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
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 (8 %)
- Molecule to CDK (7 %)
- RDKit Optimize Geometry (7 %) Streamable
Scorer(5 %) Deprecated- Loop End (3 %)
- 3D RMSD (3 %)
- Tautomer Generator (2 %)
- Generate 3D Coordinates (2 %)
- PDB Reader (2 %)
- MarvinSketch (2 %)
- MolConverter (2 %) Streamable
- CSV Reader (2 %)
- k-Means (2 %)
K Nearest Neighbor(2 %) StreamableDeprecated- Concatenate (2 %) Streamable
Column Appender(2 %) StreamableDeprecated- Column Resorter (2 %) Streamable
- Column Filter (2 %) Streamable
- Row Filter (2 %) Streamable
- GroupBy (2 %)
- Joiner (2 %)
- Denormalizer (2 %) Streamable
- Partitioning (2 %)
- Sorter (2 %)
- Molecule Type Cast (2 %) Streamable
- SDF Extractor (2 %)
- Molfile Reader (2 %)
- SDF Reader (2 %)
- Smiles Directory Reader (2 %)
- OpenBabel (2 %)
Excel Reader (XLS)(2 %) StreamableDeprecatedExcel Reader (XLS)(2 %) StreamableDeprecated- Table View (2 %)
- Image Cropper (2 %) Streamable
- Python Script (1⇒2) (2 %)
- 3D D-Similarity (2 %)
- Molecular Properties (2 %)
- Fingerprints (2 %)
- Structure Sketcher (2 %)
- RDKit Add Conformers (2 %)
- RDKit Add Hs (2 %) Streamable
- RDKit Canon SMILES (2 %) Streamable
- RDKit Interactive Table (2 %)
- RDKit From Molecule (2 %)
- RDKit Open 3D Alignment (2 %)
- RDKit RMSD Filter (2 %)
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Installation
To use this node in KNIME, install KNIME-CDK from the following update site:
Developers
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