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- a -

a : TSimpleBox3< T >
a0 : Constant
a_ : HBondShiftProcessor
a_i_ : ConjugateGradientMinimizer
ABSOLUTE_TEMPERATURE : ReissCavFreeEnergyProcessor::Default, ReissCavFreeEnergyProcessor::Option, PierottiCavFreeEnergyProcessor::Default, PierottiCavFreeEnergyProcessor::Option, PCMCavFreeEnergyProcessor::Default, PCMCavFreeEnergyProcessor::Option
acceptor_list_ : HBondShiftProcessor
add_hydrogens : FragmentDB
ALGORITHM_NAME : RingPerceptionProcessor::Default, RingPerceptionProcessor::Option
all_small_beers_ : RingPerceptionProcessor
all_small_rings_ : RingPerceptionProcessor
ALPHA : PairExpInteractionEnergyProcessor::Default, PairExpInteractionEnergyProcessor::Option, RegularExpression
alpha_ : DSN6File
ALPHANUMERIC : RegularExpression
angle : TQuaternion< T >
argument : ExpressionParser::SyntaxTree
arom : MMFF94AtomType
aspec : MMFF94AtomType
ASSIGN_CHARGES : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
ASSIGN_TYPENAMES : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
ASSIGN_TYPES : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
atom : CharmmEEF1::Data
atom_ : SmartsParser::SPAtom
atom_array : FDPB
atom_format_ : MOLFile
attributes_changed_time_ : Atom
AVERAGE_SECTION_NAME : CreateSpectrumProcessor
AVOGADRO : Constant

- b -

b : TSimpleBox3< T >
b_ : HBondShiftProcessor
b_i_ : ConjugateGradientMinimizer
backbone_dependent_ : RotamerLibrary
BATH_RELAXATION_TIME : MolecularDynamics::Option
bath_relaxation_time_ : CanonicalMD
bb_dep_sets_ : RotamerLibrary
bb_indep_sets_ : RotamerLibrary
beta_ : DSN6File
blockname : GAMESSDatFile::block
BOHR_RADIUS : Constant
BOLTZMANN : Constant
bond_ : SmartsParser::SPEdge
bond_format_ : MOLFile
bond_lengths_ : BuildBondsProcessor
bond_order_ : SmartsParser::SPBond
bond_to_index_ : RingPerceptionProcessor
BONDLENGTHS_FILENAME : BuildBondsProcessor::Default, BuildBondsProcessor::Option
book_keeping_ : PDBFile
BORDER : FDPB::Default, FDPB::Option
bound_ : CompositeIteratorTraits
BOUNDARY : FDPB::Default, FDPB::Option
bounding_box_data_size : TRRFile::TRRHeader
BOUNDING_BOX_LOWER : FDPB::Option
BOUNDING_BOX_UPPER : FDPB::Option
bucket_ : HashMap< Key, T >
build_bonds : FragmentDB

- c -

c : Constant
CAL_PER_JOULE : Constant
capacity_ : HashMap< Key, T >
cell_scaling_ : DSN6File
CHARACTER_CLASS__ASCII_ALPHA : String
CHARACTER_CLASS__ASCII_ALPHANUMERIC : String
CHARACTER_CLASS__ASCII_FLOAT : String
CHARACTER_CLASS__ASCII_LOWER : String
CHARACTER_CLASS__ASCII_NUMERIC : String
CHARACTER_CLASS__ASCII_UPPER : String
CHARACTER_CLASS__QUOTES : String
CHARACTER_CLASS__WHITESPACE : String
CHARGE_DISTRIBUTION : FDPB::Default, FDPB::Option
CHECK_AFTER_ITERATIONS : FDPB::Default, FDPB::Option
chi1 : Rotamer
chi2 : Rotamer
chi3 : Rotamer
chi4 : Rotamer
children : ExpressionParser::SyntaxTree
CHOOSE_MODEL : PDBFile::Default, PDBFile::Option
component_grouping_ : SmartsParser
component_no_ : SmartsParser, SmartsParser::SPNode
composite_iterator_ : CompositeIteratorTraits
conformation_set_ : VIEW::DockingFinishedMessage, DockResult
CONST : SLICKScore::Default, SLICKScore::Option, SLICKEnergy::Default, SLICKEnergy::Option
CONSTANT : UhligCavFreeEnergyProcessor::Default, UhligCavFreeEnergyProcessor::Option
constants_ : ParsedFunction< arg >
corr_par_ : ShiftedLVMMMinimizer
CORRECTION_PARAMETER : ShiftedLVMMMinimizer::Option
COULOMB : FDPB::Boundary
counts_format_ : MOLFile
Cp_ref : CharmmEEF1::Values
crd : MMFF94AtomType
crystal_dimension_ : DSN6File
curr_num_of_vect_pairs_ : StrangLBFGSMinimizer
curr_number_of_cols_ : ShiftedLVMMMinimizer
CURRENT_DIRECTORY : FileSystem
current_energy_ : EnergyMinimizer
current_grad_ : EnergyMinimizer
current_parser_ : SmartsParser
CURRENT_TIME : MolecularDynamics::Option
cutlo_ : EnergyMinimizer

- d -

d : TLine3< T >
D_1_ : ConjugateGradientMinimizer
D_4_ : ConjugateGradientMinimizer
data : GAMESSDatFile::block
data_ : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
DEBYE : FDPB::Boundary
DEFAULT_FRAGMENT_DB : RotamerLibrary
DEFAULT_LIBRARY : RotamerLibrary
DEG_PER_RAD : Constant
DELETE_EXISTING_BONDS : BuildBondsProcessor::Default, BuildBondsProcessor::Option
DELETE_OVERESTIMATED_BONDS : BuildBondsProcessor::Default, BuildBondsProcessor::Option
dG_free : CharmmEEF1::Values
dG_ref : CharmmEEF1::Values
dH_ref : CharmmEEF1::Values
DIELECTRIC_SMOOTHING : FDPB::Default, FDPB::Option
dimension_ : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
DIPOLE : FDPB::Boundary
direction_ : EnergyMinimizer
DISPLAYLIST_NOT_DEFINED : VIEW::GLDisplayList
DISTANCE_DEPENDENT_DIELECTRIC : MMFF94::Default, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
docking_algorithm_ : DockResult
docking_options_ : DockResult
donor_list_ : HBondShiftProcessor

- e -

E : Constant
e0 : Constant
e_size : TRRFile::TRRHeader
edges_ : SmartsParser, SmartsParser::SPNode
ELECTRON_MASS : Constant
ELECTROSTATIC_CUTOFF : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
ELECTROSTATIC_CUTON : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
element_symbol : SolventAtomDescriptor
ELEMENTARY_CHARGE : Constant
EMPTY : String
EndPos : String
ENERGY_DIFFERENCE_BOUND : EnergyMinimizer::Option
energy_difference_bound_ : EnergyMinimizer
ENERGY_OUTPUT_FREQUENCY : EnergyMinimizer::Option, MolecularDynamics::Option
energy_output_frequency_ : EnergyMinimizer
energy_update_counter_ : EnergyMinimizer
entries_ : JCAMPFile
eps_grid : FDPB
EPSILON : Constant
evaluated : ExpressionParser::SyntaxTree
extent_ : DSN6File

- f -

F : Constant
FARADAY : Constant
FILENAME : CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
filename_ : PDBInfo
FINE_STRUCTURE_CONSTANT : Constant
first : Triple< T1, T2, T3 >, Quadruple< T1, T2, T3, T4 >
first_ : SmartsParser::SPEdge
first_edge_ : SmartsParser::SPNode, SmartsParser::SPEdge
first_iter_ : StrangLBFGSMinimizer, ShiftedLVMMMinimizer, ConjugateGradientMinimizer
first_matches : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
FLUSH_TO_DISK_FREQUENCY : SnapShotManager::Default, SnapShotManager::Option
FOCUSING : FDPB::Boundary
FOLDER : MMFF94::Default, MMFF94::Option
force_data_size : TRRFile::TRRHeader
force_field_ : EnergyMinimizer
force_update_counter_ : EnergyMinimizer
forwarded_rings_ : RingPerceptionProcessor
fourth : Quadruple< T1, T2, T3, T4 >
fragment_db_ : RotamerLibrary, FragmentDB::BuildBondsProcessor
fragment_list_ : FragmentDB::BuildBondsProcessor
fragments : FragmentDistanceCollector
functions_ : ParsedFunction< arg >

- g -

gamma_ : DSN6File
GAS_CONSTANT : Constant
grad_diff_ : ShiftedLVMMMinimizer
GRAVITATIONAL_CONSTANT : Constant

- h -

h : Constant, TVector4< T >
h_bond_pairs_ : HBondProcessor
HARMONIC : FDPB::DielectricSmoothing
has_torsion_phi_ : ResidueRotamerSet
has_torsion_psi_ : ResidueRotamerSet
HEADER : INIFile
header_ : JCAMPFile
hess_factor_ : ShiftedLVMMMinimizer
HEXADECIMAL_INTEGER : RegularExpression

- i -

i : TQuaternion< T >
id_ : PDBInfo
IDENTIFIER : RegularExpression
IGNORE_SECTION_NAME : CreateSpectrumProcessor
IGNORE_XPLOR_PSEUDO_ATOMS : PDBFile::Default, PDBFile::Option
ignore_xplor_pseudo_atoms_ : PDBFile
IMPROVED : StrangLBFGSMinimizer::Option
improved_ : StrangLBFGSMinimizer
index_ : VIEW::DockResultDialog::Compare_
index_of_free_vect_ : StrangLBFGSMinimizer
info : LogStream, PDBFile
initial_atoms_ : StrangLBFGSMinimizer, ShiftedLVMMMinimizer
initial_energy_ : EnergyMinimizer
initial_grad_ : EnergyMinimizer
INTEGER : RegularExpression
internal_ : SmartsParser::SPNode, SmartsParser::SPEdge
inv_norm : Gradient
invalid_records_ : PDBInfo
ION_RADIUS : FDPB::Default, FDPB::Option
IONIC_STRENGTH : FDPB::Default, FDPB::Option
ir_size : TRRFile::TRRHeader
is_not_ : SmartsParser::SPNode, SmartsParser::SPEdge
is_orthogonal_ : TRegularData3D< ValueType >
is_proline_ : Peptides::PeptideBuilder

- j -

j : TQuaternion< T >
JOULE_PER_CAL : Constant

- k -

k : Constant, TQuaternion< T >
kappa_grid : FDPB

- l -

lambda : TRRFile::TRRHeader
last_restart_iter_ : ConjugateGradientMinimizer
lin : MMFF94AtomType
line_ : MOL2File, LineBasedFile
line_number_ : LineBasedFile
line_search_ : StrangLBFGSMinimizer, SteepestDescentMinimizer, ShiftedLVMMMinimizer, ConjugateGradientMinimizer
LJ_FILENAME : Pair6_12InteractionEnergyProcessor::Option
LOCALITY : ElectrostaticPotentialCalculator::Default, ElectrostaticPotentialCalculator::Option
log_op_ : SmartsParser::SPNode, SmartsParser::SPEdge
LOWER : FDPB::Option
LOWERCASE : RegularExpression

- m -

m11 : TMatrix4x4< T >
m12 : TMatrix4x4< T >
m13 : TMatrix4x4< T >
m14 : TMatrix4x4< T >
m21 : TMatrix4x4< T >
m22 : TMatrix4x4< T >
m23 : TMatrix4x4< T >
m24 : TMatrix4x4< T >
m31 : TMatrix4x4< T >
m32 : TMatrix4x4< T >
m33 : TMatrix4x4< T >
m34 : TMatrix4x4< T >
m41 : TMatrix4x4< T >
m42 : TMatrix4x4< T >
m43 : TMatrix4x4< T >
m44 : TMatrix4x4< T >
M_PER_FOOT : Constant
MAGIC : TRRFile::TRRHeader
mapped_atoms : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
mapping_ : TRegularData3D< ValueType >
mass_factor_ : CanonicalMD
matched_atoms : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
matrix_ : RingPerceptionProcessor
max_bond_lengths_ : BuildBondsProcessor
MAX_CRITERION : FDPB::Default, FDPB::Option
MAX_ENTRY_LENGTH : Options
MAX_GRADIENT : EnergyMinimizer::Option
max_gradient_ : EnergyMinimizer
MAX_ITERATIONS : FDPB::Default, FDPB::Option
max_length_ : BuildBondsProcessor
max_num_of_vect_pairs_ : StrangLBFGSMinimizer
max_number_of_cols_ : ShiftedLVMMMinimizer
MAX_PATH_LENGTH : FileSystem, Directory
MAX_SAME_ENERGY : EnergyMinimizer::Option
max_same_energy_ : EnergyMinimizer
MAXIMAL_NUMBER_OF_ITERATIONS : EnergyMinimizer::Option, MolecularDynamics::Option
maximal_number_of_iterations_ : EnergyMinimizer
MAXIMAL_SIMULATION_TIME : MolecularDynamics::Option
maximum_bond_length_ : HBondShiftProcessor
MAXIMUM_DISPLACEMENT : EnergyMinimizer::Option
maximum_displacement_ : EnergyMinimizer
METHOD : Pair6_12RDFIntegrator::Option
min_bond_lengths_ : BuildBondsProcessor
minimum_bond_length_ : HBondShiftProcessor
mltb : MMFF94AtomType
MM_PER_INCH : Constant
MODE_APP : File
MODE_ATE : File
MODE_BINARY : File
MODE_IN : File
MODE_OUT : File
MODE_TRUNC : File
model_read_ : PDBInfo
MODULE_LIST_SECTION : ShiftModel
MOL : Constant
movable_atoms_chi1_ : ResidueRotamerSet

- n -

n : TPlane3< T >, TCircle3< T >
NA : Constant
name_ : ResidueRotamerSet, DockResult::Scoring_, PDBInfo
needs_SSSR_ : SmartsParser
negate : Gradient, TVector3< T >, TVector2< T >, TAngle< T >, ExpressionParser::SyntaxTree
NEUTRON_MASS : Constant
nodes_ : SmartsParser
NON_ALPHA : RegularExpression
NON_ALPHANUMERIC : RegularExpression
NON_NUMERIC : RegularExpression
NON_WHITESPACE : RegularExpression
NONBONDED_CUTOFF : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
NONE : FDPB::DielectricSmoothing, NamedProperty
norm : Gradient
normal : TSurface< T >
normalize_names : FragmentDB
not_ : SmartsParser::SPBond
not_properties_ : SmartsParser::SPAtom
nre : TRRFile::TRRHeader
num_bonds_ : BuildBondsProcessor
NUM_OF_COLUMNS : ShiftedLVMMMinimizer::Option
NUM_OF_STORED_VECT_PAIRS : StrangLBFGSMinimizer::Option
number_of_atom_records_ : PDBInfo
number_of_atoms : SolventAtomDescriptor, TRRFile::TRRHeader
number_of_atoms_ : StrangLBFGSMinimizer, ShiftedLVMMMinimizer, ConjugateGradientMinimizer
number_of_hetatm_records_ : PDBInfo
NUMBER_OF_ITERATION : EnergyMinimizer::Option, MolecularDynamics::Option
number_of_iterations_ : EnergyMinimizer
number_of_models_ : PDBInfo
number_of_records_ : PDBInfo
number_of_torsions_ : ResidueRotamerSet

- o -

OBJECT_HEADER : XDRPersistenceManager
OBJECT_TRAILER : XDRPersistenceManager
OFFSET : FDPB::Option
old_energy_ : EnergyMinimizer
old_grad_ : EnergyMinimizer
old_gtg_ : ConjugateGradientMinimizer
options : GeometricFit, DockingAlgorithm, BuildBondsProcessor, UhligCavFreeEnergyProcessor, ReissCavFreeEnergyProcessor, FDPB, PierottiCavFreeEnergyProcessor, PCMCavFreeEnergyProcessor, PairExpInteractionEnergyProcessor, Pair6_12RDFIntegrator, Pair6_12InteractionEnergyProcessor, ElectrostaticPotentialCalculator, ShiftModel, EnergyMinimizer, MolecularDynamics, SnapShotManager, PeriodicBoundary, ForceField, PDBFile, ParameterSection
options_ : DockResult::Scoring_
origin_ : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >, DSN6File, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
original_coordinates_ : ResidueRotamerSet
OVERWRITE_CHARGES : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
OVERWRITE_TYPENAMES : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option

- p -

P : Rotamer
p : TSphere3< T >, TPlane3< T >, TLine3< T >, TCircle3< T >
p_i_ : ConjugateGradientMinimizer
p_t_ : ConjugateGradientMinimizer
parameters_ : MMFF94ESParameters, MMFF94VDWParameters, MMFF94PlaneParameters, MMFF94TorsionParameters, MMFF94StretchBendParameters, MMFF94BendParameters, MMFF94StretchParameters
PARENT_DIRECTORY : FileSystem
pars_ : Bruker1DFile
PARSE_PARTIAL_CHARGES : PDBFile::Default, PDBFile::Option
parse_partial_charges_ : PDBFile
parsf1_ : Bruker2DFile
PATH_SEPARATOR : FileSystem
pbcis_ : MMFF94ESParameters
periodic_boundary : ForceField
PERIODIC_BOX_ADD_SOLVENT : PeriodicBoundary::Default
PERIODIC_BOX_DISTANCE : PeriodicBoundary::Default
PERIODIC_BOX_ENABLED : PeriodicBoundary::Default
PERIODIC_BOX_LOWER : PeriodicBoundary::Default
PERIODIC_BOX_SOLVENT_FILE : PeriodicBoundary::Default
PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE : PeriodicBoundary::Default
PERIODIC_BOX_UPPER : PeriodicBoundary::Default
PERIODIC_WATER_FILE : PeriodicBoundary::Default
phi_ : ResidueRotamerSet
phi_grid : FDPB
phis_ : MMFF94ESParameters
pilp : MMFF94AtomType
PLANCK : Constant
position_data_size : TRRFile::TRRHeader
predicate : ExpressionParser::SyntaxTree
predicate_ : CompositeIteratorTraits
pres_size : TRRFile::TRRHeader
PRESSURE : ReissCavFreeEnergyProcessor::Default, ReissCavFreeEnergyProcessor::Option, PierottiCavFreeEnergyProcessor::Default, PierottiCavFreeEnergyProcessor::Option
prev_shift_val_ : ShiftedLVMMMinimizer
PRINT_TIMING : FDPB::Default, FDPB::Option
PROBE_RADIUS : UhligCavFreeEnergyProcessor::Default, UhligCavFreeEnergyProcessor::Option, ReissCavFreeEnergyProcessor::Default, ReissCavFreeEnergyProcessor::Option, FDPB::Default, FDPB::Option, PierottiCavFreeEnergyProcessor::Default, PierottiCavFreeEnergyProcessor::Option, PCMCavFreeEnergyProcessor::Default, PCMCavFreeEnergyProcessor::Option
prod_ : DSN6File
properties_ : SmartsParser::SPAtom
PROPERTY__ANISOTROPY_SHIFT : AnisotropyShiftProcessor
PROPERTY__EF_SHIFT : EFShiftProcessor
PROPERTY__RANDOM_COIL_SHIFT : RandomCoilShiftProcessor
PROPERTY__RING_CURRENT_SHIFT : JohnsonBoveyShiftProcessor, HaighMallionShiftProcessor
PROPERTY__SHIFT : ShiftModule
PROTON_MASS : Constant
psi_ : ResidueRotamerSet

- q -

q_grid : FDPB

- r -

R : Constant
r_min : CharmmEEF1::Values
RAD_PER_DEG : Constant
radius : SolventAtomDescriptor, TSphere3< T >, TCircle3< T >
RDF_FILENAME : PairExpInteractionEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Option
read_atoms_ : SDFile
REAL : RegularExpression
rec_edges_ : SmartsParser
records_ : PDBRecords
recursive_ : SmartsParser, SmartsParser::SPNode
REESTIMATE_BONDORDERS_RINGS : BuildBondsProcessor::Default, BuildBondsProcessor::Option
REFERENCE_TEMPERATURE : MolecularDynamics::Option
residue_data_ : HBondProcessor
restart_frequency_ : ConjugateGradientMinimizer
results : FDPB
rho_ : StrangLBFGSMinimizer
ring_connections_ : SmartsParser
rings_ : RingPerceptionProcessor
rms : Gradient
RMS_CRITERION : FDPB::Default, FDPB::Option
root_ : SmartsParser
rotamers_ : ResidueRotamerSet

- s -

same_energy_counter_ : EnergyMinimizer
SAMPLES : PairExpRDFIntegrator::Option, Pair6_12RDFIntegrator::Option
sampling_rate_ : DSN6File
SAS_grid : FDPB
sbmb : MMFF94AtomType
SCALING_ELECTROSTATIC_1_4 : CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
SCALING_VDW_1_4 : CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
scores_ : DockResult::Scoring_
scorings_ : DockResult
second : Triple< T1, T2, T3 >, Quadruple< T1, T2, T3, T4 >
second_ : SmartsParser::SPEdge
second_edge_ : SmartsParser::SPNode, SmartsParser::SPEdge
selected_model_ : PDBFile
shift_s_ : ShiftedLVMMMinimizer
shifted_direction_ : ShiftedLVMMMinimizer
sig_w : CharmmEEF1::Values
size_ : TRegularData3D< ValueType >, TRegularData2D< ValueType >, HashMap< Key, T >
skipped_records_ : PDBInfo
snapshot_ : EnergyMinimizer
SNAPSHOT_FREQUENCY : EnergyMinimizer::Option, MolecularDynamics::Option
snapshot_frequency_ : EnergyMinimizer
snapshot_order_ : DockResult::Scoring_, ConformationSet
SOLUTE_DC : FDPB::Default, FDPB::Option
SOLVATION_CUTOFF : CharmmFF::Default, CharmmFF::Option
SOLVATION_CUTON : CharmmFF::Default, CharmmFF::Option
SOLVENT_DC : FDPB::Default, FDPB::Option
SOLVENT_FILENAME : PairExpInteractionEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Option
SOLVENT_NUMBER_DENSITY : ReissCavFreeEnergyProcessor::Default, ReissCavFreeEnergyProcessor::Option, PierottiCavFreeEnergyProcessor::Default, PierottiCavFreeEnergyProcessor::Option, PCMCavFreeEnergyProcessor::Default, PCMCavFreeEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Default, Pair6_12InteractionEnergyProcessor::Option
sorted_by_ : DockResult
sp_atom_ : SmartsParser::SPNode
SPACING : FDPB::Default, FDPB::Option
spacing_ : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
SPEED_OF_LIGHT : Constant
sssr_ : SmartsParser
start_ : DSN6File
state : SmartsParser
step_ : EnergyMinimizer
step_width_ : RotamerLibrary
STORE_SKIPPED_RECORDS : PDBFile::Default, PDBFile::Option
store_skipped_records_ : PDBFile
stored_s_ : StrangLBFGSMinimizer
stored_y_ : StrangLBFGSMinimizer
STREAM_HEADER : XDRPersistenceManager
STREAM_TRAILER : XDRPersistenceManager
STRICT_LINE_CHECKING : PDBFile::Default, PDBFile::Option
structures_ : ConformationSet
SURFACE_FILENAME : PairExpInteractionEnergyProcessor::Default, PairExpInteractionEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Default, Pair6_12InteractionEnergyProcessor::Option
SURFACE_TENSION : UhligCavFreeEnergyProcessor::Default, UhligCavFreeEnergyProcessor::Option
SURFACE_TYPE : GeometricFit::Option, PairExpInteractionEnergyProcessor::Default, PairExpInteractionEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Default, Pair6_12InteractionEnergyProcessor::Option
swap_bytes_ : DSN6File
sym_size : TRRFile::TRRHeader
system : GAMESSLogFile
system_ : ConformationSet

- t -

TEMPERATURE : FDPB::Default, FDPB::Option
tested_beers_ : RingPerceptionProcessor
third : GraphTriangle< Vertex, Edge, Face >, Triple< T1, T2, T3 >, Quadruple< T1, T2, T3, T4 >
threshold_ : TContourSurface< T >
time_ : TimeStamp
TIME_STEP : MolecularDynamics::Option
timestep_index : TRRFile::TRRHeader
timestep_time : TRRFile::TRRHeader
title_string : TRRFile::TRRHeader
title_string_length : TRRFile::TRRHeader
tnode_to_atom_ : RingPerceptionProcessor
top_size : TRRFile::TRRHeader
TRANSFORMATION_EXEC_PREFIX : File
TRANSFORMATION_FILE_PREFIX : File
TRANSFORMATION_FTP_PREFIX : File
TRANSFORMATION_HTTP_PREFIX : File
transformation_methods_ : TransformationManager
tree : FragmentDB
triangle : TSurface< T >
TRILINEAR : FDPB::ChargeDistribution
TRIPOS : MOL2File
type : SolventAtomDescriptor, ExpressionParser::SyntaxTree
type_ : SecondaryStructure

- u -

UNDEFINED : VIEW::RepresentationMessage, VIEW::CompositeMessage, VIEW::DatasetMessage, ParameterSection, INIFile
UNIFORM : FDPB::DielectricSmoothing, FDPB::ChargeDistribution
UNKNOWN : Element
unscaled_direction_ : ConjugateGradientMinimizer
UPDATE_METHOD : ShiftedLVMMMinimizer::Option, ConjugateGradientMinimizer::Default, ConjugateGradientMinimizer::Option
updt_method_ : ShiftedLVMMMinimizer, ConjugateGradientMinimizer
updt_u_ : ShiftedLVMMMinimizer
updt_v_ : ShiftedLVMMMinimizer
UPPER : FDPB::Option
UPPERCASE : RegularExpression
USE_EEF1 : CharmmFF::Default, CharmmFF::Option
USE_RDF : PairExpInteractionEnergyProcessor::Default, PairExpInteractionEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Default, Pair6_12InteractionEnergyProcessor::Option

- v -

V : CharmmEEF1::Values
VACUUM_PERMEABILITY : Constant
VACUUM_PERMITTIVITY : Constant
val : MMFF94AtomType
valid : MMFF94AtomType
valid_ : ResidueRotamerSet, EnergyMinimizer
value : TAngle< T >
values : CharmmEEF1::Data
VDW_CUTOFF : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
VDW_CUTON : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
velocity_data_size : TRRFile::TRRHeader
VERBOSITY : UhligCavFreeEnergyProcessor::Default, UhligCavFreeEnergyProcessor::Option, ReissCavFreeEnergyProcessor::Default, ReissCavFreeEnergyProcessor::Option, FDPB::Default, FDPB::Option, PierottiCavFreeEnergyProcessor::Default, PierottiCavFreeEnergyProcessor::Option, PCMCavFreeEnergyProcessor::Default, PCMCavFreeEnergyProcessor::Option, PairExpRDFIntegrator::Option, PairExpInteractionEnergyProcessor::Default, PairExpInteractionEnergyProcessor::Option, Pair6_12RDFIntegrator::Option, Pair6_12InteractionEnergyProcessor::Default, Pair6_12InteractionEnergyProcessor::Option, PDBFile::Default, PDBFile::Option
verbosity_ : PDBFile
VERSION : TRRFile::TRRHeader
vertex : VIEW::QuadMesh, TSurface< T >
vir_size : TRRFile::TRRHeader
visited_atoms : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
visited_bonds : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
visited_edges : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_

- w -

WHITESPACE : RegularExpression
work_val_ : StrangLBFGSMinimizer

- x -

x : TVector4< T >, TVector3< T >, TVector2< T >
xaxis_ : DSN6File

- y -

y : TVector4< T >, TVector3< T >, TVector2< T >
y_i_ : ConjugateGradientMinimizer
y_t_ : ConjugateGradientMinimizer
yaxis_ : DSN6File

- z -