DiffAbXL

AstraZeneca · Oct 9, 2024 · 9e33b87 · 9e33b87
1 parent 5a01a42
commit 9e33b87
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Showing 2 changed files with 2 additions and 17 deletions.
diff --git a/config/sabdab.yaml b/config/sabdab.yaml
@@ -95,10 +95,8 @@ contact_distance: 6        # Maximum distance (in Å) for defining contacts betw
 # Fragment type IDs for different chains
 fragment_type:
   heavy: 1                 # ID for heavy chain
-  light_kappa: 2           # ID for light chain (kappa)
-  light_lambda: 3          # ID for light chain (lambda)
-  antigen: 4               # ID for antigen
-  unknown_light: 5         # ID for unknown light chains
+  light: 2                 # ID for light chain
+  antigen: 3               # ID for antigen
 
 # SabDab database filtering settings
 resolution_threshold: 4.0  # Maximum allowed resolution (in Å) for structures

diff --git a/utils/utils.py b/utils/utils.py
@@ -87,23 +87,10 @@ def set_dirs(config):
         evaluation_dir_abag = make_dir(results_dir, f"{config['antigen']}_{config['antibody']}")
         lo_dir = make_dir(evaluation_dir_abag, "lead_optimization")
         denovo_dir = make_dir(evaluation_dir_abag, "denovo")
-        docking_dir = make_dir(evaluation_dir_abag, "docking")
-        fixbb_dir = make_dir(evaluation_dir_abag, "fixbb")
-        docking_dir = make_dir(docking_dir, config['antigen'])
-        docked_structures_dir = make_dir(docking_dir, "docked_structures")
-        scheme_dir = make_dir(docking_dir, config['scheme'])
-        scores_dir = make_dir(evaluation_dir_abag, "scores")
-        preds_dir = make_dir(evaluation_dir_abag, "predictions")
 
         config.update({
             "denovo_dir": denovo_dir,
             "lo_dir": lo_dir,
-            "docking_dir": docking_dir,
-            "scores_dir": scores_dir,
-            "preds_dir": preds_dir,
-            "scheme_dir": scheme_dir,
-            "docked_structures_dir": docked_structures_dir,
-            "fixbb_dir": fixbb_dir
         })
 
     print("Directories are set.")