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protocols::backrub::BackrubProtocol Class Reference

#include <BackrubProtocol.hh>

Inheritance diagram for protocols::backrub::BackrubProtocol:
Inheritance graph
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Public Member Functions

 BackrubProtocol ()
 
 BackrubProtocol (BackrubProtocol const &bp)
 
 ~BackrubProtocol () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void set_pivot_residues (utility::vector1< core::Size > pivot_residues)
 Set the pivot residues for backrub. Will use contiguous residues as segments. Within these segments, backrub will occur. More...
 
void set_pivot_atoms (utility::vector1< std::string > pivot_atoms)
 Set the type of atoms to use for backrub. These are atom names. Default is to only use CA as pivots. More...
 
void set_movemap (core::kinematics::MoveMapCOP movemap)
 Set the movemap for the whole protocol. Uses contiguous backbone regions for backrub to set pivot residues Within these segments, backrub will occur. More...
 
void set_movemap_smallmover (core::kinematics::MoveMapCOP movemap)
 Set the MoveMap that will only be used for the SmallMover. More...
 
void set_taskfactory (core::pack::task::TaskFactoryCOP tf)
 Set the taskfactory used for sidechain moves. NOTE: Clones the TF. Sets C-Beta off as they are not compatable with branch angle optimization. More...
 
void set_scorefunction (core::scoring::ScoreFunctionCOP scorefxn)
 Set the Scorefunction. NOTE: Clones the scorefxn. More...
 
void set_backrub_mover (protocols::backrub::BackrubMoverOP backrub_mover)
 Set a pre-configured Backrub Mover. More...
 
void write_database ()
 
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 parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
utility::vector1< core::Sizeget_pivot_residues () const
 
void set_pivots_from_residue_subset (core::select::residue_selector::ResidueSubset residue_subset)
 
- 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 std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Member Functions

void read_cmd_line_options ()
 
void set_options (utility::vector1< core::Size > pivot_residues, utility::vector1< std::string > pivot_atoms, core::kinematics::MoveMapCOP minimize_movemap, core::kinematics::MoveMapCOP movemap_smallmover, core::pack::task::operation::TaskOperationCOP packing_operation, core::Size min_atoms, core::Size max_atoms, bool initial_pack, core::Real mm_bend_weight, core::Real sm_prob, core::Real sc_prob, core::Real sc_prob_uniform, core::Real sc_prob_withinrot, core::Real mc_kt, core::Size ntrials, bool trajectory, bool trajectory_gz, core::Size trajectory_stride)
 Sets all member variables that are options that control behavior. These options can be set via parse_my_tag or command line options. More...
 
void finalize_setup (core::pose::Pose &pose)
 

Private Attributes

core::scoring::ScoreFunctionOP scorefxn_
 
core::pack::task::TaskFactoryOP main_task_factory_
 
protocols::backrub::BackrubMoverOP backrubmover_
 
protocols::simple_moves::SmallMoverOP smallmover_
 
protocols::simple_moves::sidechain_moves::SidechainMoverOP sidechainmover_
 
protocols::minimization_packing::PackRotamersMoverOP packrotamersmover_
 
core::Size ntrials_
 
core::kinematics::MoveMapCOP movemap_smallmover_
 
core::kinematics::MoveMapCOP minimize_movemap_
 
core::pack::task::operation::TaskOperationCOP packing_operation_
 
utility::vector1< core::Sizepivot_residues_
 
utility::vector1< std::string > pivot_atoms_
 
core::Size min_atoms_
 
core::Size max_atoms_
 
core::Real mm_bend_weight_
 
core::Real sm_prob_
 
core::Real sc_prob_
 
core::Real sc_prob_uniform_
 
core::Real sc_prob_withinrot_
 
core::Real mc_kt_
 
bool initial_pack_
 
bool trajectory_
 
bool trajectory_gz_
 
bool recover_low_
 
core::Size trajectory_stride_
 
protocols::moves::MoverOP trajectory_apply_mover_
 
core::select::residue_selector::ResidueSelectorCOP pivots_residue_selector_
 Residue selector to select pivot residues. More...
 

