| features: |
| module: models.gcpnet.features.factory.ProteinFeaturiser |
| kwargs: |
| representation: CA |
| scalar_node_features: |
| - amino_acid_one_hot |
| - sequence_positional_encoding |
| - alpha |
| - kappa |
| - dihedrals |
| vector_node_features: |
| - orientation |
| edge_types: |
| - knn_16 |
| scalar_edge_features: |
| - edge_distance |
| vector_edge_features: |
| - edge_vectors |
| task: |
| transform: null |
| encoder: |
| module: models.gcpnet.models.graph_encoders.gcpnet.GCPNetModel |
| kwargs: |
| num_layers: 6 |
| emb_dim: 128 |
| node_s_emb_dim: 128 |
| node_v_emb_dim: 16 |
| edge_s_emb_dim: 32 |
| edge_v_emb_dim: 4 |
| r_max: 10.0 |
| num_rbf: 8 |
| activation: silu |
| pool: sum |
| module_cfg: |
| norm_pos_diff: true |
| scalar_gate: 0 |
| vector_gate: true |
| scalar_nonlinearity: silu |
| vector_nonlinearity: silu |
| nonlinearities: |
| - silu |
| - silu |
| r_max: 10.0 |
| num_rbf: 8 |
| bottleneck: 4 |
| vector_linear: true |
| vector_identity: true |
| default_bottleneck: 4 |
| predict_node_positions: false |
| predict_node_rep: true |
| node_positions_weight: 1.0 |
| update_positions_with_vector_sum: false |
| enable_e3_equivariance: false |
| pool: sum |
| model_cfg: |
| h_input_dim: 49 |
| chi_input_dim: 2 |
| e_input_dim: 9 |
| xi_input_dim: 1 |
| h_hidden_dim: 128 |
| chi_hidden_dim: 16 |
| e_hidden_dim: 32 |
| xi_hidden_dim: 4 |
| num_layers: 6 |
| dropout: 0.0 |
| layer_cfg: |
| pre_norm: false |
| use_gcp_norm: true |
| use_gcp_dropout: true |
| use_scalar_message_attention: true |
| num_feedforward_layers: 2 |
| dropout: 0.0 |
| nonlinearity_slope: 0.01 |
| mp_cfg: |
| edge_encoder: false |
| edge_gate: false |
| num_message_layers: 4 |
| message_residual: 0 |
| message_ff_multiplier: 1 |
| self_message: true |
| checkpoint_path: ./models/checkpoints/structure_denoising/gcpnet/ca_bb/last.ckpt |
| top_k: 30 |
| num_positional_embeddings: 16 |
|
|
