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SDF Extractor

KNIME Chemistry Base nodes version 4.3.0.v202011191214 by KNIME AG, Zurich, Switzerland

This node allows you to extract the different parts an SDF molecule is made up of - Ctab block, Molfile block and data properties - into columns. The properties will be extracted into different columns. In order to find out, which properties are present in the SDF structures, the node will by default scan the first 100 structures. If this is not enough to determine all properties and their types, you can enable a full scan of the input table.


SDF column
The column containing the SDF molecules.
Extract properties
Select this, if you want to extract the data properties into different columns
Scan whole table
Scans the full input table instead of the first 100 rows in order to determine the properties and their types
Extract Molfile block
Select this, if you want to extract the Molfile block into a column
Molfile column name
The new column's name that contains the Molfile blocks afterwards
Extract Ctab block
Select this, if you want to extract the Ctab block into a column
Ctab column name
The new column's name that contains the Ctab blocks afterwards

Input Ports

Table with the SDF molecules

Output Ports

Table with additional columns containing the extracted parts

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install KNIME Base Chemistry Types & Nodes from the following update site:


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

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