pyg-nightly 2.7.0.dev20250711__py3-none-any.whl → 2.7.0.dev20250713__py3-none-any.whl

{pyg_nightly-2.7.0.dev20250711.dist-info → pyg_nightly-2.7.0.dev20250713.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyg-nightly
-Version: 2.7.0.dev20250711
+Version: 2.7.0.dev20250713
 Summary: Graph Neural Network Library for PyTorch
 Keywords: deep-learning,pytorch,geometric-deep-learning,graph-neural-networks,graph-convolutional-networks
 Author-email: Matthias Fey <matthias@pyg.org>

{pyg_nightly-2.7.0.dev20250711.dist-info → pyg_nightly-2.7.0.dev20250713.dist-info}/RECORD

@@ -1,4 +1,4 @@
-torch_geometric/__init__.py,sha256=NE6Fc3xown9lpTtgn1teq5bvwDdXNjPDbqwPsMp41wI,2250
+torch_geometric/__init__.py,sha256=wobkgAtkT1v1hcj7sCzCZBYSBRjGYfs8YUNuN9sFrqc,2250
 torch_geometric/_compile.py,sha256=9yqMTBKatZPr40WavJz9FjNi7pQj8YZAZOyZmmRGXgc,1351
 torch_geometric/_onnx.py,sha256=V9ffrIKSqhDw6xUZ12lkuSfNs48cQp2EeJ6Z19GfnVw,349
 torch_geometric/backend.py,sha256=lVaf7aLoVaB3M-UcByUJ1G4T4FOK6LXAg0CF4W3E8jo,1575
@@ -463,7 +463,7 @@ torch_geometric/nn/models/neural_fingerprint.py,sha256=pTLJgU9Uh2Lnf9bggLj4cKI8Y
 torch_geometric/nn/models/node2vec.py,sha256=81Ku4Rp4IwLEAy06KEgJ2fYtXXVL_uv_Hb8lBr6YXrE,7664
 torch_geometric/nn/models/pmlp.py,sha256=dcAASVSyQMMhItSfEJWPeAFh0R3tNCwAHwdrShwQ8o4,3538
 torch_geometric/nn/models/polynormer.py,sha256=mayWdzdolT5PCt_Oo7UGG-JUripMHWB2lUWF1bh6goU,7640
-torch_geometric/nn/models/protein_mpnn.py,sha256=QXHfltiJPmakpzgJKw_1vwCGBlszv9nfY4r4F38Sg9k,11031
+torch_geometric/nn/models/protein_mpnn.py,sha256=SwTgafSbI2KJ-yqzn0trZtVWLmfo0_kPEaWSNJUCt70,12266
 torch_geometric/nn/models/re_net.py,sha256=pz66q5b5BoGDNVQvpEGS2RGoeKvpjkYAv9r3WAuvITk,8986
 torch_geometric/nn/models/rect.py,sha256=2F3XyyvHTAEuqfJpiNB5M8pSGy738LhPiom5I-SDWqM,2808
 torch_geometric/nn/models/rev_gnn.py,sha256=Bpme087Zs227lcB0ODOKWsxaly67q96wseaRt6bacjs,11796
@@ -645,7 +645,7 @@ torch_geometric/utils/undirected.py,sha256=H_nfpI0_WluOG6VfjPyldvcjL4w5USAKWu2x5
 torch_geometric/visualization/__init__.py,sha256=b-HnVesXjyJ_L1N-DnjiRiRVf7lhwKaBQF_2i5YMVSU,208
 torch_geometric/visualization/graph.py,sha256=mfZHXYfiU-CWMtfawYc80IxVwVmtK9hbIkSKhM_j7oI,14311
 torch_geometric/visualization/influence.py,sha256=CWMvuNA_Nf1sfbJmQgn58yS4OFpeKXeZPe7kEuvkUBw,477
-pyg_nightly-2.7.0.dev20250711.dist-info/licenses/LICENSE,sha256=ic-27cMJc1kWoMEYncz3Ya3Ur2Bi3bNLWib2DT763-o,1067
-pyg_nightly-2.7.0.dev20250711.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
-pyg_nightly-2.7.0.dev20250711.dist-info/METADATA,sha256=PqSq5SaAYK_6lW8wQgaKH0XuSMEmNMrtH80Dlb0O9QU,63005
-pyg_nightly-2.7.0.dev20250711.dist-info/RECORD,,
+pyg_nightly-2.7.0.dev20250713.dist-info/licenses/LICENSE,sha256=ic-27cMJc1kWoMEYncz3Ya3Ur2Bi3bNLWib2DT763-o,1067
+pyg_nightly-2.7.0.dev20250713.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+pyg_nightly-2.7.0.dev20250713.dist-info/METADATA,sha256=PRGvP632ImhKInA99VUthA2YsjaJIPcPBFnrfzYYdZE,63005
+pyg_nightly-2.7.0.dev20250713.dist-info/RECORD,,

torch_geometric/__init__.py

@@ -31,7 +31,7 @@ from .lazy_loader import LazyLoader
 contrib = LazyLoader('contrib', globals(), 'torch_geometric.contrib')
 graphgym = LazyLoader('graphgym', globals(), 'torch_geometric.graphgym')
 
-__version__ = '2.7.0.dev20250711'
+__version__ = '2.7.0.dev20250713'
 
 __all__ = [
     'Index',

torch_geometric/nn/models/protein_mpnn.py

@@ -156,6 +156,35 @@ class Decoder(MessagePassing):
 
 
 class ProteinMPNN(torch.nn.Module):
+    r"""The ProteinMPNN model from the `"Robust deep learning--based
+    protein sequence design using ProteinMPNN"
+    <https://www.biorxiv.org/content/10.1101/2022.06.03.494563v1>`_ paper.
+
+    Args:
+        hidden_dim (int): Hidden channels.
+            (default: :obj:`128`)
+        num_encoder_layers (int): Number of encode layers.
+            (default: :obj:`3`)
+        num_decoder_layers (int): Number of decode layers.
+            (default: :obj:`3`)
+        num_neighbors (int): Number of neighbors for each atom.
+            (default: :obj:`30`)
+        num_rbf (int): Number of radial basis functions.
+            (default: :obj:`16`)
+        dropout (float): Dropout rate.
+            (default: :obj:`0.1`)
+        augment_eps (float): Augmentation epsilon for input coordinates.
+            (default: :obj:`0.2`)
+        num_positional_embedding (int): Number of positional embeddings.
+            (default: :obj:`16`)
+        vocab_size (int): Number of vocabulary.
+            (default: :obj:`21`)
+
+    .. note::
+        For an example of using :class:`ProteinMPNN`, see
+        `examples/llm/protein_mpnn.py <https://github.com/pyg-team/
+        pytorch_geometric/blob/master/examples/llm/protein_mpnn.py>`_.
+    """
     def __init__(
         self,
         hidden_dim: int = 128,