jd2 → core Relation

File in src/protocols/jd2	Includes file in src/core
archive / ArchiveBase.cc	chemical / ChemicalManager.hh
archive / ArchiveBase.cc	kinematics / Jump.hh
archive / ArchiveBase.cc	pose / Pose.hh
archive / ArchiveBase.cc	conformation / Residue.hh
archive / ArchiveBase.cc	scoring / ScoreFunction.hh
archive / ArchiveBase.cc	scoring / ScoreFunctionFactory.hh
archive / ArchiveBase.cc	io / silent / SilentFileData.hh
archive / ArchiveBase.hh	pose / Pose.fwd.hh
archive / ArchiveBase.hh	scoring / ScoreFunction.fwd.hh
archive / ArchiveBase.hh	io / silent / silent.fwd.hh
archive / ArchiveBase.hh	types.hh
archive / ArchiveManager.cc	io / silent / SilentFileData.hh
archive / ArchiveManager.hh	io / silent / silent.fwd.hh
archive / ArchiveManager.hh	types.hh
archive / ArchiveMasterBase.cc	types.hh
archive / ArchiveMasterBase.hh	types.hh
AtomTreeDiffJobInputter.cc	import_pose / import_pose.hh
AtomTreeDiffJobInputter.cc	pose / Pose.hh
AtomTreeDiffJobInputter.hh	import_pose / atom_tree_diffs / atom_tree_diff.hh
AtomTreeDiffJobInputter.hh	pose / Pose.fwd.hh
AtomTreeDiffJobOutputter.cc	import_pose / atom_tree_diffs / atom_tree_diff.hh
AtomTreeDiffJobOutputter.cc	pose / Pose.hh
AtomTreeDiffJobOutputter.cc	svn_version.hh
AtomTreeDiffJobOutputter.hh	import_pose / atom_tree_diffs / atom_tree_diff.hh
AtomTreeDiffJobOutputter.hh	pose / Pose.hh
BatchJobInputter.hh	pose / Pose.fwd.hh
parser / BluePrint.cc	util / ABEGOManager.hh
parser / BluePrint.cc	kinematics / MoveMap.hh
parser / BluePrint.cc	pose / Pose.hh
parser / BluePrint.cc	types.hh
parser / BluePrint.hh	kinematics / MoveMap.fwd.hh
parser / BluePrint.hh	pose / Pose.fwd.hh
parser / BluePrint.hh	types.hh
BOINCJobDistributor.cc	io / silent / util.hh
BOINCJobDistributor.hh	types.hh
parser / DataLoader.hh	pose / Pose.fwd.hh
parser / DataLoaderCreator.hh	types.hh
DockDesignParser.cc	pose / metrics / CalculatorFactory.hh
DockDesignParser.cc	pose / metrics / simple_calculators / InterfaceDeltaEnergeticsCalculator.hh
DockDesignParser.cc	pose / metrics / simple_calculators / InterfaceNeighborDefinitionCalculator.hh
DockDesignParser.cc	pose / metrics / simple_calculators / InterfaceSasaDefinitionCalculator.hh
DockDesignParser.cc	pose / Pose.hh
DockDesignParser.cc	pose / metrics / simple_calculators / SasaCalculator.hh
DockDesignParser.cc	scoring / ScoreFunction.hh
DockDesignParser.cc	scoring / ScoreFunctionFactory.hh
DockDesignParser.cc	scoring / ScoreType.hh
DockDesignParser.cc	types.hh
DockDesignParser.hh	pose / Pose.fwd.hh
archive / EvaluatedArchive.cc	scoring / Energies.hh
archive / EvaluatedArchive.cc	pose / Pose.hh
archive / EvaluatedArchive.cc	scoring / ScoreFunction.hh
archive / EvaluatedArchive.cc	io / silent / SilentFileData.hh
archive / EvaluatedArchive.hh	scoring / constraints / ConstraintSet.fwd.hh
archive / EvaluatedArchive.hh	pose / Pose.fwd.hh
archive / EvaluatedArchive.hh	scoring / ResidualDipolarCoupling.fwd.hh
archive / EvaluatedArchive.hh	io / silent / silent.fwd.hh
archive / EvaluatedArchive.hh	types.hh
FileJobOutputter.cc	io / raw_data / ScoreFileData.hh
FileJobOutputter.hh	pose / Pose.fwd.hh
FileSystemJobDistributor.hh	types.hh
parser / FragmentReader.cc	fragment / BBTorsionSRFD.hh
parser / FragmentReader.cc	chemical / ChemicalManager.hh
