Optional Parameters


Specifies ionization environment, either neutral pH or un-ionize, to remove all ions possible. Legal values are neutral, 7.4, un-ionize, and unionize.


File for writing output. Both the output file and the -out flag are optional. The second parameter listed with no flag will be automatically mapped to the output file. Unflagged parameters must occur last in the parameter list. Any OpenEye supported molecule format can be used for output but .smi or .ism is recommended. The default setting will print .ism format to standard out.