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JOELib
Computational Chemistry Package

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A

a - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field
a - Variable in class joelib.util.types.AtomIntInt: Description of the Field
a1 - Variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: From and to atoms, respectively
a2 - Variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: From and to atoms, respectively
aalloc - Variable in class joelib.smarts.Pattern: Description of the Field
accept(JOEMol) - Method in class joelib.process.filter.SMARTSFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.SelectionFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.RuleOf5Filter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.ORFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.NOTFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.NativeValueFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.HasDataFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.HasAllDataFilter: Description of the Method
accept(JOEMol) - Method in interface joelib.process.filter.Filter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.DescriptorFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.ANDFilter: Description of the Method
acceptedProperties() - Method in class joelib.algo.DFS
acceptedProperties() - Method in class joelib.algo.BFS
acceptedProperties() - Method in class joelib.desc.SMARTSCounter
acceptedProperties() - Method in class joelib.desc.SimpleIntDesc
acceptedProperties() - Method in class joelib.desc.SimpleDoubleDesc
acceptedProperties() - Method in class joelib.desc.AtomsCounter
acceptedProperties() - Method in class joelib.desc.types.SSKey3DS
acceptedProperties() - Method in class joelib.desc.types.RotatableBonds
acceptedProperties() - Method in class joelib.desc.types.HeteroCycles
acceptedProperties() - Method in class joelib.desc.types.HeavyBonds
acceptedProperties() - Method in class joelib.desc.types.GraphPotentials
acceptedProperties() - Method in class joelib.desc.types.GeomDistanceMatrix
acceptedProperties() - Method in class joelib.desc.types.FractionRotatableBonds
acceptedProperties() - Method in class joelib.desc.types.ElectronegativityPauling
acceptedProperties() - Method in class joelib.desc.types.ElectronAffinity
acceptedProperties() - Method in class joelib.desc.types.DistanceMatrix
acceptedProperties() - Method in class joelib.desc.types.Autocorrelation
acceptedProperties() - Method in class joelib.desc.types.AtomVanDerWaalsVolume
acceptedProperties() - Method in class joelib.desc.types.AtomValence
acceptedProperties() - Method in class joelib.desc.types.AtomMass
acceptedProperties() - Method in class joelib.desc.types.AromaticBonds
acceptedProperties() - Method in class joelib.ext.SimpleExternalProcess
acceptedProperties() - Method in class joelib.molecule.charge.GasteigerMarsili
acceptedProperties() - Method in class joelib.process.SimpleProcess
acceptedProperties() - Method in class joelib.process.ProcessPipe
acceptedProperties() - Method in class joelib.process.types.MoleculeFileDeletion
acceptedProperties() - Method in class joelib.process.types.MoleculeFileCreation
acceptedProperties() - Method in class joelib.process.types.CreateFileName: Description of the Method
acceptedProperties() - Method in interface joelib.util.PropertyAcceptor
acceptObjects() - Method in class joelib.io.types.cml.MoleculeFileCDO: Procedure required by the CDOInterface.
AcidicGroups - class joelib.desc.types.AcidicGroups.: Number of acidic groups.
AcidicGroups() - Constructor for class joelib.desc.types.AcidicGroups
acount - Variable in class joelib.smarts.Pattern: Description of the Field
actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerUsage: Close the dialog on a button event
actual() - Method in class joelib.util.iterator.VectorIterator: Returns the actual Object .
actual() - Method in class joelib.util.iterator.NbrAtomIterator: Description of the Method
actualBond() - Method in class joelib.util.iterator.NbrAtomIterator: Description of the Method
actualIndex() - Method in class joelib.util.iterator.VectorIterator: Returns the index number ot the sctual Object .
actualName() - Method in class joelib.util.iterator.NativeValueIterator
add(double) - Method in class wsi.ra.tool.ArrayStatistic: Adds a value to the observed values
add(double) - Method in class wsi.ra.tool.ArrayBinning: Adds a value to the observed values
add(double, double) - Method in class wsi.ra.tool.ArrayBinning: Adds a value that has been seen n times to the observed values
add(double, int) - Method in class wsi.ra.tool.ArrayStatistic: Adds a value that has been seen n times to the observed values
add(GeoVector3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: rotat the vector by a factor add a vector to this vector
add(IntInt) - Method in class joelib.data.JOERgroupData: Add new atom-Rgroup entry.
add(int, Object) - Method in class wsi.ra.tool.SortedVector: Inserts the specified element at the specified position in this Vector.
add(JOECoordTrans) - Method in class joelib.math.JOECoordTrans: Combine two transformations.
add(JOERing) - Method in class joelib.ring.JOERingData: Description of the Method
add(Object) - Method in class wsi.ra.tool.SortedVector: Appends the specified element to the end of this Vector.
add(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
add(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
add(XYZVector, XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
addAll(Collection) - Method in class wsi.ra.tool.SortedVector: Appends all of the elements in the specified Collection to the end of this Vector, in the order that they are returned by the specified Collection's Iterator.
addAll(int, Collection) - Method in class wsi.ra.tool.SortedVector: Inserts all of the elements in in the specified Collection into this Vector at the specified position.
addAtom(JOEAtom) - Method in class joelib.molecule.JOEResidue
addAtom(JOEAtom) - Method in class joelib.molecule.JOEMol: Adds (cloned) atom to the JOEMol.
addAtom(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Add an atom to this molecule
addAtomNode(AtomNode) - Method in class joelib.gui.molviewer.java3d.graphics3D.MoleculeNode: Adds a feature to the AtomNode attribute of the MoleculeNode object
addBond(int, int, int) - Method in class joelib.molecule.JOEMol: Adds a bond to the JOEMol.
addBond(int, int, int, int) - Method in class joelib.molecule.JOEMol: Adds a bond to the JOEMol.
addBond(int, int, int, int, int) - Method in class joelib.molecule.JOEMol: Adds a bond to the JOEMol.
addBond(JOEBond) - Method in class joelib.molecule.JOEMol: Adds (cloned) bond to the JOEMol.
addBond(JOEBond) - Method in class joelib.molecule.JOEAtom: Adds a bond to this atom.
addBond(ViewerBond) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Add a bond to this molecule
addBondNode(BondNode) - Method in class joelib.gui.molviewer.java3d.graphics3D.MoleculeNode: Adds a feature to the BondNode attribute of the MoleculeNode object
addConformer(double[]) - Method in class joelib.molecule.JOEMol: Adds conformer coordinates to this molecule.
addCSEntry(JCAMPDataBlock) - Method in class joelib.jcamp.JCAMPData
addData(JOEGenericData) - Method in class joelib.molecule.JOEMol: Adds a JOEGenericData object to this molecule but don't overwrite existing data elements with the same name, if they exists already.
addData(JOEGenericData, boolean) - Method in class joelib.molecule.JOEMol: Adds a JOEGenericData object to this molecule.
addData(JOEGenericData, boolean) - Method in class joelib.molecule.GenericDataHolder: Adds a feature to the Data attribute of the GenericDataHolder object
addDXEntry(JCAMPDataBlock) - Method in class joelib.jcamp.JCAMPData
addElement(Object) - Method in class wsi.ra.tool.SortedVector: Adds the specified component to the end of this vector, increasing its size by one.
addHydrogens() - Method in class joelib.molecule.JOEMol: Adds hydrogens atoms to this molecule.
addHydrogens(boolean) - Method in class joelib.molecule.JOEMol: Adds hydrogens atoms to this molecule.
addHydrogens(boolean, boolean) - Method in class joelib.molecule.JOEMol: Adds hydrogens atoms to this molecule.
addHydrogens(boolean, boolean, boolean) - Method in class joelib.molecule.JOEMol: Adds hydrogens atoms to this molecule.
addHydrogens(JOEAtom) - Method in class joelib.molecule.JOEMol: Adds hydrogens atoms to the given atom.
adding(double[]) - Method in class joelib.math.XYZVector: Description of the Method
adding(JOECoordTrans) - Method in class joelib.math.JOECoordTrans: Changes this transform to the orginal transform followed by an additional transform.
adding(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
addLinkEntry(JCAMPDataBlock) - Method in class joelib.jcamp.JCAMPData
addMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Adds a feature to the Molecule attribute of the ViewerFrame object
addMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.Viewer: Adds a feature to the Molecule attribute of the Viewer object
addMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene: Adds a feature to the Molecule attribute of the MolecularScene object
addMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.graphics3D.JPanel3D: Adds a feature to the Molecule attribute of the Panel3D object
addObject(String, Object) - Method in class joelib.gui.molviewer.java3d.util.CentralLookup: Adds a feature to the Object attribute of the CentralLookup object
addPolarHydrogens() - Method in class joelib.molecule.JOEMol: Add polar hydrogens to molecule.
addProcess(JOEProcess) - Method in class joelib.process.ProcessPipe
addProcess(JOEProcess, Filter) - Method in class joelib.process.ProcessPipe
addProcess(JOEProcess, Filter, Hashtable) - Method in class joelib.process.ProcessPipe
addProcess(JOEProcess, Hashtable) - Method in class joelib.process.ProcessPipe
addResidue(JOEResidue) - Method in class joelib.molecule.JOEMol: Adds residue information to this molecule.
addRingFromClosure(JOEMol, JOEBond, int) - Method in class joelib.ring.JOERingSearch: Adds a feature to the RingFromClosure attribute of the JOERingSearch object
addRule(JOESmartsPattern, String) - Method in class joelib.smarts.Patty: Adds a new PATTY rule.
addRule(String, String) - Method in class joelib.smarts.Patty: Adds a new PATTY rule.
addRules(Vector) - Method in class joelib.smarts.Patty: Adds a new rules to the pattern typer.
addStringRule(String) - Method in class joelib.smarts.Patty: Adds a new rule to the pattern typer.
AE_ANDHI - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AE_ANDLO - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AE_LEAF - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AE_NOT - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AE_OR - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AE_RECUR - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_ANTICLOCKWISE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_AROM - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_CHIRAL - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_CLOCKWISE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_CONNECT - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_CONST - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_DEGREE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Degree of an atom (including explicit H), in SMARTS: D.
AL_ELECTRONEGATIVE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_ELEM - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_GROUP - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_HCOUNT - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_HEAVY_CONNECT - Static variable in class joelib.smarts.atomexpr.AtomExpr: Degree of an atom regarding only heavy atoms, in SMARTS: Q.
AL_HYB - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_IMPLICIT - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_MASS - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_NEGATIVE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_POSITIVE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_RINGS - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_SIZE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_VALENCE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
align(JOEAtom, JOEAtom, XYZVector, XYZVector) - Method in class joelib.molecule.JOEMol: Aligns atom a1 on p1 and atom a2 along p1->p2 vector.
AliphaticOHGroups - class joelib.desc.types.AliphaticOHGroups.: Number of aliphatic hydroxy groups.
AliphaticOHGroups() - Constructor for class joelib.desc.types.AliphaticOHGroups
ALL_DESCRIPTORS - Static variable in class joelib.desc.data.MolDescCounter: Description of the Field
allocAtomExpr(int) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
allocBondExpr(int) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
allocPattern() - Static method in class joelib.smarts.Pattern: Description of the Method
analyseDataset(String, GroupContributions) - Static method in class joelib.test.GroupContributionTest
and(BitSet14) - Method in class joelib.util.BitSet14: Performs a logical AND of this target bit set with the argument bit set.
and(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
and(JOEBitVec, JOEBitVec) - Static method in class joelib.util.JOEBitVec: Description of the Method
andAtomExpr(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
andAtomExprLeaf(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
andCount(BitSet14) - Method in class joelib.util.JOEBitVec: Returns the number of bits which are set in this BitSet14 AND the BitSet14 b.
ANDFilter - class joelib.process.filter.ANDFilter.: Molecule process filter AND condition.
ANDFilter() - Constructor for class joelib.process.filter.ANDFilter: Constructor for the DescriptorFilter object
ANDFilter(Filter, Filter) - Constructor for class joelib.process.filter.ANDFilter: Constructor for the DescriptorFilter object
andNot(BitSet14) - Method in class joelib.util.BitSet14: Clears all of the bits in this BitSet14 whose corresponding bit is set in the specified BitSet14.
andSet(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
Angle - class joelib.gui.molviewer.java3d.math.geometry.Angle.: A class that provides mathematical definition of geometric angle
Angle() - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Angle: default constructor: value is 0.0;
Angle(Angle) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Angle: copy constructor
Angle(double) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Angle: constructor
Angle(double, boolean) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Angle: full constructor
angle(Point3D, Point3D, Point3D) - Static method in class joelib.gui.molviewer.java3d.math.geometry.Geometry: calculate angle among three points in 3D space note: calling Point3D.distSquare() is more efficient than Point3D.distance().
angle(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector
angleWith(Point3D, Point3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: calculate angle among three points in 3D space note: calling distSquare() is more efficient than distance().
ANY - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Any bond type
append(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtoms: Append an atom to the end of vector
append(ViewerBond) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBonds: Append a bond to the end of vector
apply(JOEMol) - Method in class joelib.data.JOEChemTransformation: Description of the Method
APropDoubleArrResult - class joelib.desc.result.APropDoubleArrResult.: Atom representation.
APropDoubleArrResult() - Constructor for class joelib.desc.result.APropDoubleArrResult: Constructor for the BFSResult object
APropDoubleResult - class joelib.desc.result.APropDoubleResult.: Double value descriptor which was calculated by using an atom property (AtomProperties).
APropDoubleResult() - Constructor for class joelib.desc.result.APropDoubleResult: Constructor for the IntResult object
APropIntResult - class joelib.desc.result.APropIntResult.: Atom representation.
APropIntResult() - Constructor for class joelib.desc.result.APropIntResult: Constructor for the IntResult object
arg - Variable in class joelib.smarts.atomexpr.MonAtomExpr: Description of the Field
arg - Variable in class joelib.smarts.bondexpr.MonBondExpr: Description of the Field
AROMATIC - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Aromatic bond type
AromaticBonds - class joelib.desc.types.AromaticBonds.: Number of aromatic bonds.
AromaticBonds() - Constructor for class joelib.desc.types.AromaticBonds: Constructor for the KierShape1 object
AromaticOHGroups - class joelib.desc.types.AromaticOHGroups.: Number of aromatic hydroxy groups.
AromaticOHGroups() - Constructor for class joelib.desc.types.AromaticOHGroups
aromflag - Variable in class joelib.molecule.Element: Description of the Field
ArrayBinning - class wsi.ra.tool.ArrayBinning.: A class to store simple binning statistics
ArrayBinning(int, ArrayStatistic) - Constructor for class wsi.ra.tool.ArrayBinning: Constructor for the ArrayBinning object
ArrayHelper - class joelib.util.ArrayHelper.: Array helper methods for writing and loading arrays.
arrayStat - Variable in class wsi.ra.tool.ArrayBinning: Description of the Field
ArrayStatistic - class wsi.ra.tool.ArrayStatistic.: A class to store simple statistics
ArrayStatistic() - Constructor for class wsi.ra.tool.ArrayStatistic
ArrayStatistic(int, double, double, double, double, double, double) - Constructor for class wsi.ra.tool.ArrayStatistic
assignAromaticFlags(JOEMol) - Method in class joelib.data.JOEAromaticTyper: Description of the Method
assignBonds(JOEMol, JOEBitVec) - Method in class joelib.data.JOEResidueData
assignCisTrans(JOESmiNode) - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
assignHyb(JOEMol) - Method in class joelib.data.JOEAtomTyper: Description of the Method
assignImplicitValence(JOEMol) - Method in class joelib.data.JOEAtomTyper: Description of the Method
assignPartialCharges(JOEMol) - Method in class joelib.molecule.charge.JOEGastChrg: Description of the Method
assignSeedPartialCharge(JOEMol) - Method in class joelib.data.JOEPhModel: Description of the Method
assignTypes(JOEMol) - Method in class joelib.data.JOEAtomTyper: Description of the Method
assignTypes(JOEMol) - Method in class joelib.smarts.Patty: Assigns identifier's to the first matching atom in the SMARTS pattern.
assignTypes(JOEMol, int[]) - Method in class joelib.smarts.Patty: Assigns identifier's to the first matching atom in the SMARTS pattern.
assignTypes2All(JOEMol) - Method in class joelib.smarts.Patty: Assigns identifier's to all matching atoms in the SMARTS pattern.
assignTypes2All(JOEMol, int[]) - Method in class joelib.smarts.Patty: Assigns identifier's to all matching atoms in the SMARTS pattern.
assignTypes2Groups(JOEMol) - Method in class joelib.smarts.Patty: Assigns identifier's to all matching atoms in the SMARTS pattern and returns all matching lists.
assignTypes2Groups(JOEMol, int[], Vector) - Method in class joelib.smarts.Patty: Assigns identifier's to all matching atoms in the SMARTS pattern and returns all matching lists.
ASYM_BOND_PROPERTY_INDEX - Static variable in class joelib.io.types.ClearTextFormat: Data element for storing the access information for the asymmetric bond properties.
atom - Variable in class joelib.smarts.Pattern: Description of the Field
atom - Variable in class joelib.util.types.StackType: Description of the Field
atom - Variable in class joelib.util.types.AtomZPos: Description of the Field
atom - Variable in class joelib.util.types.AtomHCount: Description of the Field
ATOM_NUMBERS - Static variable in class joelib.desc.AtomsCounter
ATOM_PROPERTY - Static variable in class joelib.desc.result.AtomDynamicResult
ATOM_PROPERTY - Static variable in class joelib.desc.types.Autocorrelation
ATOM_PROPERTY - Static variable in class joelib.desc.types.AtomValence
AtomArrayInt - class joelib.util.types.AtomArrayInt.: Atom array and integer value.
AtomArrayInt() - Constructor for class joelib.util.types.AtomArrayInt
AtomAtomProperties - interface joelib.molecule.types.AtomAtomProperties.: Interface to access atom-atom properties.
atomContributions - Variable in class joelib.algo.contribution.GroupContributions
AtomDouble - class joelib.algo.morgan.AtomDouble.: Helper class for resolving renumbering ties.
AtomDouble() - Constructor for class joelib.algo.morgan.AtomDouble: Constructor for the IntInt object
AtomDouble(int, double) - Constructor for class joelib.algo.morgan.AtomDouble: Constructor for the IntInt object
AtomDoubleComparator - class joelib.algo.morgan.AtomDoubleComparator.: Comparator for resolving renumbering ties..
AtomDoubleComparator() - Constructor for class joelib.algo.morgan.AtomDoubleComparator: Initializes the RingSizeComparator-Comparator.
AtomDoubleParent - class joelib.algo.morgan.AtomDoubleParent.: Helper class for resolving renumbering ties.
AtomDoubleParent() - Constructor for class joelib.algo.morgan.AtomDoubleParent: Constructor for the IntInt object
AtomDoubleParent(int, double, int, boolean) - Constructor for class joelib.algo.morgan.AtomDoubleParent: Constructor for the IntInt object
AtomDoubleResult - class joelib.desc.result.AtomDoubleResult.: Double results of atom properties.
AtomDoubleResult() - Constructor for class joelib.desc.result.AtomDoubleResult: Constructor for the DoubleResult object
AtomDynamicResult - class joelib.desc.result.AtomDynamicResult.: Dynamic results of atom properties.
AtomDynamicResult() - Constructor for class joelib.desc.result.AtomDynamicResult: Constructor for the DoubleResult object
AtomExpr - class joelib.smarts.atomexpr.AtomExpr.: Atom expression in SMARTS substructure search.
AtomExpr() - Constructor for class joelib.smarts.atomexpr.AtomExpr: Constructor for the AtomExpr object
AtomExpr(int) - Constructor for class joelib.smarts.atomexpr.AtomExpr: Constructor for the AtomExpr object
atomExprConflict(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
atomExprImplied(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
atomExprImplies(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
ATOMEXPRPOOL - Static variable in class joelib.smarts.ParseSmart: Description of the Field
AtomHCount - class joelib.util.types.AtomHCount.: Atom and number of hydrogen atoms.
AtomHCount(JOEAtom, int) - Constructor for class joelib.util.types.AtomHCount: Constructor for the AtomHCount object
atomIdx - Variable in class joelib.algo.morgan.AtomDoubleParent: Description of the Field
atomIdx - Variable in class joelib.algo.morgan.AtomDouble: Description of the Field
AtomIntInt - class joelib.util.types.AtomIntInt.: Atom and IntInt.
AtomIntInt(JOEAtom, IntInt) - Constructor for class joelib.util.types.AtomIntInt: Constructor for the AtomIntInt object
AtomIntResult - class joelib.desc.result.AtomIntResult.: Integer results of atom properties.
AtomIntResult() - Constructor for class joelib.desc.result.AtomIntResult: Constructor for the DoubleResult object
AtomIterator - class joelib.util.iterator.AtomIterator.: Gets an iterator over all atoms in a molecule.
atomIterator() - Method in class joelib.molecule.JOEResidue: Gets an iterator over all atoms in this residue.
atomIterator() - Method in class joelib.molecule.JOEMol: Gets an iterator over all atoms in this molecule.
AtomIterator(Vector) - Constructor for class joelib.util.iterator.AtomIterator: Constructor for the AtomIterator object
atomLeafConflict(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
atomLeafImplies(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
AtomMass - class joelib.desc.types.AtomMass.: Atom mass.
AtomMass() - Constructor for class joelib.desc.types.AtomMass: Constructor for the KierShape1 object
AtomNode - class joelib.gui.molviewer.java3d.graphics3D.AtomNode.: Description of the Class
ATOMPOOL - Static variable in class joelib.smarts.Pattern: Description of the Field
AtomProperties - interface joelib.molecule.types.AtomProperties.: Interface to access atom properties.
atomProperty - Variable in class joelib.desc.result.APropIntResult: Description of the Field
atomProperty - Variable in class joelib.desc.result.APropDoubleResult: Description of the Field
atomProperty - Variable in class joelib.desc.result.APropDoubleArrResult: Description of the Field
atoms - Variable in class joelib.util.types.AtomArrayInt: Description of the Field
AtomsCounter - class joelib.desc.AtomsCounter.: Abstract descriptor class for counting the number of atoms.
AtomsCounter() - Constructor for class joelib.desc.AtomsCounter: Constructor for the HBA1 object
atomSmarts - Variable in class joelib.algo.contribution.GroupContributions
AtomSpec - class joelib.smarts.AtomSpec.: Atom specification of a SMARTS bond expression.
AtomSpec() - Constructor for class joelib.smarts.AtomSpec: Constructor for the AtomSpec object
AtomValence - class joelib.desc.types.AtomValence.: Atom valence.
AtomValence() - Constructor for class joelib.desc.types.AtomValence: Constructor for the KierShape1 object
AtomVanDerWaalsVolume - class joelib.desc.types.AtomVanDerWaalsVolume.: Atom Van der Waals volume.
AtomVanDerWaalsVolume() - Constructor for class joelib.desc.types.AtomVanDerWaalsVolume: Constructor for the KierShape1 object
AtomZPos - class joelib.util.types.AtomZPos.: Atom and double z value.
AtomZPos(JOEAtom, double) - Constructor for class joelib.util.types.AtomZPos: Constructor for the AtomZPos object
AtomZPosComparator - class joelib.molecule.AtomZPosComparator.: Comparator for the z position of molecules.
AtomZPosComparator() - Constructor for class joelib.molecule.AtomZPosComparator: Initializes the z position Comparator.
Autocorrelation - class joelib.desc.types.Autocorrelation.: Moreau-Broto autocorrelation.
Autocorrelation() - Constructor for class joelib.desc.types.Autocorrelation
automaticFormalCharge() - Method in class joelib.molecule.JOEMol: Gets the flag if the automatic calculation of the formal charge of the atoms is allowed.
automaticPartialCharge() - Method in class joelib.molecule.JOEMol: Gets the flag if the automatic calculation of the partial charge of the atoms is allowed.
availableDescriptors() - Method in class joelib.desc.data.MolDescCounter: Description of the Method
availableMolIdentifiers() - Method in class joelib.desc.data.MolDescCounter: Description of the Method
availableMolNames() - Method in class joelib.desc.data.MolDescCounter: Description of the Method

