|
JOELib Computational Chemistry Package |
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| joelib.algo.* |
| joelib.algo.APropertyBFS | ||
public static final String |
DESC_KEY |
"Atom_property_breadth_first_search" |
public static final String |
STARTING_ATOM |
"STARTING_ATOM" |
| joelib.algo.BFS | ||
public static final String |
DESC_KEY |
"Breadth_first_search" |
public static final String |
STARTING_ATOM |
"STARTING_ATOM" |
| joelib.algo.DFS | ||
public static final String |
DESC_KEY |
"Depth_first_search" |
public static final String |
STARTING_ATOM |
"STARTING_ATOM" |
| joelib.data.* |
| joelib.data.JOEKernel | ||
public static final String |
CML_HARD_KERNEL |
"hardCoded" |
public static final String |
CML_KERNEL_REFERENCE |
"dictRef" |
public static final String |
CML_KERNEL_REFERENCE_PREFIX |
"jk:k" |
public static final String |
CML_SOFT_KERNEL |
"softCoded" |
| joelib.desc.* |
| joelib.desc.AtomsCounter | ||
public static final String |
ATOM_NUMBERS |
"ATOM_NUMBERS" |
| joelib.desc.Description | ||
public static final int |
maxType |
3 |
| joelib.desc.DescriptorInfo | ||
public static final int |
REQUIRED_DIMENSION_ENERGETIC |
4 |
public static final int |
REQUIRED_DIMENSION_GEOMETRICAL |
3 |
public static final int |
REQUIRED_DIMENSION_NO_COORDINATES |
0 |
public static final int |
REQUIRED_DIMENSION_TOPOLOGICAL |
2 |
public static final int |
REQUIRED_DIMENSION_UNKNOWN |
-1 |
public static final String |
TYPE_ENERGETIC |
"energegetic" |
public static final String |
TYPE_GEOMETRICAL |
"geometrical" |
public static final String |
TYPE_NO_COORDINATES |
"no_coordinates" |
public static final String |
TYPE_TOPOLOGICAL |
"topological" |
public static final String |
TYPE_UNKNOWN |
"unknown" |
| joelib.desc.SMARTSCounter | ||
public static final String |
SMARTS |
"SMARTS" |
| joelib.desc.data.MolDescCounter | ||
public static final int |
ALL_DESCRIPTORS |
0 |
public static final int |
NATIVE_DESCRIPTORS |
1 |
| joelib.desc.result.AtomDynamicResult | ||
public static final String |
ATOM_PROPERTY |
"atom_property" |
| joelib.desc.result.BondDynamicResult | ||
public static final String |
BOND_PROPERTY |
"bond_property" |
| joelib.desc.result.DynamicArrayResult | ||
public static final String |
BOOLEAN |
"boolean" |
public static final String |
DOUBLE |
"double" |
public static final String |
INT |
"int" |
| joelib.desc.types.AcidicGroups | ||
public static final String |
DEFAULT |
"[$([O;H1]-[C,S,P]=O),$([*;-;!$(*~[*;+])]),$([NH](S(=O)=O)C(F)(F)F),$(n1nnnc1),$(n1nncn1)]" |
public static final String |
DESC_KEY |
"Number_of_acidic_groups" |
| joelib.desc.types.AliphaticOHGroups | ||
public static final String |
DESC_KEY |
"Number_of_aliphatic_OH_groups" |
| joelib.desc.types.APropertyDistanceMatrix | ||
public static final String |
DESC_KEY |
"Atom_property_distance_matrix" |
| joelib.desc.types.AromaticBonds | ||
public static final String |
DESC_KEY |
"Number_of_aromatic_bonds" |
| joelib.desc.types.AromaticOHGroups | ||
public static final String |
DESC_KEY |
"Number_of_aromatic_OH_groups" |
| joelib.desc.types.AtomInAcceptor | ||
public static final String |
DESC_KEY |
"Atom_in_acceptor" |
| joelib.desc.types.AtomInAromaticSystem | ||
public static final String |
DESC_KEY |
"Atom_in_aromatic_system" |
| joelib.desc.types.AtomInConjEnvironment | ||
public static final String |
DESC_KEY |
"Atom_in_conjugated_environment" |
| joelib.desc.types.AtomInDonAcc | ||
public static final String |
DESC_KEY |
"Atom_in_donor_or_acceptor" |
| joelib.desc.types.AtomInDonor | ||
public static final String |
DESC_KEY |
"Atom_in_donor" |
| joelib.desc.types.AtomInRing | ||
public static final String |
DESC_KEY |
"Atom_in_ring" |
| joelib.desc.types.AtomInTerminalCarbon | ||
public static final String |
DESC_KEY |
