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protocols::loop_grower::LoopGrower Class Reference

#include <LoopGrower.hh>

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

 LoopGrower ()=default
 
 LoopGrower (core::sequence::SequenceOP seq, protocols::loops::Loop loop, int resstart, int resstop, utility::vector1< core::fragment::FragSetOP > const &fragments)
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
core::Real single_grow (core::pose::Pose &pose, core::pose::Pose &pose_cen, LoopPartialSolutionStore &solutionset, const core::chemical::ResidueTypeCOPs &restypes_pose, const core::chemical::ResidueTypeCOPs &restypes_pos_cen, core::Size lower_pose, core::Size upper_pose, core::Size upper_term, int lower_fasta, int upper_fasta, core::Size torsionrangelo, core::Size torsionrangehi, bool insert_lower, core::Size initial_melt_left, bool is_cterm, bool is_nterm, core::Size cycle, int n_to_insert)
 
void update_to_stored (core::pose::Pose &growpose, core::pose::Pose &growpose_cen, const core::chemical::ResidueTypeCOPs &restypes_pose, const core::chemical::ResidueTypeCOPs &restypes_pose_cen, int &lower_pose, int &upper_pose, int &lower_fasta, int &upper_fasta, core::Size newreslow, core::Size newreshi, bool is_cterm, bool is_nterm)
 
void update_and_writelps (LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &pose_cen, core::chemical::ResidueTypeCOPs &restypes_pose, core::chemical::ResidueTypeCOPs &restypes_pose_cen, int lower_pose, int upper_pose, bool is_nterm, bool is_cterm, core::Size fasta_range_low, core::Size fasta_range_hi, core::Size pose_range_low, core::Size pose_range_hi, int torsionrangelo, int torsionrangehi, int tgt_jump, bool update_pose)
 
core::Real nton3_hbond_score (core::pose::Pose &pose)
 
core::Real get_resrange_hbond_energy (core::pose::Pose &pose, core::Size lower, core::Size upper)
 
core::Real modifiedscore (core::pose::Pose &fapose, core::pose::Pose &cen_pose, core::Size rangelo, core::Size rangehi)
 
core::Real modifieddensity (core::pose::Pose &pose, core::Size rangelo, core::Size rangehi, core::Real density_weight, core::Size &includesheets)
 
core::Real sheetscore (core::pose::Pose &fapose, core::pose::Pose &cen_pose, core::Size rangelo, core::Size rangehi)
 
bool is_beta (core::Real phi, core::Real psi)
 
void rescoresolutionset (LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &cen_pose, core::Size torsionrangelo, core::Size torsionrangehi)
 
void coordinate_filter (LoopPartialSolutionStore &solutionset, core::pose::Pose pose, bool lower, core::Size lower_fasta, core::Size upper_fasta, core::Size lower_pose, core::Size rangehi)
 
void addnativesolution (LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &cen_pose, int natlowerstart, int natlowerstop, int natupperstart, int natupperstop, int lower_pose, core::Size torsionrangelo, core::Size torsionrangehi)
 
void store_sheets (core::pose::Pose &pose, LoopPartialSolution &lps)
 
void refine_cycle (core::pose::Pose &pose, core::pose::Pose &cen_pose, int loop_start, int loop_end, bool finalrefinement, int cycle, int beam, int fragment, core::Size is_lower)
 
void full_atom_beam (LoopPartialSolutionStore &solutionset, core::pose::Pose &fa_pose, core::pose::Pose &cen_pose, core::Size lower_pos, core::Size upper_pos)
 
void set_scorefunction (core::scoring::ScoreFunctionOP sf)
 
void set_cen_scorefunction (core::scoring::ScoreFunctionOP sf)
 
void set_cenrot_scorefunction (core::scoring::ScoreFunctionOP sf)
 
void set_beamwidth (core::Size beamwidth)
 
void set_fragtrials (core::Size fragtrials)
 
void set_chainbreak (core::Real chainbreak)
 
void set_continuous_weight (core::Real continuous_weight)
 
void set_rmscutoff (core::Real rmscutoff)
 
void set_master_beam_cutoff (core::Real master_beam_cutoff)
 
void set_sheetbonus (core::Real sheetbonus)
 
void set_sheet_tolerance (core::Real sheet_tolerance)
 
void set_sc_scale (core::Real sc_scale)
 
void set_windowdensweight (core::Real windowdensweight)
 
void set_master_beam_width (core::Size master_beam_width)
 
void set_rmswindow (core::Size rmswindow)
 
void set_steps (core::Size steps)
 
void set_pcount (core::Size parallelcount)
 
void set_sheetcriteria (core::Size sheetcriteria)
 
void set_loopnumber (core::Size loopnumber)
 
void set_beamscorecutoff (core::Real beamscorecutoff)
 
