MolecularEnsemble contains all the molecules used by
an application. For example, a protein plus surrounding solvent in a
molecular dynamics simulation. A MolecularEnsemble contains
at least one Molecule. It can also contain some
InterAtomicArcs (which represent interactions between any
atom pairs), some HydrogenBonds and some
ImproperTorsions (these are torsion angles where not all
4 atoms are directly connected by covalent bonds).
A Molecule may or may not contain a
GroupOfAtoms. A molecular structure need not contain
information at the atomic level. An example where this is the case
is a protein for which the sequence is known but structure has not been
solved. A Molecule can contain some BondAngles,
some CovalentBonds and some TorsionAngles.
Any questions and bug reports to
Mark Williams.
Page last updated on the 25th of May 1999.