"Atom_in_terminal_carbon" |
| joelib.desc.types.AtomIsNegative | ||
public static final String |
DESC_KEY |
"Atom_is_negative" |
| joelib.desc.types.AtomIsPositive | ||
public static final String |
DESC_KEY |
"Atom_is_positive" |
| joelib.desc.types.AtomMass | ||
public static final String |
DESC_KEY |
"Atom_mass" |
| joelib.desc.types.AtomType | ||
public static final String |
DESC_KEY |
"Atom_type" |
| joelib.desc.types.AtomValence | ||
public static final String |
DESC_KEY |
"Atom_valence" |
| joelib.desc.types.AtomVanDerWaalsVolume | ||
public static final String |
DESC_KEY |
"Atom_van_der_waals_volume" |
| joelib.desc.types.Autocorrelation | ||
public static final String |
ATOM_PROPERTY |
"ATOM_PROPERTY" |
public static final String |
DESC_KEY |
"Auto_correlation" |
| joelib.desc.types.BasicGroups | ||
public static final String |
DEFAULT |
"[$([NH2]-[CX4]),$([NH](-[CX4])-[CX4]),$(N(-[CX4])(-[CX4])-[CX4]),$([*;+;!$(*~[*;-])])$(N=C-N),$(N-C=N)]" |
public static final String |
DESC_KEY |
"Number_of_basic_groups" |
| joelib.desc.types.BCUT | ||
public static final String |
ATOM_PROPERTY |
"ATOM_PROPERTY" |
public static final String |
ATOM_PROPERTY_WEIGHT |
"ATOM_PROPERTY_WEIGHT" |
public static final String |
DESC_KEY |
"BCUT" |
| joelib.desc.types.BurdenEigenvalues | ||
public static final String |
ATOM_PROPERTY |
"ATOM_PROPERTY" |
public static final String |
ATOM_PROPERTY_WEIGHT |
"ATOM_PROPERTY_WEIGHT" |
public static final String |
DESC_KEY |
"Burden_eigenvalues" |
| joelib.desc.types.BurdenModifiedEigenvalues | ||
public static final String |
ATOM_PROPERTY |
"ATOM_PROPERTY" |
public static final String |
ATOM_PROPERTY_WEIGHT |
"ATOM_PROPERTY_WEIGHT" |
public static final String |
DESC_KEY |
"Burden_modified_eigenvalues" |
| joelib.desc.types.ConjElectroTopolState | ||
public static final double |
DEFAULT_DISTANCE_INFLUENCE |
2.0d |
public static final String |
DESC_KEY |
"Conjugated_electrotopological_state_index" |
public static final String |
DISTANCE_INFLUENCE |
"DISTANCE_INFLUENCE" |
| joelib.desc.types.ConjugatedTopologicalDistance | ||
public static final String |
DESC_KEY |
"Conjugated_topological_distance" |
| joelib.desc.types.DistanceDistanceMatrix | ||
public static final String |
DESC_KEY |
"Distance_distance_matrix" |
| joelib.desc.types.DistanceMatrix | ||
public static final String |
DESC_KEY |
"Distance_matrix" |
| joelib.desc.types.ElectrogeometricalState | ||
public static final String |
DESC_KEY |
"Electrogeometrical_state_index" |
public static final String |
DISTANCE_INFLUENCE |
"DISTANCE_INFLUENCE" |
| joelib.desc.types.ElectronAffinity | ||
public static final String |
DESC_KEY |
"Electron_affinity" |
| joelib.desc.types.ElectronegativityPauling | ||
public static final String |
DESC_KEY |
"Electronegativity_pauling" |
| joelib.desc.types.ElectrotopologicalState | ||
public static final double |
DEFAULT_DISTANCE_INFLUENCE |
2.0d |
public static final String |
DESC_KEY |
"Electrotopological_state_index" |
public static final String |
DISTANCE_INFLUENCE |
"DISTANCE_INFLUENCE" |
| joelib.desc.types.FractionRotatableBonds | ||
public static final String |
DESC_KEY |
"Fraction_of_rotatable_bonds" |
| joelib.desc.types.GeomDistanceMatrix | ||
public static final String |
DESC_KEY |
"Geometrical_distance_matrix" |
| joelib.desc.types.GeometricalDiameter | ||
public static final String |
DESC_KEY |
"Geometrical_diameter" |
| joelib.desc.types.GeometricalRadius | ||
public static final String |
DESC_KEY |
"Geometrical_radius" |
| joelib.desc.types.GeometricalShapeCoefficient | ||
public static final String |
DESC_KEY |
"Geometrical_shape_coefficient" |
| joelib.desc.types.GlobalTopologicalChargeIndex | ||
public static final String |
ATOM_PROPERTY |
"ATOM_PROPERTY" |
public static final String |
