From c221efb17d961604883d0addefcb2f5c4f838417 Mon Sep 17 00:00:00 2001 From: Samantha Cox Date: Mon, 5 Aug 2024 21:06:20 -0700 Subject: [PATCH] irrelevant or outdated nbs --- .../individual_eval_20240422-181241.json | 69 -- .../individual_eval_20240422-181533.json | 69 -- notebooks/eval_demo/eval_demo.ipynb | 951 ------------------ .../evaluation_results/eval_table.tex | 8 - .../mega_eval_20240422-181533.json | 142 --- .../llama-v3p1-70b-instruct/exp_1 copy.ipynb | 420 -------- .../llama-v3p1-70b-instruct/exp_2 copy.ipynb | 227 ----- .../llama-v3p1-70b-instruct/exp_3 copy.ipynb | 208 ---- notebooks/radius_of_gyration/proteins.txt | 10 - notebooks/radius_of_gyration/rgy_1A3N.ipynb | 280 ------ notebooks/radius_of_gyration/rgy_1ATN.ipynb | 276 ----- notebooks/radius_of_gyration/rgy_1BO9.ipynb | 235 ----- notebooks/radius_of_gyration/rgy_1BR1.ipynb | 242 ----- notebooks/radius_of_gyration/rgy_1IGT.ipynb | 297 ------ notebooks/radius_of_gyration/rgy_1PQ2.ipynb | 297 ------ notebooks/radius_of_gyration/rgy_1TRZ.ipynb | 275 ----- notebooks/radius_of_gyration/rgy_1TUP.ipynb | 305 ------ notebooks/radius_of_gyration/rgy_2RH1.ipynb | 355 ------- notebooks/radius_of_gyration/rgy_2TNF.ipynb | 264 ----- notebooks/rdf/rdf.ipynb | 107 -- notebooks/rmsd/13AN_gpt4.ipynb | 261 ----- notebooks/rmsd/1ATN_gpt4.ipynb | 288 ------ notebooks/rmsd/1B09_gpt4.ipynb | 342 ------- notebooks/rmsd/1BR1_gpt4_fail.ipynb | 358 ------- notebooks/rmsd/1IGT_gpt4.ipynb | 381 ------- notebooks/rmsd/1PQ2_gpt4.ipynb | 326 ------ notebooks/rmsd/1TRZ_gpt4.ipynb | 345 ------- notebooks/rmsd/1TUP_gpt4.ipynb | 272 ----- notebooks/rmsd/2RH1_gpt4.ipynb | 335 ------ notebooks/rmsd/2TNF_gpt4_fail.ipynb | 821 --------------- notebooks/rmsd/2TNF_gpt4_try2.ipynb | 357 ------- 31 files changed, 9123 deletions(-) delete mode 100644 notebooks/eval_demo/ckpt_eval/individual_eval_20240422-181241.json delete mode 100644 notebooks/eval_demo/ckpt_eval/individual_eval_20240422-181533.json delete mode 100644 notebooks/eval_demo/eval_demo.ipynb delete mode 100644 notebooks/eval_demo/evaluation_results/eval_table.tex delete mode 100644 notebooks/eval_demo/evaluation_results/mega_eval_20240422-181533.json delete mode 100644 notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_1 copy.ipynb delete mode 100644 notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_2 copy.ipynb delete mode 100644 notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_3 copy.ipynb delete mode 100644 notebooks/radius_of_gyration/proteins.txt delete mode 100644 notebooks/radius_of_gyration/rgy_1A3N.ipynb delete mode 100644 notebooks/radius_of_gyration/rgy_1ATN.ipynb delete mode 100644 notebooks/radius_of_gyration/rgy_1BO9.ipynb delete mode 100644 notebooks/radius_of_gyration/rgy_1BR1.ipynb delete mode 100644 notebooks/radius_of_gyration/rgy_1IGT.ipynb delete mode 100644 notebooks/radius_of_gyration/rgy_1PQ2.ipynb delete mode 100644 notebooks/radius_of_gyration/rgy_1TRZ.ipynb delete mode 100644 notebooks/radius_of_gyration/rgy_1TUP.ipynb delete mode 100644 notebooks/radius_of_gyration/rgy_2RH1.ipynb delete mode 100644 notebooks/radius_of_gyration/rgy_2TNF.ipynb delete mode 100644 notebooks/rdf/rdf.ipynb delete mode 100644 notebooks/rmsd/13AN_gpt4.ipynb delete mode 100644 notebooks/rmsd/1ATN_gpt4.ipynb delete mode 100644 notebooks/rmsd/1B09_gpt4.ipynb delete mode 100644 notebooks/rmsd/1BR1_gpt4_fail.ipynb delete mode 100644 notebooks/rmsd/1IGT_gpt4.ipynb delete mode 100644 notebooks/rmsd/1PQ2_gpt4.ipynb delete mode 100644 notebooks/rmsd/1TRZ_gpt4.ipynb delete mode 100644 notebooks/rmsd/1TUP_gpt4.ipynb delete mode 100644 notebooks/rmsd/2RH1_gpt4.ipynb delete mode 100644 notebooks/rmsd/2TNF_gpt4_fail.ipynb delete mode 100644 notebooks/rmsd/2TNF_gpt4_try2.ipynb diff --git a/notebooks/eval_demo/ckpt_eval/individual_eval_20240422-181241.json b/notebooks/eval_demo/ckpt_eval/individual_eval_20240422-181241.json deleted file mode 100644 index 79e61998..00000000 --- a/notebooks/eval_demo/ckpt_eval/individual_eval_20240422-181241.json +++ /dev/null @@ -1,69 +0,0 @@ -{ - "agent_settings": { - "llm": "gpt-4-1106-preview", - "agent_type": "Structured", - "tools_llm": "gpt-4-1106-preview", - "subagents_llm": "gpt-4-1106-preview", - "resume": false, - "learn": false, - "curriculum": true - }, - "user_prompt": "Download and clean 1A3N.", - "prompt_success": true, - "total_steps": 3, - "failed_steps": 0, - "total_time_seconds": "42.115", - "total_time_minutes": "0.702", - "final_answer": "The fibronectin PDB file has been successfully downloaded and cleaned. It is now ready for further analysis or simulation steps.", - "tools_used": { - "PDBFileDownloader": 1, - "CleaningToolFunction": 2 - }, - "num_skills_before": 0, - "num_skills_after": 0, - "tools_details": { - "Step 1": { - "tool": "PDBFileDownloader", - "tool_input": { - "query": "fibronectin" - }, - "observation": "Succeeded. Downloaded the PDB file:5TFY_181207", - "status_complete": true, - "step_elapsed_time (sec)": "7.614", - "timestamp_from_start (sec)": "7.614" - }, - "Step 2": { - "tool": "CleaningToolFunction", - "tool_input": { - "pdb_id": "5TFY", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - }, - "observation": "Failed. Check your file path. File not found: [Errno 2] No such file or directory: 'Name not found in path registry.'", - "status_complete": false, - "step_elapsed_time (sec)": "9.472", - "timestamp_from_start (sec)": "17.086" - }, - "Step 3": { - "tool": "CleaningToolFunction", - "tool_input": { - "pdb_id": "5TFY_181207", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - }, - "observation": "Succeeded. File cleaned!\nFile ID:{file_id}\nPath:{directory}/{file_name}", - "status_complete": true, - "step_elapsed_time (sec)": "19.394", - "timestamp_from_start (sec)": "36.481" - } - }, - "run_id": "31fef58f-1863-4a7e-b694-71d129cb8bfa" -} diff --git a/notebooks/eval_demo/ckpt_eval/individual_eval_20240422-181533.json b/notebooks/eval_demo/ckpt_eval/individual_eval_20240422-181533.json deleted file mode 100644 index 9e11a6d8..00000000 --- a/notebooks/eval_demo/ckpt_eval/individual_eval_20240422-181533.json +++ /dev/null @@ -1,69 +0,0 @@ -{ - "agent_settings": { - "llm": "gpt-4-1106-preview", - "agent_type": "Structured", - "tools_llm": "gpt-4-1106-preview", - "subagents_llm": "gpt-4-1106-preview", - "resume": false, - "learn": false, - "curriculum": true - }, - "user_prompt": "Download and clean 1A3N.", - "prompt_success": true, - "total_steps": 3, - "failed_steps": 0, - "total_time_seconds": "40.278", - "total_time_minutes": "0.671", - "final_answer": "The fibronectin PDB file has been successfully downloaded and cleaned. The file is ready for further use.", - "tools_used": { - "PDBFileDownloader": 1, - "CleaningToolFunction": 2 - }, - "num_skills_before": 0, - "num_skills_after": 0, - "tools_details": { - "Step 1": { - "tool": "PDBFileDownloader", - "tool_input": { - "query": "fibronectin" - }, - "observation": "Succeeded. Downloaded the PDB file:5TFY_181459", - "status_complete": true, - "step_elapsed_time (sec)": "5.994", - "timestamp_from_start (sec)": "5.994" - }, - "Step 2": { - "tool": "CleaningToolFunction", - "tool_input": { - "pdb_id": "5TFY", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - }, - "observation": "Failed. Check your file path. File not found: [Errno 2] No such file or directory: 'Name not found in path registry.'", - "status_complete": false, - "step_elapsed_time (sec)": "11.529", - "timestamp_from_start (sec)": "17.522" - }, - "Step 3": { - "tool": "CleaningToolFunction", - "tool_input": { - "pdb_id": "5TFY_181459", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - }, - "observation": "Succeeded. File cleaned!