Welcome to isoenum’s documentation!¶

isoenum¶

Isotopic (iso) enumerator (enum) - enumerates isotopically resolved InChI (International Chemical Identifier) for metabolites.

The isoenum Python package provides command-line interface that allows you to enumerate the possible isotopically-resolved InChI from one of the Chemical Table file (CTfile) formats (i.e. molfile, SDfile) used to describe chemical molecules and reactions as well as from InChI itself.

See Tutorial documentation for usage examples of isoenum Python package as well as isoenum docker container.

Links¶

isoenum @ GitHub

isoenum @ PyPI

isoenum @ DockerHub

isoenum @ ReadTheDocs

Installation¶

The isoenum package runs under Python 2.7 and Python 3.4+. Use pip to install.

Install on Linux, Mac OS X¶

python3 -m pip install isoenum

Install on Windows¶

py -3 -m pip install isoenum

Dependencies¶

The isoenum Python package requires a non-pip-installable dependency: the Open Babel chemistry library version 2.3.90 or later, which relies on InChI library version 1.0.4 or later to perform InChI conversions.

Refer to the official documentation to install Open Babel on your system:

Official Installation Instructions: http://openbabel.org/wiki/Category:Installation

Docker¶

In addition to PyPI package, Dockerfile and the automatically built DockerHub container, which contains the isoenum Python package and all its dependencies, are also provided.

To use the isoenum Python package, you will need to setup docker for your system and pull or build the docker container.

Install docker¶

Install docker:

Follow the instructions to install docker on your system: https://docs.docker.com/engine/installation

Ubuntu

Debian

CentOS

Fedora

Mac

Windows

Setup container¶

Setup the isoenum container:

pull the built image from the DockerHub:
# docker pull moseleybioinformaticslab/isoenum
# docker tag moseleybioinformaticslab/isoenum:latest isoenum:latest  # retag docker image
# docker rmi moseleybioinformaticslab/isoenum  # remove after you have retagged it
or build an image using Dockerfile at the root of this repo by running docker build from the directory containing Dockerfile:
# docker build -t isoenum .

Development version installation¶

Install development version on Linux, Mac OS X¶

python3 -m pip install git+git://github.com/MoseleyBioinformaticsLab/isoenum.git

Install development version on Windows¶

py -3 -m pip install git+git://github.com/MoseleyBioinformaticsLab/isoenum.git

License¶

This package is distributed under the BSD license.

Documentation index:¶

The isoenum Tutorial¶

Note

Read The isoenum Docker Tutorial to see examples provided below but with the use of a docker container with the isoenum Python package and all its dependencies instead of using the isoenum Python package directly.

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 display all available options, run:

$ python3 -m 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.

Usage examples¶

Input files¶

We will use several input files to generate isotopically-resolved InChI.

Molfile example:

pentane-2_2-diol
OpenBabel02101812223D

18  0  0  0  0  0  0  0  0999 V2000
8986   -0.0477    0.0323 C   0  0  0  0  0  0  0  0  0  0  0  0
0960    0.7629    2.7277 C   0  0  0  0  0  0  0  0  0  0  0  0
4213   -0.0579   -0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
0115    0.3840    1.3416 C   0  0  0  0  0  0  0  0  0  0  0  0
5473    0.3524    1.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
9506   -0.9689    1.0442 O   0  0  0  0  0  0  0  0  0  0  0  0
0892    1.2477    0.4081 O   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
5151    0.9566    0.2461 H   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
7913    0.0636    3.5124 H   0  0  0  0  0  0  0  0  0  0  0  0
7734    1.7738    2.9979 H   0  0  0  0  0  0  0  0  0  0  0  0
1923    0.7728    2.7063 H   0  0  0  0  0  0  0  0  0  0  0  0
7620    0.6098   -0.8011 H   0  0  0  0  0  0  0  0  0  0  0  0
7573   -1.0707   -0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
6291   -0.2841    2.1226 H   0  0  0  0  0  0  0  0  0  0  0  0
6589    1.3989    1.5754 H   0  0  0  0  0  0  0  0  0  0  0  0
5197   -1.2976    1.7554 H   0  0  0  0  0  0  0  0  0  0  0  0
6303    2.0937    0.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
3  1  0  0  0  0
8  1  0  0  0  0
9  1  0  0  0  0
10  1  0  0  0  0
5  1  0  0  0  0
11  1  0  0  0  0
12  1  0  0  0  0
13  1  0  0  0  0
4  1  0  0  0  0
14  1  0  0  0  0
15  1  0  0  0  0
5  1  0  0  0  0
16  1  0  0  0  0
17  1  0  0  0  0
6  1  0  0  0  0
7  1  0  0  0  0
18  1  0  0  0  0
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

18  0  0  0  0  0  0  0  0999 V2000
8986   -0.0477    0.0323 C   0  0  0  0  0  0  0  0  0  0  0  0
0960    0.7629    2.7277 C   0  0  0  0  0  0  0  0  0  0  0  0
4213   -0.0579   -0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
0115    0.3840    1.3416 C   0  0  0  0  0  0  0  0  0  0  0  0
5473    0.3524    1.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
9506   -0.9689    1.0442 O   0  0  0  0  0  0  0  0  0  0  0  0
0892    1.2477    0.4081 O   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
5151    0.9566    0.2461 H   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
7913    0.0636    3.5124 H   0  0  0  0  0  0  0  0  0  0  0  0
7734    1.7738    2.9979 H   0  0  0  0  0  0  0  0  0  0  0  0
1923    0.7728    2.7063 H   0  0  0  0  0  0  0  0  0  0  0  0
7620    0.6098   -0.8011 H   0  0  0  0  0  0  0  0  0  0  0  0
7573   -1.0707   -0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
6291   -0.2841    2.1226 H   0  0  0  0  0  0  0  0  0  0  0  0
6589    1.3989    1.5754 H   0  0  0  0  0  0  0  0  0  0  0  0
5197   -1.2976    1.7554 H   0  0  0  0  0  0  0  0  0  0  0  0
6303    2.0937    0.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
3  1  0  0  0  0
8  1  0  0  0  0
9  1  0  0  0  0
10  1  0  0  0  0
5  1  0  0  0  0
11  1  0  0  0  0
12  1  0  0  0  0
13  1  0  0  0  0
4  1  0  0  0  0
14  1  0  0  0  0
15  1  0  0  0  0
5  1  0  0  0  0
16  1  0  0  0  0
17  1  0  0  0  0
6  1  0  0  0  0
7  1  0  0  0  0
18  1  0  0  0  0
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:

Path to CTfile (i.e. Molfile or SDfile).

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol

Path to the file containing an InChI.

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.inchi

InChI string.

$ python3 -m isoenum name 'InChI=1S/C5H12O2/c1-3-4-5(2,6)7/h6-7H,3-4H2,1-2H3'

or

$ python3 -m 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 a 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”:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -s 13:C:2

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -s 13:C:1 -s 13:C:2

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -s 13:C:1 -s 13:C:2 -i

or

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol --specific=C-13-1 --specific=C-13-2 --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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -a 13:C

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -a 13:C -a 18:O

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -a 13:C -a 18:O -i

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -a 13:C -s 12:C:3 -i

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -e 13:C

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -e 13:C:3:4

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -e 13:C:3:4 -i

or

$ python3 -m isoenum name tests/example_data/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 just repeat the -e or --enumerate option for the desired element:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -e 13:C:3:4 -e 18:O:1:2

or

$ python3 -m isoenum name tests/example_data/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.

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -e 13:C:2:4 -a 18:O -s 12:C:3

or

$ python3 -m isoenum name tests/example_data/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”:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -e 13:C:2 -e 12:C:2

or

$ python3 -m isoenum name tests/example_data/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:

To create InChI that represents the zwitterion form:

$ python3 -m 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

$ python3 -m 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:

Note

Notice that the InChI is non-standard. This is because zwitterionic forms of molecules cannot be represented in standard InChI, but can be represented with the standard fixed hydrogen layer (FixedH) extension.

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:

To create the biochemically-relevant ionized InChI:

$ python3 -m 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

$ python3 -m 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:

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:

To create the theoretically possible set of InChI for “1D1H” NMR experiment:

$ python3 -m 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

$ python3 -m 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¶

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

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:

$ python3 -m 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

$ python3 -m 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:

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

$ python3 -m 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

$ python3 -m 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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -s 13:C:2 -f inchi

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -s 13:C:2 -f sdf

or

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol --specific=13:C:2 --format=sdf

Output:

pentane-2_2-diol
OpenBabel04241818183D

18  0  0  0  0  0  0  0  0999 V2000
8564    0.0224   -0.0199   C 0  0  0  0  0  0  0  0  0  0  0  0
0590   -2.7653   -0.2642   C 0  0  0  0  0  0  0  0  0  0  0  0
3767    0.0633   -0.0253   C 0  0  0  0  0  0  0  0  0  0  0  0
9725   -1.3472   -0.1203   C 0  0  0  0  0  0  0  0  0  0  0  0
5036   -1.3472   -0.1439   C 0  0  0  0  0  0  0  0  0  0  0  0
9424   -0.5621   -1.2388   O 0  0  0  0  0  0  0  0  0  0  0  0
0329   -0.7920    1.0484   O 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
4813   -0.5495    0.8345   H 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
7458   -3.2426   -1.1982   H 0  0  0  0  0  0  0  0  0  0  0  0
7417   -3.3903    0.5788   H 0  0  0  0  0  0  0  0  0  0  0  0
1556   -2.7490   -0.2585   H 0  0  0  0  0  0  0  0  0  0  0  0
7259    0.5602    0.8869   H 0  0  0  0  0  0  0  0  0  0  0  0
7092    0.6719   -0.8743   H 0  0  0  0  0  0  0  0  0  0  0  0
5969   -1.8221   -1.0358   H 0  0  0  0  0  0  0  0  0  0  0  0
6148   -1.9367    0.7329   H 0  0  0  0  0  0  0  0  0  0  0  0
0489   -1.1442   -2.0068   H 0  0  0  0  0  0  0  0  0  0  0  0
6612   -1.2841    1.7969   H 0  0  0  0  0  0  0  0  0  0  0  0
3  1  0  0  0  0
8  1  0  0  0  0
9  1  0  0  0  0
10  1  0  0  0  0
5  1  0  0  0  0
11  1  0  0  0  0
12  1  0  0  0  0
13  1  0  0  0  0
4  1  0  0  0  0
14  1  0  0  0  0
15  1  0  0  0  0
5  1  0  0  0  0
16  1  0  0  0  0
17  1  0  0  0  0
6  1  0  0  0  0
7  1  0  0  0  0
18  1  0  0  0  0
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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -s 13:C:2 -f json

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -s 13:C:2 -f csv

or

$ python3 -m isoenum name tests/example_data/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¶

To save the generated output into a file, use the -o or --output option followed by the filename. For example, save the generated output in inchi format:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -a 13:C -f inchi -o outfile.inchi

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -a 13:C -f sdf -o outfile.sdf

or

$ python3 -m isoenum name tests/example_data/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

18  0  0  0  0  0  0  0  0999 V2000
9237   -0.0881    0.1091   C 0  0  0  0  0  0  0  0  0  0  0  0
1259   -2.4797    1.5667   C 0  0  0  0  0  0  0  0  0  0  0  0
4438   -0.0580    0.0798   C 0  0  0  0  0  0  0  0  0  0  0  0
0394   -1.2473    0.8454   C 0  0  0  0  0  0  0  0  0  0  0  0
5756   -1.2658    0.8182   C 0  0  0  0  0  0  0  0  0  0  0  0
9993   -1.2893   -0.5316   O 0  0  0  0  0  0  0  0  0  0  0  0
1095   -0.1114    1.4395   O 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
5500   -0.0378    1.1365   H 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
8066   -3.4184    1.1046   H 0  0  0  0  0  0  0  0  0  0  0  0
8189   -2.4761    2.6168   H 0  0  0  0  0  0  0  0  0  0  0  0
2250   -2.4670    1.5528   H 0  0  0  0  0  0  0  0  0  0  0  0
7928    0.8838    0.5163   H 0  0  0  0  0  0  0  0  0  0  0  0
7749   -0.0753   -0.9642   H 0  0  0  0  0  0  0  0  0  0  0  0
6598   -2.1729    0.3950   H 0  0  0  0  0  0  0  0  0  0  0  0
6864   -1.2108    1.8833   H 0  0  0  0  0  0  0  0  0  0  0  0
1891   -2.2082   -0.7786   H 0  0  0  0  0  0  0  0  0  0  0  0
7262   -0.0485    2.3265   H 0  0  0  0  0  0  0  0  0  0  0  0
3  1  0  0  0  0
8  1  0  0  0  0
9  1  0  0  0  0
10  1  0  0  0  0
5  1  0  0  0  0
11  1  0  0  0  0
12  1  0  0  0  0
13  1  0  0  0  0
4  1  0  0  0  0
14  1  0  0  0  0
15  1  0  0  0  0
5  1  0  0  0  0
16  1  0  0  0  0
17  1  0  0  0  0
6  1  0  0  0  0
7  1  0  0  0  0
18  1  0  0  0  0
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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -a 13:C -f json -o outfile.json

or

$ python3 -m isoenum name tests/example_data/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:

$ python3 -m isoenum name tests/example_data/pentane-2_2-diol.mol -a 13:C -f csv -o outfile.csv

or

$ python3 -m isoenum name tests/example_data/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

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

18  0  0  0  0  0  0  0  0999 V2000
8986   -0.0477    0.0323 C   0  0  0  0  0  0  0  0  0  0  0  0
0960    0.7629    2.7277 C   0  0  0  0  0  0  0  0  0  0  0  0
4213   -0.0579   -0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
0115    0.3840    1.3416 C   0  0  0  0  0  0  0  0  0  0  0  0
5473    0.3524    1.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
9506   -0.9689    1.0442 O   0  0  0  0  0  0  0  0  0  0  0  0
0892    1.2477    0.4081 O   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
5151    0.9566    0.2461 H   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
7913    0.0636    3.5124 H   0  0  0  0  0  0  0  0  0  0  0  0
7734    1.7738    2.9979 H   0  0  0  0  0  0  0  0  0  0  0  0
1923    0.7728    2.7063 H   0  0  0  0  0  0  0  0  0  0  0  0
7620    0.6098   -0.8011 H   0  0  0  0  0  0  0  0  0  0  0  0
7573   -1.0707   -0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
6291   -0.2841    2.1226 H   0  0  0  0  0  0  0  0  0  0  0  0
6589    1.3989    1.5754 H   0  0  0  0  0  0  0  0  0  0  0  0
5197   -1.2976    1.7554 H   0  0  0  0  0  0  0  0  0  0  0  0
6303    2.0937    0.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
3  1  0  0  0  0
8  1  0  0  0  0
9  1  0  0  0  0
10  1  0  0  0  0
5  1  0  0  0  0
11  1  0  0  0  0
12  1  0  0  0  0
13  1  0  0  0  0
4  1  0  0  0  0
14  1  0  0  0  0
15  1  0  0  0  0
5  1  0  0  0  0
16  1  0  0  0  0
17  1  0  0  0  0
6  1  0  0  0  0
7  1  0  0  0  0
18  1  0  0  0  0
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

18  0  0  0  0  0  0  0  0999 V2000
8986   -0.0477    0.0323 C   0  0  0  0  0  0  0  0  0  0  0  0
0960    0.7629    2.7277 C   0  0  0  0  0  0  0  0  0  0  0  0
4213   -0.0579   -0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
0115    0.3840    1.3416 C   0  0  0  0  0  0  0  0  0  0  0  0
5473    0.3524    1.3660 C   0  0  0  0  0  0  0  0  0  0  0  0
9506   -0.9689    1.0442 O   0  0  0  0  0  0  0  0  0  0  0  0
0892    1.2477    0.4081 O   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
5151    0.9566    0.2461 H   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
7913    0.0636    3.5124 H   0  0  0  0  0  0  0  0  0  0  0  0
7734    1.7738    2.9979 H   0  0  0  0  0  0  0  0  0  0  0  0
1923    0.7728    2.7063 H   0  0  0  0  0  0  0  0  0  0  0  0
7620    0.6098   -0.8011 H   0  0  0  0  0  0  0  0  0  0  0  0
7573   -1.0707   -0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
6291   -0.2841    2.1226 H   0  0  0  0  0  0  0  0  0  0  0  0
6589    1.3989    1.5754 H   0  0  0  0  0  0  0  0  0  0  0  0
5197   -1.2976    1.7554 H   0  0  0  0  0  0  0  0  0  0  0  0
6303    2.0937    0.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
3  1  0  0  0  0
8  1  0  0  0  0
9  1  0  0  0  0
10  1  0  0  0  0
5  1  0  0  0  0
11  1  0  0  0  0
12  1  0  0  0  0
13  1  0  0  0  0
4  1  0  0  0  0
14  1  0  0  0  0
15  1  0  0  0  0
5  1  0  0  0  0
16  1  0  0  0  0
17  1  0  0  0  0
6  1  0  0  0  0
7  1  0  0  0  0
18  1  0  0  0  0
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:

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:

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:

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:

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:

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¶

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

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:

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

18  0  0  0  0  0  0  0  0999 V2000
8564    0.0224   -0.0199   C 0  0  0  0  0  0  0  0  0  0  0  0
0590   -2.7653   -0.2642   C 0  0  0  0  0  0  0  0  0  0  0  0
3767    0.0633   -0.0253   C 0  0  0  0  0  0  0  0  0  0  0  0
9725   -1.3472   -0.1203   C 0  0  0  0  0  0  0  0  0  0  0  0
5036   -1.3472   -0.1439   C 0  0  0  0  0  0  0  0  0  0  0  0
9424   -0.5621   -1.2388   O 0  0  0  0  0  0  0  0  0  0  0  0
0329   -0.7920    1.0484   O 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
4813   -0.5495    0.8345   H 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
7458   -3.2426   -1.1982   H 0  0  0  0  0  0  0  0  0  0  0  0
7417   -3.3903    0.5788   H 0  0  0  0  0  0  0  0  0  0  0  0
1556   -2.7490   -0.2585   H 0  0  0  0  0  0  0  0  0  0  0  0
7259    0.5602    0.8869   H 0  0  0  0  0  0  0  0  0  0  0  0
7092    0.6719   -0.8743   H 0  0  0  0  0  0  0  0  0  0  0  0
5969   -1.8221   -1.0358   H 0  0  0  0  0  0  0  0  0  0  0  0
6148   -1.9367    0.7329   H 0  0  0  0  0  0  0  0  0  0  0  0
0489   -1.1442   -2.0068   H 0  0  0  0  0  0  0  0  0  0  0  0
6612   -1.2841    1.7969   H 0  0  0  0  0  0  0  0  0  0  0  0
3  1  0  0  0  0
8  1  0  0  0  0
9  1  0  0  0  0
10  1  0  0  0  0
5  1  0  0  0  0
11  1  0  0  0  0
12  1  0  0  0  0
13  1  0  0  0  0
4  1  0  0  0  0
14  1  0  0  0  0
15  1  0  0  0  0
5  1  0  0  0  0
16  1  0  0  0  0
17  1  0  0  0  0
6  1  0  0  0  0
7  1  0  0  0  0
18  1  0  0  0  0
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

