make_motif_tables.cc File Reference

#include <core/scoring/motif/motif_hash_stuff.hh>
#include <core/scoring/motif/util.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/mh.OptionKeys.gen.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/motif/reference_frames.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <devel/init.hh>
#include <protocols/sic_dock/read_biounit.hh>
#include <utility/io/ozstream.hh>
#include <utility/fixedsizearray1.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/geometry/hashing/SixDHasher.fwd.hh>
#include <core/scoring/ScoreFunction.hh>
#include <basic/options/option.hh>

Typedefs
typedef numeric::xyzTransform< core::Real >	Xform

Functions
Size	sicdock_max_threads ()
Size	sicdock_num_threads ()
Size	sicdock_thread_num ()
void	print_motifs (std::ostream &out)
void	merge_motifs ()
template<class T >
T	sqr (T const &x)
void	harvest_scores ()
void	print_scores ()
bool	harvest_motifs_one (ResPairMotifs &motifs, string const &tag0, Pose const &pose, core::scoring::dssp::Dssp &dssp, Size const &ir, core::scoring::EnergyEdge const &edge, vector1< Real > const &, vector1< Real > const &bfactors, vector1< Real > const &, vector1< Real > const &nbrs, int &nbad, int &, int &nbadocc, int &, int &)
void	harvest_motifs ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("motif_hash_util")

Typedef Documentation

Xform

typedef numeric::xyzTransform<core::Real> Xform

Function Documentation

harvest_motifs()

void harvest_motifs ( )

inline

References utility::graph::Node::const_upper_edge_list_end(), basic::options::OptionKeys::in::file::dssp, basic::Tracer::Error, utility::file::file_exists(), basic::options::OptionKeys::mh::filter::filter_harvest, PREcst::fname, utility::graph::Edge::get_node(), get_sasa(), basic::options::OptionKeys::mh::harvest_motifs, harvest_motifs_one(), test.T110_numeric::I, enumerate_junctions::int, basic::options::OptionKeys::mh::harvest::max_res, basic::options::OptionKeys::mh::motif_out_file, motifs, basic::options::OptionKeys::out::file::o, basic::options::OptionKeys::mh::filter::occupancy, basic::options::option, erraser_single_res_analysis::out, lactamize::outfile, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, tag, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main(), and sicdock_thread_num().

harvest_motifs_one()

bool harvest_motifs_one ( ResPairMotifs &  motifs, string const &  tag0, Pose const &  pose, core::scoring::dssp::Dssp &  dssp, Size const &  ir, core::scoring::EnergyEdge const &  edge, vector1< Real > const &  , vector1< Real > const &  bfactors, vector1< Real > const &  , vector1< Real > const &  nbrs, int &  nbad, int &  , int &  nbadocc, int &  , int &    )

inline

References numeric::xyzTransform< T >::bad(), utility::io::oc::cout, utility::file::create_directory_recursive(), basic::options::OptionKeys::in::file::dssp, basic::options::OptionKeys::mh::harvest::dump, test.T220_AtomAtomPairEnergies::fa_elec, basic::options::OptionKeys::mh::filter::hb_bb_sc, basic::options::OptionKeys::mh::filter::hb_sc, header(), basic::options::OptionKeys::out::file::o, basic::options::option, beta_nonlocal::pose, loops_kic::rms, ObjexxFCL::string_of(), tag, and utility_exit_with_message.

Referenced by harvest_motifs(), and sicdock_thread_num().

harvest_scores()

void harvest_scores ( )

inline

References basic::options::OptionKeys::mh::harvest::agg_with_max, utility::io::oc::cout, utility::file::create_directory_recursive(), basic::options::OptionKeys::mh::harvest::dump, end, ObjexxFCL::format::F(), run_backbone::float, basic::options::OptionKeys::mh::harvest_scores, basic::options::OptionKeys::mh::harvest::hash_angle_resl, basic::options::OptionKeys::mh::harvest::hash_cart_resl, create_a3b_hbs::i, create_a3b_hbs::ii, enumerate_junctions::int, subloop_histogram::iterator, basic::options::key(), predPRE::label, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, max(), min(), basic::options::OptionKeys::mh::harvest::min_bin_val, basic::options::OptionKeys::mh::motif_out_file, basic::options::OptionKeys::mh::filter::motif_type, motifs, basic::options::OptionKeys::mh::harvest::multiplier, basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, PATH, basic::options::OptionKeys::canonical_sampling::probabilities::sc, sicdock_max_threads(), sicdock_thread_num(), basic::options::OptionKeys::mh::harvest::smoothing_factor, sqr(), basic::options::TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, basic::options::OptionKeys::mh::harvest::weight_by_energy, and orn_macrocycle::wt.

Referenced by main(), and sicdock_thread_num().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, utility::io::oc::cout, basic::options::OptionKeys::mh::dump_input_pdb, test.T009_Exceptions::e, basic::Tracer::Error, utility::options::OptionKeys::options::exit, harvest_motifs(), basic::options::OptionKeys::mh::harvest_motifs, harvest_scores(), basic::options::OptionKeys::mh::harvest_scores, basic::init(), enumerate_junctions::int, basic::options::OptionKeys::mh::harvest::max_res, merge_motifs(), basic::options::OptionKeys::mh::merge_motifs, basic::options::OptionKeys::mh::filter::occupancy, basic::options::option, beta_nonlocal::pose, print_header(), print_motifs(), basic::options::OptionKeys::mh::print_motifs, print_scores(), basic::options::OptionKeys::mh::print_scores, basic::options::OptionKeys::frags::scoring::scoring, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

merge_motifs()

void merge_motifs ( )

inline

References create_a3b_hbs::i, create_a3b_hbs::k, predPRE::label, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::mh::merge_motifs, basic::options::OptionKeys::mh::motif_out_file, motifs, basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main(), and sicdock_thread_num().

print_motifs()

void print_motifs ( std::ostream &  out )

inline

References create_a3b_hbs::i, motifs, basic::options::option, and basic::options::OptionKeys::mh::print_motifs.

Referenced by main(), and sicdock_thread_num().

print_scores()

void print_scores ( )

inline

References utility::io::oc::cout, basic::options::OptionKeys::mh::harvest::hash_angle_resl, basic::options::OptionKeys::mh::harvest::hash_cart_resl, basic::options::option, basic::options::OptionKeys::mh::print_scores, ObjexxFCL::read_binary(), and basic::options::TR.

Referenced by main(), and sicdock_thread_num().

sicdock_max_threads()

Size sicdock_max_threads ( )

inline

Referenced by harvest_scores().

sicdock_num_threads()

Size sicdock_num_threads ( )

inline

sicdock_thread_num()

Size sicdock_thread_num ( )

inline

Referenced by harvest_scores().

sqr()

template<class T >

T sqr

(

T const &

x

)

References x.

Referenced by harvest_scores().

Variable Documentation

TR

basic::Tracer TR("motif_hash_util") ( "motif_hash_util"  )

static