#include <SurfaceDockingProtocol.hh>

Inheritance diagram for protocols::surface_docking::SurfaceDockingProtocol:

[legend]

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

	SurfaceDockingProtocol (SurfaceDockingProtocol const &src)
	Copy constructor. More...

	~SurfaceDockingProtocol () override

void	show (std::ostream &ouput=std::cout) const override
	Register options with the option system. More...

std::string	get_name () const override
	Insertion operator (overloaded so that SurfaceDockingProtocol can be "printed" in Pyrosetta). More...

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

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

void	apply (core::pose::Pose &pose) override
	Apply the corresponding move to the pose. More...

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 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...

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 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
void	init ()

void	copy_data (SurfaceDockingProtocol object_to_copy_to, SurfaceDockingProtocol object_to_copy_from)

bool	valid_surface_pose (core::pose::Pose const &pose)

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

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

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

void	initialize_surface_energies (core::pose::Pose &pose, core::Size first_protein_residue)

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

void	setup_movers (core::pose::Pose const &pose, core::Size const first_protein_residue)

void	setup_abinitio ()

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

void	split_protein_surface_poses (core::pose::Pose const &pose, core::pose::Pose &surface, core::pose::Pose &protein)

void	merge_protein_surface_poses (core::pose::Pose &pose, core::pose::Pose const &surface, core::pose::Pose const &protein)

core::pack::task::PackerTaskOP	create_surface_packer_task (core::pose::Pose const &pose, core::Size const first_protein_residue)

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::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

◆ SurfaceDockingProtocol() [1/2]

protocols::surface_docking::SurfaceDockingProtocol::SurfaceDockingProtocol ( )

Default constructor.

References init().

◆ SurfaceDockingProtocol() [2/2]

protocols::surface_docking::SurfaceDockingProtocol::SurfaceDockingProtocol ( SurfaceDockingProtocol const & src )

Copy constructor.

References copy_data().

◆ ~SurfaceDockingProtocol()

protocols::surface_docking::SurfaceDockingProtocol::~SurfaceDockingProtocol ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::surface_docking::SurfaceDockingProtocol::apply ( core::pose::Pose & pose )

overridevirtual

◆ calc_secondary_structure()

void protocols::surface_docking::SurfaceDockingProtocol::calc_secondary_structure ( core::pose::Pose & pose )

private

References protocols::simple_filters::dssp(), sec_struct_, core::pose::Pose::secstruct(), and core::pose::Pose::size().

◆ calc_secondary_structure_with_surface()

void protocols::surface_docking::SurfaceDockingProtocol::calc_secondary_structure_with_surface ( core::pose::Pose const & pose )

private

References protocols::simple_filters::dssp(), sec_struct_, and core::pose::Pose::split_by_chain().

◆ clone()

protocols::moves::MoverOP protocols::surface_docking::SurfaceDockingProtocol::clone ( ) const

overridevirtual

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.

◆ copy_data()

void protocols::surface_docking::SurfaceDockingProtocol::copy_data	(	SurfaceDockingProtocol	object_to_copy_to,
		SurfaceDockingProtocol	object_to_copy_from
	)

private

References abinitio_, centroid_relax_, fullatom_relax_, pack_rotamers_fullatom_, score_sidechain_pack_, sec_struct_, slide_away_from_surface_, slide_into_surface_, surface_orient_, surface_parameters_, to_centroid_, and to_full_atom_.

Referenced by SurfaceDockingProtocol().

◆ create_surface_packer_task()

core::pack::task::PackerTaskOP protocols::surface_docking::SurfaceDockingProtocol::create_surface_packer_task	(	core::pose::Pose const &	pose,
		core::Size const	first_protein_residue
	)

private

References protocols::constraint_generator::first_protein_residue(), and core::pose::Pose::size().

Referenced by setup_movers().

◆ fresh_instance()

protocols::moves::MoverOP protocols::surface_docking::SurfaceDockingProtocol::fresh_instance ( ) const

overridevirtual

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.

◆ get_name()

std::string protocols::surface_docking::SurfaceDockingProtocol::get_name ( ) const

overridevirtual

Insertion operator (overloaded so that SurfaceDockingProtocol can be "printed" in Pyrosetta).

Assignment operator

Return the name of the Mover.

Implements protocols::moves::Mover.

◆ init()

void protocols::surface_docking::SurfaceDockingProtocol::init ( void )

private

References abinitio_, centroid_relax_, core::scoring::fa_elec, fullatom_relax_, core::scoring::get_score_function(), pack_rotamers_fullatom_, score_sidechain_pack_, sec_struct_, slide_away_from_surface_, surface_orient_, surface_parameters_, to_centroid_, to_full_atom_, protocols::TR(), and protocols::moves::Mover::type().

