The isoenum Docker Tutorial

The isoenum docker container

This section contains the examples provided above but with the use of a docker container with isoenum Python package and all its dependencies instead of using isoenum Python package directly.

After you docker pull or docker build the isoenum container, you can verify that it is available.

# docker images

You should see output similar to the following:

REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
isoenum             latest              0e4c431aa519        1 day ago           862MB

Command-line interface

The isoenum package provides an easy-to-use command-line interface that allows the specification of isotopes for the creation of isotopically-resolved InChI.

  • To access the isoenum command-line interface from docker container:
# docker run isoenum --help

Output:

Isotopic enumerator (isoenum) command-line interface

Usage:
    isoenum -h | --help
    isoenum --version
    isoenum name (<path-to-ctfile-file-or-inchi-file-or-inchi-string>)
                 [--specific=<isotope:element:position>...]
                 [--all=<isotope:element>...]
                 [--enumerate=<isotope:element:min:max>...]
                 [--complete | --partial]
                 [--ignore-iso]
                 [--format=<format>]
                 [--output=<path>]
                 [--verbose]
    isoenum ionize (<path-to-ctfile-file-or-inchi-file-or-inchi-string>)
                (--state=<element:position:charge>)
                [--format=<format>]
                [--output=<path>]
    isoenum nmr (<path-to-ctfile-file-or-inchi-file-or-inchi-string>)
                [--type=<experiment-type>]
                [--jcoupling=<name>...]
                [--decoupled=<element>...]
                [--format=<format>]
                [--output=<path>]
                [--subset]
                [--verbose]

Options:
    -h, --help                                 Show this screen.
    --verbose                                  Print more information.
    -v, --version                              Show version.
    -a, --all=<isotope:element>                Specify element and isotope, e.g. -a 13:C or --all=13:C
    -s, --specific=<isotope:element:position>  Specify element, isotope and specific position,
                                               e.g. -s 13:C:1 or --specific=13:C:1.
    -e, --enumerate=<isotope:element:min:max>  Enumerate all isotopically-resolved CTfile or InChI,
                                               e.g. -e 13:C:2:4 or --enumerate=13:C:2:4
    -c, --complete                             Use complete labeling schema, i.e. every atom must specify
                                               "ISO" property, partial labeling schema will be used otherwise
                                               for specified labeling information only.
    -p, --partial                              Use partial labeling schema, i.e. generate labeling schema
                                               from the provided labeling information.
    -i, --ignore-iso                           Ignore existing "ISO" specification in the CTfile or InChI.
    -f, --format=<format>                      Format of output: inchi, mol, sdf, csv, json [default: inchi].
    -o, --output=<path>                        Path to output file.
    -t, --type=<experiment-type>               Type of NMR experiment [default: 1D1H].
    -j, --jcoupling=<type>                     Allowed J couplings.
    -d, --decoupled=<element>                  Turn off J coupling for a given element.
    -z, --state=<element:position:charge>      Create ionized form of InChI from neutral molecule,
                                               e.g. N:6:+1, O:8:-1.
    --subset                                   Create atom subsets for each resonance.

Docker usage examples

Input files

We will use the same input files as above to generate isotopically-resolved InChI. Repeated here for convenience.

  • Molfile example:
pentane-2_2-diol
OpenBabel02101812223D

 19 18  0  0  0  0  0  0  0  0999 V2000
    0.8986   -0.0477    0.0323 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0960    0.7629    2.7277 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4213   -0.0579   -0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0115    0.3840    1.3416 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5473    0.3524    1.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9506   -0.9689    1.0442 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0892    1.2477    0.4081 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4966   -0.3656   -0.9348 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5151    0.9566    0.2461 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5209   -0.7306    0.7986 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7913    0.0636    3.5124 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7734    1.7738    2.9979 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1923    0.7728    2.7063 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7620    0.6098   -0.8011 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7573   -1.0707   -0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6291   -0.2841    2.1226 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6589    1.3989    1.5754 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5197   -1.2976    1.7554 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6303    2.0937    0.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  2  5  1  0  0  0  0
  2 11  1  0  0  0  0
  2 12  1  0  0  0  0
  2 13  1  0  0  0  0
  3  4  1  0  0  0  0
  3 14  1  0  0  0  0
  3 15  1  0  0  0  0
  4  5  1  0  0  0  0
  4 16  1  0  0  0  0
  4 17  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6 18  1  0  0  0  0
  7 19  1  0  0  0  0
M  ISO  1   1  12
M  END
  • Text file containing InChI string:
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3
  • SDfile (i.e. Molfile plus data) example:
pentane-2_2-diol
OpenBabel02101812223D

