Property Options Dialog Box

Set options for the calculation of properties in the Add Standard Molecular Property Panel. The dialog box shows options for any properties that require them. If none of the selected properties requires options, the dialog box does not open, and the property calculation proceeds.

  • Features
  • Additional Resources

Property Options Dialog Box Features

The sections listed below are only present in the dialog box if the corresponding property was chosen.

Molecular formula section

Enter a limit on the number of atoms in the Ignore entries with more than N atoms text box, The default is 100 atoms.

Substructure section

Enter a SMARTS pattern to define the substructure in the SMARTS pattern text box, or select atoms in the Workspace and click Get from Workspace Selection.

Enter a limit on the number of atoms in the Ignore entries with more than N atoms text box, The default is 100 atoms.

Enter the name for the substructure count property in the Property name text box.

Total surface area section

Set up the surface type and its parameters, and choose the types of surface area to calculate. The following controls are displayed:

Surface type options

Choose the surface type, from Extended radius or Molecular. These are the same as the surfaces available under Workspace → Surface (see the Advanced Surfaces Panel topics for details).

Probe radius text box

Enter the probe radius for the surface. The default value of 1.4 Å is the value for water.

Grid spacing text box

Enter the grid spacing. Only available for the molecular surface.

Hydrophobic surface area option

Calculate the hydrophobic surface area of the molecule. Selecting this option produces the Hydrophobic SA property. Hydrophobic atoms are defined in the same way as in Glide for hydrophobic constraints.

Buried surface area option

Calculate the buried surface area of a receptor in the presence of a ligand. Selecting this option requires you to choose a receptor, and produces the Buried SA property. For meaningful results, the entries you calculate the property for should be docked to the receptor. The buried surface area is the area that is not solvent-accessible when the ligand is present.

Buried hydrophobic surface area option

Calculate the buried hydrophobic surface area of a receptor in the presence of a ligand. Selecting this option requires you to choose a receptor, and produces the Buried Hydrophobic SA property. For meaningful results, the entries you calculate the property for should be docked to the receptor. The buried hydrophobic surface area is the hydrophobic area that is not solvent-accessible when the ligand is present.

Receptor controls

When calculating buried surface areas, these controls enable you to choose a receptor. You can either pick a receptor in the Workspace, if Pick is selected, or click Choose to choose an entry for the receptor.

Sequential index section

Select Index each group separately if you want the indexing to be restarted for each group. Specify the name of the index property in the Property name text box.

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