B

b - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field
BABEL_VERSION - Static variable in class joelib.util.JOEHelper: Description of the Field
BALL_AND_STICK - Static variable in interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle: Description of the Field
BALL_AND_STICK - Static variable in class joelib.io.types.POVRay: Description of the Field
BALL_AND_STICK - Static variable in class joelib.io.types.Matlab: Description of the Field
BALL_RADIUS - Static variable in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: The Radius of the balls int ball and stick mode *
balloc - Variable in class joelib.smarts.Pattern: Description of the Field
BasicFactoryInfo - class joelib.util.types.BasicFactoryInfo.: Basic factory element informations.
BasicFactoryInfo(String, String, String) - Constructor for class joelib.util.types.BasicFactoryInfo: Constructor for the DescriptorInfo object
BasicGroups - class joelib.desc.types.BasicGroups.: Number of basic groups.
BasicGroups() - Constructor for class joelib.desc.types.BasicGroups
BatchScriptReplacer - class wsi.ra.io.BatchScriptReplacer.: Contains static methods for reading data from temporary files.
bcount - Variable in class joelib.smarts.Pattern: Description of the Field
BE_ANDHI - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BE_ANDLO - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BE_LEAF - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BE_NOT - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BE_OR - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
beginModify() - Method in class joelib.molecule.JOEMol: Begins modification of atoms and increase modification counter.
BF_NONRINGDOUBLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_NONRINGDOWN - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_NONRINGTRIPLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_NONRINGUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_NONRINGUP - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGAROM - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGDOUBLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGDOWN - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGTRIPLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGUP - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BFS - class joelib.algo.BFS.: Breadh First Search.
BFS() - Constructor for class joelib.algo.BFS: Constructor for the KierShape1 object
BFSResult - class joelib.algo.BFSResult.: Result of a BFS.
BFSResult() - Constructor for class joelib.algo.BFSResult: Constructor for the BFSResult object
BinaryValue - interface joelib.desc.BinaryValue.: Interface to have a fast method to getting binary (bit string) descriptor values.
BinAtomExpr - class joelib.smarts.atomexpr.BinAtomExpr.: Binary atom expression for SMARTS substructure search.
BinAtomExpr() - Constructor for class joelib.smarts.atomexpr.BinAtomExpr: Constructor for the BinAtomExpr object
BinAtomExpr(int) - Constructor for class joelib.smarts.atomexpr.BinAtomExpr: Constructor for the BinAtomExpr object
BinBondExpr - class joelib.smarts.bondexpr.BinBondExpr.: Binary bond expression for SMARTS.
BinBondExpr() - Constructor for class joelib.smarts.bondexpr.BinBondExpr: Constructor for the BinBondExpr object
BinBondExpr(int) - Constructor for class joelib.smarts.bondexpr.BinBondExpr: Constructor for the BinBondExpr object
binning - Variable in class wsi.ra.tool.ArrayBinning: Description of the Field
binomialStandardError(double, int) - Static method in class wsi.ra.tool.Statistics: Computes standard error for observed values of a binomial random variable.
BitArrayResult - class joelib.desc.result.BitArrayResult.: Atom representation.
BitArrayResult() - Constructor for class joelib.desc.result.BitArrayResult: Constructor for the IntResult object
bitIsOn(int) - Method in class joelib.util.JOEBitVec: Description of the Method
bitIsSet(int) - Method in class joelib.util.JOEBitVec: Description of the Method
BitResult - class joelib.desc.result.BitResult.: Atom representation.
BitResult() - Constructor for class joelib.desc.result.BitResult: Constructor for the IntResult object
BitSet14 - class joelib.util.BitSet14.: This class implements a vector of bits that grows as needed.
BitSet14() - Constructor for class joelib.util.BitSet14: Creates a new bit set.
BitSet14(int) - Constructor for class joelib.util.BitSet14: Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range 0 through nbits-1.
BL_CONST - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BL_TYPE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
bond - Variable in class joelib.smarts.Pattern: Description of the Field
bond - Variable in class joelib.util.types.StackType: Description of the Field
bond - Variable in class joelib.util.types.BondInt: Description of the Field
BOND_PROPERTY - Static variable in class joelib.desc.result.BondDynamicResult
BondComparator - class joelib.molecule.BondComparator.: Comparator for bonds.
BondComparator() - Constructor for class joelib.molecule.BondComparator: Initializes the bond comparator.
BondDoubleResult - class joelib.desc.result.BondDoubleResult.: Double results of bond properties.
BondDoubleResult() - Constructor for class joelib.desc.result.BondDoubleResult: Constructor for the DoubleResult object
BondDynamicResult - class joelib.desc.result.BondDynamicResult.: Dynamic results of bond properties.
BondDynamicResult() - Constructor for class joelib.desc.result.BondDynamicResult: Constructor for the DoubleResult object
BondExpr - class joelib.smarts.bondexpr.BondExpr.: Bond expression for SMARTS.
BondExpr() - Constructor for class joelib.smarts.bondexpr.BondExpr: Constructor for the BondExpr object
BondExpr(int) - Constructor for class joelib.smarts.bondexpr.BondExpr: Constructor for the BondExpr object
BONDEXPRPOOL - Static variable in class joelib.smarts.ParseSmart: Description of the Field
bondflags - Variable in class joelib.smiles.ClosureBond: Flags of the bond.
BondInt - class joelib.util.types.BondInt.: Bond and integer value.
BondInt(JOEBond, int) - Constructor for class joelib.util.types.BondInt: Constructor for the BondInt object
BondIntResult - class joelib.desc.result.BondIntResult.: Integer results of atom properties.
BondIntResult() - Constructor for class joelib.desc.result.BondIntResult: Constructor for the DoubleResult object
BondIterator - class joelib.util.iterator.BondIterator.: Gets an iterator over all bonds in a molecule.
bondIterator() - Method in class joelib.molecule.JOEMol: Gets an iterator over all bonds.
bondIterator() - Method in class joelib.molecule.JOEAtom: Returns a BondIterator for all bonds in this atom.
BondIterator(Vector) - Constructor for class joelib.util.iterator.BondIterator: Constructor for the BondIterator object
BondNode - class joelib.gui.molviewer.java3d.graphics3D.BondNode.: Description of the Class
BONDPOOL - Static variable in class joelib.smarts.Pattern: Description of the Field
BondProperties - interface joelib.molecule.types.BondProperties.: Interface to access bond properties.
BondSpec - class joelib.smarts.BondSpec.: Bond specification of a SMARTS bond expression.
BondSpec() - Constructor for class joelib.smarts.BondSpec
BOOLEAN - Static variable in class joelib.desc.result.DynamicArrayResult: Description of the Field
booleanArrayFromSimpleString(String) - Method in class joelib.util.ArrayHelper
booleanArrayFromSimpleString(String, String) - Static method in class joelib.util.ArrayHelper: Loads boolean array from String .
booleanArrayFromString(Reader) - Static method in class joelib.util.LineArrayHelper: Description of the Method
booleanArrayFromString(Reader, int) - Static method in class joelib.util.LineArrayHelper: Gets boolean arrays from a Reader.
booleanArrayFromString(String) - Static method in class joelib.util.LineArrayHelper: Description of the Method
booleanArrayFromString(String) - Method in class joelib.util.ArrayHelper: Loads boolean array from String .
booleanArrayFromString(String, int) - Static method in class joelib.util.LineArrayHelper: Description of the Method
booleanArrayFromString(String, String, int) - Static method in class joelib.util.ArrayHelper: Loads boolean array from String .
booleans - Variable in class joelib.smarts.RSCacheEntry: Description of the Field
BOSum() - Method in class joelib.molecule.JOEAtom: Sum of the bond orders of the bonds to the atom.
BS_ALL - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_AROM - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_DEFAULT - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_DOUBLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_DOWN - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_DOWNUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_RING - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_SINGLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_TRIPLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_UP - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_UPUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_AROM - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_DOUBLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_DOWN - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_DOWNUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_RING - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_SINGLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_TRIPLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_UP - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_UPUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BUFF_SIZE - Static variable in class joelib.util.JOEHelper: Description of the Field
buffer - Variable in class joelib.smarts.ParseSmart: Description of the Field
BUFMAX - Static variable in class joelib.smarts.ParseSmart: Description of the Field
buildAtomBin(int, AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
buildAtomLeaf(int, int) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
buildAtomNot(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
buildAtomRecurs(Pattern) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
buildBondBin(int, BondExpr, BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
buildBondLeaf(int, int) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
buildBondNot(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
buildOERTreeVector(JOEAtom, JOERTree, JOERTree[], JOEBitVec) - Static method in class joelib.util.JHM
buildTree(JOESmiNode) - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
byteMatrixFromString(String) - Method in class joelib.util.MatrixHelper: Description of the Method
byteMatrixFromString(String, String) - Static method in class joelib.util.MatrixHelper: Description of the Method

