diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v1.pt b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..8225bc857bd925dc5ec28a3bc35519308d464831 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:05bc72f12954bcc52e85dee0d23e02574f8810ebb5327fbf72ad695660b915a7 +size 29908010 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v1_config.json b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..1a279823c2f19f981a96579bba658f2c8b703d5c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v2.pt b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..c874ed1ba232bd5be1794c42bb87bea3151d8738 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1c4aefaeb9fccad5dda4f0f5d67d7024727cfb2abb34897f9a3caa041c2bcc06 +size 29908010 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v2_config.json b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..1a279823c2f19f981a96579bba658f2c8b703d5c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v3.pt b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..ef5b9791fb8244c3fc593d0885237d7b8df78ffe --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:199e2aeb8fe93818aacef3edc981500882d27035f61670496f3a5808ca6d6c41 +size 29908010 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v3_config.json b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..1a279823c2f19f981a96579bba658f2c8b703d5c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CA/CA_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v1.pt b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..8d3e99ece490739f47f52ada239e12353b082dd9 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a8bc05c2fbd0c1af5d2361d06b959ad61da155acb50de0e131a1152e8b40a64f +size 29902698 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v1_config.json b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..8e645b8f1c4787961398cfe9179d71e96e4743c2 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v2.pt b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..44a674038618071eb13852768f372b3adf02b5e3 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0fd67a6961b369ef231a5562836339701dded1e9c733aa9014291a0e600138aa +size 29902698 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v2_config.json b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..8e645b8f1c4787961398cfe9179d71e96e4743c2 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v3.pt b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..85ad02d5c72ddc8889391c264d8edf4a221df7dd --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d53653666370e12bfc0e51867f0153144fec0ad34b5a8d230ff5e2e3d32f2285 +size 29902698 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v3_config.json b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..8e645b8f1c4787961398cfe9179d71e96e4743c2 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CO/CO_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v1.pt b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..c8917da8919f54cde66802a76860b809bfa7d72f --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6aba2d9fc9095ab03c1ea375a1a9e4b6152a6f8eaa795e1d1271af1dbd249cd2 +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v1_config.json b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..d45b3a97b3cdb228c273ee770279bb2300fbe470 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v2.pt b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..690e79b536a1af68802f5adc47763f8e846344bf --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bcd9d92d86a131ed98d81fa1eb4a8821610869fb3f787d04ee2423fea38c29b9 +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v2_config.json b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..d45b3a97b3cdb228c273ee770279bb2300fbe470 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v3.pt b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..b581e7ad8deacf19904f427e0d747157ea81ab2a --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8a640bf11cd783021738b686b4fd35505f8891a7360277963b41f6b95b487767 +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v3_config.json b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..d45b3a97b3cdb228c273ee770279bb2300fbe470 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/CU/CU_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v1.pt b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..0166a1c5f3a6493492948874c0f7e3daf1a86e80 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b7c6b46f763303b44d33b2c3834323e01db6291d78e2ddfe0f1580d2d1db8f8a +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v1_config.json b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..d45b3a97b3cdb228c273ee770279bb2300fbe470 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v2.pt b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..1b99e252b3e9a3e8aad825a7935c3ad21450eab6 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ffb0f96cedb425bed1edb7b0b9e2bc91a2abfbc4550b98eab980499ee2bc1639 +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v2_config.json b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..d45b3a97b3cdb228c273ee770279bb2300fbe470 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v3.pt b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..ff6317c82400b2f6cfeee05e29fdd62aeee3d3f8 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:671757b89a03803ae50fb5f5251460c6bc7aaecb632ffe0d55523a48302d50f8 +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v3_config.json b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..d45b3a97b3cdb228c273ee770279bb2300fbe470 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/FE/FE_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/K/K_v1.pt b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..451ddaeac463cd992eb4e2e748e58b9ac61aa73f --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9031f8d3c1edbdeb97c1d905ba6cf3e796e9a45c6bf50303554357947f694bdd +size 29924598 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/K/K_v1_config.json