Main Symmetric Docking protocol class. More...

#include <SymDockProtocol.hh>

Inheritance diagram for protocols::symmetric_docking::SymDockProtocol:

[legend]

Public Types
typedef core::conformation::symmetry::SymmetricConformation	SymmetricConformation

typedef core::conformation::symmetry::SymmetryInfo	SymmetryInfo

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

Public Member Functions
	SymDockProtocol ()
	Default Constructor for Symmetric Docking Protocol. More...

	SymDockProtocol (bool const fullatom, bool const local_refine, bool const view=false)
	Custom Constructor - Symmetric docking protocol. More...

	SymDockProtocol (bool const fullatom, bool const local_refine, bool const view, core::scoring::ScoreFunctionOP docking_score_low, core::scoring::ScoreFunctionOP docking_score_high)
	Custom Constructor - Symmetric Docking Protocol. More...

	~SymDockProtocol () override
	Destructor. More...

void	register_options ()
	Register Options from the Commandline. More...

void	set_default ()
	Setup options based on constructors. More...

void	set_dock_rtmin (bool dock_rtmin_in)
	Setters for Protocol Options. More...

void	set_sc_min (bool sc_min_in)

void	set_max_repeats (core::Size const max_repeats_in)

void	set_dock_ppk (bool dock_ppk_in)

void	set_fullatom (bool const fullatom_in)

void	set_local_refine (bool const local_refine_in)

void	set_view (bool view_in)

void	set_lowres_scorefxn (core::scoring::ScoreFunctionOP docking_score_low_in)

void	set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_score_high_in)

void	set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_score_high_in, core::scoring::ScoreFunctionOP docking_score_pack_in)

bool	docking_lowres_filter (core::pose::Pose &pose)

bool	docking_highres_filter (core::pose::Pose &pose)

core::Real	calc_interaction_energy (core::pose::Pose &pose)
	Calculate Interaction energy between partners. More...

core::Real	calc_rms (core::pose::Pose &pose)
	Calculate RMSD from partner to symmetric starting structure. More...

core::Real	calc_Irms (core::pose::Pose &pose)
	Calculate interface RMSD of one chain to symmetric starting structure assuming correct native chain order. More...

core::Real	calc_fnat (core::pose::Pose &pose, core::scoring::ScoreFunctionOP dock_scorefxn)
	Calculate fraction of native contacts recovered for one chain assuming correct native chain order. More...

bool	calc_res_contact (core::conformation::ResidueOP const rsd1, core::conformation::ResidueOP const rsd2, core::Real const dist_cutoff)
	Calculate whether two residues are within a distance cutoff of each other. More...

core::Real	calc_CAPRI_rank (core::Real const Irmsd, core::Real const Lrmsd, core::Real const Fnat)
	Calculate fraction of native contacts recovered for one chain assuming correct native chain order. More...

void	recover_sidechains (core::pose::Pose &pose, const core::pose::Pose &native_pose)
	Recover sidechains from the native pose. More...

void	task_factory (core::pack::task::TaskFactoryOP task_factory)
	Set Task Factory for Packing. More...

void	design (bool const des)
	Turn on Design of partner 2 during docking - not thoroughly tested. More...

bool	design () const

void	hurry (bool const hurry)
	Skip population of the score map. More...

core::pack::task::TaskFactoryOP	task_factory () const
	Methods for task factory? More...

core::pack::task::TaskFactoryOP &	task_factory ()

void	score_only (core::pose::Pose &pose)
	Only score the pose using docking config. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	RosettaScripts Methods //////. More...

void	apply (core::pose::Pose &pose) override
	Mover Methods /////////. More...

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

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

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

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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Member Functions
void	classic_mcm_protocol (core::pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles, core::Size repack_every_Nth) const
	Classic MCM Protocol for symmetric docking protocol. More...

protocols::moves::MoverOP	make_dockmcm_mover (core::pose::Pose const &pose, protocols::moves::MoverOP repack_mover, protocols::moves::MoverOP rigbod_mover, core::kinematics::MoveMapOP movemap, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo) const
	Setup Docking Monte Carlo mover. More...

