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Public Member Functions | Private Attributes | List of all members
protocols::loop_grower::LoopPartialSolutionStore Class Reference

#include <LoopGrower.hh>

Public Member Functions

 LoopPartialSolutionStore ()=default
 
 LoopPartialSolutionStore (core::Size N, core::Real rmscutoff, core::Size master_beam_width, core::Real master_beam_cutoff)
 
void setfilterparams (core::Size fragmelt, core::Size rmswindow, core::Size parallelcount, core::Real beamscorecutoff, bool dump_errors, bool dump_beam, bool writebeams, bool clustercheck, bool fafilter, bool samplesheets, bool filterprevious, bool checksymm, bool asymmdump, bool dumpfinalbeam)
 
void store (LoopPartialSolution const &new_entry)
 
void set_filterprevious (bool filterprevious)
 
void filter (core::pose::Pose &pose, core::Size maxbeam, core::Size total_lower, core::Size lower_res, core::Size upper_res, core::Size cycle)
 
void diversityfilter (core::Size maxbeamsize, core::Size total_lower)
 
void parametercheck_filter (core::pose::Pose &pose, core::Size fragmelt, core::Size total_lower, core::Size lower_res, core::Size upper_res, core::Size rmswindow, bool dump_beam, core::Size &totalreqbeam, core::Size &totalreqmaxbeam, core::Real &totalreqscorecut, bool writebeams, core::Size cycle, core::Size parallelcount)
 
void zscoretransform ()
 
void cluster_check (LoopPartialSolution nearnativelps, core::pose::Pose &pose, core::Size total_lower, core::Size lower_res, core::Size upper_res)
 
void push (core::pose::Pose &pose, LoopPartialSolution const &new_entry, core::Size fragmelt, core::Real beamscorecutoff, core::Size total_lower, bool lower, bool dump_errors, core::Real RMS, core::Size lower_res, core::Size upper_res)
 
void report_rms_and_scores (core::Size rangelo, core::Size rangehi)
 
void sort ()
 
void sortrms ()
 
bool filterprevious (LoopPartialSolution lps, core::Size total_lower, core::Size fragmelt, core::Real rmscutoff, core::Size masterbeamwidth)
 
void skeleton_filter (core::pose::Pose &pose, DensSkeleton &skeleton, core::Size start_res, core::Size stop_res, core::Size lower_term, core::Size res_gap)
 
LoopPartialSolution operator[] (core::Size solutions_index)
 
void clear ()
 
void set_fastas (core::Size lower, core::Size upper)
 
void set_poses (core::Size lower, core::Size upper)
 
void set_cutpoint (core::Size cutpoint)
 
core::Size get_lower_fasta ()
 
core::Size get_upper_fasta ()
 
core::Size get_lower_pose ()
 
core::Size get_upper_pose ()
 
core::Size get_cutpoint ()
 
utility::vector1
< LoopPartialSolution
get_solutions ()
 
utility::vector1
< LoopPartialSolution
get_filteronly_solutions ()
 
void store_filteronly_solutions (utility::vector1< LoopPartialSolution > filteronly)
 
bool is_empty ()
 
core::Size size ()
 
void writelpsstore (core::Size loopid, core::Size jobid)
 

Private Attributes

core::Real rmscutoff_ = 0.0
 
core::Real master_beam_cutoff_ = 3.0
 
core::Real beamscorecutoff_ = 0.85
 
core::Size maxelts_ = 1
 
core::Size master_beam_width_ = 1
 
core::Size upper_fasta_ = 0
 
core::Size lower_fasta_ = 0
 
core::Size lower_pose_ = 0
 
core::Size upper_pose_ = 0
 
core::Size cutpoint_ = 0
 
core::Size fragmelt_ = 1
 
core::Size rmswindow_ = 1
 
core::Size parallelcount_ = 0
 
core::Size rank_ = 0
 
utility::vector1
< LoopPartialSolution
solutions_
 
utility::vector1
< LoopPartialSolution
old_solutions_
 
utility::vector1
< LoopPartialSolution
filteronly_solutions_
 
bool dump_errors_ = false
 
bool dump_beam_ = false
 
bool writebeams_ = false
 
bool clustercheck_ = false
 
bool fafilter_ = true
 
bool samplesheets_ = true
 
bool filterprevious_ = false
 
bool checksymm_ = false
 
bool asymmdump_ = true
 
bool dumpfinalbeam_ = false
 

Constructor & Destructor Documentation

protocols::loop_grower::LoopPartialSolutionStore::LoopPartialSolutionStore ( )
default
protocols::loop_grower::LoopPartialSolutionStore::LoopPartialSolutionStore ( core::Size  N,
core::Real  rmscutoff,
core::Size  master_beam_width,
core::Real  master_beam_cutoff 
)
inline