C

c - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field
calcPerpUnitVec(float, float, float, float, float[], float[]) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Calculates 2D vector perpendicular to bond
calcTorsionAngle(XYZVector, XYZVector, XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
calculate(JOEMol) - Method in class joelib.algo.DFS: Description of the Method
calculate(JOEMol) - Method in class joelib.algo.BFS: Description of the Method
calculate(JOEMol) - Method in class joelib.algo.morgan.Morgan: Calculate the morgan numbers of a molecule.
calculate(JOEMol) - Method in class joelib.desc.SMARTSCounter: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.SimpleIntDesc: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.SimpleDoubleDesc: Description of the Method
calculate(JOEMol) - Method in interface joelib.desc.Descriptor: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.AtomsCounter: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.SSKey3DS: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.RotatableBonds: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.HeteroCycles: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.HeavyBonds: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.GraphPotentials: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.FractionRotatableBonds: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.ElectronegativityPauling: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.ElectronAffinity: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.Autocorrelation: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.AtomVanDerWaalsVolume: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.AtomValence: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.AtomMass: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.AromaticBonds: Description of the Method
calculate(JOEMol) - Method in class joelib.molecule.charge.GasteigerMarsili: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.algo.DFS: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.algo.BFS: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.SMARTSCounter: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.SimpleIntDesc: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.SimpleDoubleDesc: Description of the Method
calculate(JOEMol, DescResult) - Method in interface joelib.desc.Descriptor: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.AtomsCounter: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.SSKey3DS: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.RotatableBonds: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.HeteroCycles: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.HeavyBonds: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.GraphPotentials: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.FractionRotatableBonds: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.ElectronegativityPauling: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.ElectronAffinity: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.Autocorrelation: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.AtomVanDerWaalsVolume: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.AtomValence: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.AtomMass: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.AromaticBonds: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.molecule.charge.GasteigerMarsili: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.algo.DFS: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.algo.BFS: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.SMARTSCounter: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.SimpleIntDesc: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.SimpleDoubleDesc: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in interface joelib.desc.Descriptor: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.AtomsCounter: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.SSKey3DS: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.RotatableBonds: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.HeteroCycles: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.HeavyBonds: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.GraphPotentials: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.FractionRotatableBonds: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.ElectronegativityPauling: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.ElectronAffinity: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.Autocorrelation: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.AtomVanDerWaalsVolume: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.AtomValence: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.AtomMass: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.AromaticBonds: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.molecule.charge.GasteigerMarsili: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.algo.DFS: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.algo.BFS: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.SMARTSCounter: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.SimpleIntDesc: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.SimpleDoubleDesc: Description of the Method
calculate(JOEMol, Map) - Method in interface joelib.desc.Descriptor: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.AtomsCounter: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.SSKey3DS: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.RotatableBonds: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.HeteroCycles: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.HeavyBonds: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.GraphPotentials: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.FractionRotatableBonds: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.ElectronegativityPauling: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.ElectronAffinity: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.Autocorrelation: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.AtomVanDerWaalsVolume: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.AtomValence: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.AtomMass: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.AromaticBonds: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.molecule.charge.GasteigerMarsili: Description of the Method
calculateDerived() - Method in class wsi.ra.tool.ArrayStatistic: Tells the object to calculate any statistics that don't have their values automatically updated during add.
calculateDerived() - Method in class wsi.ra.tool.ArrayBinning: Tells the object to calculate any statistics that don't have their values automatically updated during add.
calcVarianceNorm(DescStatistic) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method Description of the Method Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object Description of the Method
canonicaliseBond(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
canReadExtension(String) - Method in class joelib.io.IOTypeHolder: Description of the Method
canWriteExtension(String) - Method in class joelib.io.IOTypeHolder: Description of the Method
capExternalBonds(JOEMol) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
cardinality() - Method in class joelib.util.BitSet14: Returns the number of bits set to true in this BitSet14.
CDKTools - class joelib.util.CDKTools.: Helper class to faciliate access to tools of the Chemical Development Kit (CDK).
CDKTools() - Constructor for class joelib.util.CDKTools: Constructor for the CDKTools.
center() - Method in class joelib.molecule.JOEMol: Centers molecule.
center(int) - Method in class joelib.molecule.JOEMol: Centers conformer.
CentralDisplayAdapter - class joelib.gui.molviewer.java3d.util.CentralDisplayAdapter.: Description of the Class
CentralDisplayAdapter(JPanel3D) - Constructor for class joelib.gui.molviewer.java3d.util.CentralDisplayAdapter: Constructor for the CentralDisplayAdapter object
centralDisplayChange(MolViewerEvent) - Method in interface joelib.gui.molviewer.java3d.util.MolViewerEventListener: Description of the Method
centralDisplayChange(MolViewerEvent) - Method in class joelib.gui.molviewer.java3d.util.MolViewerEventAdapter: Description of the Method
centralDisplayChange(MolViewerEvent) - Method in class joelib.gui.molviewer.java3d.util.CentralDisplayAdapter: Description of the Method
CentralLookup - class joelib.gui.molviewer.java3d.util.CentralLookup.: Description of the Class
cformat - package cformat: Provides classes allowing printf and scanf functionality for Java.
checkAromaticity(JOEAtom, int) - Method in class joelib.data.JOEAromaticTyper: Description of the Method
checkProperties(PropertyAcceptor, Map) - Static method in class joelib.util.JOEPropertyHelper: Description of the Method
CHEMICAL_STRUCTURE - Static variable in class joelib.jcamp.JCAMPParser: data representation: definition for the parameter of a chemical structure
ChemicalMarkupLanguage - class joelib.io.types.ChemicalMarkupLanguage.: Reader/Writer for Chemical Markup Language (CML) files.
ChemicalMarkupLanguage() - Constructor for class joelib.io.types.ChemicalMarkupLanguage
chi - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field
chiral - Variable in class joelib.smarts.AtomSpec: Chiral flag.
chiSquaredProbability(double, double) - Static method in class wsi.ra.tool.Statistics: Returns chi-squared probability for given value and degrees of freedom.
clear() - Method in class joelib.algo.DFS: Description of the Method
clear() - Method in class joelib.algo.BFS: Description of the Method
clear() - Method in class joelib.desc.SMARTSCounter: Description of the Method
clear() - Method in class joelib.desc.SimpleIntDesc: Description of the Method
clear() - Method in class joelib.desc.SimpleDoubleDesc: Description of the Method
clear() - Method in interface joelib.desc.Descriptor: Description of the Method
clear() - Method in class joelib.desc.AtomsCounter: Description of the Method
clear() - Method in class joelib.desc.data.MolDescCounter: Description of the Method
clear() - Method in class joelib.desc.types.SSKey3DS: Description of the Method
clear() - Method in class joelib.desc.types.RotatableBonds: Description of the Method
clear() - Method in class joelib.desc.types.HeteroCycles: Description of the Method
clear() - Method in class joelib.desc.types.HeavyBonds: Description of the Method
clear() - Method in class joelib.desc.types.GraphPotentials: Description of the Method
clear() - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
clear() - Method in class joelib.desc.types.FractionRotatableBonds: Description of the Method
clear() - Method in class joelib.desc.types.ElectronegativityPauling: Description of the Method
clear() - Method in class joelib.desc.types.ElectronAffinity: Description of the Method
clear() - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
clear() - Method in class joelib.desc.types.Autocorrelation: Description of the Method
clear() - Method in class joelib.desc.types.AtomVanDerWaalsVolume: Description of the Method
clear() - Method in class joelib.desc.types.AtomValence: Description of the Method
clear() - Method in class joelib.desc.types.AtomMass: Description of the Method
clear() - Method in class joelib.desc.types.AromaticBonds: Description of the Method
clear() - Method in class joelib.ext.SimpleExternalProcess
clear() - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method
clear() - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene: Description of the Method
clear() - Method in class joelib.gui.molviewer.java3d.graphics3D.JPanel3D: Sets the fast attribute of the JPanel3D object Sets the nice attribute of the JPanel3D object Description of the Method
clear() - Method in class joelib.math.JOECoordTrans: Clears the object as if it were just constructed.
clear() - Method in class joelib.molecule.JOEResidue
clear() - Method in class joelib.molecule.JOEMol: Clears molecule.
clear() - Method in class joelib.molecule.JOEBond
clear() - Method in class joelib.molecule.JOEAtom: Deletes all contained informations in this atom.
clear() - Method in class joelib.molecule.GenericDataHolder: Description of the Method
clear() - Method in class joelib.molecule.charge.GasteigerMarsili: Description of the Method
clear() - Method in class joelib.process.SimpleProcess
clear() - Method in class joelib.process.ProcessPipe
clear() - Method in interface joelib.process.JOEProcess
clear() - Method in class joelib.process.types.MoleculeFileDeletion
clear() - Method in class joelib.process.types.MoleculeFileCreation
clear() - Method in class joelib.process.types.DistanceCalculation: Description of the Method
clear() - Method in class joelib.process.types.DescVarianceNorm: Description of the Method
clear() - Method in class joelib.process.types.DescStatistic: Description of the Method
clear() - Method in class joelib.process.types.DescSelectionWriter: Description of the Method
clear() - Method in class joelib.process.types.DescBinning: Description of the Method
clear() - Method in class joelib.process.types.CreateFileName: Description of the Method
clear() - Method in class joelib.util.BitSet14: Sets all of the bits in this BitSet14 to false.
clear(int) - Method in class joelib.util.BitSet14: Sets the bit specified by the index to false.
clear(int, int) - Method in class joelib.util.BitSet14: Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to false.
clearCoordPtr() - Method in class joelib.molecule.JOEAtom: Clear coordinate array.
clearLookAheadChar() - Method in class cformat.ScanfReader: Clears the look-ahead character.
ClearTextFormat - class joelib.io.types.ClearTextFormat.: Reader/Writer for ClearTeXt (CTX) files.
ClearTextFormat() - Constructor for class joelib.io.types.ClearTextFormat
clone() - Method in class joelib.algo.DFSResult
clone() - Method in class joelib.algo.BFSResult
clone() - Method in interface joelib.desc.DescResult
clone() - Method in class joelib.desc.result.IntResult
clone() - Method in class joelib.desc.result.IntMatrixResult
clone() - Method in class joelib.desc.result.IntBitArrayResult
clone() - Method in class joelib.desc.result.IntArrayResult
clone() - Method in class joelib.desc.result.DynamicArrayResult
clone() - Method in class joelib.desc.result.DoubleResult
clone() - Method in class joelib.desc.result.DoubleMatrixResult
clone() - Method in class joelib.desc.result.DoubleArrayResult
clone() - Method in class joelib.desc.result.BondIntResult
clone() - Method in class joelib.desc.result.BondDynamicResult
clone() - Method in class joelib.desc.result.BondDoubleResult
clone() - Method in class joelib.desc.result.BitResult
clone() - Method in class joelib.desc.result.BitArrayResult
clone() - Method in class joelib.desc.result.AtomIntResult
clone() - Method in class joelib.desc.result.AtomDynamicResult
clone() - Method in class joelib.desc.result.AtomDoubleResult
clone() - Method in class joelib.desc.result.APropIntResult
clone() - Method in class joelib.desc.result.APropDoubleResult
clone() - Method in class joelib.desc.result.APropDoubleArrResult
clone() - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Returns a clone (Object) of matrix
clone() - Method in class joelib.math.XYZVector: Description of the Method
clone() - Method in class joelib.molecule.JOEResidue
clone() - Method in class joelib.molecule.JOEMol: Clones molecule without additional data (e.g. descriptor data).
clone() - Method in class joelib.molecule.JOEBond
clone() - Method in class joelib.molecule.JOEAtom: Clone this JOEAtom object.
clone() - Method in class joelib.sort.XYIntArray: Description of the Method
clone() - Method in class joelib.sort.XYDoubleArray: Description of the Method
clone() - Method in class joelib.util.BitSet14: Cloning this BitSet14 produces a new BitSet14 that is equal to it.
clone() - Method in class joelib.util.iterator.VectorIterator: Description of the Method
clone() - Method in class joelib.util.iterator.AtomIterator
clone() - Method in class wsi.ra.tool.SortedVector: Returns a clone of this vector.
clone(APropDoubleArrResult) - Method in class joelib.desc.result.APropDoubleArrResult
clone(APropDoubleResult) - Method in class joelib.desc.result.APropDoubleResult
clone(APropIntResult) - Method in class joelib.desc.result.APropIntResult
clone(AtomDoubleResult) - Method in class joelib.desc.result.AtomDoubleResult
clone(AtomDynamicResult, int) - Method in class joelib.desc.result.AtomDynamicResult
clone(AtomIntResult) - Method in class joelib.desc.result.AtomIntResult
clone(BFSResult) - Method in class joelib.algo.BFSResult
clone(BitArrayResult) - Method in class joelib.desc.result.BitArrayResult
clone(BitResult) - Method in class joelib.desc.result.BitResult
clone(BondDoubleResult) - Method in class joelib.desc.result.BondDoubleResult
clone(BondDynamicResult, int) - Method in class joelib.desc.result.BondDynamicResult
clone(BondIntResult) - Method in class joelib.desc.result.BondIntResult
clone(boolean) - Method in class joelib.molecule.JOEMol: Clones this molecule.
clone(boolean, String[]) - Method in class joelib.molecule.JOEMol: Clones this molecule.
clone(DFSResult) - Method in class joelib.algo.DFSResult
clone(DoubleArrayResult) - Method in class joelib.desc.result.DoubleArrayResult
clone(DoubleMatrixResult) - Method in class joelib.desc.result.DoubleMatrixResult
clone(DoubleResult) - Method in class joelib.desc.result.DoubleResult
clone(DynamicArrayResult, int) - Method in class joelib.desc.result.DynamicArrayResult
clone(IntArrayResult) - Method in class joelib.desc.result.IntArrayResult
clone(IntBitArrayResult) - Method in class joelib.desc.result.IntBitArrayResult
clone(IntMatrixResult) - Method in class joelib.desc.result.IntMatrixResult
clone(IntResult) - Method in class joelib.desc.result.IntResult
clone(JOEAtom, JOEAtom) - Static method in class joelib.molecule.JOEAtom: Clone the JOEAtom src to the JOEAtom to.
clone(JOEBond, JOEBond) - Static method in class joelib.molecule.JOEBond: Clone the JOEBond src to the JOEBond to.
clone(JOEResidue) - Method in class joelib.molecule.JOEResidue
clone(JOEResidue, JOEResidue) - Static method in class joelib.molecule.JOEResidue
clone(MoleculesDescriptorMatrix) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
close() - Method in class cformat.ScanfReader: Closes the stream.
close() - Method in class joelib.io.SimpleWriter: Description of the Method
close() - Method in class joelib.io.SimpleReader: Description of the Method
closeReader() - Method in interface joelib.io.MoleculeFileType: Description of the Method
closeReader() - Method in class joelib.io.types.XYZ
closeReader() - Method in class joelib.io.types.Undefined
closeReader() - Method in class joelib.io.types.Tinker
closeReader() - Method in class joelib.io.types.SybylMol2
closeReader() - Method in class joelib.io.types.Smiles: Description of the Method
closeReader() - Method in class joelib.io.types.POVRay: Description of the Method
closeReader() - Method in class joelib.io.types.PDB: Description of the Method
closeReader() - Method in class joelib.io.types.MolconnZ: Description of the Method
closeReader() - Method in class joelib.io.types.MDLSD: Description of the Method
closeReader() - Method in class joelib.io.types.Matlab: Description of the Method
closeReader() - Method in class joelib.io.types.JCAMP: Description of the Method
closeReader() - Method in class joelib.io.types.Flat: Description of the Method
closeReader() - Method in class joelib.io.types.ClearTextFormat
closeReader() - Method in class joelib.io.types.ChemicalMarkupLanguage
closeWriter() - Method in interface joelib.io.MoleculeFileType: Description of the Method
closeWriter() - Method in class joelib.io.types.XYZ
closeWriter() - Method in class joelib.io.types.Undefined
closeWriter() - Method in class joelib.io.types.Tinker
closeWriter() - Method in class joelib.io.types.SybylMol2
closeWriter() - Method in class joelib.io.types.Smiles: Description of the Method
closeWriter() - Method in class joelib.io.types.POVRay: Description of the Method
closeWriter() - Method in class joelib.io.types.PDB: Description of the Method
closeWriter() - Method in class joelib.io.types.MolconnZ: Description of the Method
closeWriter() - Method in class joelib.io.types.MDLSD: Description of the Method
closeWriter() - Method in class joelib.io.types.Matlab: Description of the Method
closeWriter() - Method in class joelib.io.types.JCAMP: Description of the Method
closeWriter() - Method in class joelib.io.types.Flat: Description of the Method
closeWriter() - Method in class joelib.io.types.ClearTextFormat
closeWriter() - Method in class joelib.io.types.ChemicalMarkupLanguage
closindex - Variable in class joelib.smarts.ParseState: Description of the Field
closord - Variable in class joelib.smarts.ParseState: Description of the Field
closure - Variable in class joelib.smarts.ParseState: Description of the Field
ClosureBond - class joelib.smiles.ClosureBond.: Closure bond of an SMILES expression.
ClosureBond(int, int, int, int, int) - Constructor for class joelib.smiles.ClosureBond: Initialize the ClosureBond
closureNumber - Variable in class joelib.smiles.ClosureBond: Number of the closure bond.
CMLMoleculeWriter - interface joelib.io.types.cml.CMLMoleculeWriter.: Interface for a CML molecule writer.
Combine - class joelib.test.Combine.: Example for converting molecules.
Combine() - Constructor for class joelib.test.Combine: Constructor for the ConvertSkip object
commonLDRs - Static variable in class joelib.jcamp.JCAMPParser: An array of the commonly used LDR's (Label Data Records).
compare(JOEMol) - Method in class joelib.util.ComparisonHelper: Description of the Method
compare(JOEMol, String, double[]) - Method in class joelib.util.ComparisonHelper: Description of the Method.
compare(Object, Object) - Method in class joelib.algo.morgan.AtomDoubleComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.molecule.BondComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.molecule.AtomZPosComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.ring.RingSizeComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.sort.VVIntComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.sort.RotorComparator: Compares two objects.
compareBonds(JOEBond, JOEBond) - Method in class joelib.util.JHM: Description of the Method
Comparison - class joelib.test.Comparison.: Example for converting molecules.
Comparison() - Constructor for class joelib.test.Comparison
ComparisonHelper - class joelib.util.ComparisonHelper.: Example for converting molecules.
ComparisonHelper(IOType, String) - Constructor for class joelib.util.ComparisonHelper
ComparisonHelper(IOType, String, int) - Constructor for class joelib.util.ComparisonHelper: Constructor for the ComparisonHelper object
ComparisonHelper(JOEMol) - Constructor for class joelib.util.ComparisonHelper: Constructor for the ComparisonHelper object
ConformerIterator - class joelib.util.iterator.ConformerIterator.: Gets an iterator over all conformers in a molecule.
conformerIterator() - Method in class joelib.molecule.JOEMol: Gets an iterator over all conformers.
ConformerIterator(Vector) - Constructor for class joelib.util.iterator.ConformerIterator
conformerNum() - Method in class joelib.molecule.JOEMol: Returns the number of conformers.
connectTheDots() - Method in class joelib.molecule.JOEMol: Use inter-atomic distances to identify bonds.
constrainRecursion(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
CONTACT_E_MAIL - Static variable in class joelib.util.JOEHelper: Description of the Field
contains(String) - Method in class joelib.util.MDMatrixCache
contains(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the Renderer which draws this molecule Return true iff the atom in the parameter is one of the atoms in this molecule
contains(ViewerBond) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return true iff the bond in the parameter is one of the bonds in this molecule
contigFragList(Vector) - Method in class joelib.molecule.JOEMol: Each Vector contains the atom numbers of a contig fragment the vectors are sorted by size from largest to smallest.
CONTINUE - Static variable in class joelib.test.ConvertSkip
CONTINUE - Static variable in class joelib.test.Convert
Convert - class joelib.test.Convert.: Example for converting molecules and calculating descriptors.
convert() - Method in class joelib.test.ConvertSkip: Convert and skip test.
convert() - Method in class joelib.test.Convert: A unit test for JUnit
Convert() - Constructor for class joelib.test.Convert
ConvertSkip - class joelib.test.ConvertSkip.: Example for converting/skipping molecules.
ConvertSkip() - Constructor for class joelib.test.ConvertSkip: Constructor for the ConvertSkip object
copyAtomExpr(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
copyBondExpr(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
copyConformer(double[], int) - Method in class joelib.molecule.JOEMol: Copies given conformer to this molecule.
copyConformer(float[], int) - Method in class joelib.molecule.JOEMol: Copies given conformer to this molecule.
copyInto(Object[]) - Method in class wsi.ra.tool.SortedVector: Copies the components of this vector into the specified array.
copyPattern(Pattern) - Static method in class joelib.smarts.Pattern: Description of the Method
correctAromaticAmineCharge(JOEMol) - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
correctAromaticNitrogens(JOEMol) - Method in class joelib.data.JOEAtomTyper: Description of the Method
correctBadResonanceForm(JOEMol) - Static method in class joelib.util.JHM: Description of the Method
correctedBondRad(int) - Method in class joelib.data.JOEElementTable: Description of the Method
correctedBondRad(int, int) - Method in class joelib.data.JOEElementTable: Description of the Method
correctedVdwRad(int) - Method in class joelib.data.JOEElementTable: Description of the Method
correctedVdwRad(int, int) - Method in class joelib.data.JOEElementTable: Description of the Method
correctForPH() - Method in class joelib.molecule.JOEMol: Corrects pH value of the molecule.
correctForPH(JOEMol) - Method in class joelib.data.JOEPhModel: Corrects the molecule for PH.
correlation(double[], double[], int) - Static method in class wsi.ra.tool.StatisticUtils: Returns the correlation coefficient of two double vectors.
count - Variable in class joelib.util.types.Template: Description of the Field
count - Variable in class wsi.ra.tool.ArrayStatistic: The number of values seen
count(IOType, String) - Method in class joelib.desc.data.MolDescCounter: Description of the Method
countBits() - Method in class joelib.util.JOEBitVec: Description of the Method
countBondsOfOrder(int) - Method in class joelib.molecule.JOEAtom: Count the bonds of the bond order order .
countDescriptors(JOEMol) - Method in class joelib.desc.data.MolDescCounter: Description of the Method
countFreeOxygens() - Method in class joelib.molecule.JOEAtom: Count the number of free oxygens.
CPK - Static variable in interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle: Description of the Field
createAtom() - Method in class joelib.molecule.JOEMol: Creates only a new atom.
createAtom(Pattern, AtomExpr, int) - Static method in class joelib.smarts.Pattern: Description of the Method
createAtom(Pattern, AtomExpr, int, int) - Static method in class joelib.smarts.Pattern: Description of the Method
createBatchFile(Reader, Writer, Hashtable) - Method in class wsi.ra.io.BatchScriptReplacer: Description of the Method
createBond() - Method in class joelib.molecule.JOEMol: Creates only a new bond.
createBond(Pattern, BondExpr, int, int) - Static method in class joelib.smarts.Pattern: Description of the Method
CreateFileName - class joelib.process.types.CreateFileName.: Calling processor classes if the filter rule fits.
CreateFileName() - Constructor for class joelib.process.types.CreateFileName: Constructor for the DescSelectionWriter object
createLastDirectory(File) - Method in class wsi.ra.io.FileUtilities: Description of the Method
createNewFileName(String) - Method in class wsi.ra.io.FileUtilities
createNewFileName(String, int) - Method in class wsi.ra.io.FileUtilities
createOrthoXYZVector(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
createSmiString(JOEMol, StringBuffer) - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
createWire(ViewerBond) - Static method in class joelib.gui.molviewer.java3d.graphics3D.BondNode: Description of the Method
cross(GeoVector3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: cross product with another vector
cross(XYZVector) - Method in class joelib.math.XYZVector
cross(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
cross(XYZVector, XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
CS_TYPE - Static variable in class joelib.jcamp.JCAMPDataBlock
Cylinder - class joelib.gui.molviewer.java3d.graphics3D.Cylinder.: Description of the Class
Cylinder(float, float, int, Appearance) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.Cylinder: Constructor for the Cylinder object

