Release Date: 1 February 2008
Nametautomer - calculate tautomers for molecules
Unix Synopsistautomer [options] [infile.tdt [outfile.tdt]]
Descriptiontautomer is a non-interactive program that takes Thor Data Tree (TDT) input containing SMILES and provides output in TDT format. If present, tautomer will read in the input from infile.tdt and write it's output to outfile.tdt. If filenames are not specified tautomer will read from standard input and write to standard output.
tautomertalk is usually invoked as a program object (see dt_alloc_program(3)), and uses the "talk" protocol for input/output. See the Daylight Properties Package Manual for more information about the program object messages which tautomertalk uses.
If a valid estimate can't be made, tautomer copies the input TDT to its output unaltered.
The TAUT datatype has 1 field: $TAUT<tautomer>.
OptionsThe following apply to tautomer(1):
Displays command line summary and halts.-VERSION [TRUE]
Displays the version number of the toolkit program.-NO_ENOL [TRUE|FALSE]
This option allows only heteroatoms to participate as hydrogen donors or acceptors. This option suppresses keto-enol type tautomerism. The default is FALSE.-ISO [TRUE|FALSE]
The -ISO FALSE option returns the tautomers as unique SMILES. When true the program returns the tautomers as absolute SMILES. The default is FALSE.-KEKULE [TRUE|FALSE]
The KEKULE option when TRUE generates kekule structures using dt_xsmiles(). When FALSE the program generates canonical SMILES using dt_cansmiles(); The default is FALSE.-UNIQUE [TRUE|FALSE]
When TRUE the UNIQUE option writes out the canonical tautomer. The canonical tautomer is the one generated by using the relative electronegativities of the atom types (O > S > Se > Te > N > C) as graph invariants to preferentially assign double bond and hydrogen positions in the tautomer. Although this tautomer often corresponds to the lowest energy form, it is not guaranteed, as it's generated from graph theory and does not consider extended electronic factors. The default is FALSE.-ITERATION_LIMIT [LIMIT]
This is the maximum number of donor or acceptor positions to iterate. If a structure has more than lIMIT of either donors or acceptors, then no tautomer enumeration is performed. The default limit is 0, which causes teh program to generate tautomers for every input structure until all possible tautomers have been generated. A reasonable value for limit to minimize long-running , pathological cases, is 10.-FIXED_SUBSTRUCTURE [SMARTS,SMARTS]
A comma-separated list of SMARTS which are matched against each input molecule. Any atoms which match are marked as non-tautomerizable and hence stay fixed throughout the enumeration. Useful for excluding specific functional groups from the calculation.
Return ValueReturns 0 to its environment if the program initializes correctly. Returns 1 if initialization fails, e.g. an invalid option or a file that can't be opened.
Daylight Licenseprograms: tautomer
Daylight Theory Manual Daylight Toolkit Programmer's Guide Daylight Tautomer Reference Guide