Main AntibodyDesignMover, tieing together individual movers and classes. Main mover for application. More...

#include <AntibodyDesignMover.hh>

Public Member Functions
	AntibodyDesignMover ()

virtual	~AntibodyDesignMover ()

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

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

void	set_graft_designer (AntibodyGraftDesignMoverOP graft_designer)

void	set_sequence_designer (AntibodySeqDesignMoverOP seq_designer)

void	set_modeler (AntibodyDesignModelerOP modeler)

void	set_scorefxn (ScoreFunctionOP scorefxn)

void	set_design_scorefxn (ScoreFunctionOP design_scorefxn)

void	set_ab_info (AntibodyInfoOP ab_info)

void	set_use_graft_designer (bool setting)
	Use low-resolution graft designer for structural sampling. Default true. More...

void	set_use_sequence_designer (bool setting)
	Use high-resolution sequence designer for sequence sampling. Default true. More...

void	set_do_post_graft_design_modeling (bool setting)
	Run dock/min modeling step after the graft design step if run. More...

void	set_do_post_design_modeling (bool setting)
	Run dock/min modeling step after sequence design if run. More...

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

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

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

Private Member Functions
void	read_command_line_design_options ()
	Sets command line driven CDR design. This is mainly for testing, but makes the whole algorithm controllable without a specific instruction file. More...

void	setup_scorefxn (ScoreFunctionOP scorefxn)
	Set constraint and chainbreak score on scorefunction if not already set. More...

void	model_post_graft (core::pose::Pose &pose)
	Post-graft step modeling. If no graft step, no need to do post-graft modeling. Default false. More...

void	model_post_design (core::pose::Pose &pose)
	Post-design step modeling. Less aggressive, more high resolution. Default false. More...

void	read_options ()

void	init_on_new_input (core::pose::Pose const &pose)

void	output_ensemble (vector1< core::pose::PoseOP > ensemble, Size range_start, Size range_end, std::string prefix)
	Used to output ongoing current ensembles during the protocol. Specify a range in the vector to output. More...

void	add_cluster_comments_to_pose (core::pose::Pose &pose)
	add cluster info to the pose. Needs to go into pose and not jd2 due to Ensemble generation. More...

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...

Detailed Description

Main AntibodyDesignMover, tieing together individual movers and classes. Main mover for application.

Constructor & Destructor Documentation

protocols::antibody::design::AntibodyDesignMover::AntibodyDesignMover ( )

References ab_info_, cdr_db_parser_, get_score_function(), read_options(), set_scorefxn(), and protocols::moves::Mover::type().

Referenced by clone().

protocols::antibody::design::AntibodyDesignMover::~AntibodyDesignMover ( )

virtual

Member Function Documentation

void protocols::antibody::design::AntibodyDesignMover::add_cluster_comments_to_pose ( core::pose::Pose & pose )

private

add cluster info to the pose. Needs to go into pose and not jd2 due to Ensemble generation.

References ab_info_, core::pose::add_comment(), protocols::antibody::AntibodyInfo::get_CDR_cluster(), protocols::antibody::AntibodyInfo::get_CDR_name(), protocols::antibody::AntibodyInfo::get_cluster_name(), output, and utility::to_string().

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::apply ( core::pose::Pose & pose )

virtual

Implements protocols::moves::Mover.

protocols::moves::MoverOP protocols::antibody::design::AntibodyDesignMover::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 AntibodyDesignMover().

std::string protocols::antibody::design::AntibodyDesignMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::antibody::design::AntibodyDesignMover::init_on_new_input ( core::pose::Pose const & pose )

private

void protocols::antibody::design::AntibodyDesignMover::model_post_design ( core::pose::Pose & pose )

private

Post-design step modeling. Less aggressive, more high resolution. Default false.

References protocols::antibody::AHO_Scheme, core::scoring::ScoreFunction::clone(), modeler_, protocols::antibody::North, and scorefxn_.

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::model_post_graft ( core::pose::Pose & pose )

private

Post-graft step modeling. If no graft step, no need to do post-graft modeling. Default false.

References protocols::moves::MonteCarlo::boltzmann(), mc, modeler_, protocols::moves::MonteCarlo::recover_low(), scorefxn_, and protocols::antibody::TR.

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::output_ensemble	(	vector1< core::pose::PoseOP >	ensemble,
		core::Size	range_start,
		core::Size	range_end,
		std::string	prefix
	)

private

Used to output ongoing current ensembles during the protocol. Specify a range in the vector to output.

References protocols::nonlocal::current_job(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::job_outputter(), tag, utility::to_string(), and protocols::antibody::TR.

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::read_command_line_design_options ( )

private

Sets command line driven CDR design. This is mainly for testing, but makes the whole algorithm controllable without a specific instruction file.

References ab_info_, protocols::antibody::CDRNameEnum_start, protocols::antibody::CDRNameEnum_total, protocols::antibody::AntibodyInfo::get_CDR_name_enum(), graft_designer_, option, seq_designer_, and user.

