Rosetta  2020.37
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Functions | Variables
avrg_silent.cc File Reference
#include <basic/options/option.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <core/types.hh>
#include <core/id/AtomID.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>
#include <core/scoring/rms_util.hh>
#include <numeric/model_quality/rms.hh>
#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/SilentFileData.hh>
#include <devel/init.hh>
#include <utility/excn/Exceptions.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/format.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <cstdio>

Functions

utility::vector1< Real > calculate_variations (utility::vector1< utility::vector1< Real > > const deviation)
 
void smoothen_values (utility::vector1< Real > &CAvars, core::Size const winsize=9)
 
void add_deviations (pose::Pose ref_pose, utility::vector1< Vector > &crds, utility::vector1< id::AtomID > const &atomid, utility::vector1< utility::vector1< Real > > &deviation)
 
utility::vector1< Vector > get_avrgcrd (utility::vector1< utility::vector1< Vector > > const &crds, Size const n, utility::vector1< bool > const &exclid)
 
void report (utility::vector1< Real > const &CAvars)
 
utility::vector1< Vector > get_aligned_crd (pose::Pose pose_ref, pose::Pose pose, core::Real &rmsd, core::Real &Sd, utility::vector1< id::AtomID > const &atomid)
 
utility::vector1< id::AtomID > get_atomindex (pose::Pose const &pose_ref)
 
pose::Pose get_avrgpose (utility::vector1< Vector > const &avrgcrd, pose::Pose const &pose_ref, utility::vector1< Real > const &CAvar, utility::vector1< id::AtomID > const &atomid, utility::vector1< Size > &constres, Real const varcut)
 
bool myComparison (const std::pair< Real, Size > &a, const std::pair< Real, Size > &b)
 
Size get_close_and_lowE (utility::vector1< Real > const &scores, utility::vector1< bool > const &excluded)
 
void relax_with_restraints_on_constres (pose::Pose &pose_avrg, utility::vector1< Size > const &constres, scoring::ScoreFunctionCOP sfxn)
 
bool reavrg (utility::vector1< Vector > &avrgcrd, utility::vector1< utility::vector1< Vector > > const &crds, Real const dcut, bool const use_Sd, utility::vector1< Size > &exclid)
 
utility::vector1< Size > get_exclid (utility::vector1< Real > const &dists, Real &dcut, bool dcut_dynamic)
 
void calc_rmsf_and_avrg ()
 
int main (int argc, char *argv[])
 

Variables

static basic::Tracer TR ("app.public.comparative_modeling.avrg_silent")
 

Function Documentation

void add_deviations ( pose::Pose  ref_pose,
utility::vector1< Vector > &  crds,
utility::vector1< id::AtomID > const &  atomid,
utility::vector1< utility::vector1< Real > > &  deviation 
)

Referenced by calc_rmsf_and_avrg().

void calc_rmsf_and_avrg ( )
utility::vector1< Real > calculate_variations ( utility::vector1< utility::vector1< Real > > const  deviation)
utility::vector1< Vector > get_aligned_crd ( pose::Pose  pose_ref,
pose::Pose  pose,
core::Real &  rmsd,
core::Real &  Sd,
utility::vector1< id::AtomID > const &  atomid 
)

Referenced by calc_rmsf_and_avrg().

utility::vector1< id::AtomID > get_atomindex ( pose::Pose const &  pose_ref)

Referenced by calc_rmsf_and_avrg().

utility::vector1< Vector > get_avrgcrd ( utility::vector1< utility::vector1< Vector > > const &  crds,
Size const  n,
utility::vector1< bool > const &  exclid 
)

Referenced by calc_rmsf_and_avrg(), and reavrg().

pose::Pose get_avrgpose ( utility::vector1< Vector > const &  avrgcrd,
pose::Pose const &  pose_ref,
utility::vector1< Real > const &  CAvar,
utility::vector1< id::AtomID > const &  atomid,
utility::vector1< Size > &  constres,
Real const  varcut 
)

References TR.

Referenced by calc_rmsf_and_avrg().

Size get_close_and_lowE ( utility::vector1< Real > const &  scores,
utility::vector1< bool > const &  excluded 
)

References myComparison(), and TR.

Referenced by calc_rmsf_and_avrg().

utility::vector1< Size > get_exclid ( utility::vector1< Real > const &  dists,
Real &  dcut,
bool  dcut_dynamic 
)
int main ( int  argc,
char *  argv[] 
)
bool myComparison ( const std::pair< Real, Size > &  a,
const std::pair< Real, Size > &  b 
)

Referenced by get_close_and_lowE().

bool reavrg ( utility::vector1< Vector > &  avrgcrd,
utility::vector1< utility::vector1< Vector > > const &  crds,
Real const  dcut,
bool const  use_Sd,
utility::vector1< Size > &  exclid 
)
void relax_with_restraints_on_constres ( pose::Pose pose_avrg,
utility::vector1< Size > const &  constres,
scoring::ScoreFunctionCOP  sfxn 
)
void report ( utility::vector1< Real > const &  CAvars)
void smoothen_values ( utility::vector1< Real > &  CAvars,
core::Size const  winsize = 9 
)

References numeric::statistics::w().

Referenced by calc_rmsf_and_avrg().

Variable Documentation

basic::Tracer TR("app.public.comparative_modeling.avrg_silent")
static