Welcome to isoenum-webgui’s documentation!¶

isoenum-webgui¶

isoenum-webgui provides Flask-based web user interface that uses isoenum package to generate accurate InChI (International Chemical Identifier) for NMR metabolite features based on standard NMR experimental descriptions (currently 1D-1H and 1D-CHSQC) in order to improve data reusability of metabolomics data.

Links¶

isoenum @ GitHub
isoenum @ PyPI
isoenum @ ReadTheDocs

Installation¶

The isoenum-webgui package runs under Python 3.4+. Use pip to install.

Install on Linux, Mac OS X¶

python3 -m pip install isoenum-webgui

Install on Windows¶

py -3 -m pip install isoenum-webgui

Dependencies¶

The isoenum-webgui requires a non-pip-installable dependency: the Open Babel chemistry library version 2.4.1 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

Development version installation¶

Install development version on Linux, Mac OS X¶

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

Install development version on Windows¶

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

License¶

This package is distributed under the BSD license.

The isoenum-webgui GUI Reference¶

Home View¶

The home view allows the user to select a CSV or JSON file or create an example project.

Accepted File Formats¶

CSV¶

CSV file containing InChI strings:

Base Identifier
"InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)"
"InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1"

CSV file containing “Base Identifier” header and InChI strings:

Base Identifier
"InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)"
"InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1"

CSV file saved from the InChI Table View:

Name,Base Identifier,ISO,CHG,Repr Identifier
acetic acid,"InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)",13:C:1<br>13:C:2,O:4:-1,"InChI=1/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1/i1+1,2+1/fC2H3O2/q-1"
benzene,InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H,,,InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1",,,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1"

JSON¶

JSON file saved from the InChI Table View:

{
    "d3f60ba7-0098-4af7-999a-a506823539c1": {
        "Name": "acetic acid",
        "Base Identifier": "InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)",
        "Base SVG Str": "<?xml version=\"1.0\"?>\n<svg version=\"1.1\" id=\"topsvg\"\nxmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\nxmlns:cml=\"http://www.xml-cml.org/schema\" x=\"0\" y=\"0\" width=\"200px\" height=\"200px\" viewBox=\"0 0 100 100\">\n<title> - Open Babel Depiction</title>\n<g transform=\"translate(0,0)\">\n<svg width=\"100\" height=\"100\" x=\"0\" y=\"0\" viewBox=\"0 0 149.282 140\"\nfont-family=\"sans-serif\" stroke=\"rgb(76,76,76)\" stroke-width=\"2\"  stroke-linecap=\"round\">\n<line x1=\"98.0\" y1=\"93.5\" x2=\"74.6\" y2=\"80.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"71.6\" y1=\"80.0\" x2=\"71.6\" y2=\"53.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"77.6\" y1=\"80.0\" x2=\"77.6\" y2=\"53.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"74.6\" y1=\"80.0\" x2=\"51.3\" y2=\"93.5\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<text x=\"105.282032\" y=\"108.000000\" fill=\"rgb(102,102,102)\"  stroke=\"rgb(102,102,102)\" stroke-width=\"1\" font-size=\"16\" >CH</text>\n<text x=\"129.282032\" y=\"111.680000\" fill=\"rgb(102,102,102)\"  stroke=\"rgb(102,102,102)\" stroke-width=\"1\" font-size=\"13\" >3</text>\n<text x=\"68.641016\" y=\"48.000000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >O</text>\n<text x=\"22.000000\" y=\"108.000000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >HO</text>\n<text x=\"109.282032\" y=\"100.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >1</text>\n<text x=\"74.641016\" y=\"80.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >2</text>\n<text x=\"74.641016\" y=\"40.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >3</text>\n<text x=\"40.000000\" y=\"100.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >4</text>\n</svg>\n<cml:molecule>\n <cml:atomArray>\n  <cml:atom id=\"a1\" elementType=\"C\" x2=\"1.732051\" y2=\"-0.000000\"/>\n  <cml:atom id=\"a2\" elementType=\"C\" x2=\"0.866025\" y2=\"0.500000\"/>\n  <cml:atom id=\"a3\" elementType=\"O\" x2=\"0.866025\" y2=\"1.500000\"/>\n  <cml:atom id=\"a4\" elementType=\"O\" x2=\"-0.000000\" y2=\"-0.000000\"/>\n </cml:atomArray>\n <cml:bondArray>\n  <cml:bond atomRefs2=\"a1 a2\" order=\"1\"/>\n  <cml:bond atomRefs2=\"a2 a3\" order=\"2\"/>\n  <cml:bond atomRefs2=\"a2 a4\" order=\"1\"/>\n </cml:bondArray>\n</cml:molecule>\n</g>\n<text font-size=\"18.000000\" fill =\"gray\" font-family=\"sans-serif\"\nx=\"10.000000\" y=\"20.000000\" ></text>\n</svg>\n",
        "Base SVG": "<a href=\"/molfile/d3f60ba7-0098-4af7-999a-a506823539c1/base\" class=\"popup\"><?xml version=\"1.0\"?>\n<svg version=\"1.1\" id=\"topsvg\"\nxmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\nxmlns:cml=\"http://www.xml-cml.org/schema\" x=\"0\" y=\"0\" width=\"200px\" height=\"200px\" viewBox=\"0 0 100 100\">\n<title> - Open Babel Depiction</title>\n<g transform=\"translate(0,0)\">\n<svg width=\"100\" height=\"100\" x=\"0\" y=\"0\" viewBox=\"0 0 149.282 140\"\nfont-family=\"sans-serif\" stroke=\"rgb(76,76,76)\" stroke-width=\"2\"  stroke-linecap=\"round\">\n<line x1=\"98.0\" y1=\"93.5\" x2=\"74.6\" y2=\"80.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"71.6\" y1=\"80.0\" x2=\"71.6\" y2=\"53.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"77.6\" y1=\"80.0\" x2=\"77.6\" y2=\"53.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"74.6\" y1=\"80.0\" x2=\"51.3\" y2=\"93.5\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<text x=\"105.282032\" y=\"108.000000\" fill=\"rgb(102,102,102)\"  stroke=\"rgb(102,102,102)\" stroke-width=\"1\" font-size=\"16\" >CH</text>\n<text x=\"129.282032\" y=\"111.680000\" fill=\"rgb(102,102,102)\"  stroke=\"rgb(102,102,102)\" stroke-width=\"1\" font-size=\"13\" >3</text>\n<text x=\"68.641016\" y=\"48.000000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >O</text>\n<text x=\"22.000000\" y=\"108.000000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >HO</text>\n<text x=\"109.282032\" y=\"100.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >1</text>\n<text x=\"74.641016\" y=\"80.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >2</text>\n<text x=\"74.641016\" y=\"40.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >3</text>\n<text x=\"40.000000\" y=\"100.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >4</text>\n</svg>\n<cml:molecule>\n <cml:atomArray>\n  <cml:atom id=\"a1\" elementType=\"C\" x2=\"1.732051\" y2=\"-0.000000\"/>\n  <cml:atom id=\"a2\" elementType=\"C\" x2=\"0.866025\" y2=\"0.500000\"/>\n  <cml:atom id=\"a3\" elementType=\"O\" x2=\"0.866025\" y2=\"1.500000\"/>\n  <cml:atom id=\"a4\" elementType=\"O\" x2=\"-0.000000\" y2=\"-0.000000\"/>\n </cml:atomArray>\n <cml:bondArray>\n  <cml:bond atomRefs2=\"a1 a2\" order=\"1\"/>\n  <cml:bond atomRefs2=\"a2 a3\" order=\"2\"/>\n  <cml:bond atomRefs2=\"a2 a4\" order=\"1\"/>\n </cml:bondArray>\n</cml:molecule>\n</g>\n<text font-size=\"18.000000\" fill =\"gray\" font-family=\"sans-serif\"\nx=\"10.000000\" y=\"20.000000\" ></text>\n</svg>\n</a>",
        "Base Molfile": "\nOpenBabel08091912052D\n\n  8  7  0  0  0  0  0  0  0  0999 V2000\n    1.7321   -0.0000    0.0000   C 0  0  0  0  0  0  0  0  0  0  0  0\n    0.8660    0.5000    0.0000   C 0  0  0  0  0  0  0  0  0  0  0  0\n    0.8660    1.5000    0.0000   O 0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0000   -0.0000    0.0000   O 0  0  0  0  0  0  0  0  0  0  0  0\n    1.7321   -1.0700    0.0000   H 0  0  0  0  0  0  0  0  0  0  0  0\n    2.6587    0.5350    0.0000   H 0  0  0  0  0  0  0  0  0  0  0  0\n    2.6587   -0.5350    0.0000   H 0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8115    0.4685    0.0000   H 0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  1  5  1  0  0  0  0\n  1  6  1  0  0  0  0\n  1  7  1  0  0  0  0\n  2  3  2  0  0  0  0\n  2  4  1  0  0  0  0\n  4  8  1  0  0  0  0\nM  END\n",
        "ISO": "13:C:1<br>13:C:2",
        "CHG": "O:4:-1",
        "Repr Identifier": "InChI=1/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1/i1+1,2+1/fC2H3O2/q-1",
        "Repr SVG Str": "<?xml version=\"1.0\"?>\n<svg version=\"1.1\" id=\"topsvg\"\nxmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\nxmlns:cml=\"http://www.xml-cml.org/schema\" x=\"0\" y=\"0\" width=\"200px\" height=\"200px\" viewBox=\"0 0 100 100\">\n<title> - Open Babel Depiction</title>\n<g transform=\"translate(0,0)\">\n<svg width=\"100\" height=\"100\" x=\"0\" y=\"0\" viewBox=\"0 0 149.282 140\"\nfont-family=\"sans-serif\" stroke=\"rgb(76,76,76)\" stroke-width=\"2\"  stroke-linecap=\"round\">\n<line x1=\"98.0\" y1=\"93.5\" x2=\"74.6\" y2=\"80.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"71.6\" y1=\"80.0\" x2=\"71.6\" y2=\"53.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"77.6\" y1=\"80.0\" x2=\"77.6\" y2=\"53.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"74.6\" y1=\"80.0\" x2=\"51.3\" y2=\"93.5\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<text x=\"105.282032\" y=\"108.000000\" fill=\"rgb(102,102,102)\"  stroke=\"rgb(102,102,102)\" stroke-width=\"1\" font-size=\"16\" >CH</text>\n<text x=\"129.282032\" y=\"111.680000\" fill=\"rgb(102,102,102)\"  stroke=\"rgb(102,102,102)\" stroke-width=\"1\" font-size=\"13\" >3</text>\n<text x=\"68.641016\" y=\"48.000000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >O</text>\n<text x=\"44.800000\" y=\"85.888000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >_</text>\n<text x=\"34.000000\" y=\"108.000000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >O</text>\n<text x=\"109.282032\" y=\"100.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >1</text>\n<text x=\"74.641016\" y=\"80.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >2</text>\n<text x=\"74.641016\" y=\"40.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >3</text>\n<text x=\"40.000000\" y=\"100.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >4</text>\n</svg>\n<cml:molecule formalCharge=\"-1\">\n <cml:atomArray>\n  <cml:atom id=\"a1\" elementType=\"C\" isotope=\"13\" x2=\"1.732051\" y2=\"-0.000000\"/>\n  <cml:atom id=\"a2\" elementType=\"C\" isotope=\"13\" x2=\"0.866025\" y2=\"0.500000\"/>\n  <cml:atom id=\"a3\" elementType=\"O\" x2=\"0.866025\" y2=\"1.500000\"/>\n  <cml:atom id=\"a4\" elementType=\"O\" formalCharge=\"-1\" x2=\"-0.000000\" y2=\"-0.000000\"/>\n </cml:atomArray>\n <cml:bondArray>\n  <cml:bond atomRefs2=\"a1 a2\" order=\"1\"/>\n  <cml:bond atomRefs2=\"a2 a3\" order=\"2\"/>\n  <cml:bond atomRefs2=\"a2 a4\" order=\"1\"/>\n </cml:bondArray>\n</cml:molecule>\n</g>\n<text font-size=\"18.000000\" fill =\"gray\" font-family=\"sans-serif\"\nx=\"10.000000\" y=\"20.000000\" ></text>\n</svg>\n",
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        "record_id": "d3f60ba7-0098-4af7-999a-a506823539c1",
        "error_message": ""
    },
    "3f003e7b-0e5d-40b8-a3f9-cc6581f0ee15": {
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JSON file saved from NMR specific tables view:

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        "ISO": "13:C:1<br>13:C:2",
        "CHG": "O:4:-1",
        "Repr Identifier": "InChI=1/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1/i1+1,2+1/fC2H3O2/q-1",
        "Repr SVG Str": "<?xml version=\"1.0\"?>\n<svg version=\"1.1\" id=\"topsvg\"\nxmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\nxmlns:cml=\"http://www.xml-cml.org/schema\" x=\"0\" y=\"0\" width=\"200px\" height=\"200px\" viewBox=\"0 0 100 100\">\n<title> - Open Babel Depiction</title>\n<g transform=\"translate(0,0)\">\n<svg width=\"100\" height=\"100\" x=\"0\" y=\"0\" viewBox=\"0 0 149.282 140\"\nfont-family=\"sans-serif\" stroke=\"rgb(76,76,76)\" stroke-width=\"2\"  stroke-linecap=\"round\">\n<line x1=\"98.0\" y1=\"93.5\" x2=\"74.6\" y2=\"80.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"71.6\" y1=\"80.0\" x2=\"71.6\" y2=\"53.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"77.6\" y1=\"80.0\" x2=\"77.6\" y2=\"53.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"74.6\" y1=\"80.0\" x2=\"51.3\" y2=\"93.5\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<text x=\"105.282032\" y=\"108.000000\" fill=\"rgb(102,102,102)\"  stroke=\"rgb(102,102,102)\" stroke-width=\"1\" font-size=\"16\" >CH</text>\n<text x=\"129.282032\" y=\"111.680000\" fill=\"rgb(102,102,102)\"  stroke=\"rgb(102,102,102)\" stroke-width=\"1\" font-size=\"13\" >3</text>\n<text x=\"68.641016\" y=\"48.000000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >O</text>\n<text x=\"44.800000\" y=\"85.888000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >_</text>\n<text x=\"34.000000\" y=\"108.000000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >O</text>\n<text x=\"109.282032\" y=\"100.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >1</text>\n<text x=\"74.641016\" y=\"80.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >2</text>\n<text x=\"74.641016\" y=\"40.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >3</text>\n<text x=\"40.000000\" y=\"100.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >4</text>\n</svg>\n<cml:molecule formalCharge=\"-1\">\n <cml:atomArray>\n  <cml:atom id=\"a1\" elementType=\"C\" isotope=\"13\" x2=\"1.732051\" y2=\"-0.000000\"/>\n  <cml:atom id=\"a2\" elementType=\"C\" isotope=\"13\" x2=\"0.866025\" y2=\"0.500000\"/>\n  <cml:atom id=\"a3\" elementType=\"O\" x2=\"0.866025\" y2=\"1.500000\"/>\n  <cml:atom id=\"a4\" elementType=\"O\" formalCharge=\"-1\" x2=\"-0.000000\" y2=\"-0.000000\"/>\n </cml:atomArray>\n <cml:bondArray>\n  <cml:bond atomRefs2=\"a1 a2\" order=\"1\"/>\n  <cml:bond atomRefs2=\"a2 a3\" order=\"2\"/>\n  <cml:bond atomRefs2=\"a2 a4\" order=\"1\"/>\n </cml:bondArray>\n</cml:molecule>\n</g>\n<text font-size=\"18.000000\" fill =\"gray\" font-family=\"sans-serif\"\nx=\"10.000000\" y=\"20.000000\" ></text>\n</svg>\n",
        "Repr SVG": "<a href=\"/molfile/d3f60ba7-0098-4af7-999a-a506823539c1/repr\" class=\"popup\"><?xml version=\"1.0\"?>\n<svg version=\"1.1\" id=\"topsvg\"\nxmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\nxmlns:cml=\"http://www.xml-cml.org/schema\" x=\"0\" y=\"0\" width=\"200px\" height=\"200px\" viewBox=\"0 0 100 100\">\n<title> - Open Babel Depiction</title>\n<g transform=\"translate(0,0)\">\n<svg width=\"100\" height=\"100\" x=\"0\" y=\"0\" viewBox=\"0 0 149.282 140\"\nfont-family=\"sans-serif\" stroke=\"rgb(76,76,76)\" stroke-width=\"2\"  stroke-linecap=\"round\">\n<line x1=\"98.0\" y1=\"93.5\" x2=\"74.6\" y2=\"80.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"71.6\" y1=\"80.0\" x2=\"71.6\" y2=\"53.