This document provides an overview of working with chemistry data in KNIME Analytics Platform. It introduces common chemistry formats like SMILES, SDF, MOL and MOL2 that can be used in KNIME. It describes nodes for reading, writing and converting between file formats, as well as standardizing structures. The File Reader node is highlighted as the workhorse for importing text-based files. Sketching structures using MarvinSketch in node configurations is also covered. Additional resources for learning more about chemistry in KNIME are listed at the end.

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Chemistry Data Basics
with KNIME Analytics Platform

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Chemistry basics
• Chemistry formats
• Standardization
• Saving files

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Overview of types in KNIME
• Basic KNIME types
• string, integer, double
• KNIME core chemistry types:
• smiles, sdf, mol, mol2
• Structures in these formats
can be rendered in KNIME
tables

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New Node: File Reader
Workhorse of KNIME Source nodes
• Reads text based files
• Many advanced features allow it to read most ‘weird’ files
• Short lines, inline comments, headers, and special encoding
• Distinguishes smiles and smarts formats
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YouTube KNIME TV Channel video:
https://youtu.be/flaHQw-Qhlg

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Using knime:// URLs in file dialogs
Convenient and portable approach to reference files
in workflows.

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Nodes for reading and writing files
Reader and writers provided for:
- sdf, smiles, mol, mol2

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A bit more about reading SD files

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Sketching chemical structures – use Marvin
MarvinSketch
• Provided by Chemaxon/Infocom
• Sketch structures in the configuration dialog
• Execute node to inject structures into workflow

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Nodes for type manipulation
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• Molecule Type Cast
• Casts any string as a chemical type (i.e. It
tells KNIME “This is a smiles string”)
• Useful when reading data form a csv file or
database.
• Marvin MolConverter
• Provided by Chemaxon/Infocom
• Translates seamlessly between types
(smiles ó sdf ó mrv)

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Standardization
• Generate canonical SMILES

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Saving files with writer nodes
Reader and writers provided for:
- sdf, smiles, mol, mol2

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Additional Resources
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KNIME pages (https://www.knime.com)
• SOLUTIONS for example workflows
• RESOURCES/LEARNING HUB https://www.knime.com/learning-hub
• RESOURCES/NODE GUIDE https://www.knime.com/nodeguide
• Book WILL THEY BLEND https://www.knime.com/knimepress/will-they-blend
KNIME Tech pages
• FORUM for questions and answers https://forum.knime.com
• DOCUMENTATION for docs, FAQ, changelogs, ...
• COMMUNITY CONTRIBUTIONS for dev instructions and third party nodes
KNIME TV on YouTube https://www.youtube.com/user/KNIMETV

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The KNIME® trademark and logo and OPEN FOR INNOVATION® trademark are used by
KNIME.com AG under license from KNIME GmbH, and are registered in the United States.
KNIME® is also registered in Germany.