void set_debug (bool debug)
 
void set_fragmelt (core::Size fragmelt)
 
void set_minmelt (core::Size minmelt)
 
void set_pack_min_cycles (core::Size pack_min_cycles)
 
void set_dumpbeam (bool dumpbeam)
 
void set_dumpfinalbeam (bool dumpfinalbeam)
 
void set_dumprms (bool dumprms)
 
void set_dumperrors (bool dumperrors)
 
void set_direction (core::Size direction)
 
void set_minimize (bool minimize)
 
void set_native (core::pose::PoseOP native)
 
void set_nativegrow (bool nativegrow)
 
void set_greedy (bool greedy)
 
void set_parametercheck (bool parametercheck)
 
void set_cenrot (bool cenrot)
 
void set_writebeams (bool writebeams)
 
void set_readbeams (bool readbeams)
 
void set_clustercheck (bool clustercheck)
 
void set_rescorebeams (bool rescorebeams)
 
void set_writelps (bool writelps)
 
void set_fafilter (bool fafilter)
 
void set_famin (bool famin)
 
void set_samplesheets (bool samplesheets)
 
void set_trackfragments (bool trackfragments)
 
void set_filterprevious (bool filterprevious)
 
void set_rephasemap (bool rephasemap)
 
void set_checksymm (bool checksymm)
 
void set_asymmdump (bool asymmdump)
 
void set_continuous_sheets (bool continuous_sheets)
 
void set_auto_stop (bool auto_stop)
 
void set_storedbeams (std::string storedbeams)
 
void set_filterbeams (std::string filterbeams)
 
void set_coordfile (std::string coordfile)
 
void set_skeletonfile (std::string skeletonfile)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void update_fragment_library_pointers ()
 
void add_fragment_csts (core::pose::Pose &pose, core::Size startfasta, core::Size endfasta, core::Size natstoplow, core::Size natstarthi, core::Size startlower)
 
void add_user_csts (core::pose::Pose &pose)
 
void write_to_disk (LoopPartialSolutionStore solutionset, core::Size step, core::Size added_lower, core::Size added_upper, bool filteronly, bool lower)
 
void read_from_disk (LoopPartialSolutionStore &solutionset, int &cycle, bool &lower, bool filterbeams)
 
void read_coordfile ()
 
void fafilter (LoopPartialSolutionStore &solutionset, core::pose::Pose &fapose, core::pose::Pose &cenpose, core::Size total_lower, core::Size torsionrangelo, core::Size torsionrangehi, core::Size cycle, core::Size lower_fasta, core::Size upper_fasta, core::Size lower_pose)
 
core::Real GDThatonative (core::pose::Pose const &pose, int natlow, int nathi, int natstoplow, int natstarthi, int startlow, int stoplow, int starthi, int stophi)
 
core::Real RMStonative (core::pose::Pose const &pose, int natlow, int nathi, int natstoplow, int natstarthi, int startlow, int stoplow, int starthi, int stophi)
 
void atomGDTha (core::Vector atom1, core::Vector atom2, core::Size &GDTha)
 
core::Size check_coordinates (core::pose::Pose &pose, core::Size lower_pose, core::Size upper_pose, core::Size lower_fasta, core::Real radius)
 
bool check_auto_stop (core::pose::Pose &pose, core::Size lower_res, core::Size upper_res)
 
LoopPartialSolutionStore getSolutionSet ()
 
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...
 
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
 
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_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...
 

Private Attributes

core::Size beamwidth_ = 1
 
core::Size fragtrials_ = 10
 
core::Size fragmelt_ = 1
 
core::Size minmelt_ = 1
 
core::Size lowest_ranked_native_ = 0
 
core::Size storelow_ = 0
 
core::Size storehi_ = 0
 
core::scoring::ScoreFunctionOP sf_
 
core::scoring::ScoreFunctionOP cen_sf_
 
core::scoring::ScoreFunctionOP cenrot_sf_
 
bool debug_ = false
 
core::sequence::SequenceOP seq_
 
protocols::loops::Loop loop_
 
int resstart_ = 0
 
int resstop_ = 0
 
int upper_fasta_ = 0
 
int lower_fasta_ = 0
 
int rmsrangelo_ = 0
 
int rmsrangehi_ = 0
 
core::Real chainbreak_ = 1.5
 
core::Real continuous_weight_ = 0.3
 
core::Real rmscutoff_ = 0.0
 
core::Real beamscorecutoff_ = 0.85
 
core::Real master_beam_cutoff_ = 3.0
 
core::Real windowdensweight_ = 30
 
core::Real startingscore_ = 0.0
 
core::Real censtartingscore_ = 0.0
 
core::Real sheetbonus_ = 0.5
 
core::Real sheet_tolerance_ = 0.7
 
core::Real sc_scale_ = 1
 
utility::vector1
< core::fragment::FragSetOP
fragments_
 
utility::vector1
< boost::unordered_map
< core::Size,
core::fragment::Frame > > 
library_
 
