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protocols::antibody::AntibodyModelerProtocol Class Reference

#include <AntibodyModelerProtocol.hh>

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

 AntibodyModelerProtocol ()
 
 ~AntibodyModelerProtocol () 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 sync_objects_with_flags ()
 Instantiates non-primitive members based on the value of the primitive members. 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 set_BenchMark (bool setting)
 
void set_ModelH3 (bool setting)
 
void set_SnugFit (bool setting)
 
void set_refine_h3 (bool setting)
 
void set_sc_min (bool setting)
 
void set_rt_min (bool setting)
 
void set_packonly_after_graft (bool setting)
 
void set_cst_weight (core::Real const cst_weight)
 
void set_h3_loop_csts_lr (bool const setting)
 
void set_h3_loop_csts_hr (bool const setting)
 
void set_auto_h3_constraint (bool const setting)
 
void set_constrain_vlvh_qq (bool const setting)
 
void set_middle_pack_min (bool middle_pack_min)
 
void set_extend_h3_before_modeling (bool setting)
 
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 init_from_options ()
 Assigns user specified values to primitive members using command line options. More...
 
void finalize_setup (core::pose::Pose &pose)
 Performs the portion of setup of non-primitive members that requires a pose - called on apply. More...
 
void init ()
 Sets up the instance of AntibodyModeler and initializes all members based on values passed in at construction or via the command line. More...
 
void setup_objects ()
 
void echo_metrics_to_output (core::pose::Pose &pose)
 Output of various metrics of final model. More...
 
protocols::loops::Loop get_cdr_h3_loop ()
 Access AntibodyInfo to return loop for modeling, current 93-102 in Chothia numbering. More...
 

Private Attributes

bool model_h3_
 
bool snugfit_
 
bool refine_h3_
 
bool LH_repulsive_ramp_
 
bool sc_min_
 
bool rt_min_
 
bool middle_pack_min_
 
bool packonly_after_graft_
 
core::Real cen_cst_
 
core::Real high_cst_
 
bool extend_h3_before_modeling_
 
bool constrain_vlvh_qq_
 
bool h3_loop_csts_lr_
 
bool h3_loop_csts_hr_
 
bool auto_h3_constraint_
 
bool run_snugdock_ = false
 
bool benchmark_
 
bool user_defined_
 
bool flags_and_objects_are_in_sync_
 
core::Real cst_weight_
 
core::scoring::ScoreFunctionOP loop_scorefxn_highres_
 
core::scoring::ScoreFunctionOP loop_scorefxn_centroid_
 
core::scoring::ScoreFunctionOP dock_scorefxn_highres_
 
core::scoring::ScoreFunctionOP pack_scorefxn_
 
protocols::constraint_movers::ConstraintSetMoverOP cdr_constraint_
 
AntibodyInfoOP ab_info_
 

Friends

std::ostream & operator<< (std::ostream &out, const AntibodyModelerProtocol &ab_m)
 

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
 
- 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::AntibodyModelerProtocol::AntibodyModelerProtocol ( )

References init(), and user_defined_.

protocols::antibody::AntibodyModelerProtocol::~AntibodyModelerProtocol ( )
overridedefault

Member Function Documentation

void protocols::antibody::AntibodyModelerProtocol::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References ab_info_, protocols::loops::add_cutpoint_variants(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::antibody::AntibodyNumberingConverterMover::apply(), protocols::analysis::InterfaceAnalyzerMover::apply(), core::scoring::atom_pair_constraint, auto_h3_constraint_, cdr_constraint_, core::chemical::CENTROID, constrain_vlvh_qq_, cst_weight_, dock_scorefxn_highres_, echo_metrics_to_output(), extend_h3_before_modeling_, core::chemical::FA_STANDARD, finalize_setup(), flags_and_objects_are_in_sync_, core::pose::Pose::fold_tree(), get_cdr_h3_loop(), protocols::antibody::design::get_dock_chains_from_ab_dock_chains(), protocols::antibody::kink_constrain_antibody_H3(), LH_repulsive_ramp_, loop_scorefxn_centroid_, loop_scorefxn_highres_, model_h3_, protocols::moves::MS_SUCCESS, core::chemical::ResidueTypeBase::name(), pack_scorefxn_, packonly_after_graft_, protocols::antibody::qq_constrain_antibody(), refine_h3_, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue_type(), rt_min_, run_snugdock_, sc_min_, protocols::loops::Loop::set_extended(), protocols::moves::Mover::set_last_move_status(), core::pose::set_ss_from_phipsi(), core::pose::Pose::size(), snugfit_, protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), sync_objects_with_flags(), protocols::medal::to_centroid(), and protocols::antibody::TR().

protocols::moves::MoverOP protocols::antibody::AntibodyModelerProtocol::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::AntibodyModelerProtocol::display_constraint_residues ( core::pose::Pose pose)
void protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output ( core::pose::Pose pose)
private
void protocols::antibody::AntibodyModelerProtocol::finalize_setup ( core::pose::Pose pose)
private
loops::Loop protocols::antibody::AntibodyModelerProtocol::get_cdr_h3_loop ( )
private

Access AntibodyInfo to return loop for modeling, current 93-102 in Chothia numbering.

References ab_info_, and protocols::antibody::h3.

Referenced by apply().

std::string protocols::antibody::AntibodyModelerProtocol::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

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

Sets up the instance of AntibodyModeler and initializes all members based on values passed in at construction or via the command line.

References init_from_options(), set_default(), setup_objects(), and protocols::moves::Mover::type().

Referenced by AntibodyModelerProtocol().

void protocols::antibody::AntibodyModelerProtocol::init_from_options ( )
private
void protocols::antibody::AntibodyModelerProtocol::register_options ( )
static

Associates relevant options with the AntibodyModeler class.

void protocols::antibody::AntibodyModelerProtocol::set_auto_h3_constraint ( bool const  setting)
inline

References auto_h3_constraint_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_BenchMark ( bool  setting)
inline

References benchmark_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_constrain_vlvh_qq ( bool const  setting)
inline

References constrain_vlvh_qq_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_cst_weight ( core::Real const  cst_weight)
inline

References cst_weight_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_default ( )
void protocols::antibody::AntibodyModelerProtocol::set_extend_h3_before_modeling ( bool  setting)
inline

References extend_h3_before_modeling_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_h3_loop_csts_hr ( bool const  setting)
inline

References h3_loop_csts_hr_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_h3_loop_csts_lr ( bool const  setting)
inline

References h3_loop_csts_lr_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_middle_pack_min ( bool  middle_pack_min)
inline

References middle_pack_min_.

void protocols::antibody::AntibodyModelerProtocol::set_ModelH3 ( bool  setting)
inline

References model_h3_.

Referenced by init_from_options().

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

References packonly_after_graft_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_refine_h3 ( bool  setting)
inline

References refine_h3_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_rt_min ( bool  setting)
inline

References rt_min_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_sc_min ( bool  setting)
inline

References sc_min_.

Referenced by init_from_options().

void protocols::antibody::AntibodyModelerProtocol::set_SnugFit ( bool  setting)
inline

References snugfit_.

Referenced by init_from_options().

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

Show the complete setup of the antibody modeler protocol

Reimplemented from protocols::moves::Mover.

void protocols::antibody::AntibodyModelerProtocol::sync_objects_with_flags ( )

Instantiates non-primitive members based on the value of the primitive members.

References flags_and_objects_are_in_sync_.

Referenced by apply(), and setup_objects().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const AntibodyModelerProtocol ab_m 
)
friend

Member Data Documentation

AntibodyInfoOP protocols::antibody::AntibodyModelerProtocol::ab_info_
private
bool protocols::antibody::AntibodyModelerProtocol::auto_h3_constraint_
private
bool protocols::antibody::AntibodyModelerProtocol::benchmark_
private

Referenced by set_BenchMark(), and set_default().

protocols::constraint_movers::ConstraintSetMoverOP protocols::antibody::AntibodyModelerProtocol::cdr_constraint_
private

Referenced by apply(), and set_default().

core::Real protocols::antibody::AntibodyModelerProtocol::cen_cst_
private

Referenced by set_default().

bool protocols::antibody::AntibodyModelerProtocol::constrain_vlvh_qq_
private
core::Real protocols::antibody::AntibodyModelerProtocol::cst_weight_
private
core::scoring::ScoreFunctionOP protocols::antibody::AntibodyModelerProtocol::dock_scorefxn_highres_
private

Referenced by apply(), and setup_objects().

bool protocols::antibody::AntibodyModelerProtocol::extend_h3_before_modeling_
private
bool protocols::antibody::AntibodyModelerProtocol::flags_and_objects_are_in_sync_
private

Referenced by apply(), and sync_objects_with_flags().

bool protocols::antibody::AntibodyModelerProtocol::h3_loop_csts_hr_
private
bool protocols::antibody::AntibodyModelerProtocol::h3_loop_csts_lr_
private
core::Real protocols::antibody::AntibodyModelerProtocol::high_cst_
private

Referenced by set_default().

bool protocols::antibody::AntibodyModelerProtocol::LH_repulsive_ramp_
private
core::scoring::ScoreFunctionOP protocols::antibody::AntibodyModelerProtocol::loop_scorefxn_centroid_
private

Referenced by apply(), and setup_objects().

core::scoring::ScoreFunctionOP protocols::antibody::AntibodyModelerProtocol::loop_scorefxn_highres_
private

Referenced by apply(), and setup_objects().

bool protocols::antibody::AntibodyModelerProtocol::middle_pack_min_
private

Referenced by set_default(), and set_middle_pack_min().

bool protocols::antibody::AntibodyModelerProtocol::model_h3_
private
core::scoring::ScoreFunctionOP protocols::antibody::AntibodyModelerProtocol::pack_scorefxn_
private

Referenced by apply(), and setup_objects().

bool protocols::antibody::AntibodyModelerProtocol::packonly_after_graft_
private
bool protocols::antibody::AntibodyModelerProtocol::refine_h3_
private

Referenced by apply(), set_default(), and set_refine_h3().

bool protocols::antibody::AntibodyModelerProtocol::rt_min_
private

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

bool protocols::antibody::AntibodyModelerProtocol::run_snugdock_ = false
private

Referenced by apply(), and init_from_options().

bool protocols::antibody::AntibodyModelerProtocol::sc_min_
private

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

bool protocols::antibody::AntibodyModelerProtocol::snugfit_
private
bool protocols::antibody::AntibodyModelerProtocol::user_defined_
private

Referenced by AntibodyModelerProtocol().


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