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protocols::minimization_packing::PackRotamersMover Class Reference

A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing. More...

#include <PackRotamersMover.hh>

Inheritance diagram for protocols::minimization_packing::PackRotamersMover:
Inheritance graph
[legend]

Public Types

typedef
core::pack::interaction_graph::AnnealableGraphBaseOP 
AnnealableGraphBaseOP
 
typedef
core::pack::interaction_graph::AnnealableGraphBaseCOP 
AnnealableGraphBaseCOP
 
typedef
core::pack::rotamer_set::RotamerSetsOP 
RotamerSetsOP
 
typedef
core::pack::rotamer_set::RotamerSetsCOP 
RotamerSetsCOP
 
typedef
core::pack::task::PackerTaskCOP 
PackerTaskCOP
 
typedef
core::pack::task::TaskFactoryCOP 
TaskFactoryCOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
- 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

 PackRotamersMover ()
 default constructor; reads the nloop_ value from the global options system. More...
 
 PackRotamersMover (utility::options::OptionCollection const &options)
 constructor that reads from the (possibly local) options collection object More...
 
 PackRotamersMover (std::string const &)
 constructor with typename; reads the nloop_ value from the global options system. More...
 
 PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=nullptr, core::Size nloop=1)
 Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn> More...
 
 ~PackRotamersMover () override
 
 PackRotamersMover (PackRotamersMover const &other)
 
void apply (Pose &pose) override
 Performs side-chain packing based on the input PackerTask using the input ScoreFunction. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
bool task_is_valid (Pose const &pose) const
 when the PackerTask was not generated locally, verify compatibility with pose More...
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
virtual void parse_score_function (TagCOP, basic::datacache::DataMap const &)
 parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...
 
virtual void parse_task_operations (TagCOP, basic::datacache::DataMap const &)
 parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...
 
void initialize_task_factory_with_operations (std::list< core::pack::task::operation::TaskOperationCOP > const &)
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
void score_function (ScoreFunctionCOP sf)
 Sets the ScoreFunction to <sf> More...
 
virtual void task_factory (TaskFactoryCOP tf)
 Sets the TaskFactory to <tf> More...
 
void task (PackerTaskCOP t)
 Sets the PackerTask to <t> More...
 
void nloop (core::Size nloop_in)
 
ScoreFunctionCOP score_function () const
 Returns the ScoreFunction. More...
 
PackerTaskCOP task () const
 Returns the PackerTask. More...
 
core::Size nloop () const
 
TaskFactoryCOP task_factory () const
 Returns the TaskFactory. More...
 
RotamerSetsCOP rotamer_sets () const
 Returns the RotamerSets object being used for packing. 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_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 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
utility::tag::XMLSchemaComplexTypeGeneratorOP 
complex_type_generator_for_pack_rotamers_mover (utility::tag::XMLSchemaDefinition &xsd)
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static void list_options_read (utility::options::OptionKeyList &opts)
 
- 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...
 

Protected Member Functions

virtual void setup (Pose &pose)
 get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask. More...
 
virtual core::PackerEnergy run (Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const
 
virtual void cleanup (core::pose::Pose &pose)
 Clean up cached pose and mover data after the fact. More...
 
virtual void note_packertask_settings (Pose const &)
 note PackerTask's packable and designable residues as string info More...
 
- 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...
 

Private Member Functions

void initialize_from_options (utility::options::OptionCollection const &options)
 

Private Attributes

ScoreFunctionCOP scorefxn_
 
PackerTaskCOP task_
 
core::Size nloop_
 
TaskFactoryCOP task_factory_
 
RotamerSetsOP rotamer_sets_
 
AnnealableGraphBaseOP ig_
 

Detailed Description

A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing.

Common Methods: PackRotamersMover.apply

Note
please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here!

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::minimization_packing::PackRotamersMover::PackRotamersMover ( )

default constructor; reads the nloop_ value from the global options system.

References initialize_from_options().

protocols::minimization_packing::PackRotamersMover::PackRotamersMover ( utility::options::OptionCollection const &  options)

constructor that reads from the (possibly local) options collection object

References initialize_from_options().

protocols::minimization_packing::PackRotamersMover::PackRotamersMover ( std::string const &  type_name)

constructor with typename; reads the nloop_ value from the global options system.

References initialize_from_options().

protocols::minimization_packing::PackRotamersMover::PackRotamersMover ( ScoreFunctionCOP  scorefxn,
PackerTaskCOP  task = nullptr,
core::Size  nloop = 1 
)

Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn>

ScoreFunction scorefxn /function to minimize while changine rotamers PackerTask task /object specifying what to design/pack core::Size (int) nloop /number of rounds to run packing

protocols::minimization_packing::PackRotamersMover::~PackRotamersMover ( )
overridedefault
protocols::minimization_packing::PackRotamersMover::PackRotamersMover ( PackRotamersMover const &  other)

Member Function Documentation

void protocols::minimization_packing::PackRotamersMover::apply ( Pose pose)
overridevirtual

Performs side-chain packing based on the input PackerTask using the input ScoreFunction.

example(s): packmover.apply(pose) See Also: PackerTask ScoreFunction

Implements protocols::moves::Mover.

Reimplemented in protocols::testing::BenchmarkBuildRotamersMover, protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover, protocols::minimization_packing::SetReturningPackRotamersMover, and protocols::protein_interface_design::movers::PrepackMover.

References cleanup(), nloop_, run(), and setup().

