SMILES are not visualized

hi,

today i've encountered some problems with visualisaiton of smiles in KNIME. it occurs both if i choose column type in the Table Creator node or if i use Molecule Type Cast node - i just can't see molecules when i look in the node output, only empty cells.

it doesn't work only for smiles: for example, if i treat smiles strings as smarts, everything's ok. moreover, 'unvisible' smiles could be successfully translated into other molecule formats as rkdit; it's also possible to write a textfile containing molecules - no errors or exceptions.

i've attached an example screenshot.

is it a recent update (maybe i've just overslept one)? or problem is on my machine?

 

thank you in advance and have a nice day,

 

lana.

 

not to say it's crucial problem, but.. a somewhat puzzling one.

Using the latest KNIME Analytics Platform (3.4.1 - released yesterday). I couldn't reproduce the issue with the smiles: CCCCCC=CCC=CCC=CCC=CCCCC(=O)O

However, the images that you sent show that the smiles must be reasonably complex, perhaps the rendering just takes a long time in this case? Could you try with a simple smiles, and also with the latest version of the Analytics Platform? Is it also possible to share the smiles in the reply?

Thanks in advance.

hi,

thank you for your reply.

complexity of smiles was the first thing i've thought of, but even simple structures are not rendered.

i've just updated KNIME, and nothing had changed(

simpler structures are attached:

CCCn1c(c(c(n1)C)[N+](=O)[O-])C
CC1CCN(CC1)c2ccc(cc2Cl)[N+](=O)[O-]
c1cc(c(c(c1)Cl)N2CCOCC2)[N+](=O)[O-]

 

regards,

lana.