End of Line after SMILES

I have a workflow that I've been using for a while now with no issues, but my most recent set of compounds produced an odd error.

The output is a table with the following columns:

SMILES,Name,Activity,SMILES 2,Name,Activity 2,Tanimoto,delta(Activity)

In all past cases, this produces a nice CSV file using the CSV reader. With my most recent input structures (from an SD file), the CSV has a line break following each SMILES string. If I use different SD files, no problem, but with this particular SD file, each row of output gives this:

SMILES,
Name,Activity,SMILES 2
Name,Activity 2,Tanimoto,delta(Activity)

rather than the single line of output listed above. If I look at the data table just prior to the CSV Writer using Interactive Table, it seems fine.

Has anyone ever seen anything like this before? Any ideas?

-Kirk

Hi Kirk,

Which node are you using for converting the SDF structures to Smiles?
The Interactive Table does not support line breaks in cells except for SDF- or Mol2Cells (and maybe PDB). So even if the Smiles string contained a line break at the end you won't see it there.

Thorsten

Thor,

I'm using the CDK to SMILES node for conversion. I have not tried the OpenBabel node due to the limit on the number of structures that node can handle on Windows. (I should just get this whole thing running on LINUX!)

I tested a few other SD files and so far only this one seems to result in line breaks after the SMILES string. Strange.

-Kirk

Weird. Looking at the CDK code that does the conversion into Smiles, every Smiles string should have a newline at the end. Which is nonsense in any case I believe. I will change that, so that all newlines are removed.

Indeed the behavior is very strange. I've tested a number of SD files and this particular one is the only one I've found that causes the issue. It is easy enough to fix with a 5 minute script, but nonetheless.

Thank you for taking a look at it for me.

-kirk

Fixed in release 1.3.3 due this week.