0 ×

SDF Writer

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

This node writes SDF or Mol cells into a continuous SDF file. You may also add additional properties from columns to the SDF molecules while they are written out.


Default Settings

The path to the output file.
Overwrite OK
If unchecked, the node refuses to execute when the output file exists (prevent unintentional overwrite).
Structure column
Select the column containing the structures that should be written to the output file here. You can select SDF, Mol or Ctab columns. For Ctab column it is mandatory to also select a title column, see below.
Use column as molecule title
If selected, the molecules' titles will be exchanged by the values in the selected column or the row ID.
Omit properties with missing values
If selected, columns that contain missing values are not inserted into the molecule as properties but rather they are omitted. Otherwise they will be inserted but with an empty value.
Add 'no structure' molecules for missing values
If selected, rows with missing molecule entries are written as molecules with no structure into the file. Otherwise missing molecules are simply ignored and not written into the file.
Insert Properties
Select the columns that should be used as properties in the output file. If the structure column is a SDF column and a property already exists in the SDF block, it will be overwritten by the values in the selected column.


File Encoding
To write an SDF file with a different encoding, you can select a character set in this tab (UTF-8, UTF-16, etc.) or specify any other encoding supported by your Java VM. By default, the node uses US-ASCII (7 bit encoding).

Input Ports

A table with at least an SDF or Mol column

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.

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.


You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.