any atom type with isotope causing rendering issue

Hi

We have come across a case where SMILES datasets are being labelled with isotopes on atom types defined as 'ANY' i.e. [1*].  This is being done to preserve attachment points following some processing.

This causes some issues when rendering these with JChem.

Firstly, when this [1*] is attached to an aromatic atom, the bond is changed from single to 'aliphatic or aromatic' bond type.

Secondly, all terminal bonds in the rest of the molecule are given an '(A)' label.

The attached image shows an example using smiles [1*]c1ccc(C)cc1.  If it is changed to [1*]-c1ccc(C)cc1 it fixes the first issue.   Removing the istotop

• c1ccc(C)cc1 produces a correct image (but without the isotope information).
  
  

  We may decide to migrate what scripts we can to use atom map labels instead.  I believe this would be cleaner i.e [*:1]c1ccc(C)cc1 - plus it doesn't have these rendering issues in JChem.  I can't see any other way to retain this information using vanilla smiles.

I don't think i'll be taking that atom map route - we also want to align these molecules and having the isotope makes it work.  MolSearch/MCS ignores the atom map but not the isotope on those '*' atoms.

Hi Shane,

[1*]c1ccc(C)cc1 was read as SMARTS string. We have solved this problem, the correction will be available in Marvin 5.3.1. The string will be read as SMILES.

Erika

Hi Erika,

That's great news.  Thanks for you attention on this.

Shane

Hi Shane,

I would like to inform you that we had to make an urgent patch release that was named 5.3.1, therefore the fix promised in this topic will be included only in the patch release coming at the end of March (probably named 5.3.2).

Best regards,

Akos

Hi Akos,

Thanks for that information, it saved me some work to test v5.3.1.  I'll hold on till 5.3.2 is available.

Much appreciated,

Shane