padepy stops calculating descriptors from .smi files

[totocotonio1]

Hi

padepy stops calculating descriptors from .smi files, the problem is not related to an error of a smile string, it stops calculating anywhere in the smi file, it should be fixed

Thank you

[tjkessler]

Hi @totocotonio1,

Could you please provide a code snippet and a .smi file so I can help troubleshoot?

Best,
Travis

[totocotonio1]

Hi @tjkessler

here is the script,

` pip install padelpy

from padelpy import padeldescriptor

padeldescriptor(mol_dir='/content/drive/MyDrive/test/test1.smi', d_file='/content/drive/MyDrive/test/descriptors1.csv', fingerprints=True)`

to be noted that I am using google colab

I am generating the files in myDrive

Thank you

test1.zip

[tjkessler]

@totocotonio1,

I was able to generate the descriptors for your .smi file locally with everything located in the same directory:

from padelpy import padeldescriptor

padeldescriptor(
    mol_dir='test1.smi',
    d_file='descriptors1.csv',
    fingerprints=True
)

I've attached a ZIP file containing your .smi file, the resulting descriptors1.csv file, and the notebook I used: smiles_file_test.zip

I don't have too much experience with using PaDELPy in Google Colab, hopefully someone else can weigh in! Given that I was able to run everything locally, maybe the error is a file path issue...

Best,
Travis

[totocotonio1]

Hi @tjkessler

Thank you very much for your help,

I will generate the descriptors locally