#include <SnugDockProtocol.hh>

Public Member Functions
	SnugDockProtocol ()
	default constructor More...

	SnugDockProtocol (SnugDockProtocol const &rhs)
	copy constructor More...

SnugDockProtocol &	operator= (SnugDockProtocol const &rhs)
	assignment operator More...

virtual	~SnugDockProtocol ()

virtual void	apply (Pose &)

virtual std::string	get_name () const
	Each derived class must specify its name. More...

virtual protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	fresh_instance returns a default-constructed object for JD2 More...

virtual bool	reinitialize_for_new_input () const
	This mover retains state such that a fresh version is needed if the input Pose is about to change. More...

void	show (std::ostream &out=std::cout) const
	Outputs details about the Mover, including current settings. More...

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...

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 SnugDockProtocol 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	setup_objects (Pose const &pose)

void	setup_loop_refinement_movers ()

void	init ()

void	init_for_equal_operator_and_copy_constructor (SnugDockProtocol &lhs, SnugDockProtocol const &rhs)

void	init_options ()

docking::DockingProtocolOP	docking () const

Private Attributes
AntibodyInfoOP	antibody_info_

RefineOneCDRLoopOP	low_res_refine_cdr_h2_

RefineOneCDRLoopOP	low_res_refine_cdr_h3_

docking::DockingProtocolOP	docking_

std::string	loop_refinement_method_

bool	h3_filter_

Size	h3_filter_tolerance_

Friends
std::ostream &	operator<< (std::ostream &out, SnugDockProtocol const &snugdockprotocol)

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::SnugDockProtocol::SnugDockProtocol ( )

default constructor

References init().

Referenced by clone(), and fresh_instance().

protocols::antibody::SnugDockProtocol::SnugDockProtocol ( SnugDockProtocol const & rhs )

copy constructor

References init_for_equal_operator_and_copy_constructor().

protocols::antibody::SnugDockProtocol::~SnugDockProtocol ( )

virtual

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

References antibody_info_, docking(), core::pose::Pose::fold_tree(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), get_name(), setup_objects(), show(), and protocols::antibody::TR.

protocols::moves::MoverOP protocols::antibody::SnugDockProtocol::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 SnugDockProtocol().

docking::DockingProtocolOP protocols::antibody::SnugDockProtocol::docking ( ) const

private

References docking_.

Referenced by apply(), and setup_objects().

protocols::moves::MoverOP protocols::antibody::SnugDockProtocol::fresh_instance ( ) const

virtual

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

References SnugDockProtocol().

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