Comments (4)
Oxer11
commented on June 19, 2024
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.
pearl-rabbit
commented on June 19, 2024
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.
Oxer11
commented on June 19, 2024
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.
pearl-rabbit
commented on June 19, 2024
Thank you for patiently answering my question. It has been resolved.
from gearnet.
Related Issues (20)
- Edge_list set to [0,0,0] HOT 2
- The pre-trained GearNet-Edge model for Fold Classification HOT 5
- atom view HOT 1
- Non-deterministic embeddings HOT 2
- confusion on epochs HOT 3
- A dataset not found when I run "python script/pretrain.py -c config/pretrain/mc_gearnet_edge.yaml --gpus [0]" HOT 5
- Solution when alpha carbon coordinate is missing HOT 1
- RuntimeError: addmm: Argument #3 (dense), for training ESM_GearNet on EC
- Pre-training on different datasets HOT 1
- Pre-trained weight for ESM-GearNet HOT 4
- secondary structure evaluation HOT 2
- Node classification tasks HOT 3
- Custom dataset. Data preprocessing HOT 1
- Asking about implementation of series connection of PLM & GNN in the FusionNetwork. HOT 2
- Passing CIF files directly into GearNet? HOT 2
- Inference on PDB file by conversion into torchdrug.data.PackedProtein or TorchDrug.data.Protein HOT 4
- TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases HOT 2
- What is input (Tensor) – input node representations for GearNet HOT 1
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