KNIME nodes to configure, run and analyze PLANTS protein-ligand docking
This project uses Eclipse Tycho to perform build steps.
Included in PLANTS nodes plugin is the PLANTS executable with academic license (http://www.mnf.uni-tuebingen.de/fachbereiche/pharmazie-und-biochemie/pharmazie/pharmazeutische-chemie/pd-dr-t-exner/research/plants.html). When installing the plugin you have to accept this license agreement, you agree to use the included PLANTS executable only for academic usage. To use these nodes in a commercial manner you need to acquire a valid license yourself and configure the PLANTS node to use the commercial executable.
The PLANTS KNIME nodes themselves have the Apache 2.0 license.
- KNIME, https://www.knime.org, version 3.3 or higher
Steps to get the PLANTS KNIME node inside KNIME:
- Goto Help > Install new software ... menu
- Press add button
- Fill text fields with the
https://3d-e-chem.github.io/updatesupdate site url.
- Select --all sites-- in
- Select the node
- Install software
- Restart KNIME
- Create a new KNIME workflow.
- Find node in Node navigator panel.
- Drag node to workflow canvas.
examples/ folder contains example KNIME workflows.
An Eclipse update site will be made in
The update site can be used to perform a local installation.
Steps to get development environment setup:
Download KNIME SDK from https://www.knime.org/downloads/overview
Install/Extract/start KNIME SDK
Install m2e (Maven integration for Eclipse) + KNIME Testing framework + Vernalis + SWTBot
- Goto Window -> Preferences -> Install/Update -> Available Software Sites
- Make sure the following Software Sites (or a version of them) are present otherwise add them:
- Goto Help -> Check for updates
- Install any updates found & restart
- Goto Help > Install new software ...
- Select --All Available sites-- in work with pulldown
- Wait for list to be filled,
- Select the following items:
- m2e (Maven integration for Eclipse)
- Test Knime workflows from a Junit test
- Splash & node category for 3D-e-Chem KNIME nodes
- SWTBot for Eclipse Testing
- SWtBot JUnit Headless launchers for Eclipse
- Install software & restart
Import this repo as an Existing Maven project
After the import the Maven plugin connections must be setup, a Discover m2e connections dialog will popup to install all requested connectors, after the installation restart eclipse.
This plugin uses metanodes as it's public nodes. The are created in the following way:
- The meta nodes are first created and tested inside the example workflows in the
- The examples are fully run and committed
- The meta nodes are internally completely reset, so we don't ship public nodes with example data in them.
- The meta nodes from the example workflows are then copied to the
- The meta nodes are added to the
plugin/plugin.xmlas PersistedMetaNode in the
- The examples are checked-out to their fully run state.
Tests for the node are in
Tests can be executed with
mvn verify, they will be run in a separate KNIME environment.
Test results will be written to
Code coverage reports (html+xml) can be found in the
There are no tests for the meta nodes as they are copied from the plugin to a workflow each time, which would make the test test itself.
Unit tests written in Junit4 format can be put in
Speed up builds
Running mvn commands can take a long time as Tycho fetches indices of all p2 update sites.
This can be skipped by running maven offline using
- Update versions in pom files with
mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOTcommand.
- Create package with
mvn package, will create update site in
- Run tests with
- Optionally, test node by installing it in KNIME from a local update site
- Append new release to an update site
- Make clone of an update site repo
- Append release to the update site with
mvn install -Dtarget.update.site=<path to update site>
- Commit and push changes in this repo and update site repo.
- Create a GitHub release
- Update Zenodo entry
- Correct authors
- Correct license
- Add https://doi.org/10.1007/11839088_22 as
is referenced by this uploadrelated identifier
- Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release