SlideShare a Scribd company logo
© 2018 KNIME AG. All Rights Reserved.
Chemistry Data Basics
with KNIME Analytics Platform
© 2018 KNIME AG. All Rights Reserved. 2
Chemistry basics
• Chemistry formats
• Standardization
• Saving files
© 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
© 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
© 2018 KNIME AG. All Rights Reserved. 5
Using knime:// URLs in file dialogs
Convenient and portable approach to reference files
in workflows.
© 2018 KNIME AG. All Rights Reserved. 6
Nodes for reading and writing files
Reader and writers provided for:
- sdf, smiles, mol, mol2
© 2018 KNIME AG. All Rights Reserved. 7
A bit more about reading SD files
© 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
© 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)
© 2018 KNIME AG. All Rights Reserved. 10
Standardization
• Generate canonical SMILES
© 2018 KNIME AG. All Rights Reserved. 11
Saving files with writer nodes
Reader and writers provided for:
- sdf, smiles, mol, mol2
© 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© 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.

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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.