motif_hash_util.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/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/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/motif/reference_frames.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/MoveMap.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/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 <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <devel/init.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 <protocols/idealize/IdealizeMover.hh>
#include <protocols/sic_dock/SICFast.hh>
#include <protocols/sic_dock/util.hh>
#include <protocols/sic_dock/read_biounit.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/constraint_movers/AddConstraintsToCurrentConformationMover.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/fixedsizearray1.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/geometry/hashing/SixDHasher.hh>
#include <numeric/HomogeneousTransform.hh>
#include <apps/pilot/will/will_util.ihh>

Typedefs
typedef numeric::xyzVector< core::Real >	Vec
typedef numeric::xyzMatrix< core::Real >	Mat
typedef numeric::xyzTransform< core::Real >	Xform
typedef utility::vector1< core::id::AtomID >	AIDs

Functions
Size	sicdock_max_threads ()
Size	sicdock_num_threads ()
Size	sicdock_thread_num ()

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

Typedef Documentation

AIDs

typedef utility::vector1<core::id::AtomID> AIDs

Mat

typedef numeric::xyzMatrix<core::Real> Mat

Vec

typedef numeric::xyzVector<core::Real> Vec

Xform

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

Function Documentation

sicdock_max_threads()

Size sicdock_max_threads

(

)

Referenced by sicdock_thread_num().

sicdock_num_threads()

Size sicdock_num_threads

(

)

sicdock_thread_num()

Size sicdock_thread_num

(

)

References basic::options::OptionKeys::mh::harvest::agg_with_max, argv, numeric::xyzTransform< T >::bad(), basic::options::OptionKeys::mh::path::biounit_ideal, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, utility::options::FileOptionKey::clone(), utility::io::ozstream::close(), utility::graph::Node::const_upper_edge_list_end(), count, utility::io::oc::cout, utility::file::create_directory_recursive(), enumerate_junctions::default, basic::options::OptionKeys::in::file::dssp, basic::options::OptionKeys::mh::harvest::dump, basic::options::OptionKeys::mh::dump_input_pdb, basic::options::OptionKeys::mh::dump_matching_motifs, basic::options::OptionKeys::mh::dump_motif_pdbs, test.T009_Exceptions::e, end, basic::Tracer::Error, ObjexxFCL::format::F(), utility::file_basename(), utility::file::file_exists(), basic::options::OptionKeys::mh::filter::filter_harvest, run_backbone::float, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, PREcst::fname, utility::graph::Edge::get_node(), get_sasa(), harvest_motifs(), basic::options::OptionKeys::mh::harvest_motifs, harvest_motifs_one(), harvest_scores(), basic::options::OptionKeys::mh::harvest_scores, basic::options::OptionKeys::mh::harvest::hash_angle_resl, basic::options::OptionKeys::mh::harvest::hash_cart_resl, basic::options::OptionKeys::mh::filter::hb_sc, header(), create_a3b_hbs::i, test.T110_numeric::I, basic::options::OptionKeys::mh::harvest::idealize, numeric::xyzTransform< core::Real >::identity(), create_a3b_hbs::ii, basic::init(), enumerate_junctions::int, subloop_histogram::iterator, create_a3b_hbs::k, basic::options::key(), extract_by_sidechain_sasa_score::l, predPRE::label, basic::options::OptionKeys::mh::dump::limit_per_pair, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, compare_times::main(), max(), basic::options::OptionKeys::mh::harvest::max_res, basic::options::OptionKeys::mh::harvest::max_rmsd, merge_motifs(), basic::options::OptionKeys::mh::merge_motifs, basic::options::OptionKeys::mh::merge_scores, basic::options::OptionKeys::mh::mh, 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, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, natoms(), basic::options::OptionKeys::out::file::o, basic::options::OptionKeys::mh::filter::occupancy, basic::options::option, erraser_single_res_analysis::out, lactamize::outfile, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, PATH, beta_nonlocal::pose, test.T008_Serialization::pose1, test.T008_Serialization::pose2, pyrosetta.distributed.io::pose_from_file, print_header(), print_motifs(), basic::options::OptionKeys::mh::print_motifs, print_scores(), basic::options::OptionKeys::mh::print_scores, ObjexxFCL::read_binary(), basic::options::OptionKeys::mh::remove_duplicates, loops_kic::rms, runtime_assert, docking::s, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::canonical_sampling::probabilities::sc, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, sicdock_max_threads(), subloop_histogram::size, sm, basic::options::OptionKeys::mh::harvest::smoothing_factor, sqr(), ObjexxFCL::string_of(), basic::options::OptionKeys::symmetry::symmetry_definition, predPRE::t, pyrosetta.distributed.cluster.exceptions::T, tag, 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, orn_macrocycle::wt, x, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::xs.

Variable Documentation

TR

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

static