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protocols::rigid::RigidBodyTransMover Class Reference

This Mover translate down an axis. More...

#include <RigidBodyMover.hh>

Inheritance diagram for protocols::rigid::RigidBodyTransMover:
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

 RigidBodyTransMover (bool vary_stepsize=false)
 
 RigidBodyTransMover (core::pose::Pose const &pose_in, int const rb_jump_in=1, bool vary_stepsize=false)
 
 RigidBodyTransMover (core::Vector const &trans_axis, int const rb_jump_in=1, bool vary_stepsize=false)
 
 ~RigidBodyTransMover () override
 
 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)
 
core::Real step_size ()
 
void vary_stepsize (bool vary)
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 
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_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 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::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

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

Private Attributes

core::Real step_size_
 
core::Vector trans_axis_
 
bool vary_stepsize_
 

Additional Inherited Members

- 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 ( bool  vary_stepsize = false)
protocols::rigid::RigidBodyTransMover::RigidBodyTransMover ( core::pose::Pose const &  pose_in,
int const  rb_jump_in = 1,
bool  vary_stepsize = false 
)
protocols::rigid::RigidBodyTransMover::RigidBodyTransMover ( core::Vector const &  trans_axis,
int const  rb_jump_in = 1,
bool  vary_stepsize = false 
)
protocols::rigid::RigidBodyTransMover::~RigidBodyTransMover ( )
overridedefault
protocols::rigid::RigidBodyTransMover::RigidBodyTransMover ( RigidBodyTransMover const &  src)
default

Member Function Documentation

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

Main Method.

Implements protocols::rigid::RigidBodyMover.

References centroid_axis(), core::pose::Pose::conformation(), core::kinematics::distance(), 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(), core::conformation::Conformation::upstream_jump_stub(), and vary_stepsize_.

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::docking::EllipsoidalRandomizationMover::apply(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::rigid::UniformSphereTransMover::apply(), protocols::simple_filters::NonSequentialNeighborsFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::hotspot_hashing::HotspotStubSet::generate_unbound_pose_(), protocols::ligand_docking::get_interface_deltas(), protocols::nmr::pcs::PCSLigandTransformMover::move_ligand_close_to_surface(), protocols::ligand_docking::move_ligand_neighbor_to_desired_position(), protocols::ligand_docking::move_ligand_to_desired_centroid(), protocols::ligand_docking::LigandBaseProtocol::move_ligand_to_desired_centroid(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::surface_docking::FullatomRelaxMover::reposition_above_surface(), protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), protocols::protein_interface_design::filters::BindingStrainFilter::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
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.

moves::MoverOP protocols::rigid::RigidBodyTransMover::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::rigid::RigidBodyTransMover::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::rigid::RigidBodyMover.

References mover_name().

std::string protocols::rigid::RigidBodyTransMover::mover_name ( )
static
void protocols::rigid::RigidBodyTransMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

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

void protocols::rigid::RigidBodyTransMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::rigid::RigidBodyTransMover::step_size ( core::Real  step_size_in)
inline

References step_size_.

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::docking::EllipsoidalRandomizationMover::apply(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::rigid::UniformSphereTransMover::apply(), protocols::simple_filters::NonSequentialNeighborsFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::hotspot_hashing::HotspotStubSet::generate_unbound_pose_(), protocols::ligand_docking::get_interface_deltas(), protocols::nmr::pcs::PCSLigandTransformMover::move_ligand_close_to_surface(), protocols::ligand_docking::move_ligand_neighbor_to_desired_position(), protocols::ligand_docking::move_ligand_to_desired_centroid(), protocols::ligand_docking::LigandBaseProtocol::move_ligand_to_desired_centroid(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::surface_docking::FullatomRelaxMover::reposition_above_surface(), protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::separate_protein_and_ligand(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), protocols::protein_interface_design::filters::BindingStrainFilter::unbind(), protocols::simple_filters::DeltaFilter::unbind(), and protocols::protein_interface_design::filters::FilterScanFilter::unbind().

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

References step_size_.

Referenced by parse_my_tag().

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_.

void protocols::rigid::RigidBodyTransMover::vary_stepsize ( bool  vary)
inline

References vary_stepsize_.

Referenced by RigidBodyTransMover().

Member Data Documentation

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

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