core::Size pack_min_cycles_ = 1
 
core::Size fafilter_pmcycles_ = 1
 
core::Size direction_ = 0
 
core::Size master_beam_width_ = 1
 
core::Size rmswindow_ = 1
 
core::Size steps_ = 1e4
 
core::Size parallelcount_ = 0
 
core::Size sheetcriteria_ = 2
 
core::Size loopnumber_ = 0
 
core::Size sheetsize_ = 4
 
core::Size total_residues_ = 0
 
core::Size insert_pose_ = 0
 
core::Size maxfrag_ = 0
 
core::Size numjumps_ = 0
 
bool dumpbeam_ = false
 
bool dumpfinalbeam_ = false
 
bool dumprms_ = false
 
bool dumperrors_ = false
 
bool minimize_ = true
 
bool nativegrow_ = false
 
bool greedy_ = true
 
bool parametercheck_ = false
 
bool cenrot_ = false
 
bool writebeams_ = false
 
bool readbeams_ = false
 
bool clustercheck_ = false
 
bool rescorebeams_ = false
 
bool writelps_ = false
 
bool fafilter_ = true
 
bool famin_ = false
 
bool samplesheets_ = true
 
bool trackfragments_ = false
 
bool cenrotfilter_ = false
 
bool filterprevious_ = false
 
bool rephasemap_ = false
 
bool checksymm_ = false
 
bool continuous_sheets_ = true
 
bool auto_stop_ = false
 
bool asymmdump_ = true
 
std::string storedbeams_
 
std::string filterbeams_
 
std::string coordfile_
 
std::string skeleton_file_
 
std::map< std::pair
< core::Size, core::Size >
, utility::vector1
< numeric::xyzVector
< core::Real > > > 
scoringcoords_
 
core::pose::PoseOP native_
 
core::pose::Pose fa_seqpose_
 
core::pose::Pose cen_seqpose_
 
DensSkeleton skeleton_
 
LoopPartialSolutionStore solutionset_
 

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
 
- 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 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::LoopGrower::LoopGrower ( )
default
protocols::loop_grower::LoopGrower::LoopGrower ( core::sequence::SequenceOP  seq,
protocols::loops::Loop  loop,
int  resstart,
int  resstop,
utility::vector1< core::fragment::FragSetOP > const &  fragments 
)
inline

Member Function Documentation

void protocols::loop_grower::LoopGrower::add_fragment_csts ( core::pose::Pose pose,
core::Size  startfasta,
core::Size  endfasta,
core::Size  natstoplow,
core::Size  natstarthi,
core::Size  startlower 
)
void protocols::loop_grower::LoopGrower::add_user_csts ( core::pose::Pose pose)
void protocols::loop_grower::LoopGrower::addnativesolution ( LoopPartialSolutionStore solutionset,
core::pose::Pose fa_pose,
core::pose::Pose cen_pose,
int  natlowerstart,
int  natlowerstop,
int  natupperstart,
int  natupperstop,
int  lower_pose,
core::Size  torsionrangelo,
core::Size  torsionrangehi 
)
void protocols::loop_grower::LoopGrower::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::Pose::add_constraint(), core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), core::conformation::add_lower_terminus_type_to_conformation_residue(), core::conformation::add_upper_terminus_type_to_conformation_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::loop_grower::LoopPartialSolution::apply(), core::conformation::Residue::atom_index(), core::scoring::atom_pair_constraint, core::pose::PDBInfo::attach_to(), core::scoring::chainbreak, core::conformation::Conformation::chains_from_termini(), core::fragment::chop_fragments(), core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoint_by_jump(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint(), core::pose::Pose::dump_pdb(), core::scoring::elec_dens_fast, core::pose::Pose::energies(), core::pose::Pose::fold_tree(), protocols::loop_grower::gapdist(), core::conformation::symmetry::get_asymm_unit_fold_tree(), protocols::loop_grower::LoopPartialSolutionStore::get_solutions(), core::scoring::hbond_sr_bb, core::kinematics::FoldTree::is_cutpoint(), core::pose::symmetry::is_symmetric(), core::pose::make_pose_from_sequence(), protocols::antibody::design::minimize, core::kinematics::FoldTree::num_cutpoint(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::num_jump(), core::pose::Pose::remove_constraints(), core::conformation::remove_lower_terminus_type_from_conformation_residue(), core::conformation::remove_upper_terminus_type_from_conformation_residue(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::pose::Pose::residue_type_set_for_pose(), core::pose::residue_types_from_sequence(), protocols::hybridization::score, core::scoring::score_type_from_name(), protocols::loop_grower::LoopPartialSolution::set_bonus_score(), protocols::loop_grower::LoopPartialSolutionStore::set_fastas(), protocols::loop_grower::LoopPartialSolutionStore::setfilterparams(), protocols::loop_grower::LoopPartialSolutionStore::size(), protocols::loop_grower::LoopPartialSolutionStore::store(), protocols::loop_grower::LoopPartialSolution::store_coordinates(), core::conformation::symmetry::symmetrize_fold_tree(), core::id::to_string(), core::pose::Pose::total_residue(), protocols::loop_grower::TR(), and protocols::loop_grower::TRACER().