18  0  0  0  0  0  0  0  0999 V2000
9237   -0.0881    0.1091   C 0  0  0  0  0  0  0  0  0  0  0  0
1259   -2.4797    1.5667   C 0  0  0  0  0  0  0  0  0  0  0  0
4438   -0.0580    0.0798   C 0  0  0  0  0  0  0  0  0  0  0  0
0394   -1.2473    0.8454   C 0  0  0  0  0  0  0  0  0  0  0  0
5756   -1.2658    0.8182   C 0  0  0  0  0  0  0  0  0  0  0  0
9993   -1.2893   -0.5316   O 0  0  0  0  0  0  0  0  0  0  0  0
1095   -0.1114    1.4395   O 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
5500   -0.0378    1.1365   H 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
8066   -3.4184    1.1046   H 0  0  0  0  0  0  0  0  0  0  0  0
8189   -2.4761    2.6168   H 0  0  0  0  0  0  0  0  0  0  0  0
2250   -2.4670    1.5528   H 0  0  0  0  0  0  0  0  0  0  0  0
7928    0.8838    0.5163   H 0  0  0  0  0  0  0  0  0  0  0  0
7749   -0.0753   -0.9642   H 0  0  0  0  0  0  0  0  0  0  0  0
6598   -2.1729    0.3950   H 0  0  0  0  0  0  0  0  0  0  0  0
6864   -1.2108    1.8833   H 0  0  0  0  0  0  0  0  0  0  0  0
1891   -2.2082   -0.7786   H 0  0  0  0  0  0  0  0  0  0  0  0
7262   -0.0485    2.3265   H 0  0  0  0  0  0  0  0  0  0  0  0
3  1  0  0  0  0
8  1  0  0  0  0
9  1  0  0  0  0
10  1  0  0  0  0
5  1  0  0  0  0
11  1  0  0  0  0
12  1  0  0  0  0
13  1  0  0  0  0
4  1  0  0  0  0
14  1  0  0  0  0
15  1  0  0  0  0
5  1  0  0  0  0
16  1  0  0  0  0
17  1  0  0  0  0
6  1  0  0  0  0
7  1  0  0  0  0
18  1  0  0  0  0
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

The isoenum API Reference¶

This package provides routines to generate isotopically-resolved InChI (International Chemical Identifier) from non-isotopically labeled CTfile formatted files (e.g. Molfiles, SDfiles) or non-isotopically labeled InChI identifiers.

This package includes the following modules:

cli: This module provides the command-line interface for the isoenum package.
api: This module provides routines to augment CTfile objects with additional information and used by isoenum package CLI.
labeling: This module provides functions for generating a labeling schema.
nmr: This module provides descriptions of coupling combinations that could be observed within NMR experiments.
openbabel: This module provides functions to call the Open Babel software to convert between InChI and CTfile formatted files.
conf: This module provides the processing of configuration files necessary for isotopic enumerator.
fileio: This module provides functions for generating CTfile objects and convert CTfile objects into InChI.
utils: This module provides reusable utility functions.
exceptions: This module provides isoenum package custom exceptions.

isoenum.cli¶

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]
isoenum vis (<path-to-ctfile-file-or-inchi-file-or-inchi-string>): (–format=<format>) (–output=<path>)

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.

isoenum.cli.cli(cmdargs)[source]¶

Process command-line arguments.

Parameters:	cmdargs (dict) – Command-line arguments.
Returns:	None.
Return type:	`None`

isoenum.cli.save_output(outputstr, path, file_format)[source]¶

Save output results into file or print to stdout.

Parameters:	outputstr (str) – Output string. path (str) – Where to save results. file_format (str) – File format to create file extension.
Returns:	None.
Return type:	`None`

isoenum.cli.create_output(sdfile, path=None, file_format='inchi')[source]¶

Create output containing conversion results.

Parameters:	sdfile (`SDfile`.) – `SDfile` instance. path (str) – Path to where file will be saved. file_format (str) – File format: ‘inchi’, ‘mol’, ‘sdf’, ‘json’, or ‘csv’.
Returns:	None.
Return type:	`None`

isoenum.labeling¶

This module contains a function to generate a labeling schema based on provided cli parameters.

isoenum.labeling.create_labeling_schema(complete_labeling_schema, ignore_existing_isotopes, all_iso, specific_iso, existing_iso, enumerate_iso, isotopes_conf, ctfile)[source]¶

Create labeling schema.

Parameters:	complete_labeling_schema (bool) – Specifies if default isotopes to be added to isotopic layer. ignore_existing_isotopes (bool) – Specifies if will ignore existing isotopic layer. all_iso (dict) – Atom specific isotopes –all option. specific_iso (dict) – Atom number specific isotopes from –specific option. existing_iso (dict) – Atom number specific isotopes from `Molfile`. enumerate_iso (list) – List of isotopes from –enumerate option. isotopes_conf (dict) – Default isotopes. ctfile (`Molfile`) – Instance of `Molfile`.
Returns:	Labeling schema.
Return type:	`list`

isoenum.nmr¶

This module provides descriptions of coupling combinations that could be observed within NMR experiments.

class isoenum.nmr.ResonanceAtom(atom, isotope)[source]¶: Resonance atom - part of the coupling path.

class isoenum.nmr.Coupling(coupling_path=None, nmr_active_atoms=None, subset_atoms=None)[source]¶

Coupling provides information on the connectivity of molecules.

coupling_type¶

Coupling type.

