boltz-vsynthes 1.0.17__py3-none-any.whl → 1.0.19__py3-none-any.whl

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Files changed (9) hide show
  1. boltz/data/parse/pdb.py +3 -4
  2. boltz/data/parse/pdb_download.py +4 -5
  3. boltz/data/parse/sdf.py +3 -4
  4. {boltz_vsynthes-1.0.17.dist-info → boltz_vsynthes-1.0.19.dist-info}/METADATA +1 -1
  5. {boltz_vsynthes-1.0.17.dist-info → boltz_vsynthes-1.0.19.dist-info}/RECORD +9 -9
  6. {boltz_vsynthes-1.0.17.dist-info → boltz_vsynthes-1.0.19.dist-info}/WHEEL +0 -0
  7. {boltz_vsynthes-1.0.17.dist-info → boltz_vsynthes-1.0.19.dist-info}/entry_points.txt +0 -0
  8. {boltz_vsynthes-1.0.17.dist-info → boltz_vsynthes-1.0.19.dist-info}/licenses/LICENSE +0 -0
  9. {boltz_vsynthes-1.0.17.dist-info → boltz_vsynthes-1.0.19.dist-info}/top_level.txt +0 -0
boltz/data/parse/pdb.py CHANGED
@@ -48,14 +48,13 @@ def parse_pdb(
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  for pp in ppb.build_peptides(chain):
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  seq = str(pp.get_sequence())
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  if seq: # Only add if sequence is not empty
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- molecule = {
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+ sequences.append({
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  "protein": {
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  "id": chain.id,
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  "sequence": seq,
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  "modifications": [],
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- },
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- }
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- sequences.append(molecule)
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+ }
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+ })
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  data = {
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  "sequences": sequences,
boltz/data/parse/pdb_download.py CHANGED
@@ -5,7 +5,7 @@ from typing import Optional
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  import requests
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  from Bio import PDB
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  from Bio.PDB.PDBParser import PDBParser
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- from Bio.PDB.PPBuilder import PPBuilder
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+ from Bio.PDB.Polypeptide import PPBuilder
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  from rdkit import Chem
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  from rdkit.Chem.rdchem import Mol
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@@ -91,14 +91,13 @@ def parse_pdb_id(
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  for pp in ppb.build_peptides(chain):
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  seq = str(pp.get_sequence())
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  if seq: # Only add if sequence is not empty
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- molecule = {
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+ sequences.append({
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  "protein": {
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  "id": chain.id,
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  "sequence": seq,
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  "modifications": [],
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- },
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- }
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- sequences.append(molecule)
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+ }
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+ })
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  data = {
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  "sequences": sequences,
boltz/data/parse/sdf.py CHANGED
@@ -72,14 +72,13 @@ def parse_sdf(
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  # Convert to yaml format
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  sequences = []
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  for mol_name, smiles in mol_dict.items():
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- molecule = {
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+ sequences.append({
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  "ligand": {
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  "id": mol_name,
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  "sequence": smiles,
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  "modifications": [],
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- },
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- }
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- sequences.append(molecule)
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+ }
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+ })
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  data = {
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  "sequences": sequences,
{boltz_vsynthes-1.0.17.dist-info → boltz_vsynthes-1.0.19.dist-info}/METADATA 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: 1.0.17
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+ Version: 1.0.19
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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-1.0.17.dist-info → boltz_vsynthes-1.0.19.dist-info}/RECORD RENAMED
@@ -38,10 +38,10 @@ boltz/data/parse/csv.py,sha256=Hcq8rJW2njczahEr8jfd_o-zxLaNSgJ3YIoC9srIqpw,2518
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  boltz/data/parse/fasta.py,sha256=taI4s_CqPtyF0XaLJAsVAJHCL0GXm2g1g8Qeccdxikk,3906
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  boltz/data/parse/mmcif.py,sha256=25kEXCkx-OuaawAs7cdz0fxdRu5_CCO0AV00u84PrjQ,36822
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  boltz/data/parse/mmcif_with_constraints.py,sha256=WHYZckSqUwu-Nb9vmVmxHmC7uxwVrF7AVUeVKsc5wGQ,51473
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- boltz/data/parse/pdb.py,sha256=R6rDCh6AKLn7n9ELltF1wDORDtR1CFgFnjFdYXKJCNg,1697
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- boltz/data/parse/pdb_download.py,sha256=YEvSoYqKAan6EizCICMruC_3v-Vpvc4vpCpwmHPY67E,2808
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+ boltz/data/parse/pdb.py,sha256=X4u1ZzSFk0Xy8LRbCCMVlbAzWeGddo2O4SQuk_WyS-k,1656
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+ boltz/data/parse/pdb_download.py,sha256=YLxCidVkRLlvZ0uCCSnRTP7Yz1-AYv9hz_SO3_xecWk,2769
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  boltz/data/parse/schema.py,sha256=pq9PRrm3pyaOH0kJEjtG-rVHEPpr_KmiykvxKsMWnn0,60979
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- boltz/data/parse/sdf.py,sha256=z7XTH-a38Rq-grC8bEZUPxGmLyP-g17LCxYWzVkBS_0,2107
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+ boltz/data/parse/sdf.py,sha256=Kc9CwyyNgs6IrXtEN1MLZbm6-A-DFRpPCDgMGgFEr9w,2078
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  boltz/data/parse/yaml.py,sha256=GRFRMtDD4PQ4PIpA_S1jj0vRaEu2LlZd_g4rN1zUrNo,1505
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  boltz/data/sample/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  boltz/data/sample/cluster.py,sha256=9Sx8qP7zGZOAyEspwYFtCTbGTBZnuN-zfCKFbbA_6oI,8175
@@ -107,9 +107,9 @@ boltz/model/optim/scheduler.py,sha256=nB4jz0CZ4pR4n08LQngExL_pNycIdYI8AXVoHPnZWQ
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  boltz/model/potentials/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  boltz/model/potentials/potentials.py,sha256=vev8Vjfs-ML1hyrdv_R8DynG4wSFahJ6nzPWp7CYQqw,17507
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  boltz/model/potentials/schedules.py,sha256=m7XJjfuF9uTX3bR9VisXv1rvzJjxiD8PobXRpcBBu1c,968
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- boltz_vsynthes-1.0.17.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
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- boltz_vsynthes-1.0.17.dist-info/METADATA,sha256=s2lJPUPQJ4BMEFa2Hc57Q8e5EYMPuEKr5IO_SxCVTmc,7171
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- boltz_vsynthes-1.0.17.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- boltz_vsynthes-1.0.17.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
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- boltz_vsynthes-1.0.17.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
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- boltz_vsynthes-1.0.17.dist-info/RECORD,,
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+ boltz_vsynthes-1.0.19.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
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+ boltz_vsynthes-1.0.19.dist-info/METADATA,sha256=-sNg3xpkJoj4lVSYxkDH_noDhJzFI_k5RMmw3C7xnsg,7171
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+ boltz_vsynthes-1.0.19.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ boltz_vsynthes-1.0.19.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
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+ boltz_vsynthes-1.0.19.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
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+ boltz_vsynthes-1.0.19.dist-info/RECORD,,