- 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
DEG2RAD : spacegroup.cc , util.hh , refinable_lattice.cc
DIM : PCA.cc , superimpose.cc
DIM6 : PCA.cc , superimpose.cc
DIST_TH : SuckerEnergy.cc , GaussianOverlapEnergy.cc

- f -

foreach : ABEGOHashedFragmentStore.cc , reference_frames.cc , MPI_Refine_Master.cc , metalloproteins_util.cc , LoopProtocol.cc , EnergyPerResidueFilter.cc , ParsedProtocol.cc , TaskOperationFeatures.cc , ClosureProblem.cc , LoopMoverGroup.cc , LoopMover.cc , LoopModeler.cc , PerturberSet.cc , LogFilePerturber.cc , IdealizeNonPhiPsi.cc
foreach_ : LocalRelax.cc , EnzdesBaseProtocol.cc , ResidueArrayAnnealingEvaluator.cc
FOREACH_Chi_BB : SingleResidueDunbrackLibrary.cc

- g -

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

- 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_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_OptimizeProteinEmbeddingMover_cc : OptimizeProteinEmbeddingMover.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_relax_membrane_MPRangeRelaxMover_cc : MPRangeRelaxMover.cc
INCLUDED_protocols_relax_RangeRelaxMover_cc : RangeRelaxMover.cc
INCLUDED_protocols_rosetta_scripts_PosePropertyReporter_CC : PosePropertyReporter.cc
INCLUDED_protocols_rosetta_scripts_PoseSelector_CC : PoseSelector.cc
INIT : SingleResidueDunbrackLibrary.cc

- m -

Math_PI : FACTSResidue.cc
MAX : ShapeComplementarityCalculator_Private.hh , ANN.cc
MAX_INCLUDES : RosettaScriptsParser.cc
MAX_MOTIF_D2 : MotifHashRigidScore.cc
MAX_SUBDIV : ShapeComplementarityCalculator_Private.hh
MAX_UINT16 : read_biounit.cc , motif_hash_stuff.cc , util.cc , xfrags.cc
MAX_UINT8 : xfrags.cc , motif_hash_stuff.cc , util.cc , read_biounit.cc
MIN : ShapeComplementarityCalculator_Private.hh , ANN.cc
MOVING_RES : StepWiseWorkingParameters.hh
MPI_ANY_SOURCE : MPI_WorkUnitManager_Slave.hh , MPI_WorkUnitManager.hh

- n -

- o -

O3I_C5I_MAX_DIST : StepWiseRNA_Classes.hh
O3I_C5I_MIN_DIST : StepWiseRNA_Classes.hh
O3I_C5I_PLUS_ONE_MAX_DIST : StepWiseRNA_Classes.hh
O3I_C5I_PLUS_TWO_MAX_DIST : StepWiseRNA_Classes.hh
O3I_O3I_PLUS_ONE_MAX_DIST : StepWiseRNA_Classes.hh
OBSOLETE : EvaluatedArchive.cc , IterativeBase.cc
opt_read_out_macro : PeakAssignmentParameters.cc
opt_read_out_macro2 : PeakAssignmentParameters.cc

- p -

PI : ShapeComplementarityCalculator_Private.hh

- r -

RAD2DEG : refinable_lattice.cc , spacegroup.cc , util.hh
ROTATE : PCA.cc , ResidualDipolarCoupling.cc , superimpose.cc

- s -

SALT : Chunk.cc
SD_MULTIPLIER : Chunk.cc
SimpleCycpepPredictApplication_PEPBOND_C_ANGLE : SimpleCycpepPredictApplication.hh
SimpleCycpepPredictApplication_PEPBOND_LENGTH : SimpleCycpepPredictApplication.hh
SimpleCycpepPredictApplication_PEPBOND_N_ANGLE : SimpleCycpepPredictApplication.hh
SPARTA_MAX_NUM : constants.hh
SPARTA_MAXNUM : constants.hh
SQRT_2PI : USOGFunc.cc
STANDARD_CENTROID_BIN_SIZE : util.hh
STANDARD_EULER_ANGLE_BIN_SIZE : util.hh
STANDARD_EULER_Z_BIN_SIZE : util.hh

- t -

TAG_NUM_FORMAT_LENGTH : JobDistributors.hh
THROW_EXCEPTION : serialize_pose.cc
TRDEBUG : MPI_WorkUnitManager.cc , MPI_Refinement.cc , MPI_Refine_Master.cc , MPI_Refine_Emperor.cc , MPI_LoopHashRefine_Master.cc , MPI_LoopHashRefine_Emperor.cc , MPI_LoopHashRefine.cc , MPI_WorkUnitManager_Slave.cc

- u -

UPPER_MULTIPLE : ShapeComplementarityCalculator.cc

- x -

XFORM_SCORE_FILE_VERSION : util.cc , xfrags.cc
XX : superimpose.cc , PCA.cc , ResidualDipolarCoupling.cc , superimpose.cc

- y -

YY : ResidualDipolarCoupling.cc , superimpose.cc , PCA.cc

- z -

ZZ : ResidualDipolarCoupling.cc , superimpose.cc , PCA.cc