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protocols::antibody::GraftCDRLoopsProtocol Class Reference

#include <GraftCDRLoopsProtocol.hh>

Inheritance diagram for protocols::antibody::GraftCDRLoopsProtocol:
Inheritance graph
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Public Types

typedef std::map< std::string,
bool
GraftMap
 
- 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
 

Public Member Functions

 GraftCDRLoopsProtocol ()
 
 ~GraftCDRLoopsProtocol () override
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void set_default ()
 Assigns default values to primitive members. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void set_graft_l1 (bool graft_l1)
 
void set_graft_l2 (bool graft_l2)
 
void set_graft_l3 (bool graft_l3)
 
void set_graft_h1 (bool graft_h1)
 
void set_graft_h2 (bool graft_h2)
 
void set_graft_h3 (bool graft_h3)
 
void set_h3_stem_graft (bool h3_stem_graft)
 
void set_packonly_after_graft (bool setting)
 
void set_stem_optimize (bool setting)
 
void set_camelid (bool camelid)
 
void set_camelid_constraints (bool camelid_constraints)
 
void set_benchmark (bool benchmark)
 
void set_cst_weight (core::Real cst_weight)
 
void set_sc_min (bool scmin)
 
void set_rt_min (bool rtmin)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void display_constraint_residues (core::pose::Pose &pose)
 
void show (std::ostream &out=std::cout) const override
 
- 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 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...
 

Static Public Member Functions

static void register_options ()
 Associates relevant options with the AntibodyModeler 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 finalize_setup (core::pose::Pose &pose)
 
void init ()
 
void setup_objects ()
 
void init_from_options ()
 

Private Attributes

bool graft_l1_
 
bool graft_l2_
 
bool graft_l3_
 
bool graft_h1_
 
bool graft_h2_
 
bool graft_h3_
 
bool h3_no_stem_graft_
 
bool packonly_after_graft_
 
bool camelid_
 
bool camelid_constraints_
 
bool sc_min_
 
bool rt_min_
 
bool benchmark_
 
bool stem_optimize_
 
core::Real cst_weight_
 
core::scoring::ScoreFunctionOP scorefxn_pack_
 
AntibodyInfoOP ab_info_
 
Ab_TemplateInfoOP ab_t_info_
 
core::pack::task::TaskFactoryOP tf_
 
protocols::moves::SequenceMoverOP graft_sequence_
 
protocols::moves::SequenceMoverOP optimize_sequence_
 
CDRsMinPackMinOP cdrs_min_pack_min_
 

Friends

std::ostream & operator<< (std::ostream &out, const GraftCDRLoopsProtocol &ab_m_2)
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::antibody::GraftCDRLoopsProtocol::GraftCDRLoopsProtocol ( )

References init().

protocols::antibody::GraftCDRLoopsProtocol::~GraftCDRLoopsProtocol ( )
overridedefault

Member Function Documentation

void protocols::antibody::GraftCDRLoopsProtocol::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::antibody::GraftCDRLoopsProtocol::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::GraftCDRLoopsProtocol::display_constraint_residues ( core::pose::Pose pose)
void protocols::antibody::GraftCDRLoopsProtocol::finalize_setup ( core::pose::Pose pose)
private
std::string protocols::antibody::GraftCDRLoopsProtocol::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::antibody::GraftCDRLoopsProtocol::init ( void  )
private
void protocols::antibody::GraftCDRLoopsProtocol::init_from_options ( )
private
void protocols::antibody::GraftCDRLoopsProtocol::register_options ( )
static

Associates relevant options with the AntibodyModeler class.