Referenced by protocols::loop_grower::FragmentExtension::apply().

void protocols::loop_grower::LoopGrower::atomGDTha ( core::Vector  atom1,
core::Vector  atom2,
core::Size GDTha 
)
bool protocols::loop_grower::LoopGrower::check_auto_stop ( core::pose::Pose pose,
core::Size  lower_res,
core::Size  upper_res 
)
Size protocols::loop_grower::LoopGrower::check_coordinates ( core::pose::Pose pose,
core::Size  lower_pose,
core::Size  upper_pose,
core::Size  lower_fasta,
core::Real  radius 
)
protocols::moves::MoverOP protocols::loop_grower::LoopGrower::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::LoopGrower::coordinate_filter ( LoopPartialSolutionStore solutionset,
core::pose::Pose  pose,
bool  lower,
core::Size  lower_fasta,
core::Size  upper_fasta,
core::Size  lower_pose,
core::Size  rangehi 
)
void protocols::loop_grower::LoopGrower::fafilter ( LoopPartialSolutionStore solutionset,
core::pose::Pose fapose,
core::pose::Pose cenpose,
core::Size  total_lower,
core::Size  torsionrangelo,
core::Size  torsionrangehi,
core::Size  cycle,
core::Size  lower_fasta,
core::Size  upper_fasta,
core::Size  lower_pose 
)
protocols::moves::MoverOP protocols::loop_grower::LoopGrower::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.

void protocols::loop_grower::LoopGrower::full_atom_beam ( LoopPartialSolutionStore solutionset,
core::pose::Pose fa_pose,
core::pose::Pose cen_pose,
core::Size  lower_pos,
core::Size  upper_pos 
)
Real protocols::loop_grower::LoopGrower::GDThatonative ( core::pose::Pose const &  pose,
int  natlow,
int  nathi,
int  natstoplow,
int  natstarthi,
int  startlow,
int  stoplow,
int  starthi,
int  stophi 
)
std::string protocols::loop_grower::LoopGrower::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

Real protocols::loop_grower::LoopGrower::get_resrange_hbond_energy ( core::pose::Pose pose,
core::Size  lower,
core::Size  upper 
)
LoopPartialSolutionStore protocols::loop_grower::LoopGrower::getSolutionSet ( )
inline
bool protocols::loop_grower::LoopGrower::is_beta ( core::Real  phi,
core::Real  psi 
)
Real protocols::loop_grower::LoopGrower::modifieddensity ( core::pose::Pose pose,
core::Size  rangelo,
core::Size  rangehi,
core::Real  density_weight,
core::Size includesheets 
)
Real protocols::loop_grower::LoopGrower::modifiedscore ( core::pose::Pose fapose,
core::pose::Pose cen_pose,
core::Size  rangelo,
core::Size  rangehi 
)
bool protocols::loop_grower::LoopGrower::mover_provides_citation_info ( ) const
overridevirtual

Indiciate that this mover is published.

Reimplemented from protocols::moves::Mover.

