SMILES starting with a parenthesis

We've observed some unexpected behavior when importing some SMILES that start with parentheses (using either MarvinSketch or MolImporter directly). In most cases it treats the input as SMARTS, not SMILES.





Consider the following examples. (These are contrived examples; obviously there are other ways of writing these molecules without the leading parentheses.)

Code:

(OC)C           Treated as SMARTS (C)C1CC(N)CC1   Also treated as SMARTS    (N)C1CC(C)CC1   Treated as SMILES

All the examples should be valid SMILES, at least according to Daylight.


http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html#RTFToC18





So, two questions:


1) Why are the first two examples above treated as SMARTS?


2) What's different about the third example that makes it work?





Thanks,


Chris

Hi Chris,





I have tried with Marvin 4.0.4. I couldn't reproduce the problem with the following code which prints out the input format (part from SomeImport.java):

Code:

InputStream is = new BufferedInputStream( new FileInputStream( args[ 0 ] ) );         MolImporter molimp = new MolImporter( new MolInputStream( is ) );    MolImporter strimp = new MolImporter();    Molecule m = new Molecule();    Molecule molFromSmi =  new Molecule();    int n = 0;    while(molimp.read(m)){        System.err.println(m.getInputFormat());    }    System.err.println();     }

Saving the 3 molecule strings to '1.txt' and running the code shows that all the 3 string is imported as SMILES:

Code:

java SomeImport 1.txt smiles smiles smiles

How did you import the strings?





All the best


Andras

Hello Andras,





We've tried several things. This is what I did for the tests above:





1) Create a .smi file for one of the molecules above, using a text editor


2) Open the .smi file in MarvinSketch


3) Look at how MarvinSketch draws the image: if it imported as SMARTS, it draws an explicit "C" in some cases


4) Go to File > Save As... > SMILES. If it imported as SMARTS, you'll get an exception like the following (for (OC)C, the first example above):

Code:

Chemaxon.marvin.util.MolExportException: Some features of [#6]C[#8]) cannot be converted to smiles/cxsmiles. Use the smarts or cxsmarts format.

I did these tests after observing similar things in our code, with more complex molecules. Our import code is similar to yours. I didn't explicitly check the input format (as you did); I just observed that it failed with a MolExportException when I tried to convert the Molecule back to SMILES, with mol.toObject("smiles").





I added the check for the input format, and you're right: it says "smiles". But the molecule can't be converted to SMILES!

Code:

Molecule mol = MolImporter.importMol("(OC)C"); System.err.println(mol.getInputFormat());     // prints "smiles" System.err.println(mol.toObject("smiles"));   // throws exception

Thanks,


Chris

Hi Chris,





I have found what makes the problem:


SMILES string started with a parentheses '(' is interpreted as SMARTS with component level grouping. We fix this bug.


Thank you for the report.





Andras

Thank you, Andras!





Do you know when the fix will be released?





Chris

Hi Chris,





The fix is ready. The new release will contain this fix also.


I hope it will be available in a few weeks.





All the best


Andras