Public Types | Public Member Functions | Private Attributes | List of all members
protocols::rigid::RigidBodyDofSeqTransMover Class Reference

A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a selected jump. Jumps are visited in random order. More...

#include <RigidBodyMover.hh>

Inheritance diagram for protocols::rigid::RigidBodyDofSeqTransMover:
Inheritance graph

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

 RigidBodyDofSeqTransMover ()
 RigidBodyDofSeqTransMover (std::map< core::Size, core::conformation::symmetry::SymDof > dofs)
 RigidBodyDofSeqTransMover (RigidBodyDofSeqTransMover const &)
 ~RigidBodyDofSeqTransMover () override
core::Vectortrans_axis ()
core::Vector trans_axis () const
void trans_axis (core::Vector trans_axis_in)
void step_size (core::Real step_size_in)
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...
- 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...
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. 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_Rangetorsion_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_Rangedof_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 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...

Private Attributes

std::map< core::Size, core::conformation::symmetry::SymDofdofs_
utility::vector1< int > rb_jumps_
core::Real step_size_
core::Vector trans_axis_

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...
- 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_

Detailed Description

A Mover that translates down an axis determined by the available DOFs. Translations are made along all allowed directions (x,y or z) for a selected jump. Jumps are visited in random order.

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ RigidBodyDofSeqTransMover() [1/3]

protocols::rigid::RigidBodyDofSeqTransMover::RigidBodyDofSeqTransMover ( )

◆ RigidBodyDofSeqTransMover() [2/3]

protocols::rigid::RigidBodyDofSeqTransMover::RigidBodyDofSeqTransMover ( std::map< core::Size, core::conformation::symmetry::SymDof dofs)

◆ RigidBodyDofSeqTransMover() [3/3]

protocols::rigid::RigidBodyDofSeqTransMover::RigidBodyDofSeqTransMover ( RigidBodyDofSeqTransMover const &  )

◆ ~RigidBodyDofSeqTransMover()

protocols::rigid::RigidBodyDofSeqTransMover::~RigidBodyDofSeqTransMover ( )

Member Function Documentation

◆ apply()

void protocols::rigid::RigidBodyDofSeqTransMover::apply ( core::pose::Pose )

◆ get_name()

std::string protocols::rigid::RigidBodyDofSeqTransMover::get_name ( ) const

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

Reimplemented from protocols::rigid::RigidBodyMover.

◆ step_size()

void protocols::rigid::RigidBodyDofSeqTransMover::step_size ( core::Real  step_size_in)

◆ trans_axis() [1/3]

core::Vector& protocols::rigid::RigidBodyDofSeqTransMover::trans_axis ( )

◆ trans_axis() [2/3]

core::Vector protocols::rigid::RigidBodyDofSeqTransMover::trans_axis ( ) const

References trans_axis_.

◆ trans_axis() [3/3]

void protocols::rigid::RigidBodyDofSeqTransMover::trans_axis ( core::Vector  trans_axis_in)

References trans_axis_.

Member Data Documentation

◆ dofs_

std::map< core::Size, core::conformation::symmetry::SymDof > protocols::rigid::RigidBodyDofSeqTransMover::dofs_

Referenced by apply(), and RigidBodyDofSeqTransMover().

◆ rb_jumps_

utility::vector1< int > protocols::rigid::RigidBodyDofSeqTransMover::rb_jumps_

Referenced by apply(), and RigidBodyDofSeqTransMover().

◆ step_size_

core::Real protocols::rigid::RigidBodyDofSeqTransMover::step_size_

◆ trans_axis_

core::Vector protocols::rigid::RigidBodyDofSeqTransMover::trans_axis_

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