Merge pull request #39 from RMeli/cache

Expose structures cache from CLI

gninatorch/gnina.py

@@ -222,6 +222,13 @@ def options(args: Optional[List[str]] = None):
         help=".molcache2 file for receptors",
     )
 
+    parser.add_argument(
+        "--no_cache",
+        action="store_false",
+        help="Disable structure caching",
+        dest="cache_structures",
+    )
+
     return parser.parse_args(args)
 
 

gninatorch/inference.py

@@ -108,6 +108,12 @@ def options(args: Optional[List[str]] = None):
         help="Disable CSV output",
         dest="csv",
     )
+    parser.add_argument(
+        "--no_cache",
+        action="store_false",
+        help="Disable structure caching",
+        dest="cache_structures",
+    )
 
     return parser.parse_args(args)
 

gninatorch/setup.py

@@ -53,7 +53,7 @@ def setup_example_provider(
             stratify_max=args.stratify_max,
             stratify_min=args.stratify_min,
             stratify_step=args.stratify_step,
-            cache_structs=True,
+            cache_structs=args.cache_structures,
         )
     else:
         # Use command line option for training
@@ -66,7 +66,7 @@ def setup_example_provider(
             ligmolcache=args.ligmolcache,
             recmolcache=args.recmolcache,
             stratify_receptor=False,
-            cache_structs=True,
+            cache_structs=args.cache_structures,
         )
 
     example_provider.populate(examples_file)

gninatorch/training.py

@@ -261,6 +261,13 @@ def options(args: Optional[List[str]] = None):
         dest="roc_auc",
     )
 
+    parser.add_argument(
+        "--no_cache",
+        action="store_false",
+        help="Disable structure caching",
+        dest="cache_structures",
+    )
+
     parser.add_argument("-s", "--seed", type=int, default=None, help="Random seed")
     parser.add_argument("--silent", action="store_true", help="No console output")
 

tests/test_gnina.py

@@ -5,6 +5,7 @@
 import pytest
 import torch
 
+import gninatorch
 from gninatorch import gnina, models
 from gninatorch.dataloaders import GriddedExamplesLoader
 
@@ -318,3 +319,12 @@ def test_gnina_ensemble(
     assert np.allclose(1 - score, 1 - CNNscore, atol=1e-6)
     assert np.allclose(affinity, CNNaffinity, atol=1e-6)
     assert np.allclose(1 - variance, 1 - CNNvariance, atol=1e-6)
+
+
+def test_header(capsys):
+    gnina._header()
+
+    captured = capsys.readouterr()
+
+    assert gninatorch.__version__ in captured.out
+    assert gninatorch.__git_revision__ in captured.out