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Fingerprint calculation limited to 99 compounds #56

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debnathk opened this issue Jan 30, 2024 · 0 comments
Open

Fingerprint calculation limited to 99 compounds #56

debnathk opened this issue Jan 30, 2024 · 0 comments

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@debnathk
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debnathk commented Jan 30, 2024

I have a .smi file containing 207 compounds, with corresponding SMILES. While calculating fingerprints for those, it is limited to 99 compounds only, which can also be seen in the log file. Is there any parameter to bypass that limit? I tried setting maxcpdperfile=500, but it didn't work. Here is the snippet:

from padelpy import padeldescriptor
fingerprints = ['CDK', 'CDKextended', 'CDKgraphonly']
for fingerprint in fingerprints:
    fingerprint_output_file = ''.join([fingerprint,'.csv'])
    fingerprint_descriptortypes = fp[fingerprint]
    print(fingerprint_output_file)
    padeldescriptor(mol_dir='molecule_prad.smi', 
                    d_file=fingerprint_output_file,
                    descriptortypes= fingerprint_descriptortypes,
                    detectaromaticity=True,
                    standardizenitro=True,
                    standardizetautomers=True,
                    threads=10,
                    removesalt=True,
                    log=True,
                    fingerprints=True,
                    retainorder=True)

Screenshot 2024-01-29 202228

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