Member Function Documentation

void protocols::loop_grower::LoopPartialSolutionStore::clear ( )
inline
void protocols::loop_grower::LoopPartialSolutionStore::cluster_check ( LoopPartialSolution  nearnativelps,
core::pose::Pose pose,
core::Size  total_lower,
core::Size  lower_res,
core::Size  upper_res 
)
void protocols::loop_grower::LoopPartialSolutionStore::diversityfilter ( core::Size  maxbeamsize,
core::Size  total_lower 
)
void protocols::loop_grower::LoopPartialSolutionStore::filter ( core::pose::Pose pose,
core::Size  maxbeam,
core::Size  total_lower,
core::Size  lower_res,
core::Size  upper_res,
core::Size  cycle 
)
bool protocols::loop_grower::LoopPartialSolutionStore::filterprevious ( LoopPartialSolution  lps,
core::Size  total_lower,
core::Size  fragmelt,
core::Real  rmscutoff,
core::Size  masterbeamwidth 
)
core::Size protocols::loop_grower::LoopPartialSolutionStore::get_cutpoint ( )
inline
utility::vector1<LoopPartialSolution> protocols::loop_grower::LoopPartialSolutionStore::get_filteronly_solutions ( )
inline
core::Size protocols::loop_grower::LoopPartialSolutionStore::get_lower_fasta ( )
inline
core::Size protocols::loop_grower::LoopPartialSolutionStore::get_lower_pose ( )
inline
utility::vector1<LoopPartialSolution> protocols::loop_grower::LoopPartialSolutionStore::get_solutions ( )
inline
core::Size protocols::loop_grower::LoopPartialSolutionStore::get_upper_fasta ( )
inline
core::Size protocols::loop_grower::LoopPartialSolutionStore::get_upper_pose ( )
inline
bool protocols::loop_grower::LoopPartialSolutionStore::is_empty ( )
inline

References solutions_.

LoopPartialSolution protocols::loop_grower::LoopPartialSolutionStore::operator[] ( core::Size  solutions_index)
inline

References solutions_.

void protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter ( core::pose::Pose pose,
core::Size  fragmelt,
core::Size  total_lower,
core::Size  lower_res,
core::Size  upper_res,
core::Size  rmswindow,
bool  dump_beam,
core::Size totalreqbeam,
core::Size totalreqmaxbeam,
core::Real totalreqscorecut,
bool  writebeams,
core::Size  cycle,
core::Size  parallelcount 
)
void protocols::loop_grower::LoopPartialSolutionStore::push ( core::pose::Pose pose,
LoopPartialSolution const &  new_entry,
core::Size  fragmelt,
core::Real  beamscorecutoff,
core::Size  total_lower,
bool  lower,
bool  dump_errors,
core::Real  RMS,
core::Size  lower_res,
core::Size  upper_res 
)
void protocols::loop_grower::LoopPartialSolutionStore::report_rms_and_scores ( core::Size  rangelo,
core::Size  rangehi 
)
void protocols::loop_grower::LoopPartialSolutionStore::set_cutpoint ( core::Size  cutpoint)
inline
void protocols::loop_grower::LoopPartialSolutionStore::set_fastas ( core::Size  lower,
core::Size  upper 
)
inline
void protocols::loop_grower::LoopPartialSolutionStore::set_filterprevious ( bool  filterprevious)
inline
void protocols::loop_grower::LoopPartialSolutionStore::set_poses ( core::Size  lower,
core::Size  upper 
)
inline
void protocols::loop_grower::LoopPartialSolutionStore::setfilterparams ( core::Size  fragmelt,
core::Size  rmswindow,
core::Size  parallelcount,
core::Real  beamscorecutoff,
bool  dump_errors,
bool  dump_beam,
bool  writebeams,
bool  clustercheck,
bool  fafilter,
bool  samplesheets,
bool  filterprevious,
bool  checksymm,
bool  asymmdump,
bool  dumpfinalbeam 
)
inline
core::Size protocols::loop_grower::LoopPartialSolutionStore::size ( )
inline
void protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter ( core::pose::Pose pose,
DensSkeleton skeleton,
core::Size  start_res,
core::Size  stop_res,
core::Size  lower_term,
core::Size  res_gap 
)
void protocols::loop_grower::LoopPartialSolutionStore::sort ( )
inline
void protocols::loop_grower::LoopPartialSolutionStore::sortrms ( )
inline

