Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::symmetric_docking::SymDockProtocol Class Reference

#include <SymDockProtocol.hh>

Public Types

typedef
core::conformation::symmetry::SymmetricConformation 
SymmetricConformation
 
typedef
core::conformation::symmetry::SymmetryInfo 
SymmetryInfo
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 

Public Member Functions

 SymDockProtocol ()
 
 SymDockProtocol (bool const fullatom, bool const local_refine, bool const view=false)
 
 SymDockProtocol (bool const fullatom, bool const local_refine, bool const view, core::scoring::ScoreFunctionOP docking_score_low, core::scoring::ScoreFunctionOP docking_score_high)
 
virtual ~SymDockProtocol ()
 
void set_default ()
 setup that is called from constructor More...
 
void register_options ()
 
void set_dock_rtmin (bool dock_rtmin_in)
 setter More...
 
void set_sc_min (bool sc_min_in)
 
void set_max_repeats (Size const max_repeats_in)
 
void set_dock_ppk (bool dock_ppk_in)
 
void set_fullatom (bool const fullatom_in)
 
void set_local_refine (bool const local_refine_in)
 
void set_view (bool view_in)
 
void set_lowres_scorefxn (core::scoring::ScoreFunctionOP docking_score_low_in)
 
void set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_score_high_in)
 
void set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_score_high_in, core::scoring::ScoreFunctionOP docking_score_pack_in)
 
bool docking_lowres_filter (core::pose::Pose &pose)
 
bool docking_highres_filter (core::pose::Pose &pose)
 
core::Real calc_interaction_energy (core::pose::Pose &pose)
 
core::Real calc_rms (core::pose::Pose &pose)
 
void recover_sidechains (core::pose::Pose &pose, const core::pose::Pose &native_pose)
 recovers the side-chains from the native-pose More...
 
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 
void design (bool const des)
 
bool design () const
 
void hurry (bool const hurry)
 
core::pack::task::TaskFactoryOP task_factory () const
 
core::pack::task::TaskFactoryOPtask_factory ()
 
void score_only (core::pose::Pose &pose)
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::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...
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. 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)
 
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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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 Member Functions

void classic_mcm_protocol (core::pose::Pose &pose, core::scoring::symmetry::SymmetricScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles, core::Size repack_every_Nth) const
 
protocols::moves::MoverOP make_dockmcm_mover (core::pose::Pose const &pose, protocols::moves::MoverOP repack_mover, protocols::moves::MoverOP rigbod_mover, core::kinematics::MoveMapOP movemap, core::scoring::symmetry::SymmetricScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo) const
 

Private Attributes

bool fullatom_
 information about the mode More...
 
bool local_refine_
 
bool rtmin_
 
bool sc_min_
 
Size max_repeats_
 
bool dock_ppk_
 
utility::vector1< core::Sizemovable_jumps_
 the jump number across which to do rigid_body transformations More...
 
bool autofoldtree_
 should docking change the foldtree? More...
 
bool view_
 whether or not to initialize the viewer (for opengl) More...
 
bool design_
 
bool passed_lowres_filter_
 
bool passed_highres_filter_
 
bool hurry_
 
std::map< std::string, core::Realscore_map_
 
core::scoring::ScoreFunctionOP docking_score_low_
 
core::scoring::ScoreFunctionOP docking_score_high_
 
core::scoring::ScoreFunctionOP docking_score_high_min_
 
core::scoring::ScoreFunctionOP docking_score_pack_
 
moves::MonteCarloOP mc_
 
protocols::symmetric_docking::SymDockingLowResOP docking_low_
 
protocols::symmetric_docking::SymDockingHiResOP docking_high_
 
core::pack::task::TaskFactoryOP init_task_factory_
 

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::symmetric_docking::SymDockProtocol::SymDockProtocol ( )
protocols::symmetric_docking::SymDockProtocol::SymDockProtocol ( bool const  fullatom,
bool const  local_refine,
bool const  view = false 
)
protocols::symmetric_docking::SymDockProtocol::SymDockProtocol ( bool const  fullatom,
bool const  local_refine,
bool const  view,
core::scoring::ScoreFunctionOP  docking_score_low,
core::scoring::ScoreFunctionOP  docking_score_high 
)
protocols::symmetric_docking::SymDockProtocol::~SymDockProtocol ( )
virtual

