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Fix imports in tools notebooks (#103)

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This commit is contained in:
santiag0m
2024-09-03 16:47:13 -07:00
committed by GitHub
parent 4a92fb222c
commit e87f84912e
4 changed files with 47 additions and 39 deletions
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12
esm/tokenization/structure_tokenizer.py
View File

@@ -6,13 +6,13 @@ class StructureTokenizer(EsmTokenizerBase):
"""A convenince class for accessing special token ids of
the StructureTokenEncoder and StructureTokenDecoder."""
def __init__(self, cookbook_size: int = C.VQVAE_CODEBOOK_SIZE):
def __init__(self, codebook_size: int = C.VQVAE_CODEBOOK_SIZE):
self.vq_vae_special_tokens = {
"MASK": cookbook_size,
"EOS": cookbook_size + 1,
"BOS": cookbook_size + 2,
"PAD": cookbook_size + 3,
"CHAINBREAK": cookbook_size + 4,
"MASK": codebook_size,
"EOS": codebook_size + 1,
"BOS": codebook_size + 2,
"PAD": codebook_size + 3,
"CHAINBREAK": codebook_size + 4,
}
def mask_token(self) -> str:

24
tools/generate.ipynb
View File

@@ -33,11 +33,7 @@
"metadata": {},
"outputs": [],
"source": [
"import huggingface_hub\n",
"import nest_asyncio\n",
"from esm.widgets.utils.types import ClientInitContainer\n",
"from esm.widgets.views.generation import create_generation_ui\n",
"from esm.widgets.views.login import create_login_ui\n",
"\n",
"nest_asyncio.apply()"
]
@@ -57,6 +53,8 @@
"metadata": {},
"outputs": [],
"source": [
"import huggingface_hub\n",
"\n",
"huggingface_hub.login()"
]
},
@@ -67,6 +65,17 @@
"### Inference Settings"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from esm.widgets.utils.types import ClientInitContainer\n",
"from esm.widgets.views.generation import create_generation_ui\n",
"from esm.widgets.views.login import create_login_ui"
]
},
{
"cell_type": "code",
"execution_count": null,
@@ -95,13 +104,6 @@
"client = client_init()\n",
"create_generation_ui(client)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {

21
tools/invfold.ipynb
View File

@@ -33,13 +33,7 @@
"metadata": {},
"outputs": [],
"source": [
"import huggingface_hub\n",
"import nest_asyncio\n",
"from esm.widgets.utils.types import ClientInitContainer\n",
"from esm.widgets.views.inverse_folding import (\n",
" create_inverse_folding_ui,\n",
")\n",
"from esm.widgets.views.login import create_login_ui\n",
"\n",
"nest_asyncio.apply()"
]
@@ -59,6 +53,8 @@
"metadata": {},
"outputs": [],
"source": [
"import huggingface_hub\n",
"\n",
"huggingface_hub.login()"
]
},
@@ -69,6 +65,19 @@
"### Inference Settings"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from esm.widgets.utils.types import ClientInitContainer\n",
"from esm.widgets.views.inverse_folding import (\n",
" create_inverse_folding_ui,\n",
")\n",
"from esm.widgets.views.login import create_login_ui"
]
},
{
"cell_type": "code",
"execution_count": null,

29
tools/predict.ipynb
View File

@@ -33,11 +33,7 @@
"metadata": {},
"outputs": [],
"source": [
"import huggingface_hub\n",
"import nest_asyncio\n",
"from esm.widgets.utils.types import ClientInitContainer\n",
"from esm.widgets.views.login import create_login_ui\n",
"from esm.widgets.views.prediction import create_prediction_ui\n",
"\n",
"nest_asyncio.apply()"
]
@@ -57,6 +53,8 @@
"metadata": {},
"outputs": [],
"source": [
"import huggingface_hub\n",
"\n",
"huggingface_hub.login()"
]
},
@@ -67,6 +65,17 @@
"### Inference Settings"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from esm.widgets.utils.types import ClientInitContainer\n",
"from esm.widgets.views.login import create_login_ui\n",
"from esm.widgets.views.prediction import create_prediction_ui"
]
},
{
"cell_type": "code",
"execution_count": null,
@@ -109,18 +118,6 @@
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.0"
}
},
"nbformat": 4,