Edit Feature Dialog Box

Summary
Opening the Edit Feature Dialog Box
Using the Edit Feature Dialog Box
Edit Feature Dialog Box Features
Related Topics

Summary

The Edit Feature dialog box allows you to edit the feature that the ligand must match. Features are defined in terms of SMARTS patterns. You can add patterns, edit and delete custom patterns, and you can exclude patterns in a feature definition.

Opening the Edit Feature Dialog Box

To open the Edit Feature dialog box, you can:

Click Edit Feature in the Constraints tab of the Ligand Docking panel.

Using the Edit Feature Dialog Box

Loading and Saving Feature Sets

Built-in feature sets are stored with the distribution.

You can import a feature set for the selected constraint from a file by clicking Import, and navigating to the feature file. When you import a feature set, the definitions of all features are replaced, not just the selected feature. The feature definitions are replaced only for the selected constraint, but are replaced for that constraint in all groups.

Feature sets can be saved to a file by clicking Export, and specifying the file location in the file selector that is displayed.

The patterns that define a feature are displayed in the Pattern list table when you choose the feature from the Feature option menu.

Adding, Editing, and Deleting Patterns

If the patterns in a given feature definition do not cover all the functional groups that you want to include in the feature, you can add extra patterns. To add a new SMARTS pattern, click the table row above which you want the pattern to be inserted, then click New. In the New Pattern dialog box, you can enter a SMARTS pattern and enter the atom numbers in the pattern that must satisfy the constraint.

To edit a pattern, select the table row for the pattern, then click Edit. In the Edit Pattern dialog box, you can modify the SMARTS pattern and the atoms in the pattern that must match.

To delete a pattern, select the table row for the pattern, then click Delete.

Setting the Status of Patterns

Matching of patterns to ligand structures is done in the order specified in the Pattern list table. You cannot change the order of the patterns once they are in the table, so you must add new patterns in the appropriate place. If you want to move patterns, you must delete them then add them back in the appropriate place. Excluded patterns are processed first, regardless of their position in the table.

If you want to ensure that certain functional groups are not matched, you can select the check box in the Exclude column for the pattern for that group. For example, you might want to exclude a carboxylic acid group from being considered as a hydrogen bond donor, because it will be ionized under physiological conditions.

Visualizing Patterns

If you want to see a pattern for a given ligand or group of ligands, you can select the check box in the Mark column for the pattern. Any occurrences of the pattern are marked in the Workspace.

Feature controls

This section has three controls:

Feature option menu

Select a feature type. The selected feature type is assigned to the constraint and appears in the Available constraints table of the Constraints tab. The patterns that define the selected feature type are listed in the Pattern list table. You must select a feature type to edit its definition. The available feature types are:

Acceptor—Neutral or charged acceptor.
Charged Acceptor—Acceptor that has a formal charge. Includes O⁻, S⁻, F⁻, Cl⁻.Both oxygens in a carboxylate are included as charged acceptor atoms.
Neutral Acceptor—Acceptor that does not have a formal charge. Includes a range of groups containing N and O.
Acceptor Including Halogens—Neutral or charged acceptor or a neutral halogen (F, Cl, Br, I).
Donor—Hydrogen attached to any neutral nitrogen, oxygen or sulfur; also includes OH⁻
Donor Including Aromatic H—Donor as defined above and any hydrogen attached to an aromatic carbon.
Donor Including Halogens—Donor as defined above and any neutral halogen other than F. Halogens can make nonbonded interactions with acceptor groups.
Donor Including Aromatic H + Halogens—Donor, hydrogen attached to aromatic carbon, or halogen, as defined above.
Hydrophobic—A range of patterns of aliphatic and aromatic carbons, and neutral halogens other than F.
Custom—Specify your own feature type by defining SMARTS patterns that match the feature.

Import button

Opens a file selector in which you can browse for feature files. (Note: the feature file format changed for the 2014-3 release, so feature files from earlier releases cannot be read in.)

Export button

Opens a file selector in which you can browse to a location to write a feature file.

Pattern list table

The Pattern list table lists all the patterns that are used to define the feature. You can only select one row at a time in the table, and the text fields are not editable. The table columns are described below.

Mark: Column of check boxes. Selecting a check box marks the pattern on any structures that are displayed in the Workspace.
Pattern: Pattern definition. The definitions are SMARTS strings.
Atoms: The list of atoms that must satisfy the constraint, numbered according to the SMARTS string.
Exclude: Column of check boxes. If a check box is selected, atoms in a ligand are matched by other patterns only if they do not match this pattern. This is essentially a NOT operator. Excluded patterns are processed before other patterns.

Pattern editing buttons

New button: Opens the New Pattern dialog box, in which you can enter a SMARTS pattern and choose the atoms that are used to match the ligand feature.
Edit button: Opens the Edit Pattern dialog box, in which you can edit the selected pattern.
Delete button: Deletes the selected pattern.