 19 18  0  0  0  0  0  0  0  0999 V2000
    0.8986   -0.0477    0.0323 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0960    0.7629    2.7277 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4213   -0.0579   -0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0115    0.3840    1.3416 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5473    0.3524    1.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9506   -0.9689    1.0442 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0892    1.2477    0.4081 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4966   -0.3656   -0.9348 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5151    0.9566    0.2461 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5209   -0.7306    0.7986 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7913    0.0636    3.5124 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7734    1.7738    2.9979 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1923    0.7728    2.7063 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7620    0.6098   -0.8011 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7573   -1.0707   -0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6291   -0.2841    2.1226 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6589    1.3989    1.5754 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5197   -1.2976    1.7554 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6303    2.0937    0.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  2  5  1  0  0  0  0
  2 11  1  0  0  0  0
  2 12  1  0  0  0  0
  2 13  1  0  0  0  0
  3  4  1  0  0  0  0
  3 14  1  0  0  0  0
  3 15  1  0  0  0  0
  4  5  1  0  0  0  0
  4 16  1  0  0  0  0
  4 17  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6 18  1  0  0  0  0
  7 19  1  0  0  0  0
M  ISO  1   1  12
M  END
> <InChI>
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0

$$$$

Input file/string specification

As shown above, the isoenum command-line interface asks the user to provide one required parameter <path-to-ctfile-file-or-inchi-file-or-inchi-string>, which is the file or string with information required to create isotopically-resolved InChI.

In order to provide the input file path to the isoenum docker container, you will need to mount it as a volume for the docker container so the container can see it.

Warning

You need to provide the absolute path to the input file, otherwise the docker container will not be able to see it.

For example, -v /absolute/path/to/input.txt:/input.txt, where path on the left side of : is the absolute path on the host machine and the path on the right side of : is the path within the docker container.

To illustrate, let’s invoke the isoenum docker container and provide input files:

  • Path to CTfile (i.e. Molfile or SDfile).
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol
  • Path to the file containing an InChI.
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol
  • InChI string.
# docker run isoenum name 'InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3'

or

# docker run isoenum name '1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3'

The isoenum name command

The name command of the isoenum command-line interface provides facilities to add isotopic layer information to molecule in order to create isotopically-resolved InChI.

Isotopic layer specification: specific atoms option

The -s or --specific option allows the user to specify the isotopic information for an atom at a specific position within a molecule (e.g. carbon at position “2” will have absolute mass “13”).

  • To designate the isotope of a specific atom within a given Molfile, use the -s or --specific option. For example, specify the second carbon atom as carbon “13”:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -s 13:C:2

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --specific=13:C:2

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1
  • To designate the isotope for several atoms, repeat the -s or --specific option:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -s 13:C:1 -s 13:C:2

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --specific=13:C:1 --specific=13:C:2

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1

Note

Since the original file already contained the ISO specification for the first carbon atom, it did not change the designation of that atom (i.e. i1+0 was retained).

  • To ignore existing ISO specifications, provide the -i or --ignore-iso option:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -s 13:C:1 -s 13:C:2 -i

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --specific=13:C:1 --specific=13:C:2 --ignore-iso

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,2+1

Isotopic layer specification: all atoms of a specific type option

The -a or --all option allows the user to specify the isotopic information for all atoms of a specific type (e.g. all carbons within a molecule will have absolute mass “13” etc.)

  • To add isotope designations to all atoms of a specific element, use the -a or --all option:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -a 13:C

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --all=13:C

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1
  • To add isotope designations to different types of atoms, repeat the -a or --all option for each desired element:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -a 13:C -a 18:O

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --all=13:C --all=18:O

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1,6+2,7+2
  • To ignore existing ISO specifications, combine with the -i or --ignore-iso option:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -a 13:C -a 18:O -i

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --all=13:C --all=18:O --ignore-iso

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,2+1,3+1,4+1,5+1,6+2,7+2
  • Also the -a or --all option can be combined with the -s or --specific option which has higher priority:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -a 13:C -s 12:C:3 -i

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --all=13:C --specific=12:C:3 --ignore-iso

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,2+1,3+0,4+1,5+1

Isotopic layer specification: enumerate atoms of specific type option

The -e or --enumerate option allows the user to create a set of InChI for a molecule with a different number of isotopes (e.g. create all InChI where the number of carbon atoms with absolute mass “13” ranges from 0 to 5).

