boltz-vsynthes 1.0.10__tar.gz → 1.0.12__tar.gz

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Files changed (123) hide show
  1. {boltz_vsynthes-1.0.10/src/boltz_vsynthes.egg-info → boltz_vsynthes-1.0.12}/PKG-INFO +1 -1
  2. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/pyproject.toml +1 -1
  3. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/pdb.py +2 -2
  4. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/pdb_download.py +2 -2
  5. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12/src/boltz_vsynthes.egg-info}/PKG-INFO +1 -1
  6. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/LICENSE +0 -0
  7. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/README.md +0 -0
  8. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/setup.cfg +0 -0
  9. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/__init__.py +0 -0
  10. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/__init__.py +0 -0
  11. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/const.py +0 -0
  12. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/crop/__init__.py +0 -0
  13. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/crop/affinity.py +0 -0
  14. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/crop/boltz.py +0 -0
  15. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/crop/cropper.py +0 -0
  16. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/feature/__init__.py +0 -0
  17. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/feature/featurizer.py +0 -0
  18. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/feature/featurizerv2.py +0 -0
  19. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/feature/symmetry.py +0 -0
  20. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/__init__.py +0 -0
  21. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/dynamic/__init__.py +0 -0
  22. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/dynamic/date.py +0 -0
  23. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/dynamic/filter.py +0 -0
  24. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/dynamic/max_residues.py +0 -0
  25. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/dynamic/resolution.py +0 -0
  26. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/dynamic/size.py +0 -0
  27. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/dynamic/subset.py +0 -0
  28. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/static/__init__.py +0 -0
  29. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/static/filter.py +0 -0
  30. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/static/ligand.py +0 -0
  31. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/filter/static/polymer.py +0 -0
  32. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/module/__init__.py +0 -0
  33. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/module/inference.py +0 -0
  34. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/module/inferencev2.py +0 -0
  35. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/module/training.py +0 -0
  36. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/module/trainingv2.py +0 -0
  37. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/mol.py +0 -0
  38. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/msa/__init__.py +0 -0
  39. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/msa/mmseqs2.py +0 -0
  40. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/pad.py +0 -0
  41. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/__init__.py +0 -0
  42. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/a3m.py +0 -0
  43. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/csv.py +0 -0
  44. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/fasta.py +0 -0
  45. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/mmcif.py +0 -0
  46. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/mmcif_with_constraints.py +0 -0
  47. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/schema.py +0 -0
  48. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/sdf.py +0 -0
  49. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/yaml.py +0 -0
  50. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/sample/__init__.py +0 -0
  51. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/sample/cluster.py +0 -0
  52. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/sample/distillation.py +0 -0
  53. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/sample/random.py +0 -0
  54. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/sample/sampler.py +0 -0
  55. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/tokenize/__init__.py +0 -0
  56. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/tokenize/boltz.py +0 -0
  57. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/tokenize/boltz2.py +0 -0
  58. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/tokenize/tokenizer.py +0 -0
  59. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/types.py +0 -0
  60. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/write/__init__.py +0 -0
  61. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/write/mmcif.py +0 -0
  62. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/write/pdb.py +0 -0
  63. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/write/utils.py +0 -0
  64. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/write/writer.py +0 -0
  65. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/main.py +0 -0
  66. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/__init__.py +0 -0
  67. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/__init__.py +0 -0
  68. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/attention.py +0 -0
  69. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/attentionv2.py +0 -0
  70. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/confidence_utils.py +0 -0
  71. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/dropout.py +0 -0
  72. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/initialize.py +0 -0
  73. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/outer_product_mean.py +0 -0
  74. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/pair_averaging.py +0 -0
  75. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/pairformer.py +0 -0
  76. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/relative.py +0 -0
  77. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/transition.py +0 -0
  78. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/triangular_attention/__init__.py +0 -0
  79. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/triangular_attention/attention.py +0 -0
  80. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/triangular_attention/primitives.py +0 -0
  81. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/triangular_attention/utils.py +0 -0
  82. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/layers/triangular_mult.py +0 -0
  83. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/loss/__init__.py +0 -0
  84. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/loss/bfactor.py +0 -0
  85. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/loss/confidence.py +0 -0
  86. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/loss/confidencev2.py +0 -0
  87. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/loss/diffusion.py +0 -0
