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protocols::antibody::H3RefineCCD Class Reference

#include <H3RefineCCD.hh>

Inheritance diagram for protocols::antibody::H3RefineCCD:
Inheritance graph
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Public Member Functions

 H3RefineCCD ()
 default constructor More...
 
 H3RefineCCD (AntibodyInfoOP antibody_info, CDRNameEnum loop_name)
 constructor with arguments More...
 
 H3RefineCCD (AntibodyInfoOP antibody_info, CDRNameEnum loop_name, core::scoring::ScoreFunctionCOP highres_scorefxn)
 constructor with arguments More...
 
 H3RefineCCD (AntibodyInfoOP antibody_info)
 constructor with arguments More...
 
void set_task_factory (core::pack::task::TaskFactoryCOP tf)
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
 ~H3RefineCCD () override
 default destructor More...
 
void pass_start_pose (core::pose::Pose &start_pose)
 
void turn_on_benchmark ()
 
void turn_off_flank_relax ()
 
void turn_off_h3_filter ()
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_highres_score_func (core::scoring::ScoreFunctionCOP highres_scorefxn)
 
- 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 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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Member Functions

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

Private Attributes

AntibodyInfoOP ab_info_
 
CDRNameEnum loop_name_
 
loops::Loop the_loop_
 
core::Real high_cst_
 
core::Size loop_begin_
 
core::Size loop_end_
 
core::Size loop_size_
 
core::Size cutpoint_
 
core::Size n_small_moves_
 
core::Size inner_cycles_
 
core::Size outer_cycles_
 
bool include_neighbors_
 
core::kinematics::MoveMapOP cdrh3_map_
 
core::kinematics::MoveMapOP flank_cdrh3_map_
 
std::string minimization_type_
 
bool user_defined_
 
bool benchmark_
 
bool is_camelid_
 
moves::ChangeFoldTreeMoverOP change_FT_to_simpleloop_
 
moves::ChangeFoldTreeMoverOP change_FT_to_flankloop_
 
minimization_packing::MinMoverOP loop_min_mover_
 
moves::SequenceMoverOP wiggle_cdr_h3_
 
minimization_packing::PackRotamersMoverOP loop_repack_
 
moves::MonteCarloOP mc_
 
utility::vector1< boolallow_repack_
 
core::Real init_temp_
 
core::Real last_temp_
 
core::Real gamma_
 
core::Real min_tolerance_
 
core::Real high_move_temp_
 
core::Real neighbor_dist_
 
core::scoring::ScoreFunctionOP highres_scorefxn_
 
bool H3_filter_
 actually enables H3 filter for H3 operations More...
 
core::Size flank_size_
 number of flanking residues:default 5 More...
 
bool flank_relax_
 relax flanking regions of h3 More...
 
core::pose::Pose start_pose_
 
core::pack::task::TaskFactoryOP tf_
 
bool refine_input_loop_
 just refine input loop More...
 
core::Size max_cycle_close_trial_
 

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::H3RefineCCD::H3RefineCCD ( )

default constructor

protocols::antibody::H3RefineCCD::H3RefineCCD ( AntibodyInfoOP  antibody_info,
CDRNameEnum  loop_name 
)

constructor with arguments

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

protocols::antibody::H3RefineCCD::H3RefineCCD ( AntibodyInfoOP  antibody_info,
CDRNameEnum  loop_name,
core::scoring::ScoreFunctionCOP  highres_scorefxn 
)

constructor with arguments

References ab_info_, highres_scorefxn_, init(), loop_name_, and user_defined_.

protocols::antibody::H3RefineCCD::H3RefineCCD ( AntibodyInfoOP  antibody_info)

constructor with arguments

References ab_info_, and init().

protocols::antibody::H3RefineCCD::~H3RefineCCD ( )
overridedefault

default destructor

Member Function Documentation

void protocols::antibody::H3RefineCCD::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::antibody::H3RefineCCD::clone ( ) const
overridevirtual

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.

void protocols::antibody::H3RefineCCD::finalize_setup ( core::pose::Pose pose)
private
std::string protocols::antibody::H3RefineCCD::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::antibody::H3RefineCCD::init ( void  )
private
void protocols::antibody::H3RefineCCD::pass_start_pose ( core::pose::Pose start_pose)

References start_pose_.

void protocols::antibody::H3RefineCCD::set_default ( )
private
void protocols::antibody::H3RefineCCD::set_highres_score_func ( core::scoring::ScoreFunctionCOP  highres_scorefxn)
inline

References highres_scorefxn_.

void protocols::antibody::H3RefineCCD::set_task_factory ( core::pack::task::TaskFactoryCOP  tf)

References tf_.

void protocols::antibody::H3RefineCCD::turn_off_flank_relax ( )
inline

References flank_relax_.

void protocols::antibody::H3RefineCCD::turn_off_h3_filter ( )
inline

References H3_filter_.

void protocols::antibody::H3RefineCCD::turn_on_benchmark ( )
inline

References benchmark_.