Referenced by apply().

void protocols::antibody::design::AntibodyDesignMover::read_options ( )

private

References core::scoring::ScoreFunctionFactory::create_score_function(), get_score_function(), option, post_graft_ensemble_output_, set_design_scorefxn(), set_do_post_design_modeling(), set_do_post_graft_design_modeling(), set_use_graft_designer(), set_use_sequence_designer(), and user.

Referenced by AntibodyDesignMover().

void protocols::antibody::design::AntibodyDesignMover::set_ab_info ( AntibodyInfoOP ab_info )

References ab_info_.

void protocols::antibody::design::AntibodyDesignMover::set_design_scorefxn ( ScoreFunctionOP design_scorefxn )

References design_scorefxn_.

Referenced by read_options().

void protocols::antibody::design::AntibodyDesignMover::set_do_post_design_modeling ( bool setting )

Run dock/min modeling step after sequence design if run.

References run_post_design_modeling_.

Referenced by read_options().

void protocols::antibody::design::AntibodyDesignMover::set_do_post_graft_design_modeling ( bool setting )

Run dock/min modeling step after the graft design step if run.

References run_post_graft_modeling_.

Referenced by read_options().

void protocols::antibody::design::AntibodyDesignMover::set_graft_designer ( AntibodyGraftDesignMoverOP graft_designer )

References graft_designer_.

void protocols::antibody::design::AntibodyDesignMover::set_modeler ( AntibodyDesignModelerOP modeler )

References modeler_.

void protocols::antibody::design::AntibodyDesignMover::set_scorefxn ( ScoreFunctionOP scorefxn )

References scorefxn_.

Referenced by AntibodyDesignMover().

void protocols::antibody::design::AntibodyDesignMover::set_sequence_designer ( AntibodySeqDesignMoverOP seq_designer )

References seq_designer_.

void protocols::antibody::design::AntibodyDesignMover::set_use_graft_designer ( bool setting )

Use low-resolution graft designer for structural sampling. Default true.

References run_graft_designer_.

Referenced by read_options().

void protocols::antibody::design::AntibodyDesignMover::set_use_sequence_designer ( bool setting )

Use high-resolution sequence designer for sequence sampling. Default true.

References run_sequence_designer_.

Referenced by read_options().

void protocols::antibody::design::AntibodyDesignMover::setup_scorefxn ( ScoreFunctionOP scorefxn )

private

Set constraint and chainbreak score on scorefunction if not already set.

References chainbreak, and dihedral_constraint.

Referenced by apply().

Member Data Documentation

AntibodyInfoOP protocols::antibody::design::AntibodyDesignMover::ab_info_

private

Referenced by add_cluster_comments_to_pose(), AntibodyDesignMover(), apply(), read_command_line_design_options(), and set_ab_info().

AntibodyDatabaseManagerOP protocols::antibody::design::AntibodyDesignMover::cdr_db_parser_

private

Referenced by AntibodyDesignMover().

ScoreFunctionOP protocols::antibody::design::AntibodyDesignMover::design_scorefxn_

private

Referenced by apply(), and set_design_scorefxn().

AntibodyGraftDesignMoverOP protocols::antibody::design::AntibodyDesignMover::graft_designer_

private

Referenced by apply(), read_command_line_design_options(), and set_graft_designer().

AntibodyDesignModelerOP protocols::antibody::design::AntibodyDesignMover::modeler_

private

Referenced by apply(), model_post_design(), model_post_graft(), and set_modeler().

bool protocols::antibody::design::AntibodyDesignMover::post_graft_ensemble_output_

private

Referenced by apply(), and read_options().

bool protocols::antibody::design::AntibodyDesignMover::run_graft_designer_

private

Referenced by apply(), and set_use_graft_designer().

bool protocols::antibody::design::AntibodyDesignMover::run_post_design_modeling_

private

Referenced by apply(), and set_do_post_design_modeling().

bool protocols::antibody::design::AntibodyDesignMover::run_post_graft_modeling_

private

Referenced by apply(), and set_do_post_graft_design_modeling().

bool protocols::antibody::design::AntibodyDesignMover::run_sequence_designer_

private

Referenced by apply(), and set_use_sequence_designer().

ScoreFunctionOP protocols::antibody::design::AntibodyDesignMover::scorefxn_

private

Referenced by apply(), model_post_design(), model_post_graft(), and set_scorefxn().

AntibodySeqDesignMoverOP protocols::antibody::design::AntibodyDesignMover::seq_designer_

private

Referenced by apply(), read_command_line_design_options(), and set_sequence_designer().

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

src/protocols/antibody/design/AntibodyDesignMover.hh
src/protocols/antibody/design/AntibodyDesignMover.cc

Private Attributes
AntibodyGraftDesignMoverOP	graft_designer_

AntibodySeqDesignMoverOP	seq_designer_

AntibodyDesignModelerOP	modeler_

ScoreFunctionOP	scorefxn_

ScoreFunctionOP	design_scorefxn_

AntibodyInfoOP	ab_info_

AntibodyDatabaseManagerOP	cdr_db_parser_

bool	run_graft_designer_

bool	run_sequence_designer_

bool	run_post_graft_modeling_

bool	run_post_design_modeling_

bool	post_graft_ensemble_output_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation