New Pattern Dialog Box

The New Pattern dialog box provides tools for adding a new SMARTS pattern and associated data to a pharmacophore feature.

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

Using
Features
Additional Resources

Using the New Pattern Dialog Box

To add a pattern to a feature, you must provide the SMARTS string for the desired arrangement of atoms, and define the corresponding pharmacophore site. The pharmacophore site can be a group, such as an aromatic ring, a single point, such as an atom, or a vector, such as a hydrogen bond acceptor or donor.

Type the SMARTS string into the SMARTS pattern text box, or click Get from selection to generate a SMARTS string corresponding to the Workspace selection.
Choose Group, Point, or Vector from the Geometry option menu.
Choose the projected point type from the Projected point type option menu:
- Group: Choose aromatic ring if the SMARTS pattern defines an aromatic ring, otherwise select none
- Point: none is the only available choice.
- Vector: Choose donor if the pattern represents a hydrogen bond donor, or choose the item that defines the type of acceptor (hybridization and number of lone pairs at the acceptor) if the pattern represents a hydrogen bond acceptor.
Choose the atoms that define the pharmacophore site:
- Group: Select All if all atoms in the SMARTS pattern are to be used to define the group centroid, or select Numbers and type the atom numbers for the group centroid in the text box.
- Point: Type the atom number for the pharmacophore site in the Point atom text box.
- Vector:Type the atom number for the pharmacophore site in the Vector atom text box. This should be the donor or acceptor atom.

SMARTS Pattern Text Box

Type the desired SMARTS pattern 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

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.