Molecular Descriptors Panel

Compute topological descriptors, QikProp properties and semiempirical electronic (MOPAC) properties for a set of structures. Details of the descriptors can be found in "Handbook of Molecular Descriptors", ed. Mannhold, R.; Kubinyi, H.; Timmerman, H. (Wiley, 2008).

To open this panel: click the Tasks button and browse to ADME and Molecular Properties → Molecular Descriptors.

  • Features
  • Additional Resources

Molecular Descriptors Panel Features

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
  • Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Topological Descriptors tab

In this tab you can choose the topological descriptors to calculate.

Descriptor lists

The list on the left contains the descriptors to be left out; the list on the right contains the descriptors to be calculated. You can move the descriptors between the lists with the buttons between the list. The double arrow moves all descriptors, the single arrows move the selected descriptors. Selection does not use shift-click and control-click; rather clicking on an item toggles the selection. You can select multiple descriptors by clicking each one individually.

Search descriptor text box

Search for a descriptor in the left-hand list by entering its name or its code in the text box. The list is pruned for each character that is entered. To clear the text box, click the X button.

QikProp Properties tab

In this tab you can choose the QikProp properties to calculate - see QikProp Properties for more information.

Do NOT run QikProp with -fast option option

Run QikProp in normal mode, which includes the semiempirical PM3 calculation of the IP, EA, dipole moment and derived properties.

Property lists

The list on the left contains the properties to be left out; the list on the right contains the properties to be calculated. You can move the properties between the lists with the buttons between the list. The double arrow moves all properties, the single arrows move the selected properties. Selection does not use shift-click and control-click; rather clicking on an item toggles the selection. You can select multiple properties by clicking each one individually.

Search property text box

Search for a property in the left-hand list by entering its name in the text box. The list is pruned for each character that is entered. To clear the text box, click the X button.

Semiempirical Properties tab

In this tab you can choose to calculate electronic properties with the MOPAC default method, and control some of the parameters of the calculation.

Compute semiempirical properties option

Compute semiempirical properties. The properties include the dipole moment and its breakdown in terms of point charge and hybrid contributions, the heat of formation (in kcal/mol and kJ/mol), the total, electronic, and core-core repulsion energy in eV, and the ionization potential (also in eV).

Do not optimize geometry option

Do not optimize the geometry of the structures. By default the geometry is optimized.

Method to use for semiempirical calculations option menu

Select the method to use for the semiempirical calculations. A description of the methods and their coverage of elements is given in the Semiempirical Module Guide.

Output format options

If you want to write out a CSV file as well as a Maestro file, select CSV file. A Maestro file is always written out.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Molecular Descriptors - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

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