OMEGA Release 2.5.1.4 OpenEye Scientific Software, Inc.

CHAPTER
FIVE
MAKEFRAGLIB: CREATING A
FRAGMENT LIBRARY
makefraglib identifies, extracts, and generates conformers of molecular fragments. The model builder in OMEGA
fragments input molecules, retrieves corresponding fragment conformers, and assembles them into a three dimensional
structure. Pregenerating fragment conformers using makefraglib accelerates the model building procedure.
5.1 makefraglib Theory
The model builder in OMEGA attempts to capture all of the relevant bond length and angles, and ring conformations
for an input molecule. Fragment assembly allows for a ‘divide and conquer’ approach to model building. Much of
the relevant information for building a molecular models is contained in carefully chosen fragments. makefraglib
uses distance constraints and geometry optimization to generate fragment conformations. Only a single conformation
is stored for acyclic fragments, while all possible unique ring conformers are retained within user defined limits.
Libraries created with makefraglib can then be provided to OMEGA using the -setfraglib or -addfraglib flags.
5.2 makefraglib Usage
makefraglib can be used from the command-line to generate ring templates for use with OMEGA starting from only
a collection of molecules. The output file from makefraglib can then be passed directly into OMEGA using the -
setfraglib or -addfraglib flag. Although fragment libraries may be concatenated using the Unix ‘cat’ command, this is
not strictly necessary as multiple fragment libraries may be specified as one argument to the flag.
5.2.1 Required Parameters
-in
File containing one or more molecules from which fragments will be generated
-out
File to write fragments generated by makefraglib. OEBinary format is required and Gzipped OEBinary is
recommended.
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