legacy → core Relation

File in src/protocols/stepwise/legacy	Includes file in src/core
modeler / protein / StepWiseProteinMinimizer.cc	conformation / Conformation.hh
modeler / protein / StepWiseProteinMinimizer.cc	conformation / util.hh
modeler / protein / StepWiseProteinMinimizer.cc	id / TorsionID.hh
modeler / protein / StepWiseProteinMinimizer.cc	pose / Pose.hh
modeler / protein / StepWiseProteinMinimizer.cc	scoring / constraints / util.hh
modeler / protein / StepWiseProteinMinimizer.cc	scoring / Energies.hh
modeler / protein / StepWiseProteinMinimizer.cc	scoring / EnergyGraph.hh
modeler / protein / StepWiseProteinMinimizer.cc	scoring / ScoreFunction.hh
modeler / protein / StepWiseProteinMinimizer.cc	scoring / constraints / ConstraintSet.hh
modeler / protein / StepWiseProteinMinimizer.cc	optimization / AtomTreeMinimizer.hh
modeler / protein / StepWiseProteinMinimizer.cc	optimization / CartesianMinimizer.hh
modeler / protein / StepWiseProteinMinimizer.cc	optimization / MinimizerOptions.hh
modeler / protein / StepWiseProteinMinimizer.cc	kinematics / MoveMap.hh
modeler / protein / StepWiseProteinMinimizer.hh	pose / Pose.fwd.hh
modeler / protein / StepWiseProteinMinimizer.hh	scoring / ScoreFunction.fwd.hh
modeler / protein / StepWiseProteinMinimizer.hh	types.hh
modeler / protein / StepWiseProteinMinimizer.hh	kinematics / MoveMap.fwd.hh
modeler / protein / StepWiseProteinPoseSetup.cc	chemical / ChemicalManager.hh
modeler / protein / StepWiseProteinPoseSetup.cc	chemical / VariantType.hh
modeler / protein / StepWiseProteinPoseSetup.cc	chemical / ResidueType.hh
modeler / protein / StepWiseProteinPoseSetup.cc	conformation / Residue.hh
modeler / protein / StepWiseProteinPoseSetup.cc	conformation / ResidueFactory.hh
modeler / protein / StepWiseProteinPoseSetup.cc	conformation / Conformation.hh
modeler / protein / StepWiseProteinPoseSetup.cc	scoring / func / Func.fwd.hh
modeler / protein / StepWiseProteinPoseSetup.cc	scoring / func / FadeFunc.hh
modeler / protein / StepWiseProteinPoseSetup.cc	scoring / constraints / AtomPairConstraint.hh
modeler / protein / StepWiseProteinPoseSetup.cc	scoring / constraints / ConstraintSet.hh
modeler / protein / StepWiseProteinPoseSetup.cc	scoring / constraints / ConstraintIO.hh
modeler / protein / StepWiseProteinPoseSetup.cc	scoring / ScoreType.hh
modeler / protein / StepWiseProteinPoseSetup.cc	scoring / ScoreFunction.hh
modeler / protein / StepWiseProteinPoseSetup.cc	types.hh
modeler / protein / StepWiseProteinPoseSetup.cc	pose / util.hh
modeler / protein / StepWiseProteinPoseSetup.cc	pose / Pose.hh
modeler / protein / StepWiseProteinPoseSetup.cc	pose / full_model_info / FullModelInfo.hh
modeler / protein / StepWiseProteinPoseSetup.cc	pose / full_model_info / FullModelParameters.hh
modeler / protein / StepWiseProteinPoseSetup.cc	io / raw_data / DisulfideFile.hh
modeler / protein / StepWiseProteinPoseSetup.cc	import_pose / import_pose.hh
modeler / protein / StepWiseProteinPoseSetup.cc	pose / annotated_sequence.hh
modeler / protein / StepWiseProteinPoseSetup.cc	pose / variant_util.hh
modeler / protein / StepWiseProteinPoseSetup.cc	pose / subpose_manipulation_util.hh
modeler / protein / StepWiseProteinPoseSetup.cc	pose / rna / util.hh
modeler / protein / StepWiseProteinPoseSetup.cc	id / TorsionID.hh
modeler / protein / StepWiseProteinPoseSetup.cc	kinematics / FoldTree.hh
modeler / protein / StepWiseProteinPoseSetup.cc	chemical / rna / util.hh
modeler / protein / StepWiseProteinPoseSetup.cc	scoring / rms_util.hh
modeler / protein / StepWiseProteinPoseSetup.hh	pose / Pose.fwd.hh
modeler / protein / StepWiseProteinPoseSetup.hh	chemical / ResidueType.fwd.hh
modeler / protein / StepWiseProteinPoseSetup.hh	chemical / ResidueTypeSet.fwd.hh
modeler / protein / StepWiseProteinPoseSetup.hh	scoring / constraints / ConstraintSet.fwd.hh
modeler / protein / StepWiseProteinPoseSetup.hh	id / AtomID_Map.hh
modeler / protein / StepWiseProteinPoseSetup.hh	types.hh
modeler / protein / util.cc	io / silent / util.hh
modeler / protein / util.cc	types.hh
modeler / protein / util.cc	io / silent / BinarySilentStruct.hh
modeler / protein / util.cc	io / silent / SilentFileData.hh
modeler / protein / util.cc	io / silent / SilentFileOptions.hh
modeler / protein / util.cc	id / NamedAtomID.hh
