protein_helix_assemble.cc File Reference

#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/scoring/dunbrack/DunbrackRotamer.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/AtomICoor.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Ramachandran.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/viewer/viewers.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/RT.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID_Map.Pose.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/DOF_ID.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/stepwise/StepWiseLegacyClusterer.hh>
#include <protocols/stepwise/StepWiseProteinPoseSetup.hh>
#include <protocols/stepwise/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <protocols/stepwise/StepWiseDoNothingSampleGenerator.hh>
#include <protocols/stepwise/StepWiseCombineSampleGenerator.hh>
#include <protocols/stepwise/StepWiseIdentitySampleGenerator.hh>
#include <protocols/stepwise/StepWisePoseCombineSampleGenerator.hh>
#include <protocols/stepwise/protein/StepWiseBetaAntiParallelJumpSampleGenerator.hh>
#include <protocols/stepwise/protein/util.hh>
#include <protocols/stepwise/protein/StepWiseProteinFilterer.hh>
#include <protocols/stepwise/protein/StepWiseProteinLoopBridger.hh>
#include <protocols/stepwise/protein/StepWiseProteinPoseMinimizer.hh>
#include <protocols/stepwise/protein/StepWiseProteinScreener.hh>
#include <protocols/stepwise/protein/StepWiseProteinPacker.hh>
#include <protocols/stepwise/protein/StepWiseProteinFragmentSampleGenerator.hh>
#include <protocols/stepwise/protein/StepWiseProteinJumpSampleGenerator.hh>
#include <protocols/stepwise/protein/StepWiseProteinMainChainSampleGenerator.hh>
#include <protocols/stepwise/protein/MainChainTorsionSet.hh>
#include <protocols/stepwise/InputStreamWithResidueInfo.hh>
#include <protocols/cluster/cluster.hh>
#include <protocols/minimization_packing/GreenPacker.hh>
#include <protocols/minimization_packing/GreenPacker.fwd.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/optimizeH.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/options/option.hh>
#include <core/options/after_opts.hh>
#include <core/options/util.hh>
#include <core/options/option_macros.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/io/pose_stream/ExtendedPoseInputStream.hh>
#include <core/io/pose_stream/PoseInputStream.fwd.hh>
#include <core/io/pose_stream/PDBPoseInputStream.hh>
#include <core/io/pose_stream/SilentFilePoseInputStream.hh>
#include <core/util/datacache/BasicDataCache.hh>
#include <core/util/datacache/CacheableString.hh>
#include <core/util/basic.hh>
#include <core/io/database/open.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/angle.functions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <protocols/jobdist/JobDistributors.hh>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <deque>
#include <vector>
#include <core/util/Tracer.hh>
#include <core/options/keys/out.OptionKeys.gen.hh>
#include <core/options/keys/in.OptionKeys.gen.hh>
#include <core/options/keys/swa.OptionKeys.gen.hh>
#include <core/options/keys/score.OptionKeys.gen.hh>
#include <core/options/keys/cluster.OptionKeys.gen.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
void	build_helix_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

build_helix_test()

void build_helix_test

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::rna::denovo::denovo, create_a3b_hbs::i, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, basic::options::OptionKeys::optimization::optimization, option, options, beta_nonlocal::pose, test.T500_Packing::rotamer_trials, test.T200_Scoring::rsd1, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, basic::options::OptionKeys::relax::sequence, and vancomycin::task.

Referenced by main(), and my_main().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), NEW_OPT, beta_sc_scan::seq, and viewer_main().

my_main()

void* my_main

(

void *

)

References build_helix_test(), and utility::options::OptionKeys::options::exit.

Referenced by main().