Rosetta Protocols  2014.35
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>

Public Types

typedef core::Real Real
typedef core::Size Size
typedef core::kinematics::MoveMap MoveMap
typedef core::pose::Pose Pose
typedef protocols::moves::MoverOP MoverOP
- 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::stringStrings

Public Member Functions

 RemodelDesignMover ()
 RemodelDesignMover (RemodelData const &remodel_data, RemodelWorkingSet const &working_model, ScoreFunctionOP const &sfxn)
 value constructor More...
virtual ~RemodelDesignMover ()
 default destructor More...
virtual MoverOP clone () const
 clone this object More...
virtual MoverOP fresh_instance () const
 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< Size, Size > > &disulf_partners, const core::Energy &match_rt_limit, const Size &rosetta_scripts_min_loop_, const bool &rosetta_scripts_include_current_ds_, const bool &rosetta_scripts_keep_current_ds_)
void make_disulfide (Pose &pose, utility::vector1< std::pair< Size, Size > > &disulf_partners, core::kinematics::MoveMapOP mm)
void make_disulfide_fast (Pose &pose, utility::vector1< std::pair< Size, Size > > &disulf_partners)
virtual void apply (Pose &pose)
 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...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
- 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
void set_type (std::string const &setting)
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)
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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
 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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 ( )

default destructor

Member Function Documentation

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

References basic::options::TR.

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

clone this object

Reimplemented from protocols::moves::Mover.

bool protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood ( Pose pose,
utility::vector1< std::pair< Size, Size > > &  disulf_partners,
const core::Energy match_rt_limit,
const Size rosetta_scripts_min_loop_,
const bool rosetta_scripts_include_current_ds_,
const bool rosetta_scripts_keep_current_ds_ 
RemodelDesignMover::MoverOP protocols::forge::remodel::RemodelDesignMover::fresh_instance ( ) const

create this type of object

Reimplemented from protocols::moves::Mover.

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

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< Size, Size > > &  disulf_partners,
core::kinematics::MoveMapOP  mm 
void protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast ( Pose pose,
utility::vector1< std::pair< Size, Size > > &  disulf_partners 
void protocols::forge::remodel::RemodelDesignMover::mode1_1_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode1_packertask ( Pose pose)
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)

References basic::options::TR.

void protocols::forge::remodel::RemodelDesignMover::mode5_packertask ( Pose pose)
void protocols::forge::remodel::RemodelDesignMover::mode6_packertask ( Pose pose)

References basic::options::TR.

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 
void protocols::forge::remodel::RemodelDesignMover::scorefunction ( ScoreFunctionOP const &  sfxn)
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_
utility::vector1<bool> protocols::forge::remodel::RemodelDesignMover::non_default_positions_
RemodelData protocols::forge::remodel::RemodelDesignMover::remodel_data_
ScoreFunctionOP protocols::forge::remodel::RemodelDesignMover::score_fxn_
std::string protocols::forge::remodel::RemodelDesignMover::state_
RemodelWorkingSet protocols::forge::remodel::RemodelDesignMover::working_model_

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