Similarity Calculator (FTrees)

Computes an FTrees similarity matrix based on your query and library molecules.
For each query three columns are added to the table containing the total similarity to that query, as well as the individual feature similarity scores and smiles of the respective matching features. The feature scores and feature smiles are semicolon-separated vectors stored as simple text.

FTrees has to be licensed separately, see http://www.biosolveit.de/FTrees for more details.

Options

Query column
The molecules provided in this column are used as queries for the FTrees comparison. Accepted molecule formats are sdf, mol2 or smiles.
Library column
The molecules provided in this column are compared to the query molecules. Accepted molecule formats are sdf, mol2 or smiles.
Similarity threshold
Only those library molecules exceeding the similarity threshold will be piped into the output matrix. If you want to retrieve a result for every molecule, set this value to zero.
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.

Append input columns
Append the corresponding input table row to each result table row.
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.
Generate similarity images (significantly slower)
Enable similarity view. The similarity images will also be shown in the output table (similarity matrix), to the right of each query score column.

Note: When having enabled the view option, execution time will be significantly slower!

Input Ports

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

Output Ports

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Similarity Matrix: Output table that contains the FTrees similarity matrix. The score columns are named "Query 1", "Query 2", etc. The original query molecule names are annotated to the corresponding columns in the "Properties" tab of the similarity matrix result table.
The feature scores and feature smiles columns are named "Feature Scores Q1", "Feature Scores Q2", etc, and "Feature Smiles Q1", "Feature Smiles Q2", etc.
When having enabled "similarity view / images", the similarity images will be shown to the right of each query score column.

Popular Predecessors

Popular Successors

Views

Similarity View
Display each query-library-pair with a similarity higher than the requested threshold in a side-by-side 2d image.

Note: When having enabled the view option, execution time will be significantly slower!

Workflows

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Links

Developers

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Installation

To use this node in KNIME, install the extension BioSolveIT FTrees for Knime from the below update site following our NodePit Product and Node Installation Guide:

v5.2
Plugin provider: BioSolveIT GmbH
Plugin version: 2.29.3.202309291626
On NodePit since: 2023-12-06
Last update: 2024-04-17
KNIME versions: Since v3.6

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