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protocols::antibody2::RefineOneCDRLoop Class Reference

#include <RefineOneCDRLoop.hh>

Inheritance diagram for protocols::antibody2::RefineOneCDRLoop:
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Collaboration diagram for protocols::antibody2::RefineOneCDRLoop:
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Public Member Functions

 RefineOneCDRLoop ()
 default constructor More...
 
 RefineOneCDRLoop (AntibodyInfoOP antibody_info)
 constructor with arguments More...
 
 RefineOneCDRLoop (AntibodyInfoOP antibody_info, std::string refine_mode)
 constructor with arguments More...
 
 RefineOneCDRLoop (AntibodyInfoOP antibody_info, std::string refine_mode, core::scoring::ScoreFunctionCOP scorefxn)
 constructor with arguments More...
 
 RefineOneCDRLoop (AntibodyInfoOP antibody_info, AntibodyCDRNameEnum const &cdr_loop_name, std::string refine_mode, core::scoring::ScoreFunctionCOP scorefxn)
 constructor with arguments More...
 
 ~RefineOneCDRLoop ()
 default destructor More...
 
void turn_on_benchmark ()
 
void set_h3_filter (bool setting)
 
void set_num_filter_tries (core::Size setting)
 
void set_flank_relax (bool setting)
 
void set_flank_size (core::Size setting)
 
void set_refine_mode (std::string refine_mode)
 
virtual void apply (core::pose::Pose &pose)
 
void set_score_function (core::scoring::ScoreFunctionCOP scorefxn)
 
void pass_start_pose (core::pose::Pose &start_pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. 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
 
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...
 
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 set_default ()
 
void init ()
 
void finalize_setup (core::pose::Pose &pose)
 

Private Attributes

AntibodyInfoOP ab_info_
 
bool user_defined_
 
bool benchmark_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Size flank_size_
 
bool flank_relax_
 
core::pose::Pose start_pose_
 
core::pack::task::TaskFactoryOP tf_
 
bool H3_filter_
 
core::Size num_filter_tries_
 
std::string refine_mode_
 
AntibodyCDRNameEnum cdr_loop_name_
 
core::Real high_cst_
 

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
protocols::filters::Filters_map 
Filters_map
 
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::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::antibody2::RefineOneCDRLoop::RefineOneCDRLoop ( )

default constructor

Referenced by clone().

protocols::antibody2::RefineOneCDRLoop::RefineOneCDRLoop ( AntibodyInfoOP  antibody_info)

constructor with arguments

References ab_info_, init(), and user_defined_.

protocols::antibody2::RefineOneCDRLoop::RefineOneCDRLoop ( AntibodyInfoOP  antibody_info,
std::string  refine_mode 
)

constructor with arguments

References ab_info_, init(), refine_mode_, and user_defined_.

protocols::antibody2::RefineOneCDRLoop::RefineOneCDRLoop ( AntibodyInfoOP  antibody_info,
std::string  refine_mode,
core::scoring::ScoreFunctionCOP  scorefxn 
)
protocols::antibody2::RefineOneCDRLoop::RefineOneCDRLoop ( AntibodyInfoOP  antibody_info,
AntibodyCDRNameEnum const &  cdr_loop_name,
std::string  refine_mode,
core::scoring::ScoreFunctionCOP  scorefxn 
)

constructor with arguments

References ab_info_, cdr_loop_name_, init(), refine_mode_, scorefxn_, and user_defined_.

protocols::antibody2::RefineOneCDRLoop::~RefineOneCDRLoop ( )

default destructor

Member Function Documentation

void protocols::antibody2::RefineOneCDRLoop::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::antibody2::RefineOneCDRLoop::clone ( ) const
virtual

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 RefineOneCDRLoop().

void protocols::antibody2::RefineOneCDRLoop::finalize_setup ( core::pose::Pose pose)
private
std::string protocols::antibody2::RefineOneCDRLoop::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::antibody2::RefineOneCDRLoop::init ( void  )
private

References set_default().

Referenced by RefineOneCDRLoop().

void protocols::antibody2::RefineOneCDRLoop::pass_start_pose ( core::pose::Pose start_pose)

References start_pose_.

Referenced by apply().

void protocols::antibody2::RefineOneCDRLoop::set_default ( )
private
void protocols::antibody2::RefineOneCDRLoop::set_flank_relax ( bool  setting)
inline
void protocols::antibody2::RefineOneCDRLoop::set_flank_size ( core::Size  setting)
inline
void protocols::antibody2::RefineOneCDRLoop::set_h3_filter ( bool  setting)
inline
void protocols::antibody2::RefineOneCDRLoop::set_num_filter_tries ( core::Size  setting)
inline
void protocols::antibody2::RefineOneCDRLoop::set_refine_mode ( std::string  refine_mode)
inline
void protocols::antibody2::RefineOneCDRLoop::set_score_function ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_.

void protocols::antibody2::RefineOneCDRLoop::turn_on_benchmark ( )
inline

Member Data Documentation

AntibodyInfoOP protocols::antibody2::RefineOneCDRLoop::ab_info_
private

Referenced by apply(), and RefineOneCDRLoop().

bool protocols::antibody2::RefineOneCDRLoop::benchmark_
private
AntibodyCDRNameEnum protocols::antibody2::RefineOneCDRLoop::cdr_loop_name_
private
bool protocols::antibody2::RefineOneCDRLoop::flank_relax_
private

Referenced by apply(), and set_default().

core::Size protocols::antibody2::RefineOneCDRLoop::flank_size_
private

Referenced by apply(), and set_default().

bool protocols::antibody2::RefineOneCDRLoop::H3_filter_
private

Referenced by apply(), and set_default().

core::Real protocols::antibody2::RefineOneCDRLoop::high_cst_
private

Referenced by set_default().

core::Size protocols::antibody2::RefineOneCDRLoop::num_filter_tries_
private

Referenced by apply(), and set_default().

std::string protocols::antibody2::RefineOneCDRLoop::refine_mode_
private
core::scoring::ScoreFunctionOP protocols::antibody2::RefineOneCDRLoop::scorefxn_
private
core::pose::Pose protocols::antibody2::RefineOneCDRLoop::start_pose_
private

Referenced by apply(), and pass_start_pose().

core::pack::task::TaskFactoryOP protocols::antibody2::RefineOneCDRLoop::tf_
private
bool protocols::antibody2::RefineOneCDRLoop::user_defined_
private

Referenced by RefineOneCDRLoop(), and set_default().


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