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protocols::antibody::H3PerturbCCD Class Reference

#include <H3PerturbCCD.hh>

Inheritance diagram for protocols::antibody::H3PerturbCCD:
Inheritance graph
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Public Member Functions

 H3PerturbCCD ()
 default constructor More...
 
 H3PerturbCCD (AntibodyInfoOP antibody_in)
 constructor with arguments More...
 
 H3PerturbCCD (AntibodyInfoOP antibody_in, core::scoring::ScoreFunctionCOP highres_scorefxn)
 constructor with arguments More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
 ~H3PerturbCCD () override
 default destructor More...
 
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 read_and_store_fragments ()
 
void pass_the_loop (loops::Loop &input_loop)
 
void turn_off_H3_filter ()
 
void set_lowres_score_func (core::scoring::ScoreFunctionCOP lowres_scorefxn)
 set scorefunction for low resolution of CDR H3 modeling More...
 
- 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)
 
void build_centroid_loop (core::pose::Pose &pose)
 Build centroid mode CDR H3 loop. More...
 
void scored_frag_close (core::pose::Pose &pose_in, loops::Loop const trimmed_cdr_h3)
 

Private Attributes

AntibodyInfoOP ab_info_
 
loops::Loop input_loop_
 
bool user_defined_
 
bool is_camelid_
 
core::Size cutoff_9_
 size of loop above which 9mer frags are used More...
 
core::Size cutoff_3_
 size of loop above which 3mer frags are used More...
 
core::scoring::ScoreFunctionOP lowres_scorefxn_
 
core::Real cen_cst_
 
bool current_loop_is_H3_
 flag indicating that current loop being modeled is CDR H3 More...
 
bool H3_filter_
 actually enables H3 filter for H3 operations More...
 
core::Size num_cycles1_
 
core::Size max_ccd_cycles_
 
utility::vector1
< core::fragment::FragSetOP
cdr_h3_frags_
 
core::Real h3_fraction_
 
core::Real ccd_threshold_
 
core::Real Temperature_
 
protocols::moves::MonteCarloOP mc_
 
protocols::moves::MonteCarloOP outer_mc_
 

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::H3PerturbCCD::H3PerturbCCD ( )

default constructor

References user_defined_.

protocols::antibody::H3PerturbCCD::H3PerturbCCD ( AntibodyInfoOP  antibody_in)

constructor with arguments

References ab_info_, init(), and user_defined_.

protocols::antibody::H3PerturbCCD::H3PerturbCCD ( AntibodyInfoOP  antibody_in,
core::scoring::ScoreFunctionCOP  highres_scorefxn 
)

constructor with arguments

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

protocols::antibody::H3PerturbCCD::~H3PerturbCCD ( )
overridedefault

default destructor

Member Function Documentation

void protocols::antibody::H3PerturbCCD::apply ( core::pose::Pose )
overridevirtual
void protocols::antibody::H3PerturbCCD::build_centroid_loop ( core::pose::Pose pose)
private

Build centroid mode CDR H3 loop.

protocols::moves::MoverOP protocols::antibody::H3PerturbCCD::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::H3PerturbCCD::finalize_setup ( core::pose::Pose pose)
private
std::string protocols::antibody::H3PerturbCCD::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

void protocols::antibody::H3PerturbCCD::init ( void  )
private

References set_default().

Referenced by H3PerturbCCD().

void protocols::antibody::H3PerturbCCD::pass_the_loop ( loops::Loop input_loop)
inline

References input_loop_.

void protocols::antibody::H3PerturbCCD::read_and_store_fragments ( )
void protocols::antibody::H3PerturbCCD::scored_frag_close ( core::pose::Pose pose_in,
loops::Loop const  trimmed_cdr_h3 
)
private
void protocols::antibody::H3PerturbCCD::set_default ( )
private
void protocols::antibody::H3PerturbCCD::set_lowres_score_func ( core::scoring::ScoreFunctionCOP  lowres_scorefxn)
inline

set scorefunction for low resolution of CDR H3 modeling

References lowres_scorefxn_.

void protocols::antibody::H3PerturbCCD::turn_off_H3_filter ( )
inline

References H3_filter_.

Member Data Documentation

AntibodyInfoOP protocols::antibody::H3PerturbCCD::ab_info_
private
core::Real protocols::antibody::H3PerturbCCD::ccd_threshold_
private

Referenced by apply(), and set_default().

utility::vector1< core::fragment::FragSetOP > protocols::antibody::H3PerturbCCD::cdr_h3_frags_
private

Referenced by apply(), and read_and_store_fragments().

core::Real protocols::antibody::H3PerturbCCD::cen_cst_
private

Referenced by set_default().

bool protocols::antibody::H3PerturbCCD::current_loop_is_H3_
private

flag indicating that current loop being modeled is CDR H3

Referenced by apply(), and set_default().

core::Size protocols::antibody::H3PerturbCCD::cutoff_3_
private

size of loop above which 3mer frags are used

Referenced by set_default().

core::Size protocols::antibody::H3PerturbCCD::cutoff_9_
private

size of loop above which 9mer frags are used

Referenced by apply(), and set_default().

bool protocols::antibody::H3PerturbCCD::H3_filter_
private

actually enables H3 filter for H3 operations

Referenced by apply(), set_default(), and turn_off_H3_filter().

core::Real protocols::antibody::H3PerturbCCD::h3_fraction_
private

Referenced by apply(), and set_default().

loops::Loop protocols::antibody::H3PerturbCCD::input_loop_
private

Referenced by apply(), and pass_the_loop().

bool protocols::antibody::H3PerturbCCD::is_camelid_
private

Referenced by apply(), and set_default().

core::scoring::ScoreFunctionOP protocols::antibody::H3PerturbCCD::lowres_scorefxn_
private
core::Size protocols::antibody::H3PerturbCCD::max_ccd_cycles_
private

Referenced by apply(), and set_default().

protocols::moves::MonteCarloOP protocols::antibody::H3PerturbCCD::mc_
private

Referenced by apply(), and finalize_setup().

core::Size protocols::antibody::H3PerturbCCD::num_cycles1_
private

Referenced by apply(), and set_default().

protocols::moves::MonteCarloOP protocols::antibody::H3PerturbCCD::outer_mc_
private

Referenced by apply(), and finalize_setup().

core::Real protocols::antibody::H3PerturbCCD::Temperature_
private

Referenced by finalize_setup(), and set_default().

bool protocols::antibody::H3PerturbCCD::user_defined_
private

Referenced by H3PerturbCCD(), and set_default().


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