Edit Feature Dialog Box DEPRECATED

The Edit Feature dialog box allows you to edit a 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.

To open this dialog box, click Edit Feature in the Receptor subtab of the Constraints tab in the Ligand Docking panel.

  • Using
  • Features
  • Additional Resources

Using the Edit Feature Dialog Box

Changing the feature type

To change only the feature type assigned to the constraint, choose the feature type from the Feature menu, and click OK. The change applies to all groups.

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 Feature, 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 Feature, 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 DEPRECATED, 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 DEPRECATED, 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.

You should make sure that you have a suitable molecule, such as a known active ligand, in the Workspace. Getting the SMARTS pattern from the selection can be slow if large molecules, such as a receptor, are displayed in the Workspace. The molecule should be displayed before you open the Edit Feature dialog box.

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. Excluded patterns are processed first, regardless of their position in the Pattern list table. Thus, an excluded pattern prevents the atoms that match it from being matched by any other pattern.

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.

Edit Feature Dialog Box Features

Feature controls

In this section you can choose the feature type, add and delete custom features, and import and export feature definitions.

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, Custom-n—Specify your own feature type by providing SMARTS patterns that match the feature. By default, three custom features are available on this menu, labeled Custom, Custom-2 and Custom-3.

The donor or acceptor feature type is coordinated with the settings for aromatic and halogen H-bonds in the Settings - Advanced Settings Dialog Box DEPRECATED. A change in either place changes the setting in the other.

Add Custom Feature button

Add a custom feature to the Feature menu, labeled Custom-n, where n is chosen to make the label unique.

Delete Custom Feature button

Delete the selected custom feature, which must be labeled Custom-n. You cannot delete the custom feature labeled Custom.

Import Feature button

Import a set of features for the selected constraint. All feature definitions are replaced. 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.)

When you import a feature set, the definitions of all feature types are replaced, not just the feature type chosen from the Feature option menu. The feature definitions are replaced only for the selected constraint, but they are replaced for that constraint in all groups.

Export Feature button

Export the current set of feature definitions to a file. Opens a file selector in which you can browse to a location to write the 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. You can display markers for more than one pattern, but the markers do not distinguish between patterns.

Pattern

Pattern definition. The definitions are SMARTS patterns.

Atoms

The list of atoms that must satisfy the constraint, numbered according to the SMARTS patterns: atom 1 is the first atom in the SMARTS pattern, and so on.

For positional, metal, and H-bond constraints, you can specify multiple atoms, but only one of the specified atoms is constrained. Normally, only one atom should be specified, to ensure that the correct atom is constrained. However, if the functional group contains multiple acceptors or donors, for example, you can specify all of them if you want any one of them to be constrained. This is not necessary for groups such as carboxylates, where the local symmetry of the functional group is used and either of the oxygen atoms in the carboxylate can be selected for the constraint, even though only one of them is specified.

For hydrophobic constraints, the non-hydrogen atoms of the hydrophobic group should be specified. The number of atoms that is constrained is specified in the Required Ligand Atoms column of the Available constraints table, in theReceptor tab of the Ligand Docking Panel DEPRECATED.

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 DEPRECATED, 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 DEPRECATED, in which you can edit the selected pattern.

Delete button

Deletes the selected pattern.

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