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protocols::loop_grower::FragmentExtension Class Reference

#include <FragmentExtension.hh>

Inheritance diagram for protocols::loop_grower::FragmentExtension:
Inheritance graph
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Public Member Functions

 FragmentExtension ()
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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 cluster_fragments (utility::vector1< core::fragment::FragSetOP > &fragments, core::Real fragfilter)
 
utility::vector1
< protocols::loops::Loop
get_unaligned (core::id::SequenceMapping const &seqmap) const
 
bool mover_provides_citation_info () const override
 Indiciate that this mover is published. More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide authorship information for a published Rosetta module. 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 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_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 Attributes

core::Size beamwidth_
 
core::Size fragtrials_
 
core::Size pack_min_cycles_
 
core::Size direction_
 
core::Size maxloopsize_
 
core::Size master_beam_width_
 
core::Size rmswindow_
 
core::Size steps_
 
core::Size parallelcount_
 
core::Size montecarlorounds_
 
core::Size sheetcriteria_
 
bool debug_
 
bool dumpbeam_
 
bool dumpfinalbeam_
 
bool dumpfragments_
 
bool dumprms_
 
bool dumperrors_
 
bool minimize_
 
bool nativegrow_
 
bool greedy_
 
bool read_from_file_
 
bool assign_incomplete_
 
bool parametercheck_
 
bool cenrot_
 
bool writebeams_
 
bool readbeams_
 
bool clustercheck_
 
bool rescorebeams_
 
bool writelps_
 
bool fafilter_
 
bool samplesheets_
 
bool trackfragments_
 
bool filterprevious_
 
bool famin_
 
bool rephasemap_
 
bool checksymm_
 
bool asymmdump_
 
bool continuous_sheets_
 
bool auto_stop_
 
core::Real chainbreak_
 
core::Real continuous_weight_
 
core::Real rmscutoff_
 
core::Real fragcluster_
 
core::Real beamscorecutoff_
 
core::Real fa_bonus_
 
core::Real window_dens_weight_
 
core::Real master_beam_cutoff_
 
core::Real sheetbonus_
 
core::Real sheet_tolerance_
 
core::Real sc_scale_
 
core::scoring::ScoreFunctionOP sf_
 
core::scoring::ScoreFunctionOP cen_sf_
 
core::scoring::ScoreFunctionOP cenrot_sf_
 
int looporder_
 
core::pose::PoseOP native_
 
core::sequence::SequenceOP fullength_seq_
 
utility::vector1< core::Sizecbreaks_
 
std::string fastaname_
 
std::string storedbeams_
 
std::string filterbeams_
 
std::string coordfile_
 
std::string skeleton_file_
 
core::sequence::SequenceOP fragseq
 
utility::vector1< core::Sizefrag_sizes_
 
core::Size nfrags_
 
core::Size fragmelt_
 
core::Size minmelt_
 
utility::vector1
< core::fragment::FragSetOP
fragments_
 

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::loop_grower::FragmentExtension::FragmentExtension ( )