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"77.6\" y1=\"80.0\" x2=\"77.6\" y2=\"53.0\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<line x1=\"74.6\" y1=\"80.0\" x2=\"51.3\" y2=\"93.5\" stroke=\"rgb(76,76,76)\"  stroke-width=\"2.0\"/>\n<text x=\"105.282032\" y=\"108.000000\" fill=\"rgb(102,102,102)\"  stroke=\"rgb(102,102,102)\" stroke-width=\"1\" font-size=\"16\" >CH</text>\n<text x=\"129.282032\" y=\"111.680000\" fill=\"rgb(102,102,102)\"  stroke=\"rgb(102,102,102)\" stroke-width=\"1\" font-size=\"13\" >3</text>\n<text x=\"68.641016\" y=\"48.000000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >O</text>\n<text x=\"44.800000\" y=\"85.888000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >_</text>\n<text x=\"34.000000\" y=\"108.000000\" fill=\"rgb(255,12,12)\"  stroke=\"rgb(255,12,12)\" stroke-width=\"1\" font-size=\"16\" >O</text>\n<text x=\"109.282032\" y=\"100.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >1</text>\n<text x=\"74.641016\" y=\"80.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >2</text>\n<text x=\"74.641016\" y=\"40.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >3</text>\n<text x=\"40.000000\" y=\"100.000000\" fill=\"rgb(255,0,0)\"  stroke=\"rgb(255,0,0)\" stroke-width=\"1\" font-size=\"12\" >4</text>\n</svg>\n<cml:molecule formalCharge=\"-1\">\n <cml:atomArray>\n  <cml:atom id=\"a1\" elementType=\"C\" isotope=\"13\" x2=\"1.732051\" y2=\"-0.000000\"/>\n  <cml:atom id=\"a2\" elementType=\"C\" isotope=\"13\" x2=\"0.866025\" y2=\"0.500000\"/>\n  <cml:atom id=\"a3\" elementType=\"O\" x2=\"0.866025\" y2=\"1.500000\"/>\n  <cml:atom id=\"a4\" elementType=\"O\" formalCharge=\"-1\" x2=\"-0.000000\" y2=\"-0.000000\"/>\n </cml:atomArray>\n <cml:bondArray>\n  <cml:bond atomRefs2=\"a1 a2\" order=\"1\"/>\n  <cml:bond atomRefs2=\"a2 a3\" order=\"2\"/>\n  <cml:bond atomRefs2=\"a2 a4\" order=\"1\"/>\n </cml:bondArray>\n</cml:molecule>\n</g>\n<text font-size=\"18.000000\" fill =\"gray\" font-family=\"sans-serif\"\nx=\"10.000000\" y=\"20.000000\" ></text>\n</svg>\n</a>",
        "Repr Molfile": "\nOpenBabel08091912052D\n\n  7  6  0  0  0  0  0  0  0  0999 V2000\n    1.7321   -0.0000    0.0000   C 0  0  0  0  0  0  0  0  0  0  0  0\n    0.8660    0.5000    0.0000   C 0  0  0  0  0  0  0  0  0  0  0  0\n    0.8660    1.5000    0.0000   O 0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0000   -0.0000    0.0000   O 0  5  0  0  0  0  0  0  0  0  0  0\n    1.7321   -1.0700    0.0000   H 0  0  0  0  0  0  0  0  0  0  0  0\n    2.6587    0.5350    0.0000   H 0  0  0  0  0  0  0  0  0  0  0  0\n    2.6587   -0.5350    0.0000   H 0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  1  5  1  0  0  0  0\n  1  6  1  0  0  0  0\n  1  7  1  0  0  0  0\n  2  3  2  0  0  0  0\n  2  4  1  0  0  0  0\nM  ISO  1   1  13\nM  ISO  1   2  13\nM  CHG  1   4  -1\nM  END\n",
        "record_id": "d3f60ba7-0098-4af7-999a-a506823539c1",
        "error_message": "",
        "NMR": {
            "1D1H": {
                "InChI=1/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1/i1+1,2+1/fC2H3O2/q-1": {
                    "d3f60ba7-0098-4af7-999a-a506823539c1_1": {
                        "descr": [
                            "[1H5,1H6,1H7:C1]HResonance"
                        ],
                        "inchi": "InChI=1/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1/i1+1H3,2+1/fC2H3O2/q-1",
                        "me_group": "ME1",
                        "row_id": "d3f60ba7-0098-4af7-999a-a506823539c1_1"
                    },
                    "d3f60ba7-0098-4af7-999a-a506823539c1_2": {
                        "descr": [
                            "[1H5,1H6,1H7:C1]HResonance",
                            "[1H5,1H6,1H7:13C1]J1CH"
                        ],
                        "inchi": "InChI=1/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1/i1+1H3,2+1/fC2H3O2/q-1",
                        "me_group": "ME2",
                        "row_id": "d3f60ba7-0098-4af7-999a-a506823539c1_2"
                    }
                }
            }
        }
    }
}

