Optional Parameters¶

-ch3¶: Allows carbon atoms that are close by appropriate heteroatoms to change hybridization state. This permits structures such as cyclohexa-2,4-dien-1-one to be considered a tautomer of phenol, and other examples of keto-enol tautomerism. Unfortunately, the -ch3 flag may cause the calculation time to increase by many orders of magnitude for some molecules. [default = true]

-maxtoreturn¶: Specify a maximum number of tautomers to enumerate for a single input structure. Over 99% of compounds require less than 100 tautomers, indeed most organic compounds gave only a single tautomer, however some pathological dyes and chromophores may individually have nearly a million possible tautomeric forms. The current default is a limit of 256 tautomers per input structure. [default = 256]

-maxgenerated¶: Specify a maximum number of tautomers that may be generated per input molecule.. [default = 4096]

-maxtautomericatoms¶: Specify a maximum number of tautomeric atoms allowed in a molecule. [default = 70]

-maxtime¶: This flag limits the amount of time (in seconds) spent generating tautomer for each molecule. [default = 120.0]

-maxzonesize¶: Specify a maximum number of atoms allowed in a continuous tautomerization zone. [default = 35]

-out¶: Output filename, where the file extension indicates the output format. All OpenEye supported molecule formats are allowed but .smi and .ism are recommended. The default setting will print .ism format to standard out.

-param¶: The argument for this flag is the name of a file containing control parameters. The control parameter file acts to either replace or augment the command line interface. All parameters necessary for program execution may be provided in the control parameter file, although any command given explicitly on the command line will supersede options found in the parameter file. tautomers generates a new parameter file containing the full set of execution parameters upon every execution. The name of the parameter file written by tautomers is created by combining the prefix base name with the .parm extension.

-paramfile¶: The filename for the output parameter file can be set with this flag and it overrides -prefix flag for the name of parameter file.

-pkanorm¶: This flag determines whether to apply pKa normalization. If it is true the ionization state of each tautomer will be assigned to a predominate state at pH~7.4. [default = true]

-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 = tautomers]

-rank¶: Specify whether or not tautomers are ranked and ordered before being returned. If this is false, i.e., the canonical tautomer is returned as the first molecule in the iterator. As opposed to the most “reasonable” tautomer being returned first. [default = true]

-stereo¶: Specify a stereo loss behavior for the tautomer algorithm. There are three valid values: None means that atoms and bonds with labeled stereochemistry are fixed to participate in tautomerization; LocalSampled means that individual tautomers that have double bonds to tetrahedral stereocenters will have the stereo removed; EverSampled means that if an atom which are tetrahedral stereocenters has a double bonds in any of the tautomers returned by the function, then those tetrahedral stereocenters will have the stereo removed in ALL of the returned tautomers. [default = Localsampled]