Describe the bug
Chem.Pharma2D.Gen2DFingerprint uses an unnecessarily slow GetUniqueCombinations. There is a much faster implementation called GetUniqueCombinations_new.
Here are direct links to the respective functions in order:

To Reproduce
This code takes about 75 seconds to execute currently:

from rdkit import Chem
from rdkit.Chem.Pharm2D import Generate, Gobbi_Pharm2D

smi = "CC=CC=C(S1C=C)C(O)C=C1NCCCCCCCCCCCCCCCCCCCCCCCCCCCC=CCCCCCCCCCCCCCCCCCCCCCCCCC=CCCCCCCCCCCCCCCC=CC=CCCC=CC=CCC=CCC=CCCCCCC=CCCC[P+1][P+1][P+1][P+1][P+1][P+1][P+1][P+1][P+1][P+1][P+1][P+1][P+1][P+1]"
mol = Chem.MolFromSmiles(smi)

Generate.Gen2DFingerprint(mol, Gobbi_Pharm2D.factory)

Expected behavior
If you replace the call with GetUniqueCombinations_new, the code takes about 1 second.

Configuration (please complete the following information):

• RDKit version: 2024.09.4
• OS: OpenSUSE Tumbleweed
• Python version (if relevant): 3.12.8
• Are you using conda? No
• If you are using conda, which channel did you install the rdkit from?
• If you are not using conda: how did you install the RDKit?