b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/K/K_v2.pt b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..8ed14c143bcd942c1864b011b7aec17ae8e0792c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b2a3e466444fa0a473d7ab8677f3d528d9dd2beaa1ae0007095b97ef5e0387be +size 29924598 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/K/K_v2_config.json b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/K/K_v3.pt b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..575b00a22f1eee6fcb7290501195570a7893c706 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d96114fb1efeedbd0134ea888a73446691bf584519df6077c01dbb435f59e23d +size 29924598 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/K/K_v3_config.json b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/K/K_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v1.pt b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..ad892c245421d36f6f977022b721e2e32eaf804d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3d2025bbf8f6cb71258f6002ffdb7b421567cdd721ab9ba17efe93ce46cc5169 +size 29942050 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v1_config.json b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..550cb4d36b13111a0e2dc31a9c67b0d9dc8a568d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v2.pt b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..4fde6f3d6d8f02e829f5abb825cdf9be542080d2 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6b6a0edb5adb718479c96a7cbd3f17cfd36fc350825759aa42100438a40975ca +size 29942050 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v2_config.json b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..550cb4d36b13111a0e2dc31a9c67b0d9dc8a568d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v3.pt b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..b5c76742c29f190b6932f6a80a7a4a6bf6523736 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:81e12e93ac7a0326560be7464b21e0c2ee467c1eb22e4dc62936e15a82c5d7cb +size 29942050 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v3_config.json b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..550cb4d36b13111a0e2dc31a9c67b0d9dc8a568d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MG/MG_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v1.pt b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..a9bc2913b59bdead91e7b1b8d7dde48da6d55291 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ac58f3c8eb664d44ec139c96aa98f52a895751b3d7596bf7297416ce195f067c +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v1_config.json b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..253bc73c3b453b0652d06150c243bf980dea38af --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v2.pt b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..2be8be5ded03dd565f3180e0f557975fc109d3de --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2602b6f347c4735a256bcdad531558716634d185f818cabc1d4193f60d79b7ce +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v2_config.json b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..253bc73c3b453b0652d06150c243bf980dea38af --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v3.pt b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..01e3e48ec6637fd2cde6458be028beb08014640c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:debdd78f12e20d66047f31508fc8d82728d3fd76f14e3241bd92dcfc516c6f6f +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v3_config.json b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..253bc73c3b453b0652d06150c243bf980dea38af --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/MN/MN_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v1.pt b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..836ebdad338c37d20a905e020ef2e122dad776ed --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d24b229db228bbee5eb23c2b6b061bddd349fe7b5a0482f8d99d082b2ab40ac6 +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v1_config.json b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v2.pt b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..636d1234c5397bb8cb24ecf51e6031e59d8204ff --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2ca24d6b1919c7451af47b4946273e4026c353e12d1289236eb7cd56adb271a0 +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v2_config.json b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v3.pt b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..3bb126988a143e0a7320611fa58617423fb75a2b --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d4042df07e77e785eed0e7ea8b90e734e1e21b8ab17d5284e833d8e0f02b129c +size 29924778 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v3_config.json b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/NA/NA_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v1.pt b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..4aea1a8636de283d03cbc4dcaf53ca34d0be434f --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:432404b7d73262c38a1aaf7e87b268036817ef99fea5c7192147a49688b3025d +size 29902698 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v1_config.json b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..8e645b8f1c4787961398cfe9179d71e96e4743c2 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v2.pt b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..c27fea54bfc7609c6bf17d04b1e6805fcaeb4d08 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9b5e2a2c339e82a400df1163bf92a8f06b8b02b0fc9fa10eca277aff13fab893 +size 29902698 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v2_config.json b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..8e645b8f1c4787961398cfe9179d71e96e4743c2 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v3.pt b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..e4b3b8ac0be3698c9e4367ec8c7450d8ab0fc14b --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b22b19e40923d2388dd5133e3fc95a5d63cbda9fc2d17971736d54233155cb69 +size 29902698 diff --git a/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v3_config.json