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RDKit Salt Stripper

RDKit Nodes for Knime version 3.8.0.v201906261723 by NIBR

This node is used for removing salts from RDKit molecules and display the salt stripped molecules in an additional column in the output table. The user can optionally input salt definitions into the node. If no salt definition table is provided by the user then the default salt definitions will be applied.

Options

RDKit Mol column
The name of the column in first table containing RDKit molecules for stripping.
New column name
The new name of the column that will contained the salt stripped molecule.
Remove source column
Toggles removal of the input RDKit Mol column in the output table.
Salt definition column
The name of the column in the optional second table containing RDKit molecules as salt definitions (generated usually from SMARTS). This only applies, if a second table is connected.
Keep only largest fragment after salt stripping
Option to reduce the salt stripping outcome even more keeping only the largest fragment of all remaining fragments. If there are multiple fragments with the same number of atoms identified as largest fragments, it will keep only the first one it encounters.

Input Ports

Table having at least one RDKit molecule type column containing RDKit molecules for stripping.
Table containing RDKit molecules as salt definitions (generated usually from SMARTS). This table is optional.

Output Ports

Table containing the column with salt stripped RDKit molecules.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install RDKit KNIME JUnit Test from the following update site:

KNIME 4.0
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