Free chemistry structure and data browser
Look at your compounds in a new way
Ocura is Windows and Mac software for browsing chemical structures and data
The following information describes how to install and use Ocura. Please contact [email protected] with any questions
- Opening files
Ocura is a graphical application for viewing files containing molecules and/or data. Downloads are located here. To install Ocura run the setup installer file and follow the instructions, choosing the directory in which to install the application.
To work with previously saved files Ocura supports the following data file types:
- *.add – StarDrop file
- *.skd – Sentira file
- *.csv – Comma separated variable file
- *.smi – SMILES file
- *.sd and *.sdf – MDL SD file
- *.mol – MDL Mol file
- *.mol2 – Tripos Mol2 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 as a new tab.
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 strings.
Multiple data files can be opened in the application at any one time and can be maximised or minimised within the data window. From the View menu you can select which of the open data sets you wish to view at any time. On Windows® you can toggle between data sets by pressing Ctrl+Tab. Data sets can be arranged by clicking on the View menu and selecting Cascade or Tile. Alternatively, a Tabbed View menu option provides tabs at the bottom enabling you to easily switch between data sets.
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 View menu), select menu 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.
- The 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 enable these to be changed.
- To pair any other columns select the appropriate column name from the drop-down list.
- Click the OK 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 combined, but which contain different values for the same molecules then these will be represented by separate rows.
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.
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 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 Ocura to allow you to easily manipulate a data set.
To change the order in which properties are displayed:
- Click the button on the tool-bar to bring up the Select Data to View dialogue
– This option is also available under the Data Set Menu as Manage Data.
- 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 un-check 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.
A data set can be sorted by values within a specific column.
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 multiple columns, select Sort… from the Data Set menu or click the tool-bar button. In the Sort Data dialogue add properties to the list specifying a sort order for each before clicking OK.
Values within a specific selection (or the whole data set if there are no selections) can be found by searching (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:
- From the tool-bar click the Find button or 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 Ocura 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
Cut, copy and paste are also available on the Edit menu and via the short-cuts Ctrl-x (cut), Ctrl-c (copy) and Ctrl-v (paste).
To edit one or more columns of data, right-click on the column name to display the menu.
- 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 duplicate a column choose Duplicate.
- To edit the column properties select Edit….
To edit the value in an individual cell double-click on the cell and enter the new value in the dialogue box.
After working with a data set it is likely that data will need to be saved or exported for future analysis.
- 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 comma-separated variable (CSV) file choose file suffix .csv
– To save the file as an 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.
Free Ocura support is available via the community.