  88. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/loss/diffusionv2.py +0 -0
  89. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/loss/distogram.py +0 -0
  90. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/loss/distogramv2.py +0 -0
  91. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/loss/validation.py +0 -0
  92. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/models/__init__.py +0 -0
  93. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/models/boltz1.py +0 -0
  94. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/models/boltz2.py +0 -0
  95. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/__init__.py +0 -0
  96. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/affinity.py +0 -0
  97. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/confidence.py +0 -0
  98. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/confidence_utils.py +0 -0
  99. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/confidencev2.py +0 -0
  100. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/diffusion.py +0 -0
  101. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/diffusion_conditioning.py +0 -0
  102. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/diffusionv2.py +0 -0
  103. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/encoders.py +0 -0
  104. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/encodersv2.py +0 -0
  105. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/transformers.py +0 -0
  106. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/transformersv2.py +0 -0
  107. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/trunk.py +0 -0
  108. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/trunkv2.py +0 -0
  109. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/modules/utils.py +0 -0
  110. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/optim/__init__.py +0 -0
  111. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/optim/ema.py +0 -0
  112. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/optim/scheduler.py +0 -0
  113. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/potentials/__init__.py +0 -0
  114. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/potentials/potentials.py +0 -0
  115. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/model/potentials/schedules.py +0 -0
  116. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz_vsynthes.egg-info/SOURCES.txt +0 -0
  117. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz_vsynthes.egg-info/dependency_links.txt +0 -0
  118. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz_vsynthes.egg-info/entry_points.txt +0 -0
  119. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz_vsynthes.egg-info/requires.txt +0 -0
  120. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz_vsynthes.egg-info/top_level.txt +0 -0
  121. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/tests/test_kernels.py +0 -0
  122. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/tests/test_regression.py +0 -0
  123. {boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/tests/test_utils.py +0 -0
{boltz_vsynthes-1.0.10/src/boltz_vsynthes.egg-info → boltz_vsynthes-1.0.12}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: boltz-vsynthes
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- Version: 1.0.10
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+ Version: 1.0.12
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  Summary: Boltz for VSYNTHES
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  Requires-Python: <3.13,>=3.10
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  Description-Content-Type: text/markdown
{boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "boltz-vsynthes"
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- version = "1.0.10"
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+ version = "1.0.12"
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  requires-python = ">=3.10,<3.13"
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  description = "Boltz for VSYNTHES"
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  readme = "README.md"
{boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/pdb.py RENAMED
@@ -2,7 +2,7 @@ from pathlib import Path
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  from typing import Optional
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  from Bio import PDB
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- from Bio.PDB.Polypeptide import three_to_one
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+ from Bio.Data.IUPACData import protein_letters_3to1
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  from rdkit import Chem
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  from rdkit.Chem.rdchem import Mol
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@@ -47,7 +47,7 @@ def parse_pdb(
47
47
  for residue in chain:
48
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  if residue.id[0] == " ": # Only standard residues
49
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  try:
50
- seq += three_to_one(residue.resname)
50
+ seq += protein_letters_3to1[residue.resname]
51
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  except KeyError:
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  continue
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{boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/src/boltz/data/parse/pdb_download.py RENAMED
@@ -4,7 +4,7 @@ from typing import Optional
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  import requests
6
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  from Bio import PDB
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- from Bio.PDB.Polypeptide import three_to_one
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+ from Bio.Data.IUPACData import protein_letters_3to1
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  from rdkit import Chem
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  from rdkit.Chem.rdchem import Mol
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@@ -91,7 +91,7 @@ def parse_pdb_id(
91
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  for residue in chain:
92
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  if residue.id[0] == " ": # Only standard residues
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  try:
94
- seq += three_to_one(residue.resname)
94
+ seq += protein_letters_3to1[residue.resname]
95
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  except KeyError:
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  continue
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{boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12/src/boltz_vsynthes.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: boltz-vsynthes
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- Version: 1.0.10
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+ Version: 1.0.12
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  Summary: Boltz for VSYNTHES
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  Requires-Python: <3.13,>=3.10
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  Description-Content-Type: text/markdown
{boltz_vsynthes-1.0.10 → boltz_vsynthes-1.0.12}/LICENSE RENAMED
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