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Rosetta
2020.50
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#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/RotamerSampleOptions.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/pack/dunbrack/DunbrackRotamer.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>
#include <core/io/CrystInfo.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/types.hh>
#include <devel/init.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <utility>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/mpistream.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/random/random.hh>
#include <numeric/NumericTraits.hh>
#include <numeric/fourier/FFT.hh>
#include <numeric/constants.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/format.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/option_macros.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <basic/datacache/CacheableString.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <boost/algorithm/string.hpp>
#include <fstream>
#include <iostream>
#include <cmath>
#include <sstream>
#include <string>
#include <queue>
#include <cstdarg>
Classes | |
struct | FragInfo |
struct | ScoreFragInfo |
Functions | |
core::Size | getRotID (core::Size r1, core::Size r2=0, core::Size r3=0, core::Size r4=0) |
core::Real | distance (FragInfo const &f1, FragInfo const &f2) |
core::Size | getbin (core::Real theta) |
void | read_rama_map_file (std::string const &filename, utility::vector1< ObjexxFCL::FArray2D< Real > > &data) |
bool | is_semi_rot (core::chemical::AA aa) |
void | mutate_to_ala (core::pose::Pose &pose, int center) |
template<class C > | |
void | dump_table (ObjexxFCL::FArray2D< C > const &table, std::string const &filename, std::string const &tag) |
void | correct_rama () |
void | calc_rama_scores () |
void | correct_dunbrack () |
void | calc_scores () |
void | make_fragments () |
int | main (int argc, char *argv[]) |
Variables | |
static basic::Tracer | TR ("torsion.corrections") |
void calc_rama_scores | ( | ) |
References basic::options::OptionKeys::in::file::dssp, getbin(), test.T200_Scoring::ii, basic::options::OptionKeys::frags::j, min(), loops_kic::mm, option, options, erraser_single_res_analysis::out, demo.D010_Pose_structure::pose, basic::options::OptionKeys::remodel::rama, test.T200_Scoring::score_types, basic::options::OptionKeys::out::file::scorefile, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::mh::match::ss, utility::to_string(), TR, and basic::options::OptionKeys::optE::weights.
Referenced by main().
void calc_scores | ( | ) |
References basic::options::OptionKeys::mh::match::aa, basic::options::OptionKeys::mp::setup::center, basic::options::OptionKeys::chemical::chemical, basic::Tracer::Debug, utility::pointer::dynamic_pointer_cast(), basic::options::OptionKeys::cutoutdomain::end, getRotID(), test.T200_Scoring::ii, is_semi_rot(), min(), loops_kic::mm, option, options, erraser_single_res_analysis::out, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, runtime_assert, basic::options::OptionKeys::out::file::scorefile, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::cutoutdomain::start, utility::string_split(), tag, test.G200_Module_Region::tf, TR, and basic::options::OptionKeys::sc::weight.
Referenced by main().
void correct_dunbrack | ( | ) |
References basic::options::OptionKeys::mh::match::aa, basic::options::OptionKeys::loodo::cap, basic::options::OptionKeys::chemical::chemical, clean_pdb_keep_ligand::count, erraser_single_res_analysis::data, utility::pointer::dynamic_pointer_cast(), numeric::fourier::fft2(), getRotID(), ScoreFragInfo::id_, numeric::fourier::ifft2(), test.T200_Scoring::ii, basic::options::OptionKeys::in::in, is_semi_rot(), basic::options::OptionKeys::frags::j, min(), option, erraser_single_res_analysis::outfile, demo.D010_Pose_structure::pose, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, basic::options::OptionKeys::mh::filter::restype, basic::options::OptionKeys::out::file::scorefile, basic::options::OptionKeys::out::path::scratch, basic::options::OptionKeys::cutoutdomain::start, basic::options::OptionKeys::full_model::working_res, numeric::crick_equations::x(), and numeric::crick_equations::y().
Referenced by main().
void correct_rama | ( | ) |
References basic::options::OptionKeys::mh::match::aa, basic::options::OptionKeys::loodo::cap, utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, clean_pdb_keep_ligand::count, erraser_single_res_analysis::data, ObjexxFCL::FArray2D< typename >::dimension(), numeric::fourier::fft2(), ScoreFragInfo::id_, numeric::fourier::ifft2(), basic::options::OptionKeys::in::in, basic::options::OptionKeys::frags::j, numeric::log(), max(), min(), basic::options::option, option, erraser_single_res_analysis::outfile, basic::options::OptionKeys::corrections::score::rama_pp_map, read_rama_map_file(), basic::options::OptionKeys::out::file::scorefile, basic::options::OptionKeys::inout::dbms::user, numeric::crick_equations::x(), and numeric::crick_equations::y().
Referenced by main().
References FragInfo::center_, and FragInfo::pose_.
Referenced by make_fragments().
void dump_table | ( | ObjexxFCL::FArray2D< C > const & | table, |
std::string const & | filename, | ||
std::string const & | tag | ||
) |
core::Size getbin | ( | core::Real | theta | ) |
Referenced by calc_rama_scores(), and make_fragments().
core::Size getRotID | ( | core::Size | r1, |
core::Size | r2 = 0 , |
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core::Size | r3 = 0 , |
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core::Size | r4 = 0 |
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) |
References basic::options::OptionKeys::motifs::r1, and basic::options::OptionKeys::motifs::r2.
Referenced by calc_scores(), and correct_dunbrack().
bool is_semi_rot | ( | core::chemical::AA | aa | ) |
References basic::options::OptionKeys::chemical::chemical.
Referenced by calc_scores(), and correct_dunbrack().
References calc_rama_scores(), calc_scores(), basic::options::OptionKeys::loodo::cap, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, correct_dunbrack(), correct_rama(), utility::excn::Exception::display(), test.T009_Exceptions::e, packing::flip_HNQ(), devel::init(), make_fragments(), min(), in::missing_density_to_jump(), basic::options::OptionKeys::dna::specificity::mode, NEW_OPT, packing::no_optH(), option, basic::options::OptionKeys::out::file::scorefile, and in::file::silent_struct_type().
void make_fragments | ( | ) |
References a, basic::options::OptionKeys::mp::setup::center, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, utility::graph::Node::const_edge_list_end(), basic::options::OptionKeys::in::path::database, debug_assert, distance(), basic::options::OptionKeys::in::file::dssp, utility::graph::Edge::get_node(), getbin(), basic::options::OptionKeys::frags::j, min(), mutate_to_ala(), basic::options::OptionKeys::ddg::nfrags, option, erraser_single_res_analysis::outfile, demo.D010_Pose_structure::pose, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::mh::match::ss, utility::to_string(), and numeric::crick_equations::x().
Referenced by main().
void mutate_to_ala | ( | core::pose::Pose & | pose, |
int | center | ||
) |
References basic::options::OptionKeys::in::file::residue_type_set, and TR.
Referenced by make_fragments().
void read_rama_map_file | ( | std::string const & | filename, |
utility::vector1< ObjexxFCL::FArray2D< Real > > & | data | ||
) |
References basic::options::OptionKeys::mh::match::aa, utility::io::izstream::close(), erraser_single_res_analysis::data, utility::io::izstream::eof(), utility::io::izstream::getline(), utility::io::izstream::good(), basic::options::OptionKeys::frags::j, line, basic::database::open(), utility::io::izstream::open(), and utility_exit_with_message.
Referenced by correct_rama().
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static |
Referenced by calc_rama_scores(), calc_scores(), and mutate_to_ala().