Define Actives and Inactives Dialog Box

Assign ligands to the active set or the inactive set for pharmacophore model development from multiple ligands, and optionally set the activities of the ligands.

To open this dialog box, click the Define button in the Actives / Inactives Split section of the Develop Pharmacophore Model Panel.

  • Using
  • Features
  • Additional Resources

Using the Define Actives and Inactives Dialog Box

The primary task in this dialog box is to assign ligands to the active set for pharmacophore model development from multiple ligands. You can also assign ligands to the inactive set, which will be used in scoring and can be used to create excluded volumes. A secondary task is to assign activities to the ligands.

There are two main ways to make the assignment:

  • Manual—assign the ligands to a set by changing the values in the Pharm Set column of the ligand table.To change the value for a single ligand, click the cell and choose from the menu. To change the values for multiple ligands, select them in the table, then right-click and choose from the shortcut menu.
  • By values of a property—assign the ligands to a set using conditions on a chosen ligand property. This method requires either actual activities or a property that distinguishes actives from inactives. You can set values for this property in the Activity column for single ligands by editing the table cells, or for all ligands by choosing a property from the Available properties list. To assign the ligands, choose the activity-related property, choose the relational operator and enter the threshold value, then click Apply.

Define Actives and Inactives Dialog Box Features

Selected Project Table entries table

This table lists the entries selected for development of a pharmacophore model. You can use this table to designate which entries are actives and which are inactives, and set the activity for the entries. You can select multiple rows in the table and apply an action from the shortcut (right-click) menu: set the Pharm Set property, modify the selection, or remove the ligands from the table. If the ligands are grouped, any action you take on one ligand in the group is applied to all ligands in the group.

Name Title of the project entry for the ligand. Noneditable.
Conformers Number of conformers for the ligand. Noneditable.
Activity Activity of the ligand. You can set the activity of a single ligand by editing the table cell. You can set the activity of all ligands by choosing a property from the Choose an activity property list. To clear the activities for all ligands, right-click on the header and choose Reset Column.
Pharm Set Indicates whether the ligand is in the active set, the inactive set, or neither. You can change the value for a single ligand by clicking in the table cell and choosing from the menu. You can change the value for the selected ligands by right-clicking and choosing from the shortcut menu. By default all ligands are assigned to the active set. You can clear all the settings by right-clicking on the header and choosing Reset Column.
Ligand Group Index of the group that the ligand is in (if any). You can clear the grouping of ligands by right-clicking on the header and choosing Reset Column.
Must Match A checked box indicates that the ligand must match all hypotheses in the pharmacophore model. The checkboxes can ony be checked for the active ligands. The requirement is only relevant when the number of actives required to match a hypothesis is less than the total. You can clear all the settings by right-clicking on the header and choosing Reset Column.
Assign ligand groups by option menu and Group button

Choose an option to use for grouping ligands that are to be considered identical for the purposes of model building. Click Group to group the ligands. The table rows for each ligand group are colored to indicate the group membership, and the group index is displayed in the Ligand Group column. The Pharm Set and Must Match settings are taken from the first ligand in the group, and applied to all the group members. The options are:

  • Stereochemistry—group ligands that differ in their stereochemistry but have the same connectivity. Stereochemistry includes R/S, E/Z, cis/trans, and amino nitrogens with three substituents.The ligands must be in a contiguous set in the table.
  • Title—group ligands that have the same title. The ligands must be in a contiguous set in the table.
  • Selected Rows—group the ligands in the rows that are selected in the table. No checking is done on this grouping.
Ungroup button

Ungroup the selected rows. The button is only active when rows are selected. To ungroup all rows, you can right-click on the column header and choose Reset Column.

Choose an activity property list

Lists properties that are available for selection as the activity or activity-related property of the ligands. Select a single property to populate the Activity column of the table with the values for the ligands. The property does not have to be an actual activity: it can be any property that distinguishes actives from inactives, real, integer, string, or boolean.

Show family option menu

Prune the list of available properties to show only the properties for the chosen family.

Active if Activityoption menu and text box

Set the condition on the chosen activity property for assigning ligands as actives in the table, using the relation chosen from the option menu and the value entered into the text box. All ligands whose activity meets the condition that you set are assigned to the active set.

Inactive if Activity option menu and text box

Set the condition on the chosen activity property for assigning ligands as inactives in the table, using the relation chosen from the option menu and the value entered into the text box. All ligands whose activity meets the condition that you set are assigned to the inactive set.

Apply button

Apply the criteria for assigning ligands to the active and inactive sets. Sets the value in the Pharm Set column according to the ligand activity thresholds.

Reset button

Clear all changes made in the panel and reset settings to the defaults.

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