  • To enumerate atoms of a specific element type, use the -e or --enumerate option:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -e 13:C

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --enumerate=13:C

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0
  • A minimum and maximum number can be set to limit InChI generation to desired minimum and maximum number of atoms of the specified element. For example, generate all possible InChI where the number of carbon “13” atoms is in the range from 3 to 4:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -e 13:C:3:4

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --enumerate=13:C:3:4

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,4+1,5+1
  • To ignore existing ISO specifications, combine it with the -i or ignore-iso option:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -e 13:C:3:4 -i

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --enumerate=13:C:3:4 --ignore-iso

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,2+1,3+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,2+1,3+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,2+1,3+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,2+1,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,2+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,2+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,3+1,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,3+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,3+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+1,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i2+1,3+1,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i2+1,3+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i2+1,3+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i2+1,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i3+1,4+1,5+1
  • To enumerate multiple atom types, repeat the -e or --enumerate option for the desired element:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -e 13:C:3:4 -e 18:O:1:2

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --enumerate=13:C:3:4 --enumerate=18:O:1:2

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1,6+2,7+2
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1,6+2/t5-/m0/s1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1,6+2/t5-/m1/s1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,6+2,7+2
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,6+2/t5-/m0/s1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,6+2/t5-/m1/s1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,5+1,6+2,7+2
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,5+1,6+2/t5-/m0/s1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,5+1,6+2/t5-/m1/s1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,4+1,5+1,6+2,7+2
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,4+1,5+1,6+2/t5-/m0/s1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,4+1,5+1,6+2/t5-/m1/s1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,4+1,5+1,6+2,7+2
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,4+1,5+1,6+2/t5-/m0/s1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,4+1,5+1,6+2/t5-/m1/s1
  • The -e (--enumerate) option can be combined with the -a (--all) and -s (--specific) options except the -e (--enumerate) option cannot specify the same element as the -a (--all) option.
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -e 13:C:2:4 -a 18:O -s 12:C:3

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --enumerate=13:C:2:4 --all=18:O --specific=12:C:3

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+0,4+1,5+1,6+2,7+2
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+0,4+1,6+2,7+2
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+0,5+1,6+2,7+2
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+0,4+1,5+1,6+2,7+2
  • It is also possible to combine the -e or --enumerate option for the same element but different isotopes (also note that we are not specifying minimum number in this example, it will be set to 0 by default). For example, we want to generate InChI with up to 2 carbon “12” and up to 2 carbon “13”:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -e 13:C:2 -e 12:C:2

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --enumerate=13:C:2 --enumerate=12:C:2

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,5+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,4+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,4+0,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,4+1,5+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+0,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+0,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+0,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,5+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,4+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,4+0,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,3+1,4+1,5+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+0,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+0,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+0,4+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+0,3+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+0,3+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+0,3+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,5+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,4+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,4+0,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,4+1,5+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+0,5+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+0,4+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,5+0
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+0

The isoenum ionize command

The ionize command of isoenum command-line interface provides facilities to add charge information to a given molecule.

For example, the following InChI represents amino acid L-Valine:

InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1

with the following chemical structure:

_images/l-valine.svg
  • To create InChI that represents the zwitterion form:
# docker run isoenum ionize 'InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1' -z N:6:+1 -z O:8:-1 -f inchi

or

# docker run isoenum ionize 'InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1' --state=N:6:+1 --state=O:8:-1 --format=inchi

Output:

InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/f/h6H

The generated InChI corresponds to the following structure:

_images/l-valine-zwitterion.svg

For a second example, the following InChI represents neutral Adenosine monophosphate (AMP):

InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1

with the following chemical structure:

_images/amp.svg
  • To create the biochemically-relevant ionized InChI:
# docker run isoenum ionize 'InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1' -z O:18:-1 -z O:19:-1 -f inchi

or

# docker run isoenum ionize 'InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1' --state=O:18:-1 --state=O:19:-1 --format=inchi

Output:

InChI=1/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/p-2/t4-,6-,7-,10-/m1/s1/fC10H12N5O7P/h11H2/q-2

The generated InChI corresponds to the following structure:

_images/amp-ion.svg

The isoenum nmr command

The nmr command of the isoenum command-line interface provides facilities to create isotopically-resolved InChI based on theoretical NMR coupling patterns (e.g. J1CH, J3HH, etc.).

For example, the following InChI represents amino acid L-Valine:

InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1

with the following chemical structure:

_images/l-valine.svg
  • To create the theoretically possible set of InChI for “1D1H” NMR experiment:
# docker run isoenum nmr 'InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1' --type=1D1H --format=csv

or

# docker run isoenum nmr 'InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1' -t 1D1H -f csv

Output:

[1H9,1H10,1H11]HResonance   InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3/t3-,4-
[1H9,1H10,1H11]HResonance + [1H9,1H10,1H11:13C1]J1CH        InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1+1H3/t3-,4-
[1H9,1H10,1H11]HResonance + [1H9,1H10,1H11:1H15]J3HH        InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H/t3-,4-
[1H9,1H10,1H11]HResonance + [1H9,1H10,1H11:13C1]J1CH + [1H9,1H10,1H11:1H15]J3HH     InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1+1H3,3H/t3-,4-
[1H12,1H13,1H14]HResonance  InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3/t3-,4+/m1
[1H12,1H13,1H14]HResonance + [1H12,1H13,1H14:13C2]J1CH      InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1+1H3/t3-,4+/m1
[1H12,1H13,1H14]HResonance + [1H12,1H13,1H14:1H15]J3HH      InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H/t3-,4+/m1
[1H12,1H13,1H14]HResonance + [1H12,1H13,1H14:13C2]J1CH + [1H12,1H13,1H14:1H15]J3HH  InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1+1H3,3H/t3-,4+/m1
[1H15]HResonance    InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3H
[1H15]HResonance + [1H15:13C3]J1CH  InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3+1H
[1H15]HResonance + [1H15:1H9,1H10,1H11]J3HH InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H/t3-,4-
[1H15]HResonance + [1H15:1H12,1H13,1H14]J3HH        InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H/t3-,4+/m1
[1H15]HResonance + [1H15:1H16]J3HH  InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3H,4H
[1H15]HResonance + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H12,1H13,1H14]J3HH     InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,2H3,3H
[1H15]HResonance + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H16]J3HH       InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H,4H/t3-,4-
[1H15]HResonance + [1H15:1H12,1H13,1H14]J3HH + [1H15:1H16]J3HH      InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H,4H/t3-,4+/m1
[1H15]HResonance + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H12,1H13,1H14]J3HH + [1H15:1H16]J3HH   InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,2H3,3H,4H
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H9,1H10,1H11]J3HH       InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3+1H/t3-,4-
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H12,1H13,1H14]J3HH      InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3+1H/t3-,4+/m1
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H16]J3HH        InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3+1H,4H
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H12,1H13,1H14]J3HH   InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,2H3,3+1H
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H16]J3HH     InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3+1H,4H/t3-,4-
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H12,1H13,1H14]J3HH + [1H15:1H16]J3HH    InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3+1H,4H/t3-,4+/m1
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H12,1H13,1H14]J3HH + [1H15:1H16]J3HH InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,2H3,3+1H,4H
[1H16]HResonance    InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i4H
[1H16]HResonance + [1H16:13C4]J1CH  InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i4+1H
[1H16]HResonance + [1H16:1H15]J3HH  InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3H,4H
[1H16]HResonance + [1H16:13C4]J1CH + [1H16:1H15]J3HH        InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3H,4+1H

Note

Notice that the csv output includes a J-coupling description of the transient peak and the representative InChI.

Workflow to generate InChI for data deposition from NMR experiments

  1. Obtain standard InChI with correct bonded structure and stereochemistry.
  2. Convert to fully representative InChI with proper ionization states if necessary (the ionize command).
  3. Enumerate partial isotopomer InChI (the nmr command).
  4. Select appropriate partial isotopomer InChI.