\nFile ID:{file_id}\nPath:{directory}/{file_name}", - "status_complete": true, - "step_elapsed_time (sec)": "16.831", - "timestamp_from_start (sec)": "34.353" - } - }, - "run_id": "866c3c27-c5ff-4e21-bf5a-3bd02672f399" -} diff --git a/notebooks/eval_demo/eval_demo.ipynb b/notebooks/eval_demo/eval_demo.ipynb deleted file mode 100644 index b69b8876..00000000 --- a/notebooks/eval_demo/eval_demo.ipynb +++ /dev/null @@ -1,951 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# this is slightly old - the latest evaluator now has memory info and correct run_id" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Evaluating prompt: Download and clean fibronectin.\n", - "Thought: The user's main task is to download and clean the fibronectin protein structure. The first subtask is to download the fibronectin PDB file. I will use the PDBFileDownloader tool to download the PDB file for fibronectin.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"fibronectin\"\n", - " }\n", - "}\n", - "```" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-04-22 18:11:21.984 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "PDB file found with this ID: 5TFY\n", - "No names found. The JSON file is empty or does not contain name mappings.\n", - "The next subtask is to clean and preprocess the downloaded fibronectin PDB file. This typically involves removing heterogens, adding missing atoms and hydrogens, replacing nonstandard residues, and/or removing water. I will use the CleaningToolFunction to perform these tasks on the downloaded PDB file.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"5TFY\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```file path: Name not found in path registry.\n", - "The previous attempt to clean the fibronectin PDB file failed because the file was not found in the path registry. It seems there was a misunderstanding with the PDB ID used in the CleaningToolFunction. The PDB ID should be the one that was downloaded, which is '5TFY_181122'. I will correct the PDB ID and attempt to clean the file again using the CleaningToolFunction.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"5TFY_181122\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```file path: /Users/quinny/repos/md-agent_eval/ckpt/ckpt_9/pdb/5TFY_raw_20240422_181122.pdb\n", - "Names found in registry: 5TFY_181122\n", - "The fibronectin PDB file has been successfully downloaded and cleaned. The next steps in the user's initial plan are not specified, but typically after cleaning, the file would be prepared for molecular dynamics simulation. This could include setting up the simulation environment, selecting a force field, and solvating the protein if necessary. However, without further instructions from the user, I cannot proceed with these steps.\n", - "\n", - "Since the main task and the subtasks outlined by the user have been completed, I will provide the final answer with the details of the cleaned PDB file for fibronectin.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"Final Answer\",\n", - " \"action_input\": \"The fibronectin PDB file has been successfully downloaded and cleaned. The cleaned file is available and can be used for further molecular dynamics simulation steps.\"\n", - "}\n", - "```\n", - "----- Evaluation Summary -----\n", - "Run ID: 670ff44b-48a1-41ea-aaa8-30bf701a34dd\n", - "Total Steps: 4\n", - "Total Time: 49.63 seconds (0.83 minutes)\n", - "Evaluating prompt: Download and clean 1A3N.\n", - "Thought: The user's main task is to download and clean the fibronectin protein structure. The first subtask is to download the fibronectin PDB file. I will use the PDBFileDownloader tool to download the PDB file for fibronectin.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"fibronectin\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 5TFY\n", - "Names found in registry: 5TFY_181122, 5TFY_181149\n", - "The PDB file for fibronectin has been successfully downloaded. The next subtask is to clean and preprocess the fibronectin PDB file. This involves removing heterogens, adding missing atoms and hydrogens, replacing nonstandard residues, and removing water if necessary. I will use the CleaningToolFunction to perform these tasks on the downloaded PDB file.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"5TFY\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```file path: Name not found in path registry.\n", - "The attempt to clean the fibronectin PDB file failed because the file was not found in the path registry. This could be due to an incorrect PDB ID or an issue with the file path. Since the PDB file was successfully downloaded with the ID \"5TFY_181207\", I need to use the correct ID that includes the date suffix to ensure the file is found in the path registry. I will retry the CleaningToolFunction with the full PDB ID including the date suffix.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"5TFY_181207\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```file path: /Users/quinny/repos/md-agent_eval/ckpt/ckpt_9/pdb/5TFY_raw_20240422_181207.pdb\n", - "Names found in registry: 5TFY_181122, 5TFY_181149, 5TFY_181207\n", - "The fibronectin PDB file has been successfully cleaned and preprocessed. This completes the subtasks outlined in the user's initial plan. The cleaned PDB file is now ready for further molecular dynamics simulations or analysis as required by the user.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"Final Answer\",\n", - " \"action_input\": \"The fibronectin PDB file has been successfully downloaded and cleaned. It is now ready for further analysis or simulation steps.\"\n", - "}\n", - "```\n", - "----- Evaluation Summary -----\n", - "Run ID: 31fef58f-1863-4a7e-b694-71d129cb8bfa\n", - "Total Steps: 4\n", - "Total Time: 42.12 seconds (0.70 minutes)\n", - "All evaluations saved to evaluation_results/mega_eval_20240422-181241.json.\n" - ] - } - ], - "source": [ - "from mdagent import Evaluator\n", - "\n", - "evaluator = Evaluator(eval_dir=\"evaluation_results\") # that's the default - change base_dir if desired\n", - "\n", - "# to do it manually\n", - "agent_params = {\n", - " \"agent_type\": \"Structured\",\n", - " \"learn\": False,\n", - " 'model': 'gpt-3.5-turbo',\n", - " 'tools_model': 'gpt-3.5-turbo',\n", - "}\n", - "prompts = [\n", - " 'Download and clean fibronectin.',\n", - " 'Download and clean 1A3N.',\n", - "]\n", - "evaluator.run_and_evaluate(prompts, agent_params=agent_params)\n", - "evaluator.save()" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[{'agent_settings': {'llm': 'gpt-4-1106-preview',\n", - " 'agent_type': 'Structured',\n", - " 'tools_llm': 'gpt-4-1106-preview',\n", - " 'subagents_llm': 'gpt-4-1106-preview',\n", - " 'resume': False,\n", - " 'learn': False,\n", - " 'curriculum': True},\n", - " 'user_prompt': 'Download and clean fibronectin.',\n", - " 'prompt_success': True,\n", - " 'total_steps': 3,\n", - " 'failed_steps': 0,\n", - " 'total_time_seconds': '49.630',\n", - " 'total_time_minutes': '0.827',\n", - " 'final_answer': 'The fibronectin PDB file has been successfully downloaded and cleaned. The cleaned file is available and can be used for further molecular dynamics simulation steps.',\n", - " 'tools_used': {'PDBFileDownloader': 1, 'CleaningToolFunction': 2},\n", - " 'num_skills_before': 0,\n", - " 'num_skills_after': 0,\n", - " 'tools_details': {'Step 1': {'tool': 'PDBFileDownloader',\n", - " 'tool_input': {'query': 'fibronectin'},\n", - " 'observation': 'Succeeded. Downloaded the PDB file:5TFY_181122',\n", - " 'status_complete': True,\n", - " 'step_elapsed_time (sec)': '12.319',\n", - " 'timestamp_from_start (sec)': '12.319'},\n", - " 'Step 2': {'tool': 'CleaningToolFunction',\n", - " 'tool_input': {'pdb_id': '5TFY',\n", - " 'replace_nonstandard_residues': True,\n", - " 'add_missing_atoms': True,\n", - " 'remove_heterogens': True,\n", - " 'remove_water': True,\n", - " 'add_hydrogens': True,\n", - " 'add_hydrogens_ph': 7.0},\n", - " 'observation': \"Failed. Check your file path. File not found: [Errno 2] No such file or directory: 'Name not found in path registry.'\",\n", - " 'status_complete': False,\n", - " 'step_elapsed_time (sec)': '10.498',\n", - " 'timestamp_from_start (sec)': '22.817'},\n", - " 'Step 3': {'tool': 'CleaningToolFunction',\n", - " 'tool_input': {'pdb_id': '5TFY_181122',\n", - " 'replace_nonstandard_residues': True,\n", - " 'add_missing_atoms': True,\n", - " 'remove_heterogens': True,\n", - " 'remove_water': True,\n", - " 'add_hydrogens': True,\n", - " 'add_hydrogens_ph': 7.0},\n", - " 'observation': 'Succeeded. File cleaned!\\nFile ID:{file_id}\\nPath:{directory}/{file_name}',\n", - " 'status_complete': True,\n", - " 'step_elapsed_time (sec)': '17.433',\n", - " 'timestamp_from_start (sec)': '40.250'}},\n", - " 'run_id': '670ff44b-48a1-41ea-aaa8-30bf701a34dd',\n", - " 'execution_success': True},\n", - " {'agent_settings': {'llm': 'gpt-4-1106-preview',\n", - " 'agent_type': 'Structured',\n", - " 'tools_llm': 'gpt-4-1106-preview',\n", - " 'subagents_llm': 'gpt-4-1106-preview',\n", - " 'resume': False,\n", - " 'learn': False,\n", - " 'curriculum': True},\n", - " 'user_prompt': 'Download and clean 1A3N.',\n", - " 'prompt_success': True,\n", - " 'total_steps': 3,\n", - " 'failed_steps': 0,\n", - " 'total_time_seconds': '42.115',\n", - " 'total_time_minutes': '0.702',\n", - " 'final_answer': 'The fibronectin PDB file has been successfully downloaded and cleaned. It is now ready for further analysis or simulation steps.',\n", - " 'tools_used': {'PDBFileDownloader': 1, 'CleaningToolFunction': 2},\n", - " 'num_skills_before': 0,\n", - " 'num_skills_after': 0,\n", - " 'tools_details': {'Step 1': {'tool': 'PDBFileDownloader',\n", - " 'tool_input': {'query': 'fibronectin'},\n", - " 'observation': 'Succeeded. Downloaded the PDB file:5TFY_181207',\n", - " 'status_complete': True,\n", - " 'step_elapsed_time (sec)': '7.614',\n", - " 'timestamp_from_start (sec)': '7.614'},\n", - " 'Step 2': {'tool': 'CleaningToolFunction',\n", - " 'tool_input': {'pdb_id': '5TFY',\n", - " 'replace_nonstandard_residues': True,\n", - " 'add_missing_atoms': True,\n", - " 'remove_heterogens': True,\n", - " 'remove_water': True,\n", - " 'add_hydrogens': True,\n", - " 'add_hydrogens_ph': 7.0},\n", - " 'observation': \"Failed. Check your file path. File not found: [Errno 2] No such file or directory: 'Name not found in path registry.'\",\n", - " 'status_complete': False,\n", - " 'step_elapsed_time (sec)': '9.472',\n", - " 'timestamp_from_start (sec)': '17.086'},\n", - " 'Step 3': {'tool': 'CleaningToolFunction',\n", - " 'tool_input': {'pdb_id': '5TFY_181207',\n", - " 'replace_nonstandard_residues': True,\n", - " 'add_missing_atoms': True,\n", - " 'remove_heterogens': True,\n", - " 'remove_water': True,\n", - " 'add_hydrogens': True,\n", - " 'add_hydrogens_ph': 7.0},\n", - " 'observation': 'Succeeded. File cleaned!\\nFile ID:{file_id}\\nPath:{directory}/{file_name}',\n", - " 'status_complete': True,\n", - " 'step_elapsed_time (sec)': '19.394',\n", - " 'timestamp_from_start (sec)': '36.481'}},\n", - " 'run_id': '31fef58f-1863-4a7e-b694-71d129cb8bfa',\n", - " 'execution_success': True}]" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "evaluator.evaluations" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "evaluator.reset() # clear evaluations" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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LLMAgent TypeUser PromptPrompt SuccessExecution SuccessError MessageTotal StepsFailed StepsTime (s)Time (min)
0gpt-4-1106-previewStructuredNoneTrueTrueNone3049.6300.827
1gpt-4-1106-previewStructuredNoneTrueTrueNone3042.1150.702