InChI Table View¶

The InChI Table View provides an editable table interface where the user can update/change the metabolite name, base identifier, isotopic properties and atom charges.

How to update isotopic properties.¶

Use isotope:atom:atom_number format to specify ISO properties. For example:
- 13:C:1 means that carbon atom at position 1 is isotope 13.
- 13:C:2 means that carbon atom at position 2 is isotope 13.

How to update charge properties.¶

Use atom:atom_number:charge format to specify CHG properties. For example:
- O:4:-1 means that oxygen atom at position 4 has charge -1

How to add/remove new row to table.¶

The user can also add a new editable row by using “Add row” button and insert valid InChI string.

The user can update the row by using the “Update” button to generate base and representative identifiers and their corresponding visualizations.

The user can remove the row by using the “Remove” button in the corresponding table row.

How to view corresponding Molfile.¶

The user can view the corresponding Molfile for both base and representative InChI by clicking on the metabolite image (i.e. Base SVG or Repr SVG columns).
- Base Molfile:
- Repr Molfile:

How to save table view.¶

The user can save the table into CSV or JSON files to save their progress.

How to generate NMR specific InChI.¶

To generate NMR specific InChI for metabolites, the user needs to select the appropriate NMR experiment type and click the “Use NMR specific InChI”.

NMR specific InChI Table View¶

NMR specific InChI table view provides the interface where the user can see NMR specific InChI tables based upon selected NMR experiment type description.

How to select NMR specific InChI.¶

The user can examine tables that contain “Resonance Description” and corresponding “NMR specific InChI” to save the appropriate identifiers that correspond to peaks in their NMR spectra.

