renamed to mdcrow in notebooks

ur-whitelab · Feb 13, 2025 · c9f6b95 · c9f6b95
1 parent e1d333b
commit c9f6b95
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Showing 371 changed files with 2,354 additions and 2,785 deletions.
diff --git a/mdagent.yaml b/mdagent.yaml
diff --git a/notebooks/chat_examples.ipynb b/notebooks/chat_examples.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mdagent import MDAgent"
+    "from mdcrow import MDCrow"
    ]
   },
   {
@@ -25,7 +25,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "agent_with_memory = MDAgent(agent_type=\"Structured\", model=llm_var, top_k_tools=tools, use_memory=True)"
+    "agent_with_memory = MDCrow(agent_type=\"Structured\", model=llm_var, top_k_tools=tools, use_memory=True)"
    ]
   },
   {
@@ -90,7 +90,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "agent_with_memory_2 = MDAgent(agent_type=\"Structured\", model=llm_var, top_k_tools=tools, use_memory=True,ckpt_dir=\"ckpt_0\",run_id=\"55JRTQCS\")"
+    "agent_with_memory_2 = MDCrow(agent_type=\"Structured\", model=llm_var, top_k_tools=tools, use_memory=True,ckpt_dir=\"ckpt_0\",run_id=\"55JRTQCS\")"
    ]
   },
   {
@@ -214,7 +214,7 @@
     }
    ],
    "source": [
-    "agent_with_memory_3 = MDAgent(agent_type=\"Structured\", model=llm_var, top_k_tools=tools, use_memory=True,ckpt_dir=\"ckpt_0\",run_id=\"55JRTQCS\")\n",
+    "agent_with_memory_3 = MDCrow(agent_type=\"Structured\", model=llm_var, top_k_tools=tools, use_memory=True,ckpt_dir=\"ckpt_0\",run_id=\"55JRTQCS\")\n",
     "agent_with_memory_3.run(\"You're doing great so far\")"
    ]
   },
@@ -665,7 +665,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "agent_with_memory_3 = MDAgent(agent_type=\"Structured\",use_memory=True,ckpt_dir=\"ckpt_0\",run_id=\"55JRTQCS\")\n",
+    "agent_with_memory_3 = MDCrow(agent_type=\"Structured\",use_memory=True,ckpt_dir=\"ckpt_0\",run_id=\"55JRTQCS\")\n",
     "registry = agent_with_memory_3.path_registry"
    ]
   },
@@ -760,7 +760,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mdagent2",
+   "display_name": "mdcrow2",
    "language": "python",
    "name": "python3"
   },

diff --git a/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt1.ipynb b/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt1.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mdagent import MDAgent\n",
+    "from mdcrow import MDCrow\n",
     "import os"
    ]
   },
@@ -83,7 +83,7 @@
     }
    ],
    "source": [
-    "agent_1 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_1 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_1.run(descriptive_prompt_1)"
    ]
   },
@@ -159,7 +159,7 @@
     }
    ],
    "source": [
-    "agent_2 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_2 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_2.run(non_descriptive_prompt_1)"
    ]
   },
@@ -193,7 +193,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mdagent2",
+   "display_name": "mdcrow2",
    "language": "python",
    "name": "python3"
   },

diff --git a/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt10.ipynb b/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt10.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mdagent import MDAgent\n",
+    "from mdcrow import MDCrow\n",
     "import os \n",
     "import mdtraj as md"
    ]
@@ -424,7 +424,7 @@
     }
    ],
    "source": [
-    "agent_1 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_1 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_1.run(descriptive_prompt_10)"
    ]
   },
@@ -967,7 +967,7 @@
     }
    ],
    "source": [
-    "agent_2 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_2 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_2.run(non_descriptive_prompt_10)"
    ]
   },
@@ -1053,7 +1053,7 @@
     }
    ],
    "source": [
-    "from mdagent.tools.base_tools import ComputeDSSP\n",
+    "from mdcrow.tools.base_tools import ComputeDSSP\n",
     "\n",
     "dssp = ComputeDSSP(registry)\n",
     "dssp._run(traj_file=\"rec0_204122\", top_file=\"top_sim0_204118\", target_frames=\"last\")"
@@ -1207,7 +1207,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mdagent2",
+   "display_name": "mdcrow2",
    "language": "python",
    "name": "python3"
   },