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::backrub::BackrubProtocol::BackrubProtocol ( )
protocols::backrub::BackrubProtocol::BackrubProtocol ( BackrubProtocol const &  bp)
protocols::backrub::BackrubProtocol::~BackrubProtocol ( )
overridedefault

Member Function Documentation

void protocols::backrub::BackrubProtocol::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::backrub::BackrubProtocol::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.

void protocols::backrub::BackrubProtocol::finalize_setup ( core::pose::Pose pose)
private
protocols::moves::MoverOP protocols::backrub::BackrubProtocol::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::backrub::BackrubProtocol::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

utility::vector1< core::Size > protocols::backrub::BackrubProtocol::get_pivot_residues ( ) const

References pivot_residues_.

std::string protocols::backrub::BackrubProtocol::mover_name ( )
static
void protocols::backrub::BackrubProtocol::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::select::residue_selector::get_residue_selector(), core::pose::get_resnum_selector(), main_task_factory_, protocols::rosetta_scripts::parse_mover(), core::pack::task::parse_task_operations(), pivots_residue_selector_, recover_low_, set_options(), and trajectory_apply_mover_.

void protocols::backrub::BackrubProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::backrub::BackrubProtocol::read_cmd_line_options ( )
private

References movemap_smallmover_, and set_options().

Referenced by BackrubProtocol().

void protocols::backrub::BackrubProtocol::set_backrub_mover ( protocols::backrub::BackrubMoverOP  backrub_mover)

Set a pre-configured Backrub Mover.

References backrubmover_.

void protocols::backrub::BackrubProtocol::set_movemap ( core::kinematics::MoveMapCOP  movemap)

Set the movemap for the whole protocol. Uses contiguous backbone regions for backrub to set pivot residues Within these segments, backrub will occur.

References protocols::backrub::get_pivot_residues_from_movemap(), set_movemap_smallmover(), and set_pivot_residues().

void protocols::backrub::BackrubProtocol::set_movemap_smallmover ( core::kinematics::MoveMapCOP  movemap)

Set the MoveMap that will only be used for the SmallMover.

References movemap_smallmover_.

Referenced by set_movemap(), and set_options().

void protocols::backrub::BackrubProtocol::set_options ( utility::vector1< core::Size pivot_residues,
utility::vector1< std::string >  pivot_atoms,
core::kinematics::MoveMapCOP  minimize_movemap,
core::kinematics::MoveMapCOP  movemap_smallmover,
core::pack::task::operation::TaskOperationCOP  packing_operation,
core::Size  min_atoms,
core::Size  max_atoms,
bool  initial_pack,
core::Real  mm_bend_weight,
core::Real  sm_prob,
core::Real  sc_prob,
core::Real  sc_prob_uniform,
core::Real  sc_prob_withinrot,
core::Real  mc_kt,
core::Size  ntrials,
bool  trajectory,
bool  trajectory_gz,
core::Size  trajectory_stride 
)
private

Sets all member variables that are options that control behavior. These options can be set via parse_my_tag or command line options.

References initial_pack_, max_atoms_, mc_kt_, min_atoms_, minimize_movemap_, mm_bend_weight_, ntrials_, packing_operation_, sc_prob_, sc_prob_uniform_, sc_prob_withinrot_, set_movemap_smallmover(), set_pivot_atoms(), set_pivot_residues(), sm_prob_, trajectory_, trajectory_gz_, and trajectory_stride_.

Referenced by BackrubProtocol(), parse_my_tag(), and read_cmd_line_options().

void protocols::backrub::BackrubProtocol::set_pivot_atoms ( utility::vector1< std::string >  pivot_atoms)

Set the type of atoms to use for backrub. These are atom names. Default is to only use CA as pivots.

References pivot_atoms_.

Referenced by set_options().

void protocols::backrub::BackrubProtocol::set_pivot_residues ( utility::vector1< core::Size pivot_residues)

Set the pivot residues for backrub. Will use contiguous residues as segments. Within these segments, backrub will occur.

References pivot_residues_.

Referenced by set_movemap(), and set_options().

void protocols::backrub::BackrubProtocol::set_pivots_from_residue_subset ( core::select::residue_selector::ResidueSubset  residue_subset)

References pivot_residues_.

