Merge Duplicates Panel

Combine a set of structures into a single file with elimination of duplicates. The elimination is done by comparing SMILES strings, and the output is either a SMILES file or a 2D SD file; in either case the output contains no 3D information other than chirality properties.

To open this panel: click the Tasks button and browse to Project Table and Project Operations → Merge Duplicate Ligands.

  • Features

Merge Duplicates Panel Features

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
Open Project Table button

Open the Project Table panel, so you can select the entries for the structure source.

File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Merge properties option

When a property has a value for more than one structure in a set of duplicates, concatenate the values of the property into a comma-separated list. The property with all its values is then preserved as a string. If this option is not selected, one of the values is chosen. This applies only to properties that duplicates have in common: properties that are unique to one of the set are kept as they are.

Desalt before merging option

Remove small molecules such as solvent or ions before merging, so that only the ligand-sized molecule remains.

Neutralize before merging option

Protonate or deprotonate the structures so that they have a zero net charge before merging. This ensures that duplicates that differ only in the ionization state are eliminated.

Output format option

Choose the output format for the structures.

  • 2D SD—Write 2D structures with properties to an SD file.
  • SMILES—Write SMILES strings only to a .smi file with a title. No properties are kept.
  • SMILES CSV—Write SMILES strings with properties to a .csv file.