DESC_KEY |
"Global_topological_charge_index" |
| joelib.desc.types.GraphPotentials | ||
public static final String |
DESC_KEY |
"Graph_potentials" |
| joelib.desc.types.GraphShapeCoefficient | ||
public static final String |
DESC_KEY |
"Graph_shape_coefficient" |
| joelib.desc.types.HBA1 | ||
public static final String |
DEFAULT |
"[$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]" |
public static final String |
DESC_KEY |
"Number_of_HBA_1" |
| joelib.desc.types.HBA2 | ||
public static final String |
DEFAULT |
"[$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])]" |
public static final String |
DESC_KEY |
"Number_of_HBA_2" |
| joelib.desc.types.HBD1 | ||
public static final String |
DEFAULT |
"[!#6;!H0]" |
public static final String |
DESC_KEY |
"Number_of_HBD_1" |
| joelib.desc.types.HBD2 | ||
public static final String |
DEFAULT |
"[$([O;H1,-&!$(*-N=O)]),$([S;H1&X2,-&X1]),$([#7;H;!$(*(S(=O)=O)C(F)(F)F);!$(n1nnnc1);!$(n1nncn1)]),$([#7;-])]" |
public static final String |
DESC_KEY |
"Number_of_HBD_2" |
| joelib.desc.types.HeavyBonds | ||
public static final String |
DESC_KEY |
"Number_of_heavy_bonds" |
| joelib.desc.types.HeteroCycles | ||
public static final String |
DESC_KEY |
"Number_of_heterocycles" |
| joelib.desc.types.HydrophobicGroups | ||
public static final String |
DEFAULT |
"[C;!$(C-[!C]);!$(C-C-[!C]);!$(C=,#*);!$(C-C=,#*)]" |
public static final String |
DESC_KEY |
"Number_of_hydrophobic_groups" |
| joelib.desc.types.IntrinsicState | ||
public static final String |
DESC_KEY |
"Intrinsic_state" |
| joelib.desc.types.KierShape1 | ||
public static final String |
DESC_KEY |
"Kier_shape_1" |
| joelib.desc.types.KierShape2 | ||
public static final String |
DESC_KEY |
"Kier_shape_2" |
| joelib.desc.types.KierShape3 | ||
public static final String |
DESC_KEY |
"Kier_shape_3" |
| joelib.desc.types.LogP | ||
public static final String |
DESC_KEY |
"LogP" |
| joelib.desc.types.MolarRefractivity | ||
public static final String |
DESC_KEY |
"MolarRefractivity" |
| joelib.desc.types.MolecularWeight | ||
public static final String |
DESC_KEY |
"Molecular_weight" |
| joelib.desc.types.NO2Groups | ||
public static final String |
DEFAULT |
"[#7D3;$(N(~O)~O)]-*" |
public static final String |
DESC_KEY |
"Number_of_NO2_groups" |
| joelib.desc.types.NumberOfAtoms | ||
public static final String |
DESC_KEY |
"Number_of_atoms" |
| joelib.desc.types.NumberOfB | ||
public static final String |
DESC_KEY |
"Number_of_B_atoms" |
| joelib.desc.types.NumberOfBonds | ||
public static final String |
DESC_KEY |
"Number_of_bonds" |
| joelib.desc.types.NumberOfBr | ||
public static final String |
DESC_KEY |
"Number_of_Br_atoms" |
| joelib.desc.types.NumberOfC | ||
public static final String |
DESC_KEY |
"Number_of_C_atoms" |
| joelib.desc.types.NumberOfCl | ||
public static final String |
DESC_KEY |
"Number_of_Cl_atoms" |
| joelib.desc.types.NumberOfF | ||
public static final String |
DESC_KEY |
"Number_of_F_atoms" |
| joelib.desc.types.NumberOfHal | ||
public static final String |
DESC_KEY |
"Number_of_halogen_atoms" |
| joelib.desc.types.NumberOfI | ||
public static final String |
DESC_KEY |
"Number_of_I_atoms" |
| joelib.desc.types.NumberOfN | ||
public static final String |
DESC_KEY |
"Number_of_N_atoms" |
| joelib.desc.types.NumberOfO | ||
public static final String |
DESC_KEY |
"Number_of_O_atoms" |
| joelib.desc.types.NumberOfP | ||
public static final String |
DESC_KEY |
"Number_of_P_atoms" |
| joelib.desc.types.NumberOfS | ||
public static final String |
DESC_KEY |
"Number_of_S_atoms" |
| joelib.desc.types.OSOGroups | ||
public static final String |
DESC_KEY |
"Number_of_OSO_groups" |
| joelib.desc.types.PolarSurfaceArea | ||
public static final String |
DESC_KEY |
"PolarSurfaceArea" |
| joelib.desc.types.RadialDistributionFunction | ||
public static final String |
ATOM_PROPERTY |
"ATOM_PROPERTY" |
public static final String |
DESC_KEY |
"RDF" |
public static final String |
MAX_SPHERICAL_VOLUME |
"MAX_SPHERICAL_VOLUME" |
public static final String |
MIN_SPHERICAL_VOLUME |
"MIN_SPHERICAL_VOLUME" |
public static final String |
REMOVE_HYDROGENS |
"REMOVE_HYDROGENS" |
public static final String |
SMOOTHING_FACTOR |
"SMOOTHING_FACTOR" |
public static final String |
SPHERICAL_VOLUME_RESOLUTION |
"SPHERICAL_VOLUME_RESOLUTION" |
| joelib.desc.types.RotatableBonds | ||
public static final String |
DESC_KEY |
"Number_of_rotatable_bonds" |
| joelib.desc.types.SO2Groups | ||
public static final String |
DEFAULT |
"[#16D4;$(S(=O)(=O))]-*" |
public static final String |
DESC_KEY |
"Number_of_SO2_groups" |
| joelib.desc.types.SOGroups | ||
public static final String |
DEFAULT |
"[#16D2;$(S~O);!$(S(~O)~O)]-*" |
public static final String |
DESC_KEY |
"Number_of_SO_groups" |
| joelib.desc.types.SSKey3DS | ||
public static final String |
DESC_KEY |
"Pharmacophore_fingerprint_1" |
| joelib.desc.types.TopologicalDiameter | ||
public static final String |
DESC_KEY |
"Topological_diameter" |
| joelib.desc.types.TopologicalRadius | ||
public static final String |
DESC_KEY |
"Topological_radius" |
| joelib.desc.types.WeightedBurdenEigenvalues | ||
public static final String |
ATOM_PROPERTY1 |
"ATOM_PROPERTY1" |
public static final String |
ATOM_PROPERTY1_WEIGHT |
"ATOM_PROPERTY1_WEIGHT" |
public static final String |
ATOM_PROPERTY2 |
"ATOM_PROPERTY2" |
public static final String |
ATOM_PROPERTY2_WEIGHT |
"ATOM_PROPERTY2_WEIGHT" |
public static final String |
ATOM_PROPERTY3 |
"ATOM_PROPERTY3" |
public static final String |
ATOM_PROPERTY3_WEIGHT |
"ATOM_PROPERTY3_WEIGHT" |
public static final String |
ATOM_PROPERTY4 |
"ATOM_PROPERTY4" |
public static final String |
ATOM_PROPERTY4_WEIGHT |
"ATOM_PROPERTY4_WEIGHT" |
public static final String |
ATOM_PROPERTY5 |
"ATOM_PROPERTY5" |
public static final String |
ATOM_PROPERTY5_WEIGHT |
"ATOM_PROPERTY5_WEIGHT" |
public static final String |
ATOM_PROPERTY6 |
"ATOM_PROPERTY6" |
public static final String |
ATOM_PROPERTY6_WEIGHT |
"ATOM_PROPERTY6_WEIGHT" |
public static final String |
DESC_KEY |
"Weighted_burden_eigenvalues" |
| joelib.desc.types.WeightedBurdenModifiedEigenvalues | ||
public static final String |
ATOM_PROPERTY1 |
"ATOM_PROPERTY1" |
public static final String |
ATOM_PROPERTY1_WEIGHT |
"ATOM_PROPERTY1_WEIGHT" |
public static final String |
ATOM_PROPERTY2 |
"ATOM_PROPERTY2" |
public static final String |
ATOM_PROPERTY2_WEIGHT |
"ATOM_PROPERTY2_WEIGHT" |
public static final String |
ATOM_PROPERTY3 |
"ATOM_PROPERTY3" |
public static final String |
ATOM_PROPERTY3_WEIGHT |
"ATOM_PROPERTY3_WEIGHT" |
public static final String |
ATOM_PROPERTY4 |
"ATOM_PROPERTY4" |
public static final String |
ATOM_PROPERTY4_WEIGHT |
"ATOM_PROPERTY4_WEIGHT" |
public static final String |
ATOM_PROPERTY5 |
"ATOM_PROPERTY5" |
public static final String |
ATOM_PROPERTY5_WEIGHT |
"ATOM_PROPERTY5_WEIGHT" |
public static final String |
ATOM_PROPERTY6 |
"ATOM_PROPERTY6" |
public static final String |
ATOM_PROPERTY6_WEIGHT |
"ATOM_PROPERTY6_WEIGHT" |
public static final String |
DESC_KEY |
"Weighted_burden_modified_eigenvalues" |
| joelib.desc.types.ZagrebIndex1 | ||
public static final String |
DESC_KEY |
"Zagreb_group_index_1" |
| joelib.desc.types.ZagrebIndex2 | ||
public static final String |
DESC_KEY |
"Zagreb_group_index_2" |
| joelib.desc.types.atompair.TopologicalAtomPair | ||
public static final String |
ATOM_PROPERTIES |
"ATOM_PROPERTIES" |
public static final String |
DESC_KEY |
"Topological_atom_pair" |
| joelib.ext.* |
| joelib.ext.ExternalHelper | ||
public static final String |
OS_LINUX |
"linux" |
