OMEGA Release 2.5.1.4 OpenEye Scientific Software, Inc.

OMEGA, Release 2.5.1.4
-fromCT
This boolean flag determines whether makefraglib should generate an initial set of 3D coordinates using only the
connection table of the input molecule. Initial model generation is always necessary for molecule file formats
devoid of coordinates (i.e SMILES). Bond lengths and angles taken from molecule files containing coordinates
may be retained by setting this flag to false. [default = true]
-rms
The -rms flag sets the minimum Root Mean Square (RMS) Cartesian distance below which two fragments are
duplicates. The RMS calculation is performed after superposition such that the true minimum distance between
fragments is calculated. Lowering the -rms value may cause makefraglib to generate ensembles that contain
more fragment conformers of a similar shape. Higher -rms values may result in smaller, yet possibly more
shape diverse ensembles. [default = 0.1]
-startfact
Factor for determining number of random starting geometries when generating fragments.
5.2.3 Example Executions
The following section shows several common command-line executions of makefraglib. Each example is followed by
an explanation of what the program will do. Sample data files can be found in the data directory.
prompt> makefraglib -in drugs.smi -out fraglib.oeb
All of the molecules in drugs.smi will be processed. The set of all unique fragments (according to OMEGA fragmentation
rules) from all of the molecules in drugs.smi will be collected.
prompt> makefraglib -in vendor.smi -out new_fraglib.oeb -skip fraglib.oeb -ewindow 5.0
Conformers will be generated for all of the unique fragments found in the user supplied file vendor.smi that are not
present in fraglib.oeb. An energy window of 5 Kcal above the global minimum conformer will be used to accept or
reject conformations of flexible ring systems.
5.2. makefraglib Usage 25