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# tautomers Usage¶

## Required Parameters¶

-in

File containing one or more molecules for which tautomers will be generated. An input file is required, but the -in flag is optional. The first parameter listed with no flag will be automatically mapped to the input file. Unflagged parameters must occur last in the parameter list. Any OpenEye supported molecule format can be used for input.

### Optional parameters¶

-can

By default, output the OpenEye canonical SMILES for each tautomer. When -can has a value of false, tautomers writes arbitrary SMILES where the order of the atoms in each tautomer is the same for a given input molecule, which often makes it easier to see the differences between tautomers when reading the SMILES. [default = true]

-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 = false]

-count

Output just the number of tautomers per compound rather than listing the tautomers. This option writes to a text file or stdout. [default = false]

-kekule

Output is in Kekule format for .smi, .ism. and .can. Disabling aromaticity often makes it easier to understand the differences between tautomers. [default = false]

-level

Manually set the acceptable approximate tautomer energy level to use in enumeration. This takes an integer value between zero and seven inclusive, where zero corresponds to lowest energy states and seven corresponds to the highest energy state. By default, the tautomers program enumerates all tautomers in the lowest non-empty low energy state; first trying level zero and if no tautomers are found increasing to one, then two and so on. [default = 0]

-max

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 1000 tautomers per input structure. [default = 1000]

-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 .smi 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.

-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]

-reasonable

Only for those who want a unique tautomer which is reasonable looking. The program will output the most aromatic tautomer of the first 64 attempted. [default = false]

-savestereo

This allows for any atom or bond with stereochemistry set to not take part in tautomerization. Without this setting it is possible for stereochemistry to removed during tautomerization. [default = false]

-uniq

Run in canonicalization mode, where for each molecule in the input file, a single “canonical” tautomer is written to the output file. By default, tautomers runs in enumeration mode. [default = false]

-maxtime

This flag limits the amount of time (in seconds) spent generating tautomer for each molecule. [default = 60.0]

-warts

Add wart number with _ to each tautomer. [default = true]

## Example Executions¶

The following section shows several common command-line executions of tautomers. Each example is followed by an explanation of what the program will do.

Consider the following input file, guanine.smi, that contains just the following line: c1[nH]c2c(=O)[nH]c(nc2n1)N

prompt> tautomers guanine.smi output.smi


Which should write the following 15 structures to the file output.smi.

c1[nH]c2c(n1)[nH]c(nc2=O)N output_1_1
c1[nH]c2c(=O)[nH]c(nc2n1)N output_1_2
c1[nH]c2c(n1)c(=O)nc([nH]2)N output_1_3
c1[nH]c2c(n1)c(=O)[nH]c(n2)N output_1_4
c1[nH]c2c(n1)[nH]c(=N)[nH]c2=O output_1_5
c1[nH]c2c(n1)c(=O)[nH]c(=N)[nH]2 output_1_6
c1[nH]c2c(n1)nc(nc2O)N output_1_7
c1nc-2c(nc([nH]c2n1)N)O output_1_8
c1[nH]c2c(n1)c(nc(n2)N)O output_1_9
c1nc-2c([nH]c(nc2n1)N)O output_1_10
c1[nH]c2c(n1)[nH]c(=N)nc2O output_1_11
c1[nH]c2c([nH]c(=N)nc2n1)O output_1_12
c1[nH]c2c(n1)c(nc(=N)[nH]2)O output_1_13
c1nc-2c([nH]c(=N)[nH]c2n1)O output_1_14
c1[nH]c2c(n1)c([nH]c(=N)n2)O output_1_15


Please note that if tautomers fails to find tautomers for a molecule, it will output the molecule to a fail file. Name of the fail file is either ‘tautomers.fail’ or ‘prefix.fail’ if prefix is specified by -prefix flag.