Referenced by protocols::calc_taskop_movers::ForceDisulfidesMover::apply(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::splice::SpliceInTail::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::calc_taskop_movers::ConsensusDesignMover::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::splice::Splice::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::calc_taskop_movers::CreateSequenceMotifMover::apply(), protocols::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight_lazy(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::splice::SpliceIn::pack(), protocols::pose_creation::MergePDBMover::pack_and_minimize(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::fold_from_loops::NubInitioMover::repack(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::repack(), protocols::optimize_weights::IterativeOptEDriver::repack_and_minimize_pose(), protocols::antibody::design::GeneralAntibodyModeler::repack_antibody_interface(), protocols::antibody::design::GeneralAntibodyModeler::repack_antigen_ab_interface(), protocols::antibody::design::GeneralAntibodyModeler::repack_antigen_interface(), protocols::carbohydrates::run_shear_min_pack(), and protocols::topology_broker::TopologyBroker::switch_to_fullatom().

void protocols::minimization_packing::PackRotamersMover::cleanup ( core::pose::Pose pose)
protectedvirtual

Clean up cached pose and mover data after the fact.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References ig_, core::pack::pack_rotamers_cleanup(), and rotamer_sets_.

Referenced by apply().

protocols::moves::MoverOP protocols::minimization_packing::PackRotamersMover::clone ( ) const
overridevirtual
utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover ( utility::tag::XMLSchemaDefinition &  xsd)
static
protocols::moves::MoverOP protocols::minimization_packing::PackRotamersMover::fresh_instance ( ) const
overridevirtual
std::string protocols::minimization_packing::PackRotamersMover::get_name ( ) const
overridevirtual
void protocols::minimization_packing::PackRotamersMover::initialize_from_options ( utility::options::OptionCollection const &  options)
private

References nloop().

Referenced by PackRotamersMover().

void protocols::minimization_packing::PackRotamersMover::initialize_task_factory_with_operations ( std::list< core::pack::task::operation::TaskOperationCOP > const &  operations)

References task_factory().

void protocols::minimization_packing::PackRotamersMover::list_options_read ( utility::options::OptionKeyList &  opts)
static
std::string protocols::minimization_packing::PackRotamersMover::mover_name ( )
static
void protocols::minimization_packing::PackRotamersMover::nloop ( core::Size  nloop_in)
core::Size protocols::minimization_packing::PackRotamersMover::nloop ( ) const
inline
void protocols::minimization_packing::PackRotamersMover::note_packertask_settings ( Pose const &  pose)
protectedvirtual

note PackerTask's packable and designable residues as string info

References core::sequence::end, protocols::moves::Mover::info(), core::pose::Pose::pdb_info(), and task_.

Referenced by setup().

void protocols::minimization_packing::PackRotamersMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void protocols::minimization_packing::PackRotamersMover::parse_score_function ( TagCOP  tag,
basic::datacache::DataMap const &  datamap 
)
virtual
void protocols::minimization_packing::PackRotamersMover::parse_task_operations ( TagCOP  tag,
basic::datacache::DataMap const &  datamap 
)
virtual
void protocols::minimization_packing::PackRotamersMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
rotamer_set::RotamerSetsCOP protocols::minimization_packing::PackRotamersMover::rotamer_sets ( ) const
core::PackerEnergy protocols::minimization_packing::PackRotamersMover::run ( Pose pose,
utility::vector0< int >  rot_to_pack = utility::vector0< int >() 
) const
protectedvirtual
void protocols::minimization_packing::PackRotamersMover::score_function ( ScoreFunctionCOP  sf)

Sets the ScoreFunction to <sf>

example(s): packmover.score_function(scorefxn) See Also: PackRotamersMover PackRotamersMover.task

References scorefxn_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply(), and PackRotamersMover().

ScoreFunctionCOP protocols::minimization_packing::PackRotamersMover::score_function ( ) const
void protocols::minimization_packing::PackRotamersMover::setup ( Pose pose)
protectedvirtual
void protocols::minimization_packing::PackRotamersMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References score_function().

Referenced by protocols::minimization_packing::operator<<().

void protocols::minimization_packing::PackRotamersMover::task ( PackerTaskCOP  t)
PackerTaskCOP protocols::minimization_packing::PackRotamersMover::task ( ) const
void protocols::minimization_packing::PackRotamersMover::task_factory ( TaskFactoryCOP  tf)
virtual
TaskFactoryCOP protocols::minimization_packing::PackRotamersMover::task_factory ( ) const
bool protocols::minimization_packing::PackRotamersMover::task_is_valid ( Pose const &  pose) const

when the PackerTask was not generated locally, verify compatibility with pose

the pose residue types must be equivalent to the ones used to generate the ResidueLevelTasks, because of the way that prevent_repacking and its associated flags work

References core::pose::Pose::residue_type_ptr(), core::pose::Pose::size(), and task_.

Referenced by protocols::minimization_packing::SetReturningPackRotamersMover::apply(), and setup().

Member Data Documentation

AnnealableGraphBaseOP protocols::minimization_packing::PackRotamersMover::ig_
private

Referenced by cleanup(), PackRotamersMover(), run(), and setup().

core::Size protocols::minimization_packing::PackRotamersMover::nloop_
private
RotamerSetsOP protocols::minimization_packing::PackRotamersMover::rotamer_sets_
private
ScoreFunctionCOP protocols::minimization_packing::PackRotamersMover::scorefxn_
private
PackerTaskCOP protocols::minimization_packing::PackRotamersMover::task_
private
TaskFactoryCOP protocols::minimization_packing::PackRotamersMover::task_factory_
private

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