For example, the following InChI represents amino acid L-Valine:

InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1

with the following chemical structure:

_images/l-valine.svg

We want to generate partial isotopomer InChI for the zwitterionic form of l-valine. To change the ionization state within molecule, we need to use the ionize command on a standard InChI:

# docker run isoenum ionize 'InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1' -z N:6:+1 -z O:8:-1 -f inchi

or

# docker run isoenum ionize 'InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1' --state=N:6:+1 --state=O:8:-1 --format=inchi

Output:

InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/f/h6H

The generated InChI corresponds to the following structure:

_images/l-valine-zwitterion.svg

Next, we want to enumerate all possible isotopomers for “1D1H” NMR experiment:

# docker run isoenum nmr 'InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/f/h6H' --type=1D1H --format=csv

or

# docker run isoenum nmr 'InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/f/h6H' -t 1D1H -f csv

Output:

[1H9,1H10,1H11]HResonance   InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3/t3-,4-/f/h6H/i/tM
[1H9,1H10,1H11]HResonance + [1H9,1H10,1H11:13C1]J1CH        InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1+1H3/t3-,4-/f/h6H/i/tM
[1H9,1H10,1H11]HResonance + [1H9,1H10,1H11:1H15]J3HH        InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H/t3-,4-/f/h6H/i/tM
[1H9,1H10,1H11]HResonance + [1H9,1H10,1H11:13C1]J1CH + [1H9,1H10,1H11:1H15]J3HH     InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1+1H3,3H/t3-,4-/f/h6H/i/tM
[1H12,1H13,1H14]HResonance  InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3/t3-,4+/m1/f/h6H/i/tM/m1
[1H12,1H13,1H14]HResonance + [1H12,1H13,1H14:13C2]J1CH      InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1+1H3/t3-,4+/m1/f/h6H/i/tM/m1
[1H12,1H13,1H14]HResonance + [1H12,1H13,1H14:1H15]J3HH      InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H/t3-,4+/m1/f/h6H/i/tM/m1
[1H12,1H13,1H14]HResonance + [1H12,1H13,1H14:13C2]J1CH + [1H12,1H13,1H14:1H15]J3HH  InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1+1H3,3H/t3-,4+/m1/f/h6H/i/tM/m1
[1H15]HResonance    InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3H/f/h6H
[1H15]HResonance + [1H15:13C3]J1CH  InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3+1H/f/h6H
[1H15]HResonance + [1H15:1H9,1H10,1H11]J3HH InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H/t3-,4-/f/h6H/i/tM
[1H15]HResonance + [1H15:1H12,1H13,1H14]J3HH        InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H/t3-,4+/m1/f/h6H/i/tM/m1
[1H15]HResonance + [1H15:1H16]J3HH  InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3H,4H/f/h6H
[1H15]HResonance + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H12,1H13,1H14]J3HH     InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,2H3,3H/f/h6H
[1H15]HResonance + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H16]J3HH       InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H,4H/t3-,4-/f/h6H/i/tM
[1H15]HResonance + [1H15:1H12,1H13,1H14]J3HH + [1H15:1H16]J3HH      InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3H,4H/t3-,4+/m1/f/h6H/i/tM/m1
[1H15]HResonance + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H12,1H13,1H14]J3HH + [1H15:1H16]J3HH   InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,2H3,3H,4H/f/h6H
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H9,1H10,1H11]J3HH       InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3+1H/t3-,4-/f/h6H/i/tM
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H12,1H13,1H14]J3HH      InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3+1H/t3-,4+/m1/f/h6H/i/tM/m1
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H16]J3HH        InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3+1H,4H/f/h6H
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H12,1H13,1H14]J3HH   InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,2H3,3+1H/f/h6H
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H16]J3HH     InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3+1H,4H/t3-,4-/f/h6H/i/tM
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H12,1H13,1H14]J3HH + [1H15:1H16]J3HH    InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,3+1H,4H/t3-,4+/m1/f/h6H/i/tM/m1
[1H15]HResonance + [1H15:13C3]J1CH + [1H15:1H9,1H10,1H11]J3HH + [1H15:1H12,1H13,1H14]J3HH + [1H15:1H16]J3HH InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1H3,2H3,3+1H,4H/f/h6H
[1H16]HResonance    InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i4H/f/h6H
[1H16]HResonance + [1H16:13C4]J1CH  InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i4+1H/f/h6H
[1H16]HResonance + [1H16:1H15]J3HH  InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3H,4H/f/h6H
[1H16]HResonance + [1H16:13C4]J1CH + [1H16:1H15]J3HH        InChI=1/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3H,4+1H/f/h6H

Finally, select appropriate InChI from the generated possibilities and associate them with the appropriate transient peak (chemical shift).