Referenced by init().

void protocols::antibody::GraftCDRLoopsProtocol::set_benchmark ( bool  benchmark)
inline

References benchmark_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_camelid ( bool  camelid)
inline

References camelid_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_camelid_constraints ( bool  camelid_constraints)
inline

References camelid_constraints_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_cst_weight ( core::Real  cst_weight)
inline

References cst_weight_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_default ( )
void protocols::antibody::GraftCDRLoopsProtocol::set_graft_h1 ( bool  graft_h1)
inline

References graft_h1_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_h2 ( bool  graft_h2)
inline

References graft_h2_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_h3 ( bool  graft_h3)
inline

References graft_h3_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_l1 ( bool  graft_l1)
inline

References graft_l1_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_l2 ( bool  graft_l2)
inline

References graft_l2_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_graft_l3 ( bool  graft_l3)
inline

References graft_l3_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_h3_stem_graft ( bool  h3_stem_graft)
inline

References h3_no_stem_graft_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_packonly_after_graft ( bool  setting)
inline

References packonly_after_graft_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::set_rt_min ( bool  rtmin)
inline

References rt_min_.

void protocols::antibody::GraftCDRLoopsProtocol::set_sc_min ( bool  scmin)
inline

References sc_min_.

void protocols::antibody::GraftCDRLoopsProtocol::set_stem_optimize ( bool  setting)
inline

References stem_optimize_.

Referenced by init_from_options().

void protocols::antibody::GraftCDRLoopsProtocol::setup_objects ( )
private
void protocols::antibody::GraftCDRLoopsProtocol::show ( std::ostream &  out = std::cout) const
overridevirtual

Show the complete setup of the docking protocol

Reimplemented from protocols::moves::Mover.

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const GraftCDRLoopsProtocol ab_m_2 
)
friend

Member Data Documentation

AntibodyInfoOP protocols::antibody::GraftCDRLoopsProtocol::ab_info_
private
Ab_TemplateInfoOP protocols::antibody::GraftCDRLoopsProtocol::ab_t_info_
private

Referenced by finalize_setup(), and setup_objects().

bool protocols::antibody::GraftCDRLoopsProtocol::benchmark_
private
bool protocols::antibody::GraftCDRLoopsProtocol::camelid_
private
bool protocols::antibody::GraftCDRLoopsProtocol::camelid_constraints_
private
CDRsMinPackMinOP protocols::antibody::GraftCDRLoopsProtocol::cdrs_min_pack_min_
private

Referenced by apply(), and finalize_setup().

core::Real protocols::antibody::GraftCDRLoopsProtocol::cst_weight_
private
bool protocols::antibody::GraftCDRLoopsProtocol::graft_h1_
private
bool protocols::antibody::GraftCDRLoopsProtocol::graft_h2_
private
bool protocols::antibody::GraftCDRLoopsProtocol::graft_h3_
private
bool protocols::antibody::GraftCDRLoopsProtocol::graft_l1_
private
bool protocols::antibody::GraftCDRLoopsProtocol::graft_l2_
private
bool protocols::antibody::GraftCDRLoopsProtocol::graft_l3_
private
protocols::moves::SequenceMoverOP protocols::antibody::GraftCDRLoopsProtocol::graft_sequence_
private
bool protocols::antibody::GraftCDRLoopsProtocol::h3_no_stem_graft_
private
protocols::moves::SequenceMoverOP protocols::antibody::GraftCDRLoopsProtocol::optimize_sequence_
private

Referenced by apply(), and finalize_setup().

bool protocols::antibody::GraftCDRLoopsProtocol::packonly_after_graft_
private
bool protocols::antibody::GraftCDRLoopsProtocol::rt_min_
private
bool protocols::antibody::GraftCDRLoopsProtocol::sc_min_
private
core::scoring::ScoreFunctionOP protocols::antibody::GraftCDRLoopsProtocol::scorefxn_pack_
private

Referenced by setup_objects().

bool protocols::antibody::GraftCDRLoopsProtocol::stem_optimize_
private
core::pack::task::TaskFactoryOP protocols::antibody::GraftCDRLoopsProtocol::tf_
private

Referenced by finalize_setup(), and setup_objects().


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