About query molecules

Hi


I make a program to compute some properties of my structures (atom


count...), the program was interrupted when found query molecules as:


OS(=O)(=O)c1ccc2O[#30-10]-,:3(Oc4ccc(c5ccc[n+]-,:3c45)S(O)(=O)=O)[n+]3cccc1c23





Is possible with chemaxon run a program or script that show me this kind of


molecules, to remove it from my files.





Thanks in advance.

Hi,





Have you been using cxcalc ( http://www.chemaxon.com/marvin/help/applications/calc.html )


or evaluate ( http://www.chemaxon.com/jchem/doc/user/Evaluator.html ) to calculate these properties ?





Both have an ignore error option which can help:

Code:

-g, --ignore-error             continue with next molecule on error

If you were using something else, please let us know.





In short, there is no such application that would remove query molecules from a file,


but a small Java program can be written in a few lines using the API. I can provide more details on this if needed.





Best regards,





Szilard

I will be very grateful if you show me this kind of script, beacuse withe the evaluate and cxcalc program I lost the smile and the Id from the structure smile file.





Thanks for all.

I attached a short code example that will do the query molecule filtering.





Usage: java QueryFilter <input file> <output file> [query file]





Usage example (1):

Code:

java QueryFilter mols.smiles out.smiles

Content of the input file (mols.smiles):

Code:

OC1=CC=CC=C1 OS(=O)(=O)c1ccc2O[#30-10]-,:3(Oc4ccc(c5ccc[n+]-,:3c45)S(O)(=O)=O)[n+]3cccc1c23 CCCN

The result (out.smiles) does not contain query molecules:

Code:

OC1=CC=CC=C1 CCCN

Usage example (2):

Code:

java QueryFilter mols.smiles out.smiles queries.smarts

In this case the generated out.smiles is the same as in the prev. example, and the queries from the input file are written to queries.smarts file:

Code:

OS(=O)(=O)c1ccc2O[#30-10]-,:3(Oc4ccc(c5ccc[n+]-,:3c45)S(O)(=O)=O)[n+]3cccc1c23

I hope this helps.





Zsolt

thanks for all