rcsb-embedding-model 0.0.19__py3-none-any.whl → 0.0.21__py3-none-any.whl
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- rcsb_embedding_model/cli/inference.py +3 -0
- rcsb_embedding_model/utils/data.py +1 -1
- {rcsb_embedding_model-0.0.19.dist-info → rcsb_embedding_model-0.0.21.dist-info}/METADATA +3 -3
- {rcsb_embedding_model-0.0.19.dist-info → rcsb_embedding_model-0.0.21.dist-info}/RECORD +7 -7
- {rcsb_embedding_model-0.0.19.dist-info → rcsb_embedding_model-0.0.21.dist-info}/WHEEL +0 -0
- {rcsb_embedding_model-0.0.19.dist-info → rcsb_embedding_model-0.0.21.dist-info}/entry_points.txt +0 -0
- {rcsb_embedding_model-0.0.19.dist-info → rcsb_embedding_model-0.0.21.dist-info}/licenses/LICENSE.md +0 -0
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@@ -8,6 +8,9 @@ from rcsb_embedding_model.types.api_types import StructureFormat, Accelerator, S
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StructureLocation, SrcAssemblyFrom, SrcTensorFrom, OutFormat
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from rcsb_embedding_model.utils.data import adapt_csv_to_embedding_chain_stream
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import os
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os.environ["TOKENIZERS_PARALLELISM"] = "false"
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app = typer.Typer(
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add_completion=False
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)
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@@ -76,7 +76,7 @@ def concatenate_tensors(file_list, max_residues, dim=0):
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tensor_cat = torch.cat(tensors, dim=dim)
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return tensor_cat
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else:
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raise ValueError("No valid tensors were loaded to concatenate.")
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raise ValueError(f"No valid tensors were loaded to concatenate. {', '.join(file_list)}")
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def adapt_csv_to_embedding_chain_stream(src_file, res_embedding_location):
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def __parse_row(row):
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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: 0.0.21
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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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@@ -17,7 +17,7 @@ Description-Content-Type: text/markdown
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# RCSB Embedding Model
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**Version** 0.0.
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**Version** 0.0.21
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## Overview
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@@ -48,7 +48,7 @@ If you are interested in training the model with a new dataset, visit the [rcsb-
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**Requirements:**
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- Python ≥ 3.10
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- ESM
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- ESM >= 3.2.0
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- Lightning ≥ 2.5.0
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- Typer ≥ 0.15.0
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@@ -1,7 +1,7 @@
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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=dKp9hXQO0JAnO4SEfjJ_mG_jHu3UxAPguv6jkOjp-BI,4487
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rcsb_embedding_model/cli/args_utils.py,sha256=7nP2q8pL5dWK_U7opxtWmoFcYVwasky6elHk-dASFaI,165
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rcsb_embedding_model/cli/inference.py,sha256=
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rcsb_embedding_model/cli/inference.py,sha256=JckVWVaMJ6-X1U0Md-wwYY0Sl6g-ITRovbylwuvFMvo,18289
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rcsb_embedding_model/dataset/esm_prot_from_chain.py,sha256=3hWo2nWunFZNTfYCTiPvVoJlkWQbRmvlehFw-6B4z6A,3506
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rcsb_embedding_model/dataset/esm_prot_from_structure.py,sha256=TeITPdi1uc3qLQ-Pgn807oH6eM0LYv-67RE50ZT4dLI,2551
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rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py,sha256=worRiNqOJRjyr693TaillsS65bdTdGOoHfwyT9yE1O4,2866
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@@ -18,13 +18,13 @@ rcsb_embedding_model/modules/chain_module.py,sha256=sDSPXJmWuU2C3lt1NorlbUVWZvRS
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rcsb_embedding_model/modules/esm_module.py,sha256=MzE-9_25262m80yW7Pb-Pkf8L-R_xb3FPcz9gOlNgAI,705
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rcsb_embedding_model/modules/structure_module.py,sha256=dEtDNdWo1j2sSDa0JiOHQfEfQzIWqSLEKpvOX0GrXZ4,1048
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rcsb_embedding_model/types/api_types.py,sha256=SCwALwvEb0KRKaoWKbuN7JyfOH-1whsI0Z4ki41dht8,1235
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rcsb_embedding_model/utils/data.py,sha256=
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rcsb_embedding_model/utils/data.py,sha256=ATgHC6d7xgc2eYtCsEsgMxhAFvYp4R9C0TlNStc1jG0,3254
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rcsb_embedding_model/utils/model.py,sha256=rpZa-gfm3cEtbBd7UXMHrZv3x6f0AC8TJT3gtrSxr5I,852
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rcsb_embedding_model/utils/structure_parser.py,sha256=IWMQ8brlEMe6_ND-DBESOli8vlqHxladTssjbM9RSKw,2751
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rcsb_embedding_model/utils/structure_provider.py,sha256=eWtxjkPpmRfmil_DKR1J6miaXR3lQ28DF5O0qrqSgGA,786
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rcsb_embedding_model/writer/batch_writer.py,sha256=rTFNasB0Xp4-XCNTXKeEWZxSrb7lvZytoRldJUWn9Jg,3312
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rcsb_embedding_model-0.0.21.dist-info/METADATA,sha256=wfjwwwQccZ13sJdw5DV_nZ-tsGt6P9WLRcuiDdMV9t0,5310
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rcsb_embedding_model-0.0.21.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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rcsb_embedding_model-0.0.21.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
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rcsb_embedding_model-0.0.21.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
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rcsb_embedding_model-0.0.21.dist-info/RECORD,,
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{rcsb_embedding_model-0.0.19.dist-info → rcsb_embedding_model-0.0.21.dist-info}/entry_points.txt
RENAMED
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File without changes
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{rcsb_embedding_model-0.0.19.dist-info → rcsb_embedding_model-0.0.21.dist-info}/licenses/LICENSE.md
RENAMED
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