Referenced by SurfaceDockingProtocol().

◆ initialize_surface_energies()

void protocols::surface_docking::SurfaceDockingProtocol::initialize_surface_energies	(	core::pose::Pose &	pose,
		core::Size	first_protein_residue
	)

private

References protocols::constraint_generator::first_protein_residue(), core::pose::Pose::set_new_energies_object(), and core::pose::Pose::size().

Referenced by apply().

◆ merge_protein_surface_poses()

void protocols::surface_docking::SurfaceDockingProtocol::merge_protein_surface_poses	(	core::pose::Pose &	pose,
		core::pose::Pose const &	surface,
		core::pose::Pose const &	protein
	)

private

References core::pose::Pose::copy_segment(), set_secondary_structure(), and core::scoring::surface.

Referenced by apply().

◆ set_secondary_structure()

void protocols::surface_docking::SurfaceDockingProtocol::set_secondary_structure ( core::pose::Pose & pose )

private

References core::pose::Pose::num_jump(), sec_struct_, core::pose::Pose::set_secstruct(), core::pose::Pose::size(), and protocols::TR().

Referenced by merge_protein_surface_poses().

◆ set_surface_parameters()

void protocols::surface_docking::SurfaceDockingProtocol::set_surface_parameters ( core::pose::Pose & pose )

private

References protocols::surface_docking::SurfaceVectorLoader::create_surface_params(), and surface_parameters_.

Referenced by apply().

◆ setup_abinitio()

void protocols::surface_docking::SurfaceDockingProtocol::setup_abinitio ( )

private

References abinitio_, protocols::abinitio::ClassicAbinitio::register_options(), core::scoring::rg, and protocols::TR().

Referenced by setup_movers().

◆ setup_movers()

void protocols::surface_docking::SurfaceDockingProtocol::setup_movers	(	core::pose::Pose const &	pose,
		core::Size const	first_protein_residue
	)

private

References centroid_relax_, create_surface_packer_task(), protocols::constraint_generator::first_protein_residue(), fullatom_relax_, pack_rotamers_fullatom_, score_sidechain_pack_, setup_abinitio(), setup_slide_movers(), core::pose::Pose::size(), slide_into_surface_, surface_orient_, surface_parameters_, to_centroid_, and to_full_atom_.

Referenced by apply().

◆ setup_slide_movers()

void protocols::surface_docking::SurfaceDockingProtocol::setup_slide_movers ( core::pose::Pose const & pose )

private

References protocols::geometry::centroids_by_jump(), core::pose::Pose::num_jump(), position_above_surface_, slide_away_from_surface_, slide_into_surface_, and surface_parameters_.

Referenced by setup_movers().

◆ show()

void protocols::surface_docking::SurfaceDockingProtocol::show ( std::ostream & ouput = std::cout ) const

overridevirtual

Register options with the option system.

Generate string representation of SurfaceDockingProtocol for debugging purposes

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

◆ split_protein_surface_poses()

void protocols::surface_docking::SurfaceDockingProtocol::split_protein_surface_poses	(	core::pose::Pose const &	pose,
		core::pose::Pose &	surface,
		core::pose::Pose &	protein
	)

private

References core::pose::Pose::split_by_chain(), core::scoring::surface, and valid_surface_pose().

Referenced by apply().

◆ valid_surface_pose()

bool protocols::surface_docking::SurfaceDockingProtocol::valid_surface_pose ( core::pose::Pose const & pose )

private

References core::conformation::Conformation::chain_endings(), and core::pose::Pose::conformation().

Referenced by split_protein_surface_poses().

Member Data Documentation

◆ abinitio_

protocols::abinitio::ClassicAbinitioOP protocols::surface_docking::SurfaceDockingProtocol::abinitio_

private

Referenced by apply(), copy_data(), init(), and setup_abinitio().

◆ centroid_relax_

protocols::surface_docking::CentroidRelaxMoverOP protocols::surface_docking::SurfaceDockingProtocol::centroid_relax_

private

Referenced by apply(), copy_data(), init(), and setup_movers().

◆ fullatom_relax_

protocols::surface_docking::FullatomRelaxMoverOP protocols::surface_docking::SurfaceDockingProtocol::fullatom_relax_

private

Referenced by apply(), copy_data(), init(), and setup_movers().

