Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::rigid::RigidBodyTransMover Class Reference

This Mover translate down an axis. More...

#include <RigidBodyMover.hh>

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 

Public Member Functions

 RigidBodyTransMover ()
 
 RigidBodyTransMover (core::pose::Pose const &pose_in, int const rb_jump_in=1)
 
 RigidBodyTransMover (core::Vector const trans_axis, int const rb_jump_in=1)
 
virtual ~RigidBodyTransMover ()
 
 RigidBodyTransMover (RigidBodyTransMover const &src)
 
core::Vectortrans_axis ()
 
core::Vector trans_axis () const
 
void trans_axis (core::Vector trans_axis_in)
 
void step_size (core::Real step_size_in)
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
- Public Member Functions inherited from protocols::rigid::RigidBodyMover
 RigidBodyMover ()
 
 RigidBodyMover (int const rb_jump_in, Direction dir_in=n2c)
 
 RigidBodyMover (RigidBodyMover const &src)
 
virtual ~RigidBodyMover ()
 
void rot_center (core::Vector const rot_center_in)
 Manual override of rotation center. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual bool preserve_detailed_balance () const
 Return true if detailed balance is being preserved (i.e. no branch angle optimization). More...
 
virtual void set_preserve_detailed_balance (bool)
 set whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...
 
virtual utility::vector1
< core::id::TorsionID_Range
torsion_id_ranges (core::pose::Pose &pose)
 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...
 
virtual ~ThermodynamicMover ()
 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...
 
virtual core::Real last_proposal_density_ratio ()
 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_temperature_delta ()
 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 ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
std::string const & type () const
 
void set_type (std::string const &setting)
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

core::Vector centroid_axis (core::pose::Pose const &pose_in) const
 

Private Attributes

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

This Mover translate down an axis.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::rigid::RigidBodyTransMover::RigidBodyTransMover ( )

References protocols::moves::Mover::type().

Referenced by clone(), and fresh_instance().

protocols::rigid::RigidBodyTransMover::RigidBodyTransMover ( core::pose::Pose const &  pose_in,
int const  rb_jump_in = 1 
)
protocols::rigid::RigidBodyTransMover::RigidBodyTransMover ( core::Vector const  trans_axis,
int const  rb_jump_in = 1 
)
protocols::rigid::RigidBodyTransMover::~RigidBodyTransMover ( )
virtual
protocols::rigid::RigidBodyTransMover::RigidBodyTransMover ( RigidBodyTransMover const &  src)

Member Function Documentation

void protocols::rigid::RigidBodyTransMover::apply ( core::pose::Pose pose)
virtual

Implements protocols::rigid::RigidBodyMover.

References centroid_axis(), core::pose::Pose::conformation(), numeric::xyzVector< class >::is_zero(), core::pose::Pose::jump(), protocols::rigid::RigidBodyMover::rb_jump_, core::pose::Pose::set_jump(), step_size_, trans_axis_, core::kinematics::Jump::translation_along_axis(), protocols::rigid::TRBM, and core::conformation::Conformation::upstream_jump_stub().

Referenced by protocols::ligand_docking::append_interface_deltas(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::docking::EllipsoidalRandomizationMover::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::rigid::UniformSphereTransMover::apply(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::NonSequentialNeighborsFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::protein_interface_design::filters::InterfaceHolesFilter::compute(), protocols::simple_filters::DdgFilter::compute(), protocols::hotspot_hashing::HotspotStubSet::generate_unbound_pose_(), protocols::ligand_docking::LigandBaseProtocol::move_ligand_to_desired_centroid(), protocols::ligand_docking::move_ligand_to_desired_centroid(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::protein_interface_design::movers::part_complex(), protocols::surface_docking::FullatomRelaxMover::reposition_above_surface(), protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface(), protocols::simple_filters::RelativePoseFilter::thread_seq(), protocols::protein_interface_design::filters::BindingStrainFilter::unbind(), protocols::simple_moves::ddG::unbind(), protocols::simple_filters::DeltaFilter::unbind(), and protocols::protein_interface_design::filters::FilterScanFilter::unbind().

core::Vector protocols::rigid::RigidBodyTransMover::centroid_axis ( core::pose::Pose const &  pose_in) const
private
moves::MoverOP protocols::rigid::RigidBodyTransMover::clone ( ) const
virtual

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.

References RigidBodyTransMover().

moves::MoverOP protocols::rigid::RigidBodyTransMover::fresh_instance ( ) const
virtual

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.

References RigidBodyTransMover().

std::string protocols::rigid::RigidBodyTransMover::get_name ( ) const
virtual

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

Reimplemented from protocols::rigid::RigidBodyMover.

void protocols::rigid::RigidBodyTransMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References protocols::rigid::RigidBodyMover::rb_jump(), step_size(), and trans_axis().

void protocols::rigid::RigidBodyTransMover::step_size ( core::Real  step_size_in)
inline

References step_size_.

Referenced by protocols::ligand_docking::append_interface_deltas(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::docking::EllipsoidalRandomizationMover::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::rigid::UniformSphereTransMover::apply(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::NonSequentialNeighborsFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::protein_interface_design::filters::InterfaceHolesFilter::compute(), protocols::simple_filters::DdgFilter::compute(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::hotspot_hashing::HotspotStubSet::generate_unbound_pose_(), protocols::ligand_docking::LigandBaseProtocol::move_ligand_to_desired_centroid(), protocols::ligand_docking::move_ligand_to_desired_centroid(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), parse_my_tag(), protocols::protein_interface_design::movers::part_complex(), protocols::surface_docking::FullatomRelaxMover::reposition_above_surface(), protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::separate_protein_and_ligand(), protocols::surface_docking::SurfaceDockingProtocol::setup_slide_movers(), protocols::simple_filters::RelativePoseFilter::thread_seq(), protocols::protein_interface_design::filters::BindingStrainFilter::unbind(), protocols::simple_moves::ddG::unbind(), protocols::simple_filters::DeltaFilter::unbind(), and protocols::protein_interface_design::filters::FilterScanFilter::unbind().

core::Vector& protocols::rigid::RigidBodyTransMover::trans_axis ( )
inline
core::Vector protocols::rigid::RigidBodyTransMover::trans_axis ( ) const
inline

References trans_axis_.

void protocols::rigid::RigidBodyTransMover::trans_axis ( core::Vector  trans_axis_in)
inline

References trans_axis_.

Member Data Documentation

core::Real protocols::rigid::RigidBodyTransMover::step_size_
private
core::Vector protocols::rigid::RigidBodyTransMover::trans_axis_
private

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