SMARTSViewer

This Node Is Deprecated — This version of the node has been replaced with a new and improved version. The old version is kept for backwards-compatibility, but for all new workflows we suggest to use the version linked below.

Provides a SMARTSviewer visualisation of a column of SMARTs strings (SMARTS, Smiles or String cell types accepted as inputs) using the service provided by the University of Hamburg. The node performs no validation of the SMARTs strings prior to sending to the webservice. For more detailed information about the implementation see either the Help file at http://smartsview.zbh.uni-hamburg.de/smartsview/view or the following reference:
K. Schomburg, H.-C. Ehrlich, K. Stierand, M.Rarey; From Structure Diagrams to Visual Chemical Patterns, J. Chem. Inf. Model., 2010, 50, pp 1529-1535

The Communication Error Settings tab allows setting of behaviour relating to server communication problem handling. The values set are applied to each row in turn. The server will only be contacted until a successful result is returned. The settings allow the user to control the behaviour of the node should the SMARTSviewer server be functioning incorrectly. Note that it is not currently possible to cancel execution during a row, so use long delay settings with care!

Note that SMARTs strings are transferred to the remote server unencrypted, and the the server maintains an anonymous record of query SMARTs strings to aid future development.

This node was developed by Vernalis (Cambridge, UK). For feedback and more information, please contact knime@vernalis.com

Options

Select a column contaning the SMARTs Strings: Select a column containing SMARTs strings for visualsation. Accepted column types are SMARTS, Smiles and String. No SMARTS validation is carried out prior to sending to the remote server, which will return a blank image for invalid SMARTS strings
Select legend type: Choose the desired legend type: Dynamic - detailed text description of each atom and bond; Static - short description of how each symbol is depicted in the visualisation
Select Visualisation modus: Element symbols uses text representation of the element symbols in the depiction

Communication Error Settings

Number of retries to contact server: Set the number of times the server will be re-contacted following a failure.
Delay between attempts (secs): The delay period between each re-try
Ignore server errors: If set, the node will return a 'missing value' cell for each row which failed to contact the server after the defined number of attempts - allowing workflow execution to continue, otherwise node execution will fail. Setting a long delay interval (max 10 minutes) and large number of attempts (max 20) allows the workflow a chance to restore functionality (it will take over 3 hours between the first and last attempt for each row in these circumstances)
Restore Defaults: Restore the default server settings.

Input Ports

: Input port containing a column of SMARTS strings, either as String, SMARTS or Smiles format

Output Ports

: The input table with the SMARTSViewer representations appended as a PNG column

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Installation

To use this node in KNIME, install the extension Vernalis KNIME Nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.3

A zipped version of the software site can be downloaded here.

Plugin provider: Vernalis Research, UK

Plugin version: 1.36.7.v202405281205

On NodePit since: 2024-07-11

Last update: 2024-11-21

Tags: Deprecated

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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