How can I remove duplicates from a set of ligand-like structures?

To remove duplicates, you can use one of the following methods:

• Run $SCHRODINGER/utilities/uniquesmiles. This utility has three options for handling duplicates.
• Use the Unique Smiles node in KNIME, which is under Schrödinger → Tools. The node has two output ports, one of which is for the duplicates. There is also a duplicates option in the node configuration.
• Use the Python script "Compare ligands in different files" from the Script Center. This script has four options for structure retention.

Several other methods are available in Suite 2012:

• In Maestro, use the Merge Duplicates panel (Tools → Merge Duplicate Ligands). This produces a list of SMILES strings for the unique structures and writes them to a new file.
• In Canvas, you can remove duplicate structures from a file when you import it, by selecting Skip duplicate structures. Any structure that duplicates a structure that has already been read is discarded. If the structure already exists in the Canvas project, you can update it with the structure (and properties) from the file by selecting Update existing records. You can then export the structures in the project to obtain a file without duplicates.
• In Canvas, you can identify duplicate structures by choosing Structure → Detect Duplicates. Two properties, "Has duplicate" and "Duplicate of" are added to the project, specifying the row number (ID) of the duplicate. You can then select the rows that are not duplicates and export the unique structures to a file.

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