Real protocols::loop_grower::LoopGrower::nton3_hbond_score ( core::pose::Pose pose)
utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::loop_grower::LoopGrower::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::LoopGrower::read_coordfile ( )
void protocols::loop_grower::LoopGrower::read_from_disk ( LoopPartialSolutionStore solutionset,
int &  cycle,
bool lower,
bool  filterbeams 
)
void protocols::loop_grower::LoopGrower::refine_cycle ( core::pose::Pose pose,
core::pose::Pose cen_pose,
int  loop_start,
int  loop_end,
bool  finalrefinement,
int  cycle,
int  beam,
int  fragment,
core::Size  is_lower 
)
void protocols::loop_grower::LoopGrower::rescoresolutionset ( LoopPartialSolutionStore solutionset,
core::pose::Pose fa_pose,
core::pose::Pose cen_pose,
core::Size  torsionrangelo,
core::Size  torsionrangehi 
)
Real protocols::loop_grower::LoopGrower::RMStonative ( core::pose::Pose const &  pose,
int  natlow,
int  nathi,
int  natstoplow,
int  natstarthi,
int  startlow,
int  stoplow,
int  starthi,
int  stophi 
)
void protocols::loop_grower::LoopGrower::set_asymmdump ( bool  asymmdump)
inline
void protocols::loop_grower::LoopGrower::set_auto_stop ( bool  auto_stop)
inline
void protocols::loop_grower::LoopGrower::set_beamscorecutoff ( core::Real  beamscorecutoff)
inline
void protocols::loop_grower::LoopGrower::set_beamwidth ( core::Size  beamwidth)
inline
void protocols::loop_grower::LoopGrower::set_cen_scorefunction ( core::scoring::ScoreFunctionOP  sf)
inline
void protocols::loop_grower::LoopGrower::set_cenrot ( bool  cenrot)
inline
void protocols::loop_grower::LoopGrower::set_cenrot_scorefunction ( core::scoring::ScoreFunctionOP  sf)
inline
void protocols::loop_grower::LoopGrower::set_chainbreak ( core::Real  chainbreak)
inline
void protocols::loop_grower::LoopGrower::set_checksymm ( bool  checksymm)
inline
void protocols::loop_grower::LoopGrower::set_clustercheck ( bool  clustercheck)
inline
void protocols::loop_grower::LoopGrower::set_continuous_sheets ( bool  continuous_sheets)
inline
void protocols::loop_grower::LoopGrower::set_continuous_weight ( core::Real  continuous_weight)
inline
void protocols::loop_grower::LoopGrower::set_coordfile ( std::string  coordfile)
inline
void protocols::loop_grower::LoopGrower::set_debug ( bool  debug)
inline
void protocols::loop_grower::LoopGrower::set_direction ( core::Size  direction)
inline
void protocols::loop_grower::LoopGrower::set_dumpbeam ( bool  dumpbeam)
inline
void protocols::loop_grower::LoopGrower::set_dumperrors ( bool  dumperrors)
inline
void protocols::loop_grower::LoopGrower::set_dumpfinalbeam ( bool  dumpfinalbeam)
inline
void protocols::loop_grower::LoopGrower::set_dumprms ( bool  dumprms)
inline
void protocols::loop_grower::LoopGrower::set_fafilter ( bool  fafilter)
inline
void protocols::loop_grower::LoopGrower::set_famin ( bool  famin)
inline
void protocols::loop_grower::LoopGrower::set_filterbeams ( std::string  filterbeams)
inline
void protocols::loop_grower::LoopGrower::set_filterprevious ( bool  filterprevious)
inline
void protocols::loop_grower::LoopGrower::set_fragmelt ( core::Size  fragmelt)
inline
void protocols::loop_grower::LoopGrower::set_fragtrials ( core::Size  fragtrials)
inline
void protocols::loop_grower::LoopGrower::set_greedy ( bool  greedy)
inline
void protocols::loop_grower::LoopGrower::set_loopnumber ( core::Size  loopnumber)
inline
void protocols::loop_grower::LoopGrower::set_master_beam_cutoff ( core::Real  master_beam_cutoff)
inline
void protocols::loop_grower::LoopGrower::set_master_beam_width ( core::Size  master_beam_width)
inline
void protocols::loop_grower::LoopGrower::set_minimize ( bool  minimize)
inline
void protocols::loop_grower::LoopGrower::set_minmelt ( core::Size  minmelt)
inline
void protocols::loop_grower::LoopGrower::set_native ( core::pose::PoseOP  native)
inline
void protocols::loop_grower::LoopGrower::set_nativegrow ( bool  nativegrow)
inline
void protocols::loop_grower::LoopGrower::set_pack_min_cycles ( core::Size  pack_min_cycles)
inline
void protocols::loop_grower::LoopGrower::set_parametercheck ( bool  parametercheck)
inline
void protocols::loop_grower::LoopGrower::set_pcount ( core::Size  parallelcount)
inline
void protocols::loop_grower::LoopGrower::set_readbeams ( bool  readbeams)
inline
void protocols::loop_grower::LoopGrower::set_rephasemap ( bool  rephasemap)
inline
void protocols::loop_grower::LoopGrower::set_rescorebeams ( bool  rescorebeams)
inline
void protocols::loop_grower::LoopGrower::set_rmscutoff ( core::Real  rmscutoff)
inline
void protocols::loop_grower::LoopGrower::set_rmswindow ( core::Size  rmswindow)
inline
void protocols::loop_grower::LoopGrower::set_samplesheets ( bool  samplesheets)
inline
void protocols::loop_grower::LoopGrower::set_sc_scale ( core::Real  sc_scale)
inline
void protocols::loop_grower::LoopGrower::set_scorefunction ( core::scoring::ScoreFunctionOP  sf)
inline
void protocols::loop_grower::LoopGrower::set_sheet_tolerance ( core::Real  sheet_tolerance)
inline
void protocols::loop_grower::LoopGrower::set_sheetbonus ( core::Real  sheetbonus)
inline
void protocols::loop_grower::LoopGrower::set_sheetcriteria ( core::Size  sheetcriteria)
inline
void protocols::loop_grower::LoopGrower::set_skeletonfile ( std::string  skeletonfile)
inline
void protocols::loop_grower::LoopGrower::set_steps ( core::Size  steps)
inline
void protocols::loop_grower::LoopGrower::set_storedbeams ( std::string  storedbeams)
inline
void protocols::loop_grower::LoopGrower::set_trackfragments ( bool  trackfragments)
inline
void protocols::loop_grower::LoopGrower::set_windowdensweight ( core::Real  windowdensweight)
inline
void protocols::loop_grower::LoopGrower::set_writebeams ( bool  writebeams)
inline
void protocols::loop_grower::LoopGrower::set_writelps ( bool  writelps)
inline
Real protocols::loop_grower::LoopGrower::sheetscore ( core::pose::Pose fapose,
core::pose::Pose cen_pose,
core::Size  rangelo,
core::Size  rangehi 
)
Real protocols::loop_grower::LoopGrower::single_grow ( core::pose::Pose pose,
core::pose::Pose pose_cen,
LoopPartialSolutionStore solutionset,
const core::chemical::ResidueTypeCOPs restypes_pose,
const core::chemical::ResidueTypeCOPs restypes_pos_cen,
core::Size  lower_pose,
core::Size  upper_pose,
core::Size  upper_term,
int  lower_fasta,
int  upper_fasta,
core::Size  torsionrangelo,
core::Size  torsionrangehi,
bool  insert_lower,
core::Size  initial_melt_left,
bool  is_cterm,
bool  is_nterm,
core::Size  cycle,
int  n_to_insert 
)

