rcsb-embedding-model 0.0.29__py3-none-any.whl → 0.0.30__py3-none-any.whl
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- rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py +10 -4
- rcsb_embedding_model/utils/structure_parser.py +1 -1
- {rcsb_embedding_model-0.0.29.dist-info → rcsb_embedding_model-0.0.30.dist-info}/METADATA +1 -1
- {rcsb_embedding_model-0.0.29.dist-info → rcsb_embedding_model-0.0.30.dist-info}/RECORD +7 -7
- {rcsb_embedding_model-0.0.29.dist-info → rcsb_embedding_model-0.0.30.dist-info}/WHEEL +0 -0
- {rcsb_embedding_model-0.0.29.dist-info → rcsb_embedding_model-0.0.30.dist-info}/entry_points.txt +0 -0
- {rcsb_embedding_model-0.0.29.dist-info → rcsb_embedding_model-0.0.30.dist-info}/licenses/LICENSE.md +0 -0
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@@ -1,3 +1,4 @@
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import argparse
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import sys
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import pandas as pd
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@@ -76,12 +77,17 @@ class ResidueAssemblyEmbeddingFromTensorFile(Dataset):
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if __name__ == "__main__":
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parser = argparse.ArgumentParser()
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parser.add_argument('--file_list', type=argparse.FileType('r'), required=True)
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parser.add_argument('--res_embeddings_path', required=True)
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args = parser.parse_args()
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dataset = ResidueAssemblyEmbeddingFromTensorFile(
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src_stream=
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res_embedding_location=
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src_stream=args.file_list,
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res_embedding_location=args.res_embeddings_path,
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src_location=SrcLocation.file,
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structure_location=StructureLocation.
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structure_format=StructureFormat.
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structure_location=StructureLocation.remote,
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structure_format=StructureFormat.bciff
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)
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dataloader = DataLoader(
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@@ -32,7 +32,7 @@ def get_protein_chains(structure, min_res_n=0):
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for atom_ch in chain_iter(structure):
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atom_res = atom_ch[filter_polymer(atom_ch)]
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atom_res = atom_res[filter_amino_acids(atom_res)]
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if len(atom_res) > 0 and len(get_residues(atom_res)) > min_res_n:
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if len(atom_res) > 0 and len(get_residues(atom_res)[0]) > min_res_n:
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chain_ids.append(str(get_chains(atom_res)[0]))
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return tuple(chain_ids)
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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: 0.0.30
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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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@@ -5,7 +5,7 @@ rcsb_embedding_model/cli/inference.py,sha256=tfMvHAhkUIzJ2RbTtQjq7eWmOUrSyVfH5bj
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rcsb_embedding_model/dataset/esm_prot_from_chain.py,sha256=l8pRgRpz-8gEzR6QsNcmdnX_KkgvgF1vdqNAsP8Lrc8,3960
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rcsb_embedding_model/dataset/esm_prot_from_structure.py,sha256=3HzXCCc-UqmZNbJaeXHyUsSIZZxMc2erbxAPGIxSmfE,2621
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rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py,sha256=69h1VkrIXesHZi1cG3BOMMytSDeRzcBBP0_Z3Xz3dM8,2869
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rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py,sha256=
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rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py,sha256=Hd9oH-IVgY6d7Dxy5VfiwHvSaK-Wwhk6ccUBgOwl0TU,3740
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rcsb_embedding_model/dataset/residue_embedding_from_structure.py,sha256=1jmeEcCK41cAi2ZnqQkd667NWCAIGS3k6jGDF-WxtTk,2854
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rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py,sha256=4OPaw55yGKHjY2iPpCnemcfwfmTZ4j5VrGQ2oIMQw6A,1343
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rcsb_embedding_model/inference/assembly_inferece.py,sha256=8fPJjEXy1WsM5XB5U7KfdO5-Du6nEsawsaAjmWoXA9I,2329
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@@ -20,11 +20,11 @@ rcsb_embedding_model/modules/structure_module.py,sha256=4js02XzKvhc_G26ELsGhJ9SC
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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=BOjYdIRHrFqk8qFuKGrgCtVyfDupzgOVmH_0C-ecMvg,3813
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rcsb_embedding_model/utils/model.py,sha256=xr3p02ohOgJ5UInwdIupN68Oq4yvNFhxobZRacS1adg,953
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rcsb_embedding_model/utils/structure_parser.py,sha256=
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rcsb_embedding_model/utils/structure_parser.py,sha256=eq1Jpmeo5oqqo_kzYbyIrqDysBAZR3II0mZK3ygaYhs,2754
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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.
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rcsb_embedding_model-0.0.
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rcsb_embedding_model-0.0.
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rcsb_embedding_model-0.0.30.dist-info/METADATA,sha256=IjxTnTFbYAIGu99NNAH2MII46PvFMZXEkim5STOCNTU,5310
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rcsb_embedding_model-0.0.30.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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rcsb_embedding_model-0.0.30.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
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rcsb_embedding_model-0.0.30.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
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rcsb_embedding_model-0.0.30.dist-info/RECORD,,
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{rcsb_embedding_model-0.0.29.dist-info → rcsb_embedding_model-0.0.30.dist-info}/entry_points.txt
RENAMED
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File without changes
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{rcsb_embedding_model-0.0.29.dist-info → rcsb_embedding_model-0.0.30.dist-info}/licenses/LICENSE.md
RENAMED
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