Knime plugin for calculating distance of bitvector using Modifed Tanimoto similarity index
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nl.esciencecenter.e3dchem.modifiedtanimoto.feature
nl.esciencecenter.e3dchem.modifiedtanimoto.tests
nl.esciencecenter.e3dchem.modifiedtanimoto
nl.esciencecenter.e3dchem.p2
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README.md
pom.xml

README.md

Modified Tanimoto distance measure for Knime

Build Status Codacy Badge DOI

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:

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
  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 enviroment setup:

  1. Download KNIME SDK from https://www.knime.org/downloads/overview

  2. Install/Extract/start KNIME SDK

  3. Start SDK

  4. Install distance matrix nodes + m2e (Maven integration for Eclipse)

    1. Goto Help > Install new software ...
    2. Make sure Update site is http://update.knime.org/analytics-platform/3.1 in the pull down list otherwise add it
    3. Select --all sites-- in work with pulldown
    4. Open KNIME & Extensions folder
    5. Select KNIME Distance Matrix
    6. Open General Purpose Tools folder
    7. Select m2e (Maven integration for Eclipse)
    8. Install sofware & restart
  5. Import this repo as an Existing Maven project

During import the Tycho Eclipse providers must be installed.

New release

  1. Update versions in pom files with mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version> command.
  2. Manually update version of "source" feature in nl.esciencecenter.e3dchem.p2/category.xml file.
  3. Commit and push changes
  4. Create package with mvn package, will create update site in nl.esciencecenter.e3dchem.p2/target/repository
  5. Append new release to 3D-e-Chem update site
  6. Make clone of https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
  7. Append release to 3D-e-Chem update site with mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>
  8. Commit and push changes in this repo and 3D-e-Chem.github.io repo
  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