parser / FragmentReader.cc	fragment / ConstantLengthFragSet.hh
parser / FragmentReader.cc	fragment / FragData.hh
parser / FragmentReader.cc	fragment / FragmentIO.hh
parser / FragmentReader.cc	fragment / FragSet.hh
parser / FragmentReader.cc	fragment / Frame.hh
parser / FragmentReader.cc	fragment / FrameIterator.hh
parser / FragmentReader.cc	fragment / FrameIteratorWorker_.hh
parser / FragmentReader.cc	fragment / FrameList.hh
parser / FragmentReader.cc	import_pose / import_pose.hh
parser / FragmentReader.cc	fragment / IndependentBBTorsionSRFD.hh
parser / FragmentReader.cc	fragment / OrderedFragSet.hh
parser / FragmentReader.cc	pose / Pose.hh
parser / FragmentReader.cc	chemical / ResidueType.hh
parser / FragmentReader.cc	import_pose / pose_stream / SilentFilePoseInputStream.hh
parser / FragmentReader.cc	fragment / picking_old / vall / util.hh
parser / FragmentReader.cc	fragment / util.hh
parser / FragmentReader.hh	fragment / FragSet.fwd.hh
parser / FragmentReader.hh	pose / Pose.fwd.hh
parser / FragSetLoader.cc	fragment / FragmentIO.hh
parser / FragSetLoader.cc	fragment / FragSet.hh
parser / FragSetLoader.cc	fragment / OrderedFragSet.hh
parser / FragSetLoader.hh	pose / Pose.fwd.hh
InnerJob.cc	pose / Pose.hh
InnerJob.cc	pose / util.hh
InnerJob.hh	pose / Pose.fwd.hh
InnerJob.hh	types.hh
InnerMultiThreadingJob.cc	pose / Pose.hh
InnerMultiThreadingJob.hh	pose / Pose.fwd.hh
InnerMultiThreadingJob.hh	sequence / SequenceAlignment.fwd.hh
InnerMultiThreadingJob.hh	types.hh
JD2ResourceManagerJobInputter.cc	chemical / ChemicalManager.hh
JD2ResourceManagerJobInputter.cc	pose / Pose.hh
JD2ResourceManagerJobInputter.cc	chemical / ResidueType.hh
JD2ResourceManagerJobInputter.cc	chemical / ResidueTypeSet.hh
Job.cc	pose / Pose.hh
Job.hh	pose / Pose.fwd.hh
Job.hh	types.hh
JobDistributor.cc	pose / Pose.hh
JobDistributor.cc	scoring / ScoreFunction.hh
JobDistributor.cc	scoring / ScoreFunctionFactory.hh
JobDistributor.cc	scoring / symmetry / SymmetricScoreFunction.hh
JobDistributor.cc	pose / symmetry / util.hh
JobDistributor.hh	pose / Pose.fwd.hh
JobDistributor.hh	types.hh
JobInputter.cc	pose / Pose.hh
JobInputter.hh	pose / Pose.fwd.hh
JobInputter.hh	types.hh
JobOutputter.hh	pose / Pose.fwd.hh
JobOutputter.hh	io / silent / SilentStruct.fwd.hh
LazySilentFileJobInputter.cc	pose / Pose.hh
LazySilentFileJobInputter.cc	pose / util.hh
LazySilentFileJobInputter.hh	pose / Pose.fwd.hh
LazySilentFileJobInputter.hh	io / silent / SilentFileData.hh
LazySilentFileJobInputter.hh	io / silent / SilentStruct.fwd.hh
parser / MonteCarloLoader.cc	scoring / ScoreFunction.hh
parser / MonteCarloLoader.hh	pose / Pose.fwd.hh
archive / MPIArchiveJobDistributor.hh	pose / Pose.fwd.hh
archive / MPIArchiveJobDistributor.hh	types.hh
MpiFileBuffer.hh	types.hh
MPIFileBufJobDistributor.hh	pose / Pose.fwd.hh
MPIFileBufJobDistributor.hh	types.hh
MPIMultiCommJobDistributor.hh	pose / Pose.fwd.hh
MPIMultiCommJobDistributor.hh	types.hh
MPIWorkPartitionJobDistributor.hh	pose / Pose.fwd.hh
MPIWorkPartitionJobDistributor.hh	types.hh
MPIWorkPoolJobDistributor.hh	pose / Pose.fwd.hh
MPIWorkPoolJobDistributor.hh	types.hh
MultiThreadingJob.cc	types.hh
MultiThreadingJob.hh	pose / Pose.fwd.hh
MultiThreadingJob.hh	types.hh
NoOutputJobOutputter.hh	pose / Pose.fwd.hh
