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protocols::simple_moves::CoupledMover Class Reference

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

#include <CoupledMover.hh>

Inheritance diagram for protocols::simple_moves::CoupledMover:
Inheritance graph
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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 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 boolget_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)
 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 Stringsinfo ()
 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

Constructor & Destructor Documentation

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

References uniform_backrub_.

std::string protocols::simple_moves::CoupledMover::mover_name ( )
static
void protocols::simple_moves::CoupledMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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)
void protocols::simple_moves::CoupledMover::set_boltzmann_rotamer_mover ( protocols::minimization_packing::BoltzmannRotamerMoverOP  boltzmann_rotamer_mover)
void protocols::simple_moves::CoupledMover::set_bump_check ( bool  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)
void protocols::simple_moves::CoupledMover::set_ligand_resnum ( core::Size  ligand_resnum,
core::pose::PoseCOP  pose 
)
void protocols::simple_moves::CoupledMover::set_ligand_weight ( core::Real  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)
void protocols::simple_moves::CoupledMover::set_rotation_std_dev ( core::Real  rotation_std_dev)
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)
void protocols::simple_moves::CoupledMover::set_translation_magnitude ( core::Real  translation_magnitude)
void protocols::simple_moves::CoupledMover::set_uniform_backrub ( bool  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
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().

bool protocols::simple_moves::CoupledMover::repack_neighborhood_
private

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

Referenced by apply(), CoupledMover(), get_repack_neighborhood(), and set_repack_neighborhood().

core::Size protocols::simple_moves::CoupledMover::resnum_
private

residue number specifying the residue for the next move

Referenced by apply(), CoupledMover(), get_resnum(), and set_resnum().

protocols::rigid::RigidBodyPerturbMoverOP protocols::simple_moves::CoupledMover::rigid_body_mover_
private
core::Real protocols::simple_moves::CoupledMover::rotation_magnitude_
private

the magnitude of ligand rotation used by the RigidBodyMover (in degrees)

Referenced by CoupledMover(), get_rotation_magnitude(), set_ligand_jump_id(), and set_rotation_magnitude().

core::Real protocols::simple_moves::CoupledMover::rotation_std_dev_
private

standard deviation of rotation angle (degrees) used for ShortBackrubMover

Referenced by CoupledMover(), get_rotation_std_dev(), and set_rotation_std_dev().

core::scoring::ScoreFunctionOP protocols::simple_moves::CoupledMover::score_fxn_
private

score function needed for the BoltzmannRotamerMover

Referenced by apply(), get_score_fxn(), and set_score_fxn().

protocols::simple_moves::ShortBackrubMoverOP protocols::simple_moves::CoupledMover::short_backrub_mover_
private

mover used for backbone moves when option set to backrub

Referenced by apply(), CoupledMover(), get_short_backrub_mover(), set_input_pose(), set_rotation_std_dev(), set_short_backrub_mover(), and set_uniform_backrub().

core::Real protocols::simple_moves::CoupledMover::temperature_
private

kT value used for Boltzmann probability calculation

Referenced by CoupledMover(), get_temperature(), and set_temperature().

core::Real protocols::simple_moves::CoupledMover::translation_magnitude_
private

the magnitude of ligand translation used by the RigidBodyMover (in angstroms)

Referenced by CoupledMover(), get_translation_magnitude(), set_ligand_jump_id(), and set_translation_magnitude().

bool protocols::simple_moves::CoupledMover::uniform_backrub_
private

if true, sample rotation angle from a uniform distribution from -20 to 20

Referenced by CoupledMover(), get_uniform_backrub(), and set_uniform_backrub().


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