https://github.com/larsgw/gpml-rhea

Collect chemical reactions from a GPML file and look for matching Rhea equations.
https://github.com/larsgw/gpml-rhea

biology chemistry gpml pathways wikipathways wikipathways-gpml-files

Last synced: about 1 month ago
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Collect chemical reactions from a GPML file and look for matching Rhea equations.

• Host: GitHub
• URL: https://github.com/larsgw/gpml-rhea
• Owner: larsgw
• License: mit
• Created: 2020-11-04T02:53:46.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2020-11-04T15:46:06.000Z (about 4 years ago)
• Last Synced: 2024-09-05T15:11:00.325Z (4 months ago)
• Topics: biology, chemistry, gpml, pathways, wikipathways, wikipathways-gpml-files
• Language: JavaScript
• Homepage:
• Size: 31.3 KB
• Stars: 0
• Watchers: 3
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# GPML-Rhea

Collect chemical reactions from a GPML file and look for matching Rhea equations.

Pathway requirements:

  - MIM interactions compatible with https://github.com/BiGCAT-UM/WikiPathwaysInteractions/tree/master/FilesGPML#readme

  - Metabolites with ChEBI identifiers

## Install

System requirements:

  - [Node.js v14](https://nodejs.org/en/download/)

  - npm (usually comes with Node.js)

### Installing Node.js on Linux

    sudo apt-get install nodejs-dev node-gyp libssl1.0-dev

    sudo apt install npm

### Installing GPML-Rhea

    npm install --global @larsgw/gpml-rhea

Alternatively, run "without" installing:

    npx @larsgw/gpml-rhea [options]

## Usage

    GPML-Rhea

    

      gpml-rhea [file]             Read file

      gpml-rhea -                  Read from standard in

      gpml-rhea -v, --version      Get the version

      gpml-rhea -h, --help         Print this message

## Example

    > curl -L -o pathway.gpml https://webservice.wikipathways.org/getPathwayAs?fileType=gpml&pwId=WP5019&revision=113587

    > gpml-rhea pathway.gpml

    id192c7b4a: 5,10-Methenyltetrahydrofolate + NADH → 5,10-Methylenetetrahydrofolate + NAD(1-)

    ---------------------------------------------

    Rhea: 0 results

    ---------------------------------------------

    id4f3af248: Oxidised ferredoxin → Reduced ferredoxin

    ---------------------------------------------

    Rhea: 0 results

    ---------------------------------------------

    id59fbd0e3: 10-Formyltetrahydrofolate + dihydrogen → 5,10-Methenyltetrahydrofolate

    ---------------------------------------------

    Rhea: 0 results

    ---------------------------------------------

    id8e976caf: 5-Methyltetrahydrofolate → methyl + Tetrahydrofolate

    ---------------------------------------------

    Rhea: 0 results

    ---------------------------------------------

    idb70e2922: NAD(1-) → NADH

    ---------------------------------------------

    Rhea: 0 results

    ---------------------------------------------

    idcb0cc195: formate + ATP + Tetrahydrofolate → 10-Formyltetrahydrofolate + hydrogenphosphate + ADP

    ---------------------------------------------

    Rhea: 0 results

    ---------------------------------------------

    ide2e37f0: 5,10-Methylenetetrahydrofolate + NADH → 5-Methyltetrahydrofolate + NAD(1-)

    ---------------------------------------------

    Rhea: 0 results

    ---------------------------------------------

    ideb932d04: carbon monooxide + HSCoA + methyl → acetyl-CoA

    ---------------------------------------------

    Rhea: 0 results

    ---------------------------------------------

    idee9950c3: carbon dioxide + dihydrogen → formate + hydron

    ---------------------------------------------

    Rhea: 1 results

        27610: formate + H(+) = CO2 + H2

    ---------------------------------------------

    idf6f6d75: dihydrogen → hydron

    ---------------------------------------------

    Rhea: 13 results

        24636: H2 + NAD(+) = H(+) + NADH

        27610: formate + H(+) = CO2 + H2

        29047: a menaquinone + 2 H(+)(in) + H2 = a menaquinol + 2 H(+)(out)

        29051: 2 H(+)(in) + H2 + menaquinone-8 = 2 H(+)(out) + menaquinol-8

        29055: a ubiquinone + 2 H(+)(in) + H2 = a ubiquinol + 2 H(+)(out)

        29059: 2 H(+)(in) + H2 + ubiquinone-8 = 2 H(+)(out) + ubiquinol-8

        30279: 2 H2 + NAD(+) + 2 oxidized [2Fe-2S]-[ferredoxin] = 3 H(+) + NADH + 2 reduced [2Fe-2S]-[ferredoxin]

        35591: H2 + n sulfur = H(+) + hydrogen sulfide + (n-1) sulfur

        17445: H2 + 2 oxidized [2Fe-2S]-[ferredoxin] = 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin]

        18637: H2 + NADP(+) = H(+) + NADPH

        20017: 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H2 = 5,10-methylenetetrahydromethanopterin + H(+)

        20625: 2 [Fe(III)-cytochrome c3] + H2 = 2 [Fe(II)-cytochrome c3] + 2 H(+)

        55748: coenzyme B + coenzyme M + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] = coenzyme M-coenzyme B heterodisulfide + 2 H2 + 2 oxidized [2Fe-2S]-[ferredoxin]

    ---------------------------------------------