archive / NormalizedEvaluatedArchive.cc	scoring / ScoreFunction.hh
archive / NormalizedEvaluatedArchive.hh	scoring / constraints / ConstraintSet.fwd.hh
archive / NormalizedEvaluatedArchive.hh	pose / Pose.fwd.hh
archive / NormalizedEvaluatedArchive.hh	scoring / ResidualDipolarCoupling.fwd.hh
archive / NormalizedEvaluatedArchive.hh	io / silent / silent.fwd.hh
archive / NormalizedEvaluatedArchive.hh	types.hh
Parser.cc	pose / Pose.hh
Parser.hh	pose / Pose.fwd.hh
PDBJobInputter.cc	import_pose / import_pose.hh
PDBJobInputter.cc	pose / Pose.hh
PDBJobInputter.hh	pose / Pose.fwd.hh
PDBJobOutputter.cc	io / pdb / file_data.hh
PDBJobOutputter.cc	io / pdb / pose_io.hh
PDBJobOutputter.cc	types.hh
PDBJobOutputter.hh	pose / Pose.fwd.hh
PoseInputStreamJobInputter.cc	kinematics / Jump.hh
PoseInputStreamJobInputter.cc	import_pose / pose_stream / MetaPoseInputStream.hh
PoseInputStreamJobInputter.cc	pose / Pose.hh
PoseInputStreamJobInputter.cc	conformation / Residue.hh
PoseInputStreamJobInputter.cc	chemical / ResidueTypeSet.fwd.hh
PoseInputStreamJobInputter.cc	chemical / util.hh
PoseInputStreamJobInputter.cc	import_pose / pose_stream / util.hh
PoseInputStreamJobInputter.hh	import_pose / pose_stream / MetaPoseInputStream.hh
parser / ScoreFunctionLoader.cc	scoring / methods / EnergyMethodOptions.hh
parser / ScoreFunctionLoader.cc	scoring / hbonds / HBondOptions.hh
parser / ScoreFunctionLoader.cc	scoring / ScoreFunction.hh
parser / ScoreFunctionLoader.cc	scoring / ScoreFunctionFactory.hh
parser / ScoreFunctionLoader.cc	scoring / ScoringManager.fwd.hh
parser / ScoreFunctionLoader.cc	scoring / symmetry / SymmetricScoreFunction.hh
parser / ScoreFunctionLoader.hh	pose / Pose.fwd.hh
ScoreMap.cc	scoring / Energies.hh
ScoreMap.cc	pose / Pose.hh
ScoreMap.cc	scoring / ScoreFunction.hh
ScoreMap.hh	pose / Pose.fwd.hh
ScoreMap.hh	scoring / ScoreFunction.fwd.hh
ScoreMap.hh	types.hh
ScoreOnlyJobOutputter.cc	io / silent / SilentFileData.hh
ScoreOnlyJobOutputter.hh	pose / Pose.fwd.hh
ScoreOnlyJobOutputter.hh	types.hh
ShuffleJobDistributor.hh	types.hh
SilentFileJobInputter.cc	pose / Pose.hh
SilentFileJobInputter.cc	pose / symmetry / util.hh
SilentFileJobInputter.cc	pose / util.hh
SilentFileJobInputter.hh	pose / Pose.fwd.hh
SilentFileJobInputter.hh	io / silent / SilentFileData.hh
SilentFileJobInputter.hh	io / silent / SilentStruct.fwd.hh
SilentFileJobOutputter.cc	pose / Pose.hh
SilentFileJobOutputter.cc	io / silent / SilentFileData.hh
SilentFileJobOutputter.cc	io / silent / SilentStructFactory.hh
SilentFileJobOutputter.hh	pose / Pose.fwd.hh
SilentFileJobOutputter.hh	types.hh
SingleFileBuffer.hh	types.hh
parser / TaskOperationLoader.cc	pack / task / operation / TaskOperation.hh
parser / TaskOperationLoader.cc	pack / task / operation / TaskOperationFactory.hh
util.cc	chemical / ChemicalManager.hh
util.cc	import_pose / import_pose.hh
util.cc	pose / Pose.hh
util.cc	io / silent / SilentFileData.hh
util.cc	io / silent / SilentStruct.hh
util.cc	io / silent / SilentStructFactory.hh
util.hh	pose / Pose.fwd.hh
util.hh	io / silent / SilentStruct.fwd.hh
util.hh	types.hh
archive / VarianceStatisticsArchive.cc	io / silent / SilentStruct.hh
archive / VarianceStatisticsArchive.hh	pose / Pose.fwd.hh
archive / VarianceStatisticsArchive.hh	types.hh