Indigo errors on some SMILES strings

[David Sharpe]

Hi,

We have .Net application which allows users to perform searches by inputting a structure into Ketcher (version2.0.0-RC) and then we pass the SMILES produced by Ketcher to perform exact, similarity and substructure searches using Indigo version1.4.0-beta.12-g12ec19ed win64build.

While this works for most cases we have observed in one of our test cases that Indigo throws an error when passed the SMILES string.

Our process is:

1. Draw structure in Ketcher --> SMILES.

2. our application calls the Indigo aromatize() method on the SMILES.

3. The resulting SMILES is then used in the exact search:

exactMatch(molecule.Target, queryMolecule, "ALL -FRA -STE")

4. Indigo throws an exception: SMILES loader: invalid character within atom description: ' ''  

The SMILES string that we have seen caused this issue is: 

C[C@@H]([C@H]1CC(=O)[C@H]2[C@@]1(CC[C@H]3[C@H]2[C@H]([C@@H]([C@@H]4[C@@]3(CC[C@@H]([C@H]4O)O)C)O)OS(=O)(=O)[O-])C)[C@H]([C@@H]([C@@H](C)C(C)C)O)O.[Na+]

From some trial and error it seems that the cause of the exception is the sodium ion part of the SMILES

We've also tested with the latest release 1.4.1 and still observe the same issue.

[David Sharpe]

Is anyone able to advise if the above problem is a known issue, or if there is some error we are making in how we are using Indigo/ketcher. Alternatively, is there some kind of work around?

Kind regards,

Dave

[David Sharpe]

As an update - we were able to resolve the issue ourselves.  We determined that between generating the smiles and passing it to indigo there had been an encoding issue that had modified the smiles string.

Kind regards,

Dave