Entering SMILES Notations into SRC Estimation Programs

Direct Entry

Most users familiar with SMILES notations are able to look at a chemical structure and directly enter the corresponding SMILES notation into a program. Complicated ring structures can be difficult, and usually require that users have experience with entering complex structures directly.

SMILECAS Database

SRC sells a separate product known as the SMILECAS Database that contains SMILES notations, chemical names, and CAS (Chemical Abstract Service) numbers for 103,000 compounds. This product works in conjunction with all SRC estimation programs. By pressing the F8 key or clicking the "CAS Input" button, a CAS data entry box appears (an example is shown at the right). Simply enter the chemical's CAS number; if the CAS number is in the database, the corresponding SMILES notation and chemical name are automatically entered into the estimation program. The SMILECAS Database can also be used for "batch-mode" runs using a text file containing a list of CAS numbers.

User Files
Pressing the F4 key or clicking the "Get User" button opens and displays a user input file of chemical names and SMILES notations. See the program User's Guide for a description of this method. The input file must have been created previously by the user; otherwise, the entry selection will be blank.

Structure Drawing Programs That Can Create a SMILES Notation
We are currently aware of two commercial drawing programs that allow a user to draw a chemical structure and then directly write the SMILES notation for it to the Windows clipboard for transfer (pasting) to another program:

• CS ChemDraw Pro
• Kekule for Windows

Importing Structures
The Windows versions of SRC estimation programs can import chemical structure files from other programs. This "import" features allows other chemical structure formats to be imported directly into these SRC estimation programs. The "import" feature is accessed from the Menu Bar via: "File"...."Import Structure" as shown in the figure. The "import" feature uses the structure format conversion engine of the commercial software package ConSystantJ available from ExoGraphics, PO Box 655, West Milford, NJ 07480, (201) 728-0188. Syracuse Research Corporation has a license agreement with ExoGraphics that permits incorporation of the ConSystant DLL with the Windows versions of SRC programs. Imported structures are converted to SMILES notations and placed in the SMILES data entry field. These programs filter the conversion to make the SMILES notation as compatible as possible with SRC programs. However, some converted SMILES notations (especially SMILES with charged ions) will require some user modification before a program can estimate the structure.

Importable structure formats include:

Commercial chemical drawing programs (such as ISIS/Draw, ChemWindow, ChemDraw, Kekule, and others) can be used to draw a structure. The structure can be saved to a file format (such as a MDL MOL file) which can then be imported into the Windows version of all SRC estimation programs. This method has some advantages over the clipboard pasting method described above because the import program filters the conversion for SRC program compatibility.