◆ pack_rotamers_fullatom_

protocols::minimization_packing::PackRotamersMoverOP protocols::surface_docking::SurfaceDockingProtocol::pack_rotamers_fullatom_

private

Referenced by apply(), copy_data(), init(), and setup_movers().

◆ position_above_surface_

protocols::rigid::RigidBodyTransMoverOP protocols::surface_docking::SurfaceDockingProtocol::position_above_surface_

private

Referenced by apply(), and setup_slide_movers().

◆ score_sidechain_pack_

core::scoring::ScoreFunctionOP protocols::surface_docking::SurfaceDockingProtocol::score_sidechain_pack_

private

Referenced by copy_data(), init(), and setup_movers().

◆ sec_struct_

std::string protocols::surface_docking::SurfaceDockingProtocol::sec_struct_

private

Referenced by calc_secondary_structure(), calc_secondary_structure_with_surface(), copy_data(), init(), and set_secondary_structure().

◆ slide_away_from_surface_

protocols::rigid::RigidBodyTransMoverOP protocols::surface_docking::SurfaceDockingProtocol::slide_away_from_surface_

private

Referenced by copy_data(), init(), and setup_slide_movers().

◆ slide_into_surface_

protocols::docking::FaDockingSlideIntoContactOP protocols::surface_docking::SurfaceDockingProtocol::slide_into_surface_

private

Referenced by copy_data(), setup_movers(), and setup_slide_movers().

◆ surface_orient_

SurfaceOrientMoverOP protocols::surface_docking::SurfaceDockingProtocol::surface_orient_

private

Referenced by apply(), copy_data(), init(), and setup_movers().

◆ surface_parameters_

protocols::surface_docking::SurfaceParametersOP protocols::surface_docking::SurfaceDockingProtocol::surface_parameters_

private

Referenced by copy_data(), init(), set_surface_parameters(), setup_movers(), and setup_slide_movers().

◆ to_centroid_

simple_moves::SwitchResidueTypeSetMoverOP protocols::surface_docking::SurfaceDockingProtocol::to_centroid_

private

Referenced by apply(), copy_data(), init(), and setup_movers().

◆ to_full_atom_

simple_moves::SwitchResidueTypeSetMoverOP protocols::surface_docking::SurfaceDockingProtocol::to_full_atom_

private

Referenced by apply(), copy_data(), init(), and setup_movers().

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

src/protocols/surface_docking/SurfaceDockingProtocol.hh
src/protocols/surface_docking/SurfaceDockingProtocol.cc

Private Attributes
core::scoring::ScoreFunctionOP	score_sidechain_pack_

std::string	sec_struct_

protocols::surface_docking::SurfaceParametersOP	surface_parameters_

simple_moves::SwitchResidueTypeSetMoverOP	to_centroid_

simple_moves::SwitchResidueTypeSetMoverOP	to_full_atom_

SurfaceOrientMoverOP	surface_orient_

protocols::abinitio::ClassicAbinitioOP	abinitio_

protocols::surface_docking::CentroidRelaxMoverOP	centroid_relax_

protocols::minimization_packing::PackRotamersMoverOP	pack_rotamers_fullatom_

protocols::rigid::RigidBodyTransMoverOP	slide_away_from_surface_

protocols::docking::FaDockingSlideIntoContactOP	slide_into_surface_

protocols::surface_docking::FullatomRelaxMoverOP	fullatom_relax_

protocols::rigid::RigidBodyTransMoverOP	position_above_surface_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ SurfaceDockingProtocol() [1/2]

◆ SurfaceDockingProtocol() [2/2]

◆ ~SurfaceDockingProtocol()

Member Function Documentation

◆ apply()

◆ calc_secondary_structure()

◆ calc_secondary_structure_with_surface()

◆ clone()

◆ copy_data()

◆ create_surface_packer_task()

◆ fresh_instance()

◆ get_name()

◆ init()

◆ initialize_surface_energies()

◆ merge_protein_surface_poses()

◆ set_secondary_structure()

◆ set_surface_parameters()

◆ setup_abinitio()

◆ setup_movers()

◆ setup_slide_movers()

◆ show()

◆ split_protein_surface_poses()

◆ valid_surface_pose()

Member Data Documentation

◆ abinitio_

◆ centroid_relax_

◆ fullatom_relax_

◆ pack_rotamers_fullatom_

◆ position_above_surface_

◆ score_sidechain_pack_

◆ sec_struct_

◆ slide_away_from_surface_

◆ slide_into_surface_

◆ surface_orient_

◆ surface_parameters_

◆ to_centroid_

◆ to_full_atom_