#include <DockingEnsemblePrepackProtocol.hh>

Inheritance diagram for protocols::docking::DockingEnsemblePrepackProtocol:

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Public Member Functions
	DockingEnsemblePrepackProtocol ()
	Default constructor. More...

	~DockingEnsemblePrepackProtocol () override

void	setup_defaults ()
	Assigns default values to members. More...

void	setup_pack_operation_movers ()
	Instantiates and configures movers used by DockingEnsemblePrepackProtocol. More...

utility::vector1< char >	get_pose_chains (core::pose::Pose &)
	Returns a vector1 of the pdb chains in a pose, in order. More...

void	check_ensemble_member_compatibility ()
	Ensures all members of either ensemble are compatible with one another. More...

void	move_away (core::pose::Pose &pose)

void	move_back (core::pose::Pose &pose)

void	apply (core::pose::Pose &) override
	Main Method. More...

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

void	set_ensemble1 (std::string const &ensemble1)

void	set_ensemble2 (std::string const &ensemble2)

void	set_spanfile1 (std::string const &spanfile1)

void	set_spanfile2 (std::string const &spanfile2)

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)

	~DockingHighRes () override

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

void	set_movable_jumps (DockJumps movable_jumps)

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)

std::string	get_partners () const

void	set_interface_definition_task_operation (protocols::simple_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 MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

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

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...

virtual MoverOP	clone () const
	Return a clone of the Mover object. 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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

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

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
std::string	copy_ensemble (std::string const &inputfile_name)

void	finalize_setup (core::pose::Pose &)
	Performs setup that requires a pose. More...

void	register_options ()

void	init_from_options ()

Private Attributes
utility::vector1< rigid::RigidBodyTransMoverOP >	trans_away_vec_

utility::vector1< rigid::RigidBodyTransMoverOP >	trans_back_vec_

core::Real	trans_magnitude_

bool	membrane_
	membrane for translating in the membrane plane More...

bool	movers_setup_

protocols::minimization_packing::RotamerTrialsMinMoverOP	rtmin_mover_

protocols::minimization_packing::PackRotamersMoverOP	prepack_full_repack_

SidechainMinMoverOP	scmin_mover_

protocols::moves::SequenceMoverOP	pack_operations_

DockingEnsembleOP	ensemble1_

DockingEnsembleOP	ensemble2_

std::string	ensemble1_filename_

std::string	ensemble2_filename_

std::string	span1_filename_

std::string	span2_filename_

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

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

◆ DockingEnsemblePrepackProtocol()

protocols::docking::DockingEnsemblePrepackProtocol::DockingEnsemblePrepackProtocol ( )

Default constructor.

References init_from_options(), register_options(), and setup_defaults().

◆ ~DockingEnsemblePrepackProtocol()

protocols::docking::DockingEnsemblePrepackProtocol::~DockingEnsemblePrepackProtocol ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::docking::DockingEnsemblePrepackProtocol::apply ( core::pose::Pose & )

overridevirtual

◆ check_ensemble_member_compatibility()

void protocols::docking::DockingEnsemblePrepackProtocol::check_ensemble_member_compatibility ( )

Ensures all members of either ensemble are compatible with one another.

References ensemble1_, ensemble2_, protocols::docking::DockingHighRes::get_partners(), get_pose_chains(), protocols::docking::DockingHighRes::partners(), core::pose::Pose::sequence(), core::id::to_string(), and protocols::docking::TR().

Referenced by apply().

◆ copy_ensemble()

std::string protocols::docking::DockingEnsemblePrepackProtocol::copy_ensemble ( std::string const & inputfile_name )

inlineprivate

Referenced by set_ensemble1(), and set_ensemble2().

◆ finalize_setup()

void protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup ( core::pose::Pose & pose )

private

◆ get_name()

std::string protocols::docking::DockingEnsemblePrepackProtocol::get_name ( ) const

overridevirtual

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

Implements protocols::docking::DockingHighRes.

◆ get_pose_chains()

utility::vector1< char > protocols::docking::DockingEnsemblePrepackProtocol::get_pose_chains ( core::pose::Pose & pose )

Returns a vector1 of the pdb chains in a pose, in order.

References core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by check_ensemble_member_compatibility().

◆ init_from_options()

void protocols::docking::DockingEnsemblePrepackProtocol::init_from_options ( )

private

References membrane_, set_ensemble1(), set_ensemble2(), protocols::docking::DockingHighRes::set_partners(), protocols::docking::DockingHighRes::set_rt_min(), protocols::docking::DockingHighRes::set_sc_min(), set_spanfile1(), and set_spanfile2().

Referenced by DockingEnsemblePrepackProtocol().

◆ move_away()

void protocols::docking::DockingEnsemblePrepackProtocol::move_away ( core::pose::Pose & pose )

References membrane_, protocols::membrane::membrane_axis(), protocols::docking::DockingHighRes::movable_jumps(), protocols::docking::TR(), and trans_magnitude_.

Referenced by apply().

◆ move_back()

void protocols::docking::DockingEnsemblePrepackProtocol::move_back ( core::pose::Pose & pose )

References membrane_, protocols::membrane::membrane_axis(), protocols::docking::DockingHighRes::movable_jumps(), protocols::docking::TR(), and trans_magnitude_.

Referenced by apply().

◆ register_options()

void protocols::docking::DockingEnsemblePrepackProtocol::register_options ( )

private

Referenced by DockingEnsemblePrepackProtocol().

◆ set_ensemble1()

void protocols::docking::DockingEnsemblePrepackProtocol::set_ensemble1 ( std::string const & ensemble1 )

References copy_ensemble(), and ensemble1_filename_.

Referenced by init_from_options().

