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NiBoyang / AutoDock-SS

Use AutoDock for Ligand-based Virtual Screening
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Stuck After Creating grid.txt #4

Open cmwilson252 opened 2 months ago

cmwilson252 commented 2 months ago

Hello, thanks for all the previous help. Things have been going well. I noticed that I often get stuck here:

1 molecule converted Finished creating 'grid.txt'

Is there any insight into this? I believe the next function call is here:

create_map_files(lig_path, grid_file_path, pdbqt_path, n_jobs)
NiBoyang commented 2 months ago

Hi @cmwilson252, yes this is quite slow for now especially when the grid box size is large. I'm considering re-writing this part using Numba Cuda, but I'll probably start to do this after I complete my current project. Please wait for the following updates, many thanks.

cmwilson252 commented 2 months ago

Hello NiBoyang,

Thank you for all the replies, I am grateful for all the guidance thus far.

Do you have any timeline on this? I have found it hard to deploy this for general use due to the above function having extremely long execution times.

cmwilson252 commented 2 weeks ago

Hello NiBoyang,

I am checking in on this. This feature would still be highly desirable!

NiBoyang commented 2 weeks ago

Hi Colorado! Thanks for your message. I'd been quite busy preparing for my first-year PhD annual review, so sorry for the late reply. I'll be taking my annual leave from the next week for three weeks, however I'm very happy to improve the speed of the grid map generation during my holiday. I'll probably get back to you in a week with the updates. - Boyang

From: Colorado Wilson @.> Sent: Wednesday, July 10, 2024 16:48 To: NiBoyang/AutoDock-SS @.> Cc: Boyang Ni @.>; Comment @.> Subject: Re: [NiBoyang/AutoDock-SS] Stuck After Creating grid.txt (Issue #4)

Hello NiBoyang,

I am checking in on this. This feature would still be highly desirable!

— Reply to this email directly, view it on GitHubhttps://github.com/NiBoyang/AutoDock-SS/issues/4#issuecomment-2220883664, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AU3A5XITP6VUTMJV6MPPO7LZLVJTJAVCNFSM6AAAAABHJG2DA2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRQHA4DGNRWGQ. You are receiving this because you commented.

cmwilson252 commented 2 days ago

Congratulations on your first-year PhD review. No worries about the responses!

How is the rewrite coming?