Private Attributes
bool	fullatom_
	Data about the protocol. More...

bool	local_refine_

bool	rtmin_

bool	sc_min_

core::Size	max_repeats_

bool	dock_ppk_

utility::vector1< core::Size >	movable_jumps_
	Jumps for symmetric rigid body transformations. More...

bool	autofoldtree_
	Modified Docking foldtree for symmetry. More...

bool	view_
	Initialize the graphics viewer (opengl) More...

bool	design_
	Allow design of partner 2 during docking. More...

bool	passed_lowres_filter_
	Filters for structures during protocols. More...

bool	passed_highres_filter_

bool	hurry_
	Sip population of the score map. More...

std::map< std::string, core::Real >	score_map_
	For scorefile output. More...

core::scoring::ScoreFunctionOP	docking_score_low_
	Scorefunctions used during the protocol. More...

core::scoring::ScoreFunctionOP	docking_score_high_

core::scoring::ScoreFunctionOP	docking_score_high_min_

core::scoring::ScoreFunctionOP	docking_score_pack_

moves::MonteCarloOP	mc_
	Monte carlo object. More...

protocols::symmetric_docking::SymDockingLowResOP	docking_low_
	Child protocols - low resolution and high resolution docking & for packing. More...

protocols::symmetric_docking::SymDockingHiResOP	docking_high_

core::pack::task::TaskFactoryOP	init_task_factory_
	Used to restrict packer task during docking. More...

Additional Inherited Members
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 Symmetric Docking protocol class.

Member Typedef Documentation

◆ SymmetricConformation

typedef core::conformation::symmetry::SymmetricConformation protocols::symmetric_docking::SymDockProtocol::SymmetricConformation

◆ SymmetryInfo

typedef core::conformation::symmetry::SymmetryInfo protocols::symmetric_docking::SymDockProtocol::SymmetryInfo

Constructor & Destructor Documentation

◆ SymDockProtocol() [1/3]

protocols::symmetric_docking::SymDockProtocol::SymDockProtocol ( )

Default Constructor for Symmetric Docking Protocol.

References register_options(), and set_default().

◆ SymDockProtocol() [2/3]

protocols::symmetric_docking::SymDockProtocol::SymDockProtocol	(	bool const	fullatom,
		bool const	local_refine,
		bool const	view = `false`
	)

Custom Constructor - Symmetric docking protocol.

Custom protocol - specify if input pose is fullatom, local refinement and use graphics viewer

References register_options(), set_default(), set_fullatom(), set_local_refine(), and set_view().

◆ SymDockProtocol() [3/3]

protocols::symmetric_docking::SymDockProtocol::SymDockProtocol	(	bool const	fullatom,
		bool const	local_refine,
		bool const	view,
		core::scoring::ScoreFunctionOP	docking_score_low,
		core::scoring::ScoreFunctionOP	docking_score_high
	)

Custom Constructor - Symmetric Docking Protocol.

Custom protocol - specify if input pose is fullatom, local refinement and use graphics viewer. Also specify custom scoring functions for low and high resolution stages

References docking_score_high_, docking_score_high_min_, docking_score_low_, docking_score_pack_, register_options(), set_default(), set_fullatom(), set_local_refine(), and set_view().

◆ ~SymDockProtocol()

protocols::symmetric_docking::SymDockProtocol::~SymDockProtocol ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

void protocols::symmetric_docking::SymDockProtocol::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods /////////.

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), core::io::raw_data::ScoreMap::add_energies_data_from_scored_pose(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::symmetry::SymDockingInitialPerturbation::apply(), protocols::constraint_movers::ConstraintSetMover::apply(), calc_CAPRI_rank(), calc_fnat(), calc_interaction_energy(), calc_Irms(), calc_rms(), core::chemical::CENTROID, core::pose::Pose::conformation(), core::pose::Pose::data(), core::pack::interaction_graph::debug, design_, docking_high_, docking_highres_filter(), docking_low_, docking_lowres_filter(), docking_score_high_, docking_score_high_min_, docking_score_low_, docking_score_pack_, core::scoring::fa_rep, core::scoring::fa_sol, core::chemical::FA_STANDARD, fullatom_, protocols::moves::Mover::get_input_pose(), protocols::jd2::JobDistributor::get_instance(), protocols::moves::Mover::get_native_pose(), core::scoring::get_score_function(), hurry_, init_task_factory_, core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), local_refine_, core::chemical::element::N, core::scoring::pair, passed_highres_filter_, passed_lowres_filter_, recover_sidechains(), protocols::relax::relax_pose(), core::scoring::rms, core::pose::datacache::CacheableDataType::SCORE_MAP, score_map_, score_only(), core::scoring::score_type_from_name(), protocols::moves::Mover::set_input_pose(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), protocols::medal::to_centroid(), and protocols::symmetric_docking::TR().

◆ calc_CAPRI_rank()

core::Real protocols::symmetric_docking::SymDockProtocol::calc_CAPRI_rank	(	core::Real const	Irmsd,
		core::Real const	Lrmsd,
		core::Real const	Fnat
	)

Calculate fraction of native contacts recovered for one chain assuming correct native chain order.

References protocols::symmetric_docking::TR().

Referenced by apply().

◆ calc_fnat()

core::Real protocols::symmetric_docking::SymDockProtocol::calc_fnat	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	dock_scorefxn
	)

Calculate fraction of native contacts recovered for one chain assuming correct native chain order.

References core::kinematics::FoldTree::add_edge(), calc_res_contact(), core::pose::Pose::chain(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clone(), core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoints(), core::pose::Pose::fold_tree(), protocols::moves::Mover::get_native_pose(), core::pose::symmetry::is_symmetric(), core::chemical::element::N, core::pose::Pose::residue(), core::pose::Pose::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::id::to_string(), and protocols::symmetric_docking::TR().

Referenced by apply().

◆ calc_interaction_energy()

core::Real protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy ( core::pose::Pose & pose )

Calculate Interaction energy between partners.

References core::scoring::atom_pair_constraint, core::pose::Pose::conformation(), docking_score_low_, docking_score_pack_, fullatom_, and core::pose::symmetry::is_symmetric().

Referenced by apply().

◆ calc_Irms()

core::Real protocols::symmetric_docking::SymDockProtocol::calc_Irms ( core::pose::Pose & pose )

Calculate interface RMSD of one chain to symmetric starting structure assuming correct native chain order.

References core::kinematics::FoldTree::add_edge(), core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoints(), core::pose::Pose::fold_tree(), protocols::moves::Mover::get_native_pose(), core::pose::initialize_atomid_map(), core::scoring::is_protein_CA(), core::pose::symmetry::is_symmetric(), core::chemical::element::N, core::pose::Pose::residue(), core::scoring::rmsd_no_super(), core::pose::Pose::size(), core::scoring::superimpose_pose(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and protocols::symmetric_docking::TR().

Referenced by apply().

◆ calc_res_contact()

bool protocols::symmetric_docking::SymDockProtocol::calc_res_contact	(	core::conformation::ResidueOP const	rsd1,
		core::conformation::ResidueOP const	rsd2,
		core::Real const	dist_cutoff
	)

Calculate whether two residues are within a distance cutoff of each other.

Referenced by calc_fnat().

◆ calc_rms()

core::Real protocols::symmetric_docking::SymDockProtocol::calc_rms ( core::pose::Pose & pose )

Calculate RMSD from partner to symmetric starting structure.

References core::scoring::CA_rmsd_symmetric(), core::pose::Pose::conformation(), protocols::constraint_generator::get_native_pose(), core::scoring::is_protein_CA(), core::pose::symmetry::is_symmetric(), and core::scoring::rmsd_with_super_subset().

Referenced by apply(), and score_only().

◆ classic_mcm_protocol()

void protocols::symmetric_docking::SymDockProtocol::classic_mcm_protocol	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	scorefxn,
		protocols::moves::MonteCarloOP	monteCarlo,
		core::Size	num_cycles,
		core::Size	repack_every_Nth
	)		const

private

Classic MCM Protocol for symmetric docking protocol.

◆ clone()

protocols::moves::MoverOP protocols::symmetric_docking::SymDockProtocol::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.

References docking_score_high_, docking_score_low_, fullatom_, local_refine_, and view_.

◆ design() [1/2]

bool protocols::symmetric_docking::SymDockProtocol::design ( ) const

References design_.

Referenced by set_default().

◆ design() [2/2]

void protocols::symmetric_docking::SymDockProtocol::design ( bool const des )

Turn on Design of partner 2 during docking - not thoroughly tested.

Note: @ralford I think this is just copied over from regular docking protocol?

References design_.

◆ docking_highres_filter()

bool protocols::symmetric_docking::SymDockProtocol::docking_highres_filter ( core::pose::Pose & pose )

References core::pose::Pose::energies(), score_map_, core::scoring::Energies::total_energy(), and protocols::symmetric_docking::TR().

Referenced by apply().

◆ docking_lowres_filter()

bool protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter ( core::pose::Pose & pose )

References core::scoring::atom_pair_constraint, core::pose::Pose::conformation(), core::scoring::interchain_contact, core::scoring::interchain_vdw, core::chemical::element::N, core::energy_methods::ref_spectrum, core::scoring::ScoreFunction::set_weight(), core::pose::setPoseExtraScore(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and protocols::symmetric_docking::TR().

Referenced by apply().

◆ get_name()

std::string protocols::symmetric_docking::SymDockProtocol::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ hurry()

void protocols::symmetric_docking::SymDockProtocol::hurry ( bool const hurry )

Skip population of the score map.

References hurry_.

Referenced by set_default().

◆ make_dockmcm_mover()

protocols::moves::MoverOP protocols::symmetric_docking::SymDockProtocol::make_dockmcm_mover	(	core::pose::Pose const &	pose,
		protocols::moves::MoverOP	repack_mover,
		protocols::moves::MoverOP	rigbod_mover,
		core::kinematics::MoveMapOP	movemap,
		core::scoring::ScoreFunctionOP	scorefxn,
		protocols::moves::MonteCarloOP	monteCarlo
	)		const

private

Setup Docking Monte Carlo mover.

◆ mover_name()

std::string protocols::symmetric_docking::SymDockProtocol::mover_name ( )

static

Referenced by get_name(), protocols::symmetric_docking::SymDockProtocolCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::symmetric_docking::SymDockProtocol::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

RosettaScripts Methods //////.

Reimplemented from protocols::moves::Mover.

References core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), set_dock_ppk(), set_dock_rtmin(), set_fullatom(), set_highres_scorefxn(), set_local_refine(), set_lowres_scorefxn(), set_max_repeats(), set_sc_min(), set_view(), and task_factory().

◆ provide_xml_schema()

void protocols::symmetric_docking::SymDockProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::symmetric_docking::SymDockProtocolCreator::provide_xml_schema().

◆ recover_sidechains()

void protocols::symmetric_docking::SymDockProtocol::recover_sidechains	(	core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose
	)

Recover sidechains from the native pose.

References docking_score_pack_, rtmin_, and protocols::symmetric_docking::TR().

Referenced by apply().

◆ register_options()

void protocols::symmetric_docking::SymDockProtocol::register_options ( )

Register Options from the Commandline.

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), set_dock_ppk(), set_dock_rtmin(), set_fullatom(), set_local_refine(), set_max_repeats(), protocols::moves::Mover::set_native_pose(), and set_sc_min().

Referenced by SymDockProtocol().

◆ score_only()

void protocols::symmetric_docking::SymDockProtocol::score_only ( core::pose::Pose & pose )

Only score the pose using docking config.

References protocols::simple_moves::ScoreMover::apply(), calc_rms(), core::chemical::CENTROID, docking_score_high_, docking_score_low_, fullatom_, protocols::simple_moves::ScoreMover::insert_rms(), and protocols::medal::to_centroid().

Referenced by apply().

◆ set_default()

void protocols::symmetric_docking::SymDockProtocol::set_default ( )

Setup options based on constructors.

References core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::atom_pair_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), design(), dock_ppk_, docking_score_high_, docking_score_high_min_, docking_score_low_, docking_score_pack_, core::scoring::get_score_function(), hurry(), passed_highres_filter_, passed_lowres_filter_, and set_local_refine().

Referenced by SymDockProtocol().

◆ set_dock_ppk()

void protocols::symmetric_docking::SymDockProtocol::set_dock_ppk ( bool dock_ppk_in )

References dock_ppk_.

Referenced by parse_my_tag(), and register_options().

◆ set_dock_rtmin()

void protocols::symmetric_docking::SymDockProtocol::set_dock_rtmin ( bool dock_rtmin_in )

Setters for Protocol Options.

References rtmin_.

Referenced by parse_my_tag(), and register_options().

◆ set_fullatom()

void protocols::symmetric_docking::SymDockProtocol::set_fullatom ( bool const fullatom_in )

References fullatom_, and passed_highres_filter_.

Referenced by parse_my_tag(), register_options(), set_local_refine(), and SymDockProtocol().

◆ set_highres_scorefxn() [1/2]

void protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionOP docking_score_high_in )

References docking_high_, docking_score_high_, and docking_score_high_min_.

Referenced by parse_my_tag().

◆ set_highres_scorefxn() [2/2]

void protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn	(	core::scoring::ScoreFunctionOP	docking_score_high_in,
		core::scoring::ScoreFunctionOP	docking_score_pack_in
	)

References docking_score_high_, docking_score_high_min_, and docking_score_pack_.

◆ set_local_refine()

void protocols::symmetric_docking::SymDockProtocol::set_local_refine ( bool const local_refine_in )

References local_refine_, passed_lowres_filter_, and set_fullatom().

Referenced by parse_my_tag(), register_options(), set_default(), and SymDockProtocol().

◆ set_lowres_scorefxn()

void protocols::symmetric_docking::SymDockProtocol::set_lowres_scorefxn ( core::scoring::ScoreFunctionOP docking_score_low_in )

References docking_low_, and docking_score_low_.

Referenced by parse_my_tag().

◆ set_max_repeats()

void protocols::symmetric_docking::SymDockProtocol::set_max_repeats ( core::Size const max_repeats_in )

References max_repeats_.

Referenced by parse_my_tag(), and register_options().

◆ set_sc_min()

void protocols::symmetric_docking::SymDockProtocol::set_sc_min ( bool sc_min_in )

References sc_min_.

Referenced by parse_my_tag(), and register_options().

◆ set_view()

void protocols::symmetric_docking::SymDockProtocol::set_view ( bool view_in )

References view_.

Referenced by parse_my_tag(), and SymDockProtocol().

◆ task_factory() [1/3]

core::pack::task::TaskFactoryOP & protocols::symmetric_docking::SymDockProtocol::task_factory ( )

References init_task_factory_.

◆ task_factory() [2/3]

core::pack::task::TaskFactoryOP protocols::symmetric_docking::SymDockProtocol::task_factory ( ) const

Methods for task factory?

References init_task_factory_.

Referenced by parse_my_tag().

◆ task_factory() [3/3]

void protocols::symmetric_docking::SymDockProtocol::task_factory ( core::pack::task::TaskFactoryOP task_factory )

Set Task Factory for Packing.

References init_task_factory_.

Member Data Documentation

◆ autofoldtree_

bool protocols::symmetric_docking::SymDockProtocol::autofoldtree_

private

Modified Docking foldtree for symmetry.

◆ design_

bool protocols::symmetric_docking::SymDockProtocol::design_

private

Allow design of partner 2 during docking.

Referenced by apply(), and design().

◆ dock_ppk_

bool protocols::symmetric_docking::SymDockProtocol::dock_ppk_

private

Referenced by set_default(), and set_dock_ppk().

◆ docking_high_

protocols::symmetric_docking::SymDockingHiResOP protocols::symmetric_docking::SymDockProtocol::docking_high_

private

Referenced by apply(), and set_highres_scorefxn().

◆ docking_low_

protocols::symmetric_docking::SymDockingLowResOP protocols::symmetric_docking::SymDockProtocol::docking_low_

private

Child protocols - low resolution and high resolution docking & for packing.

Referenced by apply(), and set_lowres_scorefxn().

◆ docking_score_high_

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_high_

private

Referenced by apply(), clone(), score_only(), set_default(), set_highres_scorefxn(), and SymDockProtocol().

◆ docking_score_high_min_

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_high_min_

private

Referenced by apply(), set_default(), set_highres_scorefxn(), and SymDockProtocol().

◆ docking_score_low_

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_low_

private

Scorefunctions used during the protocol.

Referenced by apply(), calc_interaction_energy(), clone(), score_only(), set_default(), set_lowres_scorefxn(), and SymDockProtocol().

◆ docking_score_pack_

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_pack_

private

Referenced by apply(), calc_interaction_energy(), recover_sidechains(), set_default(), set_highres_scorefxn(), and SymDockProtocol().

◆ fullatom_

bool protocols::symmetric_docking::SymDockProtocol::fullatom_

private

Data about the protocol.

Referenced by apply(), calc_interaction_energy(), clone(), score_only(), and set_fullatom().

◆ hurry_

bool protocols::symmetric_docking::SymDockProtocol::hurry_

private

Sip population of the score map.

Referenced by apply(), and hurry().

◆ init_task_factory_

core::pack::task::TaskFactoryOP protocols::symmetric_docking::SymDockProtocol::init_task_factory_

private

Used to restrict packer task during docking.

Referenced by apply(), and task_factory().

◆ local_refine_

bool protocols::symmetric_docking::SymDockProtocol::local_refine_

private

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

◆ max_repeats_

core::Size protocols::symmetric_docking::SymDockProtocol::max_repeats_

private

Referenced by set_max_repeats().

◆ mc_

moves::MonteCarloOP protocols::symmetric_docking::SymDockProtocol::mc_

private

Monte carlo object.

◆ movable_jumps_

utility::vector1<core::Size> protocols::symmetric_docking::SymDockProtocol::movable_jumps_

private

Jumps for symmetric rigid body transformations.

◆ passed_highres_filter_

bool protocols::symmetric_docking::SymDockProtocol::passed_highres_filter_

private

Referenced by apply(), set_default(), and set_fullatom().

◆ passed_lowres_filter_

bool protocols::symmetric_docking::SymDockProtocol::passed_lowres_filter_

private

Filters for structures during protocols.

Referenced by apply(), set_default(), and set_local_refine().

◆ rtmin_

bool protocols::symmetric_docking::SymDockProtocol::rtmin_

private

Referenced by recover_sidechains(), and set_dock_rtmin().

◆ sc_min_

bool protocols::symmetric_docking::SymDockProtocol::sc_min_

private

Referenced by set_sc_min().

◆ score_map_

std::map< std::string, core::Real > protocols::symmetric_docking::SymDockProtocol::score_map_

private

For scorefile output.

Referenced by apply(), and docking_highres_filter().

◆ view_

bool protocols::symmetric_docking::SymDockProtocol::view_

private

Initialize the graphics viewer (opengl)

Referenced by clone(), and set_view().

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

src/protocols/symmetric_docking/SymDockProtocol.hh
src/protocols/symmetric_docking/SymDockProtocol.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SymmetricConformation

◆ SymmetryInfo

Constructor & Destructor Documentation

◆ SymDockProtocol() [1/3]

◆ SymDockProtocol() [2/3]

◆ SymDockProtocol() [3/3]

◆ ~SymDockProtocol()

Member Function Documentation

◆ apply()

◆ calc_CAPRI_rank()

◆ calc_fnat()

◆ calc_interaction_energy()

◆ calc_Irms()

◆ calc_res_contact()

◆ calc_rms()

◆ classic_mcm_protocol()

◆ clone()

◆ design() [1/2]

◆ design() [2/2]

◆ docking_highres_filter()

◆ docking_lowres_filter()

◆ get_name()

◆ hurry()

◆ make_dockmcm_mover()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ recover_sidechains()

◆ register_options()

◆ score_only()

◆ set_default()

◆ set_dock_ppk()

◆ set_dock_rtmin()

◆ set_fullatom()

◆ set_highres_scorefxn() [1/2]

◆ set_highres_scorefxn() [2/2]

◆ set_local_refine()

◆ set_lowres_scorefxn()

◆ set_max_repeats()

◆ set_sc_min()

◆ set_view()

◆ task_factory() [1/3]

◆ task_factory() [2/3]

◆ task_factory() [3/3]

Member Data Documentation

◆ autofoldtree_

◆ design_

◆ dock_ppk_

◆ docking_high_

◆ docking_low_

◆ docking_score_high_

◆ docking_score_high_min_

◆ docking_score_low_

◆ docking_score_pack_

◆ fullatom_

◆ hurry_

◆ init_task_factory_

◆ local_refine_

◆ max_repeats_

◆ mc_

◆ movable_jumps_

◆ passed_highres_filter_

◆ passed_lowres_filter_

◆ rtmin_

◆ sc_min_

◆ score_map_

◆ view_