RDKit Functional Group Filter

This node can be used for filtering sets of molecules based on named substructures (functional groups based on SMARTS). Note that the default definitions are constructed to try and define functional groups relevant for reactivity; consequently groups like -CF3 do not match the halogen pattern.

Options

RDKit Mol column

It specifies which column contains the set of RDKit molecules.

Functional group definition file

File containing functional group definitions. This input is optional. Alternatively you may press "Load Defaults" to use default functional group definitions. Pressing the info button on the very right shows the content of the currently selected definitions incl. all SMARTS that describe the functional groups.

The "Load Custom..." button lets you define your own configuration in a dialog with the following options:

Read from:
Select a file system which stores the model you want to read. There are four default file system options to choose from:

• Local File System: Allows you to select a file from your local system.
• Mountpoint: Allows you to read from a mountpoint. When selected, a new drop-down menu appears to choose the mountpoint. Unconnected mountpoints are greyed out but can still be selected (note that browsing is disabled in this case). Go to the KNIME Explorer and connect to the mountpoint to enable browsing. A mountpoint is displayed in red if it was previously selected but is no longer available. You won't be able to save the dialog as long as you don't select a valid i.e. known mountpoint.
• Relative to: Allows you to choose whether to resolve the path relative to the current mountpoint, current workflow or the current workflow's data area. When selected, a new drop-down menu appears to choose which of the two options to use.
• Custom/KNIME URL: Allows to specify a URL (e.g. file://, http:// or knime:// protocol). When selected, a spinner appears that allows you to specify the desired connection and read timeout in milliseconds. In case it takes longer to connect to the host / read the file, the node fails to execute. Browsing is disabled for this option.

It is possible to use other file systems with this node. Therefore, you have to enable the file system connection input port of this node by clicking the ... in the bottom left corner of the node's icon and choose Add File System Connection port .
Afterwards, you can simply connect the desired connector node to this node. The file system connection will then be shown in the drop-down menu. It is greyed out if the file system is not connected in which case you have to (re)execute the connector node first. Note: The default file systems listed above can't be selected if a file system is provided via the input port.

File/URL:
Enter a URL when reading from Custom/KNIME URL, otherwise enter a path to a file. The required syntax of a path depends on the chosen file system, such as "C:\path\to\file" (Local File System on Windows) or "/path/to/file" (Local File System on Linux/MacOS and Mountpoint). For file systems connected via input port, the node description of the respective connector node describes the required path format. You can also choose a previously selected file from the drop-down list, or select a location from the "Browse..." dialog. Note that browsing is disabled in some cases:

• Custom/KNIME URL: Browsing is always disabled.
• Mountpoint: Browsing is disabled if the selected mountpoint isn't connected. Go to the KNIME Explorer and connect to the mountpoint to enable browsing.
• File systems provided via input port: Browsing is disabled if the connector node hasn't been executed since the workflow has been opened. (Re)execute the connector node to enable browsing.

Warning: Although technically the location can be set via a path flow variable, the filter will always deliver empty results, because the configuration file must be present at configuration time to select for it all active entries for the filter. This step would be missing when using a flow variable, which gets only processed at execution time of the node.

List of functional group filters

Defines the conditions for filtering molecules. Select the ones that needs to be applied on the molecules. If no filter pattern is selected, molecules are sent to the matching output table.

Recording of first non-matching pattern in new column

If checked, an additional column (the name can be specified) containing the first non-matching pattern is added to the table of failing molecules.

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