In ChemDoodle 2, the SMILES widget has been upgraded to the Line Notation Pad widget. Now Sybyl Line Notation (SLN), IUPAC International Chemical Identifiers (InChI) and Beilstein’s Representation Of Structure Description Arranged Linearly (ROSDAL) can be generated in addition to Daylight SMILES. Here, I will briefly describe the features of this improved widget.
UPDATE: ChemDoodle 2 was released on 5/27/09.
Chemical line notations are interesting because they are unique ways to store chemical data. And since all the data is in a single line of text, database applications become easier. From a chemoinformaticist’s perspective, they are very intriguing puzzles that require both an encoder and decoder to play with. The Line Notation Pad widget is just that!
The following image and list will outline how to use the widget.
- Choose the line notation format with this combobox. If there already is a loaded structure, choosing a different line notation will convert the string in 2 into the new format.
- The string text field will display the generated line notation when a structure is dropped on the widget. You may also explicitly type in your line notation here and then press Return or 3 to interpret it and display the corresponding structure in 9. If the widget is currently collapsed, you can expand it by dragging a structure onto it or typing in a line notation here and pressing Return.
- The View in 2D button will interpret the current string in 2 and display the structure in 9.
- The Add to the Doodle Board button will place the current structure in 9 onto the current Doodle Sheet. Alternatively, you can click on 9 and drag onto the Doodle Sheet to place it.
- The Choose Start Point button will allow you to flag an atom in 9 as the start point for the generation of the line notation. Note that if the line notation is canonical or if such an option is set, then choosing the starting point will not affect the generated string.
- The Copy to System Clipboard as Text will copy the current text in 2 onto the system clipboard as plain text. For MIME type specific clipboard contents, choose the appropriate settings in the Advanced tab of the Preferences window, then copy from the Doodle Board.
- The Help button will display information about this widget.
- The Clear button will clear the current contents and collapse the widget.
- The corresponding structure will be displayed here. You can drag structures from this area onto the Doodle Sheet with the mouse.
- The starting point for the line notation is noted with a blue circle. You can modify the starting point with 5.
- Any errors or warnings encountered when interpreting the string in 2 will be listed here. Use these suggestions to help correct malformatted strings.
So in short, the Line Notation Pad widget generates, parses and converts chemical line notation formats with ease. This widget will be available in ChemDoodle 2 when it is released at the end of May.
ChemDoodle also contains a data conversion tool accessible by selecting the Convert… menu item in the File menu. This tool is able to convert between all the chemical filetypes available in ChemDoodle. At the current moment there are 16 such formats: Beilstein ROSDAL, Chemical Markup Language (CML), ChemDoodle Documents (ICL), ChemDraw Exchange (CDX), ChemDraw XML (CDXML), Daylight SMILES, ISIS Sketch (SKC), ISIS Sketch Transportable Graphics Files (TGF), IUPAC InChI, MDL Molfiles (MOL), MDL SDfiles (SDF), Protein Data Bank (PDB), Standard Molecular Data (SMD), Sybyl SLN, Tripos MOL2 and XYZ. ChemDoodle can manipulate one of the largest selections of chemical data formats available, and they are all supported fully to the extent of ChemDoodle objects. In other words, all properties and objects that are found in ChemDoodle can be manipulated in all formats that support them, including shapes, fonts, colors, annotations, etc. Enjoy!