References core::pose::Pose::add_constraint(), core::conformation::add_lower_terminus_type_to_conformation_residue(), core::conformation::add_upper_terminus_type_to_conformation_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::loop_grower::SheetSampler::apply(), core::fragment::Frame::apply(), protocols::loop_grower::LoopPartialSolution::apply(), core::conformation::Residue::atom_index(), core::scoring::atom_pair_constraint, core::scoring::chainbreak, core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), core::pose::Pose::dump_pdb(), core::scoring::elec_dens_fast, protocols::loop_grower::LoopPartialSolutionStore::filter(), core::fragment::Frame::fragment(), protocols::loop_grower::gapdist(), protocols::loop_grower::LoopPartialSolution::get_bonus_score(), protocols::loop_grower::LoopPartialSolutionStore::get_filteronly_solutions(), protocols::loop_grower::LoopPartialSolution::get_history(), protocols::loop_grower::LoopPartialSolution::get_rms(), protocols::loop_grower::LoopPartialSolution::get_score(), protocols::mean_field::min(), core::fragment::Frame::nr_frags(), protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::remove_constraints(), core::conformation::remove_lower_terminus_type_from_conformation_residue(), core::conformation::remove_upper_terminus_type_from_conformation_residue(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), core::fragment::FragData::secstruct(), protocols::loop_grower::LoopPartialSolution::set_bonus_score(), protocols::loop_grower::LoopPartialSolution::set_gdt(), protocols::loop_grower::LoopPartialSolution::set_history(), protocols::loop_grower::LoopPartialSolution::set_id(), protocols::loop_grower::LoopPartialSolution::set_rms(), protocols::loop_grower::LoopPartialSolutionStore::setfilterparams(), core::fragment::Frame::shift_to(), protocols::loop_grower::LoopPartialSolutionStore::size(), protocols::loop_grower::LoopPartialSolutionStore::store(), protocols::loop_grower::LoopPartialSolutionStore::store_filteronly_solutions(), core::id::to_string(), core::pose::Pose::total_residue(), protocols::loop_grower::TR(), protocols::loop_grower::TRACER(), and protocols::loop_grower::transform_to_closest_symmunit().

void protocols::loop_grower::LoopGrower::store_sheets ( core::pose::Pose pose,
LoopPartialSolution lps 
)
void protocols::loop_grower::LoopGrower::update_and_writelps ( LoopPartialSolutionStore solutionset,
core::pose::Pose fa_pose,
core::pose::Pose pose_cen,
core::chemical::ResidueTypeCOPs restypes_pose,
core::chemical::ResidueTypeCOPs restypes_pose_cen,
int  lower_pose,
int  upper_pose,
bool  is_nterm,
bool  is_cterm,
core::Size  fasta_range_low,
core::Size  fasta_range_hi,
core::Size  pose_range_low,
core::Size  pose_range_hi,
int  torsionrangelo,
int  torsionrangehi,
int  tgt_jump,
bool  update_pose 
)
void protocols::loop_grower::LoopGrower::update_fragment_library_pointers ( )

Referenced by LoopGrower().

