Matching SMARTS patterns of unwanted moieties to a chemical spreadsheet.

[Andrew Orry]

Q: Can I supply a list of ~100 SMARTS patterns (of unwanted moieties) to automatically mark/select/remove all matching compounds in a chemical spreadsheet of 500,000 compounds—without generating a separate column for each SMARTS?

A: Yes, you can. Here's how:

1. Prepare a table of SMARTS patterns (e.g., from a CSV file).

2. Load the SMARTS table as a chemical table in ICM.

3. Convert the SMARTS column to a chemical column by right-clicking the column header and selecting "Convert."

4. Add a LABEL column to your SMARTS table. This can contain any identifier (e.g., text or numbers 1,2,3,...). These labels will appear in the annotation results.

Once your SMARTS table is ready:

1. Load your large compound table (e.g., 500,000 compounds) into ICM.

2. Go to Chemistry > Annotate by Substructure.

3. Switch to the Custom Fragments tab.

4. Select:

   • The compound table you want to annotate.

   • Your SMARTS table as the fragment source.

The result will be a single column with comma-separated matches for each compound row—no need to generate one column per SMARTS