util.cc File Reference

#include <core/scoring/motif/motif_hash_stuff.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/Tracer.hh>
#include <basic/database/open.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/mh.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/pymol_chains.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/motif/reference_frames.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/pose/xyzStripeHashPose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreTypeManager.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/dssp/StrandPairing.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <numeric/conversions.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <numeric/xyzVector.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/fixedsizearray1.hh>
#include <numeric/xyzTransform.hh>
#include <numeric/geometry/hashing/SixDHasher.hh>
#include <boost/unordered_set.hpp>
#include <bitset>
#include <pthread.h>

Namespaces
	core
	A class for reading in the atom type properties.
	core::scoring
	core::scoring::motif

Macros
#define	MAX_UINT16   65535
#define	MAX_UINT8   255
#define	XFORM_SCORE_FILE_VERSION   1

Functions
static basic::Tracer	core::scoring::motif::TR ("core.scoring.motif.util")
void	core::scoring::motif::xform_pose (core::pose::Pose &pose, Xform const &s, Size sres=1, Size eres=0)
Mat	core::scoring::motif::random_rotation ()
std::string	core::scoring::motif::tag_from_pdb_fname (string const &fname0)
ostream &	core::scoring::motif::operator<< (ostream &out, Real6 const &r6)
Real	core::scoring::motif::rt6_rt6_bb_dis2_explicit_stupid (Real6 const &x1, Real6 const &x2)
Real	core::scoring::motif::rt6_rt6_dis2 (Real6 const &x1, Real6 const &x2, Real const &lever)
Real	core::scoring::motif::rt6_rt6_bb_dis2 (Real6 const &x1, Real6 const &x2)
Real6	core::scoring::motif::inverse_rt6 (Real6 const &rt)
Real6	core::scoring::motif::rt_to_real6 (core::kinematics::RT const &rt)
core::kinematics::RT	core::scoring::motif::real6_to_rt (Real6 const &rt6)
RM_Type	core::scoring::motif::rpm_type1 (RPM_Type const &type)
RM_Type	core::scoring::motif::rpm_type2 (RPM_Type const &type)
Xform	core::scoring::motif::get_residue_pair_xform (Pose const &pose1, Size ir, Pose const &pose2, Size jr, RPM_Type const &type)
Xform	core::scoring::motif::get_residue_pair_xform (Pose const &pose, Size ir, Size jr, RPM_Type const &type)
Real6	core::scoring::motif::get_residue_pair_rt6 (Pose const &pose1, Size ir, Pose const &pose2, Size jr, RPM_Type const &type)
Real6	core::scoring::motif::get_residue_pair_rt6 (Pose const &pose, Size ir, Size jr, RPM_Type const &type)
void	core::scoring::motif::set_residue_pair_xform (Xform const &x, Pose &pose, Size ir, Size jr, RPM_Type const &type)
Reals	core::scoring::motif::get_sasa (Pose const &pose, Real const &probesize)
Reals	core::scoring::motif::get_nbrs (Pose const &pose)
void	core::scoring::motif::HACK_dump_helix (Pose const &pose, string fname, int beg, int end)
int	core::scoring::motif::HACK_dump_helices (Pose const &pose, string tag, int nres, int minlen=10)
Real6	core::scoring::motif::get_bins (Real c, Real a)
core::id::AtomID_Mask	core::scoring::motif::get_motif_atom_mask (Pose const &motif_pose, RPM_Type const &type, bool with_Hpol)
Real	core::scoring::motif::align_motif_pose_NCAC_super (Pose &motif_pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr, RPM_Type const &type)
Real	core::scoring::motif::align_motif_pose_break (Pose &, Pose const &, Size const &, Pose const &, Size const &, RPM_Type const &)
Real	core::scoring::motif::align_motif_pose_by_one_frame (Pose &, Pose const &, Size const &, Pose const &, Size const &, RPM_Type const &)
Real	core::scoring::motif::align_motif_pose_super (Pose &motif_pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr, RPM_Type const &type)
Real	core::scoring::motif::align_motif_pose (Pose &motif_pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr, RPM_Type const &type)
core::Real	core::scoring::motif::aa_trustworthiness (char aa)

Macro Definition Documentation

#define MAX_UINT16   65535

#define MAX_UINT8   255

#define XFORM_SCORE_FILE_VERSION   1