I make a program to compute some properties of my structures (atom
count...), the program was interrupted when found query molecules as:
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.
Have you been using cxcalc
) to calculate these properties ?
Both have an ignore error option which can help:
|-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.
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):
|java QueryFilter mols.smiles out.smiles |
Content of the input file (mols.smiles):
The result (out.smiles) does not contain query molecules:
Usage example (2):
|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:
I hope this helps.