📥
ChEMBL Data Deposition Guide
  • Introduction
  • Overview
    • Source Identifier
    • Depositor-Defined Identifiers
      • AIDX
      • RIDX
      • CIDX
    • File types and names
  • File structure
    • File hierarchy
    • Simplified input data schema
    • Deposition file list
    • Field names and data types - basic submission
      • The CONTACT field
      • ACTION_TYPE valid names
      • TARGET_TYPE list
      • Adding context using the ACTIVITY_PROPERTIES file
    • The ASSAY_DESCRIPTION field
  • Complex results sets
    • Linking files through depositor defined IDs
    • Linking multiple result types using TEOID
    • Supplementary data in the ACTIVITY_SUPP file
    • Flexible SAMID mapping
    • Field names and data types - more complex data types
  • Example dataset
  • Common data issues
  • Advanced features and documentation
  • Depositing activities against other depositors entities
  • Creating a COMPOUND_CTAB file from a file containing SMILES strings
  • FAQs
  • Glossary
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  • Using KNIME
  • Using a Jupyter Notebook

Creating a COMPOUND_CTAB file from a file containing SMILES strings

If you need to create the file but you only have your compound structures as SMILES strings.

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Last updated 1 year ago

We provide an examble 2-column Excel workbook to show how input data should be organised for these tools.

Using KNIME

Install KNIME, which you can find here. Open the workflow in KNIME. KNIME will prompt you to let it install the plugin dependencies for this workflow.

Double-click the first node and change the File path to wherever you downloaded the CIDX_SMILES.xlxs file to.

Double-click the final node and change the File path to wherever you would like the output to go to.

Select the final node again and either press the execute button (right-facing triangle) or press F7 to run the workflow. At this point you will probably want to save the workflow to keep your own file paths.

Using a Jupyter Notebook

If you are more familiar with coding, we also have a Jupyter notebook tool here.

https://www.knime.com/installation
81KB
smiles2SDF.knwf
4KB
smiles2SDF_RDKit.ipynb
82KB
CIDX_smiles.xlsx