removing unnecesary angle tools

ur-whitelab · Jan 24, 2025 · 5467132 · 5467132
1 parent 16c0be9
commit 5467132
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Showing 3 changed files with 3 additions and 40 deletions.
diff --git a/mdagent/tools/base_tools/analysis_tools/__init__.py b/mdagent/tools/base_tools/analysis_tools/__init__.py
@@ -1,15 +1,4 @@
-from .bond_angles_dihedrals_tool import (
-    ComputeAngles,
-    ComputeChi1,
-    ComputeChi2,
-    ComputeChi3,
-    ComputeChi4,
-    ComputeDihedrals,
-    ComputeOmega,
-    ComputePhi,
-    ComputePsi,
-    RamachandranPlot,
-)
+from .bond_angles_dihedrals_tool import ComputeAngles
 from .distance_tools import ContactsTool, DistanceMatrixTool
 from .inertia import MomentOfInertia
 from .pca_tools import PCATool
@@ -22,14 +11,6 @@
 
 __all__ = [
     "ComputeAngles",
-    "ComputeChi1",
-    "ComputeChi2",
-    "ComputeChi3",
-    "ComputeChi4",
-    "ComputeDihedrals",
-    "ComputeOmega",
-    "ComputePhi",
-    "ComputePsi",
     "ComputeLPRMSD",
     "ComputeRMSD",
     "ComputeRMSF",
@@ -39,7 +20,6 @@
     "PCATool",
     "PPIDistance",
     "RadiusofGyrationTool",
-    "RamachandranPlot",
     "RMSDCalculator",
     "SimulationOutputFigures",
     "SolventAccessibleSurfaceArea",

diff --git a/mdagent/tools/base_tools/analysis_tools/bond_angles_dihedrals_tool.py b/mdagent/tools/base_tools/analysis_tools/bond_angles_dihedrals_tool.py
@@ -41,6 +41,7 @@ class ComputeAngles(BaseTool):
     analysis of the phi-psi angles, chi1-chi2 angles, or both. """
 
     path_registry: PathRegistry | None = None
+    args_schema = ComputingAnglesSchema
 
     def __init__(self, path_registry: PathRegistry):
         super().__init__()

diff --git a/mdagent/tools/maketools.py b/mdagent/tools/maketools.py
@@ -13,20 +13,12 @@
 from .base_tools import (
     CleaningToolFunction,
     ComputeAcylindricity,
+    ComputeAngles,
     ComputeAsphericity,
     ComputeDSSP,
     ComputeGyrationTensor,
-    ComputeAngles,
-    ComputeChi1,
-    ComputeChi2,
-    ComputeChi3,
-    ComputeChi4,
-    ComputeDihedrals,
     ComputeLPRMSD,
     ComputeRelativeShapeAntisotropy,
-    ComputeOmega,
-    ComputePhi,
-    ComputePsi,
     ComputeRMSD,
     ComputeRMSF,
     ContactsTool,
@@ -56,7 +48,6 @@
     PPIDistance,
     ProteinName2PDBTool,
     RadiusofGyrationTool,
-    RamachandranPlot,
     RDFTool,
     Scholar2ResultLLM,
     SetUpandRunFunction,
@@ -96,14 +87,6 @@ def make_all_tools(
         ComputeGyrationTensor(path_registry=path_instance),
         ComputeRelativeShapeAntisotropy(path_registry=path_instance),
         ComputeAngles(path_registry=path_instance),
-        ComputeChi1(path_registry=path_instance),
-        ComputeChi2(path_registry=path_instance),
-        ComputeChi3(path_registry=path_instance),
-        ComputeChi4(path_registry=path_instance),
-        ComputeDihedrals(path_registry=path_instance),
-        ComputeOmega(path_registry=path_instance),
-        ComputePhi(path_registry=path_instance),
-        ComputePsi(path_registry=path_instance),
         CleaningToolFunction(path_registry=path_instance),
         ComputeLPRMSD(path_registry=path_instance),
         ComputeRMSD(path_registry=path_instance),
@@ -117,7 +100,6 @@ def make_all_tools(
         PPIDistance(path_registry=path_instance),
         ProteinName2PDBTool(path_registry=path_instance),
         RadiusofGyrationTool(path_registry=path_instance),
-        RamachandranPlot(path_registry=path_instance),
         RDFTool(path_registry=path_instance),
         SetUpandRunFunction(path_registry=path_instance),
         SimulationOutputFigures(path_registry=path_instance),