Chemistry Data Basics with KNIME Analytics Platform
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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
- 1. © 2018 KNIME AG. All Rights Reserved. Chemistry Data Basics with KNIME Analytics Platform
- 2. © 2018 KNIME AG. All Rights Reserved. 2 Chemistry basics • Chemistry formats • Standardization • Saving files
- 3. © 2018 KNIME AG. All Rights Reserved. 3 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
- 4. © 2018 KNIME AG. All Rights Reserved. 4 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 4 YouTube KNIME TV Channel video: https://youtu.be/flaHQw-Qhlg
- 5. © 2018 KNIME AG. All Rights Reserved. 5 Using knime:// URLs in file dialogs Convenient and portable approach to reference files in workflows.
- 6. © 2018 KNIME AG. All Rights Reserved. 6 Nodes for reading and writing files Reader and writers provided for: - sdf, smiles, mol, mol2
- 7. © 2018 KNIME AG. All Rights Reserved. 7 A bit more about reading SD files
- 8. © 2018 KNIME AG. All Rights Reserved. 8 Sketching chemical structures – use Marvin MarvinSketch • Provided by Chemaxon/Infocom • Sketch structures in the configuration dialog • Execute node to inject structures into workflow
- 9. © 2018 KNIME AG. All Rights Reserved. 9 Nodes for type manipulation 9 9 • 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)
- 10. © 2018 KNIME AG. All Rights Reserved. 10 Standardization • Generate canonical SMILES
- 11. © 2018 KNIME AG. All Rights Reserved. 11 Saving files with writer nodes Reader and writers provided for: - sdf, smiles, mol, mol2
- 12. © 2018 KNIME AG. All Rights Reserved. 12 Additional Resources 12 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
- 13. 13© 2018 KNIME AG. All Rights Reserved. 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.