The user can sort NMR specific tables by “Resonance Description”, “NMR specific InChI”, and “ME Group”. “ME” stands for “Magnetically Equivalent” InChI - ones that have similar “Resonance Description” and identical InChI strings.

How to save NMR table view.¶

The user can save the NMR table into CSV or JSON files to save their progress.

Save to JSON is intended to save the project state, while save to CSV will create a CSV file that will contain NMR specific InChI that can be directly used for data deposition.

Name,Base Identifier,Repr Identifier,Resonance Description,NMR Specific InChI
acetic acid,"InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)","InChI=1/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1/i1+1,2+1/fC2H3O2/q-1","[1H5,1H6,1H7:C1]HResonance","InChI=1/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1/i1+1H3,2+1/fC2H3O2/q-1"
acetic acid,"InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)","InChI=1/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1/i1+1,2+1/fC2H3O2/q-1","[1H5,1H6,1H7:C1]HResonance + [1H5,1H6,1H7:13C1]J1CH","InChI=1/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1/i1+1H3,2+1/fC2H3O2/q-1"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","[1H9,1H10,1H11:C1]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-"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","[1H9,1H10,1H11:C1]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-"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","[1H9,1H10,1H11:C1]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-"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","[1H9,1H10,1H11:C1]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-"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","[1H12,1H13,1H14:C2]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-"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","[1H12,1H13,1H14:C2]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-"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","[1H12,1H13,1H14:C2]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-"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","[1H12,1H13,1H14:C2]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-"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1",[1H15:C3]HResonance,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i3H"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1",[1H15:C3]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"
valine,"InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1","[1H15:C3]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-"

The isoenum-webgui CLI Reference¶

The isoenum-webgui command-line interface¶

Usage:

isoenum_webgui -h | –help

isoenum_webgui –version

isoenum_webgui [–port=<port>] [–browser] [–debug]

Options:

`-h, --help`	Show this screen.
`--version`	Show version.
`-b, --browser`	Open isoenum-webgui in a default browser.
`-p, --port=<port>`
	Port [default: 5000].
`--debug`	Debug mode flag.

isoenum_webgui.cli.cli(cmdargs)[source]¶

Command-line interface entry point.

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

The isoenum-webgui API Reference¶

Isotopic enumerator web interface.

isoenum_webgui.proc¶

This module contains isoenum-webgui data processing/transformation logic, i.e. it calls the appropriate isoenum API methods in order to generate correct InChI, Molfile`s and SVG images based upon input from the `isoenum-webgui.

isoenum_webgui.proc.generate_repr_molfile(inchi_str, iso_str, chg_str)[source]¶

Generate representative Molfile using isotope and charge specification strings.

Parameters:	inchi_str (str) – InChI string. iso_str (str) – Isotope specification. chg_str (str) – Charge specification.
Returns:	Representative Molfile.
Return type:	`Molfile`

isoenum_webgui.proc.generate_table(records)[source]¶

Generate InChI table.

Parameters:	records (dict) – Global RECORDS store.

isoenum_webgui.proc.create_initial_record(header, row)[source]¶

Initialize record.

Parameters:	header (list) – Record keys. row (list) – Record values.
Returns:	Record dictionary.
Return type:	dict

isoenum_webgui.proc.update_record(record)[source]¶

Update record.

Parameters:	record (dict) – Record.
Returns:	Updated record.
Return type:	dict

isoenum_webgui.proc.create_repr_inchi(base_inchi_str, iso_str, chg_str)[source]¶

Create representative InChI string.

Parameters:	base_inchi_str (str) – Base InChI string iso_str (srr) – Isotope specification. chg_str (str) – Charge specification.
Returns:	Representative InChI string.
Return type:	str

isoenum_webgui.proc.create_svg(inchi_str)[source]¶

Create SVG from InChI string.

Parameters:	inchi_str (str) – InChI string.
Returns:	SVG string.
Return type:	str

isoenum_webgui.proc.create_svg_link(svg_str, record_id, record_type)[source]¶

Create SVG link.

