Edit Pattern Dialog Box

The Edit Pattern dialog box provides tools for editing custom SMARTS patterns and redefining the geometry of the pharmacophore site.

To open this dialog box, click Edit in the Edit Features Dialog Box

  • Features
  • Additional Resources

Edit Pattern Dialog Box Features

SMARTS Pattern Text Box

Contains the SMARTS pattern. You can change the SMARTS string in this text box.

Get From Selection Button

Click this button to generate a SMARTS string from the selected atoms in the Workspace. The string replaces the SMARTS string in the SMARTS pattern text box.

Geometry Option Menu

This option menu has three items that can be selected to define the type of site point: Group, Point, and Vector. The remaining controls in the dialog box depend on the choice you make from this menu.

Group
The pattern contributes a group of atoms to the pharmacophore feature definition, with the pharmacophore site placed at the centroid. The Projected point type menu has only none and aromatic ring options available, and the Group atoms controls are displayed.
Point
The pattern contributes a single atom to the pharmacophore feature definition, with the pharmacophore site placed at that atom. The Projected point type menu only has none available, and the Point atom text box is displayed.
Vector
The pattern contributes an atom with one or more directions to the pharmacophore feature definition, with the pharmacophore site placed at the atom. The Projected point type menu has items for donor and acceptor groups, and the Vector atom text box is displayed.

Projected Point Type Option Menu

This option menu allows you to define the type of the projected point that defines the pharmacophore site. The items available depend on what you choose from the Geometry menu:

Group:   none
aromatic ring
Point:   none
Vector:   donor
acceptor, spn, m lp

The acceptor items define the hybridization at the projected point and the number of lone pairs.

Atom definition controls

The atom definition tools depend on the choice made from the Geometry menu:

Group atoms

All includes all atoms in the SMARTS pattern in the group. Numbers includes the atoms whose atom numbers are given in a comma-separated list in the text box in the group. The pharmacophore site is the group centroid.

Point atom

The coordinates of the atom number given in this text box define the pharmacophore site for the feature.

Vector atom

The coordinates of the atom number given in this text box define the origin of the vector for the pharmacophore site.

The atom numbers given in the last three features refer to the order of the atoms in the SMARTS string (the SMARTS index). You can use the SMARTS Index Panel to determine what the SMARTS index of a particular atom in the Workspace is.

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