Rosetta
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#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/MinimizerOptions.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/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 <utility>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <numeric/fourier/FFT.hh>
#include <numeric/xyzVector.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.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/corrections.OptionKeys.gen.hh>
#include <boost/algorithm/string.hpp>
#include <fstream>
#include <iostream>
#include <cmath>
#include <sstream>
#include <string>
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(), create_a3b_hbs::i, create_a3b_hbs::ii, gaussian-sampling::input, enumerate_junctions::int, create_a3b_hbs::j, min(), beta_nonlocal::mm, option, options, erraser_single_res_analysis::out, oop_conformations::phi, kmeans_adaptive_kernel_density_bb_dependent_rotlib::phi_bin, beta_nonlocal::pose, oop_conformations::psi, kmeans_adaptive_kernel_density_bb_dependent_rotlib::psi_bin, basic::options::OptionKeys::remodel::rama, test.T200_Scoring::score_types, extract_by_sidechain_sasa_score::scorefile, oop_conformations::scorefxn, challenge::ss, str(), utility::to_string(), TR, and weights().
Referenced by main().
void calc_scores | ( | ) |
References aa, center, basic::options::OptionKeys::chemical::chemical, basic::Tracer::Debug, end, predPRE::fields, getRotID(), create_a3b_hbs::ii, enumerate_junctions::int, is_semi_rot(), subloop_histogram::iterator, beta_nonlocal::jj, kk, min(), beta_nonlocal::mm, kmeans_bb_dependent_rotlib::nrot, option, options, erraser_single_res_analysis::out, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, runtime_assert, extract_by_sidechain_sasa_score::scorefile, oop_conformations::scorefxn, sfd, basic::options::OptionKeys::cutoutdomain::start, test_mm_lj::step, utility::string_split(), tag, test.G200_Module_Region::tf, TR, and basic::options::OptionKeys::sc::weight.
Referenced by main().
void correct_dunbrack | ( | ) |
References aa, ScoreFragInfo::aa_, basic::options::OptionKeys::loodo::cap, basic::options::OptionKeys::chemical::chemical, count, data, ObjexxFCL::FArray2D< T >::dimension(), numeric::fourier::fft2(), ScoreFragInfo::fragscore_, getRotID(), create_a3b_hbs::i, ScoreFragInfo::id_, numeric::fourier::ifft2(), create_a3b_hbs::ii, basic::options::OptionKeys::in::in, enumerate_junctions::int, is_semi_rot(), create_a3b_hbs::j, beta_nonlocal::jj, create_a3b_hbs::k, kk, min(), kmeans_bb_dependent_rotlib::nrot, option, lactamize::outfile, oop_conformations::phi, ScoreFragInfo::phibin_, beta_nonlocal::pose, oop_conformations::psi, ScoreFragInfo::psibin_, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, build_restypes::restype, ScoreFragInfo::rotid_, ScoreFragInfo::rotidx_, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale, extract_by_sidechain_sasa_score::scorefile, basic::options::OptionKeys::cutoutdomain::start, test_mm_lj::step, ScoreFragInfo::weight_, basic::options::OptionKeys::full_model::working_res, x, and predPRE::y.
Referenced by main().
void correct_rama | ( | ) |
References aa, ScoreFragInfo::aa_, basic::options::OptionKeys::loodo::cap, utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, count, data, ObjexxFCL::FArray2D< T >::dimension(), numeric::fourier::fft2(), ScoreFragInfo::fragscore_, create_a3b_hbs::i, ScoreFragInfo::id_, numeric::fourier::ifft2(), basic::options::OptionKeys::in::in, enumerate_junctions::int, create_a3b_hbs::j, numeric::log(), max(), min(), basic::options::option, option, lactamize::outfile, ScoreFragInfo::phibin_, ScoreFragInfo::psibin_, basic::options::OptionKeys::corrections::score::rama_pp_map, read_rama_map_file(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale, extract_by_sidechain_sasa_score::scorefile, basic::options::OptionKeys::inout::dbms::user, ScoreFragInfo::weight_, x, and predPRE::y.
Referenced by main().
core::Real distance | ( | FragInfo const & | f1, |
FragInfo const & | f2 | ||
) |
References FragInfo::center_, vancomycin::f2, 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 aa, and basic::options::OptionKeys::chemical::chemical.
Referenced by calc_scores(), and correct_dunbrack().
int main | ( | int | argc, |
char * | argv[] | ||
) |
References argv, calc_rama_scores(), calc_scores(), basic::options::OptionKeys::loodo::cap, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, correct_dunbrack(), correct_rama(), test.T009_Exceptions::e, packing::flip_HNQ(), basic::init(), make_fragments(), min(), in::missing_density_to_jump(), SmotifHasher::mode, NEW_OPT, packing::no_optH(), option, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale, extract_by_sidechain_sasa_score::scorefile, and in::file::silent_struct_type().
void make_fragments | ( | ) |
References a, center, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, utility::graph::Node::const_edge_list_end(), kic_runner::database, debug_assert, distance(), basic::options::OptionKeys::in::file::dssp, utility::graph::Edge::get_node(), getbin(), create_a3b_hbs::i, gaussian-sampling::input, enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, min(), mutate_to_ala(), basic::options::OptionKeys::ddg::nfrags, option, lactamize::outfile, oop_conformations::phi, kmeans_adaptive_kernel_density_bb_dependent_rotlib::phi_bin, beta_nonlocal::pose, oop_conformations::psi, kmeans_adaptive_kernel_density_bb_dependent_rotlib::psi_bin, oop_conformations::scorefxn, sfd, challenge::ss, str(), utility::to_string(), and x.
Referenced by main().
void mutate_to_ala | ( | core::pose::Pose & | pose, |
int | center | ||
) |
References center, create_a3b_hbs::i, enumerate_junctions::int, beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, beta_sc_scan::restype_set, and TR.
Referenced by make_fragments().
void read_rama_map_file | ( | std::string const & | filename, |
utility::vector1< ObjexxFCL::FArray2D< Real > > & | data | ||
) |
References aa, utility::io::izstream::close(), data, utility::io::izstream::eof(), lactamize::filename, utility::io::izstream::getline(), utility::io::izstream::good(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, line, utility::io::izstream::open(), basic::database::open(), oop_conformations::phi, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, oop_conformations::psi, 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().