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protocols::antibody::AntibodyModelerProtocol Class Reference

#include <AntibodyModelerProtocol.hh>

Inheritance diagram for protocols::antibody::AntibodyModelerProtocol:
Inheritance graph

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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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_


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

◆ AntibodyModelerProtocol()

protocols::antibody::AntibodyModelerProtocol::AntibodyModelerProtocol ( )

References init(), and user_defined_.

◆ ~AntibodyModelerProtocol()

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

Member Function Documentation

◆ apply()

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

Main Method.

Implements protocols::moves::Mover.

References ab_info_, protocols::loops::add_cutpoint_variants(), protocols::analysis::InterfaceAnalyzerMover::apply(), protocols::antibody::AntibodyNumberingConverterMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::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().

◆ clone()

protocols::moves::MoverOP protocols::antibody::AntibodyModelerProtocol::clone ( ) const

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.

◆ display_constraint_residues()

void protocols::antibody::AntibodyModelerProtocol::display_constraint_residues ( core::pose::Pose pose)

◆ echo_metrics_to_output()

void protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output ( core::pose::Pose pose)

◆ finalize_setup()

void protocols::antibody::AntibodyModelerProtocol::finalize_setup ( core::pose::Pose pose)

◆ get_cdr_h3_loop()

loops::Loop protocols::antibody::AntibodyModelerProtocol::get_cdr_h3_loop ( )

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

References ab_info_, protocols::loops::Loop::cut(), protocols::antibody::h3, protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by apply().

◆ get_name()

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

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

Implements protocols::moves::Mover.

◆ init()

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

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().

◆ init_from_options()

void protocols::antibody::AntibodyModelerProtocol::init_from_options ( )

◆ register_options()

void protocols::antibody::AntibodyModelerProtocol::register_options ( )

Associates relevant options with the AntibodyModeler class.

◆ set_auto_h3_constraint()

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

References auto_h3_constraint_.

Referenced by init_from_options().

◆ set_BenchMark()

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

References benchmark_.

Referenced by init_from_options().

◆ set_constrain_vlvh_qq()

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

References constrain_vlvh_qq_.

Referenced by init_from_options().

◆ set_cst_weight()

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

References cst_weight_.

Referenced by init_from_options().

◆ set_default()

void protocols::antibody::AntibodyModelerProtocol::set_default ( )

◆ set_extend_h3_before_modeling()

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

References extend_h3_before_modeling_.

Referenced by init_from_options().

◆ set_h3_loop_csts_hr()

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

References h3_loop_csts_hr_.

Referenced by init_from_options().

◆ set_h3_loop_csts_lr()

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

References h3_loop_csts_lr_.

Referenced by init_from_options().

◆ set_middle_pack_min()

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

References middle_pack_min_.

◆ set_ModelH3()

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

References model_h3_.

Referenced by init_from_options().

◆ set_packonly_after_graft()

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

References packonly_after_graft_.

Referenced by init_from_options().

◆ set_refine_h3()

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

References refine_h3_.

Referenced by init_from_options().

◆ set_rt_min()

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

References rt_min_.

Referenced by init_from_options().

◆ set_sc_min()

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

References sc_min_.

Referenced by init_from_options().

◆ set_SnugFit()

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

References snugfit_.

Referenced by init_from_options().

◆ setup_objects()

void protocols::antibody::AntibodyModelerProtocol::setup_objects ( )

◆ show()

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

Show the complete setup of the antibody modeler protocol

Reimplemented from protocols::moves::Mover.

References core::conformation::membrane::out.

◆ sync_objects_with_flags()

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

◆ operator<<

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

Member Data Documentation

◆ ab_info_

AntibodyInfoOP protocols::antibody::AntibodyModelerProtocol::ab_info_

◆ auto_h3_constraint_

bool protocols::antibody::AntibodyModelerProtocol::auto_h3_constraint_

◆ benchmark_

bool protocols::antibody::AntibodyModelerProtocol::benchmark_

Referenced by set_BenchMark(), and set_default().

◆ cdr_constraint_

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

Referenced by apply(), and set_default().

◆ cen_cst_

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

Referenced by set_default().

◆ constrain_vlvh_qq_

bool protocols::antibody::AntibodyModelerProtocol::constrain_vlvh_qq_

◆ cst_weight_

core::Real protocols::antibody::AntibodyModelerProtocol::cst_weight_

◆ dock_scorefxn_highres_

core::scoring::ScoreFunctionOP protocols::antibody::AntibodyModelerProtocol::dock_scorefxn_highres_

Referenced by apply(), and setup_objects().

◆ extend_h3_before_modeling_

bool protocols::antibody::AntibodyModelerProtocol::extend_h3_before_modeling_

◆ flags_and_objects_are_in_sync_

bool protocols::antibody::AntibodyModelerProtocol::flags_and_objects_are_in_sync_

Referenced by apply(), and sync_objects_with_flags().

◆ h3_loop_csts_hr_

bool protocols::antibody::AntibodyModelerProtocol::h3_loop_csts_hr_

◆ h3_loop_csts_lr_

bool protocols::antibody::AntibodyModelerProtocol::h3_loop_csts_lr_

◆ high_cst_

core::Real protocols::antibody::AntibodyModelerProtocol::high_cst_

Referenced by set_default().

◆ LH_repulsive_ramp_

bool protocols::antibody::AntibodyModelerProtocol::LH_repulsive_ramp_

Referenced by apply(), and set_default().

◆ loop_scorefxn_centroid_

core::scoring::ScoreFunctionOP protocols::antibody::AntibodyModelerProtocol::loop_scorefxn_centroid_

Referenced by apply(), and setup_objects().

◆ loop_scorefxn_highres_

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

Referenced by apply(), and setup_objects().

◆ middle_pack_min_

bool protocols::antibody::AntibodyModelerProtocol::middle_pack_min_

Referenced by set_default(), and set_middle_pack_min().

◆ model_h3_

bool protocols::antibody::AntibodyModelerProtocol::model_h3_

Referenced by apply(), set_default(), and set_ModelH3().

◆ pack_scorefxn_

core::scoring::ScoreFunctionOP protocols::antibody::AntibodyModelerProtocol::pack_scorefxn_

Referenced by apply(), and setup_objects().

◆ packonly_after_graft_

bool protocols::antibody::AntibodyModelerProtocol::packonly_after_graft_

◆ refine_h3_

bool protocols::antibody::AntibodyModelerProtocol::refine_h3_

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

◆ rt_min_

bool protocols::antibody::AntibodyModelerProtocol::rt_min_

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

◆ run_snugdock_

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

Referenced by apply(), and init_from_options().

◆ sc_min_

bool protocols::antibody::AntibodyModelerProtocol::sc_min_

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

◆ snugfit_

bool protocols::antibody::AntibodyModelerProtocol::snugfit_

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

◆ user_defined_

bool protocols::antibody::AntibodyModelerProtocol::user_defined_

Referenced by AntibodyModelerProtocol().

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