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knime-molviewer

KNIME node which launches a web browser with moleculer viewer powered by webgl

https://github.com/3d-e-chem/knime-molviewer

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 3 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (14.8%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

KNIME node which launches a web browser with moleculer viewer powered by webgl

Basic Info
  • Host: GitHub
  • Owner: 3D-e-Chem
  • License: apache-2.0
  • Language: Java
  • Default Branch: master
  • Homepage:
  • Size: 19.1 MB
Statistics
  • Stars: 3
  • Watchers: 6
  • Forks: 0
  • Open Issues: 4
  • Releases: 11
Created over 9 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License Citation Zenodo

README.md

KNIME node which launches a web browser with a molecule viewer powered by NGL.

Java CI with Maven Quality Gate Status Coverage DOI

If you are using KNIME workflows with large molecules and you want to view them in 3D then the molviewer nodes are able to handle this. * Provides cheminformatics trying to model proteins within KNIME a way to view them * Adds nodes to KNIME to visualize proteins, small molecules and pharmacophores * Adds support to KNIME to handle viewing big molecules * Used to compare pharmacophore generation tools * Used to check ligand repurposing

This project uses a web user interface based on https://github.com/3D-e-Chem/molviewer-tsx .

From KNIME launch web based molviewer

Installation

Requirements:

  • KNIME, https://www.knime.org, version 5.1 or higher

Steps to get the MolViewer KNIME node inside KNIME:

  1. Goto Help > Install new software ... menu
  2. Press add button
  3. Fill text fields with https://3d-e-chem.github.io/updates/5.1
  4. Select --all sites-- in work with pulldown
  5. Select the node called MolViewer nodes for KNIME
  6. Install software
  7. Restart KNIME

Usage

  1. Create a new KNIME workflow.
  2. Find node in Node navigator panel under Community Nodes > 3D-e-Chem > Molviewer.
  3. Drag node to workflow canvas.
  4. Give molviewer nodes Proteins, Ligands and/or Pharmacophores as input.
  5. Open the view of the molviewer node, this will launch a web browser with the molecules visualized.
  6. In web browser you can
  • Rotate/translate/zoom molecules with mouse
  • Toggle which molecules are visible
  • Transmit visible molecules as HiLite selection back to KNIME or do the reverse from KNIME to molviewer
  • and more

See example workflow in examples/ directory.

Build

mvn verify

An Eclipse update site will be made in p2/target/repository repository. The update site can be used to perform a local installation.

Development

Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:

  1. Install Java 17
  2. Install Eclipse for RCP and RAP developers
  3. Configure Java 17 inside Eclipse Window > Preferences > Java > Installed JREs
  4. Import this repo as an Existing Maven project
  5. Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the KNIME Analytics Platform (5.1) - nl.esciencecenter.e3dchem.knime.molviewer.targetplatform/KNIME-AP-5.1.target target definition.
  6. A KNIME Analytics Platform instance can be started by right clicking on the targetplatform/KNIME\ Analytics\ Platform.launch file and selecting Run As → KNIME Analytics Platform. The KNIME instance will contain the target platform together with all extensions defined in the workspace.

During import the Tycho Eclipse providers must be installed.

Web interface

The web interface in the plugin/src/main/java/js-lib/molviewer directory. Is a distribution from the https://github.com/3D-e-Chem/molviewer-tsx repository.

Tests

Tests for the node are in tests/src directory. Tests can be executed with mvn verify, they will be run in a separate KNIME environment. Test results will be written to test/target/surefire-reports directory.

Workflow tests

See https://github.com/3D-e-Chem/knime-testflow#3-add-test-workflow

New release

  1. Update versions in pom files with mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOT command.
  2. Commit and push changes
  3. Create package with mvn package, will create update site in p2/target/repository
  4. Test node by installing it from local update site
  5. Append new release to an update site
    1. Make clone of an update site repo
    2. Append release to the update site with mvn install -Dtarget.update.site=<path to update site>
  6. Add files, commit and push changes of update site repo.
  7. Create a Github release
  8. Update Zenodo entry, fix authors
  9. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release
  10. Update DOI in CITATION.cff

Technical architecture

The nodes are implemented as Dynamic JavaScript nodes also known as a org.knime.dynamic.node.generation.dynamicNodes extension.

The viewer has two way binding for the molecule visibility.

This project uses Eclipse Tycho to perform build steps.

Owner

  • Name: 3D-e-Chem NLeSC project
  • Login: 3D-e-Chem
  • Kind: organization
  • Location: Amsterdam, The Netherlands

Software repositories for 3D-e-Chem project of Netherlands eScience Center

Citation (CITATION.cff) 

# YAML 1.2
# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
cff-version: 1.0.3
message: If you use this software, please cite it as below.
title: KNIME molecule viewer nodes
doi: 10.5281/zenodo.597231
authors:
- given-names: Stefan
  family-names: Verhoeven
  affiliation: Nederlands eScience Center
- given-names: Albert
  family-names: Kooistra
  name-particle: J.
  affiliation: Vrije Universiteit Amsterdam
- given-names: Marton
  family-names: Vass
  affiliation: Vrije Universiteit Amsterdam
- given-names: Ross
  family-names: McGuire
  affiliation: BioAxis Research
- given-names: Chris
  family-names: de Graaf
  affiliation: Vrije Universiteit Amsterdam
repository-code: https://github.com/3D-e-Chem/knime-molviewer
license: Apache-2.0

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