Chemical Space Searcher (FTrees)

Search an FTrees Chemical Space for molecules that are similar to the given query molecules. For each query a limited number of best matching similar molecules will be found.

FTrees has to be licensed separately, see for more details.


Query column
The molecules provided in this column are used as queries for the FTrees comparison. Accepted molecule formats are sdf, mol2 or smiles.
Chemical space
Specify a chemical space (*.space) generated by the CoLibri nodes.
Minimum similarity
Only those library molecules exceeding the minimum similarity will be piped into the output matrix. If you want to retrieve a result for every molecule, set this value to zero.
Target similarity
The desired similarity of the result molecules to the query. Typically, results are required that are not perfectly similar to the query. Alter this parameter to vary how similar to the query the results are allowed to be. The lower the value, the more varied the resulting molecules will be from the query.
Total diversity
Required diversity between any two compounds in a Feature Tree Fragment Space solution set. Values from 0.9 to 1.0 are allowed.

Note: Only available if number of results is <= 500.

Warning: Any value below 1.0 drastically extends the run time.

Maximum number of results
The number of results you want to generate.

The total number of returned library molecules with score is limited to the best ranking 100,000, so this is the highest number you can enter with this option.

Keep debug files and show the log after the run
This setting keeps all temporary files and opens an editor to show the output of the external program. This setting is very helpful for debugging.

Input Ports

Query: Input table with at least one column containing a molecule in sdf, mol2 or smiles format.

Output Ports

Similarity Matrix: Output table that contains the FTrees similarity score for each found molecule from the space.


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