OMEGA Release 2.5.1.4 OpenEye Scientific Software, Inc.

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OMEGA, Release 2.5.1.4 6.2.1 Required Parameters -in File containing one or more molecules for which stereoisomers will be generated -out This required parameter indicates the output molecule file. The output file format is limited to OEB, isomeric SMILES (.ism NOT .smi) or SD format since these are the only formats which fully specify stereocenters without the need for three-dimensional coordinates. 6.2.2 Other options -enumNitrogen The -enumNitrogen string flag controls the behavior of FLIPPER with respect to enumeration of non-planar nitrogens. Any nitrogen with pyramidal geometry in the initial model of the input molecule, and having no more than two ring bonds is considered by OMEGA to be ‘invertible’. FLIPPER will enumerate all possible puckers if the -enumNitrogens flag is set to true. [default = false] -forceflip This parameter forces flipper to modify all of the stereocenters in a molecule. If -forceflip is false (the default), flipper only enumerates stereocenters which do not already have a specified stereochemistry. [default = false] -maxcenters Obviously, the number of molecules generated by enumerating the stereocenters is 2 N , where N is the number of stereocenters. In some instances, this may be larger than is desired. The -maxcenters parameter indicates the maximum number of stereocenters which will be fully enumerated. If a molecule has more than -maxcenters stereocenters, flipper will randomly enumerate 2^(maxcenters) instances from the full set of potential isomers. [default = 12] -warts Add wart to title of each stereoisomer. [default = false] 6.2.3 Example Executions Below are three example flipper executions. Each example is followed by a brief description of the parameter’s effects. Sample data files can be found in the data directory. prompt> flipper -in drugs.smi -out enumerated.ism This execution will examine each stereocenter in drugs.smi. If the stereocenter does not have a specified stereochemistry, flipper will generate molecules with each of the stereochemistry states at each stereocenter. prompt> flipper -in drugs.smi -out enumerated_forceflip.ism -forceflip true This execution will differ from the first in that all stereocenters will be enumerated, regardless of whether the stereochemistry is specified in the input file. prompt> flipper -in drugs.smi -out enumerated_maxcenters6.ism -maxcenters 6 In this execution, flipper will exhaustively enumerate all unspecified stereocenters in molecules with up to 6 stereocenters. For molecules with more than 6 stereocenters, a random set of 64 isomers will be generated from the larger set of potential stereoisomers. 28 Chapter 6. flipper: Enumerating Stereocenters
7.1 oeb2sdconf Usage CHAPTER SEVEN OEB2SDCONF oeb2sdconf is a utility that allows OMEGA generated conformers to be used with the MOE program. Please contact Chemical Computing Group support if you require assistance with this utility. 29
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