isogen
Performs stereoisomer enumeration for a set of input molecules.
Synopsis
isogen [-hVvpabsxngruyS] [-c arg] [-l arg] [-I arg] [-O arg] [-m arg] [-R arg] -i arg [arg]… -o arg
Mandatory options
-i [ –input ] arg
Specifies one or more input file(s) with molecules for which stereoisomers 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)
Chemical Markup Language Format (*.cml)
GZip-Compressed Chemical Markup Language Format (*.cml.gz)
BZip2-Compressed Chemical Markup Language Format (*.cml.bz2)
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 stereoisomers 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)
Chemical Markup Language Format (*.cml)
GZip-Compressed Chemical Markup Language Format (*.cml.gz)
BZip2-Compressed Chemical Markup Language Format (*.cml.bz2)
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).
-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.
- 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)
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)
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.
- 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)
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)
This option is useful when the format cannot be auto-detected from the actual extension of the file (because missing, misleading or not supported).
-m [ –max-num-isomers ] arg
Maximum number of output stereoisomers per molecule (default: 0, must be >= 0, 0 disables limit).
-a [ –enum-atom-cfg ] [=arg(=1)]
Enumerate configurations of atom stereocenters (default: true).
-b [ –enum-bond-cfg ] [=arg(=1)]
Enumerate configurations of bond stereocenters (default: true).
-s [ –inc-spec-ctrs ] [=arg(=1)]
Include specified atom/bond stereocenters (default: false).
-x [ –inc-sym-ctrs ] [=arg(=1)]
Include atom/bond stereocenters with topological symmetry (default: false).
-n [ –inc-inv-nitrogens ] [=arg(=1)]
Include invertible nitrogen stereocenters (default: false).
-g [ –inc-bh-atoms ] [=arg(=1)]
Include bridgehead atom stereocenters (default: false).
-r [ –inc-ring-bonds ] [=arg(=1)]
Include ring bond stereocenters (default: false).
-R [ –min-ring-size ] arg
Minimum size of rings below which the configuration of member bonds shall not be altered (only effective if option -r is true; default: 8).
-u [ –use-2d-coords ] [=arg(=1)]
If present, use atom 2D coordinates and stereo bonds to perceive the configuration of otherwise unspecified stereocenters (default: true).
-y [ –use-3d-coords ] [=arg(=1)]
If present, use atom 3D coordinates to perceive the configuration of otherwise unspecified stereocenters (default: false).
-S [ –title-suffix ] [=arg(=1)]
Append stereoisomer number to the title of the output molecules (default: false).