D

d - Variable in class joelib.algo.morgan.AtomDoubleParent: Description of the Field
d - Variable in class joelib.algo.morgan.AtomDouble: Description of the Field
d - Variable in class joelib.util.types.DoubleInt: Description of the Field
DASH - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Wedge down bond type
data - Variable in class joelib.jcamp.LabelData
DATA_TYPE_PEAKS - Static variable in class joelib.jcamp.JCAMPParser: Description of the Field
DATA_TYPE_SPECTRUM - Static variable in class joelib.jcamp.JCAMPParser: Description of the Field
dataSize() - Method in class joelib.molecule.JOEMol: Returns the number of data elements in this molecule.
decodeData() - Method in class joelib.jcamp.JCAMPParser: Decide which data type this JCAMP data set contains and decodes this data.
decrementImplicitValence() - Method in class joelib.molecule.JOEAtom: Decrement the implicit valence.
decrementMod() - Method in class joelib.molecule.JOEMol: Decrease modification counter.
DEFAULT - Static variable in class joelib.desc.types.SOGroups
DEFAULT - Static variable in class joelib.desc.types.SO2Groups
DEFAULT - Static variable in class joelib.desc.types.OSOGroups
DEFAULT - Static variable in class joelib.desc.types.NO2Groups
DEFAULT - Static variable in class joelib.desc.types.HydrophobicGroups
DEFAULT - Static variable in class joelib.desc.types.HBD2
DEFAULT - Static variable in class joelib.desc.types.HBD1
DEFAULT - Static variable in class joelib.desc.types.HBA2
DEFAULT - Static variable in class joelib.desc.types.HBA1
DEFAULT - Static variable in class joelib.desc.types.BasicGroups
DEFAULT - Static variable in class joelib.desc.types.AromaticOHGroups
DEFAULT - Static variable in class joelib.desc.types.AliphaticOHGroups
DEFAULT - Static variable in class joelib.desc.types.AcidicGroups
DEFAULT_OUTPUT_TYPE - Static variable in class joelib.io.types.POVRay: Description of the Field
DEFAULT_OUTPUT_TYPE - Static variable in class joelib.io.types.Matlab: Description of the Field
DEFAULT_SEPARATOR - Static variable in class joelib.util.MatrixHelper: Description of the Field
DEFAULT_SEPARATOR - Static variable in class joelib.util.ArrayHelper: Description of the Field
DEG_TO_RAD - Static variable in class joelib.math.XYZVector: Description of the Field
DEG_TO_RAD - Static variable in class joelib.math.Matrix3x3: Description of the Field
DEG_TO_RAD - Static variable in class joelib.util.JHM: Description of the Field
degreeValue() - Method in class joelib.gui.molviewer.java3d.math.geometry.Angle: Return angle value in degree unit
dehighlight() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Dehighlighted all highlighted atoms.
deleteAtom(JOEAtom) - Method in class joelib.molecule.JOEMol: Delete atom from molecule.
deleteBond(JOEBond) - Method in class joelib.molecule.JOEMol: Delete the given JOEBond from this molecule.
deleteBond(JOEBond) - Method in class joelib.molecule.JOEAtom: Delete a bond from this atom.
deleteConformer(int) - Method in class joelib.molecule.JOEMol: Delete conformer from molecule.
deleteData(JOEDataType) - Method in class joelib.molecule.JOEMol: Deletes all data elements os the given JOEDataType .
deleteData(JOEDataType) - Method in class joelib.molecule.GenericDataHolder: Description of the Method
deleteData(JOEGenericData) - Method in class joelib.molecule.JOEMol: Delete all data elements which are equal to the given JOEGenericData element.
deleteData(JOEGenericData) - Method in class joelib.molecule.GenericDataHolder: Description of the Method
deleteData(String) - Method in class joelib.molecule.JOEMol: Description of the Method
deleteData(String) - Method in class joelib.molecule.GenericDataHolder: Description of the Method
deleteData(Vector) - Method in class joelib.molecule.JOEMol: Description of the Method
deleteData(Vector) - Method in class joelib.molecule.GenericDataHolder: Description of the Method
deleteFileName(String) - Method in class wsi.ra.io.FileUtilities
deleteHydrogen(JOEAtom) - Method in class joelib.molecule.JOEMol: Deletes hydrogen atom.
deleteHydrogens() - Method in class joelib.molecule.JOEMol: Delete all hydrogen atoms from molecule.
deleteHydrogens(JOEAtom) - Method in class joelib.molecule.JOEMol: Delete all hydrogen atoms from given atom.
deleteNonPolarHydrogens() - Method in class joelib.molecule.JOEMol: Delete all non polar hydrogens from molecule.
deleteResidue() - Method in class joelib.molecule.JOEAtom
deleteResidue(JOEResidue) - Method in class joelib.molecule.JOEMol: Description of the Method
denom - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field
Deque - class wsi.ra.tool.Deque.: Deque implementation.
Deque() - Constructor for class wsi.ra.tool.Deque
Deque(DequeNode) - Constructor for class wsi.ra.tool.Deque
DequeIterator - class wsi.ra.tool.DequeIterator.: Iterator class for the list.
DequeIterator(Deque) - Constructor for class wsi.ra.tool.DequeIterator
DequeNode - class wsi.ra.tool.DequeNode.: Deque node representation.
DequeNode(DequeNode, Object) - Constructor for class wsi.ra.tool.DequeNode
DequeNode(DequeNode, Object, DequeNode) - Constructor for class wsi.ra.tool.DequeNode
DequeNode(Object) - Constructor for class wsi.ra.tool.DequeNode
DESC_KEY - Static variable in class joelib.algo.DFS
DESC_KEY - Static variable in class joelib.algo.BFS
DESC_KEY - Static variable in class joelib.desc.types.ZagrebIndex2
DESC_KEY - Static variable in class joelib.desc.types.ZagrebIndex1
DESC_KEY - Static variable in class joelib.desc.types.TopologicalRadius
DESC_KEY - Static variable in class joelib.desc.types.TopologicalDiameter
DESC_KEY - Static variable in class joelib.desc.types.SSKey3DS
DESC_KEY - Static variable in class joelib.desc.types.SOGroups
DESC_KEY - Static variable in class joelib.desc.types.SO2Groups
DESC_KEY - Static variable in class joelib.desc.types.RotatableBonds
DESC_KEY - Static variable in class joelib.desc.types.OSOGroups
DESC_KEY - Static variable in class joelib.desc.types.NumberOfS
DESC_KEY - Static variable in class joelib.desc.types.NumberOfP
DESC_KEY - Static variable in class joelib.desc.types.NumberOfO
DESC_KEY - Static variable in class joelib.desc.types.NumberOfN
DESC_KEY - Static variable in class joelib.desc.types.NumberOfI
DESC_KEY - Static variable in class joelib.desc.types.NumberOfHal
DESC_KEY - Static variable in class joelib.desc.types.NumberOfF
DESC_KEY - Static variable in class joelib.desc.types.NumberOfCl
DESC_KEY - Static variable in class joelib.desc.types.NumberOfC
DESC_KEY - Static variable in class joelib.desc.types.NumberOfBr
DESC_KEY - Static variable in class joelib.desc.types.NumberOfBonds
DESC_KEY - Static variable in class joelib.desc.types.NumberOfB
DESC_KEY - Static variable in class joelib.desc.types.NumberOfAtoms
DESC_KEY - Static variable in class joelib.desc.types.NO2Groups
DESC_KEY - Static variable in class joelib.desc.types.MolecularWeight
DESC_KEY - Static variable in class joelib.desc.types.KierShape3
DESC_KEY - Static variable in class joelib.desc.types.KierShape2
DESC_KEY - Static variable in class joelib.desc.types.KierShape1
DESC_KEY - Static variable in class joelib.desc.types.HydrophobicGroups
DESC_KEY - Static variable in class joelib.desc.types.HeteroCycles
DESC_KEY - Static variable in class joelib.desc.types.HeavyBonds
DESC_KEY - Static variable in class joelib.desc.types.HBD2
DESC_KEY - Static variable in class joelib.desc.types.HBD1
DESC_KEY - Static variable in class joelib.desc.types.HBA2
DESC_KEY - Static variable in class joelib.desc.types.HBA1
DESC_KEY - Static variable in class joelib.desc.types.GraphShapeCoefficient
DESC_KEY - Static variable in class joelib.desc.types.GraphPotentials
DESC_KEY - Static variable in class joelib.desc.types.GeometricalShapeCoefficient
DESC_KEY - Static variable in class joelib.desc.types.GeometricalRadius
DESC_KEY - Static variable in class joelib.desc.types.GeometricalDiameter
DESC_KEY - Static variable in class joelib.desc.types.GeomDistanceMatrix
DESC_KEY - Static variable in class joelib.desc.types.FractionRotatableBonds
DESC_KEY - Static variable in class joelib.desc.types.ElectronegativityPauling
DESC_KEY - Static variable in class joelib.desc.types.ElectronAffinity
DESC_KEY - Static variable in class joelib.desc.types.DistanceMatrix
DESC_KEY - Static variable in class joelib.desc.types.BasicGroups
DESC_KEY - Static variable in class joelib.desc.types.Autocorrelation
DESC_KEY - Static variable in class joelib.desc.types.AtomVanDerWaalsVolume
DESC_KEY - Static variable in class joelib.desc.types.AtomValence
DESC_KEY - Static variable in class joelib.desc.types.AtomMass
DESC_KEY - Static variable in class joelib.desc.types.AromaticOHGroups
DESC_KEY - Static variable in class joelib.desc.types.AromaticBonds
DESC_KEY - Static variable in class joelib.desc.types.AliphaticOHGroups
DESC_KEY - Static variable in class joelib.desc.types.AcidicGroups
DESC_KEY - Static variable in class joelib.molecule.charge.GasteigerMarsili
DescBinning - class joelib.process.types.DescBinning.: Calling processor classes if the filter rule fits.
DescBinning() - Constructor for class joelib.process.types.DescBinning: Constructor for the DescSelectionWriter object
DescDescription - class joelib.desc.DescDescription.: Descriptor descriptons.
DescDescription(String) - Constructor for class joelib.desc.DescDescription: Constructor for the DescDescription object
descFromMol(JOEMol, String) - Method in class joelib.desc.DescriptorHelper: Getting descriptor values from a molecule and try to calculate a descriptor value if it is not already available.
descFromMol(JOEMol, String, boolean) - Static method in class joelib.desc.DescriptorHelper: Getting descriptor values from a molecule and try to calculate a descriptor value if it is not already available.
descFromMol(JOEMol, String, DescResult) - Method in class joelib.desc.DescriptorHelper: Getting descriptor values from a molecule and try to calculate a descriptor value if it is not already available.
descFromMol(JOEMol, String, DescResult, boolean) - Static method in class joelib.desc.DescriptorHelper: Getting descriptor values from a molecule and try to calculate a descriptor value if it is not already available.
descInfo - Variable in class joelib.desc.SMARTSCounter
descInfo - Variable in class joelib.desc.SimpleIntDesc
descInfo - Variable in class joelib.desc.SimpleDoubleDesc
descInfo - Variable in class joelib.desc.AtomsCounter
DescResult - interface joelib.desc.DescResult.: Interface definition for descriptor results.
Description - class joelib.desc.Description.: Description for a descriptor.
Descriptor - interface joelib.desc.Descriptor.: Interface for defining descriptors, which can be calculated by using JOELib.
DescriptorException - exception joelib.desc.DescriptorException.: Descriptor exception.
DescriptorException() - Constructor for class joelib.desc.DescriptorException: Constructor for the DescriptorException object
DescriptorException(String) - Constructor for class joelib.desc.DescriptorException: Constructor for the DescriptorException object
DescriptorFactory - class joelib.desc.DescriptorFactory.: Factory class to get descriptor calculation classes.
DescriptorFilter - class joelib.process.filter.DescriptorFilter.: Interface definition for calling external programs from JOELib.
DescriptorFilter() - Constructor for class joelib.process.filter.DescriptorFilter: Constructor for the DescriptorFilter object
DescriptorFilter(String, boolean) - Constructor for class joelib.process.filter.DescriptorFilter: Constructor for the DescriptorFilter object
DescriptorFilter(Vector) - Constructor for class joelib.process.filter.DescriptorFilter: Constructor for the DescriptorFilter object
DescriptorHelper - class joelib.desc.DescriptorHelper.: Some methods to faciliate the work with descriptors.
DescriptorInfo - class joelib.desc.DescriptorInfo.: Informations for a descriptor.
DescriptorInfo(String, String, int, String, String, String, String) - Constructor for class joelib.desc.DescriptorInfo: Constructor for the DescriptorInfo object
DESCRIPTORS - Static variable in class joelib.process.types.DescSelectionWriter: Description of the Field
descriptors() - Method in class joelib.desc.DescriptorHelper: Returns a Enumeration of all available descriptor names that could be calculated by using JOELib.
DescriptorSelection - class joelib.test.DescriptorSelection.: Example for converting molecules.
DescriptorSelection() - Constructor for class joelib.test.DescriptorSelection
DescriptorStatistic - class joelib.test.DescriptorStatistic.: Example for converting molecules.
DescriptorStatistic() - Constructor for class joelib.test.DescriptorStatistic
DescSelectionWriter - class joelib.process.types.DescSelectionWriter.: Calling processor classes if the filter rule fits.
DescSelectionWriter() - Constructor for class joelib.process.types.DescSelectionWriter: Constructor for the DescSelectionWriter object
DescStatistic - class joelib.process.types.DescStatistic.: Calling processor classes if the filter rule fits.
DescStatistic() - Constructor for class joelib.process.types.DescStatistic: Constructor for the DescSelectionWriter object
DescVarianceNorm - class joelib.process.types.DescVarianceNorm.: Scales the values in one descriptor so that they have similar magnitudes.
DescVarianceNorm() - Constructor for class joelib.process.types.DescVarianceNorm: Constructor for the DescSelectionWriter object
deselect() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Deselects all selected atoms
destroyAtom(JOEAtom) - Method in class joelib.molecule.JOEMol: Destroys atom.
destroyBond(JOEBond) - Method in class joelib.molecule.JOEMol: Destroys all bond.
determinant() - Method in class joelib.math.Matrix3x3: Description of the Method
determineFRJ(JOEMol) - Static method in class joelib.util.JHM: Description of the Method
DFS - class joelib.algo.DFS.: Depth First Search.
DFS() - Constructor for class joelib.algo.DFS: Constructor for the KierShape1 object
DFSResult - class joelib.algo.DFSResult.: Result of a DFS.
DFSResult() - Constructor for class joelib.algo.DFSResult: Constructor for the DFSResult object
differentialShannon(int[], int[], int, int, int) - Static method in class wsi.ra.tool.StatisticUtils: Computes differential shannon entropy
dimension - Static variable in class joelib.io.types.MDLSD: Description of the Field
discovered - Variable in class joelib.algo.DFSResult: Description of the Field
displayAndAromElem(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displayAtomExpr(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displayAtomLeaf(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displayBondExpr(BondExpr, OutputStream) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
displayBondLeaf(BondExpr, OutputStream) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
displayOrAromElem(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displaySimpleAtomExpr(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displaySMARTSAtom(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displaySMARTSBond(BondExpr, OutputStream) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
displaySMARTSPart(Pattern, ParseState, int, OutputStream) - Static method in class joelib.smarts.ParseSmart: Description of the Method
distance(Point3D, Point3D) - Static method in class joelib.gui.molviewer.java3d.math.geometry.Geometry: calculate distance between two points in 3D space
DistanceCalculation - class joelib.process.types.DistanceCalculation.: Calling processor classes if the filter rule fits.
DistanceCalculation() - Constructor for class joelib.process.types.DistanceCalculation: Constructor for the DescSelectionWriter object
DistanceMatrix - class joelib.desc.types.DistanceMatrix.: Calculates the Distance Matrix (shortest paths from each atom to each atom) of a molecule
DistanceMatrix() - Constructor for class joelib.desc.types.DistanceMatrix: Constructor for the DistanceMatrix object
distanceTo(Point3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: calculate distance from this point to the other
distanceTo(Point3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.Line: Return the distance from a given point to the line
distSq(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
distSquareTo(Point3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: calculate the squre of distance from this point to the other
div(int) - Method in class joelib.math.XYZVector: Description of the Method
div(XYZVector, int) - Static method in class joelib.math.XYZVector: Description of the Method
div(XYZVector, XYZVector, double) - Static method in class joelib.math.XYZVector: Description of the Method
divideAndRound(int, int) - Static method in class joelib.gui.molviewer.java3d.math.util.MathUtils: Perform a division of the input integers, and round to the next integer if the divisor is not a even multiple of the dividend.
diving(double) - Method in class joelib.math.XYZVector: Description of the Method
diving(double) - Method in class joelib.math.Matrix3x3: Description of the Method
dot(GeoVector3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: dot product with another vector
dot(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
DOUBLE - Static variable in class joelib.desc.result.DynamicArrayResult: Description of the Field
DOUBLE - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Double bond type
doubleArrayFromString(Reader) - Static method in class joelib.util.LineArrayHelper: Description of the Method
doubleArrayFromString(Reader, int) - Static method in class joelib.util.LineArrayHelper: Gets double arrays from a Reader.
doubleArrayFromString(String) - Static method in class joelib.util.LineMatrixHelper: Description of the Method
doubleArrayFromString(String) - Static method in class joelib.util.LineArrayHelper: Description of the Method
doubleArrayFromString(String) - Method in class joelib.util.ArrayHelper: Loads double array from String .
doubleArrayFromString(String, int) - Static method in class joelib.util.LineArrayHelper: Description of the Method
doubleArrayFromString(String, String, int) - Static method in class joelib.util.ArrayHelper: Loads double array from String .
DoubleArrayResult - class joelib.desc.result.DoubleArrayResult.: Double array results of variable size.
DoubleArrayResult() - Constructor for class joelib.desc.result.DoubleArrayResult: Constructor for the IntArrayResult object
DoubleInt - class joelib.util.types.DoubleInt.: Double and integer value.
DoubleInt() - Constructor for class joelib.util.types.DoubleInt: Constructor for the IntInt object
DoubleInt(double, int) - Constructor for class joelib.util.types.DoubleInt: Constructor for the IntInt object
doubleMatrixFromString(String, String) - Static method in class joelib.util.MatrixHelper: Description of the Method
doubleMatrixFromString(String, Vector) - Method in class joelib.util.MatrixHelper: Description of the Method
DoubleMatrixResult - class joelib.desc.result.DoubleMatrixResult.: Double matrix results of variable size.
DoubleMatrixResult() - Constructor for class joelib.desc.result.DoubleMatrixResult: Constructor for the IntMatrixResult object
DoubleResult - class joelib.desc.result.DoubleResult.: Double results.
DoubleResult() - Constructor for class joelib.desc.result.DoubleResult: Constructor for the DoubleResult object
DoubleType - class joelib.util.types.DoubleType.: Two integers to represent a (BINARY) double value.
DoubleType() - Constructor for class joelib.util.types.DoubleType
DragBehavior - class joelib.gui.molviewer.java3d.graphics3D.DragBehavior.: Description of the Class
dst - Variable in class joelib.smarts.BondSpec: Index of the SMARTS atom expression which is the destination of this bond expression.
dumpAtomExpr(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
dumpBondExpr(BondExpr, OutputStream) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
dumpBondLeaf(BondExpr, OutputStream) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
DX_TYPE - Static variable in class joelib.jcamp.JCAMPDataBlock
DynamicArrayResult - class joelib.desc.result.DynamicArrayResult.: Dynamic array results of variable size.
DynamicArrayResult() - Constructor for class joelib.desc.result.DynamicArrayResult: Constructor for the IntArrayResult object

E

ele - Variable in class joelib.math.Matrix3x3: Description of the Field
ElectronAffinity - class joelib.desc.types.ElectronAffinity.: Electron affinity.
ElectronAffinity() - Constructor for class joelib.desc.types.ElectronAffinity: Constructor for the KierShape1 object
ElectronegativityPauling - class joelib.desc.types.ElectronegativityPauling.: Electronegativity after Pauling.
ElectronegativityPauling() - Constructor for class joelib.desc.types.ElectronegativityPauling: Constructor for the KierShape1 object
elem - Variable in class joelib.util.types.Template: Description of the Field
Element - class joelib.molecule.Element.: Element.
Element() - Constructor for class joelib.molecule.Element
elementAt(int) - Method in class wsi.ra.tool.SortedVector: Returns the component at the specified index.
elements() - Method in class wsi.ra.tool.SortedVector: Returns an enumeration of the components of this vector.
ELEMMAX - Static variable in class joelib.smarts.ParseSmart: Description of the Field
empty() - Method in class joelib.molecule.JOEMol: Returns true if this molecule contains no atoms.
empty() - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
empty() - Method in class joelib.util.JOEBitVec: Description of the Method
endBit() - Method in class joelib.util.JOEBitVec: Description of the Method
endDocument() - Method in class joelib.io.types.cml.MoleculeFileCDO: Procedure required by the CDOInterface.
endModify() - Method in class joelib.molecule.JOEMol: Ends modification of atoms and decrease modification counter.
endModify(boolean) - Method in class joelib.molecule.JOEMol: Ends modification of atoms and decrease modification counter.
endObject(String) - Method in class joelib.io.types.cml.MoleculeFileCDO: Procedure required by the CDOInterface.
entropy - Variable in class wsi.ra.tool.ArrayBinning: Description of the Field
eol - Static variable in class joelib.util.JHM
eq(double, double) - Static method in class wsi.ra.tool.StatisticUtils: Tests if a is equal to b.
EQ(String, String) - Static method in class joelib.util.JOEHelper: Description of the Method
EQn(String, String, int) - Static method in class joelib.util.JOEHelper: Description of the Method
EQUAL - Static variable in class joelib.process.filter.SMARTSFilter
EQUAL - Static variable in class joelib.process.filter.NativeValueFilter
equalAtomExpr(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
equals(Description) - Method in class joelib.desc.Description: Description of the Method
equals(IOType) - Method in class joelib.io.IOType: Description of the Method
equals(JOEGenericData) - Method in class joelib.data.JOEGenericData
equals(Object) - Method in class joelib.algo.morgan.AtomDoubleParent
equals(Object) - Method in class joelib.algo.morgan.AtomDoubleComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.algo.morgan.AtomDouble
equals(Object) - Method in class joelib.data.JOEDataType: Description of the Method
equals(Object) - Method in class joelib.molecule.BondComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.molecule.AtomZPosComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.process.ProcessPipeEntry: Two entries are equal, if they contain the same JOEProcess object.
equals(Object) - Method in class joelib.ring.RingSizeComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.sort.VVIntComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.sort.RotorComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.util.JOEProperty
equals(Object) - Method in class joelib.util.BitSet14: Compares this object against the specified object.
equals(Object) - Method in class joelib.util.types.IntIntInt
equals(Object) - Method in class joelib.util.types.IntInt
equals(Object) - Method in class joelib.util.types.DoubleInt
equals(Object) - Method in class joelib.util.types.AtomZPos: Compare this object with another object.
equals(ViewerMolecule) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Compares this molecule with another
equals(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
equals(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
EuklidianComparison - class joelib.test.EuklidianComparison.: Example for converting molecules.
EuklidianComparison() - Constructor for class joelib.test.EuklidianComparison
evalAtomExpr(AtomExpr, JOEAtom) - Method in class joelib.smarts.ParseSmart: Description of the Method
evalBondExpr(BondExpr, JOEBond) - Static method in class joelib.smarts.ParseSmart: Description of the Method
excludeSmallRing(JOEMol) - Method in class joelib.data.JOEAromaticTyper: Description of the Method
existInstance() - Static method in class wsi.ra.tool.PropertyHolder: Description of the Method
existsBinningFileFor(String) - Static method in class joelib.process.types.DescBinning: Description of the Method
existsMatrixFileFor(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
existsStatisticFileFor(String) - Static method in class joelib.process.types.DescStatistic: Description of the Method
expandKekule(JOEMol, Vector, AtomIterator, int[], boolean) - Static method in class joelib.util.JHM
explicitHydrogenCount() - Method in class joelib.molecule.JOEAtom: Returns the number of explicit hydrogens.
expr - Variable in class joelib.smarts.BondSpec: Representation of the SMARTS bond expression.
expr - Variable in class joelib.smarts.AtomSpec: Representation of the SMARTS atom expression.
External - interface joelib.ext.External.: Interface definition for calling external programs from JOELib.
ExternalException - exception joelib.ext.ExternalException.: External molecule process exception.
ExternalException() - Constructor for class joelib.ext.ExternalException: Constructor for the DescriptorException object
ExternalException(String) - Constructor for class joelib.ext.ExternalException: Constructor for the DescriptorException object
ExternalFactory - class joelib.ext.ExternalFactory.: Factory class to get external molecule process classes.
ExternalHelper - class joelib.ext.ExternalHelper.: Some helper methods for calling external programs.
ExternalInfo - class joelib.ext.ExternalInfo.: Informations for an external process.
ExternalInfo(String, String, String, String, String, String, Vector) - Constructor for class joelib.ext.ExternalInfo: Constructor for the DescriptorInfo object
externals() - Method in class joelib.ext.ExternalFactory: Description of the Method

F

fastSingleMatch(JOEMol, Pattern, Vector) - Method in class joelib.smarts.ParseSmart
filenameToType(String) - Method in class joelib.io.IOTypeHolder: Description of the Method
FileUtilities - class wsi.ra.io.FileUtilities.: Usefull functions for file handling.
FileUtilities() - Constructor for class wsi.ra.io.FileUtilities
fillOrth(double, double, double, double, double, double) - Method in class joelib.math.Matrix3x3: Description of the Method
Filter - interface joelib.process.filter.Filter.: Interface definition for filter options for a molecule process.
FilterException - exception joelib.process.filter.FilterException.: Molecule process filter exception.
FilterException() - Constructor for class joelib.process.filter.FilterException: Constructor for the DescriptorException object
FilterException(String) - Constructor for class joelib.process.filter.FilterException: Constructor for the DescriptorException object
FilterFactory - class joelib.process.filter.FilterFactory.: Factory class to get molecule process filter classes.
FilterInfo - class joelib.process.filter.FilterInfo.: Molecule process filter informations.
FilterInfo(String, String, String) - Constructor for class joelib.process.filter.FilterInfo: Constructor for the DescriptorInfo object
filters() - Method in class joelib.process.filter.FilterFactory: Description of the Method
finalize() - Method in class joelib.data.JOETypeTable: Description of the Method
finalize() - Method in class joelib.data.JOEResidueData: Description of the Method
finalize() - Method in class joelib.data.JOEPhModel: Description of the Method
finalize() - Method in class joelib.data.JOEGroupContribution: Description of the Method
finalize() - Method in class joelib.data.JOEGlobalDataBase: Description of the Method
finalize() - Method in class joelib.data.JOEGenericData: Description of the Method
finalize() - Method in class joelib.data.JOEExternalBond: Description of the Method
finalize() - Method in class joelib.data.JOEElementTable: Description of the Method
finalize() - Method in class joelib.data.JOEChemTransformation: Description of the Method
finalize() - Method in class joelib.data.JOEAtomTyper: Description of the Method
finalize() - Method in class joelib.data.JOEAromaticTyper: Description of the Method
finalize() - Method in class joelib.io.JOEFileFormat: Description of the Method
finalize() - Method in class joelib.math.XYZVector: Description of the Method
finalize() - Method in class joelib.math.JOESqrtTbl: Description of the Method
finalize() - Method in class joelib.math.JOECoordTrans: Description of the Method
finalize() - Method in class joelib.molecule.JOERTree: Desctructor
finalize() - Method in class joelib.molecule.JOEResidue
finalize() - Method in class joelib.molecule.JOEMolVector: Functions for dealing with groups of molecules.
finalize() - Method in class joelib.molecule.JOEMol: Destructor for this molecule.
finalize() - Method in class joelib.molecule.JOEBond: Description of the Method
finalize() - Method in class joelib.molecule.JOEAtom: Destructor for the JOEAtom object.
finalize() - Method in class joelib.molecule.GenericDataHolder: Description of the Method
finalize() - Method in class joelib.molecule.charge.JOEGastChrg: Description of the Method
finalize() - Method in class joelib.molecule.charge.GasteigerState: Description of the Method
finalize() - Method in class joelib.ring.JOERingSearch: Description of the Method
finalize() - Method in class joelib.smarts.Patty
finalize() - Method in class joelib.smarts.JOESSMatch: Description of the Method
finalize() - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
finalize() - Method in class joelib.smiles.JOESmiNode: Description of the Method
finalize() - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
findAromaticBonds(JOEMol) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
findAromaticBonds(JOEMol, JOEAtom, int) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
findAtom(float, float, float, float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Returns closest atom to point within FINDRADIUS, null if nothing is found,
findBB() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Determines bounding box of a molecule (sets xmax,xmin,ymax,ymin,zmax,zmin)
findCenterAndNormal(XYZVector, XYZVector, XYZVector) - Method in class joelib.ring.JOERing: Description of the Method
findChildren(Vector, int, int) - Method in class joelib.molecule.JOEMol: Locates all atoms for which there exists a path to second without going through first children does not include second .
findChildren(Vector, JOEAtom, JOEAtom) - Method in class joelib.molecule.JOEMol: locates all atoms for which there exists a path to 'second' without going through 'first' children does not include 'second'
findChiralCenters() - Method in class joelib.molecule.JOEMol: Description of the Method
findClosureBonds(JOEMol) - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
findLargestFragment(JOEBitVec) - Method in class joelib.molecule.JOEMol: each vector contains the atom numbers of a contig fragment the vectors are sorted by size from largest to smallest
findRingAtomsAndBonds() - Method in class joelib.molecule.JOEMol: Description of the Method
findRings(JOEMol, Vector, JOEBitVec, JOEBitVec, int, int) - Static method in class joelib.ring.JOERingSearch
findRings(JOEMol, Vector, JOEBitVec, JOEBitVec, int, int) - Static method in class joelib.util.JHM
findSSSR() - Method in class joelib.molecule.JOEMol: Finds the Smallest Set of Smallest Rings (SSSR).
finished - Variable in class joelib.algo.DFSResult: Description of the Field
firstBit() - Method in class joelib.util.JOEBitVec: Returns the index of the first bit that is set to true.
firstElement() - Method in class wsi.ra.tool.SortedVector: Returns the first component (the item at index 0) of this vector.
flag - Variable in class joelib.util.types.Template: Description of the Field
Flat - class joelib.io.types.Flat.: Flat file format support.
Flat() - Constructor for class joelib.io.types.Flat: Constructor for the Smiles object
flip(int) - Method in class joelib.util.BitSet14: Sets the bit at the specified index to to the complement of its current value.
flip(int, int) - Method in class joelib.util.BitSet14: Sets each bit from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the complement of its current value.
fold(int) - Method in class joelib.util.JOEBitVec: Description of the Method
FOO - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
formatDescription(IOType) - Method in class joelib.algo.DFSResult: Description of the Method
formatDescription(IOType) - Method in class joelib.algo.BFSResult: Description of the Method
formatDescription(IOType) - Method in interface joelib.desc.DescResult
formatDescription(IOType) - Method in class joelib.desc.result.IntResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.IntMatrixResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.IntBitArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.IntArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.DynamicArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.DoubleResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.DoubleMatrixResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.DoubleArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.BitResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.BitArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.APropIntResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.APropDoubleResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.APropDoubleArrResult: Description of the Method
FProbability(double, int, int) - Static method in class wsi.ra.tool.Statistics: Computes probability of F-ratio.
FractionRotatableBonds - class joelib.desc.types.FractionRotatableBonds.: Fraction of rotatable bonds.
FractionRotatableBonds() - Constructor for class joelib.desc.types.FractionRotatableBonds: Constructor for the KierShape2 object
FREE_ELECTRONS_NOT_DEF - Static variable in class joelib.molecule.JOEAtom
freeAtomExpr(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
freeBondExpr(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
freePattern(Pattern) - Static method in class joelib.smarts.Pattern: Description of the Method
fromBoolArr(boolean[]) - Method in class joelib.util.JOEBitVec
fromFile(String) - Method in class joelib.process.types.DescStatistic: Description of the Method
fromFile(String) - Method in class joelib.process.types.DescBinning: Description of the Method
fromFileFor(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
fromFileFor(String) - Method in class joelib.process.types.DescStatistic
fromFileFor(String) - Method in class joelib.process.types.DescBinning
fromIntArr(int[]) - Method in class joelib.util.JOEBitVec: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.algo.DFSResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.algo.BFSResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in interface joelib.desc.DescResult
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.IntResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.IntMatrixResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.IntBitArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.IntArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.DynamicArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.DoubleResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.DoubleMatrixResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.DoubleArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.BitResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.BitArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.APropIntResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.APropDoubleResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.APropDoubleArrResult: Description of the Method
fromResource(String, String, Hashtable) - Method in class wsi.ra.io.BatchScriptReplacer: Description of the Method
fromString(IOType, String) - Method in class joelib.algo.DFSResult: Description of the Method
fromString(IOType, String) - Method in class joelib.algo.BFSResult: Description of the Method
fromString(IOType, String) - Method in interface joelib.desc.DescResult
fromString(IOType, String) - Method in class joelib.desc.result.IntResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.IntMatrixResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.IntBitArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.IntArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.DynamicArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.DoubleResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.DoubleMatrixResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.DoubleArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.BitResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.BitArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.APropIntResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.APropDoubleResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.APropDoubleArrResult: Description of the Method
fromString(String) - Method in class joelib.process.filter.SMARTSFilter
fromString(String) - Method in class joelib.process.filter.NativeValueFilter
fromString(String) - Method in class joelib.util.JOEBitVec: Reads this bit vector from a String.
fromString(String, boolean) - Method in class joelib.process.filter.SMARTSFilter
fromVecInt(Vector) - Method in class joelib.util.JOEBitVec

