Comments (4)
Hi, could you provide more contexts about the error? Including what command you're running and what dataset and model you're using.
from gearnet.
error infomation:
Traceback (most recent call last):
File "test230424_define_model.py", line 67, in <module>
output = gearnet_edge(protein, protein.node_feature.float(), all_loss=None, metric=None)
File "/home/admin/anaconda3/envs/test/lib/python3.7/site-packages/torch/nn/modules/module.py", line 1130, in _call_impl
return forward_call(*input, **kwargs)
File "/home/admin/anaconda3/envs/test/lib/python3.7/site-packages/torchdrug-0.2.0-py3.7.egg/torchdrug/models/gearnet.py", line 99, in forward
edge_hidden = self.edge_layers[i](line_graph, edge_input)
File "/home/admin/anaconda3/envs/test/lib/python3.7/site-packages/torch/nn/modules/module.py", line 1130, in _call_impl
return forward_call(*input, **kwargs)
File "/home/admin/anaconda3/envs/test/lib/python3.7/site-packages/torchdrug-0.2.0-py3.7.egg/torchdrug/layers/conv.py", line 91, in forward
update = self.message_and_aggregate(graph, input)
File "/home/admin/anaconda3/envs/test/lib/python3.7/site-packages/torchdrug-0.2.0-py3.7.egg/torchdrug/layers/conv.py", line 813, in message_and_aggregate
return update.view(graph.num_node, self.num_relation * self.input_dim)
RuntimeError: shape '[19, 472]' is invalid for input of size 6080
protein:
I only loaded one protein, and i provide partial information in 1A0G.pdb.The number of loaded protein residues does not seem to affect the results.
PackedProtein(batch_size=1, num_atoms=[5], num_bonds=[19], num_residues=[5]) torch.Size([5, 3])
ATOM 1 N GLY A 1 62.683 18.043 31.832 1.00 27.29 N
ATOM 2 CA GLY A 1 62.540 19.333 31.113 1.00 26.20 C
ATOM 3 C GLY A 1 61.709 20.294 31.930 1.00 26.29 C
ATOM 4 O GLY A 1 61.503 20.069 33.122 1.00 26.53 O
ATOM 5 H1 GLY A 1 63.547 17.860 31.944 1.00 27.29 H
ATOM 6 H2 GLY A 1 62.287 18.100 32.627 1.00 27.29 H
ATOM 7 H3 GLY A 1 62.302 17.394 31.357 1.00 27.29 H
ATOM 8 HA2 GLY A 1 63.415 19.715 30.943 1.00 26.20 H
ATOM 9 HA3 GLY A 1 62.122 19.186 30.250 1.00 26.20 H
ATOM 10 N TYR A 2 61.235 21.352 31.285 1.00 25.57 N
ATOM 11 CA TYR A 2 60.403 22.375 31.908 1.00 25.80 C
ATOM 12 C TYR A 2 59.040 22.446 31.212 1.00 24.57 C
ATOM 13 O TYR A 2 58.920 22.239 29.996 1.00 23.52 O
ATOM 14 CB TYR A 2 61.066 23.748 31.808 1.00 27.46 C
ATOM 15 CG TYR A 2 62.320 23.894 32.630 1.00 30.74 C
ATOM 16 CD1 TYR A 2 63.564 23.548 32.104 1.00 31.97 C
ATOM 17 CD2 TYR A 2 62.265 24.368 33.941 1.00 32.03 C
ATOM 18 CE1 TYR A 2 64.730 23.662 32.861 1.00 33.56 C
ATOM 19 CE2 TYR A 2 63.429 24.490 34.713 1.00 34.25 C
ATOM 20 CZ TYR A 2 64.659 24.131 34.162 1.00 34.25 C
ATOM 21 OH TYR A 2 65.812 24.229 34.910 1.00 36.90 O
ATOM 22 H TYR A 2 61.392 21.500 30.452 1.00 25.57 H
ATOM 23 HA TYR A 2 60.290 22.135 32.841 1.00 25.80 H
ATOM 24 HB2 TYR A 2 61.279 23.925 30.878 1.00 27.46 H
ATOM 25 HB3 TYR A 2 60.429 24.424 32.087 1.00 27.46 H
ATOM 26 HD1 TYR A 2 63.617 23.235 31.230 1.00 31.97 H
ATOM 27 HD2 TYR A 2 61.444 24.606 34.308 1.00 32.03 H
ATOM 28 HE1 TYR A 2 65.551 23.424 32.494 1.00 33.56 H
ATOM 29 HE2 TYR A 2 63.381 24.808 35.586 1.00 34.25 H
ATOM 30 HH TYR A 2 65.626 24.526 35.674 1.00 36.90 H
ATOM 31 N THR A 3 58.029 22.784 31.994 1.00 22.76 N
ATOM 32 CA THR A 3 56.674 22.908 31.512 1.00 20.04 C
ATOM 33 C THR A 3 56.145 24.288 31.854 1.00 20.22 C
ATOM 34 O THR A 3 56.566 24.902 32.840 1.00 21.09 O
ATOM 35 CB THR A 3 55.813 21.835 32.187 1.00 19.90 C
ATOM 36 OG1 THR A 3 56.348 20.551 31.868 1.00 18.58 O
ATOM 37 CG2 THR A 3 54.358 21.891 31.725 1.00 19.23 C
ATOM 38 H THR A 3 58.116 22.950 32.833 1.00 22.76 H
ATOM 39 HA THR A 3 56.647 22.789 30.550 1.00 20.04 H
ATOM 40 HB THR A 3 55.829 21.996 33.143 1.00 19.90 H
ATOM 41 HG1 THR A 3 57.091 20.455 32.247 1.00 18.58 H
ATOM 42 HG21 THR A 3 53.849 21.198 32.174 1.00 19.23 H
ATOM 43 HG22 THR A 3 53.983 22.759 31.941 1.00 19.23 H
ATOM 44 HG23 THR A 3 54.317 21.751 30.766 1.00 19.23 H
ATOM 45 N LEU A 4 55.313 24.822 30.972 1.00 18.82 N
ATOM 46 CA LEU A 4 54.661 26.099 31.184 1.00 18.80 C
ATOM 47 C LEU A 4 53.361 25.744 31.916 1.00 18.45 C
ATOM 48 O LEU A 4 52.540 24.988 31.412 1.00 18.08 O
ATOM 49 CB LEU A 4 54.363 26.774 29.843 1.00 19.09 C
ATOM 50 CG LEU A 4 53.376 27.937 29.779 1.00 19.90 C
ATOM 51 CD1 LEU A 4 53.899 29.172 30.510 1.00 19.94 C
ATOM 52 CD2 LEU A 4 53.136 28.257 28.336 1.00 20.91 C
ATOM 53 H LEU A 4 55.110 24.447 30.225 1.00 18.82 H
ATOM 54 HA LEU A 4 55.209 26.720 31.688 1.00 18.80 H
ATOM 55 HB2 LEU A 4 55.207 27.091 29.485 1.00 19.09 H
ATOM 56 HB3 LEU A 4 54.040 26.087 29.239 1.00 19.09 H
ATOM 57 HG LEU A 4 52.552 27.678 30.220 1.00 19.90 H
ATOM 58 HD11 LEU A 4 53.246 29.886 30.447 1.00 19.94 H
ATOM 59 HD12 LEU A 4 54.052 28.956 31.443 1.00 19.94 H
ATOM 60 HD13 LEU A 4 54.732 29.459 30.105 1.00 19.94 H
ATOM 61 HD21 LEU A 4 52.510 28.995 28.268 1.00 20.91 H
ATOM 62 HD22 LEU A 4 53.974 28.504 27.915 1.00 20.91 H
ATOM 63 HD23 LEU A 4 52.768 27.479 27.889 1.00 20.91 H
ATOM 64 N TRP A 5 53.244 26.216 33.147 1.00 18.81 N
ATOM 65 CA TRP A 5 52.090 25.958 33.974 1.00 19.95 C
ATOM 66 C TRP A 5 51.552 27.327 34.334 1.00 20.86 C
ATOM 67 O TRP A 5 52.060 27.978 35.250 1.00 19.16 O
ATOM 68 CB TRP A 5 52.518 25.197 35.224 1.00 21.36 C
ATOM 69 CG TRP A 5 51.379 24.766 36.083 1.00 23.63 C
