update paths

configs/screening.json

@@ -1,50 +1,19 @@
 {
     "available_gpus": ["4,5,6,7"],
-    "script": "main",
+    "script": "screen",
     "cartesian_hyperparams": {
-      "dataset_file_path": [],
-      "inference_dir": [],
-      "save_hiddens": [], 
-      "save_predictions": [], 
-      "use_as_protein_encoder": [], 
-      "use_as_reaction_encoder": [],
-      "protein_cache_dir": [],
-      "gpus": [],
+      "dataset_file_path": ["files/new_data.csv"],
+      "inference_dir": [""],
+      "save_hiddens": [false], 
+      "save_predictions": [false], 
+      "use_as_protein_encoder": [false], 
+      "use_as_reaction_encoder": [false],
+      "gpus": [1],
       "batch_size": [8],
       "precision": ["bf16"],
-      "dataset_name": ["reactions_dataset"],
-      "max_protein_length": [650], 
-      "eval_on_train_multigpu": [true],
-      "lightning_name": ["base"],
-      "model_name": ["enzyme_reaction_clip"],
-      "from_checkpoint": [true],
       "checkpoint_path": ["files/clipzyme_model.ckpt"],
-      "chemprop_node_dim": [9],
-      "chemprop_edge_dim": [3],
-      "protein_encoder": ["egnn_sparse_network"],
-      "use_protein_graphs": [true],
-      "protein_dim": [1280],
-      "neighbour_aggr": ["mean"],
-      "pool_type": ["sum"],
-      "message_dim": [24],
-      "norm_feats": [true],
-      "norm_coors": [true],
-      "update_feats": [true],
-      "update_coors": [true],
-      "egcl_layers": [6],
-      "use_sinusoidal": [true],
-      "chemprop_num_layers": [5],
-      "chemprop_hidden_dim": [1280],
-      "chemprop_pool": ["none"],
-      "dropout": [0],
-      "num_workers": [24],
-      "train": [false],
-      "dev": [false],
-      "test": [false],
-      "num_sanity_val_steps": [0],
-      "val_check_interval": [1.0],
-      "logger_name": ["tensorboard"],
-      "logger_tags": ["screen"]
+      "esm_dir": ["/data/esm/checkpoints"],
+      "num_workers": [24]
     }
   }
 

configs/train/clip_cgr.json

@@ -5,8 +5,8 @@
     "precision": ["bf16"],
     "accumulate_grad_batches": [1],
     "dataset_name": ["enzymemap_reaction_graph"],
-    "dataset_file_path": ["/home/datasets/EnzymeMap/version2/enzymemap_v2_brenda2_blip.json"],
-    "dataset_cache_path": ["/home/cache/cached_egnn_blip_dataset_version2.p"],
+    "dataset_file_path": ["files/enzymemap.json"],
+    "dataset_cache_path": ["files/cached_enzymemap.p"],
     "remove_duplicate_reactions": [true],
     "use_pesto_scores": [true],
     "max_protein_length": [650], 

configs/train/clip_cgr_rxn_string.json

@@ -5,8 +5,8 @@
       "precision": ["bf16"],
       "accumulate_grad_batches": [1],
       "dataset_name": ["enzymemap_reaction_graph"],
-      "dataset_file_path": ["/home/datasets/EnzymeMap/version2/enzymemap_v2_brenda2_blip.json"],
-      "dataset_cache_path": ["/home/cache/cached_egnn_blip_dataset_version2.p"],
+      "dataset_file_path": ["files/enzymemap.json"],
+      "dataset_cache_path": ["files/cached_enzymemap.p"],
       "remove_duplicate_reactions": [true],
       "use_pesto_scores": [false],
       "max_protein_length": [650], 

configs/train/clip_egnn.json

@@ -5,8 +5,8 @@
       "precision": ["bf16"],
       "accumulate_grad_batches": [1],
       "dataset_name": ["enzymemap_reaction_graph"],
-      "dataset_file_path": ["/home/datasets/EnzymeMap/version2/enzymemap_v2_brenda2_blip.json"],
-      "dataset_cache_path": ["/home/cache/cached_egnn_blip_dataset_version2.p"],
+      "dataset_file_path": ["files/enzymemap.json"],
+      "dataset_cache_path": ["files/cached_enzymemap.p"],
       "remove_duplicate_reactions": [true],
       "use_pesto_scores": [false],
       "max_protein_length": [650], 

configs/train/clip_esm.json

@@ -5,8 +5,8 @@
     "precision": ["bf16"],
     "accumulate_grad_batches": [2],
     "dataset_name": ["enzymemap_reaction_graph"],
-    "dataset_file_path": ["/home/datasets/EnzymeMap/version2/enzymemap_v2_brenda2_blip.json"],
-    "dataset_cache_path": ["/home/cache/cached_egnn_blip_dataset_version2.p"],
+    "dataset_file_path": ["files/enzymemap.json"],
+    "dataset_cache_path": ["files/cached_enzymemap.p"],
     "from_checkpoint": [true],
     "checkpoint_path": ["/home/snapshots/metabolomics/6a518ff6eda2b4a4299e9e1523b24d27/6a518ff6eda2b4a4299e9e1523b24d27epoch=15.ckpt"],
     "remove_duplicate_reactions": [true],

configs/train/clip_esm_frozen.json

@@ -5,8 +5,8 @@
     "precision": ["bf16"],
     "accumulate_grad_batches": [1],
     "dataset_name": ["enzymemap_reaction_graph"],
-    "dataset_file_path": ["/home/datasets/Enzymes/EnzymeMap/version2/enzymemap_v2_brenda2_blip.json"],
-    "dataset_cache_path": ["/home/cache/cached_egnn_blip_dataset_version2.p"],
+    "dataset_file_path": ["files/enzymemap.json"],
+    "dataset_cache_path": ["files/cached_enzymemap.p"],
     "remove_duplicate_reactions": [true],
     "use_pesto_scores": [false],
     "max_protein_length": [650], 

configs/train/clip_msa.json

@@ -5,8 +5,8 @@
       "precision": ["bf16"],
       "accumulate_grad_batches": [2],
       "dataset_name": ["enzymemap_reaction_graph"],
-      "dataset_file_path": ["/home/datasets/EnzymeMap/version2/enzymemap_v2_brenda2_blip.json"],
-      "dataset_cache_path": ["/home/cache/cached_egnn_blip_dataset_version2.p"],
+      "dataset_file_path": ["files/enzymemap.json"],
+      "dataset_cache_path": ["files/cached_enzymemap.p"],
       "remove_duplicate_reactions": [true],
       "use_pesto_scores": [false],
       "max_protein_length": [650], 

configs/train/clip_wldn.json

@@ -5,8 +5,8 @@
       "precision": ["bf16"],
       "accumulate_grad_batches": [1],
       "dataset_name": ["enzymemap_reaction_graph"],
-      "dataset_file_path": ["/home/datasets/EnzymeMap/version2/enzymemap_v2_brenda2_blip.json"],
-      "dataset_cache_path": ["/home/cache/cached_egnn_blip_dataset_version2.p"],
+      "dataset_file_path": ["files/enzymemap.json"],
+      "dataset_cache_path": ["files/cached_enzymemap.p"],
       "remove_duplicate_reactions": [true],
       "use_pesto_scores": [false],
       "max_protein_length": [650],