getMol('smiles') not including stereo

Hi

It does not happen every time, but once in a while MarvinSketch's getMol('smiles') does not include stereo even when students draw a valid structure.  Below is an example of student's drawing.  With this drawing, getMold('smiles') returned "CC1C[C@H]1C".

Another one here returned "C[C@H]1C[C@H]1C".

The applet parameters that we use are

        msketch_param("menubar", "false");

	msketch_param("sketchCarbonVisibility", "inChain");

	msketch_param("implicitH", "heteroterm");

	msketch_param("importConv", "");

	msketch_param("extraBonds", "wedge");

	msketch_param("lonePairsAutoCalc", "false");

	msketch_param("lonePairsVisible", "false");

	msketch_param("valenceErrorVisible", "true");

	msketch_param("templateToolbarCustomizable", "false");

	msketch_param("atomFont", "SansSerif");

	msketch_param("chiralitySupport", "off");

	msketch_param("explicitH", "true");

and the MarvinSketch version is 14.11.10.  
Like I said, it does not happen every time.  It's very hard to reproduce.  
Do you have any idea?

Mayumi

Hi Mayumi,

 

I can't reproduce this, could you send us the problematic molecule in a format that contains coordinates? (mrv, mol)

It seem like a bug in our stereo calculations.

Best regards,

Peter

Hi Peter,

Here is the mol string.

\n  Mrv0541 02251509532D          \n\n  5  5  0  0  0  0            999 V2000\n   -1.4364    2.0330    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -0.7219    2.4455    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0\n   -0.3094    1.7311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.2333    1.8195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7219    3.2705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  1  3  1  0  0  0  0\n  1  4  1  1  0  0  0\n  2  5  1  1  0  0  0\nM  END\n

When I load the mol and try to get the SMILES from the reconstructed drawing, MarvinSketch does include stereo.  So, I'm not sure how to re-produce this problem.

This is the user's browser information at the time when the problem occurred.

Mozilla/5.0 (Windows NT 6.2; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/40.0.2214.115 Safari/537.36

Thanks,

Mayumi

Thank you for the information.

We'll try to reproduce the issue and get back to you when we made any progress.

Peter