Referenced by finalize_setup().

void protocols::backrub::BackrubProtocol::set_scorefunction ( core::scoring::ScoreFunctionCOP  scorefxn)

Set the Scorefunction. NOTE: Clones the scorefxn.

ScoreFunction

References scorefxn_.

void protocols::backrub::BackrubProtocol::set_taskfactory ( core::pack::task::TaskFactoryCOP  tf)

Set the taskfactory used for sidechain moves. NOTE: Clones the TF. Sets C-Beta off as they are not compatable with branch angle optimization.

References main_task_factory_.

void protocols::backrub::BackrubProtocol::write_database ( )

References backrubmover_.

Member Data Documentation

protocols::backrub::BackrubMoverOP protocols::backrub::BackrubProtocol::backrubmover_
private
bool protocols::backrub::BackrubProtocol::initial_pack_
private

Referenced by apply(), BackrubProtocol(), and set_options().

core::pack::task::TaskFactoryOP protocols::backrub::BackrubProtocol::main_task_factory_
private
core::Size protocols::backrub::BackrubProtocol::max_atoms_
private
core::Real protocols::backrub::BackrubProtocol::mc_kt_
private

Referenced by apply(), BackrubProtocol(), and set_options().

core::Size protocols::backrub::BackrubProtocol::min_atoms_
private
core::kinematics::MoveMapCOP protocols::backrub::BackrubProtocol::minimize_movemap_
private

Referenced by apply(), BackrubProtocol(), and set_options().

core::Real protocols::backrub::BackrubProtocol::mm_bend_weight_
private
core::kinematics::MoveMapCOP protocols::backrub::BackrubProtocol::movemap_smallmover_
private
core::Size protocols::backrub::BackrubProtocol::ntrials_
private

Referenced by apply(), BackrubProtocol(), and set_options().

core::pack::task::operation::TaskOperationCOP protocols::backrub::BackrubProtocol::packing_operation_
private
protocols::minimization_packing::PackRotamersMoverOP protocols::backrub::BackrubProtocol::packrotamersmover_
private

Referenced by apply(), and finalize_setup().

utility::vector1<std::string> protocols::backrub::BackrubProtocol::pivot_atoms_
private
utility::vector1<core::Size> protocols::backrub::BackrubProtocol::pivot_residues_
private
core::select::residue_selector::ResidueSelectorCOP protocols::backrub::BackrubProtocol::pivots_residue_selector_
private

Residue selector to select pivot residues.

Referenced by finalize_setup(), and parse_my_tag().

bool protocols::backrub::BackrubProtocol::recover_low_
private

Referenced by apply(), and parse_my_tag().

core::Real protocols::backrub::BackrubProtocol::sc_prob_
private

Referenced by apply(), BackrubProtocol(), and set_options().

core::Real protocols::backrub::BackrubProtocol::sc_prob_uniform_
private
core::Real protocols::backrub::BackrubProtocol::sc_prob_withinrot_
private
core::scoring::ScoreFunctionOP protocols::backrub::BackrubProtocol::scorefxn_
private
protocols::simple_moves::sidechain_moves::SidechainMoverOP protocols::backrub::BackrubProtocol::sidechainmover_
private

Referenced by apply(), and finalize_setup().

core::Real protocols::backrub::BackrubProtocol::sm_prob_
private
protocols::simple_moves::SmallMoverOP protocols::backrub::BackrubProtocol::smallmover_
private

Referenced by apply(), and finalize_setup().

bool protocols::backrub::BackrubProtocol::trajectory_
private

Referenced by apply(), BackrubProtocol(), and set_options().

protocols::moves::MoverOP protocols::backrub::BackrubProtocol::trajectory_apply_mover_
private

Referenced by apply(), and parse_my_tag().

bool protocols::backrub::BackrubProtocol::trajectory_gz_
private

Referenced by apply(), BackrubProtocol(), and set_options().

core::Size protocols::backrub::BackrubProtocol::trajectory_stride_
private

Referenced by apply(), BackrubProtocol(), and set_options().


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