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Mol2 Reader

KNIME Chemistry Base nodes version 4.4.0.v202104131254 by KNIME AG, Zurich, Switzerland

This node reads a Mol2 file and creates a column with each molecule in a new row. The molecules' names are used as row IDs as long as they are unique (otherwise an artificial name is created based on the row index).


The path to the input file
Generate row IDs
Instead of using the molecule names in the Mol2 file, auto-generated row IDs are created.

Output Ports

Table with the read molecules

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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