alvaDesc – KNIME

The alvaDesc KNIME Plugin contains three KNIME nodes:

• Descriptor: calculates molecular descriptors
• Fingerprint: calculates molecular fingerprints
• Pattern: identifies structural patterns (using SMARTS syntax)
• Molecule Reader: reads standard molecule files and can be used as a source for the other two nodes (which are also compatible with KNIME standard molecule nodes)

In order to work, the plugin requires a licensed version of alvaDesc installed on the same computer.

Video

A short video introduction:

Multithreading

If you are using alvaDesc v3 or later, you can benefit from multithreading, which can significantly speed up calculations within the KNIME platform. To enable this performance enhancement, activate the “Multithreading” option found in the “Options” panel of the “Descriptor” node. Note that this feature is available only when working with alvaDesc v3 or above.

Example

You can download a simple example workflow of the alvaDesc KNIME Plugin from here.

Install (with External Software Site)

You can install the alvaDesc Plugin directly from KNIME:

1. Make sure you have an updated version of KNIME (at least 4.6.5)
2. Make sure you are in KNIME Classic User Interface
3. Make sure the Alvascience update site is present and checked in the list of the Available Software Sites (File -> Preferences -> Install/Update -> Available Software Sites), if it is not:
   • Go to File -> Preferences -> Install/Update -> Available Software Sites
   • Click Add…
   • Fill in the Name: Alvascience update site
   • Fill in the Location: https://www.alvascience.com/knime/latest
   • Click Add
   • Click Apply and Close
4. Click File -> Install KNIME Extensions…
5. Search for Alvascience
6. Select Alvascience alvaDesc
7. Click Next and follow KNIME instructions

The node will be then available in the section Alvascience -> alvaDesc Nodes.

Update (with External Software Site)

You can update the alvaDesc Plugin directly from KNIME:

1. Make sure you the Alvascience update site is configured (check the Install section)
2. Make sure you are in KNIME Classic User Interface
3. Click File -> Update KNIME…
4. Click Next and follow KNIME instructions

Install (with zip file / Local Software Site)

You can install the alvaDesc Plugin using a zip file:

1. Make sure you have an updated version of KNIME (at least 4.6.5)
2. Make sure you are in KNIME Classic User Interface
3. Download the zip file of Alvascience Local Software Site to your local system
4. Go to File -> Preferences -> Install/Update -> Available Software Sites
5. Remove other External or Local Software Sites related to Alvascience
6. Click Add…
7. Click Archive…
8. Fill in the Name: Alvascience local site
9. Click Add
10. Click Apply and Close
11. Click File -> Install KNIME Extensions…
12. Search for Alvascience
13. Select Alvascience alvaDesc inside Alvascience Extensions
14. Click Next and follow KNIME instructions

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