Output format

  • There are several output formats available:

    • inchi: produces InChI string.
    • sdf: produces SDfile with one or more Molfile and InChI associated with it.
    • mol: the same as sdf.
    • json: produces JSON representation of SDfile.
    • csv: produces tab-separated csv file with the information from SDfile data block.

  • To specify the inchi output format (which is set to default and does not require format specification), use the -f or --format option followed by inchi:

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -s 13:C:2 -f inchi

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --specific=13:C:2 --format=inchi

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1
  • To specify the mol or sdf output format, use the -f or --format option followed by mol or sdf:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -s 13:C:2 -f sdf

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --specific=13:C:2 --format=sdf

Output:

pentane-2_2-diol
OpenBabel04241818183D

 19 18  0  0  0  0  0  0  0  0999 V2000
    0.8564    0.0224   -0.0199   C 0  0  0  0  0  0  0  0  0  0  0  0
    5.0590   -2.7653   -0.2642   C 0  0  0  0  0  0  0  0  0  0  0  0
    2.3767    0.0633   -0.0253   C 0  0  0  0  0  0  0  0  0  0  0  0
    2.9725   -1.3472   -0.1203   C 0  0  0  0  0  0  0  0  0  0  0  0
    4.5036   -1.3472   -0.1439   C 0  0  0  0  0  0  0  0  0  0  0  0
    4.9424   -0.5621   -1.2388   O 0  0  0  0  0  0  0  0  0  0  0  0
    5.0329   -0.7920    1.0484   O 0  0  0  0  0  0  0  0  0  0  0  0
    0.4514    1.0368    0.0457   H 0  0  0  0  0  0  0  0  0  0  0  0
    0.4813   -0.5495    0.8345   H 0  0  0  0  0  0  0  0  0  0  0  0
    0.4733   -0.4367   -0.9365   H 0  0  0  0  0  0  0  0  0  0  0  0
    4.7458   -3.2426   -1.1982   H 0  0  0  0  0  0  0  0  0  0  0  0
    4.7417   -3.3903    0.5788   H 0  0  0  0  0  0  0  0  0  0  0  0
    6.1556   -2.7490   -0.2585   H 0  0  0  0  0  0  0  0  0  0  0  0
    2.7259    0.5602    0.8869   H 0  0  0  0  0  0  0  0  0  0  0  0
    2.7092    0.6719   -0.8743   H 0  0  0  0  0  0  0  0  0  0  0  0
    2.5969   -1.8221   -1.0358   H 0  0  0  0  0  0  0  0  0  0  0  0
    2.6148   -1.9367    0.7329   H 0  0  0  0  0  0  0  0  0  0  0  0
    5.0489   -1.1442   -2.0068   H 0  0  0  0  0  0  0  0  0  0  0  0
    4.6612   -1.2841    1.7969   H 0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  2  5  1  0  0  0  0
  2 11  1  0  0  0  0
  2 12  1  0  0  0  0
  2 13  1  0  0  0  0
  3  4  1  0  0  0  0
  3 14  1  0  0  0  0
  3 15  1  0  0  0  0
  4  5  1  0  0  0  0
  4 16  1  0  0  0  0
  4 17  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6 18  1  0  0  0  0
  7 19  1  0  0  0  0
M  ISO  2   1  12   2  13
M  END
> <InChI>
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1

$$$$
  • To specify the json output format, use the -f or --format option followed by json:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -s 13:C:2 -f json

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --specific=13:C:2 --format=json

Output:

{
    "1": {
        "molfile": {
            "HeaderBlock": {
                "molecule_name": "",
                "software": "OpenBabel02101812223D",
                "comment": ""
            },
            "Ctab": {
                "CtabCountsLine": {
                    "number_of_atoms": "19",
                    "number_of_bonds": "18",
                    "number_of_atom_lists": "0",
                    "not_used1": "0",
                    "chiral_flag": "0",
                    "number_of_stext_entries": "0",
                    "not_used2": "0",
                    "not_used3": "0",
                    "not_used4": "0",
                    "not_used5": "0",
                    "number_of_properties": "999",
                    "version": "V2000"
                },
                "CtabAtomBlock": [
                    {
                        "x": "0.8986",
                        "y": "-0.0477",
                        "z": "0.0323",
                        "atom_symbol": "C",
                        "mass_difference": "0",
                        "charge": "0",
                        "atom_stereo_parity": "0",
                        "hydrogen_count": "0",
                        "stereo_care_box": "0",
                        "valence": "0",
                        "h0designator": "0",
                        "not_used1": "0",
                        "not_used2": "0",
                        "atom_atom_mapping_number": "0",
                        "inversion_retention_flag": "0",
                        "exact_change_flag": "0"
                    },
                    ...
                ],
                "CtabBondBlock": [
                    {
                        "first_atom_number": "1",
                        "second_atom_number": "3",
                        "bond_type": "1",
                        "bond_stereo": "0",
                        "not_used1": "0",
                        "bond_topology": "0",
                        "reacting_center_status": "0"
                    },
                    ...
                ],
                "CtabPropertiesBlock": {
                    "ISO": [
                        {
                            "atom_number": "1",
                            "absolute_mass": "12"
                        },
                        {
                            "atom_number": "2",
                            "absolute_mass": "13"
                        }
                    ]
                }
            }
        },
        "data": {
            "InChI": [
                "InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1"
            ]
        }
    }
}
  • To specify the csv output format, use the -f or --format option followed by csv:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol -s 13:C:2 -f csv

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol isoenum name /pentane-2_2-diol.mol --specific=13:C:2 --format=csv

Output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1

Output file

In the case of using the isoenum docker container, both the input file and the output file must be mounted as volumes for the docker container to see them.

Warning

You need to provide the absolute path to the input and output files, otherwise the docker container will not be able to see them.

For example, -v /absolute/path/to/input.txt:/input.txt, where path on the left side of : is the absolute path on the host machine and the path on the right side of : is the path within the docker container.

In the same way, you will need to create an empty text file and mount it as a volume, so the docker container can write to it, -v /absolute/path/to/output.txt:/output.txt, where the path on the left side of : is the absolute path on the host machine and the path on the right side of : is the path within the docker container.

  • To save the generated output into a file, use the -o or --output option followed by filename. For example, save the generated output in inchi format:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol \
             -v /absolute/path/to/outfile.inchi:/outfile.inchi \
             isoenum name /pentane-2_2-diol.mol -a 13:C -f inchi -o /outfile.inchi

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol \
             -v /absolute/path/to/outfile.inchi:/outfile.inchi \
             isoenum name /pentane-2_2-diol.mol --all=13:C --format=inchi --output=/outfile.inchi

The generated file will contain the following output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1
  • To save the generated output in mol or sdf format:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol \
             -v /absolute/path/to/outfile.sdf:/outfile.sdf \
             isoenum name /pentane-2_2-diol.mol -a 13:C -f sdf -o /outfile.sdf

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol \
             -v /absolute/path/to/outfile.sdf:/outfile.sdf \
             isoenum name /pentane-2_2-diol.mol --all=13:C --format=sdf --output=/outfile.sdf

The generated file will contain the following output:

