Optibrium - StarVue: Free chemistry structure and data browser

The following information describes how to install and use StarVue. Please submit any questions or features requests in the forums.

Installation
Opening files
Data
Saving

Installation

StarVue is a graphical application for viewing files containing molecules and/or data. To install StarVue, insert the CD or double-click the setup installer file and follow the instructions, choosing the directories in which to install the application.

Opening files

To work with previously saved files StarVue supports the following data file types:

*.add - StarDrop file
*.csv - Comma separated variable file
*.smi - SMILES file
*.sd and *.sdf - MDL SD file
*.mol - MDL Mol file

To open a data file:

From the File menu select Open. A dialogue will be displayed.
Select the required file and either double-click on it or click the Open button.
The file will appear in the data window on the right hand side of StarVue.

Note: For files of type *.csv the first row is imported as a header row and will be the titles for columns within the data set.
Molecular structures will be automatically recognised, even within CSV files if they are represented by SMILES strnings.

Data sets

Multiple data files can be opened in the application at any one time and can be maximised or minimised within the data window. You can toggle between data sets by pressing Ctrl+Tab. Data sets can be arranged by clicking on the Windows menu and selecting Cascade or Tile. You can create a new data set by selecting rows in an existing data set and then selecting Create New Data Set From Selection from the Tools menu. or clicking the button on the toolbar

Merging data sets

The current data set can be merged with another open data set using the Merge Data Set dialogue. Merging will create a new data set with columns from the both the current data set and those of a selected set.

To merge two data sets:

Open the two data sets to be merged.
With one of the data sets being the active window (if necessary bring it to the front using the Windows menu), select menu Tools, then Data Set and then Merge....This launches the Merge Data Set dialogue.
Select the other data set to be merged from the drop-down list (assuming the other data set is not already showing).
The dialogue's table shows the columns from the active data set under Column and the respective column from the other data set, with which each will be paired, under Merge with. By default, columns with the same name and type will be paired, but the drop-down lists allow these to be changed.
To pair any other columns select the appropriate column name from the drop-down list.
Click the Apply button.

Rows from the two data sets will be considered matches, and will therefore be merged, when all the paired columns have identical values. For each match a single row will be created in the output data set. However, if there are columns in the two data sets that should be paired, but which contain different values for the same molecules, tick the Allow Duplicates checkbox and this will ensure there is only a single column of values in the final data set and where multiple values occur these will be duplicated to be merged with all the other matching rows.

Data

There are two different views that can be used for browsing the information in a data set:

The table view shows all the information in a table where each row displays a different compound and each column displays a different data type. The molecule view shows each compound at a time, making it easier to look at all the properties for a single molecule.

In molecule view you can scroll the molecules left and right. The data below will change to display values for the current molecule. You can drag and drop the data items below to arrange as desired. Clicking on a molecule will select/deselect it. Clicking to either side of the molecule will scroll the view by one molecule in the chosen direction.

On the toolbar are two buttons that can be used to switch between these views. Click on the

button to switch to molecule view and click on

to switch to table view. If there are no molecules in the data set then the molecule view will be disabled.

A number of features are available in StarVue to allow you to easily manipulate a data set.

Re-ordering columns/properties

To change the order in which properties are displayed:

Click the button on the toolbar to bring up the Select Data to View dialogue
Drag and drop properties (or highlight them and click the up and down buttons) to change the order in which properties are displayed
Check or uncheck the properties to show or hide them respectively

Note: The order will be changed in both the table view and the molecule view.
In addition, you can drag and drop columns and rows when using the table view and drag and drop individual properties when using the molecule view.

Sorting data

A data set can be sorted by values within a specific column or by structural similarity to a specific molecule. To sort data by column values click the right mouse button on the column title to display the menu and select Sort and either Ascending or Descending. To sort by rows based upon the structural similarity to a molecule in a specific row, click the right mouse button at the beginning of the row containing the comparator molecule to display the menu. Select Sort by structural similarity followed by Ascending or Descending.

Finding data

Values within a specific selection (or the whole data set if there are no selections) can be found based upon specific values without knowing where that data lies within a data set (for example, to find a molecule for which the ID is known but the position in the data set is not).

To find a value:

Select the Tools menu option and Find. Alternatively use the short-cut keys Ctrl-f. This brings up the Find dialogue
Type in the search value or, if it has been entered before, select it from a list of previous values
Click on the arrow next to the box labelled Find what to display a drop-down list and select the required value
Click Find Next to be taken to the next row of data where the matched value occurs
If the search value cannot be found StarVue will display a message

Editing rows and columns

To edit one or more rows of data, select them and then right-click on the row label to bring up the menu.

To delete the selected rows select Delete
To copy the selected rows to the clipboard select Copy. The copied rows will now be available to be pasted into this or another data set
To cut the selected rows select Cut. The selected rows will be deleted but be available on the clipboard to be pasted into this or another data set
To paste data from the clipboard select Paste

Edit

Ctrl-x

Ctrl-c

Ctrl-v

To delete the selected columns select Delete. The column will be deleted immediately
To insert a new column select Insert... to display a dialogue. Enter the name of this column and click OK. If a name is not entered or the Cancel button is clicked then no column will be inserted
To edit the column properties select Edit....

Editing values

Saving

From the File menu choose Save. If the data set has been saved before, this will update the saved version. If the data set has not been saved before the Save As dialogue will appear
Enter the File name where prompted and click the Save button
Choose the file format to use:
- To save the file as a StarDrop file choose file suffix .add
- To save the file as a comma-separated variable (CSV) file choose file suffix .csv
- To save the file as a SD file choose file suffix .sdf
- To save the file as a SMILES file choose file suffix .smi
Note: Saving as a SMILES file will only save the ID and the structure. No other data will be saved
To save the data set as a new file, select Save As... from the File menu. The same dialogue will appear giving the option to choose a new file name for the data set

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