public static final String |
OS_SOLARIS |
"solaris" |
public static final String |
OS_WINDOWS |
"windows" |
| joelib.gui.* |
| joelib.gui.molviewer.java3d.graphics3D.RenderStyle | ||
public static final int |
BALL_AND_STICK |
2 |
public static final int |
CPK |
1 |
public static final int |
INVISIBLE |
0 |
public static final int |
NONE |
-1 |
public static final int |
STICK |
3 |
public static final int |
WIRE |
4 |
| joelib.gui.molviewer.java3d.molecule.ViewerBond | ||
public static final int |
ANY |
7 |
public static final int |
AROMATIC |
4 |
public static final int |
DASH |
6 |
public static final int |
DOUBLE |
2 |
public static final int |
SINGLE |
1 |
public static final int |
TRIPLE |
3 |
public static final int |
WEDGE |
5 |
| joelib.gui.molviewer.java3d.util.MolViewerEvent | ||
public static final int |
ATOM_PICKED |
1 |
public static final int |
BOND_PICKED |
2 |
public static final int |
REPLACE_MOLECULE |
0 |
| joelib.io.* |
| joelib.io.types.ChemicalMarkupLanguage | ||
public static final float |
CML_VERSION_1 |
1.0f |
public static final float |
CML_VERSION_2 |
2.0f |
public static final String |
DEFAULT_DELIMITER |
" " |
public static final int |
OUTPUT_ARRAY |
2 |
public static final String |
OUTPUT_ARRAY_S |
"array" |
public static final int |
OUTPUT_ATTRIBUTE_ARRAY |
3 |
public static final String |
OUTPUT_ATTRIBUTE_ARRAY_S |
"attributearray" |
public static final int |
OUTPUT_HUGE |
0 |
public static final String |
OUTPUT_HUGE_S |
"huge" |
public static final int |
OUTPUT_LARGE |
1 |
public static final String |
OUTPUT_LARGE_S |
"large" |
| joelib.io.types.ClearTextFormat | ||
public static final String |
ASYM_BOND_PROPERTY_INDEX |
"ASYM_BOND_PROPERTY_INDEX" |
| joelib.io.types.Matlab | ||
public static final int |
BALL_AND_STICK |
0 |
public static final int |
DEFAULT_OUTPUT_TYPE |
1 |
public static final int |
SPHERE |
1 |
public static final int |
STICK |
2 |
| joelib.io.types.POVRay | ||
public static final int |
BALL_AND_STICK |
0 |
public static final String |
BALL_AND_STICK_S |
"ball_and_stick" |
public static final int |
DEFAULT_OUTPUT_TYPE |
0 |
public static final int |
SPHERE |
1 |
public static final String |
SPHERE_S |
"sphere" |
public static final int |
STICK |
2 |
public static final String |
STICK_S |
"stick" |
| joelib.io.types.cml.CMLCoreModule | ||
public static final int |
ANGLE |
11 |
public static final int |
ARRAY |
25 |
public static final int |
ATOM |
15 |
public static final int |
ATOMARRAY |
16 |
public static final int |
BOND |
17 |
public static final int |
BOND_STEREO |
27 |
public static final int |
BONDARRAY |
18 |
public static final int |
COORDINATE2 |
9 |
public static final int |
COORDINATE3 |
10 |
public static final int |
CRYSTAL |
21 |
public static final int |
ELECTRON |
19 |
public static final int |
FEATURE |
23 |
public static final int |
FLOAT |
3 |
public static final int |
FLOATARRAY |
6 |
public static final int |
FLOATMATRIX |
8 |
public static final int |
INTEGER |
4 |
public static final int |
INTEGERARRAY |
7 |
public static final int |
LINK |
2 |
public static final int |
LIST |
13 |
public static final int |
MATRIX |
24 |
public static final int |
MOLECULE |
14 |
public static final int |
NAME |
28 |
public static final int |
REACTION |
20 |
public static final int |
SCALAR |
26 |
public static final int |
SEQUENCE |
22 |
public static final int |
STRING |
1 |
public static final int |
STRINGARRAY |
5 |
public static final int |
SYMMETRY |
29 |
public static final int |
TORSION |
12 |
public static final int |
UNKNOWN |
-1 |
| joelib.io.types.cml.elements.ArrayCML | ||
public static final String |
DATA_TYPE |
"dataType" |
public static final String |
DELIMITER |
"delimiter" |
public static final String |
ERROR_BASIS |
"errorBasis" |
public static final String |
ERROR_VALUES |
"errorValues" |
public static final String |
MAX_VALUES |
"maxValues" |
public static final String |
MIN_VALUES |
"minValues" |
public static final String |
SIZE |
"size" |
public static final String |
TITLE |
"title" |
public static final String |
UNITS |
"units" |
| joelib.io.types.cml.elements.MatrixCML | ||
public static final String |
COLUMNS |
"columns" |
public static final String |
DATA_TYPE |
"dataType" |
public static final String |
DELIMITER |
"delimiter" |
public static final String |
DICT_REF |
"dictRef" |
public static final String |
MATRIX_TYPE |
"matrixType" |
public static final String |
ROWS |
"rows" |
public static final String |
TITLE |
"title" |
public static final String |
UNITS |
"units" |
| joelib.io.types.cml.elements.ScalarCML | ||
public static final String |
DATA_TYPE |
"dataType" |
public static final String |
DICT_REF |
"dictRef" |
public static final String |
ERROR_BASIS |
"errorBasis" |
public static final String |
ERROR_VALUE |
"errorValue" |
public static final String |
MAX |
"max" |
public static final String |
MIN |
"min" |
public static final String |
TITLE |
"title" |
public static final String |
UNITS |
"units" |
| joelib.jcamp.* |
| joelib.jcamp.JCAMPDataBlock | ||
public static final int |
CS_TYPE |
1 |
public static final int |
DX_TYPE |
2 |
public static final String |
labelEndString |
"=" |
public static final String |
labelStartString |
"##" |
public static final int |
LINK_TYPE |
0 |
public static final int |
UNDEFINED_TYPE |
-1 |
| joelib.jcamp.JCAMPParser | ||
public static final int |
CHEMICAL_STRUCTURE |
20 |
public static final int |
DATA_TYPE_PEAKS |
1 |
public static final int |
DATA_TYPE_SPECTRUM |
1 |
public static final int |
LINK |
70 |
public static final int |
PEAK_ASSIGNMENTS |
50 |
public static final int |
PEAK_TABLE |
40 |
public static final int |
RADATA |
60 |
public static final int |
XYDATA_X_YY |
10 |
public static final int |
XYPAIRS |
0 |
public static final int |
XYPOINTS |
30 |
| joelib.math.* |
| joelib.math.Matrix3x3 | ||
public static final double |
DEG_TO_RAD |
0.017453292519943295d |
public static final double |
RAD_TO_DEG |
57.29577951308232d |
| joelib.math.XYZVector | ||
public static final double |
DEG_TO_RAD |
0.017453292519943295d |
public static final double |
RAD_TO_DEG |
57.29577951308232d |
| joelib.math.symmetry.SymCoordinates | ||
public static final int |
DIMENSION |
3 |
| joelib.math.symmetry.Symmetry | ||
public static final double |
GRADIENT_STEP_DEFAULT |
1.0E-7d |
public static final int |
MAX_AXIS_ORDER_DEFAULT |
20 |
public static final int |
MAX_OPT_CYCLES_DEFAULT |
200 |
public static final double |
MAXOPT_STEP_DEFAULT |
0.5d |
public static final double |
MINOPT_STEP_DEFAULT |
1.0E-7d |
public static final int |
OPT_CHANGE_HITS_DEFAULT |
5 |
public static final double |
OPTCHANGE_THRESHOLD_DEFAULT |
1.0E-10d |
public static final double |
TOLERANCE_FINAL_DEFAULT |
0.05d |
public static final double |
TOLERANCE_PRIMARY_DEFAULT |
0.05d |
public static final double |
TOLERANCE_SAME_DEFAULT |
0.0010d |
| joelib.molecule.* |
| joelib.molecule.JOEAtom | ||
public static final int |
FREE_ELECTRONS_NOT_DEF |
-2147483648 |
public static final int |
JOE_3RING_ATOM |
4 |
public static final int |
JOE_4RING_ATOM |
2 |
public static final int |
JOE_ACCEPTOR_ATOM |
256 |
public static final int |
JOE_ACSTEREO_ATOM |
64 |
public static final int |
JOE_AROMATIC_ATOM |
8 |
public static final int |
JOE_CHIRAL_ATOM |
512 |
public static final int |
JOE_CSTEREO_ATOM |
32 |
public static final int |
JOE_DONOR_ATOM |
128 |
public static final int |
JOE_RING_ATOM |
16 |
| joelib.molecule.JOEBond | ||
public static final int |
JOE_AROMATIC_BOND |
2 |
public static final int |
JOE_AROMATIC_BOND_ORDER |
