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protocols::forge::remodel::RemodelDesignMover Class Reference

#include <RemodelDesignMover.hh>

Inheritance diagram for protocols::forge::remodel::RemodelDesignMover:
Inheritance graph
[legend]

Public Types

typedef core::Real Real
 
typedef core::Size Size
 
typedef core::kinematics::MoveMap MoveMap
 
typedef core::pose::Pose Pose
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::pack::task::PackerTaskOP 
PackerTaskOP
 
typedef
core::pack::task::PackerTask 
PackerTask
 
typedef protocols::moves::MoverOP MoverOP
 
typedef
protocols::forge::remodel::RemodelData 
RemodelData
 
typedef
protocols::forge::remodel::RemodelWorkingSet 
RemodelWorkingSet
 
- 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

 RemodelDesignMover ()
 
 RemodelDesignMover (RemodelData const &remodel_data, RemodelWorkingSet const &working_model, ScoreFunctionOP const &sfxn)
 value constructor More...
 
 ~RemodelDesignMover () override
 default destructor More...
 
MoverOP clone () const override
 clone this object More...
 
MoverOP fresh_instance () const override
 create this type of object More...
 
core::pack::task::PackerTaskOPtask ()
 packer task accessor More...
 
void scorefunction (ScoreFunctionOP const &sfxn)
 score function setter More...
 
void mode1_packertask (Pose &pose)
 these are split up for convenience reasons, so one can bypass blueprint setting if needed be More...
 
void mode1_1_packertask (Pose &pose)
 these are split up for convenience reasons, so one can bypass blueprint setting if needed be More...
 
void mode2_packertask (Pose &pose)
 
void mode3_packertask (Pose &pose)
 
void mode4_packertask (Pose &pose)
 
void mode5_packertask (Pose &pose)
 
void mode6_packertask (Pose &pose)
 
void reduce_task (Pose &pose, PackerTaskOP &task, bool core, bool boundary, bool surface)
 
bool check_state ()
 
void set_state (std::string state_tag)
 
bool find_disulfides_in_the_neighborhood (Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &disulf_partners, const core::Energy &match_rt_limit, const core::Size &rosetta_scripts_min_loop, const bool &rosetta_scripts_include_current_ds, const bool &rosetta_scripts_keep_current_ds, const bool &relax_bb_for_disulf, const bool &use_match_rt, const bool &use_disulf_fa_score, const core::Real disulf_fa_max)
 
void make_disulfide (Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &disulf_partners, core::kinematics::MoveMapOP mm)
 
void make_disulfide_fast (Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &disulf_partners)
 
void apply (Pose &pose) override
 Apply method for Mover. Checks value of option -remodel::design::no_design -remodel::design::find_neighbors -remodel::design::design_neigbors -remodel::design::skip_partial. More...
 
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
 
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 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...
 

Private Types

typedef protocols::moves::Mover Super
 

Private Member Functions

void run_calculator (core::pose::Pose const &pose, std::string const &calculator, std::string const &calculation, utility::vector1_bool &residues)
 

Private Attributes

RemodelData remodel_data_
 
RemodelWorkingSet working_model_
 
PackerTaskOP archived_starting_task_
 
utility::vector1< boolnon_default_positions_
 
std::string state_
 
ScoreFunctionOP score_fxn_
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover ( )
protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover ( RemodelData const &  remodel_data,
RemodelWorkingSet const &  working_model,
ScoreFunctionOP const &  sfxn 
)
protocols::forge::remodel::RemodelDesignMover::~RemodelDesignMover ( )
overridedefault

default destructor

Member Function Documentation

void protocols::forge::remodel::RemodelDesignMover::apply ( Pose pose)
overridevirtual
bool protocols::forge::remodel::RemodelDesignMover::check_state ( )
RemodelDesignMover::MoverOP protocols::forge::remodel::RemodelDesignMover::clone ( ) const
overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

bool protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood ( Pose pose,
utility::vector1< std::pair< core::Size, core::Size > > &  disulf_partners,
const core::Energy match_rt_limit,
const core::Size rosetta_scripts_min_loop,
const bool rosetta_scripts_include_current_ds,
const bool rosetta_scripts_keep_current_ds,
const bool relax_bb_for_disulf,
const bool use_match_rt,
const bool use_disulf_fa_score,
const core::Real  disulf_fa_max 
)
RemodelDesignMover::MoverOP protocols::forge::remodel::RemodelDesignMover::fresh_instance ( ) const
overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

std::string protocols::forge::remodel::RemodelDesignMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::forge::remodel::RemodelDesignMover::make_disulfide ( Pose pose,
utility::vector1< std::pair< core::Size, core::Size > > &  disulf_partners,
core::kinematics::MoveMapOP  mm 
)
void protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast ( Pose pose,
utility::vector1< std::pair< core::Size, core::Size > > &  disulf_partners 
)
void protocols::forge::remodel::RemodelDesignMover::mode1_1_packertask ( Pose pose)

these are split up for convenience reasons, so one can bypass blueprint setting if needed be

References protocols::forge::methods::remodel_generic_taskfactory(), core::pose::Pose::size(), and protocols::forge::remodel::TR().

void protocols::forge::remodel::RemodelDesignMover::mode1_packertask ( Pose pose)

these are split up for convenience reasons, so one can bypass blueprint setting if needed be

References protocols::forge::methods::remodel_generic_taskfactory(), core::pose::Pose::size(), and protocols::forge::remodel::TR().

void protocols::forge::remodel::RemodelDesignMover::mode2_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode3_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode4_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode5_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode6_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::reduce_task ( Pose pose,
PackerTaskOP task,
bool  core,
bool  boundary,
bool  surface 
)
void protocols::forge::remodel::RemodelDesignMover::run_calculator ( core::pose::Pose const &  pose,
std::string const &  calculator,
std::string const &  calculation,
utility::vector1_bool &  residues 
)
private
void protocols::forge::remodel::RemodelDesignMover::scorefunction ( ScoreFunctionOP const &  sfxn)

score function setter

Referenced by protocols::forge::remodel::RemodelMover::apply().

void protocols::forge::remodel::RemodelDesignMover::set_state ( std::string  state_tag)
core::pack::task::PackerTaskOP & protocols::forge::remodel::RemodelDesignMover::task ( )

packer task accessor

Member Data Documentation

PackerTaskOP protocols::forge::remodel::RemodelDesignMover::archived_starting_task_
private
utility::vector1<bool> protocols::forge::remodel::RemodelDesignMover::non_default_positions_
private
RemodelData protocols::forge::remodel::RemodelDesignMover::remodel_data_
private
ScoreFunctionOP protocols::forge::remodel::RemodelDesignMover::score_fxn_
private
std::string protocols::forge::remodel::RemodelDesignMover::state_
private
RemodelWorkingSet protocols::forge::remodel::RemodelDesignMover::working_model_
private

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