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Prior to conformer generation, Omega builds a set of three dimensional
models of a compound that contain the bond lengths, angles, and ring
conformations that will be held fixed during the torsion search.
Omega is capable of generating fragment templates on-the-fly, however,
using pregenerated templates is far more efficient and will speed
execution of conformer generation. Omega distributions include a
program called makefraglib that can be used to create libraries
of molecular fragments and ring conformers that can be used by Omega
to build three dimensional models of molecules. For an explanation of
how to use makefraglib, consult Section 4. In
practice, extensive fragment libraries need only to be constructed a
single time and rarely need to be altered. Corporate and vendor
databases can be used to construct an extensive fragment library.
Once built, the fragment libraries will rarely need to be updated, and
will provide a significant enhancement in performance.
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