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MinkaiXu / GeoDiff

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
MIT License
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test.py，How do you specify a specific molecule simles to generating？ #19

Open lonngxiang opened 1 year ago

JackAILab commented 1 year ago

I also have this problem～ I find it hard to generate the 3D structure through the test result.

MinkaiXu commented 1 year ago

Hi, indeed you can write your molecule graph into .pkl, as the same format in the provided training/test sets.

JackAILab commented 1 year ago

Dear author,

I have reproduced your entire code and now got some pkl files as shown in the picture below, but I cannot generate the 3D molecular conformation shown in your paper from these pkl files.

I would like to know whether it is necessary to use the function shown in the figure to complete the generation from the pkl file to the 3d molecular conformation map. Besides, can you provide some detailed instructions on generating 3D visualization results?

---- Replied Message ---- | From | Minkai @.> | | Date | 04/5/2023 10:59 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [MinkaiXu/GeoDiff] test.py，How do you specify a specific molecule simles to generating？ (Issue #19) |

Hi, indeed you can write your molecule graph into .pkl, as the same format in the provided training/test sets.

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MinkaiXu commented 1 year ago

Hi,

For visualization, we just use the software called PyMol, which can render molecular structures. Sorry that this is an entire software and we couldn't provide all guidelines for using the software. We suggest you can refer to their official document for full details (https://pymol.org/dokuwiki/).

Thanks!