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Rosetta
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#include <protocols/frags/VallData.hh>#include <protocols/frags/TorsionFragment.hh>#include <core/scoring/dna/setup.hh>#include <core/scoring/dna/base_geometry.hh>#include <core/scoring/dna/BasePartner.hh>#include <core/scoring/GenBornPotential.hh>#include <core/scoring/LREnergyContainer.hh>#include <core/scoring/methods/Methods.hh>#include <protocols/simple_moves/BackboneMover.hh>#include <protocols/minimization_packing/MinMover.hh>#include <protocols/moves/MonteCarlo.hh>#include <protocols/moves/Mover.hh>#include <protocols/moves/MoverContainer.hh>#include <protocols/moves/OutputMovers.hh>#include <protocols/rigid/RigidBodyMover.hh>#include <protocols/moves/TrialMover.hh>#include <protocols/minimization_packing/PackRotamersMover.hh>#include <protocols/minimization_packing/RotamerTrialsMover.hh>#include <protocols/moves/RepeatMover.hh>#include <protocols/loops/ccd_closure.hh>#include <protocols/loops/loops_main.hh>#include <protocols/viewer/viewers.hh>#include <core/types.hh>#include <core/scoring/sasa.hh>#include <core/id/SequenceMapping.hh>#include <core/chemical/AtomTypeSet.hh>#include <core/chemical/MMAtomTypeSet.hh>#include <core/chemical/AA.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueMatcher.hh>#include <core/pack/rotamer_set/RotamerCouplings.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/ResidueTypeSelector.hh>#include <core/conformation/ResidueFactory.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/ChemicalManager.hh>#include <core/scoring/etable/Etable.hh>#include <core/scoring/ScoringManager.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/scoring/Ramachandran.hh>#include <core/pack/dunbrack/RotamerLibrary.hh>#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>#include <core/scoring/hbonds/HBondSet.hh>#include <core/scoring/hbonds/hbonds.hh>#include <core/scoring/etable/count_pair/CountPairFunction.hh>#include <core/pack/rotamer_trials.hh>#include <core/pack/pack_rotamers.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pack/task/TaskOperation.hh>#include <core/kinematics/FoldTree.hh>#include <protocols/viewer/visualize.hh>#include <core/kinematics/MoveMap.hh>#include <core/kinematics/util.hh>#include <core/id/AtomID_Map.hh>#include <core/mm/MMTorsionLibrary.hh>#include <core/mm/MMTorsionLibrary.fwd.hh>#include <core/optimization/AtomTreeMinimizer.hh>#include <core/optimization/MinimizerOptions.hh>#include <core/pose/Pose.hh>#include <core/pose/PDBPoseMap.hh>#include <core/pose/PDBInfo.hh>#include <core/pose/util.hh>#include <basic/options/util.hh>#include <basic/basic.hh>#include <basic/database/open.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <utility/vector1.hh>#include <numeric/xyzVector.hh>#include <numeric/random/random.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <cstdlib>#include <fstream>#include <iostream>#include <string>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/pep_spec.OptionKeys.gen.hh>#include <basic/options/keys/constraints.OptionKeys.gen.hh>#include <basic/Tracer.hh>#include <core/import_pose/import_pose.hh>Functions | |
| void | dump_efactor_pdb (pose::Pose &pose, core::scoring::ScoreFunctionOP const scorefxn, std::string const &tag) |
| Real | get_rmsd (pose::Pose pose, Size prot_begin, Size prot_end, Size pep_begin, Size pep_anchor, Size pep_end, pose::Pose ref_pose, Size ref_prot_begin, Size ref_prot_end, Size ref_pep_begin, Size ref_pep_anchor, Size ref_pep_end) |
| std::string | pep_rmsd_analysis (pose::Pose pose, Size prot_begin, Size prot_end, Size pep_begin, Size pep_anchor, Size pep_end) |
| std::string | pep_phipsi_analysis (pose::Pose pose, Size prot_begin, Size prot_end, Size pep_begin, Size pep_anchor, Size pep_end) |
| void | pep_energies_analysis (pose::Pose pose, core::scoring::ScoreFunctionOP full_scorefxn, std::string filename, core::scoring::EMapVector &emap_total_avg, vector1< core::scoring::EMapVector > &emap_res_avg, vector1< core::scoring::EMapVector > &emap_res_sd) |
| void | pep_scan_analysis (pose::Pose pose, core::scoring::ScoreFunctionOP soft_scorefxn, core::scoring::ScoreFunctionOP full_scorefxn, std::string filename, Size pep_begin, Size pep_anchor, Size pep_end, vector1< core::scoring::EMapVector > &avg_res_avg_emap) |
| void | RunPepSpec () |
| int | main (int argc, char *argv[]) |
| void dump_efactor_pdb | ( | pose::Pose & | pose, |
| core::scoring::ScoreFunctionOP const | scorefxn, | ||
| std::string const & | tag | ||
| ) |
References val2thr::atom, predPRE::chain, chains, ObjexxFCL::format::F(), lactamize::filename, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, basic::options::option, erraser_single_res_analysis::out, basic::options::OptionKeys::out::file::output_virtual, beta_nonlocal::pose, oop_conformations::scorefxn, and tag.