pentane-2_2-diol
OpenBabel04251811053D

 19 18  0  0  0  0  0  0  0  0999 V2000
    0.9237   -0.0881    0.1091   C 0  0  0  0  0  0  0  0  0  0  0  0
    5.1259   -2.4797    1.5667   C 0  0  0  0  0  0  0  0  0  0  0  0
    2.4438   -0.0580    0.0798   C 0  0  0  0  0  0  0  0  0  0  0  0
    3.0394   -1.2473    0.8454   C 0  0  0  0  0  0  0  0  0  0  0  0
    4.5756   -1.2658    0.8182   C 0  0  0  0  0  0  0  0  0  0  0  0
    4.9993   -1.2893   -0.5316   O 0  0  0  0  0  0  0  0  0  0  0  0
    5.1095   -0.1114    1.4395   O 0  0  0  0  0  0  0  0  0  0  0  0
    0.5176    0.7650   -0.4432   H 0  0  0  0  0  0  0  0  0  0  0  0
    0.5500   -0.0378    1.1365   H 0  0  0  0  0  0  0  0  0  0  0  0
    0.5406   -1.0041   -0.3524   H 0  0  0  0  0  0  0  0  0  0  0  0
    4.8066   -3.4184    1.1046   H 0  0  0  0  0  0  0  0  0  0  0  0
    4.8189   -2.4761    2.6168   H 0  0  0  0  0  0  0  0  0  0  0  0
    6.2250   -2.4670    1.5528   H 0  0  0  0  0  0  0  0  0  0  0  0
    2.7928    0.8838    0.5163   H 0  0  0  0  0  0  0  0  0  0  0  0
    2.7749   -0.0753   -0.9642   H 0  0  0  0  0  0  0  0  0  0  0  0
    2.6598   -2.1729    0.3950   H 0  0  0  0  0  0  0  0  0  0  0  0
    2.6864   -1.2108    1.8833   H 0  0  0  0  0  0  0  0  0  0  0  0
    5.1891   -2.2082   -0.7786   H 0  0  0  0  0  0  0  0  0  0  0  0
    4.7262   -0.0485    2.3265   H 0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  2  5  1  0  0  0  0
  2 11  1  0  0  0  0
  2 12  1  0  0  0  0
  2 13  1  0  0  0  0
  3  4  1  0  0  0  0
  3 14  1  0  0  0  0
  3 15  1  0  0  0  0
  4  5  1  0  0  0  0
  4 16  1  0  0  0  0
  4 17  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6 18  1  0  0  0  0
  7 19  1  0  0  0  0
M  ISO  5   1  12   2  13   3  13   4  13   5  13
M  END
> <InChI>
InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1

$$$$
  • To save the generated output in json format:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol \
             -v /absolute/path/to/outfile.sdf:/outfile.json \
             isoenum name /pentane-2_2-diol.mol -a 13:C -f json -o outfile.json

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol \
             -v /absolute/path/to/outfile.sdf:/outfile.json \
             isoenum name /pentane-2_2-diol.mol --all=13:C --format=json --output=outfile.json

The generated file will contain the following output:

{
    "1": {
        "molfile": {
            "HeaderBlock": {
                "molecule_name": "",
                "software": "OpenBabel02101812223D",
                "comment": ""
            },
            "Ctab": {
                "CtabCountsLine": {
                    "number_of_atoms": "19",
                    "number_of_bonds": "18",
                    "number_of_atom_lists": "0",
                    "not_used1": "0",
                    "chiral_flag": "0",
                    "number_of_stext_entries": "0",
                    "not_used2": "0",
                    "not_used3": "0",
                    "not_used4": "0",
                    "not_used5": "0",
                    "number_of_properties": "999",
                    "version": "V2000"
                },
                "CtabAtomBlock": [
                    {
                        "x": "0.8986",
                        "y": "-0.0477",
                        "z": "0.0323",
                        "atom_symbol": "C",
                        "mass_difference": "0",
                        "charge": "0",
                        "atom_stereo_parity": "0",
                        "hydrogen_count": "0",
                        "stereo_care_box": "0",
                        "valence": "0",
                        "h0designator": "0",
                        "not_used1": "0",
                        "not_used2": "0",
                        "atom_atom_mapping_number": "0",
                        "inversion_retention_flag": "0",
                        "exact_change_flag": "0"
                    },
                    ...
                ],
                "CtabBondBlock": [
                    {
                        "first_atom_number": "1",
                        "second_atom_number": "3",
                        "bond_type": "1",
                        "bond_stereo": "0",
                        "not_used1": "0",
                        "bond_topology": "0",
                        "reacting_center_status": "0"
                    },
                    ...
                ],
                "CtabPropertiesBlock": {
                    "ISO": [
                        {
                            "atom_number": "1",
                            "absolute_mass": "12"
                        },
                        {
                            "atom_number": "2",
                            "absolute_mass": "13"
                        }
                    ]
                }
            }
        },
        "data": {
            "InChI": [
                "InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1"
            ]
        }
    }
}
  • To save the generated output in csv format:
# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol \
             -v /absolute/path/to/outfile.sdf:/outfile.csv \
             isoenum name /pentane-2_2-diol.mol -a 13:C -f csv -o outfile.csv

or

# docker run -v /absolute/path/to/pentane-2_2-diol.mol:/pentane-2_2-diol.mol \
             -v /absolute/path/to/outfile.sdf:/outfile.csv \
             isoenum name /pentane-2_2-diol.mol --all=13:C --format=csv --output=outfile.csv

The generated file will contain the following output:

InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3/i1+0,2+1,3+1,4+1,5+1