Returns:	Coupling type.
Return type:	`str`

subset¶

Generate coupling path subsets.

Returns:	Coupling path subsets.
Return type:	`list`

is_resonance_compatible(resonance)[source]¶

Test if coupling is compatible with resonance.

Parameters:	resonance (`Coupling`) – Subclass of `Coupling`.
Returns:	True if compatible, False otherwise.
Return type:	`True` or False

classmethod couplings(atom)[source]¶

Generate list of possible couplings for a given atom type.

Parameters:	atom (`ctfile.Atom`) – Atom type.
Returns:	List of couplings.
Return type:	`list`

name¶

Specific coupling name that indicates interacting atoms.

Returns:	Specific coupling name.
Return type:	`str`

hydrogen_coupling_path¶

Coupling path that consists of hydrogen atoms.

Returns:	Coupling path.
Return type:	`list`

hydrogen_coupling_path_repr¶

Hydrogen coupling path representation.

Returns:	List of hydrogen groups representing hydrogen coupling path.
Return type:	`list`

class isoenum.nmr.J1CH(coupling_path=None, nmr_active_atoms=None, subset_atoms=None)[source]¶

J1CH coupling type: C-H.

couplings(carbon_atom)[source]¶

Generate list of possible J1CH couplings.

Parameters:	carbon_atom – Carbon atom.
Returns:	List of couplings.
Return type:	`list`

class isoenum.nmr.J2HH(coupling_path=None, nmr_active_atoms=None, subset_atoms=None)[source]¶

J2HH coupling type: H-C-H.

couplings(carbon_atom)[source]¶

Generate list of possible J2HH couplings.

Parameters:	carbon_atom – Carbon atom.
Returns:	List of couplings.
Return type:	`list`

class isoenum.nmr.J3HH(coupling_path=None, nmr_active_atoms=None, subset_atoms=None)[source]¶

J3HH coupling type: H-C-C-H.

couplings(carbon_atom)[source]¶

Generate list of possible J3HH couplings.

Parameters:	carbon_atom – Carbon atom.
Returns:	List of couplings.
Return type:	`list`

is_resonance_compatible(resonance)[source]¶

Test if J3HH coupling is compatible with resonance.

Parameters:	resonance (`Coupling`) – Subclass of `Coupling`.
Returns:	True if compatible, False otherwise.
Return type:	`True` or False

class isoenum.nmr.HResonance(coupling_path=None, nmr_active_atoms=None, subset_atoms=None)[source]¶

Hydrogen resonance.

couplings(carbon_atom)[source]¶

Generate resonance.

Parameters:	carbon_atom – Carbon atom.
Returns:	List of couplings.
Return type:	`list`

class isoenum.nmr.NMRExperiment(name, couplings, decoupled, default_coupling_definitions)[source]¶

NMR experiment.

generate_coupling_combinations(molfile, subset=False)[source]¶: Generate possible J couplings for a Molfile.

class isoenum.nmr.NMR1D1H(name, couplings=None, decoupled=None, default_coupling_definitions=(HResonance(coupling_path=None), J1CH(coupling_path=None), J2HH(coupling_path=None), J3HH(coupling_path=None)))[source]¶

1D 1H NMR experiment.

generate_coupling_combinations(molfile, subset=False)[source]¶

Generate 1D 1H NMR experiment J couplings for a Molfile.

Parameters:	molfile (`ctfile.Molfile`) – `Molfile` object. subset (`True` or `False`) – Generate couplings subsets?
Returns:	List of possible couplings for a given `Molfile`.
Return type:	`list`

class isoenum.nmr.NMR1DCHSQC(name, couplings=None, decoupled=None, default_coupling_definitions=(HResonance(coupling_path=None), J1CH(coupling_path=None), J2HH(coupling_path=None), J3HH(coupling_path=None)))[source]¶: 1D 13C HSQC NMR experiment.

isoenum.nmr.create_nmr_experiment(name, couplings=None, decoupled=None)[source]¶

Create NMR experiment upon provided experiment type.

Parameters:	name (str) – NMR experiment type. couplings (list) – List of coupling types. decoupled (list) – List of elements.
Returns:	NMR experiment.
Return type:	`NMRExperiment`.

isoenum.conf¶

This module provides processing of configuration files necessary for isotopic enumerator.

isoenum.fileio¶

This module provides routines to generate CTfile objects and convert CTfile objects into InChI and vice versa.

isoenum.fileio.create_ctfile(path_or_id, xyx_coordinates='--gen2D', explicit_hydrogens='-h')[source]¶

Guess what type of path is provided, i.e. is it existing file in Molfile format, existing file in SDfile file format, existing file containing InChI string, or InChI string and tries to create CTfile object.

