#include <CoupledMovesProtocol.hh>

Inheritance diagram for protocols::coupled_moves::CoupledMovesProtocol:

Public Member Functions
	CoupledMovesProtocol ()

	CoupledMovesProtocol (CoupledMovesProtocol const &cmp)

void	apply (core::pose::Pose &pose) override
	Main Method. 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	configure_score_fxn ()
	adds terms for the backrub step to the scorefunction. Used by ctor; also useful when using set_score_fxn More...

core::Real	compute_ligand_score_bonus (core::pose::PoseOP pose)

void	exclude_nonclashing_positions (core::pose::PoseOP pose)

void	setup_move_and_design_positions (core::pack::task::PackerTaskCOP task, core::pose::PoseCOP pose)

protocols::simple_moves::CoupledMoverOP	setup_coupled_mover (core::pack::task::PackerTaskOP task, core::pose::PoseOP pose_copy, protocols::simple_moves::CoupledMoverOP coupled_mover)

protocols::simple_moves::CoupledMoverOP	setup_coupled_mover_for_ligand (core::pose::PoseOP pose_copy, core::pack::task::PackerTaskOP task, protocols::simple_moves::CoupledMoverOP coupled_mover)

void	setup_move_type (core::Real const move_prob)

void	setup_resnum (core::Real const move_prob, protocols::simple_moves::CoupledMoverOP coupled_mover, core::pose::PoseOP pose_copy)

void	write_info_to_log (core::pose::PoseOP pose_copy)

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	parse_my_tag More...

void	set_score_fxn (core::scoring::ScoreFunctionOP const sf)
	set the score function. NOTICE: you will want to also use the companion configure_score_fxn afterwards to add backrub terms to the SF, if you did not do so yourself! More...

void	set_main_task_factory (core::pack::task::TaskFactoryOP const tf)
	set the task factory. Note that the ctor sets InitializeFromCommandline plus either ReadResfile or RestrictToRepacking. More...

void	set_ntrials (core::Size ntrials)

void	set_loop_size (core::Size loop_size)

void	set_perturber (kinematic_closure::perturbers::PerturberOP perturber)

void	set_backbone_mover (std::string const &backbone_mover)

void	set_repack_neighborhood (bool repack_neighborhood)

void	set_ligand_mode (bool const ligand_mode)

void	set_number_ligands (core::Size const number_ligands)

void	set_ligand_weight (core::Real const ligand_weight)

void	set_ligand_prob (core::Real const ligand_prob)

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

core::Size	get_ntrials ()

std::string	get_backbone_mover () const

const bool &	get_repack_neighborhood () const

core::Size	get_loop_size () const

kinematic_closure::perturbers::PerturberOP	get_perturber () const

std::string	get_move_type () const

std::map< std::string, core::Real >	get_unique_sequences () const

utility::vector1< core::Size >	get_move_positions () const

utility::vector1< core::Size >	get_design_positions () const

bool	get_ligand_mode () const

core::Size	get_number_ligands () const

core::Real	get_ligand_weight () const

core::Real	get_ligand_prob () const

utility::vector1< core::Size >	get_ligand_resnums () 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 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

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

static std::string	mover_name ()

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	initialize_from_options ()
	sets up internal options based on options system More...

void	initialize_ligand_from_options ()
	sets up internal options for ligand mode based on the options system More...

Private Attributes
core::scoring::ScoreFunctionOP	score_fxn_

core::pack::task::TaskFactoryOP	main_task_factory_

core::Size	ntrials_ = 1000

std::string	move_type_ = "RESIDUE"

utility::vector1< core::Size >	move_positions_

utility::vector1< core::Size >	design_positions_

std::map< std::string, core::Real >	unique_sequences_

std::map< std::string, core::scoring::EnergyMap >	unique_scores_

core::Size	loop_size_ = 4
	parameter for KIC with walking perturber More...

kinematic_closure::perturbers::PerturberOP	perturber_
	mover used for side-chain moves More...

std::string	backbone_mover_ = "backrub"
	type of backbone move, e.g. backrub or kic More...

bool	repack_neighborhood_ = false
	Default false for legacy behavior (Ollikainen 2015). After the backbone move and rotamer move, repack sidechains within 5A of the design residue. More...

bool	ligand_mode_ = false
	if true, model protein ligand interaction More...

core::Size	number_ligands_ = 1
	number of ligands in the pose More...

core::Real	ligand_weight_ = 1.0
	weight for residue - ligand interactions More...

core::Real	ligand_prob_ = 0.1
	probability of making a ligand move More...

utility::vector1< core::Size >	ligand_resnums_

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

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::coupled_moves::CoupledMovesProtocol::CoupledMovesProtocol ( )

References configure_score_fxn(), core::scoring::get_score_function(), main_task_factory_, and score_fxn_.

protocols::coupled_moves::CoupledMovesProtocol::CoupledMovesProtocol ( CoupledMovesProtocol const & cmp )

default

Member Function Documentation

void protocols::coupled_moves::CoupledMovesProtocol::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

protocols::moves::MoverOP protocols::coupled_moves::CoupledMovesProtocol::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.

core::Real protocols::coupled_moves::CoupledMovesProtocol::compute_ligand_score_bonus ( core::pose::PoseOP pose )

References ligand_resnums_, and ligand_weight_.

Referenced by apply().

void protocols::coupled_moves::CoupledMovesProtocol::configure_score_fxn ( )

adds terms for the backrub step to the scorefunction. Used by ctor; also useful when using set_score_fxn

References core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::mm_bend, and score_fxn_.

Referenced by CoupledMovesProtocol(), and parse_my_tag().

void protocols::coupled_moves::CoupledMovesProtocol::exclude_nonclashing_positions ( core::pose::PoseOP pose )

References main_task_factory_.

Referenced by apply().

protocols::moves::MoverOP protocols::coupled_moves::CoupledMovesProtocol::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.

std::string protocols::coupled_moves::CoupledMovesProtocol::get_backbone_mover ( ) const

inline

References backbone_mover_.

utility::vector1<core::Size> protocols::coupled_moves::CoupledMovesProtocol::get_design_positions ( ) const

inline

References design_positions_.

bool protocols::coupled_moves::CoupledMovesProtocol::get_ligand_mode ( ) const

inline

References ligand_mode_.

core::Real protocols::coupled_moves::CoupledMovesProtocol::get_ligand_prob ( ) const

inline

References ligand_prob_.

utility::vector1<core::Size> protocols::coupled_moves::CoupledMovesProtocol::get_ligand_resnums ( ) const

inline

References ligand_resnums_.

core::Real protocols::coupled_moves::CoupledMovesProtocol::get_ligand_weight ( ) const

inline

References ligand_weight_.

core::Size protocols::coupled_moves::CoupledMovesProtocol::get_loop_size ( ) const

inline

References loop_size_.

utility::vector1<core::Size> protocols::coupled_moves::CoupledMovesProtocol::get_move_positions ( ) const

inline

References move_positions_.

std::string protocols::coupled_moves::CoupledMovesProtocol::get_move_type ( ) const

inline

References move_type_.

std::string protocols::coupled_moves::CoupledMovesProtocol::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Size protocols::coupled_moves::CoupledMovesProtocol::get_ntrials ( )

inline

References ntrials_.

core::Size protocols::coupled_moves::CoupledMovesProtocol::get_number_ligands ( ) const

inline

References number_ligands_.

kinematic_closure::perturbers::PerturberOP protocols::coupled_moves::CoupledMovesProtocol::get_perturber ( ) const

inline

References perturber_.

const bool& protocols::coupled_moves::CoupledMovesProtocol::get_repack_neighborhood ( ) const

inline

References repack_neighborhood_.

std::map<std::string,core::Real> protocols::coupled_moves::CoupledMovesProtocol::get_unique_sequences ( ) const

inline

References unique_sequences_.

void protocols::coupled_moves::CoupledMovesProtocol::initialize_from_options ( )

private

sets up internal options based on options system

References initialize_ligand_from_options(), and protocols::TR().

Referenced by apply().

void protocols::coupled_moves::CoupledMovesProtocol::initialize_ligand_from_options ( )

private

sets up internal options for ligand mode based on the options system

References set_ligand_mode(), set_ligand_prob(), set_ligand_weight(), and set_number_ligands().

Referenced by initialize_from_options().

std::string protocols::coupled_moves::CoupledMovesProtocol::mover_name ( )

static

Referenced by get_name(), protocols::coupled_moves::CoupledMovesProtocolCreator::keyname(), and provide_xml_schema().

void protocols::coupled_moves::CoupledMovesProtocol::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data_map
	)

overridevirtual

parse_my_tag

Reimplemented from protocols::moves::Mover.

References configure_score_fxn(), loop_size_, main_task_factory_, core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), protocols::loops::read_loop_fragments(), score_fxn_, set_backbone_mover(), set_loop_size(), set_perturber(), and protocols::TR().

void protocols::coupled_moves::CoupledMovesProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::attributes_for_parse_task_operations(), mover_name(), core::id::to_string(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::coupled_moves::CoupledMovesProtocolCreator::provide_xml_schema().

void protocols::coupled_moves::CoupledMovesProtocol::set_backbone_mover ( std::string const & backbone_mover )

inline

References backbone_mover_.

Referenced by parse_my_tag().

void protocols::coupled_moves::CoupledMovesProtocol::set_ligand_mode ( bool const ligand_mode )

inline

References ligand_mode_.

Referenced by initialize_ligand_from_options().

void protocols::coupled_moves::CoupledMovesProtocol::set_ligand_prob ( core::Real const ligand_prob )

inline

References ligand_prob_.

Referenced by initialize_ligand_from_options().

void protocols::coupled_moves::CoupledMovesProtocol::set_ligand_weight ( core::Real const ligand_weight )

inline

References ligand_weight_.

Referenced by initialize_ligand_from_options().

void protocols::coupled_moves::CoupledMovesProtocol::set_loop_size ( core::Size loop_size )

inline

References loop_size_.

Referenced by parse_my_tag().

void protocols::coupled_moves::CoupledMovesProtocol::set_main_task_factory ( core::pack::task::TaskFactoryOP const tf )

inline

set the task factory. Note that the ctor sets InitializeFromCommandline plus either ReadResfile or RestrictToRepacking.

References main_task_factory_.

void protocols::coupled_moves::CoupledMovesProtocol::set_ntrials ( core::Size ntrials )

inline

References ntrials_.

void protocols::coupled_moves::CoupledMovesProtocol::set_number_ligands ( core::Size const number_ligands )

inline

References number_ligands_.

Referenced by initialize_ligand_from_options().

void protocols::coupled_moves::CoupledMovesProtocol::set_perturber ( kinematic_closure::perturbers::PerturberOP perturber )

inline

References perturber_.

Referenced by parse_my_tag().

void protocols::coupled_moves::CoupledMovesProtocol::set_repack_neighborhood ( bool repack_neighborhood )

inline

References repack_neighborhood_.

void protocols::coupled_moves::CoupledMovesProtocol::set_score_fxn ( core::scoring::ScoreFunctionOP const sf )

inline

set the score function. NOTICE: you will want to also use the companion configure_score_fxn afterwards to add backrub terms to the SF, if you did not do so yourself!

References score_fxn_.

protocols::simple_moves::CoupledMoverOP protocols::coupled_moves::CoupledMovesProtocol::setup_coupled_mover	(	core::pack::task::PackerTaskOP	task,
		core::pose::PoseOP	pose_copy,
		protocols::simple_moves::CoupledMoverOP	coupled_mover
	)

References backbone_mover_, core::pack::rotamer_set::bump_check(), ligand_mode_, loop_size_, perturber_, score_fxn_, and setup_coupled_mover_for_ligand().

Referenced by apply().

protocols::simple_moves::CoupledMoverOP protocols::coupled_moves::CoupledMovesProtocol::setup_coupled_mover_for_ligand	(	core::pose::PoseOP	pose_copy,
		core::pack::task::PackerTaskOP	task,
		protocols::simple_moves::CoupledMoverOP	coupled_mover
	)

References ligand_resnums_, ligand_weight_, number_ligands_, and score_fxn_.

Referenced by setup_coupled_mover().

void protocols::coupled_moves::CoupledMovesProtocol::setup_move_and_design_positions	(	core::pack::task::PackerTaskCOP	task,
		core::pose::PoseCOP	pose
	)

References design_positions_, and move_positions_.

Referenced by apply().

void protocols::coupled_moves::CoupledMovesProtocol::setup_move_type ( core::Real const move_prob )

References ligand_mode_, ligand_prob_, and move_type_.

Referenced by apply().

void protocols::coupled_moves::CoupledMovesProtocol::setup_resnum	(	core::Real const	move_prob,
		protocols::simple_moves::CoupledMoverOP	coupled_mover,
		core::pose::PoseOP	pose_copy
	)

References ligand_mode_, ligand_prob_, ligand_resnums_, move_positions_, and protocols::rigid::random.

Referenced by apply().

void protocols::coupled_moves::CoupledMovesProtocol::write_info_to_log ( core::pose::PoseOP pose_copy )

References design_positions_, ntrials_, score_fxn_, and protocols::TR().

Referenced by apply().

Member Data Documentation

std::string protocols::coupled_moves::CoupledMovesProtocol::backbone_mover_ = "backrub"

private

type of backbone move, e.g. backrub or kic

Referenced by get_backbone_mover(), set_backbone_mover(), and setup_coupled_mover().

utility::vector1<core::Size> protocols::coupled_moves::CoupledMovesProtocol::design_positions_

private

Referenced by apply(), get_design_positions(), setup_move_and_design_positions(), and write_info_to_log().

bool protocols::coupled_moves::CoupledMovesProtocol::ligand_mode_ = false

private

if true, model protein ligand interaction

Referenced by apply(), get_ligand_mode(), set_ligand_mode(), setup_coupled_mover(), setup_move_type(), and setup_resnum().

core::Real protocols::coupled_moves::CoupledMovesProtocol::ligand_prob_ = 0.1

private

probability of making a ligand move

Referenced by get_ligand_prob(), set_ligand_prob(), setup_move_type(), and setup_resnum().

utility::vector1<core::Size> protocols::coupled_moves::CoupledMovesProtocol::ligand_resnums_

private

Referenced by compute_ligand_score_bonus(), get_ligand_resnums(), setup_coupled_mover_for_ligand(), and setup_resnum().

core::Real protocols::coupled_moves::CoupledMovesProtocol::ligand_weight_ = 1.0

private

weight for residue - ligand interactions

Referenced by compute_ligand_score_bonus(), get_ligand_weight(), set_ligand_weight(), and setup_coupled_mover_for_ligand().

core::Size protocols::coupled_moves::CoupledMovesProtocol::loop_size_ = 4

private

parameter for KIC with walking perturber

loop size for KIC

Referenced by get_loop_size(), parse_my_tag(), set_loop_size(), and setup_coupled_mover().

core::pack::task::TaskFactoryOP protocols::coupled_moves::CoupledMovesProtocol::main_task_factory_

private

Referenced by apply(), CoupledMovesProtocol(), exclude_nonclashing_positions(), parse_my_tag(), and set_main_task_factory().

utility::vector1<core::Size> protocols::coupled_moves::CoupledMovesProtocol::move_positions_

private

Referenced by apply(), get_move_positions(), setup_move_and_design_positions(), and setup_resnum().

std::string protocols::coupled_moves::CoupledMovesProtocol::move_type_ = "RESIDUE"

private

Referenced by apply(), get_move_type(), and setup_move_type().

core::Size protocols::coupled_moves::CoupledMovesProtocol::ntrials_ = 1000

private

Referenced by apply(), get_ntrials(), set_ntrials(), and write_info_to_log().

core::Size protocols::coupled_moves::CoupledMovesProtocol::number_ligands_ = 1

private

number of ligands in the pose

Referenced by get_number_ligands(), set_number_ligands(), and setup_coupled_mover_for_ligand().

kinematic_closure::perturbers::PerturberOP protocols::coupled_moves::CoupledMovesProtocol::perturber_

private

mover used for side-chain moves

perturber used by kic

Referenced by get_perturber(), set_perturber(), and setup_coupled_mover().

bool protocols::coupled_moves::CoupledMovesProtocol::repack_neighborhood_ = false

private

Default false for legacy behavior (Ollikainen 2015). After the backbone move and rotamer move, repack sidechains within 5A of the design residue.

Referenced by get_repack_neighborhood(), and set_repack_neighborhood().

core::scoring::ScoreFunctionOP protocols::coupled_moves::CoupledMovesProtocol::score_fxn_

private

Referenced by apply(), configure_score_fxn(), CoupledMovesProtocol(), parse_my_tag(), set_score_fxn(), setup_coupled_mover(), setup_coupled_mover_for_ligand(), and write_info_to_log().

std::map<std::string,core::scoring::EnergyMap> protocols::coupled_moves::CoupledMovesProtocol::unique_scores_

private

Referenced by apply().

std::map<std::string,core::Real> protocols::coupled_moves::CoupledMovesProtocol::unique_sequences_

private

Referenced by apply(), and get_unique_sequences().

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

src/protocols/coupled_moves/CoupledMovesProtocol.hh
src/protocols/coupled_moves/CoupledMovesProtocol.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation