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Rosetta
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#include <core/types.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/ResidueTypeSet.fwd.hh>#include <core/conformation/Residue.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/pose/Pose.hh>#include <core/pose/PDBInfo.hh>#include <core/scoring/electron_density/ElectronDensity.hh>#include <core/import_pose/import_pose.hh>#include <protocols/hybridization/FragmentBiasAssigner.hh>#include <protocols/electron_density/SetupForDensityScoringMover.hh>#include <protocols/electron_density/DensityZscores.hh>#include <basic/options/util.hh>#include <devel/init.hh>#include <utility/vector1.hh>#include <numeric/xyzVector.hh>#include <numeric/random/random.hh>#include <numeric/constants.hh>#include <ObjexxFCL/string.functions.hh>#include <ObjexxFCL/format.hh>#include <basic/Tracer.hh>#include <basic/options/option.hh>#include <basic/options/option_macros.hh>#include <basic/options/keys/OptionKeys.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/edensity.OptionKeys.gen.hh>#include <fstream>#include <string>Functions | |
| std::string | name2elt (std::string line) |
| void | readPDBcoords (std::string filename, poseCoords &atmlist) |
| void | find_unexplained_density (ObjexxFCL::FArray3D< float > const &dens_data, ObjexxFCL::FArray3D< double > const &mask_data, utility::vector1< numeric::xyzVector< core::Real > > &points, utility::vector1< core::Real > &scores, utility::vector1< core::Real > &buried_scores, poseCoords const &pose) |
| void | densityTools () |
| int | main (int argc, char *argv[]) |
Variables | |
| static basic::Tracer | TR ("density_tools") |
| void densityTools | ( | ) |
References out::path::all(), test.T009_Exceptions::e, ObjexxFCL::format::F(), numeric::fourier::fft3(), find_unexplained_density(), detail::get_data(), pyrosetta.distributed.io::get_score_function(), edensity::grid_spacing(), create_a3b_hbs::i, ObjexxFCL::format::I(), test.T110_numeric::I, enumerate_junctions::int, basic::options::OptionKeys::mp::dock::lowres, basic::options::OptionKeys::edensity::mapfile, edensity::mapfile(), basic::options::OptionKeys::edensity::mapreso, edensity::mapreso(), create_a3b_hbs::nres, assign_charges::ofs, basic::options::option, option, erraser_single_res_analysis::out, closure_error::path, clean_pdb_keep_ligand::pdbfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), create_a3b_hbs::r, readPDBcoords(), runtime_assert, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), TR, basic::Tracer::Trace, utility_exit_with_message, basic::options::OptionKeys::sc::verbose, and Xi.
Referenced by main().
| void find_unexplained_density | ( | ObjexxFCL::FArray3D< float > const & | dens_data, |
| ObjexxFCL::FArray3D< double > const & | mask_data, | ||
| utility::vector1< numeric::xyzVector< core::Real > > & | points, | ||
| utility::vector1< core::Real > & | scores, | ||
| utility::vector1< core::Real > & | buried_scores, | ||
| poseCoords const & | pose | ||
| ) |
References val2thr::atom, kmeans_adaptive_kernel_density_bb_dependent_rotlib::centroids, basic::Tracer::Debug, build_jacobian::distance, run_backbone::float, create_a3b_hbs::i, enumerate_junctions::int, beta_nonlocal::pose, ObjexxFCL::pow(), test.G101_Functions_Output::regions, legacy_score_vs_rmsd::scores, TR, ObjexxFCL::FArray3D< T >::u1(), ObjexxFCL::FArray3D< T >::u2(), ObjexxFCL::FArray3D< T >::u3(), x, Xi, predPRE::y, and predPRE::z.
Referenced by densityTools().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
| std::string name2elt | ( | std::string | line | ) |
References line.
Referenced by readPDBcoords().
| void readPDBcoords | ( | std::string | filename, |
| poseCoords & | atmlist | ||
| ) |
References cal_vdw_radius_pool::buf, lactamize::filename, getline(), and name2elt().
Referenced by densityTools().
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static |
Referenced by densityTools(), and find_unexplained_density().
1.9.1