Member Function Documentation

void protocols::loop_grower::FragmentExtension::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::loop_grower::LoopGrower::apply(), core::conformation::Residue::atom(), core::pose::Pose::conformation(), protocols::hybridization::create_fragment_set_no_ssbias(), core::kinematics::distance(), core::pose::Pose::dump_pdb(), core::scoring::elec_dens_fast, core::pose::symmetry::extract_asymmetric_unit(), core::chemical::FA_STANDARD, protocols::loop_grower::LoopGrower::getSolutionSet(), core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), protocols::loop_grower::LoopPartialSolutionStore::push(), core::conformation::Conformation::reset_chain_endings(), core::pose::Pose::residue(), core::scoring::rg, protocols::loop_grower::LoopGrower::set_asymmdump(), protocols::loop_grower::LoopGrower::set_auto_stop(), protocols::loop_grower::LoopGrower::set_beamscorecutoff(), protocols::loop_grower::LoopGrower::set_beamwidth(), protocols::loop_grower::LoopGrower::set_cen_scorefunction(), protocols::loop_grower::LoopGrower::set_cenrot(), protocols::loop_grower::LoopGrower::set_cenrot_scorefunction(), protocols::loop_grower::LoopGrower::set_chainbreak(), protocols::loop_grower::LoopGrower::set_checksymm(), protocols::loop_grower::LoopGrower::set_clustercheck(), protocols::loop_grower::LoopGrower::set_continuous_sheets(), protocols::loop_grower::LoopGrower::set_continuous_weight(), protocols::loop_grower::LoopGrower::set_coordfile(), protocols::loop_grower::LoopGrower::set_debug(), protocols::loop_grower::LoopGrower::set_direction(), protocols::loop_grower::LoopGrower::set_dumpbeam(), protocols::loop_grower::LoopGrower::set_dumperrors(), protocols::loop_grower::LoopGrower::set_dumpfinalbeam(), protocols::loop_grower::LoopGrower::set_dumprms(), protocols::loop_grower::LoopGrower::set_fafilter(), protocols::loop_grower::LoopGrower::set_famin(), protocols::loop_grower::LoopGrower::set_filterbeams(), protocols::loop_grower::LoopGrower::set_filterprevious(), protocols::loop_grower::LoopGrower::set_fragmelt(), protocols::loop_grower::LoopGrower::set_fragtrials(), protocols::loop_grower::LoopGrower::set_greedy(), protocols::loop_grower::LoopGrower::set_loopnumber(), protocols::loop_grower::LoopGrower::set_master_beam_cutoff(), protocols::loop_grower::LoopGrower::set_master_beam_width(), protocols::loop_grower::LoopGrower::set_minimize(), protocols::loop_grower::LoopGrower::set_minmelt(), protocols::loop_grower::LoopGrower::set_native(), protocols::loop_grower::LoopGrower::set_nativegrow(), protocols::loop_grower::LoopGrower::set_pack_min_cycles(), protocols::loop_grower::LoopGrower::set_parametercheck(), protocols::loop_grower::LoopGrower::set_pcount(), protocols::loop_grower::LoopComparator::set_read_from_file(), protocols::loop_grower::LoopGrower::set_readbeams(), protocols::loop_grower::LoopGrower::set_rephasemap(), protocols::loop_grower::LoopGrower::set_rescorebeams(), protocols::loop_grower::LoopGrower::set_rmscutoff(), protocols::loop_grower::LoopGrower::set_rmswindow(), protocols::loop_grower::LoopGrower::set_samplesheets(), protocols::loop_grower::LoopGrower::set_sc_scale(), protocols::loop_grower::LoopGrower::set_scorefunction(), protocols::loop_grower::LoopGrower::set_sheet_tolerance(), protocols::loop_grower::LoopGrower::set_sheetbonus(), protocols::loop_grower::LoopGrower::set_sheetcriteria(), protocols::loop_grower::LoopGrower::set_skeletonfile(), protocols::loop_grower::LoopGrower::set_steps(), protocols::loop_grower::LoopGrower::set_storedbeams(), protocols::loop_grower::LoopGrower::set_trackfragments(), protocols::loop_grower::LoopGrower::set_windowdensweight(), protocols::loop_grower::LoopGrower::set_writebeams(), protocols::loop_grower::LoopGrower::set_writelps(), core::pose::Pose::size(), protocols::loops::start, protocols::loops::stop, core::id::to_string(), core::pose::Pose::total_residue(), protocols::loop_grower::TR(), core::scoring::vdw, core::fragment::FragmentIO::write_data(), and core::conformation::Atom::xyz().

protocols::moves::MoverOP protocols::loop_grower::FragmentExtension::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::loop_grower::FragmentExtension::cluster_fragments ( utility::vector1< core::fragment::FragSetOP > &  fragments,
core::Real  fragfilter 
)
protocols::moves::MoverOP protocols::loop_grower::FragmentExtension::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::loop_grower::FragmentExtension::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

utility::vector1< protocols::loops::Loop > protocols::loop_grower::FragmentExtension::get_unaligned ( core::id::SequenceMapping const &  seqmap) const
std::string protocols::loop_grower::FragmentExtension::mover_name ( )
static
bool protocols::loop_grower::FragmentExtension::mover_provides_citation_info ( ) const
overridevirtual

Indiciate that this mover is published.

Reimplemented from protocols::moves::Mover.

void protocols::loop_grower::FragmentExtension::parse_my_tag ( utility::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::sequence::read_fasta_file_str(), and protocols::loop_grower::TR().

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::loop_grower::FragmentExtension::provide_citation_info ( ) const
overridevirtual

Provide authorship information for a published Rosetta module.

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

Also provides citations for movers called by the BundleGridSampler.

Author
Brandon Frenz (brand.nosp@m.on.f.nosp@m.renz@.nosp@m.bran.nosp@m.don.f.nosp@m.renz.com)

Reimplemented from protocols::moves::Mover.

void protocols::loop_grower::FragmentExtension::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

Member Data Documentation

bool protocols::loop_grower::FragmentExtension::assign_incomplete_
private
bool protocols::loop_grower::FragmentExtension::asymmdump_
private
bool protocols::loop_grower::FragmentExtension::auto_stop_
private
core::Real protocols::loop_grower::FragmentExtension::beamscorecutoff_
private
core::Size protocols::loop_grower::FragmentExtension::beamwidth_
private
utility::vector1< core::Size > protocols::loop_grower::FragmentExtension::cbreaks_
private
core::scoring::ScoreFunctionOP protocols::loop_grower::FragmentExtension::cen_sf_
private
bool protocols::loop_grower::FragmentExtension::cenrot_
private
core::scoring::ScoreFunctionOP protocols::loop_grower::FragmentExtension::cenrot_sf_
private
core::Real protocols::loop_grower::FragmentExtension::chainbreak_
private
bool protocols::loop_grower::FragmentExtension::checksymm_
private
bool protocols::loop_grower::FragmentExtension::clustercheck_
private
bool protocols::loop_grower::FragmentExtension::continuous_sheets_
private
core::Real protocols::loop_grower::FragmentExtension::continuous_weight_
private
std::string protocols::loop_grower::FragmentExtension::coordfile_
private
bool protocols::loop_grower::FragmentExtension::debug_
private
core::Size protocols::loop_grower::FragmentExtension::direction_
private
bool protocols::loop_grower::FragmentExtension::dumpbeam_
private
bool protocols::loop_grower::FragmentExtension::dumperrors_
private
bool protocols::loop_grower::FragmentExtension::dumpfinalbeam_
private
bool protocols::loop_grower::FragmentExtension::dumpfragments_
private
bool protocols::loop_grower::FragmentExtension::dumprms_
private
core::Real protocols::loop_grower::FragmentExtension::fa_bonus_
private
bool protocols::loop_grower::FragmentExtension::fafilter_
private
bool protocols::loop_grower::FragmentExtension::famin_
private
std::string protocols::loop_grower::FragmentExtension::fastaname_
private
std::string protocols::loop_grower::FragmentExtension::filterbeams_
private
bool protocols::loop_grower::FragmentExtension::filterprevious_
private
utility::vector1<core::Size> protocols::loop_grower::FragmentExtension::frag_sizes_
private
core::Real protocols::loop_grower::FragmentExtension::fragcluster_
private
core::Size protocols::loop_grower::FragmentExtension::fragmelt_
private
utility::vector1<core::fragment::FragSetOP> protocols::loop_grower::FragmentExtension::fragments_
private
core::sequence::SequenceOP protocols::loop_grower::FragmentExtension::fragseq
private
core::Size protocols::loop_grower::FragmentExtension::fragtrials_
private
core::sequence::SequenceOP protocols::loop_grower::FragmentExtension::fullength_seq_
private
bool protocols::loop_grower::FragmentExtension::greedy_
private
int protocols::loop_grower::FragmentExtension::looporder_
private
core::Real protocols::loop_grower::FragmentExtension::master_beam_cutoff_
private
core::Size protocols::loop_grower::FragmentExtension::master_beam_width_
private
core::Size protocols::loop_grower::FragmentExtension::maxloopsize_
private
bool protocols::loop_grower::FragmentExtension::minimize_
private
core::Size protocols::loop_grower::FragmentExtension::minmelt_
private
core::Size protocols::loop_grower::FragmentExtension::montecarlorounds_
private
core::pose::PoseOP protocols::loop_grower::FragmentExtension::native_
private
bool protocols::loop_grower::FragmentExtension::nativegrow_
private
core::Size protocols::loop_grower::FragmentExtension::nfrags_
private
core::Size protocols::loop_grower::FragmentExtension::pack_min_cycles_
private
core::Size protocols::loop_grower::FragmentExtension::parallelcount_
private
bool protocols::loop_grower::FragmentExtension::parametercheck_
private
bool protocols::loop_grower::FragmentExtension::read_from_file_
private
bool protocols::loop_grower::FragmentExtension::readbeams_
private
bool protocols::loop_grower::FragmentExtension::rephasemap_
private
bool protocols::loop_grower::FragmentExtension::rescorebeams_
private
core::Real protocols::loop_grower::FragmentExtension::rmscutoff_
private
core::Size protocols::loop_grower::FragmentExtension::rmswindow_
private
bool protocols::loop_grower::FragmentExtension::samplesheets_
private
core::Real protocols::loop_grower::FragmentExtension::sc_scale_
private
core::scoring::ScoreFunctionOP protocols::loop_grower::FragmentExtension::sf_
private
core::Real protocols::loop_grower::FragmentExtension::sheet_tolerance_
private
core::Real protocols::loop_grower::FragmentExtension::sheetbonus_
private
core::Size protocols::loop_grower::FragmentExtension::sheetcriteria_
private
std::string protocols::loop_grower::FragmentExtension::skeleton_file_
private
core::Size protocols::loop_grower::FragmentExtension::steps_
private
std::string protocols::loop_grower::FragmentExtension::storedbeams_
private
bool protocols::loop_grower::FragmentExtension::trackfragments_
private
core::Real protocols::loop_grower::FragmentExtension::window_dens_weight_
private
bool protocols::loop_grower::FragmentExtension::writebeams_
private
bool protocols::loop_grower::FragmentExtension::writelps_
private

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