#include <NcbbDockDesignProtocol.hh>

Public Member Functions
	NcbbDockDesignProtocol ()

	NcbbDockDesignProtocol (core::scoring::ScoreFunctionOP score_function, core::Real const mc_temp, core::Real const pert_mc_temp, core::Real const pert_dock_rot_mag, core::Real const pert_dock_trans_mag, core::Real const pert_pep_small_temp, core::Real const pert_pep_small_H, core::Real const pert_pep_small_L, core::Real const pert_pep_small_E, core::Real const pert_pep_shear_temp, core::Real const pert_pep_shear_H, core::Real const pert_pep_shear_L, core::Real const pert_pep_shear_E, core::Size const pert_pep_num_rep, core::Size const pert_num, core::Size const dock_design_loop_num, bool const no_design, bool const final_design_min, bool const use_soft_rep, bool const mc_initial_pose, bool const ncbb_design_first, bool const pymol, bool const keep_history)

	NcbbDockDesignProtocol (core::scoring::ScoreFunctionOP score_function, core::Real const mc_temp, core::Real const pert_dock_rot_mag, core::Real const pert_dock_trans_mag, core::Size const dock_design_loop_num, bool const no_design, bool const final_design_min, bool const pymol, bool const keep_history)

virtual	~NcbbDockDesignProtocol ()

virtual void	apply (core::pose::Pose &pose)

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

void	setup_filter_stats ()

protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

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

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

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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Private Member Functions
void	setup_pert_foldtree (core::pose::Pose &pose)

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

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...

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::ncbb::NcbbDockDesignProtocol::NcbbDockDesignProtocol ( )

References get_score_function(), and score_fxn_.

Referenced by clone(), and protocols::ncbb::NcbbDockDesignProtocolCreator::create_mover().

protocols::ncbb::NcbbDockDesignProtocol::NcbbDockDesignProtocol	(	core::scoring::ScoreFunctionOP	score_function,
		core::Real const	mc_temp,
		core::Real const	pert_mc_temp,
		core::Real const	pert_dock_rot_mag,
		core::Real const	pert_dock_trans_mag,
		core::Real const	pert_pep_small_temp,
		core::Real const	pert_pep_small_H,
		core::Real const	pert_pep_small_L,
		core::Real const	pert_pep_small_E,
		core::Real const	pert_pep_shear_temp,
		core::Real const	pert_pep_shear_H,
		core::Real const	pert_pep_shear_L,
		core::Real const	pert_pep_shear_E,
		core::Size const	pert_pep_num_rep,
		core::Size const	pert_num,
		core::Size const	dock_design_loop_num,
		bool const	no_design,
		bool const	final_design_min,
		bool const	use_soft_rep,
		bool const	mc_initial_pose,
		bool const	ncbb_design_first,
		bool const	pymol,
		bool const	keep_history
	)

protocols::ncbb::NcbbDockDesignProtocol::NcbbDockDesignProtocol	(	core::scoring::ScoreFunctionOP	score_function,
		core::Real const	mc_temp,
		core::Real const	pert_dock_rot_mag,
		core::Real const	pert_dock_trans_mag,
		core::Size const	dock_design_loop_num,
		bool const	no_design,
		bool const	final_design_min,
		bool const	pymol,
		bool const	keep_history
	)

virtual protocols::ncbb::NcbbDockDesignProtocol::~NcbbDockDesignProtocol ( )

inlinevirtual

Member Function Documentation

void protocols::ncbb::NcbbDockDesignProtocol::apply ( core::pose::Pose & pose )

virtual

Implements protocols::moves::Mover.

References protocols::moves::MoverContainer::add_mover(), protocols::jd2::Job::add_string_real_pair(), protocols::moves::AddPyMolObserver(), core::pack::task::ResidueLevelTask::and_extrachi_cutoff(), protocols::simple_moves::BackboneMover::angle_max(), protocols::simple_moves::PackRotamersMover::apply(), protocols::simple_moves::MinMover::apply(), protocols::moves::TrialMover::apply(), protocols::moves::SequenceMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), core::scoring::atom_pair_constraint, protocols::moves::MonteCarlo::boltzmann(), core::conformation::Conformation::chain_begin(), core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), protocols::nonlocal::current_job(), dock_design_loop_num_, core::pose::Pose::energies(), FA_STANDARD_SOFT, final_design_min_, protocols::jd2::JobDistributor::get_instance(), get_score_function(), hbond_bb_sc, hbond_lr_bb, hbond_sc, hbond_sr_bb, core::pose::ncbb::initialize_hbs(), core::pose::ncbb::initialize_ncbbs(), core::pose::ncbb::initialize_oops(), keep_history_, mc, mc_initial_pose_, mc_temp_, core::pose::Pose::metric(), ncbb_design_first_, no_design_, core::pack::task::PackerTask::nonconst_residue_task(), option, core::pack::task::ResidueLevelTask::or_ex1(), core::pack::task::ResidueLevelTask::or_ex2(), pert_dock_rot_mag_, pert_dock_trans_mag_, pert_mc_temp_, pert_num_, pert_pep_num_rep_, pert_pep_shear_E_, pert_pep_shear_H_, pert_pep_shear_L_, pert_pep_shear_temp_, pert_pep_small_E_, pert_pep_small_H_, pert_pep_small_L_, pert_pep_small_temp_, core::pack::task::TaskFactory::push_back(), pymol_, protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::reset(), protocols::simple_moves::PackRotamersMover::score_function(), score_fxn_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_bb_true_range(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), setup_pert_foldtree(), protocols::moves::MonteCarlo::show_state(), protocols::rigid::RigidBodyTransMover::step_size(), protocols::simple_moves::PackRotamersMover::task_factory(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), protocols::TR, protocols::stepwise::sampler::rigid_body::translate(), use_soft_rep_, and basic::MetricValue< T >::value().

