KNIME plugin with nodes to convert and align pharmacophores.

A pharmacophore is an abstract description of molecular features that are necessary for molecular recognition of a ligand by a biological macromolecule. Nodes in this plugin allow for converting pharmacophores, from and to molecules, by mapping elements to pharmacophore type and, reading from or writing to the phar file format used by the Silicos IT align-it tool. This plugin adds the Pharmacophore (Phar) data type to KNIME, allowing nodes to read/write/manipulate pharmacophores inside KNIME like the Silicos-it align-it, Kripo pharmacophore retrieval and molviewer pharmacophore viewer nodes.

This project uses Eclipse Tycho to perform build steps.

Installation

Requirements:

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

Steps to get the Pharmacophore KNIME nodes 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 Pharmacophore KNIME nodes
6. Install software
7. Restart KNIME

Usage

1. Create a new KNIME workflow.
2. Find node in Node navigator panel.
3. Drag node to workflow canvas.

Examples

The examples/ folder contains example KNIME workflows.

Build

mvn verify

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

Continuous Integration

Configuration files to run Continuous Integration builds on GitHub actions are present in .github/workflows.

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.pharmacophore.targetplatform/KNIME-AP-5..10.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.

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. Code coverage reports (html+xml) can be found in the tests/target/jacoco/report/ directory.

Unit tests

Unit tests written in Junit4 format can be put in tests/src/java.

Workflow tests

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

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 mvn -o.

New release

1. Update versions in pom files with mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOT command.
2. Create package with mvn package, will create update site in p2/target/repository
3. Run tests with mvn verify
4. Optionally, test node by installing it in KNIME from a 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. Commit and push changes in this repo and update site repo.
7. Create a Github release
8. Update Zenodo entry
   1. Correct 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