1.4. VIEW Menu
Hide/Unhide >>
Hides or reveals (unhides) spreadsheet rows from view. When hidden, they are ignored in operations such as substructure searching and file export. This contrasts with the effect of using [EDIT >> Delete].
The Clear Control Panel Filters and Reset Control Panel Filter Ranges options are used in conjunction with the Spreadsheet Controls (see below). The first option clears all information from the filter controls, unhiding any rows that were hidden using those controls. The second option resets the filter ranges but does not remove the names of any filter attributes you have selected; the result is the same as with the first option, unhiding any rows that were hidden using the filter controls.
Modify Structures >> provides options for modifying chemical structures or redrawing them:
>> Modify Using MedChem Designer lets you modify the chemical structure of compound. A copy of the original structure is saved in the Previous Structure column; Restore Previous restores the original and removes it from the "stack" of Previous Structures.
>> Redraw cleans up the selected chemical structures. Its effect is reversed by Undo Redraw. The ADMET Predictor installation includes a file called CoordinateGenerationTemplates.ctk that helps to draw designated structural motifs in a desired orientation. You can open this file in ADMET Predictor to see the motifs that are provided by default, and can modify the file by exporting from ADMET Predictor using CTK file format. Please note that motifs in CoordinateGenerationTemplates.ctk are currently limited to ring systems: every bond in each motif must be a ring bond. In addition, during redraw a motif will be utilized only if the structure being redrawn contains the motif and there are no additional ring bonds attached to the motif: in other words, if CoordinateGenerationTemplates.ctk contains a benzene motif, that motif will not affect the redrawing of naphthalene.
Structure Highlighting >> allows you to Set Scaffold Color, to Set Query Color and to Clear Query Highlighting.
ADMET Predictor supports two types of structural highlighting of molecules. The first results from running a spreadsheet search using [EDIT>>Query by Structure/Property]. A search for compounds containing a phenyl ring, for example, will result in a phenyl ring being highlighted in all "hit." The second type results from class generation methods that assign a structural scaffold to a class, such that all member molecules for that class display the scaffold as a highlighted substructure. Both types of compound highlighting should be visible in the Classes, Compounds, and R Tables tabs. The Pairs tab uses a different type of highlighting, as discussed in the sections describing those tabs. If a particular molecule contains both types of highlighting, the query-based highlighting will take precedence.
Resize Columns >> allows you to change the widths of all spreadsheet columns.
The Fit Header Labels option resizes columns to fit the names in the column headers; the Fit All Cell Data option resizes columns to fit the contents of all of the columns' cells; and the Defaults option restores the default column widths.
Arrange Columns (Ctrl+Alt+V)
Allows you to add, remove or reorder spreadsheet columns.
Load Star Plot Columns
Allows you to add star-plot columns to the spreadsheet by selecting a pre-defined text file containing a description of each desired column. A default file called AutoStarPlots.star is included in the ADMET Predictor installation.
Spreadsheet Heat Map
Colors spreadsheet cells based on specified attribute values. This option is also available using the toolbar, as shown below.
By default, cells containing high values are colored green and those containing low values are colored red. This can be reversed by changing the default setting. Changes to this setting does not affect star plots. If you want to color a particular attribute using a log scale, right click on the column header and choose Set Color Scale >> Log from the context menu.
Application Theme >>
Lets you specify the color scheme for the ADMET Predictor GUI as Modern Blue, Modern Light or Classic Style. The application theme used for the illustrations in this manual is Modern Blue.
Dock Charts In Main Window
Restores the charts to their default positions if they have been moved by docking them in new configurations.
Information Bar
Displays Informational messages are shown here after class generation, R-Table generation, pair generation, etc. You can hide the information bar by unchecking this menu item.
Status Bar
The blue colored bar at the bottom of the ADMET Predictor screen is called the status bar. Messages are displayed at the left side, while the right side displays information about the contents of the current tab, as well as a Hidden Items Alert.
Spreadsheet Controls
Launches the spreadsheet control panel, which can be used to modify the spreadsheet view and to hide compounds falling outside of desired property ranges.
MedChem Features
Lets you control whether toolbar items and menus specific to the MedChem Studio module are visible or are hidden, presuming that you have licensed the MedChem Studio™ module of ADMET Predictor.
Tiled Spreadsheet (Ctrl+Alt+T)
Lets you switch between a Table and Tile view of the spreadsheet.