tautgen
Performs tautomer generation/standardization for a set of input molecules.
Synopsis
tautgen [-hVvptsdzS] [-c arg] [-l arg] [-m arg] [-I arg] [-O arg] [-n arg] [–keto-enol] [–imine-enamine] [–nitroso-oxime] [–amide-imidic-acid] [–lactam-lactim] [–ketene-ynol] [–nitro-aci] [–phosphinic-acid] [–sulfenic-acid] [–generic-h13-shift] [–generic-h15-shift] -i arg [arg]… -o arg
Mandatory options
-i [ –input ] arg
Specifies one or more input file(s) with molecules for which tautomers have to be generated.
- Supported Input Formats:
JME Molecular Editor String (.jme)
MDL Structure-Data File (.sdf, .sd)
MDL Molfile (.mol)
Daylight SMILES String (.smi)
Daylight SMARTS String (.sma)
IUPAC International Chemical Identifier (.inchi, .ichi)
Native CDPL-Format (.cdf)
Tripos Sybyl MOL2 File (.mol2)
Atomic Coordinates XYZ File (.xyz)
GZip-Compressed MDL Structure-Data File (.sdf.gz, .sd.gz, .sdz)
BZip2-Compressed MDL Structure-Data File (.sdf.bz2, .sd.bz2)
GZip-Compressed Native CDPL-Format (.cdf.gz)
BZip2-Compressed Native CDPL-Format (.cdf.bz2)
GZip-Compressed Daylight SMILES String (.smi.gz)
BZip2-Compressed Daylight SMILES String (.smi.bz2)
GZip-Compressed Tripos Sybyl MOL2 File (.mol2.gz)
BZip2-Compressed Tripos Sybyl MOL2 File (.mol2.bz2)
-o [ –output ] arg
Specifies the output file where the generated tautomers will be stored.
- Supported Output Formats:
JME Molecular Editor String (.jme)
MDL Structure-Data File (.sdf, .sd)
MDL Molfile (.mol)
Daylight SMILES String (.smi)
Daylight SMARTS String (.sma)
IUPAC International Chemical Identifier (.inchi, .ichi)
Native CDPL-Format (.cdf)
Tripos Sybyl MOL2 File (.mol2)
Atomic Coordinates XYZ File (.xyz)
GZip-Compressed MDL Structure-Data File (.sdf.gz, .sd.gz, .sdz)
BZip2-Compressed MDL Structure-Data File (.sdf.bz2, .sd.bz2)
GZip-Compressed Native CDPL-Format (.cdf.gz)
BZip2-Compressed Native CDPL-Format (.cdf.bz2)
GZip-Compressed Daylight SMILES String (.smi.gz)
BZip2-Compressed Daylight SMILES String (.smi.bz2)
GZip-Compressed Tripos Sybyl MOL2 File (.mol2.gz)
BZip2-Compressed Tripos Sybyl MOL2 File (.mol2.bz2)
Other options
-h [ –help ] [=arg(=SHORT)]
Print help message and exit (ABOUT, USAGE, SHORT, ALL or ‘name of option’, default: SHORT).
-V [ –version ]
Print version information and exit.
-v [ –verbosity ] [=arg(=VERBOSE)]
Verbosity level of information output (QUIET, ERROR, INFO, VERBOSE, DEBUG, default: INFO).
-c [ –config ] arg
Use file with program options.
-l [ –log-file ] arg
Redirect text-output to file.
-p [ –progress ] [=arg(=1)]
Show progress bar (default: true).
-m [ –mode ] arg
Tautomer generation mode (STANDARDIZE, BEST_SCORING [since V1.1], BEST_SCORING_UNIQUE [since V1.1], ALL [since V1.1], ALL_UNIQUE [since V1.1], default: BEST_SCORING_UNIQUE [since V1.1])
-t [ –num-threads ] [=arg(=4)]
Number of parallel execution threads (default: no multithreading, implicit value: number of CPUs, must be >= 0, 0 disables multithreading).
-I [ –input-format ] arg
Allows to explicitly specify the format of the input file(s) by providing one of the supported file-extensions (without leading dot!) as argument. This option is useful when the format cannot be auto-detected from the actual extension of the file(s) (because missing, misleading or not supported).
-O [ –output-format ] arg
Allows to explicitly specify the output format by providing one of the supported file-extensions (without leading dot!) as argument. This option is useful when the format cannot be auto-detected from the actual extension of the file (because missing, misleading or not supported).
-s [ –regard-stereo ] [=arg(=1)]
Consider stereochemistry in topological duplicate detection (default: true).
-d [ –regard-iso ] [=arg(=1)]
Whether or not isotope information matters in topological duplicate detection (default: true).
-z [ –neutralize ] [=arg(=1)]
Neutralize molecule before generating tautomers (default: false).
-n [ –max-num-tautomers ] arg
Maximum number of output tautomers for each molecule (default: 0, must be >= 0, 0 disables limit).
-S [ –title-suffix ] [=arg(=1)]
Append tautomer number to the title of the output molecules (default: false). [since V1.1]
—keto-enol [=arg(=1)]
Enable keto <-> enol tautomerization (default: true).
—imine-enamine [=arg(=1)]
Enable imine <-> enamine tautomerization (default: true).
—nitroso-oxime [=arg(=1)]
Enable nitroso <-> oxime tautomerization (default: true).
—amide-imidic-acid [=arg(=1)]
Enable amide <-> imidic acid tautomerization (default: true).
—lactam-lactim [=arg(=1)]
Enable lactam <-> lactim tautomerization (default: true).
—ketene-ynol [=arg(=1)]
Enable ketene <-> ynol form tautomerization (default: true).
—nitro-aci [=arg(=1)]
Enable nitro <-> aci form tautomerization (default: true).
—phosphinic-acid [=arg(=1)]
Enable phosphinic acid tautomerization (default: true).
—sulfenic-acid [=arg(=1)]
Enable sulfenic acid tautomerization (default: true).
—generic-h13-shift [=arg(=1)]
Enable generic hydrogen 1 <-> 3 shift tautomerization (default: true).
—generic-h15-shift [=arg(=1)]
Enable generic hydrogen 1 <-> 5 shift tautomerization (default: false [since V1.1]).