mm, core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in=partner_downstream, bool interface_in=false)
 
 RigidBodyPerturbMover (core::Real const rot_mag_in, core::Real const trans_mag_in, Partner const partner_in=partner_downstream, bool interface_in=false)
 
 RigidBodyPerturbMover (RigidBodyPerturbMover const &)
 
 ~RigidBodyPerturbMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
void rot_magnitude (core::Real const magnitude)
 
void trans_magnitude (core::Real const magnitude)
 
core::Distance get_trans_mag () const
 
core::Angle get_rot_mag () const
 
void rot_center (core::Vector const &)
 Manual override of rotation center. More...
 
- Public Member Functions inherited from protocols::rigid::RigidBodyMover
 RigidBodyMover ()
 
 RigidBodyMover (int const rb_jump_in, Direction dir_in=n2c)
 
 RigidBodyMover (RigidBodyMover const &src)
 
 ~RigidBodyMover () override
 
void rot_center (core::Vector const &rot_center_in)
 Manual override of rotation center. More...
 
bool preserve_detailed_balance () const override
 Return true if detailed balance is being preserved (i.e. no branch angle optimization). More...
 
void set_preserve_detailed_balance (bool) override
 set whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...
 
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...
 
int rb_jump () const
 
void rb_jump (int jump_id)
 
void unfreeze ()
 
void freeze ()
 
- 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...
 
virtual utility::vector1
< core::id::DOF_ID_Range
dof_id_ranges (core::pose::Pose &pose)
 Return a list specifying which degrees of freedom may be perturbed by apply(), and the in what range each perturbation may be. 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 

Protected Attributes

core::Real rot_mag_
 
core::Real trans_mag_
 
utility::vector1< core::Realrb_delta_
 
- Protected Attributes inherited from protocols::rigid::RigidBodyMover
int rb_jump_
 
Direction dir_
 direction of folding (n-term to c-term) More...
 
core::Vector rot_center_
 center of rotation More...
 
bool freeze_
 

Private Attributes

Partner partner_
 
bool interface_
 
utility::vector1< core::Sizemovable_jumps_
 
utility::vector1< boolok_for_centroid_calculation_
 

Additional Inherited Members

- 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...
 
- 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

This Mover does a perturbation defined by the rotational and translational magnitudes.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover ( )
protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover ( int const  rb_jump_in,
core::Real const  rot_mag_in,
core::Real const  trans_mag_in,
Partner const  partner_in = partner_downstream,
bool  interface_in = false 
)
protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover ( int const  rb_jump_in,
core::Real const  rot_mag_in,
core::Real const  trans_mag_in,
Partner const  partner_in,
utility::vector1< bool > const &  ok_for_centroid_calculation 
)
protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover ( core::pose::Pose const &  pose_in,
core::kinematics::MoveMap const &  mm,
core::Real const  rot_mag_in,
core::Real const  trans_mag_in,
Partner const  partner_in = partner_downstream,
bool  interface_in = false 
)
protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover ( core::Real const  rot_mag_in,
core::Real const  trans_mag_in,
Partner const  partner_in = partner_downstream,
bool  interface_in = false 
)
protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover ( RigidBodyPerturbMover const &  src)
protocols::rigid::RigidBodyPerturbMover::~RigidBodyPerturbMover ( )
overridedefault

Member Function Documentation

void protocols::rigid::RigidBodyPerturbMover::apply ( core::pose::Pose )
overridevirtual
std::string protocols::rigid::RigidBodyPerturbMover::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::rigid::RigidBodyMover.

core::Angle protocols::rigid::RigidBodyPerturbMover::get_rot_mag ( ) const

References rot_mag_.

Referenced by show().

core::Distance protocols::rigid::RigidBodyPerturbMover::get_trans_mag ( ) const

References trans_mag_.

Referenced by show().

void protocols::rigid::RigidBodyPerturbMover::rot_center ( core::Vector const &  )

Manual override of rotation center.

void protocols::rigid::RigidBodyPerturbMover::rot_magnitude ( core::Real const  magnitude)
inline
void protocols::rigid::RigidBodyPerturbMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::rigid::RigidBodyMover.

References get_rot_mag(), get_trans_mag(), and protocols::rigid::RigidBodyMover::show().

Referenced by protocols::rigid::operator<<().

void protocols::rigid::RigidBodyPerturbMover::trans_magnitude ( core::Real const  magnitude)
inline

Member Data Documentation

bool protocols::rigid::RigidBodyPerturbMover::interface_
private

Referenced by apply().

utility::vector1<core::Size> protocols::rigid::RigidBodyPerturbMover::movable_jumps_
private

Referenced by apply(), and RigidBodyPerturbMover().

utility::vector1< bool > protocols::rigid::RigidBodyPerturbMover::ok_for_centroid_calculation_
private

Referenced by apply().

Partner protocols::rigid::RigidBodyPerturbMover::partner_
private

Referenced by apply().

utility::vector1<core::Real> protocols::rigid::RigidBodyPerturbMover::rb_delta_
protected

Referenced by apply().

core::Real protocols::rigid::RigidBodyPerturbMover::rot_mag_
protected
core::Real protocols::rigid::RigidBodyPerturbMover::trans_mag_
protected

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