modeler / protein / util.cc	id / AtomID.hh
modeler / protein / util.cc	pose / Pose.hh
modeler / protein / util.cc	conformation / Residue.hh
modeler / protein / util.cc	scoring / rms_util.hh
modeler / protein / util.hh	pose / Pose.fwd.hh
modeler / protein / util.hh	io / silent / SilentFileData.fwd.hh
modeler / protein / util.hh	types.hh
modeler / rna / RNA_AnalyticLoopCloser.cc	types.hh
modeler / rna / RNA_AnalyticLoopCloser.cc	chemical / ResidueType.hh
modeler / rna / RNA_AnalyticLoopCloser.cc	chemical / rna / RNA_Info.hh
modeler / rna / RNA_AnalyticLoopCloser.cc	id / AtomID.hh
modeler / rna / RNA_AnalyticLoopCloser.cc	id / NamedAtomID.hh
modeler / rna / RNA_AnalyticLoopCloser.cc	id / DOF_ID.hh
modeler / rna / RNA_AnalyticLoopCloser.cc	kinematics / AtomTree.hh
modeler / rna / RNA_AnalyticLoopCloser.cc	pose / Pose.hh
modeler / rna / RNA_AnalyticLoopCloser.cc	conformation / Residue.hh
modeler / rna / RNA_AnalyticLoopCloser.cc	scoring / ScoreFunction.hh
modeler / rna / RNA_AnalyticLoopCloser.hh	id / NamedAtomID.hh
modeler / rna / RNA_AnalyticLoopCloser.hh	id / DOF_ID.hh
modeler / rna / RNA_AnalyticLoopCloser.hh	pose / Pose.fwd.hh
modeler / rna / RNA_AnalyticLoopCloser.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / RNA_AnalyticLoopCloser.hh	types.hh
modeler / rna / StepWiseRNA_Clusterer.cc	types.hh
modeler / rna / StepWiseRNA_Clusterer.cc	pose / Pose.hh
modeler / rna / StepWiseRNA_Clusterer.cc	pose / extra_pose_info_util.hh
modeler / rna / StepWiseRNA_Clusterer.cc	pose / rna / util.hh
modeler / rna / StepWiseRNA_Clusterer.cc	chemical / ChemicalManager.hh
modeler / rna / StepWiseRNA_Clusterer.cc	chemical / rna / util.hh
modeler / rna / StepWiseRNA_Clusterer.cc	io / silent / SilentStruct.hh
modeler / rna / StepWiseRNA_Clusterer.cc	io / silent / SilentFileData.hh
modeler / rna / StepWiseRNA_Clusterer.cc	io / silent / SilentFileOptions.hh
modeler / rna / StepWiseRNA_Clusterer.cc	import_pose / pose_stream / SilentFilePoseInputStream.hh
modeler / rna / StepWiseRNA_Clusterer.cc	scoring / rms_util.hh
modeler / rna / StepWiseRNA_Clusterer.cc	io / silent / SilentFileData.fwd.hh
modeler / rna / StepWiseRNA_Clusterer.cc	conformation / Conformation.hh
modeler / rna / StepWiseRNA_Clusterer.hh	pose / Pose.fwd.hh
modeler / rna / StepWiseRNA_Clusterer.hh	pose / Pose.hh
modeler / rna / StepWiseRNA_Clusterer.hh	import_pose / pose_stream / SilentFilePoseInputStream.fwd.hh
modeler / rna / StepWiseRNA_Clusterer.hh	chemical / ResidueTypeSet.fwd.hh
modeler / rna / StepWiseRNA_Clusterer.hh	io / silent / SilentFileData.fwd.hh
modeler / rna / StepWiseRNA_Clusterer.hh	types.hh
modeler / rna / StepWiseRNA_Clusterer.hh	io / silent / SilentStruct.fwd.hh
modeler / rna / StepWiseRNA_PoseSelection.cc	scoring / ScoreFunction.hh
modeler / rna / StepWiseRNA_PoseSelection.cc	pose / Pose.hh
modeler / rna / StepWiseRNA_PoseSelection.cc	pose / util.hh
modeler / rna / StepWiseRNA_PoseSelection.cc	pose / extra_pose_info_util.hh
modeler / rna / StepWiseRNA_PoseSelection.cc	pose / rna / util.hh
modeler / rna / StepWiseRNA_PoseSelection.hh	pose / Pose.fwd.hh
modeler / rna / StepWiseRNA_PoseSelection.hh	types.hh
modeler / rna / StepWiseRNA_PoseSelection.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / ChemicalManager.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / VariantType.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / ResidueType.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / ResidueTypeSet.fwd.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	conformation / Residue.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	conformation / ResidueFactory.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	chemical / rna / util.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	scoring / func / Func.fwd.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	scoring / func / FadeFunc.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	scoring / constraints / AtomPairConstraint.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	scoring / constraints / ConstraintSet.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	types.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	pose / annotated_sequence.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	pose / Pose.