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3D Viewer

KNIME CDK Integration version 1.5.700.v202006231106 by KNIME GmbH, Konstanz and EMBL-EBI, Cambridge

View to display 3D depictions of molecular structures. The input table needs to contain a column containing either CDK or SDF values. The structures also need to have 3D coordinates attached. (Due to problems with the 3D generation in the CDK libraries the coordinates must be available in the input file, for instance must be contained in the SDF file.)

This node uses the JMol library as rendering engine.

Input Ports

: Table to display

Views

3D View: Select any structure in the table view at the top and see the 3D representation at the bottom. The bottom view may be empty if the structure being selected does not carry 3D coordinate information.

Best Friends (Incoming)

3D Coordinates (20 %)
Molecule to CDK (7 %)
RDKit Optimize Geometry (5 %) Streamable
SDF Reader (5 %)
RDKit Open 3D Alignment (3 %)
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Best Friends (Outgoing)

2D/3D Scatterplot (50 %)
Network Viewer (50 %)

Installation

To use this node in KNIME, install KNIME-CDK from the following update site:

KNIME 4.3

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

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Developers

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