- a -

ABS : ShapeComplementarityCalculator_Private.hh

- b -

BOINC_CHECKPOINT_COUNT_FILE : boinc.hh
BOINC_DEFAULT_MAX_CPU_RUN_TIME : boinc.hh
BOINC_INIT_COUNT_FILE : boinc.hh
BOINC_MAX_GFX_CPU : boinc.hh
BOINC_MAX_GFX_FPS : boinc.hh
BOINC_MAX_NO_PROGRESS_INIT_CNT : boinc.hh
BOINC_MAX_NSTRUCT : boinc.hh
boost_foreach : AntibodyFeatures.cc
BRIDGE_RES : StepWiseWorkingParameters.hh

- c -

C5I_C5I_PLUS_ONE_MAX_DIST : StepWiseRNA_Classes.hh
CAP_FA_REP : NestedEnergyTermOptEData.cc , OptEData.cc
CUTOFF : CartesianBondedEnergy.cc
CYS_1oSIN_CB_SG_HG : FunGroupTK.cc
CYS_CB_HG_DIS : FunGroupTK.cc
CYS_CB_SG_PERP : FunGroupTK.cc
CYS_HG_SG_PRJLEN : FunGroupTK.cc
CYS_HG_SG_X_DROP : FunGroupTK.cc
CYS_SG_CB_H : FunGroupTK.cc

- d -

DEFAULT_DIST_CUTOFF_MULTIPLIER : metalloproteins_util.hh
DEFINE_OPTIONS_NOW : PeakAssignmentParameters.cc
DIM : superimpose.cc , PCA.cc
DIM6 : superimpose.cc , PCA.cc , superimpose.cc
DIST_TH : SuckerEnergy.cc , GaussianOverlapEnergy.cc

- f -

foreach : reference_frames.cc , VallLookbackPotential.cc , LoopProtocol.cc , EnergyPerResidueFilter.cc , ParsedProtocol.cc , MPI_Refine_Master.cc , MatDesGreedyOptMutationMover.cc , metalloproteins_util.cc , PerturberSet.cc , LoopMover.cc , LoopMoverGroup.cc , TaskOperationFeatures.cc , LogFilePerturber.cc , IdealizeNonPhiPsi.cc , ClosureProblem.cc , LoopModeler.cc
foreach_ : LocalRelax.cc , EnzdesBaseProtocol.cc

- g -

GAP_SIZE_DUMMY : StepWiseBasicWorkingParameters.hh
GetCurrentDir : StepWiseRNA_PoseSetupFromCommandLine.cc
getmax : TMalign.hh
getmin : TMalign.hh

- h -

HIS_1oSIN_CA_CB_CG : FunGroupTK.cc
HIS_CB_CG_PERP : FunGroupTK.cc
HIS_CB_HG_DIS : FunGroupTK.cc
HIS_CB_HG_PAR : FunGroupTK.cc
HIS_CG_CB_H : FunGroupTK.cc
HIS_HE2_CG_PRJLEN : FunGroupTK.cc
HIS_HE2_CG_X_DROP : FunGroupTK.cc

- i -

INCLUDE_core_scoring_MembranePotential_cc : MembranePotential.cc
INCLUDED_core_pack_packer_trie_trie_vs_trie_HH : trie_vs_path.cc
INCLUDED_core_pose_stream_util_HH : util.cc
INCLUDED_core_scoring_membrane_FaMPEnvEnergy_cc : FaMPEnvEnergy.cc
INCLUDED_core_scoring_membrane_FaMPSolvEnergy_cc : FaMPSolvEnergy.cc
INCLUDED_core_scoring_membrane_MembraneData_cc : MembraneData.cc
INCLUDED_core_scoring_membrane_MPCbetaEnergy_cc : MPCBetaEnergy.cc
INCLUDED_core_scoring_membrane_MPEnvEnergy_cc : MPEnvEnergy.cc
INCLUDED_core_scoring_membrane_MPLipoEnergy_cc : MPLipoEnergy.cc
INCLUDED_core_scoring_membrane_MPNonHelixPenalty_cc : MPNonHelixPenalty.cc
INCLUDED_core_scoring_membrane_MPPairEnergy_cc : MPPairEnergy.cc
INCLUDED_core_scoring_membrane_MPTerminiPenalty_cc : MPTerminiPenalty.cc
INCLUDED_core_scoring_membrane_MPTMProjPenalty_cc : MPTMProjPenalty.cc
INCLUDED_core_scoring_sc_MolecularSurfaceCalculator_cc : MolecularSurfaceCalculator.cc
INCLUDED_core_scoring_sc_ShapeComplementarityCalculator_cc : ShapeComplementarityCalculator.cc
INCLUDED_protocols_docking_membrane_MPDockingMover_cc : MPDockingMover.cc
INCLUDED_protocols_docking_membrane_MPDockingSetupMover_cc : MPDockingSetupMover.cc
INCLUDED_protocols_docking_membrane_MPFindInterfaceMover_cc : MPFindInterfaceMover.cc
INCLUDED_protocols_docking_membrane_QuickRelaxPartnersSeparately_cc : QuickRelaxPartnersSeparately.cc
INCLUDED_protocols_flxbb_utility_HH : utility.cc
INCLUDED_protocols_membrane_AddMembraneMover_cc : AddMembraneMover.cc
INCLUDED_protocols_membrane_FlipMover_cc : FlipMover.cc
INCLUDED_protocols_membrane_MembranePositionFromTopologyMover_cc : MembranePositionFromTopologyMover.cc
INCLUDED_protocols_membrane_MPMutateRelaxMover_cc : MPMutateRelaxMover.cc
INCLUDED_protocols_membrane_MPQuickRelaxMover_cc : MPQuickRelaxMover.cc
INCLUDED_protocols_membrane_OptimizeMembranePositionMover_cc : OptimizeMembranePositionMover.cc
INCLUDED_protocols_membrane_SpinAroundPartnerMover_cc : SpinAroundPartnerMover.cc
INCLUDED_protocols_membrane_symmetry_SymmetricAddMembraneMover_cc : SymmetricAddMembraneMover.cc
INCLUDED_protocols_membrane_TiltMover_cc : TiltMover.cc
INCLUDED_protocols_membrane_TransformIntoMembraneMover_cc : TransformIntoMembraneMover.cc
INCLUDED_protocols_membrane_TranslationRotationMover_cc : TranslationRotationMover.cc
INCLUDED_protocols_membrane_visualize_VisualizeEmbeddingMover_cc : VisualizeEmbeddingMover.cc
INCLUDED_protocols_membrane_visualize_VisualizeMembraneMover_cc : VisualizeMembraneMover.cc
INCLUDED_protocols_moves_PyMolMover_CC : PyMolMover.cc
INCLUDED_protocols_pose_reporters_BasicPoseReporters_CC : BasicPosePropertyReporters.cc
INCLUDED_protocols_pose_selectors_BasicPoseSelectors_cc : BasicPoseSelectors.cc
INCLUDED_protocols_pose_selectors_ClusterPoseSelector_cc : ClusterPoseSelector.cc
INCLUDED_protocols_rosetta_scripts_PosePropertyReporter_CC : PosePropertyReporter.cc
INCLUDED_protocols_rosetta_scripts_PoseSelector_CC : PoseSelector.cc