| Real get_rmsd | ( | pose::Pose | pose, |
| Size | prot_begin, | ||
| Size | prot_end, | ||
| Size | pep_begin, | ||
| Size | pep_anchor, | ||
| Size | pep_end, | ||
| pose::Pose | ref_pose, | ||
| Size | ref_prot_begin, | ||
| Size | ref_prot_end, | ||
| Size | ref_pep_begin, | ||
| Size | ref_pep_anchor, | ||
| Size | ref_pep_end | ||
| ) |
References create_a3b_hbs::i, option, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), pep_end(), beta_nonlocal::pose, prot_begin(), prot_end(), sd(), and superimpose_pose().
Referenced by LoopHash_Analyze::apply(), RNA_ScoreMover::apply(), and RunPepSpec().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, test.T009_Exceptions::e, basic::init(), and RunPepSpec().
| void pep_energies_analysis | ( | pose::Pose | pose, |
| core::scoring::ScoreFunctionOP | full_scorefxn, | ||
| std::string | filename, | ||
| core::scoring::EMapVector & | emap_total_avg, | ||
| vector1< core::scoring::EMapVector > & | emap_res_avg, | ||
| vector1< core::scoring::EMapVector > & | emap_res_sd | ||
| ) |
References utility::io::oc::cout, lactamize::filename, beta_nonlocal::pose, and ObjexxFCL::string_of().
Referenced by RunPepSpec().
| std::string pep_phipsi_analysis | ( | pose::Pose | pose, |
| Size | prot_begin, | ||
| Size | prot_end, | ||
| Size | pep_begin, | ||
| Size | pep_anchor, | ||
| Size | pep_end | ||
| ) |
References ObjexxFCL::abs(), create_a3b_hbs::i, num_chains(), basic::options::OptionKeys::AnchoredDesign::filters::omega, option, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), basic::options::OptionKeys::pepspec::pep_chain, pep_end(), oop_conformations::phi, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::psi, ObjexxFCL::string_of(), and basic::options::OptionKeys::inout::dbms::user.
Referenced by RunPepSpec().
| std::string pep_rmsd_analysis | ( | pose::Pose | pose, |
| Size | prot_begin, | ||
| Size | prot_end, | ||
| Size | pep_begin, | ||
| Size | pep_anchor, | ||
| Size | pep_end | ||
| ) |
References create_a3b_hbs::i, num_chains(), option, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), basic::options::OptionKeys::pepspec::pep_chain, pep_end(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, prot_begin(), prot_end(), basic::options::OptionKeys::pepspec::rmsd_analysis, sd(), ObjexxFCL::string_of(), superimpose_pose(), and basic::options::OptionKeys::inout::dbms::user.
Referenced by RunPepSpec().
| void pep_scan_analysis | ( | pose::Pose | pose, |
| core::scoring::ScoreFunctionOP | soft_scorefxn, | ||
| core::scoring::ScoreFunctionOP | full_scorefxn, | ||
| std::string | filename, | ||
| Size | pep_begin, | ||
| Size | pep_anchor, | ||
| Size | pep_end, | ||
| vector1< core::scoring::EMapVector > & | avg_res_avg_emap | ||
| ) |
References utility::io::oc::cout, extract_by_sidechain_sasa_score::cutoff, create_a3b_hbs::i, create_a3b_hbs::ii, basic::options::OptionKeys::pepspec::interface_cutoff, subloop_histogram::iterator, create_a3b_hbs::j, beta_nonlocal::jj, make_sequence_change(), vancomycin::min_mover, option, vancomycin::pack, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), pep_end(), beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, beta_sc_scan::seq, skip(), ObjexxFCL::string_of(), and basic::options::OptionKeys::inout::dbms::user.
Referenced by RunPepSpec().
| void RunPepSpec | ( | ) |
References begin, utility::io::oc::cout, pyrosetta::create_score_function, extract_by_sidechain_sasa_score::cutoff, data, lactamize::filename, get_rmsd(), getline(), create_a3b_hbs::i, subloop_histogram::iterator, num_chains(), option, bur_nodon_tyr::pdb_list, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), basic::options::OptionKeys::pepspec::pep_chain, pep_end(), pep_energies_analysis(), pep_phipsi_analysis(), pep_rmsd_analysis(), pep_scan_analysis(), beta_nonlocal::pose, test.T008_Serialization::pose2, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, prot_anchor(), prot_begin(), prot_chain(), prot_end(), average_rmsds::rmsd, basic::options::OptionKeys::pepspec::rmsd_analysis, basic::options::OptionKeys::pepspec::soft_wts, ObjexxFCL::string_of(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.
Referenced by main().
1.9.1