Add Standard Molecular Property Panel

The Add Standard Molecular Property panel allows you to generate one or more new entry properties based on the attributes of the structures in the entries. The properties to generate are selected from a list.

To open this panel, do one of the following:

  • in the Project Table panel, choose Data → Add Property → Standard Molecular Property
  • click the Tasks button and browse to Project Table and Project Operations → Add Molecular Properties
  • Using
  • Features
  • Additional Resources

Using the Add Standard Molecular Property Panel

To calculate one or more properties, select them from the list, then click Add. If you chose properties that require options to be set, the Property Options dialog box opens, and you can make the required settings, then click Calculate to continue to the calculation.

If the property calculation takes some time, a progress dialog box is displayed. You can stop the property calculation; if you do, the properties already calculated are kept.

To recalculate a property, select Recalculate existing values before you click the button to calculate the properties.

Add Standard Molecular Property Panel Features

Properties list

The properties you can generate are listed in this section. To calculate one or more properties, select them from the list. The number of properties selected is displayed below the list.

The available properties are:

  • Chiral centers—calculates the number of chiral centers for ligand-sized molecules and adds the chirality properties used by LigPrep (single molecule entries only)
  • Molecular charge (single molecule entries only)
  • Molecular formula (single molecule entries only)
  • Molecular weight (single molecule entries only)
  • Number of atoms
  • Number of heavy atoms—atoms other than hydrogen
  • Number of molecules
  • Number of residues
  • Spin multiplicity—lowest spin multiplicity based on the atoms present and the charge.
  • Secondary structure content—generates three properties: percentage of helices, percentage of beta strands, and percentage of random coils
  • AlogP—see Ref. [9]
  • Hydrogen bond acceptors
  • Hydrogen bond donors
  • Number of h-bonds and halogen bonds—generates four properties: number of hydrogen bonds, number of halogen bonds, number of aromatic hydrogen bonds, and number of salt bridges
  • Number of contacts—generates three properties, one each for good, bad, and ugly contacts
  • Number of pi interactions—generates two properties: number of pi-pi interactions and number of pi-cation interactions
  • Number of rotatable bonds
  • Polar surface area—see Ref. [13]
  • Molar refractivity—see Ref. [10]
  • Polarizability—see Ref. [11]
  • Unit cell volume
  • Unit cell density
  • Unit cell formula

The interaction counts (H-bonds, contacts, pi) are evaluated according to the current interaction settings and Workspace contents. Each non-fixed entry is considered as included in the Workspace, and the counts of interactions are made with whatever is fixed in the Workspace and whatever is specified in the Interactions toolbox. This property may therefore depend on other entries.

Recalculate existing values option

If this option is selected, calculating a property that already exists replaces the property values with new values. If it is not selected and the property exists, the property will be calculated only for the entries that do not already have values.

Add properties to selected entries only option

Calculate the property values only for the selected entries. By default, the values are calculated for all entries.

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