◆ set_ensemble2()

void protocols::docking::DockingEnsemblePrepackProtocol::set_ensemble2 ( std::string const & ensemble2 )

References copy_ensemble(), and ensemble2_filename_.

Referenced by init_from_options().

◆ set_spanfile1()

void protocols::docking::DockingEnsemblePrepackProtocol::set_spanfile1 ( std::string const & spanfile1 )

References span1_filename_.

Referenced by init_from_options().

◆ set_spanfile2()

void protocols::docking::DockingEnsemblePrepackProtocol::set_spanfile2 ( std::string const & spanfile2 )

References span2_filename_.

Referenced by init_from_options().

◆ setup_defaults()

void protocols::docking::DockingEnsemblePrepackProtocol::setup_defaults ( )

Assigns default values to members.

References ensemble1_, ensemble1_filename_, ensemble2_, ensemble2_filename_, membrane_, movers_setup_, pack_operations_, and trans_magnitude_.

Referenced by DockingEnsemblePrepackProtocol().

◆ setup_pack_operation_movers()

void protocols::docking::DockingEnsemblePrepackProtocol::setup_pack_operation_movers ( )

Instantiates and configures movers used by DockingEnsemblePrepackProtocol.

References movers_setup_, pack_operations_, prepack_full_repack_, protocols::docking::DockingHighRes::rt_min(), rtmin_mover_, protocols::docking::DockingHighRes::sc_min(), scmin_mover_, protocols::docking::DockingHighRes::scorefxn_pack(), and protocols::docking::DockingHighRes::task_factory().

Referenced by finalize_setup().

Member Data Documentation

◆ ensemble1_

DockingEnsembleOP protocols::docking::DockingEnsemblePrepackProtocol::ensemble1_

private

Referenced by apply(), check_ensemble_member_compatibility(), finalize_setup(), and setup_defaults().

◆ ensemble1_filename_

std::string protocols::docking::DockingEnsemblePrepackProtocol::ensemble1_filename_

private

Referenced by finalize_setup(), set_ensemble1(), and setup_defaults().

◆ ensemble2_

DockingEnsembleOP protocols::docking::DockingEnsemblePrepackProtocol::ensemble2_

private

Referenced by apply(), check_ensemble_member_compatibility(), finalize_setup(), and setup_defaults().

◆ ensemble2_filename_

std::string protocols::docking::DockingEnsemblePrepackProtocol::ensemble2_filename_

private

Referenced by finalize_setup(), set_ensemble2(), and setup_defaults().

◆ membrane_

bool protocols::docking::DockingEnsemblePrepackProtocol::membrane_

private

membrane for translating in the membrane plane

Referenced by apply(), finalize_setup(), init_from_options(), move_away(), move_back(), and setup_defaults().

◆ movers_setup_

bool protocols::docking::DockingEnsemblePrepackProtocol::movers_setup_

private

Referenced by finalize_setup(), setup_defaults(), and setup_pack_operation_movers().

◆ pack_operations_

protocols::moves::SequenceMoverOP protocols::docking::DockingEnsemblePrepackProtocol::pack_operations_

private

Referenced by apply(), setup_defaults(), and setup_pack_operation_movers().

◆ prepack_full_repack_

protocols::minimization_packing::PackRotamersMoverOP protocols::docking::DockingEnsemblePrepackProtocol::prepack_full_repack_

private

Referenced by setup_pack_operation_movers().

◆ rtmin_mover_

protocols::minimization_packing::RotamerTrialsMinMoverOP protocols::docking::DockingEnsemblePrepackProtocol::rtmin_mover_

private

Referenced by setup_pack_operation_movers().

◆ scmin_mover_

SidechainMinMoverOP protocols::docking::DockingEnsemblePrepackProtocol::scmin_mover_

private

Referenced by setup_pack_operation_movers().

◆ span1_filename_

std::string protocols::docking::DockingEnsemblePrepackProtocol::span1_filename_

private

Referenced by apply(), finalize_setup(), and set_spanfile1().

◆ span2_filename_

std::string protocols::docking::DockingEnsemblePrepackProtocol::span2_filename_

private

Referenced by apply(), finalize_setup(), and set_spanfile2().

◆ trans_away_vec_

utility::vector1< rigid::RigidBodyTransMoverOP > protocols::docking::DockingEnsemblePrepackProtocol::trans_away_vec_

private

◆ trans_back_vec_

utility::vector1< rigid::RigidBodyTransMoverOP > protocols::docking::DockingEnsemblePrepackProtocol::trans_back_vec_

private

◆ trans_magnitude_

core::Real protocols::docking::DockingEnsemblePrepackProtocol::trans_magnitude_

private

Referenced by move_away(), move_back(), and setup_defaults().

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

src/protocols/docking/DockingEnsemblePrepackProtocol.hh
src/protocols/docking/DockingEnsemblePrepackProtocol.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ DockingEnsemblePrepackProtocol()

◆ ~DockingEnsemblePrepackProtocol()

Member Function Documentation

◆ apply()

◆ check_ensemble_member_compatibility()

◆ copy_ensemble()

◆ finalize_setup()

◆ get_name()

◆ get_pose_chains()

◆ init_from_options()

◆ move_away()

◆ move_back()

◆ register_options()

◆ set_ensemble1()

◆ set_ensemble2()

◆ set_spanfile1()

◆ set_spanfile2()

◆ setup_defaults()

◆ setup_pack_operation_movers()

Member Data Documentation

◆ ensemble1_

◆ ensemble1_filename_

◆ ensemble2_

◆ ensemble2_filename_

◆ membrane_

◆ movers_setup_

◆ pack_operations_

◆ prepack_full_repack_

◆ rtmin_mover_

◆ scmin_mover_

◆ span1_filename_

◆ span2_filename_

◆ trans_away_vec_

◆ trans_back_vec_

◆ trans_magnitude_