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protocols::minimization_packing::MinPackMover Class Reference

a mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing. More...

#include <MinPackMover.hh>

Inheritance diagram for protocols::minimization_packing::MinPackMover:
Inheritance graph
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Public Types

typedef
core::pack::task::PackerTaskCOP 
PackerTaskCOP
 
typedef
core::pack::task::TaskFactoryCOP 
TaskFactoryCOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
- 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

 MinPackMover ()
 default constructor More...
 
 MinPackMover (std::string const &)
 constructor with typename More...
 
 MinPackMover (ScoreFunctionCOP scorefxn)
 
 MinPackMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task)
 
 ~MinPackMover () override
 
 MinPackMover (MinPackMover const &other)
 
void init ()
 
void apply (Pose &pose) override
 Main Method. More...
 
bool task_is_valid (Pose const &pose) const
 when the PackerTask was not generated locally, verify compatibility with pose More...
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
virtual void parse_score_function (TagCOP, basic::datacache::DataMap const &)
 parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...
 
virtual void parse_task_operations (TagCOP, basic::datacache::DataMap const &)
 parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
void score_function (ScoreFunctionCOP sf)
 
void task_factory (TaskFactoryCOP tf)
 
void task (PackerTaskCOP t)
 
ScoreFunctionCOP score_function () const
 
PackerTaskCOP task () const
 
TaskFactoryCOP task_factory () const
 
void off_rotamer_pack (bool)
 
bool off_rotamer_pack () const
 
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 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 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 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 Attributes

ScoreFunctionCOP scorefxn_
 
PackerTaskCOP task_
 
TaskFactoryCOP task_factory_
 
bool off_rotamer_pack_
 
bool nonideal_
 
bool cartesian_
 

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...
 

Detailed Description

a mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::minimization_packing::MinPackMover::MinPackMover ( )

default constructor

References init().

protocols::minimization_packing::MinPackMover::MinPackMover ( std::string const &  type_name)

constructor with typename

References init().

protocols::minimization_packing::MinPackMover::MinPackMover ( ScoreFunctionCOP  scorefxn)

References init().

protocols::minimization_packing::MinPackMover::MinPackMover ( ScoreFunctionCOP  scorefxn,
PackerTaskCOP  task 
)

References init().

protocols::minimization_packing::MinPackMover::~MinPackMover ( )
overridedefault
protocols::minimization_packing::MinPackMover::MinPackMover ( MinPackMover const &  other)

Member Function Documentation

void protocols::minimization_packing::MinPackMover::apply ( Pose )
overridevirtual
protocols::moves::MoverOP protocols::minimization_packing::MinPackMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::minimization_packing::MinPackMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::minimization_packing::MinPackMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::minimization_packing::MinPackMover::init ( void  )

References cartesian_, and nonideal_.

Referenced by MinPackMover().

std::string protocols::minimization_packing::MinPackMover::mover_name ( )
static
void protocols::minimization_packing::MinPackMover::off_rotamer_pack ( bool  setting)

References off_rotamer_pack_.

bool protocols::minimization_packing::MinPackMover::off_rotamer_pack ( ) const

References off_rotamer_pack_.

void protocols::minimization_packing::MinPackMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

References cartesian_, nonideal_, off_rotamer_pack_, parse_score_function(), and parse_task_operations().

void protocols::minimization_packing::MinPackMover::parse_score_function ( TagCOP  tag,
basic::datacache::DataMap const &  datamap 
)
virtual

parse "scorefxn" XML option (can be employed virtually by derived Packing movers)

References core::scoring::parse_score_function(), and score_function().

Referenced by parse_my_tag().

void protocols::minimization_packing::MinPackMover::parse_task_operations ( TagCOP  tag,
basic::datacache::DataMap const &  datamap 
)
virtual

parse "task_operations" XML option (can be employed virtually by derived Packing movers)

References core::pack::task::parse_task_operations(), and task_factory().

Referenced by parse_my_tag().

void protocols::minimization_packing::MinPackMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::minimization_packing::MinPackMover::score_function ( ScoreFunctionCOP  sf)

References scorefxn_.

Referenced by MinPackMover().

ScoreFunctionCOP protocols::minimization_packing::MinPackMover::score_function ( ) const

References scorefxn_.

Referenced by parse_score_function().

void protocols::minimization_packing::MinPackMover::task ( PackerTaskCOP  t)

Referenced by MinPackMover().

PackerTaskCOP protocols::minimization_packing::MinPackMover::task ( ) const

References task_.

Referenced by apply().

void protocols::minimization_packing::MinPackMover::task_factory ( TaskFactoryCOP  tf)

References task_factory_.

Referenced by MinPackMover().

TaskFactoryCOP protocols::minimization_packing::MinPackMover::task_factory ( ) const

References task_factory_.

Referenced by parse_task_operations().

bool protocols::minimization_packing::MinPackMover::task_is_valid ( Pose const &  pose) const

when the PackerTask was not generated locally, verify compatibility with pose

the pose residue types must be equivalent to the ones used to generate the ResidueLevelTasks, because of the way that prevent_repacking and its associated flags work

References core::pose::Pose::residue_type_ptr(), core::pose::Pose::size(), and task_.

Referenced by apply().

Member Data Documentation

bool protocols::minimization_packing::MinPackMover::cartesian_
private
bool protocols::minimization_packing::MinPackMover::nonideal_
private
bool protocols::minimization_packing::MinPackMover::off_rotamer_pack_
private
ScoreFunctionCOP protocols::minimization_packing::MinPackMover::scorefxn_
private

Referenced by apply(), MinPackMover(), and score_function().

PackerTaskCOP protocols::minimization_packing::MinPackMover::task_
private
TaskFactoryCOP protocols::minimization_packing::MinPackMover::task_factory_
private

Referenced by apply(), MinPackMover(), and task_factory().


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