Public Types | Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
protocols::forge::remodel::RemodelDesignMover Class Reference

#include <RemodelDesignMover.hh>

Inheritance diagram for protocols::forge::remodel::RemodelDesignMover:
Inheritance graph

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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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< bool > non_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

◆ MoveMap

◆ MoverOP

◆ PackerTask

◆ PackerTaskOP

◆ Pose

◆ Real

◆ RemodelData

◆ RemodelWorkingSet

◆ ScoreFunction

◆ ScoreFunctionOP

◆ Size

◆ Super

Constructor & Destructor Documentation

◆ RemodelDesignMover() [1/2]

protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover ( )

◆ RemodelDesignMover() [2/2]

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

◆ ~RemodelDesignMover()

protocols::forge::remodel::RemodelDesignMover::~RemodelDesignMover ( )

default destructor

Member Function Documentation

◆ apply()

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

◆ check_state()

bool protocols::forge::remodel::RemodelDesignMover::check_state ( )

◆ clone()

RemodelDesignMover::MoverOP protocols::forge::remodel::RemodelDesignMover::clone ( ) const

clone this object

Reimplemented from protocols::moves::Mover.

◆ find_disulfides_in_the_neighborhood()

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 

◆ fresh_instance()

RemodelDesignMover::MoverOP protocols::forge::remodel::RemodelDesignMover::fresh_instance ( ) const

create this type of object

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

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

Implements protocols::moves::Mover.

◆ make_disulfide()

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

◆ make_disulfide_fast()

void protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast ( Pose pose,
utility::vector1< std::pair< core::Size, core::Size > > &  disulf_partners 

◆ mode1_1_packertask()

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().

◆ mode1_packertask()

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().

◆ mode2_packertask()

void protocols::forge::remodel::RemodelDesignMover::mode2_packertask ( Pose pose)

◆ mode3_packertask()

void protocols::forge::remodel::RemodelDesignMover::mode3_packertask ( Pose pose)

◆ mode4_packertask()

void protocols::forge::remodel::RemodelDesignMover::mode4_packertask ( Pose pose)

◆ mode5_packertask()

void protocols::forge::remodel::RemodelDesignMover::mode5_packertask ( Pose pose)

◆ mode6_packertask()

void protocols::forge::remodel::RemodelDesignMover::mode6_packertask ( Pose pose)

◆ reduce_task()

void protocols::forge::remodel::RemodelDesignMover::reduce_task ( Pose pose,
PackerTaskOP task,
bool  core,
bool  boundary,
bool  surface 

◆ run_calculator()

void protocols::forge::remodel::RemodelDesignMover::run_calculator ( core::pose::Pose const &  pose,
std::string const &  calculator,
std::string const &  calculation,
utility::vector1_bool &  residues 

◆ scorefunction()

void protocols::forge::remodel::RemodelDesignMover::scorefunction ( ScoreFunctionOP const &  sfxn)

score function setter

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

◆ set_state()

void protocols::forge::remodel::RemodelDesignMover::set_state ( std::string  state_tag)

◆ task()

core::pack::task::PackerTaskOP & protocols::forge::remodel::RemodelDesignMover::task ( )

packer task accessor

Member Data Documentation

◆ archived_starting_task_

PackerTaskOP protocols::forge::remodel::RemodelDesignMover::archived_starting_task_

◆ non_default_positions_

utility::vector1<bool> protocols::forge::remodel::RemodelDesignMover::non_default_positions_

◆ remodel_data_

RemodelData protocols::forge::remodel::RemodelDesignMover::remodel_data_

◆ score_fxn_

ScoreFunctionOP protocols::forge::remodel::RemodelDesignMover::score_fxn_

◆ state_

std::string protocols::forge::remodel::RemodelDesignMover::state_

◆ working_model_

RemodelWorkingSet protocols::forge::remodel::RemodelDesignMover::working_model_

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