5 |
public static final int |
JOE_CLOSURE_BOND |
1024 |
public static final int |
JOE_HASH_BOND |
8 |
public static final int |
JOE_KDOUBLE_BOND |
256 |
public static final int |
JOE_KSINGLE_BOND |
128 |
public static final int |
JOE_KTRIPLE_BOND |
512 |
public static final int |
JOE_RING_BOND |
16 |
public static final int |
JOE_TORDOWN_BOND |
64 |
public static final int |
JOE_TORUP_BOND |
32 |
public static final int |
JOE_WEDGE_BOND |
4 |
| joelib.molecule.JOEMol | ||
public static final int |
JOE_AROM_CORRECTED_MOL |
16384 |
public static final int |
JOE_AROMATIC_MOL |
8 |
public static final int |
JOE_ATOMTYPES_MOL |
16 |
public static final int |
JOE_CHAINS_MOL |
32768 |
public static final int |
JOE_CHIRALITY_MOL |
32 |
public static final int |
JOE_CLOSURE_MOL |
2048 |
public static final int |
JOE_CURRENT_CONFORMER |
65536 |
public static final int |
JOE_H_ADDED_MOL |
4096 |
public static final int |
JOE_HYBRID_MOL |
256 |
public static final int |
JOE_IMPVAL_MOL |
512 |
public static final int |
JOE_KEKULE_MOL |
1024 |
public static final int |
JOE_PCHARGE_MOL |
64 |
public static final int |
JOE_PH_CORRECTED_MOL |
8192 |
public static final int |
JOE_RINGFLAGS_MOL |
4 |
public static final int |
JOE_SSSR_MOL |
2 |
| joelib.molecule.charge.GasteigerMarsili | ||
public static final String |
DESC_KEY |
"Gasteiger_Marsili" |
| joelib.process.* |
| joelib.process.filter.NativeValueFilter | ||
public static final int |
EQUAL |
2 |
public static final int |
GREATER |
4 |
public static final int |
GREATER_EQUAL |
3 |
public static final int |
NOT_EQUAL |
5 |
public static final int |
SMALLER |
1 |
public static final int |
SMALLER_EQUAL |
0 |
| joelib.process.filter.SMARTSFilter | ||
public static final int |
EQUAL |
2 |
public static final int |
GREATER |
4 |
public static final int |
GREATER_EQUAL |
3 |
public static final int |
NOT_EQUAL |
5 |
public static final int |
SMALLER |
1 |
public static final int |
SMALLER_EQUAL |
0 |
| joelib.process.types.AtomPropertyMatrix | ||
public static final String |
ATOM_PROPERTIES |
"ATOM_PROPERTIES" |
public static final String |
ATOM_PROPERTY_MATRIX |
"Atom_property_matrix" |
public static final String |
INCREMENTAL_SPHERES |
"INCREMENTAL_SPHERES" |
public static final String |
SPHERES2CALCULATE |
"SPHERES2CALCULATE" |
| joelib.process.types.DescSelectionWriter | ||
public static final int |
DESCRIPTORS |
0 |
public static final int |
MOL_AND_DESCRIPTORS |
1 |
| joelib.smarts.* |
| joelib.smarts.ParseSmart | ||
public static final int |
ATOMEXPRPOOL |
1 |
public static final int |
BONDEXPRPOOL |
1 |
public static final int |
BUFMAX |
1024 |
public static final int |
ELEMMAX |
104 |
public static final int |
IFALSE |
0 |
public static final int |
ITRUE |
1 |
public static final int |
OE_EVAL_STACKSIZE |
40 |
| joelib.smarts.Pattern | ||
public static final int |
ATOMPOOL |
1 |
public static final int |
BONDPOOL |
1 |
| joelib.smarts.Patty | ||
public static final int |
TYPE_UNKNOWN |
-1 |
| joelib.smarts.atomexpr.AtomExpr | ||
public static final int |
AE_ANDHI |
4 |
public static final int |
AE_ANDLO |
6 |
public static final int |
AE_LEAF |
1 |
public static final int |
AE_NOT |
3 |
public static final int |
AE_OR |
5 |
public static final int |
AE_RECUR |
2 |
public static final int |
AL_ANTICLOCKWISE |
2 |
public static final int |
AL_AROM |
3 |
public static final int |
AL_CHIRAL |
15 |
public static final int |
AL_CLOCKWISE |
1 |
public static final int |
AL_CONNECT |
9 |
public static final int |
AL_CONST |
1 |
public static final int |
AL_DEGREE |
10 |
public static final int |
AL_ELECTRONEGATIVE |
18 |
public static final int |
AL_ELEM |
4 |
public static final int |
AL_GROUP |
17 |
public static final int |
AL_HCOUNT |
5 |
public static final int |