Parameters:	svg_str (str) – SVG string. record_id (str) – Record id. record_type (str) – Record type: base or repr.
Returns:	SVG link.
Return type:	str

isoenum_webgui.proc.generate_nmr(nmr_experiment_type, records)[source]¶

Generate NMR specific InChI tables.

Parameters:	nmr_experiment_type (str) – NMR experiment type. records (dict) – Global RECORDS dictionary.
Returns:	None.
Return type:	`None`

isoenum_webgui.proc.create_record_id()[source]¶

Create record id.

Returns:	Record id string.
Return type:	str

isoenum_webgui.proc.create_empty_record()[source]¶

Create empty record.

Returns:	Empty record dictionary.
Return type:	dict

isoenum_webgui.routes¶

Isotopic enumerator web interface routes.

isoenum_webgui.routes.home()[source]¶: Home.

isoenum_webgui.routes.example_project()[source]¶: Example project.

isoenum_webgui.routes.table()[source]¶: Display base and representative InChI.

isoenum_webgui.routes.nmrtable()[source]¶: Display NMR-specific InChI.

isoenum_webgui.routes.update()[source]¶: Update record.

isoenum_webgui.routes.add()[source]¶: Add empty record.

isoenum_webgui.routes.remove()[source]¶: Remove record.

isoenum_webgui.routes.display_molfile(record_id, record_type)[source]¶: Display Molfile.

isoenum_webgui.routes.export_json()[source]¶: Export as JSON.

isoenum_webgui.routes.export_csv()[source]¶: Export as CSV.

isoenum_webgui.routes.export_nmr_csv()[source]¶: Export NMR-specific InChI as CSV.

isoenum_webgui.routes.about()[source]¶: About page.

isoenum_webgui.routes.after_request(response)[source]¶: Do not cache responses.

isoenum_webgui.forms¶

Isotopic enumerator web interface forms.

class isoenum_webgui.forms.FileForm(formdata=<object object>, **kwargs)[source]¶: File input form with validation.

isoenum_webgui.config¶

This module contains isoenum-webgui application configurations.

class isoenum_webgui.config.Config[source]¶: Set isoenum-webgui Flask app configuration.

isoenum_webgui.errors¶

Isotopic enumerator web interface custom exception handling.

isoenum_webgui.errors.handle_error(error)[source]¶: Custom error handler.

Release History¶

0.2.0 (2019-08-14)¶

Improvements

Added popup window for base and representative molfiles.
Strip out html on paste event for editable table.
Updated templates.
Added error handling for “Base Identifier” column.
Added CLI, GUI, API documentation.
Added “isoenum_webgui” entry point.

0.1.0 (2019-07-30)¶

Initial public release.

License¶

The Clear BSD License

Copyright (c) 2019, 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-webgui’s documentation!¶

isoenum-webgui¶

Links¶

Installation¶

Install on Linux, Mac OS X¶

Install on Windows¶

Dependencies¶

Development version installation¶

Install development version on Linux, Mac OS X¶

Install development version on Windows¶

License¶

The isoenum-webgui GUI Reference¶

Home View¶

Accepted File Formats¶

CSV¶

JSON¶

InChI Table View¶

How to update isotopic properties.¶

How to update charge properties.¶

How to add/remove new row to table.¶

How to view corresponding Molfile.¶

How to save table view.¶

How to generate NMR specific InChI.¶

NMR specific InChI Table View¶

How to select NMR specific InChI.¶

How to save NMR table view.¶

The isoenum-webgui CLI Reference¶

The isoenum-webgui command-line interface¶

The isoenum-webgui API Reference¶

isoenum_webgui.proc¶

isoenum_webgui.routes¶

isoenum_webgui.forms¶

isoenum_webgui.config¶

isoenum_webgui.errors¶

Release History¶

0.2.0 (2019-08-14)¶

0.1.0 (2019-07-30)¶

License¶

Indices and tables¶