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"babel -o fpt ..." Command - Similarity Search
How to use "babel -o fpt ..." command to do similarity search?
✍: FYIcenter.com
You can use the "fpt" output file format with the "babel" command to
do similarity search using the following syntax:
babel input_section -o fpt
When you run the above commands, Open Babel will perform the following:
Example 1 - If the query molecule is stored as the first molecule in file with object molecules, you can do similarity search with a shorter syntax as shown below:
babel mymols.sdf -o fpt MOL_00000067 MOL_00000083 Tanimoto from MOL_00000067 = 0.810811 MOL_00000105 Tanimoto from MOL_00000067 = 0.833333 MOL_00000296 Tanimoto from MOL_00000067 = 0.425926 MOL_00000320 Tanimoto from MOL_00000067 = 0.534884 MOL_00000328 Tanimoto from MOL_00000067 = 0.511111 MOL_00000338 Tanimoto from MOL_00000067 = 0.522727 MOL_00000354 Tanimoto from MOL_00000067 = 0.534884 MOL_00000378 Tanimoto from MOL_00000067 = 0.489362 MOL_00000391 Tanimoto from MOL_00000067 = 0.489362 10 molecules converted
The similarity score output shows that molecule MOL_00000105 is the most similar molecule to molecule MOL_00000067 with the best similarity score of 0.833333.
Example 2 - If the query molecule is stored in file separately from the object molecule file, you can do similarity search with a more clear syntax as shown below:
babel query.sdf mymols.sdf -o fpt MOL_00000067 Tanimoto from first mol = 0.0888889 MOL_00000083 Tanimoto from first mol = 0.0869565 MOL_00000105 Tanimoto from first mol = 0.0888889 MOL_00000296 Tanimoto from first mol = 0.0714286 MOL_00000320 Tanimoto from first mol = 0.0888889 MOL_00000328 Tanimoto from first mol = 0.0851064 MOL_00000338 Tanimoto from first mol = 0.0869565 MOL_00000354 Tanimoto from first mol = 0.0888889 MOL_00000378 Tanimoto from first mol = 0.0816327 MOL_00000391 Tanimoto from first mol = 0.0816327 11 molecules converted
The similarity score output shows that molecules MOL_00000067, MOL_00000105, MOL_00000320, MOL_00000354 are 4 most similar molecules to the molecule stored in "query.sdf" with the best similarity score of 0.0888889.
⇒ Fingerprint Types Supported in Open Babel
⇐ Similarity Search with Open Babel
2020-12-15, 832👍, 0💬
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