Package no.uio.labmed.molecule

Interface Summary
Atomic Interface defining atomic elements.

Class Summary
AminoAcidElement Defines the amino acid molecular structures.
Atom An actual atom: ie. and instance of an atom, not just the atomic element.
AtomicBondings Object for storing a list of bonds: either those that a given atom participates in, or bonds in a given compound.
AtomicElement Defines a general atom.
AtomInCompound Object to identify an atom in a compound element.
Bond Abstract class of bonds between atoms specified as Atomic instances.
Compound An actual compound: ie. one refering to Atom instances.
CompoundElement Defines a general compound molecule: a compound of general molecular structure (see MolecularStructure).
CovalentBond A covalent bond between two atoms.
MolecularElement Defines a general molecular structure or substructure which may be either an atom or compound.
MolecularType Molecular structure types.
Molecule An actual molecule: ie. not just a general molecular structure, but an actual instance of a given MolecularElement refering to instances of Atom for each atom in the molecule and giving the coordinates of the atoms.
NullIterator An 'empty' iterator: ie. one that has no elements to iterate over.
Selector Class defining a selector: adapters towards the data which defines the key and interators for subelements.
SelectorByName Implementation of Selector which selects on molecule name.
SelectorByType Implementation of Selector which selects by molecular type.
SimpleCompoundElement Definitions of simple molecules that tend to be components of larger compounds: eg.
SimpleElement Definition of a family of simple molecules and their composition.
Test Test program.