Member Data Documentation

AntibodyInfoOP protocols::antibody::H3RefineCCD::ab_info_
private

Referenced by apply(), H3RefineCCD(), and init().

utility::vector1< bool> protocols::antibody::H3RefineCCD::allow_repack_
private

Referenced by apply(), and finalize_setup().

bool protocols::antibody::H3RefineCCD::benchmark_
private
core::kinematics::MoveMapOP protocols::antibody::H3RefineCCD::cdrh3_map_
private

Referenced by finalize_setup().

moves::ChangeFoldTreeMoverOP protocols::antibody::H3RefineCCD::change_FT_to_flankloop_
private

Referenced by apply(), and finalize_setup().

moves::ChangeFoldTreeMoverOP protocols::antibody::H3RefineCCD::change_FT_to_simpleloop_
private

Referenced by finalize_setup().

core::Size protocols::antibody::H3RefineCCD::cutpoint_
private

Referenced by finalize_setup(), and init().

core::kinematics::MoveMapOP protocols::antibody::H3RefineCCD::flank_cdrh3_map_
private

Referenced by finalize_setup().

bool protocols::antibody::H3RefineCCD::flank_relax_
private

relax flanking regions of h3

Referenced by finalize_setup(), set_default(), and turn_off_flank_relax().

core::Size protocols::antibody::H3RefineCCD::flank_size_
private

number of flanking residues:default 5

Referenced by finalize_setup(), and set_default().

core::Real protocols::antibody::H3RefineCCD::gamma_
private

Referenced by apply(), and init().

bool protocols::antibody::H3RefineCCD::H3_filter_
private

actually enables H3 filter for H3 operations

Referenced by apply(), set_default(), and turn_off_h3_filter().

core::Real protocols::antibody::H3RefineCCD::high_cst_
private

Referenced by set_default().

core::Real protocols::antibody::H3RefineCCD::high_move_temp_
private

Referenced by finalize_setup(), and set_default().

core::scoring::ScoreFunctionOP protocols::antibody::H3RefineCCD::highres_scorefxn_
private
bool protocols::antibody::H3RefineCCD::include_neighbors_
private

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

core::Real protocols::antibody::H3RefineCCD::init_temp_
private
core::Size protocols::antibody::H3RefineCCD::inner_cycles_
private

Referenced by apply(), and init().

bool protocols::antibody::H3RefineCCD::is_camelid_
private

Referenced by set_default().

core::Real protocols::antibody::H3RefineCCD::last_temp_
private

Referenced by init(), and set_default().

core::Size protocols::antibody::H3RefineCCD::loop_begin_
private

Referenced by finalize_setup(), and init().

core::Size protocols::antibody::H3RefineCCD::loop_end_
private

Referenced by finalize_setup(), and init().

minimization_packing::MinMoverOP protocols::antibody::H3RefineCCD::loop_min_mover_
private

Referenced by apply(), and finalize_setup().

CDRNameEnum protocols::antibody::H3RefineCCD::loop_name_
private

Referenced by H3RefineCCD(), and init().

minimization_packing::PackRotamersMoverOP protocols::antibody::H3RefineCCD::loop_repack_
private

Referenced by apply(), and finalize_setup().

core::Size protocols::antibody::H3RefineCCD::loop_size_
private

Referenced by init().

core::Size protocols::antibody::H3RefineCCD::max_cycle_close_trial_
private

Referenced by apply(), and set_default().

moves::MonteCarloOP protocols::antibody::H3RefineCCD::mc_
private

Referenced by apply(), and finalize_setup().

core::Real protocols::antibody::H3RefineCCD::min_tolerance_
private

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

std::string protocols::antibody::H3RefineCCD::minimization_type_
private

Referenced by finalize_setup(), and set_default().

core::Size protocols::antibody::H3RefineCCD::n_small_moves_
private

Referenced by finalize_setup(), and init().

core::Real protocols::antibody::H3RefineCCD::neighbor_dist_
private

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

core::Size protocols::antibody::H3RefineCCD::outer_cycles_
private

Referenced by apply(), and init().

bool protocols::antibody::H3RefineCCD::refine_input_loop_
private

just refine input loop

Referenced by init(), and set_default().

core::pose::Pose protocols::antibody::H3RefineCCD::start_pose_
private
core::pack::task::TaskFactoryOP protocols::antibody::H3RefineCCD::tf_
private
loops::Loop protocols::antibody::H3RefineCCD::the_loop_
private

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

bool protocols::antibody::H3RefineCCD::user_defined_
private

Referenced by H3RefineCCD(), and set_default().

moves::SequenceMoverOP protocols::antibody::H3RefineCCD::wiggle_cdr_h3_
private

Referenced by apply(), and finalize_setup().


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