protocols::moves::MoverOP protocols::ncbb::NcbbDockDesignProtocol::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 dock_design_loop_num_, final_design_min_, keep_history_, mc_initial_pose_, mc_temp_, ncbb_design_first_, NcbbDockDesignProtocol(), no_design_, pert_dock_rot_mag_, pert_dock_trans_mag_, pert_mc_temp_, pert_num_, pert_pep_num_rep_, pert_pep_shear_E_, pert_pep_shear_H_, pert_pep_shear_L_, pert_pep_shear_temp_, pert_pep_small_E_, pert_pep_small_H_, pert_pep_small_L_, pert_pep_small_temp_, pymol_, score_fxn_, and use_soft_rep_.

protocols::moves::MoverOP protocols::ncbb::NcbbDockDesignProtocol::fresh_instance ( ) const

inlinevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

virtual std::string protocols::ncbb::NcbbDockDesignProtocol::get_name ( ) const

inlinevirtual

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

Implements protocols::moves::Mover.

void protocols::ncbb::NcbbDockDesignProtocol::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References dock_design_loop_num_, final_design_min_, basic::datacache::DataMap::get(), basic::datacache::DataMap::has(), keep_history_, mc_initial_pose_, mc_temp_, ncbb_design_first_, no_design_, pert_dock_rot_mag_, pert_dock_trans_mag_, pert_mc_temp_, pert_num_, pert_pep_num_rep_, pert_pep_shear_E_, pert_pep_shear_H_, pert_pep_shear_L_, pert_pep_shear_temp_, pert_pep_small_E_, pert_pep_small_H_, pert_pep_small_L_, pert_pep_small_temp_, pymol_, score_fxn_, and use_soft_rep_.

void protocols::ncbb::NcbbDockDesignProtocol::setup_filter_stats ( )

void protocols::ncbb::NcbbDockDesignProtocol::setup_pert_foldtree ( core::pose::Pose & pose )

private

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), protocols::make_rot_lib::PEPTIDE, and core::pose::residue_center_of_mass().

Referenced by apply().

Member Data Documentation

core::Size protocols::ncbb::NcbbDockDesignProtocol::dock_design_loop_num_

private

Referenced by apply(), clone(), and parse_my_tag().

bool protocols::ncbb::NcbbDockDesignProtocol::final_design_min_

private

Referenced by apply(), clone(), and parse_my_tag().

bool protocols::ncbb::NcbbDockDesignProtocol::keep_history_

private

Referenced by apply(), clone(), and parse_my_tag().

bool protocols::ncbb::NcbbDockDesignProtocol::mc_initial_pose_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::mc_temp_

private

Referenced by apply(), clone(), and parse_my_tag().

bool protocols::ncbb::NcbbDockDesignProtocol::ncbb_design_first_

private

Referenced by apply(), clone(), and parse_my_tag().

bool protocols::ncbb::NcbbDockDesignProtocol::no_design_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_dock_rot_mag_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_dock_trans_mag_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_mc_temp_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Size protocols::ncbb::NcbbDockDesignProtocol::pert_num_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Size protocols::ncbb::NcbbDockDesignProtocol::pert_pep_num_rep_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_pep_shear_E_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_pep_shear_H_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_pep_shear_L_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_pep_shear_temp_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_pep_small_E_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_pep_small_H_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_pep_small_L_

private

Referenced by apply(), clone(), and parse_my_tag().

core::Real protocols::ncbb::NcbbDockDesignProtocol::pert_pep_small_temp_

private

Referenced by apply(), clone(), and parse_my_tag().

bool protocols::ncbb::NcbbDockDesignProtocol::pymol_

private

Referenced by apply(), clone(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::ncbb::NcbbDockDesignProtocol::score_fxn_

private

Referenced by apply(), clone(), NcbbDockDesignProtocol(), and parse_my_tag().

bool protocols::ncbb::NcbbDockDesignProtocol::use_soft_rep_

private

Referenced by apply(), clone(), and parse_my_tag().

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

src/protocols/ncbb/NcbbDockDesignProtocol.hh
src/protocols/ncbb/NcbbDockDesignProtocol.cc

Private Attributes
core::scoring::ScoreFunctionOP	score_fxn_

core::Real	mc_temp_

core::Real	pert_mc_temp_

core::Real	pert_dock_rot_mag_

core::Real	pert_dock_trans_mag_

core::Real	pert_pep_small_temp_

core::Real	pert_pep_small_H_

core::Real	pert_pep_small_L_

core::Real	pert_pep_small_E_

core::Real	pert_pep_shear_temp_

core::Real	pert_pep_shear_H_

core::Real	pert_pep_shear_L_

core::Real	pert_pep_shear_E_

core::Size	pert_pep_num_rep_

core::Size	pert_num_

core::Size	dock_design_loop_num_

bool	no_design_

bool	final_design_min_

bool	use_soft_rep_

bool	mc_initial_pose_

bool	ncbb_design_first_

bool	pymol_

bool	keep_history_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation