#include <AntibodyModelerProtocol.hh>

Inheritance diagram for protocols::antibody::AntibodyModelerProtocol:

[legend]

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 Strings &	info ()
	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_

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

◆ AntibodyModelerProtocol()

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

References init(), and user_defined_.

◆ ~AntibodyModelerProtocol()

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

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

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

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.

◆ display_constraint_residues()

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

References ab_info_, protocols::antibody::Extended, protocols::antibody::h3, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::loops::stop, and protocols::antibody::TR().

◆ echo_metrics_to_output()

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

private

Output of various metrics of final model.

Referenced by apply().

◆ finalize_setup()

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

private

Performs the portion of setup of non-primitive members that requires a pose - called on apply.

References ab_info_, constrain_vlvh_qq_, core::pose::Pose::fold_tree(), protocols::moves::Mover::get_input_pose(), protocols::moves::Mover::get_native_pose(), protocols::moves::Mover::set_input_pose(), protocols::moves::Mover::set_native_pose(), core::pose::set_ss_from_phipsi(), and protocols::antibody::TR().

Referenced by apply().

◆ get_cdr_h3_loop()

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_, 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

overridevirtual

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

Implements protocols::moves::Mover.

◆ init()

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().

◆ init_from_options()

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

private

Assigns user specified values to primitive members using command line options.

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), run_snugdock_, set_auto_h3_constraint(), set_BenchMark(), set_constrain_vlvh_qq(), set_cst_weight(), set_extend_h3_before_modeling(), set_h3_loop_csts_hr(), set_h3_loop_csts_lr(), set_ModelH3(), protocols::moves::Mover::set_native_pose(), set_packonly_after_graft(), set_refine_h3(), set_rt_min(), set_sc_min(), set_SnugFit(), and protocols::antibody::TR().

Referenced by init().

◆ register_options()

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

static

Associates relevant options with the AntibodyModeler class.

◆ set_auto_h3_constraint()

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

inline

References auto_h3_constraint_.

Referenced by init_from_options().

◆ set_BenchMark()

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

inline

References benchmark_.

Referenced by init_from_options().

◆ set_constrain_vlvh_qq()

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

inline

References constrain_vlvh_qq_.

Referenced by init_from_options().

◆ set_cst_weight()

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

inline

References cst_weight_.

Referenced by init_from_options().

◆ set_default()

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

Assigns default values to primitive members.

References auto_h3_constraint_, benchmark_, cdr_constraint_, cen_cst_, constrain_vlvh_qq_, cst_weight_, extend_h3_before_modeling_, h3_loop_csts_hr_, h3_loop_csts_lr_, high_cst_, LH_repulsive_ramp_, middle_pack_min_, model_h3_, packonly_after_graft_, refine_h3_, rt_min_, sc_min_, snugfit_, and protocols::antibody::TR().

Referenced by init().

◆ set_extend_h3_before_modeling()

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

inline

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 )

inline

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 )

inline

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 )

inline

References middle_pack_min_.

◆ set_ModelH3()

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

inline

References model_h3_.

Referenced by init_from_options().

◆ set_packonly_after_graft()

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

inline

References packonly_after_graft_.

Referenced by init_from_options().

◆ set_refine_h3()

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

inline

References refine_h3_.

Referenced by init_from_options().

◆ set_rt_min()

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

inline

References rt_min_.

Referenced by init_from_options().

◆ set_sc_min()

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

inline

References sc_min_.

Referenced by init_from_options().

◆ set_SnugFit()

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

inline

References snugfit_.

Referenced by init_from_options().

◆ setup_objects()

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

private

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::chainbreak, constrain_vlvh_qq_, core::scoring::ScoreFunctionFactory::create_score_function(), cst_weight_, core::scoring::dihedral_constraint, dock_scorefxn_highres_, core::scoring::get_score_function(), h3_loop_csts_hr_, h3_loop_csts_lr_, loop_scorefxn_centroid_, loop_scorefxn_highres_, core::scoring::overlap_chainbreak, pack_scorefxn_, sync_objects_with_flags(), and protocols::antibody::TR().

Referenced by init().

◆ show()

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.

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
	)

friend

Member Data Documentation

◆ ab_info_

AntibodyInfoOP protocols::antibody::AntibodyModelerProtocol::ab_info_

private

Referenced by apply(), display_constraint_residues(), echo_metrics_to_output(), finalize_setup(), and get_cdr_h3_loop().

◆ auto_h3_constraint_

bool protocols::antibody::AntibodyModelerProtocol::auto_h3_constraint_

private

Referenced by apply(), set_auto_h3_constraint(), and set_default().

◆ benchmark_

bool protocols::antibody::AntibodyModelerProtocol::benchmark_

private

Referenced by set_BenchMark(), and set_default().