Parameters:	path_or_id (str) – Path to `Molfile`, `SDfile`, `InChI`, or `InChI` string. xyx_coordinates (str) – Option that generates x, y, z coordinates (e.g., “–gen2D” or “–gen3D”). explicit_hydrogens (str) – Option that makes hydrogens atoms explicit when generating `CTfile` object.
Returns:	Subclass of `CTfile` object.
Return type:	`Molfile` or `SDfile`

isoenum.fileio.create_ctfile_from_ctfile_str(ctfile_str)[source]¶

Create CTfile object from CTfile string.

Parameters:	ctfile_str (str) – `CTfile` string.
Returns:	Subclass of `CTfile` object.
Return type:	`CTfile`

isoenum.fileio.create_ctfile_from_identifier_file(path, output_format='mol', **options)[source]¶

Create CTfile instance from InChI or SMILES identifier file.

Parameters:	path (str) – Path to file containing `InChI` or `SMILES` identifier. output_format (str) – Output file format used by Open Babel to generate `CTfile`. options – Additional options to be passed to Open Babel.
Returns:	Subclass of `CTfile` object.
Return type:	`CTfile`

isoenum.fileio.create_ctfile_from_identifier_str(identifier_str, output_format='mol', **options)[source]¶

Create CTfile instance from InChI or SMILES identifier string.

Parameters:	identifier_str (str) – `InChI` or `SMILES` identifier string. output_format (str) – Output file format used by Open Babel to generate `CTfile`. options – Additional options to be passed to Open Babel.
Returns:	Subclass of `CTfile` object.
Return type:	`CTfile`

isoenum.fileio.guess_identifier_format(identifier_str)[source]¶

Guess identifier format.

Parameters:	identifier_str (str) – Chemical identifier string.
Returns:	‘inchi’ or ‘smiles’ string.
Return type:	`str`

isoenum.fileio.create_inchi_from_ctfile_obj(ctf, **options)[source]¶

Create InChI from CTfile instance.

Parameters:	ctf (`CTfile`) – Instance of `CTfile`.
Returns:	`InChI` string.
Return type:	`str`

isoenum.fileio.normalize_ctfile_obj(ctf, xyx_coordinates='--gen2D', explicit_hydrogens='-h')[source]¶

Normalize CTfile object.

Parameters:	ctf (`CTfile`) – `CTfile` object.
Returns:	Normalized `CTfile` object.
Return type:	`CTfile`

isoenum.fileio.create_empty_sdfile_obj()[source]¶

Create empty SDfile object.

Returns:	`SDfile` object.
Return type:	`SDfile`

isoenum.fileio.create_empty_molfile_obj()[source]¶

Create empty Molfile object.

Returns:	`Molfile` object.
Return type:	`Molfile`

isoenum.fileio.create_svg_str(inchi_str, **options)[source]¶

Create SVG string from InChI identifier string.

Parameters:	inchi_str (str) – `InChI` identifier. options – Additional options to be passed to Open Babel.
Returns:	SVG XML code.
Return type:	`str`

isoenum.fileio.circular_consistency_test(inchi_str)[source]¶

Perform conversion from InChI string to Molfile and back to InChI string.

Parameters:	inchi_str (str) – `InChI` string.
Returns:	None
Return type:	`None`

isoenum.utils¶

This module provides reusable utility functions.

isoenum.utils.is_url(path)[source]¶

Test if path represents a valid URL.

Parameters:	path (str) – Path to file.
Returns:	True if path is valid url string, False otherwise.
Return type:	`True` or `False`

isoenum.utils.all_combinations(items)[source]¶

Generate combinations of variable size.

Parameters:	items – Sequence of items.
Returns:	List of all combinations.
Return type:	`list`

isoenum.openbabel¶

This module provides convert() to convert between different file formats used in molecular modeling and computational chemistry (e.g. InChI, SMILES, Molfile, etc.).

isoenum.openbabel.convert(input_file_path, output_file_path, input_format, output_format, **options)[source]¶

Convert between formats using Open Babel.

Parameters:	input_file_path (str) – Path to input file. output_file_path (str) – Path to output file. input_format (str) – Input file format. output_format (str) – Output file format. options – Additional key-value options to pass to Open Babel.
Returns:	None.
Return type:	`None`

isoenum.exceptions¶

Custom exceptions.

exception isoenum.exceptions.EmptyCTFileError[source]¶: Invalid CTFile object error.

Release History¶

0.4.1 (2019-08-12)¶

Improvements

Added custom exceptions module.

0.4.0 (2019-07-30)¶

Improvements

Added documentation on how to install development version from GitHub.
Simplified set of functions that interfaces with Open Babel.
Added default output formats configuration file.
Generalized functions that create CTfile objects to accept both InChI and SMILES.
Added API functions module.
Added functionality to annotate Molfiles that have the same InChI and coupling type but different labeling schema as magnetically equivalent.

Bugfixes

Fixed bug that used arbitrary output file format extension to save the results.
Fixed bug not being able to pass two-word options to Open Babel.

