Unable to perform ROC analysis with helper script

[wolberlab]

Unable to perform ROC analysis with helper script

[martinlju]

Dear David,

you are right, the problem was with the whitespaces all along. The script works now that I've added the quotations.

Thank you again for all of your help!

Best regards,
Martin

[schallerdavid]

Hi Martin,
any chance you can try this on linux? I never tried calling ligandscout from the command line in windows. Maybe the Problem comes from this. Also, I did not update any code for the newer python releases, so testing this with a python 3.8 environment might be worth a try as well.

[martinlju]

Dear David,

thank you for your reply and suggestion. I have tried to run the script on linux as well, but had the same problem. Sadly, using an older Python version also didn't help.

Thanks and kind regards,
Martin

[schallerdavid]

Dear Martin,

could you manually execute the first run via the command line?
First change in the terminal to the respective directory and then execute something like

C:\Program Files\LigandScout 4.0\iscreen.exe -q library/0.pml -d handpicked_screenlibrary.ldb:active -o 0.sdf -l 0.log -C  6 -M 8

[martinlju]

Dear David,

I manually executed the command (I needed to put the iscreen path in quotations to avoid the error: 'C:\Program' is not recognized as an internal or external command, operable program or batch file.)
"C:\Program Files\LigandScout 4.0\iscreen.exe" -q library/320.pml -d handpicked_screenlibrary.ldb:active -o "320.sdf" -l "320.log" -C 6 -M 8

The program worked. I did this for several pharmacophores, here is an example of pharmacophore 310, which produces hits:

Screening (10 hits) [=========================================] 100,000%
iscreen finished successfully.

The program did not always execute instantly, sometimes I had to wait up to 30 seconds for it to start (it worked fast once it actually began running)

Log file from executing the command above:
320.log

[schallerdavid]

Dear Martin,

I think we found the problem :), its about the whitespaces. Could you put the iscreen executable in quotations in the python file?

iscreen_path = '"C:\Program Files\LigandScout 4.0\iscreen.exe"'