Modified Tanimoto distance measure for Knime

KNIME plugin for calculating distance of bitvectors using Modifed Tanimoto similarity index. Implements similarity index according to Fligner, Michael A., et al. “A Modification of the Jaccard-Tanimoto Similarity Index for Diverse Selection of Chemical Compounds Using Binary Strings.” Technometrics, vol. 44, no. 2, 2002, pp. 110–119. https://www.jstor.org/stable/1271255

Followed http://tech.knime.org/wiki/distance-measure-developers-guide for this repo.

Installation

Requirements:

• KNIME, https://www.knime.org

Steps to get distance measure 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. Open KNIME 3D-e-Chem Contributions folder
6. Select Modified Tanimoto Distance measure
7. Install sofware & restart

Usage

The Modified Tanimoto distance measure can be selected inside the Bit Vector Distances node.

For description of distance measurement framework see http://tech.knime.org/wiki/distance-measure

See example workflow in examples folder.

Build

mvn verify

Jar has been made in nl.esciencecenter.e3dchem.modifiedtanimoto/target folder. An Eclipse update site will be made in nl.esciencecenter.e3dchem.p2/target/repository repository.

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 <<<<<<< HEAD
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.sstea.targetplatform/KNIME-AP-5.1.target target definition. =======
6. Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the KNIME Analytics Platform (4.0) - nl.esciencecenter.e3dchem.modifiedtanimoto.targetplatform/KNIME-AP-4.0.target target definition.

origin/master

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.

Unit tests

Unit tests written in Junit4 format can be put in nl.esciencecenter.e3dchem.modifiedtanimoto.tests/src/java.

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 nl.esciencecenter.e3dchem.p2/target/repository
4. Append new release to 3D-e-Chem update site
5. Make clone of https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
6. Append release to 3D-e-Chem update site with mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>
7. Commit and push changes in this repo and 3D-e-Chem.github.io repo
8. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release