Comments (1)
tjkessler
commented on August 25, 2024
When you use the 'padeldescriptor' function, you have to specify in the function call which descriptors you want to calculate:
from padelpy import padeldescriptor
# Calculate 2-D descriptors
padeldescriptor(mol_dir='molecule.smi', d_file='descriptors.csv', d_2d=True)
# Calculate 3-D descriptors
padeldescriptor(mol_dir='molecule.smi', d_file='descriptors.csv', d_3d=True)
# Calculate 2-D and 3-D descriptors
padeldescriptor(mol_dir='molecule.smi', d_file='descriptors.csv', d_2d=True, d_3d=True)If the 'd_2d' and 'd_3d' arguments are not specified, the output file will not be populated with descriptors.
Further, I highly suggest that you set 'retainorder' to 'True', this will ensure the descriptors in your output CSV file appear in the same order as the molecules in your input file:
padeldescriptor(mol_dir='molecule.smi', d_file='descriptors.csv', d_2d=True, d_3d=True, retainorder=True)Best,
Travis
from padelpy.
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