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•	joelib.util.cdk.* (2)	•	joelib.util.database.* (3)	•	joelib.util.ghemical.* (3)	•	joelib.util.iterator.* (12)
•	joelib.util.types.* (18)

• joelib.util: Javadoc index of package joelib.util.


Package Samples:

• joelib.util.types: Provides all kind of additional technical/molecular helper classes.  
• joelib.util.cdk
• joelib.util.database
• joelib.util.ghemical
• joelib.util.iterator

Classes:

• BitSet14: This class implements a vector of bits that grows as needed. Each component of the bit set has a boolean value. The bits of a BitSet14 are indexed by nonnegative integers. Individual indexed bits can be examined, set, or cleared. One BitSet14 may be used to modify the contents of another BitSet14 through logical AND, logical inclusive OR, and logical exclusive OR operations. By default, all bits in the set initially have the value false . Every bit set has a current size, which is the number of bits of space currently in use by the bit set. Note that the size is related to the implementation of ...
• NativeValueIterator: Gets an iterator over native descriptor values ( int or double ) of this molecule. NativeValueIterator nativeIt = mol.nativeValueIterator(); double value; String descName; while (nativeIt.hasNext()) { value = nativeIt.nextDouble(); descName = nativeIt.actualName(); }
• JOEProperty: JOELib property representation. Properties will be defined here for three reasons: Type checking, for all possible parameters you can imagine Is this an optional parameter entry ? Allow helper classes to access these data elements (easier)...
• NbrAtomIterator: Gets an iterator over all neighbour atoms in a atom. NbrAtomIterator nait = atom.nbrAtomIterator(); JOEBond bond; JOEAtom nbrAtom; while (nait.hasNext()) { nbrAtom=nait.nextNbrAtom(); bond = nait.actualBond(); }
• ConformerIterator: Gets an iterator over all conformers in a molecule. ConformerIterator cit = mol.conformerIterator(); double conformer[]; while (cit.hasNext()) { conformer = cit.nextConformer(); }
• RingIterator: Gets an iterator over all rings in a molecule. RingIterator rit = mol.getRingIterator(); JOERing ring; while(rit.hasNext()) { ring = rit.nextRing(); }
• AtomIterator: Gets an iterator over all atoms in a molecule. AtomIterator ait = mol.atomIterator(); JOEAtom atom; while (ait.hasNext()) { atom = ait.nextAtom(); }
• BondIterator: Gets an iterator over all bonds in a molecule. BondIterator ait = mol.bondIterator(); JOEBond bond; while (ait.hasNext()) { bond = bit.nextBond(); }
• JOEPropertyHelper: Some helper methods for calling classes which accept properties ( PropertyAcceptor ).
• StringPattern: java.lang.String and regular expression java.util.regex.Pattern .
• CDKTools: Helper class to faciliate access to tools of the Chemical Development Kit (CDK) .
• IntIntInt: IntInt and one more integer value.
• GhemicalInterface: This interface class to Ghemical defines some native methods for accessing parts of the Ghemical functionality.
• AtomIntInt: Atom and IntInt .
• BasicFactoryInfo: Create informations for a class which can be get by a factory class using Java reflection.
• VectorIterator: Iterator for the standard java.util.Vector .
• TestInterface: Small self-running class used to test the native methods of the 'oelib' interface.
• IteratorException: java.util.Vector iterator exception.
• LineMatrixHelper: Helper methods for writing and loading line matrices.
• ArrayHelper: Array helper methods for writing and loading arrays.
• LineArrayHelper: Helper methods for writing and loading line arrays.
• TestLayout: Example for generating 2D coordinates from SMILES.
• DoubleType: Two integers to represent a (BINARY) double value.
• MatrixHelper: Helper methods for wrinting and loading matrices.
• ResidueIterator: Gets an iterator over all residue informations.

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