rcsb-embedding-model 0.0.2__py3-none-any.whl → 0.0.3__py3-none-any.whl
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- rcsb_embedding_model/rcsb_structure_embedding.py +8 -4
- {rcsb_embedding_model-0.0.2.dist-info → rcsb_embedding_model-0.0.3.dist-info}/METADATA +3 -3
- rcsb_embedding_model-0.0.3.dist-info/RECORD +8 -0
- rcsb_embedding_model-0.0.2.dist-info/RECORD +0 -8
- {rcsb_embedding_model-0.0.2.dist-info → rcsb_embedding_model-0.0.3.dist-info}/WHEEL +0 -0
- {rcsb_embedding_model-0.0.2.dist-info → rcsb_embedding_model-0.0.3.dist-info}/licenses/LICENSE.md +0 -0
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@@ -29,10 +29,7 @@ class RcsbStructureEmbedding:
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def load_residue_embedding(self, device=None):
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if not device:
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device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
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self.__residue_embedding =
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ESM3_OPEN_SMALL,
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device
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)
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self.__residue_embedding = _load_res_model(device)
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def load_aggregator_embedding(self, device=None):
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if not device:
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@@ -146,3 +143,10 @@ def _load_model(model_path, device=None):
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aggregator_model.to(device)
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aggregator_model.eval()
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return aggregator_model
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def _load_res_model(device=None):
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return ESM3.from_pretrained(
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ESM3_OPEN_SMALL,
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device
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)
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@@ -1,6 +1,6 @@
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Metadata-Version: 2.4
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Name: rcsb-embedding-model
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Version: 0.0.
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Version: 0.0.3
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Summary: Protein Embedding Model for Structure Search
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Project-URL: Homepage, https://github.com/rcsb/rcsb-embedding-model
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Project-URL: Issues, https://github.com/rcsb/rcsb-embedding-model/issues
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@@ -11,7 +11,7 @@ Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python :: 3
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Requires-Python: >=3.10
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Requires-Dist: esm>=3.2.0
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Requires-Dist: torch>=2.
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Requires-Dist: torch>=2.2.0
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Description-Content-Type: text/markdown
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# RCSB Embedding Model: A Deep Learning Approach for 3D Structure Embeddings
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@@ -70,7 +70,7 @@ res_embedding = model.residue_embedding(
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```
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### **Generating Protein Structure**
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### **Generating Protein Structure Embeddings**
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Protein 3D structure embedding can be calculated as:
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```python
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rcsb_embedding_model/__init__.py,sha256=r3gLdeBIXkQEQA_K6QcRPO-TtYuAQSutk6pXRUE_nas,120
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rcsb_embedding_model/rcsb_structure_embedding.py,sha256=DFpq8r6s2cZIRQb7Rj-XkyWngxb_JxJuCUvimZoO4jI,5254
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rcsb_embedding_model/model/layers.py,sha256=lhKaWC4gTS_T5lHOP0mgnnP8nKTPEOm4MrjhESA4hE8,743
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rcsb_embedding_model/model/residue_embedding_aggregator.py,sha256=k3UW63Ax8DtjCMdD3O5xNxtyAu28l2n3-Ab6nS0atm0,1967
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rcsb_embedding_model-0.0.3.dist-info/METADATA,sha256=2os9xEQZJwjw_aftS4UCLKZhSLdBqiC0w07xVYc6boo,5381
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rcsb_embedding_model-0.0.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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rcsb_embedding_model-0.0.3.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
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rcsb_embedding_model-0.0.3.dist-info/RECORD,,
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rcsb_embedding_model/__init__.py,sha256=r3gLdeBIXkQEQA_K6QcRPO-TtYuAQSutk6pXRUE_nas,120
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rcsb_embedding_model/rcsb_structure_embedding.py,sha256=quxl9SnLPIYJE7yn7kXgJvCKR-W9kXIJ5fBFTTLV1YQ,5195
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rcsb_embedding_model/model/layers.py,sha256=lhKaWC4gTS_T5lHOP0mgnnP8nKTPEOm4MrjhESA4hE8,743
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rcsb_embedding_model/model/residue_embedding_aggregator.py,sha256=k3UW63Ax8DtjCMdD3O5xNxtyAu28l2n3-Ab6nS0atm0,1967
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rcsb_embedding_model-0.0.2.dist-info/METADATA,sha256=O5JNOufpbfTUJznAWaWMwwicerku0ih7TjWfzAc3OJo,5370
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rcsb_embedding_model-0.0.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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rcsb_embedding_model-0.0.2.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
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rcsb_embedding_model-0.0.2.dist-info/RECORD,,
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{rcsb_embedding_model-0.0.2.dist-info → rcsb_embedding_model-0.0.3.dist-info}/licenses/LICENSE.md
RENAMED
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File without changes
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