#include <SnugDock.hh>

Inheritance diagram for protocols::antibody2::SnugDock:

Collaboration diagram for protocols::antibody2::SnugDock:

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

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

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

virtual	~SnugDock ()

virtual void	apply (Pose &)

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

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. 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...

Size	number_of_high_resolution_cycles () const

void	number_of_high_resolution_cycles (Size const number_of_high_resolution_cycles)

void	set_antibody_info (AntibodyInfoOP antibody_info)

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

Public Member Functions inherited from protocols::docking::DockingHighRes
	DockingHighRes ()
	Default constructor. More...

	DockingHighRes (core::Size const rb_jump)
	Constructor with one argument - the jump number to dock over. More...

	DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn)
	Constructor with two arguments. The first is thejump number, the second is a scorefunction that will be used for docking and packing. More...

	DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
	Constructor with three arguments. The first is the jump number, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...

	DockingHighRes (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
	Constructor with three arguments. The first is the DockJumps, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...

	DockingHighRes (DockingHighRes const &old_instance)

virtual	~DockingHighRes ()

void	set_task_factory (core::pack::task::TaskFactoryCOP tf)

void	set_ignore_default_task (bool ignore_default_task)

bool	ignore_default_task ()

void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)

void	set_scorefxn_pack (core::scoring::ScoreFunctionOP scorefxn_pack)

DockJumps &	movable_jumps ()

DockJumps const &	movable_jumps () const

core::pack::task::TaskFactoryCOP	task_factory ()

void	set_sc_min (bool sc_min)

void	set_rt_min (bool rt_min)

void	set_partners (std::string partners)

void	set_interface_definition_task_operation (protocols::toolbox::task_operations::InterfaceTaskOperationOP interface_definition)

void	set_additional_task_operarations (utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations)

void	add_additional_task_operaration (core::pack::task::operation::TaskOperationOP task_operation)

utility::vector1 < core::pack::task::operation::TaskOperationOP >	get_additional_task_operarations ()

bool	sc_min ()

bool	rt_min ()

std::string	partners ()

core::scoring::ScoreFunctionOP	scorefxn () const

core::scoring::ScoreFunctionOP	scorefxn_pack () 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

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 (TagPtr const tag, 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
	this function informs 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 SnugDock class. More...

Private Member Functions
void	setup_objects (Pose const &pose)

void	init ()

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

void	init_options ()

Private Attributes
AntibodyInfoOP	antibody_info_

moves::MonteCarloOP	mc_

moves::RandomMoverOP	high_resolution_step_

std::string	loop_refinement_method_

antibody2::CDRsMinPackMinOP	pre_minimization_

Size	number_of_high_resolution_cycles_

Friends
std::ostream &	operator<< (std::ostream &out, SnugDock const &snugdock)

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

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::docking::DockingHighRes
protocols::docking::DockTaskFactoryOP	tf2 ()

Detailed Description

Definition at line 46 of file SnugDock.hh.

Constructor & Destructor Documentation

protocols::antibody2::SnugDock::SnugDock ( )

default constructor

Definition at line 61 of file SnugDock.cc.

References init().

Referenced by clone(), and fresh_instance().

protocols::antibody2::SnugDock::SnugDock ( SnugDock const & rhs)

copy constructor

Definition at line 67 of file SnugDock.cc.

References init_for_equal_operator_and_copy_constructor().

protocols::antibody2::SnugDock::~SnugDock ( )

virtual

Definition at line 82 of file SnugDock.cc.

Member Function Documentation

void protocols::antibody2::SnugDock::apply ( Pose & pose)

virtual

Implements protocols::docking::DockingHighRes.

Definition at line 122 of file SnugDock.cc.

References antibody_info_, core::pose::Pose::fold_tree(), get_name(), high_resolution_step_, mc_, number_of_high_resolution_cycles_, pre_minimization_, protocols::docking::DockingHighRes::scorefxn(), setup_objects(), show(), and protocols::TR().

protocols::moves::MoverOP protocols::antibody2::SnugDock::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

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.

Definition at line 92 of file SnugDock.cc.

References SnugDock().

protocols::moves::MoverOP protocols::antibody2::SnugDock::fresh_instance ( ) const

virtual

fresh_instance returns a default-constructed object for JD2

Reimplemented from protocols::moves::Mover.

Definition at line 99 of file SnugDock.cc.

References SnugDock().

std::string protocols::antibody2::SnugDock::get_name ( ) const

virtual

Each derived class must specify its name.