G

GasteigerMarsili - class joelib.molecule.charge.GasteigerMarsili.: Partial charge calculation.
GasteigerMarsili() - Constructor for class joelib.molecule.charge.GasteigerMarsili: Constructor for the partial charge calculation.
GasteigerState - class joelib.molecule.charge.GasteigerState.: Stores actual Gasteiger charge state.
GasteigerState() - Constructor for class joelib.molecule.charge.GasteigerState: Constructor for the GasteigerState object
GCPredictor - class joelib.algo.contribution.GCPredictor.: Value prediction based on a group contribution model.
GCPredictor() - Constructor for class joelib.algo.contribution.GCPredictor
generate2D(JOEMol) - Static method in class joelib.util.CDKTools
generateAromElem(int, int) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
generateDefaultBond() - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
generateDescInfo(String, Class, String, int, String, String) - Static method in class joelib.desc.DescriptorHelper: Faciliates the generation of a descriptor information.
generatedOutput - Variable in class joelib.test.EuklidianComparison: Description of the Field
generatedOutput - Variable in class joelib.test.ConvertSkip: Description of the Field
generatedOutput - Variable in class joelib.test.Convert: Description of the Field
generatedOutput - Variable in class joelib.test.Comparison: Description of the Field
generatedOutput - Variable in class joelib.test.Combine: Description of the Field
generateElement(int) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
generateSMARTSString(Pattern, OutputStream) - Static method in class joelib.smarts.ParseSmart: Description of the Method
GenericDataHolder - class joelib.molecule.GenericDataHolder.: Holder class of generic data objects for one molecule.
GenericDataHolder(JOEMol, int, int) - Constructor for class joelib.molecule.GenericDataHolder: Constructor for the GenericDataHolder object
GenericDataIterator - class joelib.util.iterator.GenericDataIterator.: Iterator over generic data elements.
genericDataIterator() - Method in class joelib.molecule.JOEMol: Gets an iterator over the generic data elements of this molecule.
genericDataIterator() - Method in class joelib.molecule.GenericDataHolder: Gets the data attribute of the JOEMol object
GenericDataIterator(Vector, Hashtable) - Constructor for class joelib.util.iterator.GenericDataIterator: Constructor for the GenericDataIterator object
GeomDistanceMatrix - class joelib.desc.types.GeomDistanceMatrix.: Geometrical distance matrix.
GeomDistanceMatrix() - Constructor for class joelib.desc.types.GeomDistanceMatrix: Constructor for the DistanceMatrix object
GeometricalDiameter - class joelib.desc.types.GeometricalDiameter.: Calculates the geometrical diameter.
GeometricalDiameter() - Constructor for class joelib.desc.types.GeometricalDiameter
GeometricalRadius - class joelib.desc.types.GeometricalRadius.: Calculates the geometrical radius.
GeometricalRadius() - Constructor for class joelib.desc.types.GeometricalRadius
GeometricalShapeCoefficient - class joelib.desc.types.GeometricalShapeCoefficient.: Calculates the geometrical shape coefficient.
GeometricalShapeCoefficient() - Constructor for class joelib.desc.types.GeometricalShapeCoefficient
Geometry - class joelib.gui.molviewer.java3d.math.geometry.Geometry.: A public class that provides mathematical calculation on some geometry entities.
Geometry() - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Geometry
GeoVector3D - class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D.: A geometric vector class that provides vector computations: length, normalize, dot and cross.
GeoVector3D() - Constructor for class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Default constructor, all component are 0.0
GeoVector3D(double, double, double) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Full constructor
GeoVector3D(GeoVector3D) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: copy constructor
GeoVector3D(Point3D, Point3D) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: constructor
get(double[]) - Method in class joelib.math.XYZVector: Description of the Method
get(double[], int) - Method in class joelib.math.XYZVector: Description of the Method
get(int) - Method in class joelib.util.BitSet14: Returns the value of the bit with the specified index.
get(int) - Method in class wsi.ra.tool.SortedVector: Returns the element at the specified position in this Vector.
get(int, int) - Method in class joelib.math.Matrix3x3: Description of the Method
get(int, int) - Method in class joelib.util.BitSet14: Returns a new BitSet14 composed of bits from this BitSet14 from fromIndex(inclusive) to toIndex(exclusive).
get(String) - Method in class joelib.util.MDMatrixCache
get(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
getAdditionalInformation(String) - Method in class joelib.jcamp.JCAMPParser: Gets the label infoType.
getAllredRochowEN() - Method in class joelib.molecule.JOEElement: Gets the atom electronegativity after Allred and Rochow.
getAllredRochowEN(int) - Method in class joelib.data.JOEElementTable: Gets the atom electronegativity after Allred and Rochow.
getAllTypes() - Static method in class joelib.data.JOEDataType
getArguments() - Method in class joelib.ext.ExternalInfo: Gets the arguments attribute of the ExternalInfo object
getArray() - Method in class joelib.desc.result.DynamicArrayResult: Gets the array attribute of the DynamicArrayResult object
getArray(double[]) - Method in class joelib.math.Matrix3x3: Gets the array attribute of the Matrix3x3 object
getArrayStatistic() - Method in class wsi.ra.tool.ArrayBinning: Gets the descriptorStatistic attribute of the DescStatistic object
getAtom() - Method in class joelib.data.JOEExternalBond: Gets the atom attribute of the JOEExternalBond object
getAtom() - Method in class joelib.smiles.JOESmiNode: Gets the atom attribute of the JOESmiNode object
getAtom(int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtoms: Returns atom at specified index
getAtom(int) - Method in class joelib.molecule.JOEMol: Gets an atom of the JOEMol object Atom index must be between 1 to numAtoms() .
getAtomFromId(int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return an atom in this molecule whose id matches the input id
getAtomicNum() - Method in class joelib.molecule.JOEElement: Gets the atomicNum attribute of the JOEElement object
getAtomicNum() - Method in class joelib.molecule.JOEAtom: Gets the atomic number of the JOEAtom object.
getAtomicNum(int) - Method in class joelib.smarts.JOESmartsPattern: Gets the atomicNum attribute of the JOESmartsPattern object
getAtomicNum(String) - Method in class joelib.data.JOEElementTable: Gets the atomicNum attribute of the JOEElementTable object
getAtomID(JOEAtom) - Method in class joelib.molecule.JOEResidue
getAtomIdToIndex() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return atomIdToIndex
getAtomIdx() - Method in class joelib.molecule.JOERTree: Gets the atom index of this atom tree node.
getAtomPropDescs() - Method in class joelib.desc.DescriptorHelper
getAtoms() - Method in class joelib.ring.JOERing: Returns all atom indexes of atoms which are contained in this ring.
getAttribute() - Method in class joelib.data.JOEGenericData: Gets the attribute attribute of the JOEGenericData object
getBack() - Method in class wsi.ra.tool.Deque: Returns the back DequeNode of this stack.
getBeginAtom() - Method in class joelib.molecule.JOEBond: Gets the beginAtom attribute of the JOEBond object
getBeginAtomIdx() - Method in class joelib.molecule.JOEBond: Gets the beginAtomIdx attribute of the JOEBond object
getBgn() - Method in class joelib.data.JOEVirtualBond: Gets the bgn attribute of the JOEVirtualBond object
getBinaryValue() - Method in interface joelib.desc.BinaryValue
getBinaryValue() - Method in class joelib.desc.result.IntBitArrayResult: Gets the double attribute of the DoubleResult object
getBinaryValue() - Method in class joelib.desc.result.BitResult
getBinaryValue() - Method in class joelib.desc.result.BitArrayResult: Gets the double attribute of the DoubleResult object
getBinning(int) - Method in class joelib.desc.data.MoleculesDescriptorMatrix
getBinning(int, boolean) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
getBlockData() - Method in class joelib.jcamp.JCAMPDataBlock: Gets the data of this JCAMP block.
getBlockID() - Method in class joelib.jcamp.JCAMPDataBlock: Gets the ID of this JCAMP block.
getBlockType() - Method in class joelib.jcamp.JCAMPDataBlock: Gets the type of this JCAMP block.
getBO() - Method in class joelib.molecule.JOEBond: Gets the bO attribute of the JOEBond object
getBond() - Method in class joelib.data.JOEExternalBond: Gets the bond attribute of the JOEExternalBond object
getBond(int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBonds: Returns bond at specified index
getBond(int) - Method in class joelib.molecule.JOEMol: Gets a bond of the JOEMol object.
getBond(int, int) - Method in class joelib.molecule.JOEMol: Gets the bond attribute of the JOEMol object Atom index must be between 1 to numAtoms() .
getBond(IntIntInt, int) - Method in class joelib.smarts.JOESmartsPattern: Gets the bond attribute of the JOESmartsPattern object
getBond(JOEAtom) - Method in class joelib.molecule.JOEAtom: Gets the bond attribute of the JOEAtom object
getBond(JOEAtom, JOEAtom) - Method in class joelib.molecule.JOEMol: Gets the bond attribute of the JOEMol object
getBondExprIndex(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Gets the bondExprIndex attribute of the ParseSmart class
getBondFromId(int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return a bond in this molecule whose id matches the input id
getBondLeafIndex(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Gets the bondLeafIndex attribute of the ParseSmart class
getBondOrder() - Method in class joelib.molecule.JOEBond: Gets the bondOrder attribute of the JOEBond object
getBondPropDescs() - Method in class joelib.desc.DescriptorHelper
getBonds() - Method in class joelib.molecule.JOEAtom: Returns a Vector for all bonds in this atom.
getBooleanArray() - Method in class joelib.desc.result.DynamicArrayResult: Gets the booleanArray attribute of the DynamicArrayResult object
getBoRad() - Method in class joelib.molecule.JOEElement: Gets the boRad attribute of the JOEElement object
getBORad(int) - Method in class joelib.data.JOEElementTable: Gets the bORad attribute of the JOEElementTable object
getBytesFromResourceLocation(String) - Method in class wsi.ra.tool.ResourceLoader: Gets the byte data from a file at the given resource location.
getChain() - Method in class joelib.molecule.JOEResidue
getChainNum() - Method in class joelib.molecule.JOEResidue
getCharge() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the atomic charge
getCharge(int) - Method in class joelib.smarts.JOESmartsPattern: Gets the charge attribute of the JOESmartsPattern object
getCharNumber() - Method in class cformat.ScanfReader: Gets the current character number (equal to the number of characters that have been consumed by the stream).
getChiralFlag(AtomExpr) - Static method in class joelib.smarts.ParseSmart: Gets the chiralFlag attribute of the ParseSmart class
getChiralStereo(JOESmiNode, StringBuffer) - Method in class joelib.smiles.JOEMol2Smi: Gets the chiralStereo attribute of the JOEMol2Smi object
getCIdx() - Method in class joelib.molecule.JOEAtom: Gets the cIdx attribute of the JOEAtom object
getClosureAtoms(JOEAtom, Vector) - Method in class joelib.smiles.JOEMol2Smi
getClosureDigits(JOEAtom) - Method in class joelib.smiles.JOEMol2Smi
getColor() - Method in class joelib.molecule.JOEElement: Gets the color attribute of the JOEElement object
getColor(int) - Method in class joelib.data.JOEElementTable: Gets the color attribute of the JOEElementTable object
getColorFromType() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Gets the colorFromType attribute of the ViewerAtom object
getComment() - Method in class joelib.gui.molviewer.java3d.math.geometry.Angle: Return comment
getComment() - Method in class joelib.process.types.DescSelectionWriter: Gets the comment attribute of the DescSelectionWriter object
getConformer(int) - Method in class joelib.molecule.JOEMol: Gets the conformer attribute of the JOEMol object
getConformers() - Method in class joelib.molecule.JOEMol: Returns a Vector of all conformer coordinates (double[] values).
getCoordinate() - Method in class joelib.molecule.JOEAtom: Gets the coordinate attribute of the JOEAtom object
getCoordinateIdx() - Method in class joelib.molecule.JOEAtom: Gets the coordinateIdx attribute of the JOEAtom object.
getCoordinates() - Method in class joelib.molecule.JOEMol: Gets the coordinate array of this molecule.
getCorrelationCoefficient(double[], double[]) - Static method in class wsi.ra.tool.StatisticUtils: Returns the correlation coefficient r^2.
getCovalentRad() - Method in class joelib.molecule.JOEElement: Gets the covalentRad attribute of the JOEElement object
getCovalentRad(int) - Method in class joelib.data.JOEElementTable: Gets the covalentRad attribute of the JOEElementTable object
getCurrentValence(JOEAtom) - Static method in class joelib.util.JHM: Gets the currentValence attribute of the JHM class
getData() - Method in class joelib.data.JOERgroupData: Gets the Rgroup informations.
getData() - Method in class joelib.data.JOECommentData: Gets the data attribute of the JOECommentData object
getData() - Method in class joelib.jcamp.LabelData
getData() - Method in class joelib.ring.JOERingData
getData(JOEDataType) - Method in class joelib.molecule.JOEMol: Returns the first data entry of the given data type.
getData(JOEDataType) - Method in class joelib.molecule.GenericDataHolder: Gets the data attribute of the GenericDataHolder object
getData(String) - Method in class joelib.molecule.JOEMol: Returns the data entry with the given name, if multiple data entries exists only the first one is taken.
getData(String, boolean) - Method in class joelib.molecule.JOEMol: Returns the data entry with the given name, if multiple data entries exists only the first one is taken.
getData(String, boolean) - Method in class joelib.molecule.GenericDataHolder: Gets the data attribute of the GenericDataHolder object
getDataDescription() - Method in class joelib.desc.result.DynamicArrayResult: Gets the dataDescription attribute of the DynamicArrayResult object
getDataInLine(String) - Static method in class joelib.jcamp.JCAMPDataBlock: Gets the 'Label Data Record'-data of the actual line.
getDataType() - Method in class joelib.data.JOEGenericData: Gets the dataType attribute of the JOEGenericData object
getDataType() - Method in class joelib.jcamp.JCAMPParser: Gets the data type of this data set.
getDataUnit() - Method in class joelib.desc.result.DynamicArrayResult: Gets the dataUnit attribute of the DynamicArrayResult object
getDefaultAtoms() - Method in class joelib.desc.AtomsCounter
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfS: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfP: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfO: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfN: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfI: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfHal: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfF: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfCl: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfC: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfBr: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfB: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAttr() - Method in class joelib.data.JOEDataType: Gets the defaultAttr attribute of the JOEDataType object
getDefaultProperty() - Method in class joelib.util.JOEProperty
getDefaultSMARTS() - Method in class joelib.desc.SMARTSCounter
getDefaultSMARTS() - Method in class joelib.desc.types.SOGroups
getDefaultSMARTS() - Method in class joelib.desc.types.SO2Groups
getDefaultSMARTS() - Method in class joelib.desc.types.OSOGroups
getDefaultSMARTS() - Method in class joelib.desc.types.NO2Groups
getDefaultSMARTS() - Method in class joelib.desc.types.HydrophobicGroups
getDefaultSMARTS() - Method in class joelib.desc.types.HBD2
getDefaultSMARTS() - Method in class joelib.desc.types.HBD1
getDefaultSMARTS() - Method in class joelib.desc.types.HBA2
getDefaultSMARTS() - Method in class joelib.desc.types.HBA1
getDefaultSMARTS() - Method in class joelib.desc.types.BasicGroups
getDefaultSMARTS() - Method in class joelib.desc.types.AromaticOHGroups
getDefaultSMARTS() - Method in class joelib.desc.types.AliphaticOHGroups
getDefaultSMARTS() - Method in class joelib.desc.types.AcidicGroups
getDelimiter() - Method in class joelib.process.types.DescSelectionWriter: Gets the delimiter attribute of the DescSelectionWriter object
getDepth() - Method in class joelib.jcamp.JCAMPDataBlock: Gets the depth of this JCAMP block.
getDequeIterator() - Method in class wsi.ra.tool.Deque: Returns an DequeIterator for this stack, which starts with the front DequeNode.
getDescBinning(IOType, String, int) - Static method in class joelib.process.types.DescBinning: Gets the descBinning attribute of the DescBinning class
getDescContainsNaN() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descContainsNaN attribute of the MoleculesDescriptorMatrix object
getDescFromMolByIdentifier(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descFromMolByIdentifier attribute of the MoleculesDescriptorMatrix object
getDescFromMolByIdentifier(String, boolean) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descFromMol attribute of the MoleculesDescriptorMatrix object
getDescFromMolByIndex(int) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descFromMolByIndex attribute of the MoleculesDescriptorMatrix object
getDescFromMolByIndex(int, boolean) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descFromMol attribute of the MoleculesDescriptorMatrix object
getDescFromMolByName(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descFromMolByName attribute of the MoleculesDescriptorMatrix object
getDescFromMolByName(String, boolean) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descFromMol attribute of the MoleculesDescriptorMatrix object
getDescInfo() - Method in class joelib.algo.DFS: Description of the Method
getDescInfo() - Method in class joelib.algo.BFS: Description of the Method
getDescInfo() - Method in class joelib.desc.SMARTSCounter: Description of the Method
getDescInfo() - Method in class joelib.desc.SimpleIntDesc: Description of the Method
getDescInfo() - Method in class joelib.desc.SimpleDoubleDesc: Description of the Method
getDescInfo() - Method in interface joelib.desc.Descriptor: Description of the Method
getDescInfo() - Method in class joelib.desc.AtomsCounter: Description of the Method
getDescInfo() - Method in class joelib.desc.types.SSKey3DS: Description of the Method
getDescInfo() - Method in class joelib.desc.types.RotatableBonds: Description of the Method
getDescInfo() - Method in class joelib.desc.types.HeteroCycles: Description of the Method
getDescInfo() - Method in class joelib.desc.types.HeavyBonds: Description of the Method
getDescInfo() - Method in class joelib.desc.types.GraphPotentials: Description of the Method
getDescInfo() - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
getDescInfo() - Method in class joelib.desc.types.FractionRotatableBonds: Description of the Method
getDescInfo() - Method in class joelib.desc.types.ElectronegativityPauling: Description of the Method
getDescInfo() - Method in class joelib.desc.types.ElectronAffinity: Description of the Method
getDescInfo() - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
getDescInfo() - Method in class joelib.desc.types.Autocorrelation: Description of the Method
getDescInfo() - Method in class joelib.desc.types.AtomVanDerWaalsVolume: Description of the Method
getDescInfo() - Method in class joelib.desc.types.AtomValence: Description of the Method
getDescInfo() - Method in class joelib.desc.types.AtomMass: Description of the Method
getDescInfo() - Method in class joelib.desc.types.AromaticBonds: Description of the Method
getDescInfo() - Method in class joelib.molecule.charge.GasteigerMarsili: Description of the Method
getDescInfo(String) - Method in class joelib.desc.DescriptorHelper: Returns a descriptor information for the given descriptor name.
getDescNames() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descNames attribute of the MoleculesDescriptorMatrix object
getDescResult(String) - Method in class joelib.desc.ResultFactory: Gets the descResult attribute of the ResultFactory class
getDescription() - Method in class joelib.algo.DFS: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.algo.BFS: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.SMARTSCounter: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.SimpleIntDesc: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.SimpleDoubleDesc: Gets the description attribute of the Descriptor object
