5.2 Usage

Flipper is a simple command-line utility program with only four parameters.

5.2.1 Command Line Interface

If you execute flipper with no arguments, it will produce the following banner.

No argument specified on the command line
Required parameters:
    -in : Input filename
    -out : Output filename (.ism or .sdf format only)
For more help type:
  flipper --help'

As described in the output above, if you desire additional command-line help, using the following prompt will result in:

prompt> flipper --help all

Complete parameter list
    Flipper
        -forceflip : Generate structures from connection-table only
        -in : Input filename
        -maxcenters : Generate structures from connection-table only
        -out : Output filename (.ism or .sdf format only)

5.2.2 Parameters

-in: This required parameter indicates the input molecule file.
-out: This required parameter indicates the output molecule file. The output file format is limited to isomeris SMILES (.ism NOT .smi) or sd format since these are the only formats which fully specify stereocenters without the need for three-dimensional coordinates.
-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: Obiously, the number of molecules generated by enumerating the stereocenters is 2N, 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]

5.2.3 Example executions

Below are three example flipper executions. Each example is followed by a brief description of the parameter's effects.

prompt> flipper -in drugs.ism -out enumerated.ism

This execution will examine each stereocenter in drugs.ism. If the stereocenter does not have a specified stereochemistry, flipper will generate moleucles with each of the stereochemistry states at each stereocenter.

prompt> flipper -in drugs.ism -out enumerated.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.ism -out enumerated.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.

				OMEGA C++ Toolkit

				OMEGA C++ Toolkit