Compare Ligand Files Panel

Compare two sets of structures, either from files or selected entries in the Project Table, and return those structures that either occur in both sets, occur only in the first set and not the second, occur in only one of the sets, or occur in either set, without duplicates. The comparison is based on titles, SMILES strings, or connectivity.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Structure Analysis → Compare Ligand Files
  • Click the Tasks button and browse to Ligand Preparation and Library Design → Compare Ligand Files
  • Features

Compare Ligand Files Panel Features

First structure set options

Select an option for specifying the first structure set:

  • File—Use the specified file as the first structure set. Enter the file name in the text box, or click Browse and navigate to the file.
  • Selected entries—Use the entries that are selected in the Project Table as the first structure set. If you choose this option for the first set, you should not choose it for the second set.
Second structure set options

  • File—Use the specified file as the second structure set. Enter the file name in the text box, or click Browse and navigate to the file.
  • Selected entries—Use the entries that are selected in the Project Table as the second structure set. If you choose this option for the second set, you should not choose it for the first set.
Save options

Select an option for the structures to save in the output file:

  • Structures from the first set that are not in the second set—Keep the structures from the first set that do not match any of the structures in the second set.
  • Structures from the first set that are also present in the second set—Keep the structures from the first set that match structures in the second set. These are the structures that are the same in both sets.
  • Structures that occur only in one set but not the other—Keep the structures from each set that are not in both sets. These are the structures that differ between the sets. This is the logical complement of the previous option.
  • All structures from the first set plus all structures from the second set that are not also in the first set—Combine the sets and eliminate duplicates, keeping only the copy from the first set for structures that are the same in both sets.
Criteria options

Select an option for the criterion used to decide whether a structure from the first set is the same as a structure from the second set:

  • PropertyStructures that have the same value of the property specified in the text box are considered the same. The internal name of the property must be used.
  • SMILESStructures that have the same SMILES pattern are considered the same. The SMILES pattern is generated automatically.
  • Tautomer—Structures that are tautomers (or have identical connectivity) are considered the same.
Do not return multiple copies of each structure option

Select this option to ensure that only one copy of each structure appears in the output file. Although the Save options ensure that duplication between the two sets is eliminated, they do not eliminate duplicates within each set. This option ensures that duplicates within the sets are also eliminated.

Don't analyze the first structure from the input files (receptor) option

Select this option to skip the first structure in each set. This is useful when the file is a pose viewer file, or an entry group is chosen with a receptor as the first entry. As this option is applied to both sets, you must ensure that the first entry in each set should be ignored.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Compare Ligand Files - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Related Topics