Knime node to calculate subfamily specific two entropy analysis (ss-TEA) score.

The ss-TEA can identify specific ligand binding residue positions for any receptor, predicated on high quality sequence information.

See reference at https://doi.org/10.1186/1471-2105-12-332 for a description of the score.

Installation

Requirements:

• KNIME, https://www.knime.org

Steps to get KripoDB Python templates 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 ss-TEA
7. Install software & restart

Usage

See example workflow at examples/ss-TEA-example.zip.

It can be run by importing it into Knime as an archive.

Build

mvn verify

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

Development

Steps to get development environment setup:

1. Download KNIME SDK from https://www.knime.org/downloads/overview
2. Install/Extract/start KNIME SDK
3. Start SDK

4. Install m2e (Maven integration for Eclipse) + Test workflows in JUnit + 3D-e-Chem node category

   1. Goto Help > Install new software ...
   2. Make sure Update site http://update.knime.org/analytics-platform/3.1 and https://3d-e-chem.github.io/updates are in the pull down list otherwise add them
   3. Select --all sites-- in work with pulldown
   4. Select m2e (Maven integration for Eclipse)
   5. Select Test Knime workflows from a Junit test
   6. Select Splash & node category for 3D-e-Chem KNIME nodes
   7. Install software & restart

5. Import this repo as an Existing Maven project

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 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> command.
2. Manually update version of "source" feature in p2/category.xml file.
3. Commit and push changes
4. Create package with mvn package, will create update site in p2/target/repository
5. Append new release to 3D-e-Chem update site
   1. Make clone of https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
   2. Append release to 3D-e-Chem update site with mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>
6. Commit and push changes in this repo and 3D-e-Chem.github.io repo
7. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release

Offline Knime update site

If Knime update site can not be contacted then use a local version.

1. Download zip of update site from https://www.knime.org/downloads/update
2. Unzip it
3. To maven commands add -Dknime.update.site=file://-Dknime.update.site=file://<path to update site directory>