diff --git a/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt2.ipynb b/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt2.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mdagent import MDAgent"
+    "from mdcrow import MDCrow"
    ]
   },
   {
@@ -127,7 +127,7 @@
     }
    ],
    "source": [
-    "agent_1 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_1 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_1.run(descriptive_prompt_2)"
    ]
   },
@@ -166,7 +166,7 @@
     }
    ],
    "source": [
-    "from mdagent.tools.base_tools import ComputeDSSP\n",
+    "from mdcrow.tools.base_tools import ComputeDSSP\n",
     "\n",
     "dssp = ComputeDSSP(registry)\n",
     "dssp._run(traj_file= \"1LYZ_001617\", target_frames=\"all\")"
@@ -247,7 +247,7 @@
     }
    ],
    "source": [
-    "agent_2 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_2 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_2.run(non_descriptive_prompt_2)"
    ]
   },
@@ -286,7 +286,7 @@
     }
    ],
    "source": [
-    "from mdagent.tools.base_tools import ComputeDSSP\n",
+    "from mdcrow.tools.base_tools import ComputeDSSP\n",
     "\n",
     "dssp = ComputeDSSP(registry)\n",
     "dssp._run(traj_file= \"1LYZ_001826\", target_frames=\"all\")"
@@ -295,7 +295,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mdagent2",
+   "display_name": "mdcrow2",
    "language": "python",
    "name": "python3"
   },

diff --git a/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt3.ipynb b/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt3.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mdagent import MDAgent\n",
+    "from mdcrow import MDCrow\n",
     "import os \n",
     "import mdtraj as md"
    ]
@@ -233,7 +233,7 @@
     }
    ],
    "source": [
-    "agent_1 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_1 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_1.run(descriptive_prompt_3)"
    ]
   },
@@ -472,7 +472,7 @@
     }
    ],
    "source": [
-    "agent_2 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_2 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_2.run(non_descriptive_prompt_3)"
    ]
   },
@@ -554,7 +554,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mdagent2",
+   "display_name": "mdcrow2",
    "language": "python",
    "name": "python3"
   },

diff --git a/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt4.ipynb b/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt4.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mdagent import MDAgent\n",
+    "from mdcrow import MDCrow\n",
     "import os\n",
     "import mdtraj as md"
    ]
@@ -236,7 +236,7 @@
     }
    ],
    "source": [
-    "agent_1 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_1 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_1.run(descriptive_prompt_4)"
    ]
   },
@@ -511,7 +511,7 @@
     }
    ],
    "source": [
-    "agent_2 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_2 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_2.run(non_descriptive_prompt_4)"
    ]
   },
@@ -596,7 +596,7 @@
     }
    ],
    "source": [
-    "from mdagent.tools.base_tools import ComputeDSSP\n",
+    "from mdcrow.tools.base_tools import ComputeDSSP\n",
     "\n",
     "dssp = ComputeDSSP(registry)\n",
     "dssp._run(traj_file=\"rec2_003616\", top_file=\"top_sim0_003614\", target_frames=\"all\")"
@@ -628,7 +628,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mdagent2",
+   "display_name": "mdcrow2",
    "language": "python",
    "name": "python3"
   },

diff --git a/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt5.ipynb b/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt5.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mdagent import MDAgent\n",
+    "from mdcrow import MDCrow\n",
     "import os \n",
     "import mdtraj as md"
    ]
@@ -247,7 +247,7 @@
     }
    ],
    "source": [
-    "agent_1 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_1 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_1.run(descriptive_prompt_5)"
    ]
   },
@@ -536,7 +536,7 @@
     }
    ],
    "source": [
-    "agent_2 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_2 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_2.run(non_descriptive_prompt_5)"
    ]
   },
@@ -622,7 +622,7 @@
     }
    ],
    "source": [
-    "from mdagent.tools.base_tools import ComputeDSSP\n",
+    "from mdcrow.tools.base_tools import ComputeDSSP\n",
     "\n",
     "dssp = ComputeDSSP(registry)\n",
     "dssp._run(traj_file=\"rec2_004346\", top_file=\"top_sim0_004346\", target_frames=\"all\")"
@@ -654,7 +654,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mdagent2",
+   "display_name": "mdcrow2",
    "language": "python",
    "name": "python3"
   },

diff --git a/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt6.ipynb b/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt6.ipynb
@@ -6,7 +6,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mdagent import MDAgent\n",
+    "from mdcrow import MDCrow\n",
     "import os \n",
     "import mdtraj as md"
    ]
@@ -280,7 +280,7 @@
     }
    ],
    "source": [
-    "agent_1 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_1 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_1.run(descriptive_prompt_6)"
    ]
   },
@@ -654,7 +654,7 @@
     }
    ],
    "source": [
-    "agent_2 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_2 = MDCrow(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
     "agent_2.run(non_descriptive_prompt_6)"
    ]
   },
@@ -744,7 +744,7 @@
     }
    ],
    "source": [
-    "from mdagent.tools.base_tools import ComputeDSSP\n",
+    "from mdcrow.tools.base_tools import ComputeDSSP\n",
     "\n",
     "dssp = ComputeDSSP(path_registry=agent_2.path_registry)\n",
     "dssp._run(traj_file= \"rec2_185013\", top_file= \"top_sim0_185013\", target_frames= \"last\")"
@@ -820,7 +820,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mdagent2",
+   "display_name": "mdcrow2",
    "language": "python",
    "name": "python3"
   },