- a -

A : BALL::LennardJones::Values
a : BALL::PDB::RecordCRYST1::UnitCell , BALL::PDB::Structure::UnitCellInfo
A : BALL::Potential1210::Values
a : BALL::SortedPosition2 , BALL::SortedPosition3 , BALL::TSimpleBox3< T >
a0 : BALL::Constant
a1 : BALL::HybridisationProcessor::AtomNames_
a2 : BALL::HybridisationProcessor::AtomNames_
a3 : BALL::HybridisationProcessor::AtomNames_
A_ : BALL::LennardJones , BALL::Pair6_12RDFIntegrator , BALL::Potential1210 , BALL::StructureMapper
a_i_ : BALL::ConjugateGradientMinimizer
A_STAR : BALL::AssignBondOrderProcessor::Algorithm
abbreviation_common : BALL::NMRStarFile::MolecularSystem
abop : BALL::BondOrderAssignmentStrategy , BALL::PartialBondOrderAssignment
abort_ : BALL::DockingAlgorithm , BALL::VIEW::DockingFinishedMessage
abort_by_energy_enabled_ : BALL::EnergyMinimizer , BALL::MolecularDynamics
abort_energy_ : BALL::EnergyMinimizer , BALL::MolecularDynamics
abort_test : BALL::VIEW::TestFramework
aborted_ : BALL::EnergyMinimizer , BALL::VIEW::DownloadElectronDensity , BALL::VIEW::DownloadPDBFile
about_to_quit_ : BALL::VIEW::MainControl , BALL::VIEW::RenderSetup
ABSOLUTE_TEMPERATURE : BALL::NonpolarSolvation::Default , BALL::NonpolarSolvation::Option , BALL::PCMCavFreeEnergyProcessor::Default , BALL::PCMCavFreeEnergyProcessor::Option , BALL::PierottiCavFreeEnergyProcessor::Default , BALL::PierottiCavFreeEnergyProcessor::Option , BALL::ReissCavFreeEnergyProcessor::Default , BALL::ReissCavFreeEnergyProcessor::Option
ac : BALL::BondOrderAssignment
ac_ : BALL::AssignBondOrderProcessor , BALL::VIEW::FieldLineCreator
acceptor_ : BALL::HBondProcessor::HBond , BALL::TCPServer
acceptor_types_ : BALL::HBondShiftProcessor
acceptors_ : BALL::HBondProcessor , BALL::HBondShiftProcessor
accession_code : BALL::NMRStarFile::MolecularSystem::RelatedDB , BALL::NMRStarFile::MonomericPolymer::HomologDB
action : BALL::VIEW::Hotkey
action1_ : BALL::VIEW::PubChemDialog
action2_ : BALL::VIEW::PubChemDialog
action_ : BALL::VIEW::TestFramework , BALL::VIEW::UndoManagerDialog
actions_ : BALL::VIEW::DatasetController , BALL::VIEW::InteractionModeManager
actions_for_one_set_ : BALL::VIEW::DatasetController
activated_item_ : BALL::VIEW::AssignBondOrderResultsDialog
active_ : BALL::VIEW::ClippingPlane
active_stereo_action_ : BALL::VIEW::Scene
activities : BALL::QSAR::InputConfiguration
activity_names : BALL::QSAR::InputConfiguration
adapt_char_ : BALL::TRRFile
adapt_double_ : BALL::TRRFile
adapt_float_ : BALL::DCDFile , BALL::TRRFile
adapt_size_ : BALL::DCDFile , BALL::TRRFile
add_button_ : BALL::VIEW::PubChemDialog
ADD_HBONDS : BALL::HBondProcessor::Default , BALL::HBondProcessor::Option
ADD_HYDROGENS : BALL::AssignBondOrderProcessor::Default , BALL::AssignBondOrderProcessor::Option
add_hydrogens : BALL::FragmentDB
add_hydrogens_action_ : BALL::VIEW::Scene
add_menu_ : BALL::VIEW::EditMode
add_missing_hydrogens_ : BALL::AssignBondOrderProcessor
additional_grid_distance_ : BALL::VIEW::ColorProcessor
adjacent_edges_ : BALL::NodeItem< Node, Edge >
advanced : BALL::ParameterDescription
advanced_options_modified_ : BALL::VIEW::DisplayProperties
ai : BALL::MMFF94VDWParameters::VDWEntry
Aij_ : BALL::LennardJones
ALGORITHM : BALL::AssignBondOrderProcessor::Default , BALL::AssignBondOrderProcessor::Option
ALGORITHM_NAME : BALL::RingPerceptionProcessor::Default , BALL::RingPerceptionProcessor::Option
all_amino_acids_ : BALL::VIEW::PeptideDialog
all_aromatic_atoms_ : BALL::Kekuliser
all_atoms_ : BALL::SmilesParser
all_fragments_ : BALL::FragmentDistanceCollector
all_hydrogen_are_targets_ : BALL::HaighMallionShiftProcessor
ALL_LIG_NONB_PAIRS : BALL::ScoringFunction::Default , BALL::ScoringFunction::Option
all_ligand_nonbonded_ : BALL::ScoringFunction
all_names_ : BALL::VIEW::GLRenderer
all_residues_hashgrid_ : BALL::ScoringFunction
all_small_beers_ : BALL::RingPerceptionProcessor
all_small_rings_ : BALL::RingPerceptionProcessor
all_torsions_ : BALL::ResidueTorsions
ALLOWED_INTERMOL_OVERLAP : BALL::ScoringFunction::Default , BALL::ScoringFunction::Option
allowed_intermolecular_overlap_ : BALL::ScoringFunction
ALLOWED_INTRAMOL_OVERLAP : BALL::ScoringFunction::Default , BALL::ScoringFunction::Option
allowed_intramolecular_overlap_ : BALL::ScoringFunction
allowed_values : BALL::ParameterDescription
ALPHA : BALL::PairExpInteractionEnergyProcessor::Default , BALL::PairExpInteractionEnergyProcessor::Option
alpha : BALL::PDB::RecordCRYST1::UnitCell , BALL::PDB::Structure::UnitCellInfo
ALPHA : BALL::RegularExpression
alpha_ : BALL::AssignBondOrderProcessor , BALL::CCP4File , BALL::CrystalInfo , BALL::DSN6File , BALL::LineSearch , BALL::PairExpInteractionEnergyProcessor , BALL::PairExpRDFIntegrator
alpha_blending_ : BALL::VIEW::ColorMap
alpha_i : BALL::MMFF94VDWParameters::VDWEntry
alpha_proton_oxygen_hydrogen_separation_distance_ : BALL::HBondShiftProcessor
ALPHA_PROTON_OXYGEN_SEPARATION_DISTANCE : BALL::HBondProcessor
ALPHANUMERIC : BALL::RegularExpression
alternate_location_indicator : BALL::PDB::RecordANISOU , BALL::PDB::RecordATOM , BALL::PDB::RecordHETATM , BALL::PDB::RecordHYDBND::HydrogenAtom , BALL::PDB::RecordHYDBND::HydrogenPartnerAtom , BALL::PDB::RecordLINK::LinkPartner , BALL::PDB::RecordSIGATM , BALL::PDB::RecordSIGUIJ , BALL::PDB::RecordSLTBRG::PartnerAtom
alternate_location_indicator_ : BALL::PDBFile
amber_nb_ : BALL::Electrostatic
ambient_ : BALL::VIEW::Stage
ambient_color : BALL::VIEW::Stage::Material
ambient_intensity : BALL::VIEW::Stage::Material
ambiguity_code : BALL::NMRStarFile::NMRAtomData
amide_proton_factor_ : BALL::HBondShiftProcessor
amide_proton_oxygen_hydrogen_separation_distance_ : BALL::HBondShiftProcessor
AMIDE_PROTON_OXYGEN_SEPARATION_DISTANCE : BALL::HBondProcessor
amide_proton_subtrahend_ : BALL::HBondShiftProcessor
amide_protons_are_targets_ : BALL::HBondShiftProcessor
angle : BALL::MMFF94Torsion::Torsion
angle_ : BALL::RSEdge , BALL::SASEdge , BALL::VIEW::LightSource
angle_action_ : BALL::VIEW::MolecularControl
angle_measure : BALL::PDB::RecordCISPEP
ANGLE_TOLERANCE : BALL::CHPI::Default , BALL::CHPI::Option , BALL::CHPISlick::Default , BALL::CHPISlick::Option
animation_export_PNG_action_ : BALL::VIEW::Scene
animation_export_POV_action_ : BALL::VIEW::Scene
animation_export_VRML_action_ : BALL::VIEW::Scene
animation_points_ : BALL::VIEW::Scene
animation_repeat_action_ : BALL::VIEW::Scene
animation_running_ : BALL::VIEW::SnapshotVisualisationDialog
animation_smoothness_ : BALL::VIEW::Scene
animation_thread_ : BALL::VIEW::Scene
anion : BALL::MMFF94AtomTyper::AromaticType
applied : BALL::GRAPH::UndoEliminateOperation< UndirectedGraph >
APPLY_FIRST_SOLUTION : BALL::AssignBondOrderProcessor::Default , BALL::AssignBondOrderProcessor::Option
apply_processor_ : BALL::VIEW::AtomOverview
aps_matcher : BALL::GAFFCESParser::CESPredicate
aps_terms : BALL::GAFFCESParser::APSMatcher
argument : BALL::ExpressionParser::SyntaxTree
argument_ : BALL::ExpressionPredicate
arom : BALL::MMFF94AtomType
arom_proc_ : BALL::SMARTSPredicate
aromat_list_ : BALL::JohnsonBoveyShiftProcessor
aromatic_atoms_ : BALL::Kekuliser
aromatic_bonds_ : BALL::MMFF94
aromatic_rings_ : BALL::AtomTyper , BALL::Kekuliser , BALL::MMFF94 , BALL::MMFF94ChargeProcessor
aromatic_systems_ : BALL::Kekuliser
aromatic_types_5_map_ : BALL::MMFF94AtomTyper
arrow_width_ : BALL::VIEW::AddCartoonModel
ASP_SEPERATION : BALL::BindingPocketProcessor::Default , BALL::BindingPocketProcessor::Option
aspec : BALL::MMFF94AtomType
ASSIGN_CHARGES : BALL::AmberFF::Default , BALL::AmberFF::Option , BALL::CharmmFF::Default , BALL::CharmmFF::Option , BALL::MMFF94::Default , BALL::MMFF94::Option
ASSIGN_TYPENAMES : BALL::AmberFF::Default , BALL::AmberFF::Option , BALL::CharmmFF::Default , BALL::CharmmFF::Option , BALL::MMFF94::Default , BALL::MMFF94::Option
ASSIGN_TYPES : BALL::AmberFF::Default , BALL::AmberFF::Option , BALL::CharmmFF::Default , BALL::CharmmFF::Option , BALL::MMFF94::Default , BALL::MMFF94::Option
assignment : BALL::FPTBondOrderStrategy::BackTrackingState_
assignment_ : BALL::FPTBondOrderStrategy::DPBackTrackingCombiner_
asu_ : BALL::CrystalGenerator
ATIJK : BALL::MMFF94StretchBend::Bend
atom : BALL::CharmmEEF1::Data , BALL::FragmentDB::BuildBondsProcessor::Connection , BALL::PDB::Structure::AtomEntry , BALL::StaticLigandFragment::Connection , BALL::VIEW::EditOperation
atom1 : BALL::AmberTorsion::SingleAmberTorsion , BALL::CharmmTorsion::SingleCharmmTorsion , BALL::CosineTorsion::Data , BALL::CosineTorsion::SingleData , BALL::LennardJones::Data , BALL::MMFF94StretchBend::Bend , BALL::MMFF94StretchBend::Stretch , BALL::MMFF94Torsion::Torsion , BALL::MOL2File::BondStruct , BALL::Potential1210::Data , BALL::QuadraticAngleBend::Data , BALL::QuadraticBondStretch::Data , BALL::QuadraticImproperTorsion::Data
atom2 : BALL::AmberTorsion::SingleAmberTorsion , BALL::CharmmTorsion::SingleCharmmTorsion , BALL::CosineTorsion::Data , BALL::CosineTorsion::SingleData , BALL::LennardJones::Data , BALL::MMFF94StretchBend::Bend , BALL::MMFF94StretchBend::Stretch , BALL::MMFF94Torsion::Torsion , BALL::MOL2File::BondStruct , BALL::Potential1210::Data , BALL::QuadraticAngleBend::Data , BALL::QuadraticBondStretch::Data , BALL::QuadraticImproperTorsion::Data
atom3 : BALL::AmberTorsion::SingleAmberTorsion , BALL::CharmmTorsion::SingleCharmmTorsion , BALL::CosineTorsion::Data , BALL::CosineTorsion::SingleData , BALL::MMFF94StretchBend::Bend , BALL::MMFF94Torsion::Torsion , BALL::QuadraticAngleBend::Data , BALL::QuadraticImproperTorsion::Data
atom4 : BALL::AmberTorsion::SingleAmberTorsion , BALL::CharmmTorsion::SingleCharmmTorsion , BALL::CosineTorsion::Data , BALL::CosineTorsion::SingleData , BALL::MMFF94Torsion::Torsion , BALL::QuadraticImproperTorsion::Data
atom_ : BALL::NodeItem< Node, Edge > , BALL::Peak< PositionType > , BALL::ReducedSurface , BALL::RSVertex , BALL::SESVertex , BALL::SmartsParser::SPAtom
atom_areas_ : BALL::NumericalSAS
atom_array : BALL::FDPB
atom_bijection_ : BALL::PoseClustering
atom_data : BALL::NMRStarFile::NMRAtomDataSet
atom_distance_ : BALL::VIEW::FieldLineCreator
ATOM_EXACT_CHANGE : BALL::MOLFile::Property
atom_forces_ : BALL::SnapShot
atom_format_ : BALL::MOLFile
atom_grid_ : BALL::VIEW::ColorProcessor
atom_group : BALL::NMRStarFile::ShiftReferenceElement
ATOM_H0_DESIGNATOR : BALL::MOLFile::Property
ATOM_HYDROGEN_COUNT : BALL::MOLFile::Property
atom_ID : BALL::NMRStarFile::NMRAtomData
atom_infos_ : BALL::Kekuliser
ATOM_INVERSION_RETENTION : BALL::MOLFile::Property
atom_list_ : BALL::JohnsonBoveyShiftProcessor
atom_map_ : BALL::PDBFile
ATOM_MASS_DIFFERENCE : BALL::MOLFile::Property
atom_name : BALL::NMRStarFile::NMRAtomData , BALL::PDB::RecordANISOU , BALL::PDB::RecordATOM , BALL::PDB::RecordHETATM , BALL::PDB::RecordHYDBND::HydrogenAtom , BALL::PDB::RecordHYDBND::HydrogenPartnerAtom , BALL::PDB::RecordLINK::LinkPartner , BALL::PDB::RecordSIGATM , BALL::PDB::RecordSIGUIJ , BALL::PDB::RecordSLTBRG::PartnerAtom
atom_name_A : BALL::ResidueTorsions::Data
atom_name_B : BALL::ResidueTorsions::Data
atom_name_C : BALL::ResidueTorsions::Data
atom_name_D : BALL::ResidueTorsions::Data
atom_name_in_current_strand : BALL::PDB::RecordSHEET
atom_name_in_previous_strand : BALL::PDB::RecordSHEET
atom_names : BALL::JohnsonBoveyShiftProcessor::Ring
atom_number_ : BALL::VIEW::EditMode
atom_overview_ : BALL::VIEW::MolecularControl
atom_overview_selection_ : BALL::VIEW::MolecularControl
atom_pairwise_ : BALL::ScoringComponent
atom_positions_ : BALL::SnapShot
atom_properties_ : BALL::VIEW::EditMode
ATOM_REACTION_COMPONENT_NUMBER : BALL::MOLFile::Property
ATOM_REACTION_COMPONENT_TYPE : BALL::MOLFile::Property
atom_serial_number : BALL::PDB::RecordCON061 , BALL::PDB::RecordCON062 , BALL::PDB::RecordCON063 , BALL::PDB::RecordCON064 , BALL::PDB::RecordCON06 , BALL::PDB::RecordCONECT
atom_status_ : BALL::RSComputer
ATOM_STEREO_CARE_BOX : BALL::MOLFile::Property
atom_surface_map_ : BALL::NumericalSAS
atom_surfaces_ : BALL::NumericalSAS
atom_to_block_ : BALL::AssignBondOrderProcessor , BALL::FPTBondOrderStrategy
atom_to_node_ : BALL::TSimpleMolecularGraph< Node, Edge >
atom_to_test : BALL::GAFFCESParser::CESPredicate
atom_to_tnode_ : BALL::RingPerceptionProcessor
atom_to_virtual_bond_index_ : BALL::AssignBondOrderProcessor
atom_type : BALL::GAFFTypeProcessor::TypeDefinition , BALL::NMRStarFile::NMRAtomData , BALL::NMRStarFile::ShiftReferenceElement
ATOM_TYPE_FF_FILENAME : BALL::HybridisationProcessor::Default , BALL::HybridisationProcessor::Option
ATOM_TYPE_FILE : BALL::NonpolarSolvation::Default , BALL::NonpolarSolvation::Option
atom_type_normalization_factor_ : BALL::AssignBondOrderProcessor
atom_type_smarts_ : BALL::HybridisationProcessor
ATOM_TYPE_SMARTS_FILENAME : BALL::HybridisationProcessor::Default , BALL::HybridisationProcessor::Option
atom_typer_ : BALL::MMFF94
atom_types_ : BALL::AssignTypeProcessor , BALL::ForceFieldParameters , BALL::GAFFTypeProcessor , BALL::GridedPLP , BALL::MMFF94 , BALL::MMFF94AtomTyper , BALL::PLPScoring , BALL::SolventParameter
atom_types_map_ : BALL::GridBasedScoring
ATOM_VALENCE : BALL::MOLFile::Property
atom_vector_ : BALL::MolecularDynamics
atom_velocities_ : BALL::SnapShot
atom_volumes_ : BALL::NumericalSAS
atomic_coordinate_records : BALL::PDB::BookKeeping
atomic_number : BALL::GAFFTypeProcessor::TypeDefinition , BALL::MMFF94AtomTyper::AromaticType
atomic_number_ : BALL::VIEW::Scene
atomic_property : BALL::GAFFTypeProcessor::TypeDefinition
atoms : BALL::PDB::Structure , BALL::RingAnalyser::Ring , BALL::StaticLigandFragment
atoms_ : BALL::AtomTyper , BALL::ForceField , BALL::MMFF94ChargeProcessor , BALL::MOL2File , BALL::MOPACOutputFile
atoms_to_delete : BALL::BondOrderAssignment
atoms_to_fragments_ : BALL::ScoringFunction
ATOMTYPE_FILENAME : BALL::GAFFTypeProcessor::Default , BALL::GAFFTypeProcessor::Option
attached_hydrogens : BALL::GAFFTypeProcessor::TypeDefinition
attenuation_ : BALL::VIEW::LightSource
authors : BALL::PDB::RecordAUTHOR
autoactivate_plugins_ : BALL::PluginManager
AVERAGE_SECTION_NAME : BALL::CreateSpectrumProcessor
AVOGADRO : BALL::Constant
axis_color_ : BALL::VIEW::RegularData1DWidget , BALL::VIEW::RegularData2DWidget