small_molecule_pdb with path_registry

ur-whitelab · Feb 23, 2024 · 25e534c · 25e534c
1 parent ef0b6b9
commit 25e534c
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Showing 5 changed files with 1,179 additions and 488 deletions.
diff --git a/mdagent/tools/base_tools/__init__.py b/mdagent/tools/base_tools/__init__.py
@@ -9,12 +9,8 @@
     RemoveWaterCleaningTool,
     SpecializedCleanTool,
 )
-from .preprocess_tools.pdb_tools import (
-    PackMolTool,
-    ProteinName2PDBTool,
-    SmallMolPDB,
-    get_pdb,
-)
+from .preprocess_tools.packing import PackMolTool
+from .preprocess_tools.pdb_tools import ProteinName2PDBTool, SmallMolPDB, get_pdb
 from .simulation_tools.create_simulation import ModifyBaseSimulationScriptTool
 from .simulation_tools.setup_and_run import (
     InstructionSummary,

diff --git a/mdagent/tools/base_tools/preprocess_tools/__init__.py b/mdagent/tools/base_tools/preprocess_tools/__init__.py
@@ -5,7 +5,8 @@
     RemoveWaterCleaningTool,
     SpecializedCleanTool,
 )
-from .pdb_tools import PackMolTool, ProteinName2PDBTool, SmallMolPDB, get_pdb
+from .packing import PackMolTool
+from .pdb_tools import ProteinName2PDBTool, SmallMolPDB, get_pdb
 
 __all__ = [
     "AddHydrogensCleaningTool",