Claude experiments

.env.example

@@ -5,7 +5,4 @@
 # OpenAI API Key
 OPENAI_API_KEY=YOUR_OPENAI_API_KEY_GOES_HERE  # pragma: allowlist secret
 
-# PQA API Key to use LiteratureSearch tool (optional) -- it also requires OpenAI key
-PQA_API_KEY=YOUR_PQA_API_KEY_GOES_HERE # pragma: allowlist secret
-
 # Optional: add TogetherAI, Fireworks, or Anthropic API key here to use their models

README.md

@@ -21,7 +21,7 @@ pip install git+https://github.com/ur-whitelab/md-agent.git
 
 ## Usage
 The next step is to set up your API keys in your environment. An API key for LLM provider is necessary for this project. Supported LLM providers are OpenAI, TogetherAI, Fireworks, and Anthropic.
-Other tools require API keys, such as paper-qa for literature searches. We recommend setting up the keys in a .env file. You can use the provided .env.example file as a template.
+We recommend setting up api keys in a .env file. You can use the provided .env.example file as a template.
 1. Copy the `.env.example` file and rename it to `.env`: `cp .env.example .env`
 2. Replace the placeholder values in `.env` with your actual keys
 

notebooks/experiments/Robustness/claude-3-5-sonnet/prompt1.ipynb

@@ -0,0 +1,215 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mdagent import MDAgent\n",
+    "import os"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "descriptive_prompt_1 = \"Complete all of the following tasks: 1. Download the PDB file 1LYZ.\"\n",
+    "non_descriptive_prompt_1 = \"Download the PDB file 1LYZ.\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Required Tasks:\n",
+    "- Download"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "llm_model = \"claude-3-5-sonnet-20240620\"\n",
+    "tools = \"all\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Certainly! I'll start by downloading the PDB file 1LYZ using the PDBFileDownloader tool.\n",
+      "\n",
+      "Thought: To download the PDB file 1LYZ, I need to use the PDBFileDownloader tool. This tool can fetch PDB files using a protein's PDB ID.\n",
+      "\n",
+      "Action:\n",
+      "```\n",
+      "{\n",
+      "    \"action\": \"PDBFileDownloader\",\n",
+      "    \"action_input\": \"1LYZ\"\n",
+      "}\n",
+      "```PDB file found with this ID: 1LYZ\n",
+      "Thought: Great, we have successfully downloaded the PDB file for 1LYZ. Now, I need to provide a final answer summarizing what we've accomplished.\n",
+      "\n",
+      "Action:\n",
+      "```\n",
+      "{\n",
+      "  \"action\": \"Final Answer\",\n",
+      "  \"action_input\": \"Task 1 has been completed successfully. The PDB file for 1LYZ has been downloaded using the PDBFileDownloader tool. The file is now available in the system with the identifier '1LYZ_001358'. This PDB file contains the structural information for lysozyme, which is a well-studied enzyme often used as a model protein in molecular biology and biochemistry research.\"\n",
+      "}\n",
+      "```"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "({'input': '\\n    You are an expert molecular dynamics scientist, and\\n    your task is to respond to the question or\\n    solve the problem to the best of your ability using\\n    the provided tools.\\n\\n    You can only respond with a single complete\\n    \\'Thought, Action, Action Input\\' format\\n    OR a single \\'Final Answer\\' format.\\n\\n    Complete format:\\n    Thought: (reflect on your progress and decide what to do next)\\n    Action:\\n    ```\\n    {\\n        \"action\": (the action name, it should be the name of a tool),\\n        \"action_input\": (the input string for the action)\\n    }\\n    \\'\\'\\'\\n\\n    OR\\n\\n    Final Answer: (the final response to the original input\\n    question, once all steps are complete)\\n\\n    You are required to use the tools provided,\\n    using the most specific tool\\n    available for each action.\\n    Your final answer should contain all information\\n    necessary to answer the question and its subquestions.\\n    Before you finish, reflect on your progress and make\\n    sure you have addressed the question in its entirety.\\n\\n    If you are asked to continue\\n    or reference previous runs,\\n    the context will be provided to you.\\n    If context is provided, you should assume\\n    you are continuing a chat.\\n\\n    Here is the input:\\n    Previous Context: None\\n    Question: Complete all of the following tasks: 1. Download the PDB file 1LYZ. ',\n",