void protocols::loop_grower::LoopGrower::update_to_stored ( core::pose::Pose growpose,
core::pose::Pose growpose_cen,
const core::chemical::ResidueTypeCOPs restypes_pose,
const core::chemical::ResidueTypeCOPs restypes_pose_cen,
int &  lower_pose,
int &  upper_pose,
int &  lower_fasta,
int &  upper_fasta,
core::Size  newreslow,
core::Size  newreshi,
bool  is_cterm,
bool  is_nterm 
)
void protocols::loop_grower::LoopGrower::write_to_disk ( LoopPartialSolutionStore  solutionset,
core::Size  step,
core::Size  added_lower,
core::Size  added_upper,
bool  filteronly,
bool  lower 
)

Member Data Documentation

bool protocols::loop_grower::LoopGrower::asymmdump_ = true
private

Referenced by set_asymmdump().

bool protocols::loop_grower::LoopGrower::auto_stop_ = false
private

Referenced by set_auto_stop().

core::Real protocols::loop_grower::LoopGrower::beamscorecutoff_ = 0.85
private

Referenced by set_beamscorecutoff().

core::Size protocols::loop_grower::LoopGrower::beamwidth_ = 1
private

Referenced by set_beamwidth().

core::pose::Pose protocols::loop_grower::LoopGrower::cen_seqpose_
private
core::scoring::ScoreFunctionOP protocols::loop_grower::LoopGrower::cen_sf_
private
bool protocols::loop_grower::LoopGrower::cenrot_ = false
private

Referenced by set_cenrot().

core::scoring::ScoreFunctionOP protocols::loop_grower::LoopGrower::cenrot_sf_
private
bool protocols::loop_grower::LoopGrower::cenrotfilter_ = false
private
core::Real protocols::loop_grower::LoopGrower::censtartingscore_ = 0.0
private
core::Real protocols::loop_grower::LoopGrower::chainbreak_ = 1.5
private

Referenced by set_chainbreak().

bool protocols::loop_grower::LoopGrower::checksymm_ = false
private

Referenced by set_checksymm().

bool protocols::loop_grower::LoopGrower::clustercheck_ = false
private

Referenced by set_clustercheck().

bool protocols::loop_grower::LoopGrower::continuous_sheets_ = true
private

Referenced by set_continuous_sheets().

core::Real protocols::loop_grower::LoopGrower::continuous_weight_ = 0.3
private

Referenced by set_continuous_weight().

std::string protocols::loop_grower::LoopGrower::coordfile_
private

Referenced by set_coordfile().

bool protocols::loop_grower::LoopGrower::debug_ = false
private

Referenced by set_debug().

core::Size protocols::loop_grower::LoopGrower::direction_ = 0
private

Referenced by set_direction().

bool protocols::loop_grower::LoopGrower::dumpbeam_ = false
private

Referenced by set_dumpbeam().

bool protocols::loop_grower::LoopGrower::dumperrors_ = false
private

Referenced by set_dumperrors().

bool protocols::loop_grower::LoopGrower::dumpfinalbeam_ = false
private

Referenced by set_dumpfinalbeam().

bool protocols::loop_grower::LoopGrower::dumprms_ = false
private

Referenced by set_dumprms().

core::pose::Pose protocols::loop_grower::LoopGrower::fa_seqpose_
private
bool protocols::loop_grower::LoopGrower::fafilter_ = true
private

Referenced by set_fafilter().

core::Size protocols::loop_grower::LoopGrower::fafilter_pmcycles_ = 1
private

Referenced by LoopGrower().

bool protocols::loop_grower::LoopGrower::famin_ = false
private

Referenced by set_famin().

std::string protocols::loop_grower::LoopGrower::filterbeams_
private

Referenced by set_filterbeams().

bool protocols::loop_grower::LoopGrower::filterprevious_ = false
private

Referenced by set_filterprevious().

core::Size protocols::loop_grower::LoopGrower::fragmelt_ = 1
private

Referenced by set_fragmelt().

utility::vector1<core::fragment::FragSetOP> protocols::loop_grower::LoopGrower::fragments_
private
core::Size protocols::loop_grower::LoopGrower::fragtrials_ = 10
private

Referenced by set_fragtrials().

bool protocols::loop_grower::LoopGrower::greedy_ = true
private

Referenced by set_greedy().

core::Size protocols::loop_grower::LoopGrower::insert_pose_ = 0
private
utility::vector1<boost::unordered_map<core::Size, core::fragment::Frame> > protocols::loop_grower::LoopGrower::library_
private
protocols::loops::Loop protocols::loop_grower::LoopGrower::loop_
private
core::Size protocols::loop_grower::LoopGrower::loopnumber_ = 0
private

Referenced by set_loopnumber().