References solutions_.

void protocols::loop_grower::LoopPartialSolutionStore::store ( LoopPartialSolution const &  new_entry)
inline
void protocols::loop_grower::LoopPartialSolutionStore::store_filteronly_solutions ( utility::vector1< LoopPartialSolution filteronly)
inline
void protocols::loop_grower::LoopPartialSolutionStore::writelpsstore ( core::Size  loopid,
core::Size  jobid 
)
void protocols::loop_grower::LoopPartialSolutionStore::zscoretransform ( )

Member Data Documentation

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

Referenced by setfilterparams().

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

Referenced by setfilterparams().

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

Referenced by setfilterparams().

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

Referenced by setfilterparams().

core::Size protocols::loop_grower::LoopPartialSolutionStore::cutpoint_ = 0
private

Referenced by get_cutpoint(), and set_cutpoint().

bool protocols::loop_grower::LoopPartialSolutionStore::dump_beam_ = false
private

Referenced by setfilterparams().

bool protocols::loop_grower::LoopPartialSolutionStore::dump_errors_ = false
private

Referenced by setfilterparams().

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

Referenced by setfilterparams().

bool protocols::loop_grower::LoopPartialSolutionStore::fafilter_ = true
private

Referenced by setfilterparams().

utility::vector1<LoopPartialSolution> protocols::loop_grower::LoopPartialSolutionStore::filteronly_solutions_
private
bool protocols::loop_grower::LoopPartialSolutionStore::filterprevious_ = false
private
core::Size protocols::loop_grower::LoopPartialSolutionStore::fragmelt_ = 1
private

Referenced by setfilterparams().

core::Size protocols::loop_grower::LoopPartialSolutionStore::lower_fasta_ = 0
private

Referenced by get_lower_fasta(), and set_fastas().

core::Size protocols::loop_grower::LoopPartialSolutionStore::lower_pose_ = 0
private

Referenced by get_lower_pose(), and set_poses().

core::Real protocols::loop_grower::LoopPartialSolutionStore::master_beam_cutoff_ = 3.0
private
core::Size protocols::loop_grower::LoopPartialSolutionStore::master_beam_width_ = 1
private
core::Size protocols::loop_grower::LoopPartialSolutionStore::maxelts_ = 1
private
utility::vector1<LoopPartialSolution> protocols::loop_grower::LoopPartialSolutionStore::old_solutions_
private
core::Size protocols::loop_grower::LoopPartialSolutionStore::parallelcount_ = 0
private

Referenced by setfilterparams().

core::Size protocols::loop_grower::LoopPartialSolutionStore::rank_ = 0
private
core::Real protocols::loop_grower::LoopPartialSolutionStore::rmscutoff_ = 0.0
private
core::Size protocols::loop_grower::LoopPartialSolutionStore::rmswindow_ = 1
private

Referenced by setfilterparams().

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

Referenced by setfilterparams().

utility::vector1<LoopPartialSolution> protocols::loop_grower::LoopPartialSolutionStore::solutions_
private
core::Size protocols::loop_grower::LoopPartialSolutionStore::upper_fasta_ = 0
private

Referenced by get_upper_fasta(), and set_fastas().

core::Size protocols::loop_grower::LoopPartialSolutionStore::upper_pose_ = 0
private

Referenced by get_upper_pose(), and set_poses().

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

Referenced by setfilterparams().


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