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protocols::antibody2::SnugDock Class Reference

#include <SnugDock.hh>

Inheritance diagram for protocols::antibody2::SnugDock:
Inheritance graph
Collaboration diagram for protocols::antibody2::SnugDock:
Collaboration graph

Public Member Functions

 SnugDock ()
 default constructor More...
 SnugDock (SnugDock const &rhs)
 copy constructor More...
SnugDockoperator= (SnugDock const &rhs)
 assignment operator More...
virtual ~SnugDock ()
virtual void apply (Pose &)
virtual std::string get_name () const
 Each derived class must specify its name. More...
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
virtual protocols::moves::MoverOP fresh_instance () const
 fresh_instance returns a default-constructed object for JD2 More...
virtual bool reinitialize_for_new_input () const
 This mover retains state such that a fresh version is needed if the input Pose is about to change. More...
Size number_of_high_resolution_cycles () const
void number_of_high_resolution_cycles (Size const number_of_high_resolution_cycles)
void set_antibody_info (AntibodyInfoOP antibody_info)
void show (std::ostream &out=std::cout)
- 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 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

Static Public Member Functions

static void register_options ()
 Associates relevant options with the SnugDock class. More...

Private Member Functions

void setup_objects (Pose const &pose)
void init ()
void init_for_equal_operator_and_copy_constructor (SnugDock &lhs, SnugDock const &rhs)
void init_options ()

Private Attributes

AntibodyInfoOP antibody_info_
moves::MonteCarloOP mc_
moves::RandomMoverOP high_resolution_step_
std::string loop_refinement_method_
antibody2::CDRsMinPackMinOP pre_minimization_
Size number_of_high_resolution_cycles_


std::ostream & operator<< (std::ostream &out, SnugDock const &snugdock)

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
- Protected Member Functions inherited from protocols::docking::DockingHighRes
protocols::docking::DockTaskFactoryOP tf2 ()

Constructor & Destructor Documentation

protocols::antibody2::SnugDock::SnugDock ( )

default constructor

References init().

Referenced by clone(), and fresh_instance().

protocols::antibody2::SnugDock::SnugDock ( SnugDock const &  rhs)

copy constructor

References init_for_equal_operator_and_copy_constructor().

protocols::antibody2::SnugDock::~SnugDock ( )

Member Function Documentation

void protocols::antibody2::SnugDock::apply ( Pose pose)
protocols::moves::MoverOP protocols::antibody2::SnugDock::clone ( ) const

clone has to be overridden only if clone invocation is expected.

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 SnugDock().

protocols::moves::MoverOP protocols::antibody2::SnugDock::fresh_instance ( ) const

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

References SnugDock().

std::string protocols::antibody2::SnugDock::get_name ( ) const

Each derived class must specify its name.

Implements protocols::docking::DockingHighRes.

References protocols::moves::Mover::type().

Referenced by apply(), and setup_objects().

void protocols::antibody2::SnugDock::init ( void  )
void protocols::antibody2::SnugDock::init_for_equal_operator_and_copy_constructor ( SnugDock lhs,
SnugDock const &  rhs 
void protocols::antibody2::SnugDock::init_options ( )

References number_of_high_resolution_cycles().

Referenced by init().

Size protocols::antibody2::SnugDock::number_of_high_resolution_cycles ( ) const
void protocols::antibody2::SnugDock::number_of_high_resolution_cycles ( Size const  number_of_high_resolution_cycles)
SnugDock & protocols::antibody2::SnugDock::operator= ( SnugDock const &  rhs)

assignment operator

References init_for_equal_operator_and_copy_constructor().

void protocols::antibody2::SnugDock::register_options ( )

Associates relevant options with the SnugDock class.

References protocols::moves::Mover::register_options().

Referenced by protocols::antibody2::SnugDockProtocol::register_options().

bool protocols::antibody2::SnugDock::reinitialize_for_new_input ( ) const

This mover retains state such that a fresh version is needed if the input Pose is about to change.

Reimplemented from protocols::moves::Mover.

void protocols::antibody2::SnugDock::set_antibody_info ( AntibodyInfoOP  antibody_info)

References antibody_info_.

void protocols::antibody2::SnugDock::setup_objects ( Pose const &  pose)
void protocols::antibody2::SnugDock::show ( std::ostream &  out = std::cout)

Referenced by apply().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
SnugDock const &  snugdock 

Member Data Documentation

AntibodyInfoOP protocols::antibody2::SnugDock::antibody_info_
moves::RandomMoverOP protocols::antibody2::SnugDock::high_resolution_step_
std::string protocols::antibody2::SnugDock::loop_refinement_method_
moves::MonteCarloOP protocols::antibody2::SnugDock::mc_
Size protocols::antibody2::SnugDock::number_of_high_resolution_cycles_
antibody2::CDRsMinPackMinOP protocols::antibody2::SnugDock::pre_minimization_

Referenced by apply(), and setup_objects().

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