int protocols::loop_grower::LoopGrower::lower_fasta_ = 0
private
core::Size protocols::loop_grower::LoopGrower::lowest_ranked_native_ = 0
private
core::Real protocols::loop_grower::LoopGrower::master_beam_cutoff_ = 3.0
private

Referenced by set_master_beam_cutoff().

core::Size protocols::loop_grower::LoopGrower::master_beam_width_ = 1
private

Referenced by set_master_beam_width().

core::Size protocols::loop_grower::LoopGrower::maxfrag_ = 0
private
bool protocols::loop_grower::LoopGrower::minimize_ = true
private

Referenced by set_minimize().

core::Size protocols::loop_grower::LoopGrower::minmelt_ = 1
private

Referenced by set_minmelt().

core::pose::PoseOP protocols::loop_grower::LoopGrower::native_
private

Referenced by LoopGrower(), and set_native().

bool protocols::loop_grower::LoopGrower::nativegrow_ = false
private

Referenced by set_nativegrow().

core::Size protocols::loop_grower::LoopGrower::numjumps_ = 0
private
core::Size protocols::loop_grower::LoopGrower::pack_min_cycles_ = 1
private

Referenced by LoopGrower(), and set_pack_min_cycles().

core::Size protocols::loop_grower::LoopGrower::parallelcount_ = 0
private

Referenced by set_pcount().

bool protocols::loop_grower::LoopGrower::parametercheck_ = false
private

Referenced by set_parametercheck().

bool protocols::loop_grower::LoopGrower::readbeams_ = false
private

Referenced by set_readbeams().

bool protocols::loop_grower::LoopGrower::rephasemap_ = false
private

Referenced by set_rephasemap().

bool protocols::loop_grower::LoopGrower::rescorebeams_ = false
private

Referenced by set_rescorebeams().

int protocols::loop_grower::LoopGrower::resstart_ = 0
private
int protocols::loop_grower::LoopGrower::resstop_ = 0
private
core::Real protocols::loop_grower::LoopGrower::rmscutoff_ = 0.0
private

Referenced by LoopGrower(), and set_rmscutoff().

int protocols::loop_grower::LoopGrower::rmsrangehi_ = 0
private
int protocols::loop_grower::LoopGrower::rmsrangelo_ = 0
private
core::Size protocols::loop_grower::LoopGrower::rmswindow_ = 1
private

Referenced by set_rmswindow().

bool protocols::loop_grower::LoopGrower::samplesheets_ = true
private

Referenced by set_samplesheets().

core::Real protocols::loop_grower::LoopGrower::sc_scale_ = 1
private

Referenced by set_sc_scale().

std::map< std::pair< core::Size, core::Size >, utility::vector1< numeric::xyzVector< core::Real > > > protocols::loop_grower::LoopGrower::scoringcoords_
private
core::sequence::SequenceOP protocols::loop_grower::LoopGrower::seq_
private
core::scoring::ScoreFunctionOP protocols::loop_grower::LoopGrower::sf_
private

Referenced by LoopGrower(), and set_scorefunction().

core::Real protocols::loop_grower::LoopGrower::sheet_tolerance_ = 0.7
private

Referenced by set_sheet_tolerance().

core::Real protocols::loop_grower::LoopGrower::sheetbonus_ = 0.5
private

Referenced by set_sheetbonus().

core::Size protocols::loop_grower::LoopGrower::sheetcriteria_ = 2
private

Referenced by set_sheetcriteria().

core::Size protocols::loop_grower::LoopGrower::sheetsize_ = 4
private
DensSkeleton protocols::loop_grower::LoopGrower::skeleton_
private
std::string protocols::loop_grower::LoopGrower::skeleton_file_
private

Referenced by set_skeletonfile().

LoopPartialSolutionStore protocols::loop_grower::LoopGrower::solutionset_
private

Referenced by getSolutionSet().

core::Real protocols::loop_grower::LoopGrower::startingscore_ = 0.0
private
core::Size protocols::loop_grower::LoopGrower::steps_ = 1e4
private

Referenced by set_steps().

std::string protocols::loop_grower::LoopGrower::storedbeams_
private

Referenced by set_storedbeams().

core::Size protocols::loop_grower::LoopGrower::storehi_ = 0
private
core::Size protocols::loop_grower::LoopGrower::storelow_ = 0
private
core::Size protocols::loop_grower::LoopGrower::total_residues_ = 0
private
bool protocols::loop_grower::LoopGrower::trackfragments_ = false
private

Referenced by set_trackfragments().

int protocols::loop_grower::LoopGrower::upper_fasta_ = 0
private
core::Real protocols::loop_grower::LoopGrower::windowdensweight_ = 30
private

Referenced by set_windowdensweight().

bool protocols::loop_grower::LoopGrower::writebeams_ = false
private

Referenced by set_writebeams().

bool protocols::loop_grower::LoopGrower::writelps_ = false
private

Referenced by set_writelps().


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