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protocols::antibody::RefineBetaBarrel Class Reference

#include <RefineBetaBarrel.hh>

Inheritance diagram for protocols::antibody::RefineBetaBarrel:
Inheritance graph

Public Member Functions

 RefineBetaBarrel ()
 default constructor More...
 ~RefineBetaBarrel () override
 default destructor More...
 RefineBetaBarrel (AntibodyInfoOP antibody_info)
 RefineBetaBarrel (AntibodyInfoOP antibody_info, core::scoring::ScoreFunctionCOP dock_scorefxn, core::scoring::ScoreFunctionCOP pack_scorefxn)
void apply (core::pose::Pose &pose_in) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void set_task_factory (core::pack::task::TaskFactoryCOP tf)
void set_dock_score_func (core::scoring::ScoreFunctionCOP dock_scorefxn)
void set_pack_score_func (core::scoring::ScoreFunctionCOP pack_scorefxn)
void turn_off_repulsive_ramp ()
void set_sc_min (bool sc_min)
void set_rt_min (bool rt_min)
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual MoverOP create ()
MoverCOP get_self_ptr () const
MoverOP get_self_ptr ()
MoverCAP get_self_weak_ptr () const
MoverAP get_self_weak_ptr ()
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
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...
virtual MoverOP clone () const
 Return a clone of the Mover object. 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...
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...
void set_type (std::string const &setting)
 Set the 'type' string. More...
std::string get_type () const
void type (const std::string &type_in)
 Set the 'type' string. More...
std::string const & type () const
 Get the set 'type' string. More...
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 parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void set_current_tag (std::string const &new_tag)
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...
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
virtual core::Real last_proposal_density_ratio ()
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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions

void init ()
void finalize_setup (core::pose::Pose &pose_in)

Private Attributes

bool sc_min_
bool rt_min_
bool user_defined_
bool repulsive_ramp_
AntibodyInfoOP ab_info_
core::pack::task::TaskFactoryOP tf_
LHRepulsiveRampOP lh_repulsive_ramp_
LHSnugFitLegacyOP lh_snugfit_
docking::DockMCMProtocolOP dock_mcm_protocol_
core::scoring::ScoreFunctionOP dock_scorefxn_
core::scoring::ScoreFunctionOP pack_scorefxn_
core::kinematics::MoveMapOP cdr_dock_map_
docking::DockJumps LH_dock_jump_

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::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. 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...

Constructor & Destructor Documentation

protocols::antibody::RefineBetaBarrel::RefineBetaBarrel ( )

default constructor

protocols::antibody::RefineBetaBarrel::~RefineBetaBarrel ( )

default destructor

protocols::antibody::RefineBetaBarrel::RefineBetaBarrel ( AntibodyInfoOP  antibody_info)

References ab_info_, init(), and user_defined_.

protocols::antibody::RefineBetaBarrel::RefineBetaBarrel ( AntibodyInfoOP  antibody_info,
core::scoring::ScoreFunctionCOP  dock_scorefxn,
core::scoring::ScoreFunctionCOP  pack_scorefxn 

Member Function Documentation

void protocols::antibody::RefineBetaBarrel::apply ( core::pose::Pose )
void protocols::antibody::RefineBetaBarrel::finalize_setup ( core::pose::Pose pose_in)
std::string protocols::antibody::RefineBetaBarrel::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::antibody::RefineBetaBarrel::init ( void  )
void protocols::antibody::RefineBetaBarrel::set_dock_score_func ( core::scoring::ScoreFunctionCOP  dock_scorefxn)

References dock_scorefxn_.

void protocols::antibody::RefineBetaBarrel::set_pack_score_func ( core::scoring::ScoreFunctionCOP  pack_scorefxn)

References pack_scorefxn_.

void protocols::antibody::RefineBetaBarrel::set_rt_min ( bool  rt_min)

References rt_min_.

Referenced by apply().

void protocols::antibody::RefineBetaBarrel::set_sc_min ( bool  sc_min)

References sc_min_.

Referenced by apply().

void protocols::antibody::RefineBetaBarrel::set_task_factory ( core::pack::task::TaskFactoryCOP  tf)

References tf_.

Referenced by apply().

void protocols::antibody::RefineBetaBarrel::turn_off_repulsive_ramp ( )

References repulsive_ramp_.

Member Data Documentation

AntibodyInfoOP protocols::antibody::RefineBetaBarrel::ab_info_

Referenced by finalize_setup(), and RefineBetaBarrel().

core::kinematics::MoveMapOP protocols::antibody::RefineBetaBarrel::cdr_dock_map_

Referenced by apply(), and finalize_setup().

docking::DockMCMProtocolOP protocols::antibody::RefineBetaBarrel::dock_mcm_protocol_

Referenced by apply().

core::scoring::ScoreFunctionOP protocols::antibody::RefineBetaBarrel::dock_scorefxn_
docking::DockJumps protocols::antibody::RefineBetaBarrel::LH_dock_jump_

Referenced by apply(), finalize_setup(), and init().

LHRepulsiveRampOP protocols::antibody::RefineBetaBarrel::lh_repulsive_ramp_

Referenced by apply().

LHSnugFitLegacyOP protocols::antibody::RefineBetaBarrel::lh_snugfit_
core::scoring::ScoreFunctionOP protocols::antibody::RefineBetaBarrel::pack_scorefxn_
bool protocols::antibody::RefineBetaBarrel::repulsive_ramp_
bool protocols::antibody::RefineBetaBarrel::rt_min_

Referenced by apply(), init(), and set_rt_min().

bool protocols::antibody::RefineBetaBarrel::sc_min_

Referenced by apply(), init(), and set_sc_min().

core::pack::task::TaskFactoryOP protocols::antibody::RefineBetaBarrel::tf_
bool protocols::antibody::RefineBetaBarrel::user_defined_

Referenced by init(), and RefineBetaBarrel().

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