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protocols::ligand_docking::RigidSearchMover Class Reference

An optimized mover for Monte Carlo trial of rigid body perturbations. More...

#include <RigidSearchMover.hh>

Inheritance diagram for protocols::ligand_docking::RigidSearchMover:
Inheritance graph
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Public Member Functions

 RigidSearchMover (int jump_id, int num_trials, core::scoring::ScoreFunctionCOP scorefxn)
 
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...
 
bool recover_low () const
 Will the absolute lowest-energy pose be recovered at the end of apply()? More...
 
void recover_low (bool b)
 Should the absolute lowest-energy pose be recovered at the end of apply()? More...
 
core::Real translation () const
 Amount of random (Gaussian) translation, in Angstroms. More...
 
void translation (core::Real angstroms)
 Amount of random (Gaussian) translation, in Angstroms. More...
 
core::Real rotation () const
 Amount of random (Gaussian) rotation, in degrees. More...
 
void rotation (core::Real degrees)
 Amount of random (Gaussian) rotation, in degrees. More...
 
void rotate_around_downstream_centroid ()
 Rotation occurs around centroid of downstream half of the jump (default) More...
 
void rotate_around_atom (core::Size rsd, core::Size atom)
 Rotation occurs around the specified atom. 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 show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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

int jump_id_
 
int num_trials_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
core::Real temperature_
 
core::Real rotate_deg_
 
core::Real translate_Ang_
 
core::Size rotate_rsd_
 
core::Size rotate_atom_
 
bool recover_low_
 

Additional Inherited Members

- 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
 
- 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

An optimized mover for Monte Carlo trial of rigid body perturbations.

Constructor & Destructor Documentation

protocols::ligand_docking::RigidSearchMover::RigidSearchMover ( int  jump_id,
int  num_trials,
core::scoring::ScoreFunctionCOP  scorefxn 
)

Member Function Documentation

void protocols::ligand_docking::RigidSearchMover::apply ( core::pose::Pose )
overridevirtual
std::string protocols::ligand_docking::RigidSearchMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

bool protocols::ligand_docking::RigidSearchMover::recover_low ( ) const
inline

Will the absolute lowest-energy pose be recovered at the end of apply()?

References recover_low_.

void protocols::ligand_docking::RigidSearchMover::recover_low ( bool  b)
inline

Should the absolute lowest-energy pose be recovered at the end of apply()?

References protocols::match::upstream::b, and recover_low_.

void protocols::ligand_docking::RigidSearchMover::rotate_around_atom ( core::Size  rsd,
core::Size  atom 
)
inline

Rotation occurs around the specified atom.

References rotate_atom_, and rotate_rsd_.

void protocols::ligand_docking::RigidSearchMover::rotate_around_downstream_centroid ( )
inline

Rotation occurs around centroid of downstream half of the jump (default)

References rotate_atom_, and rotate_rsd_.

core::Real protocols::ligand_docking::RigidSearchMover::rotation ( ) const
inline

Amount of random (Gaussian) rotation, in degrees.

References rotate_deg_.

void protocols::ligand_docking::RigidSearchMover::rotation ( core::Real  degrees)
inline

Amount of random (Gaussian) rotation, in degrees.

References rotate_deg_.

core::Real protocols::ligand_docking::RigidSearchMover::translation ( ) const
inline

Amount of random (Gaussian) translation, in Angstroms.

References translate_Ang_.

void protocols::ligand_docking::RigidSearchMover::translation ( core::Real  angstroms)
inline

Amount of random (Gaussian) translation, in Angstroms.

References translate_Ang_.

Member Data Documentation

int protocols::ligand_docking::RigidSearchMover::jump_id_
private

Referenced by apply().

int protocols::ligand_docking::RigidSearchMover::num_trials_
private

Referenced by apply().

bool protocols::ligand_docking::RigidSearchMover::recover_low_
private

Referenced by apply(), and recover_low().

core::Size protocols::ligand_docking::RigidSearchMover::rotate_atom_
private
core::Real protocols::ligand_docking::RigidSearchMover::rotate_deg_
private

Referenced by apply(), and rotation().

core::Size protocols::ligand_docking::RigidSearchMover::rotate_rsd_
private
core::scoring::ScoreFunctionCOP protocols::ligand_docking::RigidSearchMover::scorefxn_
private

Referenced by apply().

core::Real protocols::ligand_docking::RigidSearchMover::temperature_
private

Referenced by apply().

core::Real protocols::ligand_docking::RigidSearchMover::translate_Ang_
private

Referenced by apply(), and translation().


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