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.
- KNIME, https://www.knime.org, version 4.0 or higher
Steps to get the Pharmacophore KNIME nodes inside KNIME:
- Goto Help > Install new software ... menu
- Press add button
- Fill text fields with
- Select --all sites-- in
- Select the
Pharmacophore KNIME nodes
- 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.
Configuration files to run Continuous Integration builds on Linux (Travis-CI), OS X (Travis-CI) and Windows (AppVeyor) are present.
./.travis.yml file how to trigger a Travis-CI build for every push or pull request.
./.travis.yml file how to upload coverage to https://www.codacy.com .
./appveyor.yml file how to run on https://www.appveyor.com .
Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:
- Install Java 8
- Install Eclipse for RCP and RAP developers
- Configure Java 8 inside Eclipse Window > Preferences > Java > Installed JREs
- Import this repo as an Existing Maven project
- Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the
KNIME Analytics Platform (4.0) - nl.esciencecenter.e3dchem.knime.pharmacophore.targetplatform/KNIME-AP-4.0.targettarget definition.
- A KNIME Analytics Platform instance can be started by right clicking on the
targetplatform/KNIME\ Analytics\ Platform.launchfile 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 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
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
- Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release