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igashov / DiffLinker

DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design
MIT License
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Question：given the limitation of pocket but without limitataion of --anchors #8

Closed MachineGUN001 closed 1 year ago

MachineGUN001 commented 1 year ago

hi,

if using generate_with_protein.py or generate_with_pocket.py method, the para --anchors is necessary. however, In order to take into account the diversity of compounds generated, is there any approach that takes into account the combination and limitation of pockets but doesn't limit the location of the anchors for the fragment links?

many many thanks,

Sh-Y

igashov commented 1 year ago

Hello,

These scripts do not require --anchors parameter to be specified. However, if you don't specify anchors you need to make sure that you use the model that was trained without anchors. In case of pocket conditioning, there is such a model.

Hope it help!

Best regards Ilia

MachineGUN001 commented 1 year ago

hi, Llia,

thanks for your kind explanation. I'll give a try to do the modification as you mentioned. this issue will be closed.

Best,

Sh-Y