Compare Ligand Sets

Compares and writes a file that contains a subset of structures in file1 and file2, depending on the selected mode

compare_ligand_files.py
The script compare_ligand_files.py is used to implement this node.

Options

Include Input: All columns in the input table(s) are included in the output. For mode "first only", only the input tables from the first input are included. For modes both and either, both the input tables from the first and second input are included. For implementation, this node keeps a lookup for the input rows to match the output molecule with the input. If there is more than one match, then the input of the last version of the molecule is included in the output.
Criteria: Criteria to determine uniqueness by titles(default), smiles, or field name (ex: i_user_foo)
Mode: Which structures to write out. firstonly(default), both, or either.
firstonly (default): Outputs structures from the first set that are not present in the second set.

both: Outputs structures from the first set that are also present in the second set.
Note: In "both" mode, what file you specify first does matter. The first input is compared with the second input and used in the output. Thus, the order of the inputs matter, since duplicates in the first input will also be duplicated in the output, but not the other way around.
either: Outputs structures that are present in one set but not the other.
Do not return multiple copies of each structure: Do not return multiple copies of each structure. This option can also be used to find unique structures in a single list of structures, assuming this list is used for both inputs.

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

v5.5

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 25.2.133.v202505021925

On NodePit since: 2025-07-04

Last update: 2025-07-23

KNIME versions: v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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