Member Function Documentation

void protocols::symmetric_docking::SymDockProtocol::apply ( core::pose::Pose pose)
virtual

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), protocols::jd2::Job::add_string_real_pair(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ConstraintSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), calc_interaction_energy(), calc_rms(), core::chemical::CENTROID, core::pose::Pose::conformation(), protocols::nonlocal::current_job(), core::pose::Pose::data(), design_, docking_high_, docking_highres_filter(), docking_low_, docking_lowres_filter(), docking_score_high_, docking_score_high_min_, docking_score_low_, docking_score_pack_, core::chemical::FA_STANDARD, fullatom_, protocols::moves::Mover::get_input_pose(), protocols::jd2::JobDistributor::get_instance(), protocols::moves::Mover::get_native_pose(), core::scoring::get_score_function(), hurry_, init_task_factory_, core::pose::Pose::is_fullatom(), local_refine_, max_repeats, protocols::jd2::ScoreMap::nonzero_energies(), option, passed_highres_filter_, passed_lowres_filter_, basic::prof_reset(), basic::prof_show(), recover_sidechains(), protocols::relax::relax_pose(), rms, core::pose::datacache::CacheableDataType::SCORE_MAP, score_map_, score_only(), scoring, basic::datacache::BasicDataCache::set(), protocols::moves::Mover::set_input_pose(), core::scoring::symmetry::symmetrize_scorefunction(), protocols::medal::to_centroid(), protocols::symmetric_docking::TR, user, and viewer.

core::Real protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy ( core::pose::Pose pose)
core::Real protocols::symmetric_docking::SymDockProtocol::calc_rms ( core::pose::Pose pose)
void protocols::symmetric_docking::SymDockProtocol::classic_mcm_protocol ( core::pose::Pose pose,
core::scoring::symmetry::SymmetricScoreFunctionOP  scorefxn,
protocols::moves::MonteCarloOP  monteCarlo,
core::Size  num_cycles,
core::Size  repack_every_Nth 
) const
private
protocols::moves::MoverOP protocols::symmetric_docking::SymDockProtocol::clone ( ) const
virtual

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.

References docking_score_high_, docking_score_low_, fullatom_, local_refine_, SymDockProtocol(), and view_.

void protocols::symmetric_docking::SymDockProtocol::design ( bool const  des)

References design_.

bool protocols::symmetric_docking::SymDockProtocol::design ( ) const

References design_.

Referenced by set_default().

bool protocols::symmetric_docking::SymDockProtocol::docking_highres_filter ( core::pose::Pose pose)
bool protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter ( core::pose::Pose pose)
std::string protocols::symmetric_docking::SymDockProtocol::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::symmetric_docking::SymDockProtocol::hurry ( bool const  hurry)

References hurry_.

Referenced by set_default().

protocols::moves::MoverOP protocols::symmetric_docking::SymDockProtocol::make_dockmcm_mover ( core::pose::Pose const &  pose,
protocols::moves::MoverOP  repack_mover,
protocols::moves::MoverOP  rigbod_mover,
core::kinematics::MoveMapOP  movemap,
core::scoring::symmetry::SymmetricScoreFunctionOP  scorefxn,
protocols::moves::MonteCarloOP  monteCarlo 
) const
private
void protocols::symmetric_docking::SymDockProtocol::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::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 dock_ppk, dock_rtmin, fullatom, max_repeats, protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), sc_min, set_dock_ppk(), set_dock_rtmin(), set_fullatom(), set_highres_scorefxn(), set_local_refine(), set_lowres_scorefxn(), set_max_repeats(), set_sc_min(), set_view(), task_factory(), and view.

void protocols::symmetric_docking::SymDockProtocol::recover_sidechains ( core::pose::Pose pose,
const core::pose::Pose native_pose 
)
void protocols::symmetric_docking::SymDockProtocol::register_options ( )
void protocols::symmetric_docking::SymDockProtocol::score_only ( core::pose::Pose pose)
void protocols::symmetric_docking::SymDockProtocol::set_default ( )
void protocols::symmetric_docking::SymDockProtocol::set_dock_ppk ( bool  dock_ppk_in)

References dock_ppk_.

Referenced by parse_my_tag(), and register_options().

void protocols::symmetric_docking::SymDockProtocol::set_dock_rtmin ( bool  dock_rtmin_in)

setter

References rtmin_.

Referenced by parse_my_tag(), and register_options().

void protocols::symmetric_docking::SymDockProtocol::set_fullatom ( bool const  fullatom_in)
void protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionOP  docking_score_high_in)
void protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionOP  docking_score_high_in,
core::scoring::ScoreFunctionOP  docking_score_pack_in 
)
void protocols::symmetric_docking::SymDockProtocol::set_local_refine ( bool const  local_refine_in)
void protocols::symmetric_docking::SymDockProtocol::set_lowres_scorefxn ( core::scoring::ScoreFunctionOP  docking_score_low_in)

References docking_low_, and docking_score_low_.

Referenced by parse_my_tag().

void protocols::symmetric_docking::SymDockProtocol::set_max_repeats ( Size const  max_repeats_in)

References max_repeats_.

Referenced by parse_my_tag(), and register_options().

void protocols::symmetric_docking::SymDockProtocol::set_sc_min ( bool  sc_min_in)

References sc_min_.

Referenced by parse_my_tag(), and register_options().

void protocols::symmetric_docking::SymDockProtocol::set_view ( bool  view_in)

References view_.

Referenced by parse_my_tag(), and SymDockProtocol().

void protocols::symmetric_docking::SymDockProtocol::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

References init_task_factory_.

core::pack::task::TaskFactoryOP protocols::symmetric_docking::SymDockProtocol::task_factory ( ) const

References init_task_factory_.

Referenced by parse_my_tag().

core::pack::task::TaskFactoryOP & protocols::symmetric_docking::SymDockProtocol::task_factory ( )

References init_task_factory_.

Member Data Documentation

bool protocols::symmetric_docking::SymDockProtocol::autofoldtree_
private

should docking change the foldtree?

bool protocols::symmetric_docking::SymDockProtocol::design_
private

Referenced by apply(), and design().

bool protocols::symmetric_docking::SymDockProtocol::dock_ppk_
private

Referenced by set_default(), and set_dock_ppk().

protocols::symmetric_docking::SymDockingHiResOP protocols::symmetric_docking::SymDockProtocol::docking_high_
private

Referenced by apply(), and set_highres_scorefxn().

protocols::symmetric_docking::SymDockingLowResOP protocols::symmetric_docking::SymDockProtocol::docking_low_
private

Referenced by apply(), and set_lowres_scorefxn().

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_high_
private
core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_high_min_
private
core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_low_
private
core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_pack_
private
bool protocols::symmetric_docking::SymDockProtocol::fullatom_
private

information about the mode

Referenced by apply(), calc_interaction_energy(), clone(), score_only(), and set_fullatom().

bool protocols::symmetric_docking::SymDockProtocol::hurry_
private

Referenced by apply(), and hurry().

core::pack::task::TaskFactoryOP protocols::symmetric_docking::SymDockProtocol::init_task_factory_
private

Referenced by apply(), and task_factory().

bool protocols::symmetric_docking::SymDockProtocol::local_refine_
private

Referenced by apply(), clone(), and set_local_refine().

Size protocols::symmetric_docking::SymDockProtocol::max_repeats_
private

Referenced by set_max_repeats().

moves::MonteCarloOP protocols::symmetric_docking::SymDockProtocol::mc_
private
utility::vector1<core::Size> protocols::symmetric_docking::SymDockProtocol::movable_jumps_
private

the jump number across which to do rigid_body transformations

bool protocols::symmetric_docking::SymDockProtocol::passed_highres_filter_
private

Referenced by apply(), set_default(), and set_fullatom().

bool protocols::symmetric_docking::SymDockProtocol::passed_lowres_filter_
private
bool protocols::symmetric_docking::SymDockProtocol::rtmin_
private
bool protocols::symmetric_docking::SymDockProtocol::sc_min_
private

Referenced by set_sc_min().

std::map< std::string, core::Real > protocols::symmetric_docking::SymDockProtocol::score_map_
private

Referenced by apply(), and docking_highres_filter().

bool protocols::symmetric_docking::SymDockProtocol::view_
private

whether or not to initialize the viewer (for opengl)

Referenced by clone(), and set_view().


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