SDF Reader

This node reads an SDF file and creates several columns with each molecule in a new row. You can select which parts of the molecule should be extracted into columns in the output table. By default only the molecular structure is exported, but in the second tab you can select if and which properties from the SD-file should be extracted into columns of the output table.

Options

File selection

Input sources: Here you can select several input sources. They can be files (selectable with the Browse-button) or an URL. You can delete or reorder the source locations in the list. Empty location will be ignored.
Limit number of read molecules: This option lets you limit the number of molecules that will be read by the node.
Use molecule name as row ID: Instead of generating row IDs, the molecule's names are taken as row IDs. You have to make sure, that the names are unique, otherwise the node will fail.
Extract molecule name: If selected, the molecules' names are put into a column called 'Molecule name' in the output table. This option can be used together with the previous one.
Add column with source location: Enabling this option will add a column showing the source location for each molecule.
Extract SDF blocks: If the complete molecule, starting from the title up to the magic $$$$ should be extracted into a column, select this check box.
Extract Mol blocks: If you are interested in the molecules' Mol blocks (i.e. without the properties) you can select this option in order to extract a column containing the Mol blocks.
Extract Ctab blocks: If you are interested in the molecules' Ctab blocks (i.e. without the header and properties) you can select this option in order to extract a column containing the Ctab blocks.
Extract counts: If you are interested in the molecules' atom and bond counts as they are stored inside the Ctab block you can select this option in order to extract two column containing the atom and bond counts.

Property handling

Extract all properties: If this option is enabled, all source location will be scanned for all existing properties during execution. All found properties will be added to the output table. Please note that this requires two scans over all sources during execution.
Properties: If you want to extract the properties inside the SDF file into separate columns, you first have to scan the file for the properties. If you have a big file and know, that all molecules contain the same properties, you may stop scanning before the whole file has been analyzed. The table will show all found properties together with their suspected type. You may then select, which properties you want to extract. It is possible to change the properties' types, but you should only change to a more general type (Integer → Double → String), otherwise errors will very likely occur.

Encoding

File Encoding: To read 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 (7bit encoding).

Input Ports

This node has no input ports

Output Ports

: Table with the read molecules
: Table with illegal SDF records

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Installation

To use this node in KNIME, install the extension KNIME Base Chemistry Types & Nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.9

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

Plugin provider: KNIME AG, Zurich, Switzerland

Plugin version: 5.9.0.v202511130853

On NodePit since: 2025-12-11

Last update: 2026-01-21

KNIME versions: Since v3.6

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