rcsb-embedding-model 0.0.8__py3-none-any.whl → 0.0.10__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Potentially problematic release.
This version of rcsb-embedding-model might be problematic. Click here for more details.
- rcsb_embedding_model/dataset/esm_prot_from_structure.py +3 -2
- rcsb_embedding_model/utils/structure_parser.py +3 -2
- {rcsb_embedding_model-0.0.8.dist-info → rcsb_embedding_model-0.0.10.dist-info}/METADATA +2 -2
- {rcsb_embedding_model-0.0.8.dist-info → rcsb_embedding_model-0.0.10.dist-info}/RECORD +7 -7
- {rcsb_embedding_model-0.0.8.dist-info → rcsb_embedding_model-0.0.10.dist-info}/WHEEL +0 -0
- {rcsb_embedding_model-0.0.8.dist-info → rcsb_embedding_model-0.0.10.dist-info}/entry_points.txt +0 -0
- {rcsb_embedding_model-0.0.8.dist-info → rcsb_embedding_model-0.0.10.dist-info}/licenses/LICENSE.md +0 -0
|
@@ -33,8 +33,9 @@ class EsmProtFromStructure(EsmProtFromChain):
|
|
|
33
33
|
super().__init__(
|
|
34
34
|
src_stream=self.__get_chains(src_stream),
|
|
35
35
|
src_location=SrcLocation.stream,
|
|
36
|
-
structure_location=
|
|
37
|
-
structure_format=structure_format
|
|
36
|
+
structure_location=structure_location,
|
|
37
|
+
structure_format=structure_format,
|
|
38
|
+
structure_provider=structure_provider
|
|
38
39
|
)
|
|
39
40
|
|
|
40
41
|
def __get_chains(self, src_stream):
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
from biotite.structure import filter_amino_acids, chain_iter, get_chains, get_residues, AtomArray
|
|
1
|
+
from biotite.structure import filter_amino_acids, filter_polymer, chain_iter, get_chains, get_residues, AtomArray
|
|
2
2
|
from biotite.structure.io.pdb import PDBFile, get_structure as get_pdb_structure, get_assembly as get_pdb_assembly, list_assemblies as list_pdb_assemblies
|
|
3
3
|
from biotite.structure.io.pdbx import CIFFile, get_structure, get_assembly, BinaryCIFFile, list_assemblies
|
|
4
4
|
|
|
@@ -30,7 +30,8 @@ def get_structure_from_src(
|
|
|
30
30
|
def get_protein_chains(structure, min_res_n=0):
|
|
31
31
|
chain_ids = []
|
|
32
32
|
for atom_ch in chain_iter(structure):
|
|
33
|
-
atom_res = atom_ch[
|
|
33
|
+
atom_res = atom_ch[filter_polymer(atom_ch)]
|
|
34
|
+
atom_res = atom_res[filter_amino_acids(atom_res)]
|
|
34
35
|
if len(atom_res) > 0 and len(get_residues(atom_res)) > min_res_n:
|
|
35
36
|
chain_ids.append(str(get_chains(atom_res)[0]))
|
|
36
37
|
return tuple(chain_ids)
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: rcsb-embedding-model
|
|
3
|
-
Version: 0.0.