◆ cdr_constraint_

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

private

Referenced by apply(), and set_default().

◆ cen_cst_

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

private

Referenced by set_default().

◆ constrain_vlvh_qq_

bool protocols::antibody::AntibodyModelerProtocol::constrain_vlvh_qq_

private

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

◆ cst_weight_

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

private

Referenced by apply(), set_cst_weight(), set_default(), and setup_objects().

◆ dock_scorefxn_highres_

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

private

Referenced by apply(), and setup_objects().

◆ extend_h3_before_modeling_

bool protocols::antibody::AntibodyModelerProtocol::extend_h3_before_modeling_

private

Referenced by apply(), set_default(), and set_extend_h3_before_modeling().

◆ flags_and_objects_are_in_sync_

bool protocols::antibody::AntibodyModelerProtocol::flags_and_objects_are_in_sync_

private

Referenced by apply(), and sync_objects_with_flags().

◆ h3_loop_csts_hr_

bool protocols::antibody::AntibodyModelerProtocol::h3_loop_csts_hr_

private

Referenced by set_default(), set_h3_loop_csts_hr(), and setup_objects().

◆ h3_loop_csts_lr_

bool protocols::antibody::AntibodyModelerProtocol::h3_loop_csts_lr_

private

Referenced by set_default(), set_h3_loop_csts_lr(), and setup_objects().

◆ high_cst_

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

private

Referenced by set_default().

◆ LH_repulsive_ramp_

bool protocols::antibody::AntibodyModelerProtocol::LH_repulsive_ramp_

private

Referenced by apply(), and set_default().

◆ loop_scorefxn_centroid_

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

private

Referenced by apply(), and setup_objects().

◆ loop_scorefxn_highres_

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

private

Referenced by apply(), and setup_objects().

◆ middle_pack_min_

bool protocols::antibody::AntibodyModelerProtocol::middle_pack_min_

private

Referenced by set_default(), and set_middle_pack_min().

◆ model_h3_

bool protocols::antibody::AntibodyModelerProtocol::model_h3_

private

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

◆ pack_scorefxn_

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

private

Referenced by apply(), and setup_objects().

◆ packonly_after_graft_

bool protocols::antibody::AntibodyModelerProtocol::packonly_after_graft_

private

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

◆ refine_h3_

bool protocols::antibody::AntibodyModelerProtocol::refine_h3_

private

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

◆ rt_min_

bool protocols::antibody::AntibodyModelerProtocol::rt_min_

private

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

◆ run_snugdock_

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

private

Referenced by apply(), and init_from_options().

◆ sc_min_

bool protocols::antibody::AntibodyModelerProtocol::sc_min_

private

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

◆ snugfit_

bool protocols::antibody::AntibodyModelerProtocol::snugfit_

private

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

◆ user_defined_

bool protocols::antibody::AntibodyModelerProtocol::user_defined_

private

Referenced by AntibodyModelerProtocol().

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

src/protocols/antibody/AntibodyModelerProtocol.hh
src/protocols/antibody/AntibodyModelerProtocol.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

◆ AntibodyModelerProtocol()

◆ ~AntibodyModelerProtocol()

Member Function Documentation

◆ apply()

◆ clone()

◆ display_constraint_residues()

◆ echo_metrics_to_output()

◆ finalize_setup()

◆ get_cdr_h3_loop()

◆ get_name()

◆ init()

◆ init_from_options()

◆ register_options()

◆ set_auto_h3_constraint()

◆ set_BenchMark()

◆ set_constrain_vlvh_qq()

◆ set_cst_weight()

◆ set_default()

◆ set_extend_h3_before_modeling()

◆ set_h3_loop_csts_hr()

◆ set_h3_loop_csts_lr()

◆ set_middle_pack_min()

◆ set_ModelH3()

◆ set_packonly_after_graft()

◆ set_refine_h3()

◆ set_rt_min()

◆ set_sc_min()

◆ set_SnugFit()

◆ setup_objects()

◆ show()

◆ sync_objects_with_flags()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ ab_info_

◆ auto_h3_constraint_

◆ benchmark_

◆ cdr_constraint_

◆ cen_cst_

◆ constrain_vlvh_qq_

◆ cst_weight_

◆ dock_scorefxn_highres_

◆ extend_h3_before_modeling_

◆ flags_and_objects_are_in_sync_

◆ h3_loop_csts_hr_

◆ h3_loop_csts_lr_

◆ high_cst_

◆ LH_repulsive_ramp_

◆ loop_scorefxn_centroid_

◆ loop_scorefxn_highres_

◆ middle_pack_min_

◆ model_h3_

◆ pack_scorefxn_

◆ packonly_after_graft_

◆ refine_h3_

◆ rt_min_

◆ run_snugdock_

◆ sc_min_

◆ snugfit_

◆ user_defined_