0.3.1 (2018-08-27)¶

Improvements

Updated “The isoenum Tutorial” documentation.
Restructured tutorial into two sections: “The isoenum Tutorial” and “The isoenum Docker Tutorial”.
Added logic to use “FixedH” option to create InChI for charged molecules.

Bugfixes

Fixed bug that gave an error if existing “ISO” property was present.
Fixed bug generating incorrect coupling for “C” atoms that did not have any “H” attached to it (e.g. “C=O”).
Fixed bug that did not create multiple subsets for “J3HH” couplings.

0.3.0 (2018-08-22)¶

Improvements

Added ionize command and functionality in order to create charged versions of neutral molecules, e.g. zwitterion forms of amino acids (https://en.wikipedia.org/wiki/Zwitterion)
Removed Open Babel system call stdout messages.

0.2.1 (2018-08-20)¶

Improvements

Updated CLI isotope specification: --specific=<isotope:element:position>, --all=<isotope:element>, --enumerate=<isotope:element:min:max>.
Updated all documentation examples according to new CLI.
Removed trailing “n” from InChI strings.

0.2.0 (2018-08-15)¶

Improvements

Added new command-line interface command nmr and module in order to generate InChI associated with observed coupling combination for a given NMR experiment type.
Added “1D 1H” and “1D 13C HSQC” NMR experiments.
Added new output formats “json” and “csv”.
Updated API documentation.

0.1.5 (2018-04-26)¶

Bugfixes

Fixed incorrect rendering on PyPI project page.

0.1.4 (2018-04-25)¶

Improvements

Added ReadTheDocs documentation: http://isoenum.readthedocs.io

0.1.3 (2018-04-20)¶

Improvements

Added “Dockerfile” to create docker container with isoenum software and all required dependencies ready-to-use.
Changes to cli options: replaced “-f” and “–full” with “-c” and “–complete” to specify labeling schema. Used “-f” for “–format” option.

0.1.2 (2018-04-19)¶

Improvements

Added ability to save conversion results into file via “–output” cli option and in different formats (“inchi”, “mol”, and “sdf”) via “–format” cli option.

0.1.1 (2018-04-17)¶

Improvements

Added ability to process SDfiles in addition to Molfiles and InChI.
Added basic unit tests for command-line interface.

Bugfixes

Fixed bug of not including package data configuration files into source distribution.

0.1.0 (2018-04-16)¶

Initial public release.

License¶

The Clear BSD License

Copyright (c) 2018, Andrey Smelter, Hunter N.B. Moseley
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted (subject to the limitations in the disclaimer
below) provided that the following conditions are met:

     * Redistributions of source code must retain the above copyright notice,
     this list of conditions and the following disclaimer.

     * Redistributions in binary form must reproduce the above copyright
     notice, this list of conditions and the following disclaimer in the
     documentation and/or other materials provided with the distribution.

     * Neither the name of the copyright holder nor the names of its
     contributors may be used to endorse or promote products derived from this
     software without specific prior written permission.

NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.

Welcome to isoenum’s documentation!¶

isoenum¶

Links¶

Installation¶

Install on Linux, Mac OS X¶

Install on Windows¶

Dependencies¶

Docker¶

Install docker¶

Setup container¶

Development version installation¶

Install development version on Linux, Mac OS X¶

Install development version on Windows¶

License¶

Documentation index:¶

The isoenum Tutorial¶

Command-line interface¶

Usage examples¶

Input files¶

Input file/string specification¶

The isoenum name command¶

Isotopic layer specification: specific atoms option¶

Isotopic layer specification: all atoms of a specific type option¶

Isotopic layer specification: enumerate atoms of specific type option¶

The isoenum ionize command¶

The isoenum nmr command¶

Workflow to generate InChI for data deposition from NMR experiments¶

Output format¶

Output file¶

The isoenum Docker Tutorial¶

The isoenum docker container¶

Command-line interface¶

Docker usage examples¶

Input files¶

Input file/string specification¶

The isoenum name command¶

Isotopic layer specification: specific atoms option¶

Isotopic layer specification: all atoms of a specific type option¶

Isotopic layer specification: enumerate atoms of specific type option¶

The isoenum ionize command¶

The isoenum nmr command¶

Workflow to generate InChI for data deposition from NMR experiments¶

Output format¶

Output file¶

The isoenum API Reference¶

isoenum.cli¶

isoenum.labeling¶

isoenum.nmr¶

isoenum.conf¶

isoenum.fileio¶

isoenum.utils¶

isoenum.openbabel¶

isoenum.exceptions¶

Release History¶

0.4.1 (2019-08-12)¶

0.4.0 (2019-07-30)¶

0.3.1 (2018-08-27)¶

0.3.0 (2018-08-22)¶

0.2.1 (2018-08-20)¶

0.2.0 (2018-08-15)¶

0.1.5 (2018-04-26)¶

0.1.4 (2018-04-25)¶

0.1.3 (2018-04-20)¶

0.1.2 (2018-04-19)¶

0.1.1 (2018-04-17)¶

0.1.0 (2018-04-16)¶

License¶

Indices and tables¶