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protocols::enzdes::EnzRepackMinimize Class Reference

#include <EnzRepackMinimize.hh>

Inheritance diagram for protocols::enzdes::EnzRepackMinimize:
Inheritance graph
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Public Member Functions

 EnzRepackMinimize ()
 
 EnzRepackMinimize (std::string const &name)
 
 ~EnzRepackMinimize () override
 
void ensure_scofx_cstfication (core::pose::Pose const &pose)
 turns on constraint score terms in case the pose has an enzdes cst cache More...
 
void minimize_in_stages (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool const &cstopt, bool const &min_sc, bool const &min_rb, bool const &min_lig)
 
void apply (core::pose::Pose &pose) override
 Main Method. 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...
 
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...
 
utility::vector1< core::Sizerb_min_jumps () const
 
void rb_min_jumps (utility::vector1< core::Size > const )
 
void set_min_rb (bool const min_rb)
 
bool get_min_rb () const
 
void set_min_sc (bool const min_sc)
 
bool get_min_sc () const
 
void set_min_lig (bool const min_lig)
 
bool get_min_lig () const
 
void set_min_bb (bool const min_bb)
 
bool get_min_bb () const
 
bool get_design () const
 
void set_design (bool const des)
 
void set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)
 
core::scoring::ScoreFunctionOP scorefxn_repack () const
 
core::scoring::ScoreFunctionOP scorefxn_minimize () const
 
core::pack::task::PackerTaskOP create_ptask (core::pose::Pose &pose)
 
void task_factory (core::pack::task::TaskFactoryOP p)
 
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

core::scoring::ScoreFunctionOP scorefxn_repack_
 
core::scoring::ScoreFunctionOP scorefxn_minimize_
 
bool cst_opt_
 
bool design_
 
bool repack_
 
bool fix_catalytic_
 
bool minimize_in_stages_
 
bool min_rb_
 
bool min_sc_
 
bool min_bb_
 
bool min_lig_
 
bool minimize_prot_jumps_
 
bool backrub_
 
core::pack::task::PackerTaskOP task_
 
core::pack::task::TaskFactoryOP task_factory_
 
core::Size n_cycles_
 
utility::vector1< core::Sizerb_min_jumps_
 

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...
 

Constructor & Destructor Documentation

protocols::enzdes::EnzRepackMinimize::EnzRepackMinimize ( )
protocols::enzdes::EnzRepackMinimize::EnzRepackMinimize ( std::string const &  name)
protocols::enzdes::EnzRepackMinimize::~EnzRepackMinimize ( )
overridedefault

Member Function Documentation

void protocols::enzdes::EnzRepackMinimize::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::enzdes::EnzRepackMinimize::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.

core::pack::task::PackerTaskOP protocols::enzdes::EnzRepackMinimize::create_ptask ( core::pose::Pose pose)

References task_factory_, and protocols::enzdes::TR().

Referenced by apply().

void protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication ( core::pose::Pose const &  pose)
protocols::moves::MoverOP protocols::enzdes::EnzRepackMinimize::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.

bool protocols::enzdes::EnzRepackMinimize::get_design ( ) const
inline

References design_.

bool protocols::enzdes::EnzRepackMinimize::get_min_bb ( ) const
inline

References min_bb_.

bool protocols::enzdes::EnzRepackMinimize::get_min_lig ( ) const
inline

References min_lig_.

bool protocols::enzdes::EnzRepackMinimize::get_min_rb ( ) const
inline

References min_rb_.

bool protocols::enzdes::EnzRepackMinimize::get_min_sc ( ) const
inline

References min_sc_.

std::string protocols::enzdes::EnzRepackMinimize::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::enzdes::EnzRepackMinimize::minimize_in_stages ( core::pose::Pose pose,
core::pack::task::PackerTaskCOP  task,
bool const &  cstopt,
bool const &  min_sc,
bool const &  min_rb,
bool const &  min_lig 
)

References min_rb_, scorefxn_minimize(), and protocols::enzdes::TR().

Referenced by apply().

std::string protocols::enzdes::EnzRepackMinimize::mover_name ( )
static
void protocols::enzdes::EnzRepackMinimize::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 backrub_, cst_opt_, design_, fix_catalytic_, core::scoring::get_score_function_name(), min_bb_, minimize_in_stages_, minimize_prot_jumps_, n_cycles_, core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), rb_min_jumps(), repack_, scorefxn_minimize_, scorefxn_repack_, set_min_bb(), set_min_lig(), set_min_rb(), set_min_sc(), task_factory(), task_factory_, and protocols::enzdes::TR().

void protocols::enzdes::EnzRepackMinimize::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
utility::vector1< core::Size > protocols::enzdes::EnzRepackMinimize::rb_min_jumps ( ) const

References rb_min_jumps_.

Referenced by apply(), and parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::rb_min_jumps ( utility::vector1< core::Size > const  v)

References rb_min_jumps_.

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_minimize ( ) const

References scorefxn_minimize_.

Referenced by minimize_in_stages().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_repack ( ) const

References scorefxn_repack_.

void protocols::enzdes::EnzRepackMinimize::set_design ( bool const  des)
inline

References design_.

void protocols::enzdes::EnzRepackMinimize::set_min_bb ( bool const  min_bb)
inline

References min_bb_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_min_lig ( bool const  min_lig)
inline

References min_lig_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_min_rb ( bool const  min_rb)
inline

References min_rb_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_min_sc ( bool const  min_sc)
inline

References min_sc_.

Referenced by parse_my_tag().

void protocols::enzdes::EnzRepackMinimize::set_scorefxn_minimize ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_minimize_.

void protocols::enzdes::EnzRepackMinimize::set_scorefxn_repack ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_repack_.

void protocols::enzdes::EnzRepackMinimize::task_factory ( core::pack::task::TaskFactoryOP  p)

References task_factory_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::enzdes::EnzRepackMinimize::backrub_
private

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::cst_opt_
private

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::design_
private
bool protocols::enzdes::EnzRepackMinimize::fix_catalytic_
private

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::min_bb_
private
bool protocols::enzdes::EnzRepackMinimize::min_lig_
private

Referenced by apply(), get_min_lig(), and set_min_lig().

bool protocols::enzdes::EnzRepackMinimize::min_rb_
private
bool protocols::enzdes::EnzRepackMinimize::min_sc_
private

Referenced by apply(), get_min_sc(), and set_min_sc().

bool protocols::enzdes::EnzRepackMinimize::minimize_in_stages_
private

Referenced by apply(), and parse_my_tag().

bool protocols::enzdes::EnzRepackMinimize::minimize_prot_jumps_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::enzdes::EnzRepackMinimize::n_cycles_
private

Referenced by apply(), and parse_my_tag().

utility::vector1< core::Size > protocols::enzdes::EnzRepackMinimize::rb_min_jumps_
private

Referenced by rb_min_jumps().

bool protocols::enzdes::EnzRepackMinimize::repack_
private

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_minimize_
private
core::scoring::ScoreFunctionOP protocols::enzdes::EnzRepackMinimize::scorefxn_repack_
private
core::pack::task::PackerTaskOP protocols::enzdes::EnzRepackMinimize::task_
private

Referenced by apply().

core::pack::task::TaskFactoryOP protocols::enzdes::EnzRepackMinimize::task_factory_
private

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