#include <AntibodyModelerProtocol.hh>

Public Member Functions
	AntibodyModelerProtocol ()

	~AntibodyModelerProtocol ()

virtual protocols::moves::MoverOP	clone () const
	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...

virtual void	apply (pose::Pose &pose)

virtual std::string	get_name () const
	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_H3Filter (bool setting)

void	set_CterInsert (bool setting)

void	set_sc_min (bool setting)

void	set_rt_min (bool setting)

void	set_flank_residue_min (bool setting)

void	set_packonly_after_graft (bool setting)

void	set_perturb_type (std::string remodel)

void	set_refine_type (std::string refine)

void	set_H3Filter_Tolerance (core::Size const number)

void	set_cst_weight (core::Real const cst_weight)

void	set_use_constraints (bool const use_csts)

void	set_constrain_cter (bool const setting)

void	set_constrain_vlvh_qq (bool const setting)

void	set_flank_residue_size (core::Real const flank_residue_size)

void	set_middle_pack_min (bool middle_pack_min)

void	set_bad_nter (bool setting)

void	set_extend_h3_before_modeling (bool setting)

void	set_idealize_h3_stems_before_modeling (bool setting)

void	display_constraint_residues (pose::Pose &pose)

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

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

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...

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 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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

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_jd2 (core::pose::Pose &pose, protocols::jd2::JobOP job)
	Output of various metrics of final model. More...

Private Attributes
bool	model_h3_

bool	snugfit_

bool	refine_h3_

bool	h3_filter_

bool	cter_insert_

bool	LH_repulsive_ramp_

bool	sc_min_

bool	rt_min_

bool	camelid_

bool	camelid_constraints_

bool	flank_residue_min_

core::Real	flank_residue_size_

bool	middle_pack_min_

bool	packonly_after_graft_

std::string	h3_perturb_type_

std::string	h3_refine_type_

core::Real	cen_cst_

core::Real	high_cst_

bool	bad_nter_

bool	extend_h3_before_modeling_

bool	idealize_h3_stems_before_modeling_

bool	use_csts_

bool	constrain_vlvh_qq_

bool	constrain_cter_

bool	benchmark_

bool	user_defined_

bool	flags_and_objects_are_in_sync_

core::Size	h3_filter_tolerance_

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::simple_moves::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 protocols::filters::Filters_map	Filters_map

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_.

Referenced by clone().

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

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

References ab_info_, protocols::loops::add_cutpoint_variants(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), bad_nter_, camelid_constraints_, cdr_constraint_, chemical, constrain_vlvh_qq_, cst_weight_, cter_insert_, protocols::nonlocal::current_job(), display_constraint_residues(), dock_scorefxn_highres_, echo_metrics_to_jd2(), extend_h3_before_modeling_, finalize_setup(), flags_and_objects_are_in_sync_, flank_residue_min_, flank_residue_size_, core::pose::Pose::fold_tree(), protocols::antibody::AntibodyInfo::get_CDR_loop(), protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs(), protocols::jd2::JobDistributor::get_instance(), protocols::antibody::h3, h3_filter_, h3_filter_tolerance_, h3_perturb_type_, h3_refine_type_, idealize_h3_stems_before_modeling_, LH_repulsive_ramp_, loop_scorefxn_centroid_, loop_scorefxn_highres_, model_h3_, protocols::moves::MS_SUCCESS, pack_scorefxn_, packonly_after_graft_, basic::prof_reset(), basic::prof_show(), recover_sidechains, refine_h3_, protocols::loops::remove_cutpoint_variants(), rt_min_, sc_min_, scoring, protocols::antibody::RefineOneCDRLoop::set_flank_size(), protocols::moves::Mover::set_last_move_status(), snugfit_, protocols::loops::Loop::start(), protocols::loops::Loop::stop(), sync_objects_with_flags(), protocols::medal::to_centroid(), core::pose::Pose::total_residue(), and protocols::antibody::TR.

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

virtual

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.

References AntibodyModelerProtocol().

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

References ab_info_, protocols::antibody::Extended, protocols::antibody::AntibodyInfo::get_CDR_loop(), protocols::antibody::AntibodyInfo::get_H3_kink_type(), protocols::antibody::h3, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::antibody::TR.