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README.md

@@ -1,10 +1,10 @@
 ---
 library_name: transformers
 tags:
-- biology
-- protein-structure
-- esmfold2
-- multimodal-protein-model
+  - biology
+  - protein-structure
+  - esmfold2
+  - multimodal-protein-model
 ---
 
 # FastPLMs ESMFold2

esmfold2_metrics.py

@@ -5,7 +5,7 @@ from einops import rearrange
 from torch import Tensor
 from torch.amp import autocast  # type: ignore
 
-from . import esmfold2_residue_constants
+from . import esmfold2_residue_constants as residue_constants
 from .esmfold2_misc import binpack, unbinpack
 from .esmfold2_protein_structure import (
     compute_alignment_tensors,

esmfold2_mmcif_parsing.py

@@ -10,7 +10,7 @@ from typing import Union
 import biotite.structure as bs
 import biotite.structure.io.pdbx as pdbx
 
-from . import esmfold2_residue_constants
+from . import esmfold2_residue_constants as residue_constants
 
 # Define PathOrBuffer for the opensource version
 PathOrBuffer = Union[str, os.PathLike, io.StringIO]

esmfold2_molecular_complex.py

@@ -23,7 +23,7 @@ from biotite.structure.io.pdbx import (
     set_structure,
 )
 
-from . import esmfold2_residue_constants
+from . import esmfold2_residue_constants as residue_constants
 from .esmfold2_metrics import compute_lddt, compute_rmsd
 from .esmfold2_protein_complex import ProteinComplex, ProteinComplexMetadata
 

esmfold2_protein_chain.py

@@ -20,7 +20,7 @@ from biotite.structure.io.pdbx import set_structure as set_structure_pdbx
 from scipy.spatial import ConvexHull, KDTree
 from scipy.spatial.distance import cdist, pdist, squareform
 
-from . import esmfold2_residue_constants
+from . import esmfold2_residue_constants as residue_constants
 from .esmfold2_misc import slice_python_object_as_numpy
 from .esmfold2_affine3d import Affine3D
 from .esmfold2_aligner import Aligner

esmfold2_protein_complex.py

@@ -27,7 +27,7 @@ from biotite.structure.io.pdbx.convert import _get_transformations, get_structur
 from biotite.structure.util import matrix_rotate
 from scipy.spatial import KDTree
 
-from . import esmfold2_residue_constants
+from . import esmfold2_residue_constants as residue_constants
 from .esmfold2_misc import slice_python_object_as_numpy
 from .esmfold2_affine3d import Affine3D
 from .esmfold2_aligner import Aligner

esmfold2_protein_structure.py

@@ -8,7 +8,7 @@ import torch.nn.functional as F
 from torch import Tensor
 from torch.amp import autocast  # type: ignore
 
-from . import esmfold2_residue_constants
+from . import esmfold2_residue_constants as residue_constants
 from .esmfold2_misc import unbinpack
 from .esmfold2_affine3d import Affine3D