pep_nrg.cc File Reference

#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 <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	RunPepSpec ()
int	main (int argc, char *argv[])

Function Documentation

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, test.T009_Exceptions::e, basic::init(), and RunPepSpec().

RunPepSpec()

void RunPepSpec

(

)

References pyrosetta::create_score_function, data, lactamize::filename, getline(), create_a3b_hbs::i, num_chains(), out::file::o(), option, erraser_single_res_analysis::out, bur_nodon_tyr::pdb_list, 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, basic::options::OptionKeys::mp::assembly::poses, prot_anchor(), prot_begin(), prot_chain(), prot_end(), basic::options::OptionKeys::blivens::score_type, test.T200_Scoring::score_types, oop_conformations::scorefxn, ObjexxFCL::string_of(), and utility_exit_with_message.

Referenced by main().