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protocols::docking::ConformerSwitchMover Class Reference

this mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction. More...

#include <ConformerSwitchMover.hh>

Inheritance diagram for protocols::docking::ConformerSwitchMover:
Inheritance graph
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Public Member Functions

 ConformerSwitchMover ()
 
 ConformerSwitchMover (protocols::docking::DockingEnsembleOP ensemble, bool random_conformer=false)
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
void switch_conformer (core::pose::Pose &pose, core::Size conf_num)
 
void set_temperature (core::Real temp_in)
 
void set_random_confomer (bool rand)
 
core::Real get_temperature () const
 
protocols::docking::DockingEnsembleOP get_ensemble ()
 
bool use_random_conformer () const
 
void set_specific_conformer (core::Size conformer_num_in)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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 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 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

void GenerateProbTable (core::pose::Pose &pose)
 

Private Attributes

bool random_conformer_
 
core::Real temperature_
 
utility::vector1< core::Realprob_table_
 
protocols::docking::DockingEnsembleOP ensemble_
 
protocols::docking::DockingLowResFilterOP lowres_filter_
 
core::Size specific_conformer_
 

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
 
- 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 the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction.

Constructor & Destructor Documentation

protocols::docking::ConformerSwitchMover::ConformerSwitchMover ( )
protocols::docking::ConformerSwitchMover::ConformerSwitchMover ( protocols::docking::DockingEnsembleOP  ensemble,
bool  random_conformer = false 
)

References ensemble_, and lowres_filter_.

Member Function Documentation

void protocols::docking::ConformerSwitchMover::apply ( core::pose::Pose )
overridevirtual
void protocols::docking::ConformerSwitchMover::GenerateProbTable ( core::pose::Pose pose)
private

References ensemble_, prob_table_, switch_conformer(), and temperature_.

Referenced by apply().

protocols::docking::DockingEnsembleOP protocols::docking::ConformerSwitchMover::get_ensemble ( )

References ensemble_.

std::string protocols::docking::ConformerSwitchMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Real protocols::docking::ConformerSwitchMover::get_temperature ( ) const
inline

References temperature_.

Referenced by show().

std::string protocols::docking::ConformerSwitchMover::mover_name ( )
static
void protocols::docking::ConformerSwitchMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::docking::ConformerSwitchMover::set_random_confomer ( bool  rand)
inline

References random_conformer_.

void protocols::docking::ConformerSwitchMover::set_specific_conformer ( core::Size  conformer_num_in)

References specific_conformer_.

void protocols::docking::ConformerSwitchMover::set_temperature ( core::Real  temp_in)

References temperature_.

void protocols::docking::ConformerSwitchMover::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::moves::Mover.

References get_temperature(), and use_random_conformer().

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

void protocols::docking::ConformerSwitchMover::switch_conformer ( core::pose::Pose pose,
core::Size  conf_num 
)
bool protocols::docking::ConformerSwitchMover::use_random_conformer ( ) const
inline

References random_conformer_.

Referenced by show().

Member Data Documentation

protocols::docking::DockingEnsembleOP protocols::docking::ConformerSwitchMover::ensemble_
private
protocols::docking::DockingLowResFilterOP protocols::docking::ConformerSwitchMover::lowres_filter_
private

Referenced by apply(), and ConformerSwitchMover().

utility::vector1< core::Real > protocols::docking::ConformerSwitchMover::prob_table_
private

Referenced by apply(), and GenerateProbTable().

bool protocols::docking::ConformerSwitchMover::random_conformer_
private
core::Size protocols::docking::ConformerSwitchMover::specific_conformer_
private

Referenced by apply(), and set_specific_conformer().

core::Real protocols::docking::ConformerSwitchMover::temperature_
private

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