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protocols::enzdes::EnzRepackMinimize Class Reference

#include <EnzRepackMinimize.hh>

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

 EnzRepackMinimize ()
 
 EnzRepackMinimize (std::string const name)
 
virtual ~EnzRepackMinimize ()
 
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)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

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_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...
 

Constructor & Destructor Documentation

protocols::enzdes::EnzRepackMinimize::EnzRepackMinimize ( )

Referenced by clone(), and fresh_instance().

protocols::enzdes::EnzRepackMinimize::EnzRepackMinimize ( std::string const  name)
protocols::enzdes::EnzRepackMinimize::~EnzRepackMinimize ( )
virtual

Member Function Documentation

void protocols::enzdes::EnzRepackMinimize::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::enzdes::EnzRepackMinimize::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

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.

References EnzRepackMinimize().

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
virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

References EnzRepackMinimize().

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
virtual

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

Implements protocols::moves::Mover.

References protocols::enzdes::EnzRepackMinimizeCreator::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().

void protocols::enzdes::EnzRepackMinimize::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References backrub_, cst_opt_, design_, fix_catalytic_, protocols::moves::DataMap::get(), min_bb_, minimize_in_stages_, minimize_prot_jumps_, n_cycles_, protocols::rosetta_scripts::parse_task_operations(), repack_, scorefxn_minimize(), scorefxn_minimize_, scorefxn_repack(), scorefxn_repack_, set_min_bb(), set_min_lig(), set_min_rb(), set_min_sc(), task_factory(), task_factory_, and protocols::enzdes::TR().

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

References scorefxn_minimize_.

Referenced by minimize_in_stages(), and parse_my_tag().

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

References scorefxn_repack_.

Referenced by parse_my_tag().

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().

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: