This mover is called by CoupledMovesProtocol to make a single coupled move. More...

#include <CoupledMover.hh>

Inheritance diagram for protocols::simple_moves::CoupledMover:

Public Types
typedef protocols::moves::MoverOP	MoverOP

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

Public Member Functions
	CoupledMover ()

	CoupledMover (core::pose::PoseOP pose, core::scoring::ScoreFunctionOP score_fxn, core::pack::task::PackerTaskOP packer_task)
	constructor that sets input pose, score function and packer task More...

	CoupledMover (core::pose::PoseOP pose, core::scoring::ScoreFunctionOP score_fxn, core::pack::task::PackerTaskOP packer_task, core::Size ligand_resnum)
	constructor that sets input pose, score function, packer task and ligand residue number More...

	CoupledMover (CoupledMover const &rval)
	copy constructor More...

	~CoupledMover () override
	destructor More...

protocols::moves::MoverOP	clone () const override
	clone this object More...

protocols::moves::MoverOP	fresh_instance () const override
	create this type of object More...

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

void	set_resnum (core::Size resnum)

void	set_randomize_resnum (bool randomize_resnum)

void	set_fix_backbone (bool fix_backbone)

void	set_rotation_std_dev (core::Real rotation_std_dev)

void	set_uniform_backrub (bool uniform_backrub)

void	set_input_pose (core::pose::PoseCOP pose) override
	setter for poses contained for rms More...

void	set_temperature (core::Real temperature)

void	set_bias_sampling (bool bias_sampling)

void	set_bump_check (bool bump_check)

void	set_ligand_resnum (core::Size ligand_resnum, core::pose::PoseCOP pose)

void	set_ligand_jump_id (core::Size ligand_jump_id)

void	set_ligand_weight (core::Real ligand_weight)

void	set_rotation_magnitude (core::Real rotation_magnitude)

void	set_translation_magnitude (core::Real translation_magnitude)

void	set_short_backrub_mover (protocols::simple_moves::ShortBackrubMoverOP short_backrub_mover)

void	set_boltzmann_rotamer_mover (protocols::minimization_packing::BoltzmannRotamerMoverOP boltzmann_rotamer_mover)

void	set_rigid_body_mover (protocols::rigid::RigidBodyPerturbMoverOP rigid_body_mover)

void	set_score_fxn (core::scoring::ScoreFunctionOP score_fxn)

void	set_packer_task (core::pack::task::PackerTaskOP packer_task)

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)

core::Size	get_resnum () const

bool	get_randomize_resnum () const

bool	get_fix_backbone () const

core::Real	get_rotation_std_dev () const

bool	get_uniform_backrub () const

core::Real	get_temperature () const

bool	get_bias_sampling () const

bool	get_bump_check () const

core::Size	get_ligand_resnum () const

core::Size	get_ligand_jump_id () const

core::Real	get_ligand_weight () const

core::Real	get_rotation_magnitude () const

core::Real	get_translation_magnitude () const

protocols::simple_moves::ShortBackrubMoverOP	get_short_backrub_mover () const

protocols::minimization_packing::BoltzmannRotamerMoverOP	get_boltzmann_rotamer_mover () const

protocols::rigid::RigidBodyPerturbMoverOP	get_rigid_body_mover () const

core::scoring::ScoreFunctionOP	get_score_fxn () const

core::pack::task::PackerTaskOP	get_packer_task () const

core::Size	get_loop_size () const

kinematic_closure::perturbers::PerturberOP	get_perturber () const

const std::string &	get_backbone_mover () const

const bool &	get_repack_neighborhood () const

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...

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_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, 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...

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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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 Attributes
core::Size	resnum_
	residue number specifying the residue for the next move More...

bool	randomize_resnum_
	if true, choose a random residue for the next move More...

bool	fix_backbone_
	if true, do not perform backbone moves More...

core::Real	rotation_std_dev_
	standard deviation of rotation angle (degrees) used for ShortBackrubMover More...

bool	uniform_backrub_
	if true, sample rotation angle from a uniform distribution from -20 to 20 More...

core::Real	temperature_
	kT value used for Boltzmann probability calculation More...

bool	bias_sampling_
	if true, bias rotamer selection based on energy More...

bool	bump_check_
	if true, use bump check when generating rotamers More...

core::Size	ligand_resnum_
	residue number specifying the ligand (set to zero if there is no ligand) More...

core::Size	ligand_jump_id_
	jump id specifying the ligand jump (set to zero if there is no ligand) More...

core::Real	ligand_weight_
	weight of interaction between resnum_ and ligand_resnum_ More...

core::Real	rotation_magnitude_
	the magnitude of ligand rotation used by the RigidBodyMover (in degrees) More...

core::Real	translation_magnitude_
	the magnitude of ligand translation used by the RigidBodyMover (in angstroms) More...

protocols::simple_moves::ShortBackrubMoverOP	short_backrub_mover_
	mover used for backbone moves when option set to backrub More...

protocols::kinematic_closure::KicMoverOP	fullatom_kic_mover_
	mover used for backbone moves when option set to kinematic closure More...

protocols::minimization_packing::BoltzmannRotamerMoverOP	boltzmann_rotamer_mover_
	mover used for side-chain moves More...

protocols::rigid::RigidBodyPerturbMoverOP	rigid_body_mover_
	mover used for rigid body rotation and translation More...

core::scoring::ScoreFunctionOP	score_fxn_
	score function needed for the BoltzmannRotamerMover More...

core::pack::task::PackerTaskOP	packer_task_
	task factory needed to generate packer task More...

core::Size	loop_size_
	the size of the loop for KIC move. Loop is center residue + and - this number. More...

kinematic_closure::perturbers::PerturberOP	perturber_
	Which perturber to use during kinematic closure (KIC). Currently the options are fragment or walking perturber. Walking perturber adjusts torsions by degrees, the magnitude of which can be set by walking_perturber_magnitude option in CoupledMovesProtocol. More...

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

bool	repack_neighborhood_
	After the backbone move and rotamer move, repack sidechains within 5A of the design residue. Default false for legacy behavior. 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

This mover is called by CoupledMovesProtocol to make a single coupled move.

The CoupledMover apply function makes a single coupled move as follows: (1) Backbone move – As of March 2018, there are three options: backrub, kinematic closure with walking perturber, or kinematic closure with fragment perturber. (2) Side chain move – The three residues at the center of the perturbed backbone are sampled by BoltzmannRotamerMover. (3) Repack – 10A shell around the residues from step 2 is repacked.

Member Typedef Documentation

typedef protocols::moves::MoverOP protocols::simple_moves::CoupledMover::MoverOP

Constructor & Destructor Documentation

protocols::simple_moves::CoupledMover::CoupledMover ( )

References bias_sampling_, boltzmann_rotamer_mover_, bump_check_, fix_backbone_, ligand_jump_id_, ligand_resnum_, ligand_weight_, loop_size_, randomize_resnum_, repack_neighborhood_, resnum_, rotation_magnitude_, rotation_std_dev_, short_backrub_mover_, temperature_, translation_magnitude_, protocols::moves::Mover::type(), and uniform_backrub_.

protocols::simple_moves::CoupledMover::CoupledMover	(	core::pose::PoseOP	pose,
		core::scoring::ScoreFunctionOP	score_fxn,
		core::pack::task::PackerTaskOP	packer_task
	)

constructor that sets input pose, score function and packer task

References set_packer_task(), set_score_fxn(), and short_backrub_mover_.

protocols::simple_moves::CoupledMover::CoupledMover	(	core::pose::PoseOP	pose,
		core::scoring::ScoreFunctionOP	score_fxn,
		core::pack::task::PackerTaskOP	packer_task,
		core::Size	ligand_resnum
	)

constructor that sets input pose, score function, packer task and ligand residue number

constructor that sets input pose, score function, packer task, and ligand residue number

References ligand_jump_id_, ligand_resnum_, rigid_body_mover_, rotation_magnitude_, set_rigid_body_mover(), and translation_magnitude_.

protocols::simple_moves::CoupledMover::CoupledMover ( CoupledMover const & rval )

default

copy constructor

protocols::simple_moves::CoupledMover::~CoupledMover ( )

overridedefault

destructor

Member Function Documentation

void protocols::simple_moves::CoupledMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::simple_moves::MutateResidue::apply(), backbone_mover_, boltzmann_rotamer_mover_, core::conformation::Residue::chain(), protocols::loops::chainID, core::select::residue_selector::NeighborhoodResidueSelector::clone(), fix_backbone_, get_boltzmann_rotamer_mover(), get_ligand_resnum(), core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueTypeBase::is_protein(), core::conformation::Residue::is_protein(), loop_size_, packer_task_, perturber_, randomize_resnum_, repack_neighborhood_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), resnum_, core::scoring::rg, rigid_body_mover_, score_fxn_, core::pose::Pose::sequence(), core::select::residue_selector::NeighborhoodResidueSelector::set_distance(), core::select::residue_selector::NeighborhoodResidueSelector::set_focus(), core::select::residue_selector::NeighborhoodResidueSelector::set_include_focus_in_subset(), short_backrub_mover_, core::pose::Pose::size(), and protocols::simple_moves::TR().

CoupledMover::MoverOP protocols::simple_moves::CoupledMover::clone ( ) const

overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

CoupledMover::MoverOP protocols::simple_moves::CoupledMover::fresh_instance ( ) const

overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

const std::string & protocols::simple_moves::CoupledMover::get_backbone_mover ( ) const

References backbone_mover_.

bool protocols::simple_moves::CoupledMover::get_bias_sampling ( ) const

References bias_sampling_.

protocols::minimization_packing::BoltzmannRotamerMoverOP protocols::simple_moves::CoupledMover::get_boltzmann_rotamer_mover ( ) const

References boltzmann_rotamer_mover_.

Referenced by apply().

bool protocols::simple_moves::CoupledMover::get_bump_check ( ) const

References bump_check_.

bool protocols::simple_moves::CoupledMover::get_fix_backbone ( ) const

References fix_backbone_.

core::Size protocols::simple_moves::CoupledMover::get_ligand_jump_id ( ) const

References ligand_jump_id_.

core::Size protocols::simple_moves::CoupledMover::get_ligand_resnum ( ) const

References ligand_resnum_.

Referenced by apply().

core::Real protocols::simple_moves::CoupledMover::get_ligand_weight ( ) const

References ligand_weight_.

core::Size protocols::simple_moves::CoupledMover::get_loop_size ( ) const

References loop_size_.

std::string protocols::simple_moves::CoupledMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::pack::task::PackerTaskOP protocols::simple_moves::CoupledMover::get_packer_task ( ) const

References packer_task_.

kinematic_closure::perturbers::PerturberOP protocols::simple_moves::CoupledMover::get_perturber ( ) const

References perturber_.

bool protocols::simple_moves::CoupledMover::get_randomize_resnum ( ) const

References randomize_resnum_.

const bool & protocols::simple_moves::CoupledMover::get_repack_neighborhood ( ) const

References repack_neighborhood_.

core::Size protocols::simple_moves::CoupledMover::get_resnum ( ) const

References resnum_.

protocols::rigid::RigidBodyPerturbMoverOP protocols::simple_moves::CoupledMover::get_rigid_body_mover ( ) const

References rigid_body_mover_.

core::Real protocols::simple_moves::CoupledMover::get_rotation_magnitude ( ) const

References rotation_magnitude_.

core::Real protocols::simple_moves::CoupledMover::get_rotation_std_dev ( ) const

References rotation_std_dev_.

core::scoring::ScoreFunctionOP protocols::simple_moves::CoupledMover::get_score_fxn ( ) const

References score_fxn_.

protocols::simple_moves::ShortBackrubMoverOP protocols::simple_moves::CoupledMover::get_short_backrub_mover ( ) const

References short_backrub_mover_.

core::Real protocols::simple_moves::CoupledMover::get_temperature ( ) const

References temperature_.

core::Real protocols::simple_moves::CoupledMover::get_translation_magnitude ( ) const

References translation_magnitude_.

bool protocols::simple_moves::CoupledMover::get_uniform_backrub ( ) const

References uniform_backrub_.

std::string protocols::simple_moves::CoupledMover::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::CoupledMoverCreator::keyname(), and provide_xml_schema().

void protocols::simple_moves::CoupledMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::simple_moves::CoupledMoverCreator::provide_xml_schema().

void protocols::simple_moves::CoupledMover::set_backbone_mover ( std::string const & backbone_mover )

References backbone_mover_.

void protocols::simple_moves::CoupledMover::set_bias_sampling ( bool bias_sampling )

References bias_sampling_, and boltzmann_rotamer_mover_.

void protocols::simple_moves::CoupledMover::set_boltzmann_rotamer_mover ( protocols::minimization_packing::BoltzmannRotamerMoverOP boltzmann_rotamer_mover )

References boltzmann_rotamer_mover_.

void protocols::simple_moves::CoupledMover::set_bump_check ( bool bump_check )

References boltzmann_rotamer_mover_, core::pack::rotamer_set::bump_check(), and bump_check_.

void protocols::simple_moves::CoupledMover::set_fix_backbone ( bool fix_backbone )

References fix_backbone_.

void protocols::simple_moves::CoupledMover::set_input_pose ( core::pose::PoseCOP pose )

overridevirtual

setter for poses contained for rms

Reimplemented from protocols::moves::Mover.

References short_backrub_mover_.

void protocols::simple_moves::CoupledMover::set_ligand_jump_id ( core::Size ligand_jump_id )

References ligand_jump_id_, rigid_body_mover_, rotation_magnitude_, and translation_magnitude_.

Referenced by set_ligand_resnum().

void protocols::simple_moves::CoupledMover::set_ligand_resnum	(	core::Size	ligand_resnum,
		core::pose::PoseCOP	pose
	)

References boltzmann_rotamer_mover_, ligand_resnum_, and set_ligand_jump_id().

void protocols::simple_moves::CoupledMover::set_ligand_weight ( core::Real ligand_weight )

References boltzmann_rotamer_mover_, and ligand_weight_.

void protocols::simple_moves::CoupledMover::set_loop_size ( core::Size loop_size )

References loop_size_.

void protocols::simple_moves::CoupledMover::set_packer_task ( core::pack::task::PackerTaskOP packer_task )

References packer_task_.

Referenced by CoupledMover().

void protocols::simple_moves::CoupledMover::set_perturber ( kinematic_closure::perturbers::PerturberOP perturber )

References perturber_.

void protocols::simple_moves::CoupledMover::set_randomize_resnum ( bool randomize_resnum )

References randomize_resnum_.

void protocols::simple_moves::CoupledMover::set_repack_neighborhood ( bool repack_neighborhood )

References repack_neighborhood_.

void protocols::simple_moves::CoupledMover::set_resnum ( core::Size resnum )

References resnum_.

void protocols::simple_moves::CoupledMover::set_rigid_body_mover ( protocols::rigid::RigidBodyPerturbMoverOP rigid_body_mover )

References rigid_body_mover_.

Referenced by CoupledMover().

void protocols::simple_moves::CoupledMover::set_rotation_magnitude ( core::Real rotation_magnitude )

References rigid_body_mover_, and rotation_magnitude_.

void protocols::simple_moves::CoupledMover::set_rotation_std_dev ( core::Real rotation_std_dev )

References rotation_std_dev_, and short_backrub_mover_.

void protocols::simple_moves::CoupledMover::set_score_fxn ( core::scoring::ScoreFunctionOP score_fxn )

References score_fxn_.

Referenced by CoupledMover().

void protocols::simple_moves::CoupledMover::set_short_backrub_mover ( protocols::simple_moves::ShortBackrubMoverOP short_backrub_mover )

References short_backrub_mover_.

void protocols::simple_moves::CoupledMover::set_temperature ( core::Real temperature )

References boltzmann_rotamer_mover_, and temperature_.

void protocols::simple_moves::CoupledMover::set_translation_magnitude ( core::Real translation_magnitude )

References rigid_body_mover_, and translation_magnitude_.

void protocols::simple_moves::CoupledMover::set_uniform_backrub ( bool uniform_backrub )

References short_backrub_mover_, and uniform_backrub_.

Member Data Documentation

std::string protocols::simple_moves::CoupledMover::backbone_mover_

private

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

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

bool protocols::simple_moves::CoupledMover::bias_sampling_

private

if true, bias rotamer selection based on energy

Referenced by CoupledMover(), get_bias_sampling(), and set_bias_sampling().

protocols::minimization_packing::BoltzmannRotamerMoverOP protocols::simple_moves::CoupledMover::boltzmann_rotamer_mover_

private

mover used for side-chain moves

Referenced by apply(), CoupledMover(), get_boltzmann_rotamer_mover(), set_bias_sampling(), set_boltzmann_rotamer_mover(), set_bump_check(), set_ligand_resnum(), set_ligand_weight(), and set_temperature().

bool protocols::simple_moves::CoupledMover::bump_check_

private

if true, use bump check when generating rotamers

Referenced by CoupledMover(), get_bump_check(), and set_bump_check().

bool protocols::simple_moves::CoupledMover::fix_backbone_

private

if true, do not perform backbone moves

Referenced by apply(), CoupledMover(), get_fix_backbone(), and set_fix_backbone().

protocols::kinematic_closure::KicMoverOP protocols::simple_moves::CoupledMover::fullatom_kic_mover_

private

mover used for backbone moves when option set to kinematic closure

core::Size protocols::simple_moves::CoupledMover::ligand_jump_id_

private

jump id specifying the ligand jump (set to zero if there is no ligand)

Referenced by CoupledMover(), get_ligand_jump_id(), and set_ligand_jump_id().

core::Size protocols::simple_moves::CoupledMover::ligand_resnum_

private

residue number specifying the ligand (set to zero if there is no ligand)

Referenced by CoupledMover(), get_ligand_resnum(), and set_ligand_resnum().

core::Real protocols::simple_moves::CoupledMover::ligand_weight_

private

weight of interaction between resnum_ and ligand_resnum_

Referenced by CoupledMover(), get_ligand_weight(), and set_ligand_weight().

core::Size protocols::simple_moves::CoupledMover::loop_size_

private

the size of the loop for KIC move. Loop is center residue + and - this number.

Referenced by apply(), CoupledMover(), get_loop_size(), and set_loop_size().

core::pack::task::PackerTaskOP protocols::simple_moves::CoupledMover::packer_task_

private

task factory needed to generate packer task

Referenced by apply(), get_packer_task(), and set_packer_task().

kinematic_closure::perturbers::PerturberOP protocols::simple_moves::CoupledMover::perturber_

private

Which perturber to use during kinematic closure (KIC). Currently the options are fragment or walking perturber. Walking perturber adjusts torsions by degrees, the magnitude of which can be set by walking_perturber_magnitude option in CoupledMovesProtocol.

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

bool protocols::simple_moves::CoupledMover::randomize_resnum_

private

if true, choose a random residue for the next move

Referenced by apply(), CoupledMover(), get_randomize_resnum(), and set_randomize_resnum().