AL_HEAVY_CONNECT |
6 |
public static final int |
AL_HYB |
16 |
public static final int |
AL_IMPLICIT |
11 |
public static final int |
AL_MASS |
2 |
public static final int |
AL_NEGATIVE |
7 |
public static final int |
AL_POSITIVE |
8 |
public static final int |
AL_RINGS |
12 |
public static final int |
AL_SIZE |
13 |
public static final int |
AL_VALENCE |
14 |
public static final boolean |
OLDCODE |
false |
| joelib.smarts.bondexpr.BondExpr | ||
public static final int |
BE_ANDHI |
2 |
public static final int |
BE_ANDLO |
3 |
public static final int |
BE_LEAF |
1 |
public static final int |
BE_NOT |
4 |
public static final int |
BE_OR |
5 |
public static final int |
BF_NONRINGDOUBLE |
8 |
public static final int |
BF_NONRINGDOWN |
2 |
public static final int |
BF_NONRINGTRIPLE |
16 |
public static final int |
BF_NONRINGUNSPEC |
1 |
public static final int |
BF_NONRINGUP |
4 |
public static final int |
BF_RINGAROM |
256 |
public static final int |
BF_RINGDOUBLE |
512 |
public static final int |
BF_RINGDOWN |
64 |
public static final int |
BF_RINGTRIPLE |
1024 |
public static final int |
BF_RINGUNSPEC |
32 |
public static final int |
BF_RINGUP |
128 |
public static final int |
BL_CONST |
1 |
public static final int |
BL_TYPE |
2 |
public static final int |
BS_ALL |
2047 |
public static final int |
BS_AROM |
256 |
public static final int |
BS_DEFAULT |
487 |
public static final int |
BS_DOUBLE |
520 |
public static final int |
BS_DOWN |
66 |
public static final int |
BS_DOWNUNSPEC |
99 |
public static final int |
BS_RING |
2016 |
public static final int |
BS_SINGLE |
231 |
public static final int |
BS_TRIPLE |
1040 |
public static final int |
BS_UP |
132 |
public static final int |
BS_UPUNSPEC |
165 |
public static final int |
BT_AROM |
4 |
public static final int |
BT_DOUBLE |
2 |
public static final int |
BT_DOWN |
6 |
public static final int |
BT_DOWNUNSPEC |
8 |
public static final int |
BT_RING |
9 |
public static final int |
BT_SINGLE |
1 |
public static final int |
BT_TRIPLE |
3 |
public static final int |
BT_UP |
5 |
public static final int |
BT_UPUNSPEC |
7 |
public static final boolean |
FOO |
false |
public static final boolean |
ORIG |
false |
| joelib.smiles.* |
| joelib.smiles.JOESmilesParser | ||
public static final char |
DOWN_BOND_FLAG |
92 |
public static final char |
UP_BOND_FLAG |
47 |
| joelib.test.* |
| joelib.test.Convert | ||
public static final int |
CONTINUE |
0 |
public static final int |
STOP |
1 |
public static final int |
STOP_USAGE |
2 |
| joelib.test.ConvertSkip | ||
public static final int |
CONTINUE |
0 |
public static final int |
STOP |
1 |
public static final int |
STOP_USAGE |
2 |
| joelib.test.DescriptorCalculation | ||
public static final int |
CONTINUE |
0 |
public static final int |
STOP |
1 |
public static final int |
STOP_USAGE |
2 |
| joelib.test.DescriptorStatistic | ||
public static final int |
CONTINUE |
0 |
public static final int |
STOP |
1 |
public static final int |
STOP_USAGE |
2 |
| joelib.util.* |
| joelib.util.IsomerismDetection | ||
public static final int |
CIS_ISOMERISM |
1 |
public static final int |
CISTRANS_ISOMERISM_UNDEFINED |
0 |
public static final int |
E_ISOMERISM |
2 |
public static final int |
EZ_ISOMERISM_UNDEFINED |
0 |
public static final int |
TRANS_ISOMERISM |
2 |
public static final int |
Z_ISOMERISM |
1 |
| joelib.util.JHM | ||
public static final double |
DEG_TO_RAD |
0.017453292519943295d |
public static final double |
RAD_TO_DEG |
57.29577951308232d |
| joelib.util.JOEHelper | ||
public static final int |
BUFF_SIZE |
1024 |
public static final String |
CONTACT_E_MAIL |
"wegnerj@informatik.uni-tuebingen.de" |
|
JOELib Computational Chemistry Package Comments and Questions? mail to J.K.Wegner |
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