Rosetta Protocols  2014.35
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
protocols::antibody::SnugDockProtocol Class Reference

#include <SnugDockProtocol.hh>

Public Member Functions

 SnugDockProtocol ()
 default constructor More...
 SnugDockProtocol (SnugDockProtocol const &rhs)
 copy constructor More...
SnugDockProtocoloperator= (SnugDockProtocol const &rhs)
 assignment operator More...
virtual ~SnugDockProtocol ()
virtual void apply (Pose &)
virtual std::string get_name () const
 Each derived class must specify its name. More...
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. 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...
void show (std::ostream &out=std::cout) const
 Outputs details about the Mover, including current settings. 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...
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 SnugDockProtocol class. More...
- 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...

Private Member Functions

void setup_objects (Pose const &pose)
void setup_loop_refinement_movers ()
void init ()
void init_for_equal_operator_and_copy_constructor (SnugDockProtocol &lhs, SnugDockProtocol const &rhs)
void init_options ()
docking::DockingProtocolOP docking () const

Private Attributes

AntibodyInfoOP antibody_info_
RefineOneCDRLoopOP low_res_refine_cdr_h2_
RefineOneCDRLoopOP low_res_refine_cdr_h3_
docking::DockingProtocolOP docking_
std::string loop_refinement_method_
bool h3_filter_
Size h3_filter_tolerance_


std::ostream & operator<< (std::ostream &out, SnugDockProtocol const &snugdockprotocol)

Additional Inherited Members

- 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
- 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...

Constructor & Destructor Documentation

protocols::antibody::SnugDockProtocol::SnugDockProtocol ( )

default constructor

References init().

Referenced by clone(), and fresh_instance().

protocols::antibody::SnugDockProtocol::SnugDockProtocol ( SnugDockProtocol const &  rhs)

copy constructor

References init_for_equal_operator_and_copy_constructor().

protocols::antibody::SnugDockProtocol::~SnugDockProtocol ( )

Member Function Documentation

void protocols::antibody::SnugDockProtocol::apply ( Pose pose)
protocols::moves::MoverOP protocols::antibody::SnugDockProtocol::clone ( ) const

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 SnugDockProtocol().

docking::DockingProtocolOP protocols::antibody::SnugDockProtocol::docking ( ) const

References docking_.

Referenced by apply(), and setup_objects().

protocols::moves::MoverOP protocols::antibody::SnugDockProtocol::fresh_instance ( ) const

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

References SnugDockProtocol().

std::string protocols::antibody::SnugDockProtocol::get_name ( ) const

Each derived class must specify its name.

Implements protocols::moves::Mover.

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

Referenced by apply(), protocols::antibody::operator<<(), setup_loop_refinement_movers(), and setup_objects().

void protocols::antibody::SnugDockProtocol::init ( void  )
void protocols::antibody::SnugDockProtocol::init_for_equal_operator_and_copy_constructor ( SnugDockProtocol lhs,
SnugDockProtocol const &  rhs 
void protocols::antibody::SnugDockProtocol::init_options ( )
SnugDockProtocol & protocols::antibody::SnugDockProtocol::operator= ( SnugDockProtocol const &  rhs)
void protocols::antibody::SnugDockProtocol::register_options ( )
bool protocols::antibody::SnugDockProtocol::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::antibody::SnugDockProtocol::setup_loop_refinement_movers ( )
void protocols::antibody::SnugDockProtocol::setup_objects ( Pose const &  pose)
void protocols::antibody::SnugDockProtocol::show ( std::ostream &  output = std::cout) const

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

Referenced by apply().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
SnugDockProtocol const &  snugdockprotocol 

Member Data Documentation

AntibodyInfoOP protocols::antibody::SnugDockProtocol::antibody_info_
docking::DockingProtocolOP protocols::antibody::SnugDockProtocol::docking_
bool protocols::antibody::SnugDockProtocol::h3_filter_
Size protocols::antibody::SnugDockProtocol::h3_filter_tolerance_
std::string protocols::antibody::SnugDockProtocol::loop_refinement_method_
RefineOneCDRLoopOP protocols::antibody::SnugDockProtocol::low_res_refine_cdr_h2_
RefineOneCDRLoopOP protocols::antibody::SnugDockProtocol::low_res_refine_cdr_h3_

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