isogen
======

Performs stereoisomer enumeration for a set of input molecules.


Synopsis
--------

  :program:`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)
     - 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)
     - 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).