Musse #102
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Musse #102
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guolinke
reviewed
Feb 28, 2023
guolinke
reviewed
Feb 28, 2023
unifold/config.py
Outdated
| "crop": False, | ||
| "crop_size": None, | ||
| "crop": True, | ||
| "crop_size": 384, |
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remove the changes of above two lines?
guolinke
reviewed
Feb 28, 2023
unifold/config.py
Outdated
| @@ -160,6 +166,8 @@ def base_config(): | |||
| ], | |||
| "use_templates": use_templates, | |||
| "is_multimer": is_multimer, | |||
| "is_single": is_single, | |||
| "feature_src": "", | |||
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what is this? should we keep it?
guolinke
reviewed
Feb 28, 2023
guolinke
reviewed
Feb 28, 2023
guolinke
reviewed
Feb 28, 2023
guolinke
reviewed
Feb 28, 2023
guolinke
reviewed
Feb 28, 2023
ZiyaoLi
reviewed
Feb 28, 2023
unifold/ssmultimer/__init__.py
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| @@ -0,0 +1,2 @@ | |||
| from . import model | |||
unifold/ssmultimer/dataset.py
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| # total_length = sum(x["aatype"].shape[0] for x in all_chain_features) | ||
| # pair = dok_matrix( | ||
| # (total_length, total_length, all_chain_features[0]["pair"].shape[-1]), | ||
| # dtype=all_chain_features[0]["pair"].dtype, |
unifold/data/process.py
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| @@ -48,10 +50,61 @@ def nonensembled_fns(common_cfg, mode_cfg): | |||
|
|
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| operators.append(data_ops.make_atom14_masks) | |||
| operators.append(data_ops.make_target_feat) | |||
| if common_cfg.structure_refine: | |||
| operators.append(data_ops.input_atom37_to_frames()) | |||
unifold/config.py
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| @@ -21,6 +21,7 @@ | |||
| inf = mlc.FieldReference(3e4, field_type=float) | |||
| use_templates = mlc.FieldReference(True, field_type=bool) | |||
| is_multimer = mlc.FieldReference(False, field_type=bool) | |||
| is_single = mlc.FieldReference(False, field_type=bool) | |||
unifold/config.py
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| @@ -591,6 +607,23 @@ def multimer(c): | |||
| recursive_set(c, "max_msa_clusters", 256) | |||
| c.data.train.crop_size = 384 | |||
| c.loss.violation.weight = 0.5 | |||
| elif name == "single_multimer_3b_newemb": | |||
unifold/inference.py
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| sequence_ids = open(os.path.join(data_folder, "chains.txt")).readline().split() | ||
| batch, _ = load_and_process( | ||
| batch, _ = load_and_process_ss( |
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this will harm normal unifold load_and_process. check if the two functions are equivalent, and use old fn name.
guolinke
approved these changes
Mar 2, 2023
jnooree
pushed a commit
to seoklab/Uni-Fold
that referenced
this pull request
Apr 24, 2024
* Uni-Fold Musse * mv plm to ssmultimer * update readme * udpatereadme * ss to musse * rename fn * fix monomer bug
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