getDescription() - Method in interface joelib.desc.Descriptor: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.AtomsCounter: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.SSKey3DS: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.RotatableBonds: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.HeteroCycles: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.HeavyBonds: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.GraphPotentials: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.GeomDistanceMatrix: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.FractionRotatableBonds: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.ElectronegativityPauling: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.ElectronAffinity: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.DistanceMatrix: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.Autocorrelation: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.AtomVanDerWaalsVolume: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.AtomValence: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.AtomMass: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.AromaticBonds: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.molecule.charge.GasteigerMarsili: Gets the description attribute of the Descriptor object
getDescriptionFile() - Method in class joelib.desc.DescDescription: Description of the Method
getDescriptionFile() - Method in class joelib.ext.SimpleExternalProcess: Gets the descriptionFile attribute of the Corina object
getDescriptionFile() - Method in interface joelib.ext.External
getDescriptionFile() - Method in class joelib.util.types.BasicFactoryInfo: Gets the descriptionFile attribute of the ProcessInfo object
getDescriptor(String) - Static method in class joelib.desc.DescriptorFactory
getDescriptor(String, Map) - Static method in class joelib.desc.DescriptorFactory: Gets the molReader attribute of the JOEFileFormat class.
getDescriptorBinning(String) - Method in class joelib.process.types.DescBinning: Gets the descriptorBinning attribute of the DescBinning object
getDescriptors() - Method in class joelib.process.types.DescStatistic: Gets the descriptors attribute of the DescStatistic object
getDescriptors() - Method in class joelib.process.types.DescBinning: Gets the descriptors attribute of the DescBinning object
getDescriptorStatistic(String) - Method in class joelib.process.types.DescStatistic: Gets the descriptorStatistic attribute of the DescStatistic object
getDescStatistic() - Method in class joelib.process.types.DescBinning: Gets the descStatistic attribute of the DescBinning object
getDescStatistic(IOType, String) - Static method in class joelib.process.types.DescStatistic: Gets the descStatistic attribute of the DescStatistic class
getDescValues(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descValues attribute of the MoleculesDescriptorMatrix object
getDescValues(String[]) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descValues attribute of the MoleculesDescriptorMatrix object
getDescValues(String[], boolean, int[], int[]) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descValues attribute of the MoleculesDescriptorMatrix object
getDescValues(String, boolean) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descValues attribute of the MoleculesDescriptorMatrix object
getDFFVector(JOEMol, Vector, JOEBitVec) - Static method in class joelib.util.JHM
getDistanceValues() - Method in class joelib.process.types.DistanceCalculation
getDouble() - Method in class joelib.desc.result.DoubleResult: Gets the double attribute of the DoubleResult object
getDouble() - Method in class joelib.desc.result.APropDoubleResult: Gets the double attribute of the DoubleResult object
getDouble(Object, String) - Method in class wsi.ra.tool.PropertyHolder
getDouble(Properties, Object, String) - Static method in class wsi.ra.tool.PropertyHolder
getDouble(Properties, String) - Static method in class wsi.ra.tool.PropertyHolder: Gets the double attribute of the PropertyHolder class
getDouble(Properties, String, double, double, double) - Static method in class wsi.ra.tool.PropertyHolder: Gets the double attribute of the PropertyHolder class
getDoubleArray() - Method in class joelib.desc.result.DynamicArrayResult: Gets the doubleArray attribute of the DynamicArrayResult object
getDoubleArray() - Method in class joelib.desc.result.DoubleArrayResult: Gets the double attribute of the IntArrayResult object
getDoubleNV() - Method in interface joelib.desc.NativeValue
getDoubleNV() - Method in class joelib.desc.result.IntResult: Gets the doubleNV attribute of the IntResult object
getDoubleNV() - Method in class joelib.desc.result.DoubleResult: Gets the doubleNV attribute of the DoubleResult object
getDoubleNV() - Method in class joelib.desc.result.APropIntResult: Gets the doubleNV attribute of the APropIntResult object
getDoubleNV() - Method in class joelib.desc.result.APropDoubleResult: Gets the doubleNV attribute of the APropDoubleResult object
getDoubleValue(int) - Method in class joelib.desc.result.BondIntResult
getDoubleValue(int) - Method in class joelib.desc.result.BondDynamicResult: Gets the doubleValue attribute of the AtomDynamicResult object
getDoubleValue(int) - Method in class joelib.desc.result.BondDoubleResult
getDoubleValue(int) - Method in class joelib.desc.result.AtomIntResult: Gets the doubleValue attribute of the AtomIntResult object
getDoubleValue(int) - Method in class joelib.desc.result.AtomDynamicResult: Gets the doubleValue attribute of the AtomDynamicResult object
getDoubleValue(int) - Method in class joelib.desc.result.AtomDoubleResult
getDoubleValue(int) - Method in class joelib.desc.result.APropDoubleArrResult
getDoubleValue(int) - Method in interface joelib.molecule.types.BondProperties
getDoubleValue(int) - Method in interface joelib.molecule.types.AtomProperties: Gets the doubleValue attribute of the AtomProperties object
getDoubleValue(int, int) - Method in interface joelib.molecule.types.AtomAtomProperties
getDoubleValue(JOEMol) - Method in class joelib.desc.SimpleDoubleDesc
getDoubleValue(JOEMol) - Method in class joelib.desc.types.ZagrebIndex2
getDoubleValue(JOEMol) - Method in class joelib.desc.types.ZagrebIndex1: Gets the doubleValue attribute of the ZagrebIndex1 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.NumberOfBonds: Gets the doubleValue attribute of the KierShape1 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.NumberOfAtoms: Gets the doubleValue attribute of the KierShape1 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.MolecularWeight: Gets the doubleValue attribute of the KierShape1 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.KierShape3: Gets the doubleValue attribute of the KierShape3 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.KierShape2: Gets the doubleValue attribute of the KierShape2 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.KierShape1: Gets the doubleValue attribute of the KierShape1 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.GraphShapeCoefficient: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.GeometricalShapeCoefficient: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.GeometricalRadius: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.GeometricalDiameter: Gets the defaultAtoms attribute of the NumberOfC object
getDSE(ArrayBinning, ArrayBinning) - Static method in class wsi.ra.tool.ArrayBinning: Gets the differential shannon entropy.
getDXEntry(int) - Method in class joelib.jcamp.JCAMPData
getElectronAffinity() - Method in class joelib.molecule.JOEElement: Gets the electronAffinity attribute of the JOEElement object
getElectronAffinity() - Method in class joelib.molecule.JOEAtom: Gets the electronAffinity attribute of the JOEElement object
getElectronAffinity(int) - Method in class joelib.data.JOEElementTable: Gets the electronAffinity attribute of the JOEElement object
getENAllredRochow() - Method in class joelib.molecule.JOEAtom: Gets the atom electronegativity after Allred and Rochow.
getEnd() - Method in class joelib.data.JOEVirtualBond: Gets the end attribute of the JOEVirtualBond object
getEndAtom() - Method in class joelib.molecule.JOEBond: Gets the endAtom attribute of the JOEBond object
getEndAtomIdx() - Method in class joelib.molecule.JOEBond: Gets the endAtomIdx attribute of the JOEBond object
getEnergy() - Method in class joelib.molecule.JOEMol: Gets the energy attribute of the JOEMol object
getENPauling() - Method in class joelib.molecule.JOEAtom: Gets the atom electronegativity after Pauling.
getENSanderson() - Method in class joelib.molecule.JOEAtom: Gets the atom electronegativity after Pauling.
getEquibLength() - Method in class joelib.molecule.JOEBond: Gets the equibLength attribute of the JOEBond object
getEulerTranslation(double[], double[]) - Method in class joelib.math.JOECoordTrans: Returns a \b rotation and \b translation (applied in that order) corresponding to this objects transformation.
getExecutable() - Method in class joelib.ext.ExternalInfo: Gets the executable for the actual operating system.
getExecutable(String) - Method in class joelib.ext.ExternalInfo: Gets the executable attribute of the ExternalInfo object
getExprOrder(BondExpr) - Static method in class joelib.smarts.ParseSmart: Gets the exprOrder attribute of the ParseSmart class
getExteriorElectrons() - Method in class joelib.molecule.JOEElement: Gets the exteriorElectrons attribute of the JOEElement object
getExteriorElectrons(int) - Method in class joelib.data.JOEElementTable: Gets the exteriorElectrons attribute of the JOEElementTable object
getExternal(String) - Method in class joelib.ext.ExternalFactory: Gets the external attribute of the ExternalFactory class
getExternalInfo() - Method in class joelib.ext.SimpleExternalProcess: Gets the externalInfo attribute of the Corina object
getExternalInfo() - Method in interface joelib.ext.External
getExternalInfo(String) - Method in class joelib.ext.ExternalFactory: Gets the externalInfo attribute of the ExternalFactory object
getFileTypes() - Method in class joelib.io.IOTypeHolder: Gets the fileTypes attribute of the IOTypeHolder object
getFilter(String) - Method in class joelib.process.filter.FilterFactory: Gets the external attribute of the ExternalFactory class
getFilterInfo() - Method in class joelib.process.filter.SMARTSFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.SelectionFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.RuleOf5Filter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.ORFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.NOTFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.NativeValueFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.HasDataFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.HasAllDataFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in interface joelib.process.filter.Filter
getFilterInfo() - Method in class joelib.process.filter.DescriptorFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.ANDFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo(String) - Method in class joelib.process.filter.FilterFactory: Gets the externalInfo attribute of the ExternalFactory object
getFirstAtom() - Method in class joelib.molecule.JOEMol: Gets the firstAtom attribute of the JOEMol object
getFlags() - Method in class joelib.molecule.JOEMol: Gets the flags attribute of the JOEMol object
getFlags() - Method in class joelib.molecule.JOEBond: Gets the flags attribute of the JOEBond object
getFormalCharge() - Method in class joelib.molecule.JOEAtom: Gets the formal charge of the JOEAtom .
getFreeElectrons() - Method in class joelib.molecule.JOEAtom: Get the number of free electrons.
getFront() - Method in class wsi.ra.tool.Deque: Returns the front DequeNode of this stack.
getGroup() - Method in class joelib.molecule.JOEElement: Gets the group attribute of the JOEElement object
getGroupContributions(String) - Method in class joelib.data.JOEGroupContribution: Description of the Method
getGTDVector(int[]) - Method in class joelib.molecule.JOEMol: Gets the gTDVector attribute of the JOEMol object
getHeteroValence() - Method in class joelib.molecule.JOEAtom: Returns the number of heteroatoms connected to an atom.
getHighlightAtoms() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the highlighted atoms vector
getHTMLDescription() - Method in class joelib.desc.DescDescription: Gets the hTMLDescription attribute of the DescDescription object
getHTMLInfo(double, double) - Method in interface joelib.util.ToolTipInfo: Gets the tool tip text.
getHvyValence() - Method in class joelib.molecule.JOEAtom: Returns the number of non-hydrogens connected to an atom.
getHyb() - Method in class joelib.molecule.JOEAtom: Gets the hybridisation of the JOEAtom .
getId() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Draw the molecule recommend to avoid, but to use renderer approach Returns id of this molecule
getId() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Returns id of the bond
getId() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Compares this atom with another Returns String representation of Atom Returns id of the atom
getIdx() - Method in class joelib.data.JOEExternalBond: Gets the idx attribute of the JOEExternalBond object
getIdx() - Method in class joelib.molecule.JOEResidue
getIdx() - Method in class joelib.molecule.JOEBond: Gets the idx attribute of the JOEBond object
getIdx() - Method in class joelib.molecule.JOEAtom: Gets the index number of the JOEAtom object.
getImplicitValence() - Method in class joelib.molecule.JOEAtom: Gets the implicit valence attribute of the JOEAtom .
getInputType() - Method in class joelib.molecule.JOEMol: Gets the inputType attribute of the JOEMol object
getInt() - Method in class joelib.desc.result.IntResult: Gets the double attribute of the DoubleResult object
getInt() - Method in class joelib.desc.result.APropIntResult: Gets the double attribute of the DoubleResult object
getInt(Properties, String) - Static method in class wsi.ra.tool.PropertyHolder: Gets the int attribute of the PropertyHolder class
getInt(Properties, String, int, int, int) - Static method in class wsi.ra.tool.PropertyHolder: Gets the int attribute of the PropertyHolder class
getInt(String) - Method in class wsi.ra.tool.PropertyHolder: Gets the int attribute of the PropertyHolder object
getInt(String, int, int, int) - Method in class wsi.ra.tool.PropertyHolder: Gets the int attribute of the PropertyHolder object
getIntArray() - Method in class joelib.desc.result.IntArrayResult: Gets the double attribute of the IntArrayResult object
getIntArray() - Method in class joelib.desc.result.DynamicArrayResult: Gets the intArray attribute of the DynamicArrayResult object
getIntNV() - Method in interface joelib.desc.NativeValue
getIntNV() - Method in class joelib.desc.result.IntResult: Gets the intNV attribute of the IntResult object
getIntNV() - Method in class joelib.desc.result.DoubleResult: Gets the intNV attribute of the DoubleResult object
getIntNV() - Method in class joelib.desc.result.APropIntResult: Gets the intNV attribute of the APropIntResult object
getIntNV() - Method in class joelib.desc.result.APropDoubleResult: Gets the intNV attribute of the APropDoubleResult object
getIntValue(int) - Method in class joelib.desc.result.BondIntResult: Constructor for the DoubleResult object
getIntValue(int) - Method in class joelib.desc.result.BondDynamicResult: Gets the intValue attribute of the AtomDynamicResult object.
getIntValue(int) - Method in class joelib.desc.result.BondDoubleResult: Constructor for the DoubleResult object
getIntValue(int) - Method in class joelib.desc.result.AtomIntResult: Gets the intValue attribute of the AtomIntResult object
getIntValue(int) - Method in class joelib.desc.result.AtomDynamicResult: Gets the intValue attribute of the AtomDynamicResult object.
getIntValue(int) - Method in class joelib.desc.result.AtomDoubleResult: Constructor for the DoubleResult object
getIntValue(int) - Method in class joelib.desc.result.APropDoubleArrResult
getIntValue(int) - Method in interface joelib.molecule.types.BondProperties
getIntValue(int) - Method in interface joelib.molecule.types.AtomProperties: Gets the intValue attribute of the AtomProperties object
getIntValue(int, int) - Method in interface joelib.molecule.types.AtomAtomProperties
getIntValue(JOEMol) - Method in class joelib.desc.SimpleIntDesc
getIntValue(JOEMol) - Method in class joelib.desc.types.TopologicalRadius: Gets the defaultAtoms attribute of the NumberOfC object
getIntValue(JOEMol) - Method in class joelib.desc.types.TopologicalDiameter: Gets the defaultAtoms attribute of the NumberOfC object
getIOType(String) - Method in class joelib.io.IOTypeHolder: Gets the IOType from a given input/output name.
getJCAMPData() - Method in class joelib.io.types.JCAMP
getJCampDataType() - Method in class joelib.jcamp.JCAMPParser: Gets the JCAMP data type of this data set.
getLabel() - Method in class joelib.jcamp.LabelData
getLabelInLine(String) - Static method in class joelib.jcamp.JCAMPDataBlock: Gets the 'Label Data Record'-label of the actual line.
getLength() - Method in class joelib.jcamp.JCAMPParser: Gets the length of the X and Y array.
getLineCounter() - Method in class joelib.data.JOEGlobalDataBase: Gets the lineCounter attribute of the JOEGlobalDataBase object
getLineNumber() - Method in class cformat.ScanfReader: Gets the current line number.
getLookAheadChar() - Method in class cformat.ScanfReader: Returns the look-ahead character.
getLookup() - Static method in class joelib.gui.molviewer.java3d.util.CentralLookup: Gets the lookup attribute of the CentralLookup class
getMapList() - Method in class joelib.smarts.JOESmartsPattern
getMass() - Method in class joelib.molecule.JOEElement: Gets the mass attribute of the JOEElement object
getMass(int) - Method in class joelib.data.JOEElementTable: Gets the mass attribute of the JOEElementTable object
getMaterial(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: get the material for atom a*
getMatrix() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the matrix attribute of the MoleculesDescriptorMatrix object
getMatrix(boolean) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the molDescMatrix attribute of the MoleculesDescriptorMatrix object
getMatrix3D() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return 3D transformation matrix
getMaxBitSize() - Method in class joelib.desc.result.BitResult: Gets the double attribute of the DoubleResult object
getMaxBonds() - Method in class joelib.molecule.JOEElement: Gets the maxBonds attribute of the JOEElement object
getMaxBonds(int) - Method in class joelib.data.JOEElementTable: Gets the maxBonds attribute of the JOEElementTable object
getMod() - Method in class joelib.molecule.JOEMol: Gets the mod attribute of the JOEMol object
getMol(int) - Method in class joelib.molecule.JOEMolVector: Get a specific molecule from a OEMolVector.
getMoleculeFileType(IOType) - Static method in class joelib.io.JOEFileFormat: Gets the moleculeFileType attribute of the JOEFileFormat class
getMolIdentifier() - Method in class joelib.desc.data.MolDescCounter: Gets the molIdentifier attribute of the MolDescCounter object
getMolReader(InputStream, IOType) - Static method in class joelib.io.JOEFileFormat: Gets the molReader attribute of the JOEFileFormat class.
getMolWriter(OutputStream, IOType) - Static method in class joelib.io.JOEFileFormat: Description of the Method
MoleculeFileType saver = JOEFileFormat.getMolWrite(OutputStream os, IOType type) if (saver.writeable()) { boolean success = saver.write(os, mol, title); return success; } else { logger.warn(type.getRepresentation() + " is not writeable.")
getMolWt() - Method in class joelib.molecule.JOEMol: Gets the molWt attribute of the JOEMol object
getMyAtoms() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Returns atom vector of this molecule
getMyBonds() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return bond vector of this molecule
getName() - Method in class joelib.desc.DescriptorInfo
getName() - Method in class joelib.desc.Description: Gets the name attribute of the Description object
getName() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Returns name of molecule
getName() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the elemental name
getName() - Method in class joelib.io.IOType: Gets the name attribute of the IOType class
getName() - Method in class joelib.molecule.JOEResidue
getName() - Method in class joelib.util.types.BasicFactoryInfo: Gets the name attribute of the ProcessInfo object
getName(Description) - Static method in class joelib.desc.Description: Gets the name attribute of the Description class
getName(int) - Static method in class joelib.desc.Description: Gets the name attribute of the Description class
getNativeDescs() - Method in class joelib.desc.DescriptorHelper
getNbrAtom(JOEAtom) - Method in class joelib.molecule.JOEBond: Gets the nbrAtom attribute of the JOEBond object
getNbrAtomIdx(JOEAtom) - Method in class joelib.molecule.JOEBond: Gets the nbrAtomIdx attribute of the JOEBond object
getNewArray(String, int) - Static method in class joelib.desc.result.DynamicArrayResult: Gets the newArray attribute of the DynamicArrayResult class
getNewBondVector(XYZVector, double) - Method in class joelib.molecule.JOEAtom: Gets the newBondVector attribute of the JOEAtom object
getNextAtom() - Method in class joelib.molecule.JOEAtom: Gets the nextAtom attribute of the JOEAtom object
getNextAtom(int) - Method in class joelib.smiles.JOESmiNode: Gets the nextAtom attribute of the JOESmiNode object
getNextBond(int) - Method in class joelib.smiles.JOESmiNode: Gets the nextBond attribute of the JOESmiNode object
getNextNode(int) - Method in class joelib.smiles.JOESmiNode: Gets the nextNode attribute of the JOESmiNode object
getNum() - Method in class joelib.molecule.JOEResidue
getNumAtoms() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return ring vector of this molecule Return number of atoms in this molecule
getNumBonds() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return number of bonds in this molecule
getObject(String) - Method in class joelib.gui.molviewer.java3d.util.CentralLookup: Gets the object attribute of the CentralLookup object
getOperationSystemName() - Static method in class joelib.ext.ExternalHelper: Returns the name of the operation system.
getOrder() - Method in class joelib.data.JOEVirtualBond: Gets the order attribute of the JOEVirtualBond object
getOutputOrder() - Method in class joelib.smiles.JOEMol2Smi
getOutputType() - Method in class joelib.io.types.POVRay: Gets the outputType attribute of the POVRay object
getOutputType() - Method in class joelib.io.types.Matlab: Gets the outputType attribute of the POVRay object
getOutputType() - Method in class joelib.molecule.JOEMol: Gets the outputType attribute of the JOEMol object
getParam() - Method in class joelib.gui.molviewer.java3d.util.MolViewerEvent: Gets the param attribute of the MolViewerEvent object
getParameter() - Method in class joelib.jcamp.JCAMPParser: Get all LDR's (data label records) that are stored.
getParameter(String) - Method in class joelib.jcamp.JCAMPParser
getParameter(String[]) - Method in class joelib.jcamp.JCAMPParser
getParent() - Method in class joelib.molecule.JOEBond: Gets the parent attribute of the JOEBond object
getParent() - Method in class joelib.molecule.JOEAtom: Gets the parent attribute of the JOEAtom object
getParent() - Method in class joelib.ring.JOERing: Returns the parent molecule for this ring.
getParent() - Method in class joelib.smiles.JOESmiNode: Gets the parent attribute of the JOESmiNode object
getPartialCharge() - Method in class joelib.molecule.JOEAtom: Gets the partialCharge attribute of the JOEAtom object
getPassedTime() - Method in class wsi.ra.tool.StopWatch: Returns the passed time since last 'reset stop watch' call in millis.
getPaulingEN() - Method in class joelib.molecule.JOEElement: Gets the atom electronegativity after Pauling.
getPaulingEN(int) - Method in class joelib.data.JOEElementTable: Gets the atom electronegativity after Pauling.
getPeriod() - Method in class joelib.molecule.JOEElement: Gets the period attribute of the JOEElement object
getPeriod(int) - Method in class joelib.data.JOEElementTable: Gets the period of the JOEElement object.
getPrefix() - Method in class cformat.PrintfFormat: Gets the prefix string associated with the format.
getProcess(String) - Method in class joelib.process.ProcessFactory: Gets the external attribute of the ExternalFactory class
getProcessInfo() - Method in class joelib.ext.SimpleExternalProcess: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in class joelib.process.SimpleProcess: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in class joelib.process.ProcessPipe: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in interface joelib.process.JOEProcess
getProcessInfo() - Method in class joelib.process.types.MoleculeFileDeletion: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in class joelib.process.types.MoleculeFileCreation: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in class joelib.process.types.CreateFileName: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo(String) - Method in class joelib.process.ProcessFactory: Gets the externalInfo attribute of the ExternalFactory object
getProperties() - Method in class wsi.ra.tool.PropertyHolder: Gets the properties attribute of the PropertyHolder object
getProperty(Object, String) - Method in class wsi.ra.tool.PropertyHolder: Gets the property attribute of the RegressionHelper object
getProperty(Properties, Object, String) - Static method in class wsi.ra.tool.PropertyHolder
getProperty(PropertyAcceptor, String, Map) - Static method in class joelib.util.JOEPropertyHelper: Gets single process property or default value if not defined or null .
getProperty(String, Map) - Static method in class joelib.util.JOEPropertyHelper: Gets single process property.
getPropertyType() - Method in class joelib.desc.result.DynamicArrayResult: Gets the propertyType attribute of the DynamicArrayResult object
getPropFile() - Method in class wsi.ra.tool.PropertyHolder: Gets the propFile attribute of the PropertyHolder object
getQuoteCharacter() - Method in class wsi.ra.io.BatchScriptReplacer: Gets the quoteCharacter attribute of the BatchScriptReplacer object
getRadius(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: get the radius for atom a *
getRepresentation() - Method in class joelib.io.IOType: Gets the representation attribute of the IOType class
getRepresentation() - Method in class joelib.util.types.BasicFactoryInfo: Gets the representation attribute of the ProcessInfo object
getResidue() - Method in class joelib.molecule.JOEAtom
getResidue(int) - Method in class joelib.molecule.JOEMol: Gets the residue attribute of the JOEMol object
getResult() - Method in class joelib.desc.DescriptorInfo
getRGBFloats(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: get the R,G,B values (between 0.0f and 1.0f) of the color for atom a *
getRingIterator() - Method in class joelib.molecule.JOEMol: Gets iterator for the Smallest Set of Smallest Rings (SSSR).
getRingIterator() - Method in class joelib.ring.JOERingSearch: Gets the ringIterator attribute of the JOERingSearch object
getRmatrixTranslation(double[], double[]) - Method in class joelib.math.JOECoordTrans: Returns a \b rotation and \b translation (applied in that order) coresponding to this objects transformation.
getRmatrixTranslation(Matrix3x3, XYZVector) - Method in class joelib.math.JOECoordTrans: Returns a \b rotation and \b translation (applied in that order) coresponding to this objects transformation.
getSandersonEN() - Method in class joelib.molecule.JOEElement: Gets the atom electronegativity after Pauling.
getSandersonEN(int) - Method in class joelib.data.JOEElementTable
getSelectAtoms() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the selected atoms vector
getSeparator() - Method in class joelib.util.MatrixHelper: Gets the separator attribute of the MatrixHelper object
getSeparator() - Method in class joelib.util.ArrayHelper: Gets the separator attribute of the ArrayHelper object
getSerialNum(JOEAtom) - Method in class joelib.molecule.JOEResidue
getShape() - Method in class joelib.gui.molviewer.java3d.graphics3D.IcoSphere: Gets the shape attribute of the IcoSphere object
getShape() - Method in class joelib.gui.molviewer.java3d.graphics3D.Cylinder: Gets the shape attribute of the Cylinder object
getSharedAtomGroup(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: Gets the sharedAtomGroup attribute of the RenderTable object
getSharedBondGroup(ViewerAtom, float) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: Gets the sharedBondGroup attribute of the RenderTable object
getSize() - Method in class joelib.molecule.JOEMolVector: Gets the size attribute of the JOEMolVector object
getSMARTS() - Method in class joelib.smarts.JOESmartsPattern: Gets the sMARTS attribute of the JOESmartsPattern object
getSmilesElement(JOESmiNode, StringBuffer) - Method in class joelib.smiles.JOEMol2Smi: Gets the smilesElement attribute of the JOEMol2Smi object
getSSSR() - Method in class joelib.molecule.JOEMol: Gets the Smallest Set of Smallest Rings (SSSR).
getStatistic() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method Description of the Method Description of the Method Description of the Method Description of the Method Gets the statistic attribute of the MoleculesDescriptorMatrix object
getStereo() - Method in class joelib.data.JOEVirtualBond: Gets the stereo attribute of the JOEVirtualBond object
getStoreDescriptors() - Method in class joelib.desc.data.MolDescCounter: Gets the storeDescriptors attribute of the MolDescCounter object
getStoreLineInfo() - Method in class joelib.io.types.Smiles: Gets the storeLineInfo attribute of the Smiles object
getStoreLineInfo() - Method in class joelib.io.types.Flat: Gets the storeLineInfo attribute of the Smiles object
getStringFromType(int) - Method in class joelib.smarts.Patty: Gets the identifier name from the given identifier index.
getStringNV() - Method in interface joelib.desc.NativeValue
getStringNV() - Method in class joelib.desc.result.IntResult: Gets the stringNV attribute of the IntResult object
getStringNV() - Method in class joelib.desc.result.DoubleResult: Gets the stringNV attribute of the DoubleResult object
getStringNV() - Method in class joelib.desc.result.APropIntResult: Gets the stringNV attribute of the APropIntResult object
getStringNV() - Method in class joelib.desc.result.APropDoubleResult: Gets the stringNV attribute of the APropDoubleResult object
getStringValue(int) - Method in class joelib.desc.result.BondIntResult
getStringValue(int) - Method in class joelib.desc.result.BondDynamicResult: Gets the stringValue attribute of the AtomDynamicResult object
getStringValue(int) - Method in class joelib.desc.result.BondDoubleResult
getStringValue(int) - Method in class joelib.desc.result.AtomIntResult: Gets the stringValue attribute of the AtomIntResult object
getStringValue(int) - Method in class joelib.desc.result.AtomDynamicResult: Gets the stringValue attribute of the AtomDynamicResult object
getStringValue(int) - Method in class joelib.desc.result.AtomDoubleResult
getStringValue(int) - Method in class joelib.desc.result.APropDoubleArrResult
getStringValue(int) - Method in interface joelib.molecule.types.BondProperties
getStringValue(int) - Method in interface joelib.molecule.types.AtomProperties: Gets the stringValue attribute of the AtomProperties object
getStringValue(int, int) - Method in interface joelib.molecule.types.AtomAtomProperties
getStyle() - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: What is the current rendering style ?
getSuffix() - Method in class cformat.PrintfFormat: Gets the suffix string associated with the format.
getSymbol() - Method in class joelib.molecule.JOEElement: Gets the symbol attribute of the JOEElement object
getSymbol(int) - Method in class joelib.data.JOEElementTable: Gets the symbol attribute of the JOEElementTable object
getTable() - Static method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: the accessor method for rthe instance of the RenderTable *
getTargetMols() - Method in class joelib.process.types.DistanceCalculation
getTargetMols() - Method in class joelib.util.ComparisonHelper
getTempFileBase() - Static method in class joelib.util.JHM
getTextDescription() - Method in class joelib.desc.DescDescription: Gets the textDescription attribute of the DescDescription object
getTitle() - Method in class joelib.molecule.JOEMol: Gets the title attribute of the JOEMol object.
getTorsion(int, int, int, int) - Method in class joelib.molecule.JOEMol: Gets the torsion attribute of the JOEMol object
getTorsion(JOEAtom, JOEAtom, JOEAtom, JOEAtom) - Method in class joelib.molecule.JOEMol: Gets the torsion attribute of the JOEMol object
getTranslationEuler(double[], double[]) - Method in class joelib.math.JOECoordTrans: Returns a \b translation and \b rotation (applied in that order) coresponding to this objects transformation.
getTranslationRmatrix(double[], double[]) - Method in class joelib.math.JOECoordTrans: Returns a \b translation and \b rotation (applied in that order) coresponding to this objects transformation.
getTranslationRmatrix(XYZVector, Matrix3x3) - Method in class joelib.math.JOECoordTrans: Returns a \b translation and \b rotation (applied in that order) coresponding to this objects transformation.
getTx() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the transformed x coordinate of the atom
getTy() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the transformed y coordinate of the atom
getType() - Method in class joelib.desc.DescriptorInfo
getType() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Returns bond type
getType() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns SYBYL force field atom type
getType() - Method in class joelib.gui.molviewer.java3d.util.MolViewerEvent: Gets the type attribute of the MolViewerEvent object
getType() - Method in class joelib.molecule.JOEAtom: Gets the type of the JOEAtom .
getType() - Method in interface joelib.util.ToolTipInfo: Gets the information type for this tool tip, e.g "infrared data"
getType(int) - Static method in class joelib.desc.Description: Gets the type attribute of the Description class
getType(String) - Static method in class joelib.desc.Description: Gets the type attribute of the Description class
getTypeDimension() - Method in class joelib.desc.DescriptorInfo
getTypeNumber() - Method in class joelib.io.IOType: Gets the type attribute of the IOType class
getTz() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the transformed z coordinate of the atom
getUMapList() - Method in class joelib.smarts.JOESmartsPattern
getUnusedIndex() - Method in class joelib.smiles.JOEMol2Smi: Gets the unusedIndex attribute of the JOEMol2Smi object
getURLFromProperty(Properties, String) - Static method in class wsi.ra.tool.PropertyHolder: Gets the uRLFromProperty attribute of the PropertyHolder class
getURLFromProperty(Properties, String, boolean) - Static method in class wsi.ra.tool.PropertyHolder: Gets the uRLFromProperty attribute of the PropertyHolder class
getURLFromProperty(String) - Method in class wsi.ra.tool.PropertyHolder: Gets the uRLFromProperty attribute of the PropertyHolder object
getURLFromProperty(String, boolean) - Method in class wsi.ra.tool.PropertyHolder: Gets the uRLFromProperty attribute of the PropertyHolder object
getUseUnixStyle() - Method in class joelib.io.types.Tinker
getValence() - Method in class joelib.molecule.JOEAtom: Gets the valence of the JOEAtom object.
getValue() - Method in class joelib.data.JOEPairData: Gets the value attribute of the JOEPairData object
getValue() - Method in class joelib.desc.Description: Gets the value attribute of the Description object
getValue(Description) - Static method in class joelib.desc.Description: Gets the value attribute of the Description class
getValue(int) - Method in class joelib.desc.result.BondIntResult
getValue(int) - Method in class joelib.desc.result.BondDynamicResult: Gets the value attribute of the AtomDynamicResult object
getValue(int) - Method in class joelib.desc.result.BondDoubleResult
getValue(int) - Method in class joelib.desc.result.AtomIntResult: Gets the value attribute of the AtomIntResult object
getValue(int) - Method in class joelib.desc.result.AtomDynamicResult: Gets the value attribute of the AtomDynamicResult object
getValue(int) - Method in class joelib.desc.result.AtomDoubleResult
getValue(int) - Method in class joelib.desc.result.APropDoubleArrResult
getValue(int) - Method in interface joelib.molecule.types.BondProperties
getValue(int) - Method in interface joelib.molecule.types.AtomProperties: Gets the value attribute of the AtomProperties object
getValue(int, int) - Method in interface joelib.molecule.types.AtomAtomProperties
getValueFromName(String) - Static method in class joelib.desc.Description: Gets the valueFromName attribute of the Description class
getVdwRad() - Method in class joelib.molecule.JOEElement: Gets the vdwRad attribute of the JOEElement object
getVdwRad(int) - Method in class joelib.data.JOEElementTable: Gets the vdwRad attribute of the JOEElementTable object
getVector() - Method in class joelib.molecule.JOEMolVector
getVector() - Method in class joelib.molecule.JOEAtom: Gets the vector attribute of the JOEAtom object
getVectorBinding() - Method in class joelib.smarts.ParseSmart: Gets the vectorBinding attribute of the ParseSmart class
getVectorBinding(int) - Method in class joelib.smarts.JOESmartsPattern: Gets the vector binding of this smarts pattern for SMARTS atom with idx.
getX() - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: Return X coordinate
getX() - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Return component x
getX() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the x coordinate of the atom
getX() - Method in class joelib.molecule.JOEAtom: Gets the x coordinate of the JOEAtom .
getXData() - Method in class joelib.jcamp.JCAMPParser: Gets the X array.
getXLabel() - Method in class joelib.jcamp.JCAMPParser: Gets the label for the X axis.
getXmax() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the maxmum x coordinate
getXmin() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the minimum x coordinate of this molelcule
getXMLDescription() - Method in class joelib.desc.DescDescription: Gets the xMLDescription attribute of the DescDescription object
getXScale() - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Returns X scale
getY() - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: Return Y coordinate
getY() - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Return component y
getY() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the y coordinate of the atom
getY() - Method in class joelib.molecule.JOEAtom: Gets the y coordinate of the JOEAtom .
getYData() - Method in class joelib.jcamp.JCAMPParser: Gets the Y array.
getYLabel() - Method in class joelib.jcamp.JCAMPParser: Gets the label for the Y axis.
getYmax() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the maxmum y coordinate
getYmin() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the minimum y coordinate
getYScale() - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Returns Y scale
getZ() - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: Return Z coordinate
getZ() - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Return component z
getZ() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the z coordinate of the atom
getZ() - Method in class joelib.molecule.JOEAtom: Gets the z coordinate of the JOEAtom .
getZmax() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the maxmum z coordinate
getZmin() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the minimum z coordinate
getZScale() - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Returns Z scale
gr(double, double) - Static method in class wsi.ra.tool.StatisticUtils: Tests if a is greater than b.
GraphPotentials - class joelib.desc.types.GraphPotentials.: External rotational symmetry or graph potentials.
GraphPotentials() - Constructor for class joelib.desc.types.GraphPotentials
graphPotentials(JOEMol) - Static method in class joelib.desc.types.GraphPotentials: Calculate the Graph Potentials of a molecule based on V.E.
GraphShapeCoefficient - class joelib.desc.types.GraphShapeCoefficient.: Calculates the graph shape coefficient.
GraphShapeCoefficient() - Constructor for class joelib.desc.types.GraphShapeCoefficient
GREATER - Static variable in class joelib.process.filter.SMARTSFilter
GREATER - Static variable in class joelib.process.filter.NativeValueFilter
GREATER_EQUAL - Static variable in class joelib.process.filter.SMARTSFilter
GREATER_EQUAL - Static variable in class joelib.process.filter.NativeValueFilter
grOrEq(double, double) - Static method in class wsi.ra.tool.StatisticUtils: Tests if a is greater or equal to b.
GroupContributions - class joelib.algo.contribution.GroupContributions.: Group contribution informations.
GroupContributions(String) - Constructor for class joelib.algo.contribution.GroupContributions: Constructor for the StringString object
GroupContributionTest - class joelib.test.GroupContributionTest.: Test for contribution lists for different models (e.g. logP, MR, PSA).
GroupContributionTest() - Constructor for class joelib.test.GroupContributionTest
grow - Variable in class joelib.smarts.BondSpec: Growing evaluation flag.
gSVResize(int) - Method in class joelib.molecule.charge.JOEGastChrg: Description of the Method