+       "  'output': \"Task 1 has been completed successfully. The PDB file for 1LYZ has been downloaded using the PDBFileDownloader tool. The file is now available in the system with the identifier '1LYZ_001358'. This PDB file contains the structural information for lysozyme, which is a well-studied enzyme often used as a model protein in molecular biology and biochemistry research.\"},\n",
+       " '78CNEDIC')"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "agent_1 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_1.run(descriptive_prompt_1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Files found in registry: 1LYZ_001358: PDB file downloaded from RSCB, PDBFile ID: 1LYZ_001358\n"
+     ]
+    }
+   ],
+   "source": [
+    "registry = agent_1.path_registry\n",
+    "print(registry.list_path_names_and_descriptions())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assert os.path.exists(registry.get_mapped_path(\"1LYZ_001358\"))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Certainly! I'll download the PDB file for 1LYZ using the PDBFileDownloader tool.\n",
+      "\n",
+      "Thought: To download the PDB file for 1LYZ, I need to use the PDBFileDownloader tool. This tool can fetch PDB files using a protein's PDB ID.\n",
+      "\n",
+      "Action:\n",
+      "```\n",
+      "{\n",
+      "    \"action\": \"PDBFileDownloader\",\n",
+      "    \"action_input\": \"1LYZ\"\n",
+      "}\n",
+      "```PDB file found with this ID: 1LYZ\n",
+      "Thought: The PDB file for 1LYZ has been successfully downloaded using the PDBFileDownloader tool. The file is now available in the system with the identifier \"1LYZ_001500\". I should provide this information as the final answer to the user.\n",
+      "\n",
+      "Action:\n",
+      "```\n",
+      "{\n",
+      "  \"action\": \"Final Answer\",\n",
+      "  \"action_input\": \"The PDB file for 1LYZ has been successfully downloaded. The file is now available in the system with the identifier '1LYZ_001500'. This file contains the structural information for the protein with the PDB ID 1LYZ, which corresponds to lysozyme. You can now use this file for further analysis or visualization using other tools if needed.\"\n",
+      "}\n",
+      "```"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "({'input': '\\n    You are an expert molecular dynamics scientist, and\\n    your task is to respond to the question or\\n    solve the problem to the best of your ability using\\n    the provided tools.\\n\\n    You can only respond with a single complete\\n    \\'Thought, Action, Action Input\\' format\\n    OR a single \\'Final Answer\\' format.\\n\\n    Complete format:\\n    Thought: (reflect on your progress and decide what to do next)\\n    Action:\\n    ```\\n    {\\n        \"action\": (the action name, it should be the name of a tool),\\n        \"action_input\": (the input string for the action)\\n    }\\n    \\'\\'\\'\\n\\n    OR\\n\\n    Final Answer: (the final response to the original input\\n    question, once all steps are complete)\\n\\n    You are required to use the tools provided,\\n    using the most specific tool\\n    available for each action.\\n    Your final answer should contain all information\\n    necessary to answer the question and its subquestions.\\n    Before you finish, reflect on your progress and make\\n    sure you have addressed the question in its entirety.\\n\\n    If you are asked to continue\\n    or reference previous runs,\\n    the context will be provided to you.\\n    If context is provided, you should assume\\n    you are continuing a chat.\\n\\n    Here is the input:\\n    Previous Context: None\\n    Question: Download the PDB file 1LYZ. ',\n",
+       "  'output': \"The PDB file for 1LYZ has been successfully downloaded. The file is now available in the system with the identifier '1LYZ_001500'. This file contains the structural information for the protein with the PDB ID 1LYZ, which corresponds to lysozyme. You can now use this file for further analysis or visualization using other tools if needed.\"},\n",
+       " '1PCP3267')"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "agent_2 = MDAgent(agent_type=\"Structured\", model=llm_model, top_k_tools=tools)\n",
+    "agent_2.run(non_descriptive_prompt_1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Files found in registry: 1LYZ_001358: PDB file downloaded from RSCB, PDBFile ID: 1LYZ_001358\n"
+     ]
+    }
+   ],
+   "source": [
+    "registry = agent_1.path_registry\n",
+    "print(registry.list_path_names_and_descriptions())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assert os.path.exists(registry.get_mapped_path(\"1LYZ_001358\"))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "mdagent2",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}