12.9 OSRA - Optical structure recognition

OSRA is a powerful command-line utility, developed by Igor Filippov at Frederick National Laboratory for Cancer Research, that can convert graphical representation of chemical structures into SMILES or SDF file. OSRA plug-in interfaces VEGA ZZ to this software, allowing to convert 2D documents to 3D structures. The plug-in includes also a TWAIN interface to acquire documents from image scanners or other imaging devices. It can manage graphic images (Bitmap, Enhanced Metafile, GIF, Icon, JPEG, PNG TIF and Windows Metafile) and PDF documents without external software. The unsupported formats can be also used by clipboard operations because the plug-in supports both vector and bitmap objects. To show OSRA, choose File Optical structure recognition in VEGA ZZ main menu:


OSRA main window


To open a document, you can select File Open in menu bar, or drag the file object by mouse and drop it over the OSRA window, or paste any clipboard object by Edit Paste or scan selecting File Acquire image. If you installed more than one imaging devices, remember to select it by File Select TWAIN source. In some cases, the view is too small and you can change the document scale by mouse wheel, by magnifier buttons in the tool bar and by subitems of View menu. To move the document, you can drag it by moving the mouse and keeping pressed the right mouse button. OSRA can recognize multiple structures in complex documents, but if you want speed-up the process, you can restrict the search to a specific area that can selected pressing the left mouse button and drawing a box.

To start the recognition, you can select Edit Recognize or press Recognize button of the tool bar. The found structures are shown in the list box at the bottom of the window as SMILES strings. Moving the mouse over each string, the correspondent 2D structure is shown in a hint box and double clicking each results, the SMILES string is automatically converted to 3D. You can perform also the same operation, selecting Convert to 3D in the popup menu.

The popup menu allows also to copy the selected SMILES string to clipboard (Copy SMILES item).



12.8.1 The menu bar


The menu bar functions are summarized in the following table:


Menu Item Accelerator Description
File Open Ctrl+O

Open a document / image. The supported file formats are: Bitmap, Enhanced Metafile, GIF, Icon, JPEG, PDF, PNG TIF and Windows Metafile.

Save as ... Ctrl+S

Save the current image. The supported file formats are: Bitmap, GIF, JPEG and PNG.

Select TWAIN source - Select the imaging device to acquire a document.
Acquire image Ctrl+A Acquire an image by the selected TWAIN device.
Close Ctrl+Q Close the OSRA window.
Edit Copy Ctrl+C Copy the current image / document to clipboard.
Paste Ctrl+V Paste from clipboard.
Recognize Ctrl+R Recognize the structures.
View Zoom in F1 Enlarge the image / document view.
Zoom out F2 Reduce the image / document view.
Zoom reset F5 Reset the image / document view.
Help Manual Ctrl+H Show this manual.
About OSRA - Show the credits.