From 7bdd0a222a1e2447754528836213ad4ae1161e2b Mon Sep 17 00:00:00 2001
From: Sam Cox <swrig30@ur.rochester.edu>
Date: Fri, 23 Feb 2024 13:47:00 -0800
Subject: [PATCH] removed CheckDirectoryFiles

---
 mdagent/tools/base_tools/__init__.py          |  7 +----
 .../base_tools/analysis_tools/__init__.py     |  3 +-
 .../base_tools/analysis_tools/vis_tools.py    | 29 -------------------
 mdagent/tools/maketools.py                    |  2 --
 4 files changed, 2 insertions(+), 39 deletions(-)

diff --git a/mdagent/tools/base_tools/__init__.py b/mdagent/tools/base_tools/__init__.py
index 404fd3ca..fe7cc656 100644
--- a/mdagent/tools/base_tools/__init__.py
+++ b/mdagent/tools/base_tools/__init__.py
@@ -1,11 +1,7 @@
 from .analysis_tools.plot_tools import SimulationOutputFigures
 from .analysis_tools.ppi_tools import PPIDistance
 from .analysis_tools.rmsd_tools import RMSDCalculator
-from .analysis_tools.vis_tools import (
-    CheckDirectoryFiles,
-    VisFunctions,
-    VisualizeProtein,
-)
+from .analysis_tools.vis_tools import VisFunctions, VisualizeProtein
 from .preprocess_tools.clean_tools import (
     AddHydrogensCleaningTool,
     CleaningToolFunction,
@@ -32,7 +28,6 @@
 
 __all__ = [
     "AddHydrogensCleaningTool",
-    "CheckDirectoryFiles",
     "CleaningTools",
     "InstructionSummary",
     "ListRegistryPaths",
diff --git a/mdagent/tools/base_tools/analysis_tools/__init__.py b/mdagent/tools/base_tools/analysis_tools/__init__.py
index 2243f0d2..7cb79fbd 100644
--- a/mdagent/tools/base_tools/analysis_tools/__init__.py
+++ b/mdagent/tools/base_tools/analysis_tools/__init__.py
@@ -1,13 +1,12 @@
 from .plot_tools import SimulationOutputFigures
 from .ppi_tools import PPIDistance
 from .rmsd_tools import RMSDCalculator
-from .vis_tools import CheckDirectoryFiles, VisFunctions, VisualizeProtein
+from .vis_tools import VisFunctions, VisualizeProtein
 
 __all__ = [
     "PPIDistance",
     "RMSDCalculator",
     "SimulationOutputFigures",
-    "CheckDirectoryFiles",
     "VisualizeProtein",
     "VisFunctions",
 ]
diff --git a/mdagent/tools/base_tools/analysis_tools/vis_tools.py b/mdagent/tools/base_tools/analysis_tools/vis_tools.py
index 3d9ec17b..e51bc34c 100644
--- a/mdagent/tools/base_tools/analysis_tools/vis_tools.py
+++ b/mdagent/tools/base_tools/analysis_tools/vis_tools.py
@@ -1,4 +1,3 @@
-import os
 import subprocess
 from typing import Optional
 
@@ -9,14 +8,6 @@
 
 
 class VisFunctions:
-    def list_files_in_directory(self, directory):
-        files = [
-            f
-            for f in os.listdir(directory)
-            if os.path.isfile(os.path.join(directory, f))
-        ]
-        return ", ".join(files)
-
     def run_molrender(self, cif_path):
         """Function to run molrender,
         it requires node.js to be installed
@@ -114,23 +105,3 @@ def _run(self, query: str) -> str:
     async def _arun(self, query: str) -> str:
         """Use the tool asynchronously."""
         raise NotImplementedError("custom_search does not support async")
-
-
-class CheckDirectoryFiles(BaseTool):
-    name = "ListDirectoryFiles"
-    description = """This tool will
-    give you a list of comma
-    separated files in the
-    current directory."""
-
-    def _run(self, query: str) -> str:
-        """use the tool."""
-        try:
-            vis = VisFunctions()
-            return vis.list_files_in_directory(".")
-        except Exception:
-            return "An error occurred while listing files in directory"
-
-    async def _arun(self, query: str) -> str:
-        """Use the tool asynchronously."""
-        raise NotImplementedError("custom_search does not support async")
diff --git a/mdagent/tools/maketools.py b/mdagent/tools/maketools.py
index 2117afee..b9fc7441 100644
--- a/mdagent/tools/maketools.py
+++ b/mdagent/tools/maketools.py
@@ -16,7 +16,6 @@
 from mdagent.utils import PathRegistry, _make_llm
 
 from .base_tools import (
-    CheckDirectoryFiles,
     CleaningToolFunction,
     ListRegistryPaths,
     ModifyBaseSimulationScriptTool,
@@ -79,7 +78,6 @@ def make_all_tools(
     # add base tools
     base_tools = [
         CleaningToolFunction(path_registry=path_instance),
-        CheckDirectoryFiles(),
         ListRegistryPaths(path_registry=path_instance),
         #    MapPath2Name(path_registry=path_instance),
         ProteinName2PDBTool(path_registry=path_instance),