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	pose / full_model_info / FullModelInfo.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	pose / full_model_info / FullModelParameters.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	pose / util.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	pose / variant_util.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	pose / copydofs / util.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	pose / rna / util.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	import_pose / import_pose.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	id / TorsionID.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	kinematics / FoldTree.hh
modeler / rna / StepWiseRNA_PoseSetup.cc	conformation / Conformation.hh
modeler / rna / StepWiseRNA_PoseSetup.hh	pose / Pose.fwd.hh
modeler / rna / StepWiseRNA_PoseSetup.hh	chemical / ResidueTypeSet.fwd.hh
modeler / rna / StepWiseRNA_PoseSetup.hh	types.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	types.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / AA.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / ResidueTypeSet.fwd.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / ChemicalManager.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / ScoreFunctionFactory.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / ScoreFunction.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / func / CharmmPeriodicFunc.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / constraints / DihedralConstraint.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	sequence / util.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	kinematics / FoldTree.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	id / AtomID.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	pose / Pose.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	pose / rna / util.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	io / silent / util.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	import_pose / import_pose.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	chemical / ResidueType.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.cc	scoring / constraints / ConstraintSet.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.hh	scoring / ScoreFunction.fwd.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.hh	types.hh
modeler / rna / StepWiseRNA_PoseSetupFromCommandLine.hh	pose / Pose.fwd.hh
modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	chemical / ResidueTypeSet.hh
modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	chemical / ChemicalManager.hh
modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	chemical / VariantType.hh
modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	conformation / Residue.hh
modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	types.hh
modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	pose / Pose.hh
modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	pose / rna / util.hh
modeler / rna / StepWiseRNA_WorkingParametersSetup.cc	kinematics / FoldTree.hh
modeler / rna / StepWiseRNA_WorkingParametersSetup.hh	types.hh
modeler / rna / StepWiseRNA_WorkingParametersSetup.hh	kinematics / FoldTree.hh
modeler / rna / util.cc	chemical / ChemicalManager.hh
modeler / rna / util.cc	conformation / Residue.hh
modeler / rna / util.cc	pose / Pose.hh
modeler / rna / util.cc	pose / rna / util.hh
modeler / rna / util.cc	sequence / util.hh
modeler / rna / util.cc	io / silent / SilentFileData.hh
modeler / rna / util.cc	io / silent / SilentStruct.hh
modeler / rna / util.hh	kinematics / FoldTree.fwd.hh
modeler / rna / util.hh	pose / Pose.fwd.hh
modeler / rna / util.hh	types.hh
screener / ProteinAtrRepScreener.cc	pose / Pose.fwd.hh
screener / ProteinAtrRepScreener.hh	pose / Pose.fwd.hh
screener / RNA_AtrRepScreener.cc	pose / Pose.fwd.hh
screener / RNA_AtrRepScreener.hh	pose / Pose.fwd.hh
screener / SimplePoseSelection.cc	pose / Pose.hh
screener / SimplePoseSelection.hh	pose / Pose.fwd.hh
screener / SimpleRMSD_Screener.cc	pose / Pose.fwd.hh
screener / SimpleRMSD_Screener.cc	scoring / rms_util.hh
screener / SimpleRMSD_Screener.cc	scoring / rms_util.tmpl.hh
screener / SimpleRMSD_Screener.hh	pose / Pose.fwd.hh
screener / SimpleRMSD_Screener.hh	id / AtomID.fwd.hh
screener / SimpleRMSD_Screener.hh	types.hh