H has2D() - Method in class joelib.molecule.JOEMol Description of the Method has3D() - Method in class joelib.molecule.JOEMol Description of the Method HasAllDataFilter - class joelib.process.filter.HasAllDataFilter. Molecule process filter for available descriptor entries. HasAllDataFilter() - Constructor for class joelib.process.filter.HasAllDataFilter Constructor for the DescriptorFilter object HasAllDataFilter(String) - Constructor for class joelib.process.filter.HasAllDataFilter Constructor for the DescriptorFilter object HasAllDataFilter(Vector) - Constructor for class joelib.process.filter.HasAllDataFilter hasAlphaBetaUnsat() - Method in class joelib.molecule.JOEAtom Returns true if this atom is part of an alpha beta unsaturated fragment. hasAlphaBetaUnsat(boolean) - Method in class joelib.molecule.JOEAtom Returns true if this atom is part of an alpha beta unsaturated fragment. hasAromaticBond() - Method in class joelib.molecule.JOEAtom Returns true if atom has an aromatic bond. hasAromaticCorrected() - Method in class joelib.molecule.JOEMol Description of the Method hasAromaticPerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasAtomTypesPerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasBondOfOrder(int) - Method in class joelib.molecule.JOEAtom Returns true if atom has bond of given order. hasChainsPerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasChiralityPerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasChiralitySpecified() - Method in class joelib.molecule.JOEAtom Returns true if the chirality was specified for this atom. hasClosureBondsPerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasData(JOEDataType) - Method in class joelib.molecule.JOEMol Returns true if one ore more entries of the given JOEDataType exists. hasData(JOEDataType) - Method in class joelib.molecule.GenericDataHolder Description of the Method hasData(String) - Method in class joelib.molecule.JOEMol Description of the Method hasData(String) - Method in class joelib.molecule.GenericDataHolder Description of the Method HasDataFilter - class joelib.process.filter.HasDataFilter. Molecule process filter for available descriptor entries. HasDataFilter() - Constructor for class joelib.process.filter.HasDataFilter Constructor for the DescriptorFilter object HasDataFilter(String) - Constructor for class joelib.process.filter.HasDataFilter Constructor for the DescriptorFilter object hasDescriptorStatistic(String) - Method in class joelib.process.types.DescStatistic Description of the Method hasDoubleBond() - Method in class joelib.molecule.JOEAtom Returns true if atom has a double bond. hashCode() - Method in class joelib.util.BitSet14 Returns a hash code value for this bit set. hasHTMLDescription() - Method in class joelib.desc.DescDescription Description of the Method hasHybridizationPerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasHydrogensAdded() - Method in class joelib.molecule.JOEMol Description of the Method hasImplicitValencePerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasInterface(Object, String) - Static method in class joelib.util.JOEHelper Checks if an class implements an interface. hasKekulePerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasNext() - Method in class joelib.util.iterator.VectorIterator Description of the Method hasNext() - Method in class joelib.util.iterator.NativeValueIterator Description of the Method hasNext() - Method in class joelib.util.iterator.GenericDataIterator Description of the Method hasNext() - Method in class wsi.ra.tool.DequeIterator hasNonZeroCoords() - Method in class joelib.molecule.JOEMol Description of the Method hasPartialChargesPerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasResidue() - Method in class joelib.molecule.JOEAtom hasRingAtomsAndBondsPerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasSelectedAtoms() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule Returns true if molecule has selected atoms hasSingleBond() - Method in class joelib.molecule.JOEAtom Returns true if atom has a single bond. hasSSSRPerceived() - Method in class joelib.molecule.JOEMol Description of the Method hasTextDescription() - Method in class joelib.desc.DescDescription Gets the description attribute of the Descriptor object hasXMLDescription() - Method in class joelib.desc.DescDescription Description of the Method HBA1 - class joelib.desc.types.HBA1. Number of Hydrogen Bond Acceptors (HBA). HBA1() - Constructor for class joelib.desc.types.HBA1 HBA2 - class joelib.desc.types.HBA2. Number of Hydrogen Bond Acceptors (HBA). HBA2() - Constructor for class joelib.desc.types.HBA2 HBD1 - class joelib.desc.types.HBD1. Number of Hydrogen Bond Donors (HBD). HBD1() - Constructor for class joelib.desc.types.HBD1 HBD2 - class joelib.desc.types.HBD2. Number of Hydrogen Bond Donors (HBD). HBD2() - Constructor for class joelib.desc.types.HBD2 hCount - Variable in class joelib.util.types.AtomHCount Description of the Field head - Variable in class wsi.ra.tool.Deque HeavyBonds - class joelib.desc.types.HeavyBonds. Number of heavy bonds. HeavyBonds() - Constructor for class joelib.desc.types.HeavyBonds Constructor for the KierShape1 object HeteroCycles - class joelib.desc.types.HeteroCycles. Number of hetero cycles. HeteroCycles() - Constructor for class joelib.desc.types.HeteroCycles Constructor for the KierShape1 object hi - Variable in class joelib.util.types.DoubleType Description of the Field highlight(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule Designates an atom as highlighted. highlight(ViewerAtoms) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule Designates an atom list as highlighted. HTML - Static variable in class joelib.desc.Description Description of the Field HtoMethyl() - Method in class joelib.molecule.JOEAtom Modifies a hydrogen atom to methyl group with three explicit hydrogens. hydrogenContributions - Variable in class joelib.algo.contribution.GroupContributions hydrogenSmarts - Variable in class joelib.algo.contribution.GroupContributions HydrophobicGroups - class joelib.desc.types.HydrophobicGroups. Number of hydrophobic groups. HydrophobicGroups() - Constructor for class joelib.desc.types.HydrophobicGroups I i - Variable in class joelib.smarts.types.SMARTSPatternInt Description of the Field i - Variable in class joelib.util.types.StringInt Description of the Field i - Variable in class joelib.util.types.IntIntInt Description of the Field i - Variable in class joelib.util.types.DoubleInt Description of the Field i - Variable in class joelib.util.types.BondInt Description of the Field i - Variable in class joelib.util.types.AtomArrayInt Description of the Field i1 - Variable in class joelib.util.types.IntInt Description of the Field i2 - Variable in class joelib.util.types.IntInt Description of the Field IcoSphere - class joelib.gui.molviewer.java3d.graphics3D.IcoSphere. Description of the Class IcoSphere(float, int, Appearance) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.IcoSphere Constructor for the IcoSphere object IFALSE - Static variable in class joelib.smarts.ParseSmart Description of the Field ii - Variable in class joelib.smarts.types.SMARTSPatternIntInt Description of the Field ii - Variable in class joelib.util.types.IntIntInt Description of the Field ii - Variable in class joelib.util.types.AtomIntInt Description of the Field implicitHydrogenCount() - Method in class joelib.molecule.JOEAtom Returns the number of implicit hydrogens. handles H,C,N,S,O,X in(InputStream) - Method in class joelib.util.JOEBitVec Description of the Method incompleteBeta(double, double, double) - Static method in class wsi.ra.tool.Statistics Returns the Incomplete Beta Function evaluated from zero to xx. incrementImplicitValence() - Method in class joelib.molecule.JOEAtom Increment the implicit valence. incrementMod() - Method in class joelib.molecule.JOEMol Increase modification counter. IndexedCylinder - class joelib.gui.molviewer.java3d.graphics3D.IndexedCylinder. Description of the Class IndexedCylinder(float, float, int, Appearance) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.IndexedCylinder Constructor for the IndexedCylinder object indexOf(Object, int) - Method in class wsi.ra.tool.SortedVector Searches for the first occurence of the given argument, beginning the search at index, and testing for equality using the equals method. info(int[]) - Static method in class wsi.ra.tool.StatisticUtils Computes entropy for an array of integers. init() - Method in class joelib.data.JOEGroupContribution Description of the Method init() - Method in class joelib.data.JOEGlobalDataBase Description of the Method init() - Method in class joelib.smiles.JOEMol2Smi Description of the Method init(char[]) - Method in class joelib.smarts.JOESmartsPattern Description of the Method init(ComparisonHelper) - Method in class joelib.process.types.DistanceCalculation Description of the Method init(DescStatistic) - Method in class joelib.process.types.DescVarianceNorm Description of the Method init(DescStatistic, int) - Method in class joelib.process.types.DescBinning Description of the Method init(double, double) - Method in class joelib.math.JOESqrtTbl Description of the Method init(Filter) - Method in class joelib.process.filter.NOTFilter Description of the Method init(Filter, Filter) - Method in class joelib.process.filter.ORFilter Description of the Method init(Filter, Filter) - Method in class joelib.process.filter.ANDFilter Description of the Method init(InputStream, IOType) - Method in class joelib.io.SimpleReader Description of the Method init(IOType, String) - Method in class joelib.process.types.DescVarianceNorm Description of the Method init(IOType, String, int) - Method in class joelib.process.types.DescBinning Description of the Method init(IOType, String, String) - Method in class joelib.process.types.DistanceCalculation Description of the Method init(IOType, String, String[]) - Method in class joelib.process.types.DistanceCalculation init(JOEMol, String) - Method in class joelib.process.types.DistanceCalculation init(JOEMol, String[]) - Method in class joelib.process.types.DistanceCalculation init(OutputStream, IOType) - Method in class joelib.io.SimpleWriter Description of the Method init(OutputStream, IOType) - Method in class joelib.process.types.DescSelectionWriter Description of the Method init(OutputStream, IOType, Vector, int) - Method in class joelib.process.types.DescSelectionWriter Description of the Method init(String) - Method in class joelib.algo.DFSResult Constructor for the DFSResult object init(String) - Method in class joelib.algo.BFSResult Constructor for the BFSResult object init(String) - Method in interface joelib.desc.DescResult init(String) - Method in class joelib.desc.result.IntResult Constructor for the DoubleResult object init(String) - Method in class joelib.desc.result.IntMatrixResult Constructor for the IntMatrixResult object init(String) - Method in class joelib.desc.result.IntBitArrayResult Description of the Method init(String) - Method in class joelib.desc.result.IntArrayResult Constructor for the IntArrayResult object init(String) - Method in class joelib.desc.result.DynamicArrayResult Constructor for the IntArrayResult object init(String) - Method in class joelib.desc.result.DoubleResult Constructor for the DoubleResult object init(String) - Method in class joelib.desc.result.DoubleMatrixResult Constructor for the IntMatrixResult object init(String) - Method in class joelib.desc.result.DoubleArrayResult Constructor for the IntArrayResult object init(String) - Method in class joelib.desc.result.BitResult Constructor for the DoubleResult object init(String) - Method in class joelib.desc.result.BitArrayResult Description of the Method init(String) - Method in class joelib.desc.result.APropIntResult Constructor for the DoubleResult object init(String) - Method in class joelib.desc.result.APropDoubleResult Constructor for the DoubleResult object init(String) - Method in class joelib.desc.result.APropDoubleArrResult Description of the Method init(String) - Method in class joelib.process.filter.HasDataFilter Description of the Method init(String) - Method in class joelib.smarts.JOESmartsPattern Description of the Method init(String, boolean) - Method in class joelib.process.filter.DescriptorFilter Description of the Method init(String, int, double) - Method in class joelib.process.filter.NativeValueFilter Description of the Method init(String, int, int, boolean) - Method in class joelib.process.filter.SMARTSFilter Description of the Method init(String, IOType) - Method in class joelib.process.types.DescSelectionWriter Description of the Method init(String, IOType, Vector, int) - Method in class joelib.process.types.DescSelectionWriter Description of the Method init(String, String) - Method in class joelib.data.JOEChemTransformation Description of the Method init(Vector) - Method in class joelib.process.filter.HasAllDataFilter Description of the Method init(Vector) - Method in class joelib.process.filter.DescriptorFilter Description of the Method initialize() - Method in class joelib.gui.molviewer.java3d.graphics3D.DragBehavior Description of the Method initialize(Map) - Method in class joelib.algo.DFS Description of the Method initialize(Map) - Method in class joelib.algo.BFS Description of the Method initialize(Map) - Method in class joelib.desc.SMARTSCounter Description of the Method initialize(Map) - Method in class joelib.desc.SimpleIntDesc Description of the Method initialize(Map) - Method in class joelib.desc.SimpleDoubleDesc initialize(Map) - Method in interface joelib.desc.Descriptor Description of the Method initialize(Map) - Method in class joelib.desc.AtomsCounter Description of the Method initialize(Map) - Method in class joelib.desc.types.SSKey3DS Description of the Method initialize(Map) - Method in class joelib.desc.types.RotatableBonds Description of the Method initialize(Map) - Method in class joelib.desc.types.HeteroCycles Description of the Method initialize(Map) - Method in class joelib.desc.types.HeavyBonds Description of the Method initialize(Map) - Method in class joelib.desc.types.GraphPotentials Description of the Method initialize(Map) - Method in class joelib.desc.types.GeomDistanceMatrix Description of the Method initialize(Map) - Method in class joelib.desc.types.FractionRotatableBonds Description of the Method initialize(Map) - Method in class joelib.desc.types.ElectronegativityPauling Description of the Method initialize(Map) - Method in class joelib.desc.types.ElectronAffinity Description of the Method initialize(Map) - Method in class joelib.desc.types.DistanceMatrix Description of the Method initialize(Map) - Method in class joelib.desc.types.Autocorrelation Description of the Method initialize(Map) - Method in class joelib.desc.types.AtomVanDerWaalsVolume Description of the Method initialize(Map) - Method in class joelib.desc.types.AtomValence Description of the Method initialize(Map) - Method in class joelib.desc.types.AtomMass Description of the Method initialize(Map) - Method in class joelib.desc.types.AromaticBonds Description of the Method initialize(Map) - Method in class joelib.molecule.charge.GasteigerMarsili Description of the Method initializeParser() - Method in class joelib.io.types.MolconnZ initParser() - Method in class joelib.io.types.Smiles Description of the Method initParser() - Method in class joelib.io.types.Flat Description of the Method initReader(InputStream) - Method in interface joelib.io.MoleculeFileType Description of the Method initReader(InputStream) - Method in class joelib.io.types.XYZ Description of the Method initReader(InputStream) - Method in class joelib.io.types.Undefined Description of the Method initReader(InputStream) - Method in class joelib.io.types.Tinker Description of the Method initReader(InputStream) - Method in class joelib.io.types.SybylMol2 Description of the Method initReader(InputStream) - Method in class joelib.io.types.Smiles Description of the Method initReader(InputStream) - Method in class joelib.io.types.POVRay Description of the Method initReader(InputStream) - Method in class joelib.io.types.PDB Description of the Method initReader(InputStream) - Method in class joelib.io.types.MolconnZ Description of the Method initReader(InputStream) - Method in class joelib.io.types.MDLSD Description of the Method initReader(InputStream) - Method in class joelib.io.types.Matlab Description of the Method initReader(InputStream) - Method in class joelib.io.types.JCAMP Description of the Method initReader(InputStream) - Method in class joelib.io.types.Flat Description of the Method initReader(InputStream) - Method in class joelib.io.types.ClearTextFormat Description of the Method initReader(InputStream) - Method in class joelib.io.types.ChemicalMarkupLanguage Description of the Method initSMARTSParser() - Static method in class joelib.smarts.ParseSmart Description of the Method initWriter(OutputStream) - Method in interface joelib.io.MoleculeFileType Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.XYZ Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.Undefined Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.Tinker Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.SybylMol2 Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.Smiles Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.POVRay Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.PDB Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.MolconnZ Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.MDLSD Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.Matlab Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.JCAMP Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.Flat Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.ClearTextFormat Description of the Method initWriter(OutputStream) - Method in class joelib.io.types.ChemicalMarkupLanguage Description of the Method inputDescription() - Method in interface joelib.io.MoleculeFileType Description of the Method inputDescription() - Method in class joelib.io.types.XYZ Description of the Method inputDescription() - Method in class joelib.io.types.Undefined Description of the Method inputDescription() - Method in class joelib.io.types.Tinker Description of the Method inputDescription() - Method in class joelib.io.types.SybylMol2 Description of the Method inputDescription() - Method in class joelib.io.types.Smiles Description of the Method inputDescription() - Method in class joelib.io.types.POVRay Description of the Method inputDescription() - Method in class joelib.io.types.PDB Description of the Method inputDescription() - Method in class joelib.io.types.MolconnZ Description of the Method inputDescription() - Method in class joelib.io.types.MDLSD Constructor for the MDLSD object inputDescription() - Method in class joelib.io.types.Matlab Description of the Method inputDescription() - Method in class joelib.io.types.JCAMP Description of the Method inputDescription() - Method in class joelib.io.types.Flat Description of the Method inputDescription() - Method in class joelib.io.types.ClearTextFormat Description of the Method inputDescription() - Method in class joelib.io.types.ChemicalMarkupLanguage Description of the Method inputFileExtensions() - Method in interface joelib.io.MoleculeFileType Description of the Method inputFileExtensions() - Method in class joelib.io.types.XYZ Description of the Method inputFileExtensions() - Method in class joelib.io.types.Undefined Description of the Method inputFileExtensions() - Method in class joelib.io.types.Tinker Description of the Method inputFileExtensions() - Method in class joelib.io.types.SybylMol2 Description of the Method inputFileExtensions() - Method in class joelib.io.types.Smiles Description of the Method inputFileExtensions() - Method in class joelib.io.types.POVRay Description of the Method inputFileExtensions() - Method in class joelib.io.types.PDB Description of the Method inputFileExtensions() - Method in class joelib.io.types.MolconnZ Description of the Method inputFileExtensions() - Method in class joelib.io.types.MDLSD Description of the Method inputFileExtensions() - Method in class joelib.io.types.Matlab Description of the Method inputFileExtensions() - Method in class joelib.io.types.JCAMP Description of the Method inputFileExtensions() - Method in class joelib.io.types.Flat Description of the Method inputFileExtensions() - Method in class joelib.io.types.ClearTextFormat Description of the Method inputFileExtensions() - Method in class joelib.io.types.ChemicalMarkupLanguage Description of the Method insert(Object) - Method in class joelib.util.iterator.VectorIterator Description of the Method insertAfter(DequeNode, Object) - Method in class wsi.ra.tool.Deque insertAtom(JOEAtom) - Method in class joelib.molecule.JOEMol Description of the Method insertBefore(DequeNode, Object) - Method in class wsi.ra.tool.Deque insertBond(VectorIterator, JOEBond) - Method in class joelib.molecule.JOEAtom Insert a bond to this atom. insertElementAt(Object, int) - Method in class wsi.ra.tool.SortedVector Inserts the specified object as a component in this vector at the specified index. InsertSort - class joelib.sort.InsertSort. Insert Sort. InsertSort() - Method in class joelib.sort.InsertSort Description of the Method InsertSort() - Constructor for class joelib.sort.InsertSort instance() - Static method in class joelib.data.JOETypeTable Description of the Method instance() - Static method in class joelib.data.JOEResidueData Description of the Method instance() - Static method in class joelib.data.JOEPhModel Description of the Method instance() - Static method in class joelib.data.JOEGroupContribution Description of the Method instance() - Static method in class joelib.data.JOEElementTable Description of the Method instance() - Static method in class joelib.data.JOEAtomTyper Description of the Method instance() - Static method in class joelib.data.JOEAromaticTyper Description of the Method instance() - Static method in class joelib.desc.ResultFactory Description of the Method instance() - Static method in class joelib.desc.DescriptorHelper instance() - Static method in class joelib.desc.DescriptorFactory instance() - Static method in class joelib.ext.ExternalFactory Description of the Method instance() - Static method in class joelib.gui.molviewer.java3d.Viewer Description of the Method instance() - Static method in class joelib.io.IOTypeHolder Description of the Method instance() - Static method in class joelib.process.ProcessFactory Description of the Method instance() - Static method in class joelib.process.filter.FilterFactory Description of the Method instance() - Static method in class joelib.util.MDMatrixCache instance() - Static method in class joelib.util.MatrixHelper Description of the Method instance() - Static method in class joelib.util.LineMatrixHelper Description of the Method instance() - Static method in class joelib.util.LineArrayHelper Description of the Method instance() - Static method in class joelib.util.JHM Description of the Method instance() - Static method in class joelib.util.ArrayHelper Description of the Method instance() - Static method in class wsi.ra.io.FileUtilities instance() - Static method in class wsi.ra.io.BatchScriptReplacer Description of the Method instance() - Static method in class wsi.ra.tool.ResourceLoader Description of the Method instance() - Static method in class wsi.ra.tool.PropertyHolder Description of the Method instance(String) - Static method in class wsi.ra.tool.PropertyHolder Description of the Method INT - Static variable in class joelib.desc.result.DynamicArrayResult Description of the Field intArrayFromSimpleString(String) - Method in class joelib.util.ArrayHelper Loads integer array from String . intArrayFromSimpleString(String, String) - Static method in class joelib.util.ArrayHelper Loads integer array from String . intArrayFromString(Reader) - Static method in class joelib.util.LineArrayHelper Description of the Method intArrayFromString(Reader, int) - Static method in class joelib.util.LineArrayHelper Gets int arrays from a Reader. intArrayFromString(String) - Static method in class joelib.util.LineArrayHelper Description of the Method intArrayFromString(String) - Method in class joelib.util.ArrayHelper Loads integer array from String . intArrayFromString(String, int) - Static method in class joelib.util.LineArrayHelper Description of the Method intArrayFromString(String, String, int) - Static method in class joelib.util.ArrayHelper Loads integer array from String . IntArrayResult - class joelib.desc.result.IntArrayResult. Integer array results of variable size. IntArrayResult() - Constructor for class joelib.desc.result.IntArrayResult Constructor for the IntArrayResult object IntBitArrayResult - class joelib.desc.result.IntBitArrayResult. Atom representation. IntBitArrayResult() - Constructor for class joelib.desc.result.IntBitArrayResult Constructor for the IntResult object intersects(BitSet14) - Method in class joelib.util.BitSet14 Returns true if the specified BitSet14 has any bits set to true that are also set to true in this BitSet14. IntInt - class joelib.util.types.IntInt. Two integer values. IntInt() - Constructor for class joelib.util.types.IntInt Constructor for the IntInt object IntInt(int, int) - Constructor for class joelib.util.types.IntInt Constructor for the IntInt object IntIntInt - class joelib.util.types.IntIntInt. IntInt and one more integer value. IntIntInt() - Constructor for class joelib.util.types.IntIntInt Constructor for the IntIntInt object IntIntInt(IntInt, int) - Constructor for class joelib.util.types.IntIntInt Constructor for the IntIntInt object intMatrixFromString(String) - Method in class joelib.util.MatrixHelper Description of the Method intMatrixFromString(String) - Static method in class joelib.util.LineMatrixHelper Description of the Method intMatrixFromString(String, String) - Static method in class joelib.util.MatrixHelper Description of the Method IntMatrixResult - class joelib.desc.result.IntMatrixResult. Integer matrix results of variable size. IntMatrixResult() - Constructor for class joelib.desc.result.IntMatrixResult Constructor for the IntMatrixResult object IntResult - class joelib.desc.result.IntResult. Integer result. IntResult() - Constructor for class joelib.desc.result.IntResult Constructor for the IntResult object invert() - Method in class joelib.math.Matrix3x3 Description of the Method invert() - Method in class joelib.math.JOECoordTrans Inverts this objects transformation. invertRelation() - Method in class joelib.process.filter.SMARTSFilter invertRelation() - Method in class joelib.process.filter.NativeValueFilter INVISIBLE - Static variable in interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle Description of the Field IOType - class joelib.io.IOType. Input/output type for molecules. IOTypeHolder - class joelib.io.IOTypeHolder. Holder for input/output types for molecules. isAmide() - Method in class joelib.molecule.JOEBond Gets the amide attribute of the JOEBond object isAmideNitrogen() - Method in class joelib.molecule.JOEAtom Returns true if nitrogen is part of an amide. isAntiClockwise() - Method in class joelib.molecule.JOEAtom Gets the antiClockwise attribute of the JOEAtom object isAromatic() - Method in class joelib.molecule.JOEBond Gets the aromatic attribute of the JOEBond object isAromatic() - Method in class joelib.molecule.JOEAtom Returns true if this is a aromatic atom. isAromatic() - Method in class joelib.ring.JOERing Returns true if this ring is a aromatic ring. isAromaticNOxide() - Method in class joelib.molecule.JOEAtom Returns true if this is an aromatic N-Oxide atom. isAxial() - Method in class joelib.molecule.JOEAtom Returns true if this is a axial atom. isBooleanAtomLeaf(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr Gets the booleanAtomLeaf attribute of the ParseSmart class isCarbon() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom Return true if the atom is a carbon atom isCarbon() - Method in class joelib.molecule.JOEAtom Returns true if this is a carbon atom. isCarbonyl() - Method in class joelib.molecule.JOEBond Gets the carbonyl attribute of the JOEBond object isCarboxylOxygen() - Method in class joelib.molecule.JOEAtom Returns true if carbon is part of an carboxyl group. ischiral - Variable in class joelib.smarts.Pattern Description of the Field isChiral() - Method in class joelib.molecule.JOEMol Gets the chiral attribute of the JOEMol object isChiral() - Method in class joelib.molecule.JOEAtom Returns true if this is a chiral atom. isClockwise() - Method in class joelib.molecule.JOEAtom Gets the clockwise attribute of the JOEAtom object isClosure() - Method in class joelib.molecule.JOEBond Gets the closure attribute of the JOEBond object isConnected(JOEAtom) - Method in class joelib.molecule.JOEAtom Returns true if this atom is connected to the atom at . isCorrectedForPH() - Method in class joelib.molecule.JOEMol Gets the correctedForPH attribute of the JOEMol object isDouble() - Method in class joelib.molecule.JOEBond Gets the double attribute of the JOEBond object isDoubleNV() - Method in interface joelib.desc.NativeValue isDoubleNV() - Method in class joelib.desc.result.IntResult Gets the doubleNV attribute of the IntResult object isDoubleNV() - Method in class joelib.desc.result.DoubleResult Gets the doubleNV attribute of the DoubleResult object isDoubleNV() - Method in class joelib.desc.result.APropIntResult Gets the doubleNV attribute of the APropIntResult object isDoubleNV() - Method in class joelib.desc.result.APropDoubleResult Gets the doubleNV attribute of the APropDoubleResult object isDown() - Method in class joelib.molecule.JOEBond Gets the down attribute of the JOEBond object isElectronegative() - Method in class joelib.molecule.JOEAtom Returns true if electronegative atom of type N, O, F, Cl, Br. isElementOfGroup(int) - Method in class joelib.molecule.JOEAtom isEmpty() - Method in class joelib.util.BitSet14 Returns true if this BitSet14 contains no bits that are set to true. isEmpty() - Method in class wsi.ra.tool.Deque isEster() - Method in class joelib.molecule.JOEBond Gets the ester attribute of the JOEBond object isFast() - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene Gets the fast attribute of the MolecularScene object isHalogen() - Method in class joelib.molecule.JOEAtom Returns true if this is a h