Spark Fragment Selector
Cresset KNIME Nodes version 2.6.0.41359 by www.cresset-group.com
The Spark™ Fragment Selector takes the first molecule in the input and displays a dialog which allows the user to select the region of the molecule to replace. The output of this node should be connected to the input of the Spark Database Search node.
This node wraps the executable 'Spark', which must be installed with a valid license for this node to work. If this is installed in the default location on Windows, then it should be found automatically. Otherwise, you must either set the 'Cresset Home' preference or the CRESSET_HOME environment variable to the base Cresset software install directory. You may also set the 'Spark Path' preference or the CRESSET_SPARK_EXE environment variable to point directly at the executable itself.
For more information visit www.cresset-group.com or contact us at support@cresset-group.com.
Options
Basic
- Column containing molecule structures
- The column in the first input datatable containing the starter molecule which will have a region replaced. If there is more than one molecule in the file, then only the first one will be used as a starter molecule, while the others will be used as reference molecule(s) to guide the bioisosteric replacement experiment.
- Open Spark Selector
- Opens the Spark selector wizard. The starter molecule is displayed in the 2D view, while the 3D view shows both the starter and the reference molecule(s). Drag around a region of the molecule to select it for replacement or define an atom you want to grow from by clicking it with the left mouse button: this will display the attached Hydrogen atom which will be automatically be selected for replacement. Press 'OK' when you are happy with the selection. The results of the selection will be shown in the text field.
Input Ports
- The starter molecule which will have a region replaced. If there is more than one molecule in the file, then only the first one will be used as a starter molecule, while the others will be used as reference molecule(s) to guide the bioisosteric replacement experiment.
Output Ports
Best Friends (Incoming)
- SDF Reader (63 %)
- RDKit Diversity Picker (13 %)
- MAE-to-SD (13 %)
- Substructure Search (13 %)
Best Friends (Outgoing)
- Spark Database Search (77 %)
- Fragments from Molecules (15 %)
- Torch/Forge Molecule Viewer (8 %)
Workflows
R-group replacement using Spark (Cresset) - Replace a section of a molecule using Spark (Cresset)
Installation
To use this node in KNIME, install Cresset KNIME Nodes from the following update site:
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Developers
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