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extract_motifs.cc File Reference

Application to extract motifs from a set of pdb files. More...

#include <core/types.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/motifs.OptionKeys.gen.hh>
#include <basic/basic.hh>
#include <basic/Tracer.hh>
#include <protocols/motifs/Motif.hh>
#include <protocols/motifs/SingleMotif.hh>
#include <protocols/motifs/MotifLibrary.hh>
#include <fstream>
#include <protocols/jd2/JobDistributor.hh>
#include <devel/init.hh>
#include <utility/excn/Exceptions.hh>

Functions

Vector const atom1_vector (1.500, 0.000, 0.000)
 
Vector const atom2_vector (0.000, 0.000, 0.000)
 
Vector const atom3_vector (0.000, 1.500, 0.000)
 
void fetch_atom_names (core::chemical::AA const &aa, std::string &oa1, std::string &oa2, std::string &oa3)
 
void output_single_motif (Pose &src_pose, AA const &target_aa, std::string &pdb_name, int prot_pos, std::vector< Size > &contacts)
 
void motif_distances (protocols::motifs::Motif const &m1, protocols::motifs::Motif const &m2, core::Real &dist_diff, core::Real &angl_diff)
 
Real get_packing_score (Pose &pose, Size pos1, Size pos2, ScoreFunction &sf)
 
Real get_hbond_score (Pose &pose, Size pos1, Size pos2, ScoreFunction &sf)
 
Real get_elec_score (Pose &pose, Size pos1, Size pos2, ScoreFunction &sf)
 
void process_for_motifs (Pose &pose, std::string &pdb_name, chemical::AA const target_aa, protocols::motifs::MotifLibrary &motif_lib)
 
int main (int argc, char *argv[])
 

Variables

static basic::Tracer TR ("extract_motifs")
 

Detailed Description

Application to extract motifs from a set of pdb files.

Function Documentation

Vector const atom1_vector ( 1.  500,
0.  000,
0.  000 
)

Referenced by output_single_motif().

Vector const atom2_vector ( 0.  000,
0.  000,
0.  000 
)

Referenced by output_single_motif().

Vector const atom3_vector ( 0.  000,
1.  500,
0.  000 
)

Referenced by output_single_motif().

void fetch_atom_names ( core::chemical::AA const &  aa,
std::string &  oa1,
std::string &  oa2,
std::string &  oa3 
)

References TR.

Referenced by output_single_motif(), and process_for_motifs().

Real get_elec_score ( Pose pose,
Size  pos1,
Size  pos2,
ScoreFunction &  sf 
)
Real get_hbond_score ( Pose pose,
Size  pos1,
Size  pos2,
ScoreFunction &  sf 
)
Real get_packing_score ( Pose pose,
Size  pos1,
Size  pos2,
ScoreFunction &  sf 
)
int main ( int  argc,
char *  argv[] 
)
void motif_distances ( protocols::motifs::Motif const &  m1,
protocols::motifs::Motif const &  m2,
core::Real &  dist_diff,
core::Real &  angl_diff 
)

Referenced by process_for_motifs().

void output_single_motif ( Pose src_pose,
AA const &  target_aa,
std::string &  pdb_name,
int  prot_pos,
std::vector< Size > &  contacts 
)
void process_for_motifs ( Pose pose,
std::string &  pdb_name,
chemical::AA const  target_aa,
protocols::motifs::MotifLibrary &  motif_lib 
)

Variable Documentation

basic::Tracer TR("extract_motifs")
static