Chemical Structures File Reader

Use this node to read chemical structures stored on your hard drive. Different file formats are supported. These include, but are not limited to, Chemical Markup Language (CML) files; a number of Symyx (former MDL) formats - mol, sdf, rdf; SMILES; Tripos mol2 files; pdb; xyz; etc. See for an extensive list.


Select file(s)
Use the Add and Remove buttons to add to the list of files to process. Changing the list will automatically tigger a scan in either shallow or deep mode.
Scan Depth
Shallow scan is the first 10 records of each file, whilst a deep scan will scan each file completely for properties.
Properties to keep
All molecular properties found in the first 10 records of the input file are presented in the left-hand side list. Use the provided controls to select the properties you are interested in. These will be read and stored in the output of the node. Note that all properties are treated as strings - in the likely case that some or all of the properties are numeric you may use the 'String To Number' node. The 'String To Number' node is part of the default KNIME installation and may be found under the category 'Data Manipulation | Column'.
Output options -> General -> Aromatize molecules
Select this option if you want the read chemical structures to be aromatized using the default Chemaxon algorithm. Recommended.
Output options -> Additional columns
In addition to the "native" Chemaxon Molecule object a number of columns containing different text-based representations of the read molecules can be created as well. These are useful when an interaction with another chemoinformatics package is needed. For example, to use this reader with the CDK library (since it supports much more file formats) you can output an SDF column which can than be processed by CDK.

Input Ports

This node has no input ports

Output Ports

The read chemical structures are output here. A column containing Chemaxon Molecule objects is always present. Depending on the configuration, a number of other columns - representing the read molecules in another string-based format or containing properties read from the input file - may be present as well.
The chemical molecules that failed to read are output here.


Read Molecules
View the read molecules with MarvinView.


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