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)

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: