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AlgoMole / MolCRAFT

Implementation for ICML 2024 paper "MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space"
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input file contain multiple molecules #13

Open fangxintao opened 3 weeks ago

fangxintao commented 3 weeks ago

python sample_for_pocket.py ${PDB_PATH} ${SDF_PATH}

The input file（SDF file） can contain two or more small molecules？

qky18 commented 1 week ago

Hi, in that case, there might be some undefined behavior in clipping the 10A region around the ligand to obtain the binding site, though no errors will be thrown. If the input SDF contains several molecules within roughly the same binding site, I suspect it would be just fine. But if they are scattered into multiple (and often very distant) sites, it might not yield satisfactory results since the clipped pocket would be nasty.