b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..8e645b8f1c4787961398cfe9179d71e96e4743c2 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/metal_ions/ZN/ZN_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..0d8cee7d3d625ffb177c76e720354d23d4d94692 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:65c79f39a8d0ff96878bf4c68687b23000b51deed244abdd026d8908cda5938d +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..73442097d5068327b5612fa7c933ed59a6bbb1aa --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:58a91ea90268892b42cecfd054f2d0b40c78a77f8c2d40f9c433ff599623dda0 +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..107ad3a629412922c4558f31f9b9c450759e5367 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d63fab4e08068bd2ce20d35c0ffe74100d58ce81e30b500d7852883880d4e434 +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ADP/ADP_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..ba51f55e1c238729db8bd02a5c76aabc29798fa4 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a79ae0e440c0446b5094de1a650c3d53a67de5b93de3d93fb29dbce737acac75 +size 29946136 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..550cb4d36b13111a0e2dc31a9c67b0d9dc8a568d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..029ffaf92c7747252df641e2b569b454e79738fc --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9a6ac6854f9d96d64c5b515909b88986e9241bcfc1e3b54e6d4be6028ef231e7 +size 29946136 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..550cb4d36b13111a0e2dc31a9c67b0d9dc8a568d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..c0ff0679dcf79bade064ce003de14e88c863f808 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:55822a772fc34bd82e1b2eba539b8774180a7bdeca6453242745b77dcc5491bd +size 29946136 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..550cb4d36b13111a0e2dc31a9c67b0d9dc8a568d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/ATP/ATP_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..405c7614f113aa118b808e16f35dab0e78808633 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4a5bfcad3747d182febe88e56cc4391ac54a27422e092510592691648979ecac +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..6122186313ffe80281e37ea860b41fb81225b03a --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4c73560bcd874d941404aa83f39114ff9420d61c81de3341ed17eab9397245bf +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..f0ff7f6fae97002760172b6ff09139f88979686b --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:528051c7ca60a296c745398b5bce4e87753bc48ef7e835e9c12a8f7a4042543b +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CIT/CIT_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..6931e8a475fc0a2c447222380f2aa5df04c262e5 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:dd523a4450305a0d095f85d961f47a18cc7260e763ca366b710520ed6f226725 +size 29946136 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..550cb4d36b13111a0e2dc31a9c67b0d9dc8a568d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..f73a91b69a3ebd174f7abd6efe28978a218bc4ae --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:66347a48c1e3f574fa478e68b840585b75e016d9d8efd3563dbd5e3e32527ef3 +size 29946136 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..550cb4d36b13111a0e2dc31a9c67b0d9dc8a568d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..94f5651d063a43df0e99fd293d71a596460b028d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:86d5fc23947377812b6be221a5818ad662cff2e4ef803c6aed8b7d83912d06f4 +size 29946136 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..550cb4d36b13111a0e2dc31a9c67b0d9dc8a568d --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/CLA/CLA_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..9ac2dbb0bd3de83b3ac0a6222ffda57b517e9a38 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:be2513516e06b26a95aa915d7af7152a0fb112c855e395f7f3a5c5dfba9f756e +size 29906654 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..54cb64ed98e1371c5f6ece66d4ee2c270a30a177 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..e96f333c9a572b871cc53308c0846fa0013446db --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a50813dd9b2fcb4ac4704d76f00c3879d82718b4adf3c5e5ed486c69b4efdda8 +size 29906654 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..54cb64ed98e1371c5f6ece66d4ee2c270a30a177 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..bbc90103a91d4f519cc5309c2f7041de052c6fe9 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:14883d1c26b4df281c04173e63a4fe62acf9898f718e496e857c19556306d1a8 +size 29906654 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..54cb64ed98e1371c5f6ece66d4ee2c270a30a177 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/FAD/FAD_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "gelu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..6f7b4b00668e4540c55308e8ad2d4ebc280f77f2 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:734b0d65017ba2857306050a9c357daf8216e46db7e1dd947b32eec548d4ac4b +size 29921874 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..e67e9fac872e068867b32571ee2973a8e41a136c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 4, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 5, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..ec8ceece0129c142852bf6232afb7069bc6e42c9 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a2eedbb7eb8e4b5ff00fb6c67bcd9181f8cb38e053c31477ced135e598231f09 +size 29921874 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..e67e9fac872e068867b32571ee2973a8e41a136c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 4, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 5, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..7e7caa60d8fdd02ae5caedbb4482647457992518 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7dca4d0b93ce4e5bffd8d9962b6fafe07eed2e22a03e4b4004f9f8c5b6217ddb +size 29921874 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..e67e9fac872e068867b32571ee2973a8e41a136c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GDP/GDP_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 4, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 5, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..d89c22246c8b637bead830cfffe157bb46686c15 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a81dab138fd35394a394bc96db656838e1fad7d1e1522c7b8c89b8cfbbb336ce +size 29921874 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..e67e9fac872e068867b32571ee2973a8e41a136c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 4, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 5, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..2ab9410fa6d8eb25fb737b537462bd975401d527 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:95249c0de0bf81e957a0546d4a1313953b3b903fe3db75b323879168e941afb1 +size 29921874 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..e67e9fac872e068867b32571ee2973a8e41a136c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 4, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 5, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..0ba6e27ad2d154f7a382e29701fbcf16545b87a5 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cd51ebde419960dcf8cd36b239318d44a1861a50a73e04cc1f7d51eaa8482e0a +size 29921874 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..e67e9fac872e068867b32571ee2973a8e41a136c --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/GTP/GTP_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 4, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 5, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..2a8381e482ab56297633fd33aea82c14637f19d4 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0510df89ed7d827d94a2058108b5157eb8da6359746d3729ec9f83a101824bd0 +size 29906654 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..40825c7ac78a7de80b92c39cbaf153ab7ce586e8 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..8f913161ede6470fd0e05d208be58f9b5d2d82a0 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:39ca55597f284cb992e17e0386f0d67b0a735bf29d8132e58e30df222e6bf10a +size 29906654 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..40825c7ac78a7de80b92c39cbaf153ab7ce586e8 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..c837ad4ed2dd4439725915805927c509b5f375e5 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cd1e14161c7acef1aed8b85aa9c44ba833a9a2e8eefe3e0079288921d4b17f4f +size 29906654 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..40825c7ac78a7de80b92c39cbaf153ab7ce586e8 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEC/HEC_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 6, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "elu", + "pred_dropout": 0.05, + "pred_hidden_size": 16 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..c3ee6c58068fd30601a406494080bcfeb6d07a27 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:25bf7b0ac6f908ea7bd002beb1b6c2a52db8f428cdc731f86c10ff20eba6c50d +size 29946136 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..905a8c59713b659cef4a8fcfd1a7c78893e88709 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 4, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "elu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..60df0ec1e2a6fb318e20d5c8e2dd7a5815ccf229 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:58775719329c54512c11f019f2ed6b2621759aa73d22fb5a96bab487a8fd0d77 +size 29946136 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..905a8c59713b659cef4a8fcfd1a7c78893e88709 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 4, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "elu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..22e51fa9939c3608281bb8a3f21332c8b71d4086 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3758af3335a7dc6bf9780ac48b66d431f690468aa174139269a6c5d88f152544 +size 29946136 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..905a8c59713b659cef4a8fcfd1a7c78893e88709 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/HEM/HEM_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 4, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 4, + "nonlinearity": "elu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..79f9dda04a0b2d2d2a0db3506c3fd7f7a7ae70bb --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:20b34321d5da3d6361f51b28314430762215a57032459c8838a3bbaee6ced7d8 +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..e90cab4f59cda38c7f80e44ddc5c5beb7582c429 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2264b5c2fbff5027881b9b32c7b90fc01fe6b85785571064a2880d306ffc8633 +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..ca749a341f3c8ba26b05bafb4aeaec7735ab359b --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5f17e27fac1ac3d7f5b9011d41ded0d7d26b8e41e8cfe38e3b6ae1fe0ebe21c3 +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAD/NAD_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..6dc6f0f063876c6adae9aa2fa29d4d9bc754105a --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e69679597ec2c10b558fafcb464c7f104a367644b5b10cfaa83d37ae6ca35212 +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..576c2d5069a438f8e1ca6906cd36386f9b6e8e62 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b3cabbd5822384c911eb3de2b3ec9bfd916f4cb4d7e2d8dcbc6893a3a58aea22 +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..3aeedc84c4d4aa551e51f80f165e1d56d0ecf039 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bc5e40a791144fb6837938b69ee91eb14ed807e8c58c324f6bf11e4ca9ed922f +size 29928734 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7001c2ea23644d9044763b70da6ddf6f808f1580 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NAP/NAP_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.0, + "pred_hidden_size": 64 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v1.pt b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..a84bbd18f341e574aaad68791114b3c8b657e112 --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5f2aa44a1e9b9d6f990828033c3f90fae4c8581fec6699f629ec401148caacac +size 29911966 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v1_config.json b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v1_config.json new file mode 100644 index 0000000000000000000000000000000000000000..cc3a02d31a9159674cb3aaf3804be770dd275f3b --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v1_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v2.pt b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..e48cc5e16d8ee5465b4a83e608c856855f41f3ae --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:64eab4d301bdb6b8d33afcda8b4c6067987ae832623d1bb04a69bad1f7bf8027 +size 29911966 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v2_config.json b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v2_config.json new file mode 100644 index 0000000000000000000000000000000000000000..cc3a02d31a9159674cb3aaf3804be770dd275f3b --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v2_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v3.pt b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..7a26d514681dc6f33a4ede3bf1ef11eca4651fee --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1b431e22ecee89117b66c32d1d65ae549573ab97f005c1868d351ec7408a6c9d +size 29911966 diff --git a/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v3_config.json b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v3_config.json new file mode 100644 index 0000000000000000000000000000000000000000..cc3a02d31a9159674cb3aaf3804be770dd275f3b --- /dev/null +++ b/ATOMICA_checkpoints/ligand/small_molecules/NDP/NDP_v3_config.json @@ -0,0 +1,16 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "ClassifierModel", + "num_pred_layers": 3, + "nonlinearity": "relu", + "pred_dropout": 0.05, + "pred_hidden_size": 32 +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/pretrain/pretrain_model_config.json b/ATOMICA_checkpoints/pretrain/pretrain_model_config.json new file mode 100644 index 0000000000000000000000000000000000000000..ee1d19f79f179b3a2def523010ecfdb54be114c7 --- /dev/null +++ b/ATOMICA_checkpoints/pretrain/pretrain_model_config.json @@ -0,0 +1,23 @@ +{ + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "atom_noise": false, + "translation_noise": true, + "rotation_noise": true, + "torsion_noise": true, + "atom_weight": 1.0, + "translation_weight": 1.0, + "rotation_weight": 0.1, + "torsion_weight": 1.0, + "mask_weight": 1.0, + "modality_embedding": false, + "num_masked_block_classes": 436, + "model_type": "DenoisePretrainModel" +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/pretrain/pretrain_model_weights.pt b/ATOMICA_checkpoints/pretrain/pretrain_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..6aa59a99bb7fb74b0dcbd700ec0124ebb6dffac2 --- /dev/null +++ b/ATOMICA_checkpoints/pretrain/pretrain_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:008a6b70a04ce238015f53f32f4080194104b0f2919d271a5f73f8821cccbdb6 +size 33746523 diff --git a/ATOMICA_checkpoints/prot_interface/atomica_interface_v1.json b/ATOMICA_checkpoints/prot_interface/atomica_interface_v1.json new file mode 100644 index 0000000000000000000000000000000000000000..f0ce6095b43938db9db4fde6e06b19f76330d56d --- /dev/null +++ b/ATOMICA_checkpoints/prot_interface/atomica_interface_v1.json @@ -0,0 +1,15 @@ +{ + "model_type": "ProteinInterfaceModel", + "prot_model": { + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "PredictionModel" + } +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/prot_interface/atomica_interface_v1.pt b/ATOMICA_checkpoints/prot_interface/atomica_interface_v1.pt new file mode 100644 index 0000000000000000000000000000000000000000..3a31f58bc17ed0326b491c36049d9abd505a1d82 --- /dev/null +++ b/ATOMICA_checkpoints/prot_interface/atomica_interface_v1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:88dadf845cf87a140108a3b82d820817a875deb15aaf7143f223cecd3cc8f7f9 +size 59854662 diff --git a/ATOMICA_checkpoints/prot_interface/atomica_interface_v2.json b/ATOMICA_checkpoints/prot_interface/atomica_interface_v2.json new file mode 100644 index 0000000000000000000000000000000000000000..f0ce6095b43938db9db4fde6e06b19f76330d56d --- /dev/null +++ b/ATOMICA_checkpoints/prot_interface/atomica_interface_v2.json @@ -0,0 +1,15 @@ +{ + "model_type": "ProteinInterfaceModel", + "prot_model": { + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "PredictionModel" + } +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/prot_interface/atomica_interface_v2.pt b/ATOMICA_checkpoints/prot_interface/atomica_interface_v2.pt new file mode 100644 index 0000000000000000000000000000000000000000..b7b32316cb835c030e4297e8d49b1a4206434de6 --- /dev/null +++ b/ATOMICA_checkpoints/prot_interface/atomica_interface_v2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:de2d2129616f740e7e3bc3e865e9c258fc77115846f79ecb169cc5b77e47beea +size 59854662 diff --git a/ATOMICA_checkpoints/prot_interface/atomica_interface_v3.json b/ATOMICA_checkpoints/prot_interface/atomica_interface_v3.json new file mode 100644 index 0000000000000000000000000000000000000000..f0ce6095b43938db9db4fde6e06b19f76330d56d --- /dev/null +++ b/ATOMICA_checkpoints/prot_interface/atomica_interface_v3.json @@ -0,0 +1,15 @@ +{ + "model_type": "ProteinInterfaceModel", + "prot_model": { + "atom_hidden_size": 32, + "block_hidden_size": 32, + "edge_size": 32, + "n_layers": 4, + "dropout": 0.0, + "k_neighbors": 8, + "global_message_passing": true, + "bottom_global_message_passing": false, + "fragmentation_method": "PS_300", + "model_type": "PredictionModel" + } +} \ No newline at end of file diff --git a/ATOMICA_checkpoints/prot_interface/atomica_interface_v3.pt b/ATOMICA_checkpoints/prot_interface/atomica_interface_v3.pt new file mode 100644 index 0000000000000000000000000000000000000000..fdb5c8f8ef330515f5ab8292bfa34ff0c6afefde --- /dev/null +++ b/ATOMICA_checkpoints/prot_interface/atomica_interface_v3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f48c494e7dbae94bbb97210db8659e5800e88065acddd486ff3208d63857ec9f +size 59854662