Add Uni-Fold Conformer (a diffusion-based conformation sampling method) - #148

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PKUfjh wants to merge 26 commits into

dptech-corp:mainfrom

PKUfjh commented May 18, 2024

Add ufconf model code.
Add ufconf inference scripts.
Add ufconf README file

PKUfjh added 3 commits

May 18, 2024 13:45


          organize scripts for ufconf

8825e7d


          update unifold module

9c73cea


          set default ufconf model, update readme

7967d31

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unifold/msa/mmcif.py

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README.md

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example_diffold/1ake_dataset_monomer.json

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finetune_ufconf.sh Outdated

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notebooks/README.md Outdated

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notebooks/run_ufconf_denoise.py

ZiyaoLi May 21, 2024

Member

these 3 py files are noqa by me currently

PKUfjh May 23, 2024

Author

refined the scripts

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setup.py

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ufconf/README.md

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ufconf/config.py

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ufconf/dataset.py Outdated

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ufconf/dataset_clu.py Outdated

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ufconf/diffold.py

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ufconf/diffusion/angle.py

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ufconf/task.py Outdated

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ufconf/utils.py

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unifold/config.py

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unifold/data/lmdb_dataset.py

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unifold/dataset.py

ZiyaoLi May 21, 2024

Member

revert this

PKUfjh May 23, 2024

Author

this has problem running the inference scripts, need to discuss how to refine this part of the codes

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unifold/inference.py

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unifold/inference_symmetry.py

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unifold/data/msa_pairing.py

                   "rigid_group_default_frame",
                   # zy
                   "num_sym",
+                  "input_atom_positions",

ZiyaoLi May 21, 2024

Member

these 4 keywords seem never used. try removing these and see if still runnable

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unifold/refine/modules/fold.py Outdated

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unifold/symmetry/dataset.py

unifold/task.py

ZiyaoLi changed the title ~~Add ufconf scripts~~ Add Uni-Fold Conformer (a diffusion-based conformation sampling method)

ZiyaoLi changed the base branch from main to ufconformer

May 21, 2024 10:28

ZiyaoLi changed the base branch from ufconformer to main

May 21, 2024 10:30


          remove redundant codes

cc2df8b

PKUfjh added 4 commits

May 22, 2024 19:45


          refine inference scripts, update readme

793b183


          revert refine and symmetry part of unifold

b6c66b7


          fix monomer bugs

d69a9e7


          rename diffold to ufconf

e1d95e0

PKUfjh requested a review from ZiyaoLi

May 23, 2024 10:17


          add test script

4b91957

PKUfjh force-pushed the ufconf branch from 49fe427 to 4b91957 Compare

May 29, 2024 14:55

PKUfjh and others added 17 commits

May 29, 2024 22:56


          add list selection for motif

82c7fb7


          add RAC-47 dataset

56ec119


          add fasta file input option

5113f24


          minor fix

68cc4b0


          update config

daff8d1


          update inference script

bde0899


          update readme

d7d06d2


          fix multimer bugs for fasta input

7eae6f6


          fix partial generation bugs

5bb8619


          update msa generation code

bcc7a86


          update msa example

b25c02a


          fix msa generation bugs

1ed80d2


          fix label bug


          add checkpoint info

eb5f20e


          update installation guide

85a6727


          add multimer example

a7e9e6b


          update ufconf readme

c852827

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