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protocols::docking::DockingPrepackProtocol Class Reference

#include <DockingPrepackProtocol.hh>

Inheritance diagram for protocols::docking::DockingPrepackProtocol:
Inheritance graph
Collaboration diagram for protocols::docking::DockingPrepackProtocol:
Collaboration graph

Public Member Functions

 DockingPrepackProtocol ()
 Default constructor. More...
 ~DockingPrepackProtocol ()
void setup_defaults ()
 Assigns default values to members. More...
void setup_pack_operation_movers ()
 Instantiates and configures movers used by DockingPrepackProtocol More...
void apply (core::pose::Pose &)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void score_and_output (std::string filename, core::pose::Pose &)
 Scores and outputs the pose - jd2 compatible. More...
void set_dock_ppk (bool dock_ppk)
- Public Member Functions inherited from protocols::docking::DockingHighRes
 DockingHighRes ()
 Default constructor. More...
 DockingHighRes (core::Size const rb_jump)
 Constructor with one argument - the jump number to dock over. More...
 DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn)
 Constructor with two arguments. The first is thejump number, the second is a scorefunction that will be used for docking and packing. More...
 DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 Constructor with three arguments. The first is the jump number, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...
 DockingHighRes (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 Constructor with three arguments. The first is the DockJumps, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...
 DockingHighRes (DockingHighRes const &old_instance)
virtual ~DockingHighRes ()
void set_task_factory (core::pack::task::TaskFactoryCOP tf)
void set_ignore_default_task (bool ignore_default_task)
bool ignore_default_task ()
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
void set_scorefxn_pack (core::scoring::ScoreFunctionOP scorefxn_pack)
DockJumpsmovable_jumps ()
DockJumps const & movable_jumps () const
core::pack::task::TaskFactoryCOP task_factory ()
void set_sc_min (bool sc_min)
void set_rt_min (bool rt_min)
void set_partners (std::string partners)
void set_interface_definition_task_operation (protocols::toolbox::task_operations::InterfaceTaskOperationOP interface_definition)
void set_additional_task_operarations (utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations)
void add_additional_task_operaration (core::pack::task::operation::TaskOperationOP task_operation)
< core::pack::task::operation::TaskOperationOP
get_additional_task_operarations ()
bool sc_min ()
bool rt_min ()
std::string partners ()
core::scoring::ScoreFunctionOP scorefxn () const
core::scoring::ScoreFunctionOP scorefxn_pack () const
- 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)
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
virtual void parse_my_tag (TagPtr const tag, 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
 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...
virtual 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 set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

Private Member Functions

void finalize_setup (core::pose::Pose &)
 Performs setup that requires a pose. More...
void register_options ()
void init_from_options ()

Private Attributes

< rigid::RigidBodyTransMoverOP
< rigid::RigidBodyTransMoverOP
core::Real trans_magnitude_
protocols::simple_moves::RotamerTrialsMinMoverOP rtmin_mover_
protocols::simple_moves::PackRotamersMoverOP prepack_full_repack_
SidechainMinMoverOP scmin_mover_
SequenceMoverOP pack_operations_
bool dock_ppk_
FaDockingSlideIntoContactOP fa_dock_slide_into_contact_

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 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::docking::DockingHighRes
protocols::docking::DockTaskFactoryOP tf2 ()

Constructor & Destructor Documentation

protocols::docking::DockingPrepackProtocol::DockingPrepackProtocol ( )
protocols::docking::DockingPrepackProtocol::~DockingPrepackProtocol ( )

Member Function Documentation

void protocols::docking::DockingPrepackProtocol::apply ( core::pose::Pose pose)
void protocols::docking::DockingPrepackProtocol::finalize_setup ( core::pose::Pose pose)
std::string protocols::docking::DockingPrepackProtocol::get_name ( ) const

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

Implements protocols::docking::DockingHighRes.

void protocols::docking::DockingPrepackProtocol::init_from_options ( )
void protocols::docking::DockingPrepackProtocol::register_options ( )

Referenced by DockingPrepackProtocol().

void protocols::docking::DockingPrepackProtocol::score_and_output ( std::string  filename,
core::pose::Pose pose 
void protocols::docking::DockingPrepackProtocol::set_dock_ppk ( bool  dock_ppk)

References dock_ppk_.

Referenced by init_from_options().

void protocols::docking::DockingPrepackProtocol::setup_defaults ( )

Assigns default values to members.

References dock_ppk_, pack_operations_, and trans_magnitude_.

Referenced by DockingPrepackProtocol().

void protocols::docking::DockingPrepackProtocol::setup_pack_operation_movers ( )

Member Data Documentation

bool protocols::docking::DockingPrepackProtocol::dock_ppk_

Referenced by apply(), set_dock_ppk(), and setup_defaults().

FaDockingSlideIntoContactOP protocols::docking::DockingPrepackProtocol::fa_dock_slide_into_contact_

Referenced by apply().

SequenceMoverOP protocols::docking::DockingPrepackProtocol::pack_operations_
protocols::simple_moves::PackRotamersMoverOP protocols::docking::DockingPrepackProtocol::prepack_full_repack_
protocols::simple_moves::RotamerTrialsMinMoverOP protocols::docking::DockingPrepackProtocol::rtmin_mover_
SidechainMinMoverOP protocols::docking::DockingPrepackProtocol::scmin_mover_
utility::vector1< rigid::RigidBodyTransMoverOP > protocols::docking::DockingPrepackProtocol::trans_away_vec_
utility::vector1< rigid::RigidBodyTransMoverOP > protocols::docking::DockingPrepackProtocol::trans_back_vec_
core::Real protocols::docking::DockingPrepackProtocol::trans_magnitude_

Referenced by apply(), and setup_defaults().

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