Rosetta  2019.31
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torsional_potential_corrections.cc File Reference
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/RotamerSampleOptions.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/pack/dunbrack/DunbrackRotamer.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>
#include <core/io/CrystInfo.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/types.hh>
#include <devel/init.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <utility>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/mpistream.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/random/random.hh>
#include <numeric/NumericTraits.hh>
#include <numeric/fourier/FFT.hh>
#include <numeric/constants.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/format.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/option_macros.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <basic/datacache/CacheableString.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <boost/algorithm/string.hpp>
#include <fstream>
#include <iostream>
#include <cmath>
#include <sstream>
#include <string>
#include <queue>
#include <cstdarg>

Classes

struct  FragInfo
 
struct  ScoreFragInfo
 

Functions

core::Size getRotID (core::Size r1, core::Size r2=0, core::Size r3=0, core::Size r4=0)
 
core::Real distance (FragInfo const &f1, FragInfo const &f2)
 
core::Size getbin (core::Real theta)
 
void read_rama_map_file (std::string const &filename, utility::vector1< ObjexxFCL::FArray2D< Real > > &data)
 
bool is_semi_rot (core::chemical::AA aa)
 
void mutate_to_ala (core::pose::Pose &pose, int center)
 
template<class C >
void dump_table (ObjexxFCL::FArray2D< C > const &table, std::string const &filename, std::string const &tag)
 
void correct_rama ()
 
void calc_rama_scores ()
 
void correct_dunbrack ()
 
void calc_scores ()
 
void make_fragments ()
 
int main (int argc, char *argv[])
 

Variables

static basic::Tracer TR ("torsion.corrections")
 

Function Documentation

void calc_rama_scores ( )
void calc_scores ( )
void correct_dunbrack ( )
void correct_rama ( )
core::Real distance ( FragInfo const &  f1,
FragInfo const &  f2 
)

References FragInfo::center_, and FragInfo::pose_.

Referenced by make_fragments().

template<class C >
void dump_table ( ObjexxFCL::FArray2D< C > const &  table,
std::string const &  filename,
std::string const &  tag 
)
core::Size getbin ( core::Real  theta)

Referenced by calc_rama_scores(), and make_fragments().

core::Size getRotID ( core::Size  r1,
core::Size  r2 = 0,
core::Size  r3 = 0,
core::Size  r4 = 0 
)
bool is_semi_rot ( core::chemical::AA  aa)
int main ( int  argc,
char *  argv[] 
)
void make_fragments ( )
void mutate_to_ala ( core::pose::Pose pose,
int  center 
)
void read_rama_map_file ( std::string const &  filename,
utility::vector1< ObjexxFCL::FArray2D< Real > > &  data 
)

Variable Documentation

basic::Tracer TR("torsion.corrections")
static