ATOM 70 CD1 TRP A 5 50.043 24.813 35.774 1.00 24.43 C
ATOM 71 CD2 TRP A 5 51.468 24.189 37.391 1.00 25.64 C
ATOM 72 NE1 TRP A 5 49.305 24.293 36.805 1.00 25.53 N
ATOM 73 CE2 TRP A 5 50.148 23.904 37.810 1.00 25.61 C
ATOM 74 CE3 TRP A 5 52.535 23.882 38.250 1.00 25.32 C
ATOM 75 CZ2 TRP A 5 49.866 23.330 39.050 1.00 27.27 C
ATOM 76 CZ3 TRP A 5 52.254 23.312 39.483 1.00 27.22 C
ATOM 77 CH2 TRP A 5 50.928 23.040 39.872 1.00 28.11 C
ATOM 78 H TRP A 5 53.844 26.702 33.527 1.00 18.81 H
ATOM 79 HA TRP A 5 51.420 25.418 33.526 1.00 19.95 H
ATOM 80 HB2 TRP A 5 53.026 24.415 34.958 1.00 21.36 H
ATOM 81 HB3 TRP A 5 53.113 25.758 35.747 1.00 21.36 H
ATOM 82 HD1 TRP A 5 49.690 25.148 34.982 1.00 24.43 H
ATOM 83 HE1 TRP A 5 48.448 24.222 36.818 1.00 25.53 H
ATOM 84 HE3 TRP A 5 53.413 24.057 37.997 1.00 25.32 H
ATOM 85 HZ2 TRP A 5 48.992 23.150 39.311 1.00 27.27 H
ATOM 86 HZ3 TRP A 5 52.952 23.106 40.062 1.00 27.22 H
ATOM 87 HH2 TRP A 5 50.768 22.656 40.704 1.00 28.11 H
TER
END
model definition:
# protein
protein = data.Protein.from_pdb(pdb_file, atom_feature="position", bond_feature="length", residue_feature="symbol")
_protein = data.Protein.pack([protein])
protein = graph_construction_model(_protein)
# model
gearnet_edge = models.GearNet(input_dim=21, hidden_dims=[512, 512, 512, 512, 512, 512],
num_relation=7, edge_input_dim=59, num_angle_bin=8,
batch_norm=True, concat_hidden=True, short_cut=True, readout="sum")
pthfile = 'models/angle_gearnet_edge.pth'
net = torch.load(pthfile)
gearnet_edge.load_state_dict(net)
# written according to the document,
truncate_transform = transforms.TruncateProtein(max_length=350, random=False)
protein_view_transform = transforms.ProteinView(view="residue")
transform = transforms.Compose([truncate_transform, protein_view_transform])
item = {"graph": protein}
if transform:
item = transform(item)
protein = item['graph']
#output
with torch.no_grad():
output = gearnet_edge(protein, protein.node_feature.float(), all_loss=None, metric=None)
from gearnet.
It seems that the shape of edge feature in your protein is 19*40
. Have you tried the following graph_construction_model?
graph_construction_model = layers.GraphConstruction(node_layers=[geometry.AlphaCarbonNode()],
edge_layers=[geometry.SpatialEdge(radius=10.0, min_distance=5),
geometry.KNNEdge(k=10, min_distance=5),
geometry.SequentialEdge(max_distance=2)],
edge_feature="gearnet")
Note that you need to set the edge feature in graph_contruction_model as gearnet
to get a feature of 19*59
.
from gearnet.
Thank you for patiently answering my question. It has been resolved.
from gearnet.
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from gearnet.