Optional Parameters

-ionize

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

See also

• OEProton::OESetNeutralpHModel

• OEProton::OERemoveFormalCharge

-out

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. [Default=.ism]

[Aliases=**-o**]

-prefix

The argument for this flag defines the prefix to be used for parameter and log files. The parameter and log files will be written to what follows this flag plus the extension .param or .log. [Default=fixpka]