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protocols::coupled_moves::CoupledMovesProtocol Class Reference

#include <CoupledMovesProtocol.hh>

Inheritance diagram for protocols::coupled_moves::CoupledMovesProtocol:
Inheritance graph
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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 boolget_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::Realget_unique_sequences () const
 
utility::vector1< core::Sizeget_move_positions () const
 
utility::vector1< core::Sizeget_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::Sizeget_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 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 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::Sizemove_positions_
 
utility::vector1< core::Sizedesign_positions_
 
std::map< std::string, core::Realunique_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::Sizeligand_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 ( )
protocols::coupled_moves::CoupledMovesProtocol::CoupledMovesProtocol ( CoupledMovesProtocol const &  cmp)
default

Member Function Documentation

void protocols::coupled_moves::CoupledMovesProtocol::apply ( core::pose::Pose )
overridevirtual
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 ( )
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
void protocols::coupled_moves::CoupledMovesProtocol::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data_map 
)
overridevirtual
void protocols::coupled_moves::CoupledMovesProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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
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
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 
)
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 
)
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 
)
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
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
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
utility::vector1<core::Size> protocols::coupled_moves::CoupledMovesProtocol::move_positions_
private
std::string protocols::coupled_moves::CoupledMovesProtocol::move_type_ = "RESIDUE"
private
core::Size protocols::coupled_moves::CoupledMovesProtocol::ntrials_ = 1000
private
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
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: