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SDF Reader

KNIME Chemistry Base nodes version 3.7.0.v201808081048 by KNIME AG, Zurich, Switzerland

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.

Output Ports

Table with the read molecules
Table with illegal SDF records

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 3.7
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