|
|
3
|
+
Version: 0.0.10
|
|
4
4
|
Summary: Protein Embedding Model for Structure Search
|
|
5
5
|
Project-URL: Homepage, https://github.com/rcsb/rcsb-embedding-model
|
|
6
6
|
Project-URL: Issues, https://github.com/rcsb/rcsb-embedding-model/issues
|
|
@@ -18,7 +18,7 @@ Description-Content-Type: text/markdown
|
|
|
18
18
|
|
|
19
19
|
# RCSB Embedding Model
|
|
20
20
|
|
|
21
|
-
**Version** 0.0.
|
|
21
|
+
**Version** 0.0.10
|
|
22
22
|
|
|
23
23
|
|
|
24
24
|
## Overview
|
|
@@ -3,7 +3,7 @@ rcsb_embedding_model/rcsb_structure_embedding.py,sha256=dKp9hXQO0JAnO4SEfjJ_mG_j
|
|
|
3
3
|
rcsb_embedding_model/cli/args_utils.py,sha256=7nP2q8pL5dWK_U7opxtWmoFcYVwasky6elHk-dASFaI,165
|
|
4
4
|
rcsb_embedding_model/cli/inference.py,sha256=KPZLqznbxZE_CBCGigUGg7yOfGsi8ID4aWMTExniRj4,11464
|
|
5
5
|
rcsb_embedding_model/dataset/esm_prot_from_chain.py,sha256=dBD2N0Y-GoN6p3z2yLnOvv6JGn-skAxwgbOYhXKDngc,3487
|
|
6
|
-
rcsb_embedding_model/dataset/esm_prot_from_structure.py,sha256=
|
|
6
|
+
rcsb_embedding_model/dataset/esm_prot_from_structure.py,sha256=URbT_SAp60MOZlOHnI3hdOBghR73TMNBV6jrtj5YUXA,2536
|
|
7
7
|
rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py,sha256=d8C7HRJBZWuOKhPQpihv1koT4aIvyt5QN2yndC2ABuE,2842
|
|
8
8
|
rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py,sha256=KXiohnPjjfZEFbPZQ46HGE8eEYWrVX8bfbTz4zPlo7o,3451
|
|
9
9
|
rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py,sha256=cOxT--Spkel10JJCeGlqgLXN5vNCZzPdfSxDgUSrdPI,1268
|
|
@@ -19,11 +19,11 @@ rcsb_embedding_model/modules/structure_module.py,sha256=dEtDNdWo1j2sSDa0JiOHQfEf
|
|
|
19
19
|
rcsb_embedding_model/types/api_types.py,sha256=3sPh33yb3Ya9r3O5vuiTfhb1WyFuhQWCQmewSbqEyG0,1076
|
|
20
20
|
rcsb_embedding_model/utils/data.py,sha256=x6ca_bVdBXEAp9ugCi1rVEQ-G5nGTFKpzDKqZKpkFBE,2933
|
|
21
21
|
rcsb_embedding_model/utils/model.py,sha256=rpZa-gfm3cEtbBd7UXMHrZv3x6f0AC8TJT3gtrSxr5I,852
|
|
22
|
-
rcsb_embedding_model/utils/structure_parser.py,sha256=
|
|
22
|
+
rcsb_embedding_model/utils/structure_parser.py,sha256=q_MmuU1AokZ-x-6ATxknJr_D6Sn3ZuaZ2yoJAIL-VIU,2767
|
|
23
23
|
rcsb_embedding_model/utils/structure_provider.py,sha256=eWtxjkPpmRfmil_DKR1J6miaXR3lQ28DF5O0qrqSgGA,786
|
|
24
24
|
rcsb_embedding_model/writer/batch_writer.py,sha256=ekgzFZyoKpcnZ3IDP9hfOWBpuHxUQ31P35ViDAi-Edw,2843
|
|
25
|
-
rcsb_embedding_model-0.0.
|
|
26
|
-
rcsb_embedding_model-0.0.
|
|
27
|
-
rcsb_embedding_model-0.0.
|
|
28
|
-
rcsb_embedding_model-0.0.
|
|
29
|
-
rcsb_embedding_model-0.0.
|
|
25
|
+
rcsb_embedding_model-0.0.10.dist-info/METADATA,sha256=B3dnAVzWNRpSLQ-nN-KI0ntE1VIbAF5Rzc1Hx5vlGdk,5368
|
|
26
|
+
rcsb_embedding_model-0.0.10.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
|
|
27
|
+
rcsb_embedding_model-0.0.10.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
|
|
28
|
+
rcsb_embedding_model-0.0.10.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
|
|
29
|
+
rcsb_embedding_model-0.0.10.dist-info/RECORD,,
|
|
File without changes
|
{rcsb_embedding_model-0.0.8.dist-info → rcsb_embedding_model-0.0.10.dist-info}/entry_points.txt
RENAMED
|
File without changes
|
{rcsb_embedding_model-0.0.8.dist-info → rcsb_embedding_model-0.0.10.dist-info}/licenses/LICENSE.md
RENAMED
|
File without changes
|