Rxn/RD Reader

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

This node reads one or more Rxn/RD files and creates several columns with each reaction in a new row. You can select which parts of the reaction should be extracted into columns in the output table.
RD file support is limited to embedded Rxn files ($RFMT entries) and not thoroughly tested because of the lack of publicly available RD files. Moreover, it only extracts the Rxn-parts from the RDfiles.

Options

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.

Use reaction name as row ID

Instead of generating row IDs, the reactions'' names are taken as row IDs. You have to make sure, that the names are unique, otherwise the node will fail.

Extract reaction name

If selected, the reactions' names are put into a column called 'Reaction 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 reaction.

Extract counts

If you are interested in the reactant and products counts as they are stored inside the file you can select this option.

Output Ports

Table with the read reactions

Table with illegal Rxn records

Best Friends (Incoming)

• Table Row To Variable Loop Start (100 %) LoopStart

Best Friends (Outgoing)

• RDKit Two Component Reaction (100 %) Manipulator
• Combinatorial Library (< 1 %) 
• MolConverter (< 1 %) ManipulatorStreamable
• String to Molecule (< 1 %) Manipulator
• SDF Writer (< 1 %) Sink
• OpenBabel (< 1 %) Manipulator
• RDKit Chemical Transformation (< 1 %) Manipulator
• Show all 7 recommendations

Update Site

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