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" - ], - "text/plain": [ - " LLM Agent Type User Prompt Prompt Success \\\n", - "0 gpt-4-1106-preview Structured None True \n", - "1 gpt-4-1106-preview Structured None True \n", - "\n", - " Execution Success Error Message Total Steps Failed Steps Time (s) \\\n", - "0 True None 3 0 49.630 \n", - "1 True None 3 0 42.115 \n", - "\n", - " Time (min) \n", - "0 0.827 \n", - "1 0.702 " - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# you can load it later and create a table\n", - "from mdagent import Evaluator\n", - "\n", - "evaluator = Evaluator()\n", - "evaluator.load('evaluation_results/mega_eval_20240422-181241.json')\n", - "df = evaluator.create_table(simple=True) # this is default\n", - "\n", - "df.to_latex('evaluation_results/eval_table.tex', index=False) # you can create latex tables\n", - "df" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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agent_settings_llmagent_settings_agent_typeagent_settings_tools_llmagent_settings_subagents_llmagent_settings_resumeagent_settings_learnagent_settings_curriculumuser_promptprompt_successtotal_stepsfailed_stepstotal_time_secondstotal_time_minutesfinal_answertools_used_PDBFileDownloadertools_used_CleaningToolFunctionnum_skills_beforenum_skills_aftertools_details_Step 1_tooltools_details_Step 1_tool_inputtools_details_Step 1_observationtools_details_Step 1_status_completetools_details_Step 1_step_elapsed_time (sec)tools_details_Step 1_timestamp_from_start (sec)tools_details_Step 2_tooltools_details_Step 2_tool_inputtools_details_Step 2_observationtools_details_Step 2_status_completetools_details_Step 2_step_elapsed_time (sec)tools_details_Step 2_timestamp_from_start (sec)tools_details_Step 3_tooltools_details_Step 3_tool_inputtools_details_Step 3_observationtools_details_Step 3_status_completetools_details_Step 3_step_elapsed_time (sec)tools_details_Step 3_timestamp_from_start (sec)run_idexecution_success
0gpt-4-1106-previewStructuredgpt-4-1106-previewgpt-4-1106-previewFalseFalseTrueDownload and clean fibronectin.True3049.6300.827The fibronectin PDB file has been successfully...1200PDBFileDownloader{'query': 'fibronectin'}Succeeded. Downloaded the PDB file:5TFY_181122True12.31912.319CleaningToolFunction{'pdb_id': '5TFY', 'replace_nonstandard_residu...Failed. Check your file path. File not found: ...False10.49822.817CleaningToolFunction{'pdb_id': '5TFY_181122', 'replace_nonstandard...Succeeded. File cleaned!\\nFile ID:{file_id}\\nP...True17.43340.250670ff44b-48a1-41ea-aaa8-30bf701a34ddTrue
1gpt-4-1106-previewStructuredgpt-4-1106-previewgpt-4-1106-previewFalseFalseTrueDownload and clean 1A3N.True3042.1150.702The fibronectin PDB file has been successfully...1200PDBFileDownloader{'query': 'fibronectin'}Succeeded. Downloaded the PDB file:5TFY_181207True7.6147.614CleaningToolFunction{'pdb_id': '5TFY', 'replace_nonstandard_residu...Failed. Check your file path. File not found: ...False9.47217.086CleaningToolFunction{'pdb_id': '5TFY_181207', 'replace_nonstandard...Succeeded. File cleaned!\\nFile ID:{file_id}\\nP...True19.39436.48131fef58f-1863-4a7e-b694-71d129cb8bfaTrue
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" - ], - "text/plain": [ - " agent_settings_llm agent_settings_agent_type agent_settings_tools_llm \\\n", - "0 gpt-4-1106-preview Structured gpt-4-1106-preview \n", - "1 gpt-4-1106-preview Structured gpt-4-1106-preview \n", - "\n", - " agent_settings_subagents_llm agent_settings_resume agent_settings_learn \\\n", - "0 gpt-4-1106-preview False False \n", - "1 gpt-4-1106-preview False False \n", - "\n", - " agent_settings_curriculum user_prompt prompt_success \\\n", - "0 True Download and clean fibronectin. True \n", - "1 True Download and clean 1A3N. True \n", - "\n", - " total_steps failed_steps total_time_seconds total_time_minutes \\\n", - "0 3 0 49.630 0.827 \n", - "1 3 0 42.115 0.702 \n", - "\n", - " final_answer \\\n", - "0 The fibronectin PDB file has been successfully... \n", - "1 The fibronectin PDB file has been successfully... \n", - "\n", - " tools_used_PDBFileDownloader tools_used_CleaningToolFunction \\\n", - "0 1 2 \n", - "1 1 2 \n", - "\n", - " num_skills_before num_skills_after tools_details_Step 1_tool \\\n", - "0 0 0 PDBFileDownloader \n", - "1 0 0 PDBFileDownloader \n", - "\n", - " tools_details_Step 1_tool_input \\\n", - "0 {'query': 'fibronectin'} \n", - "1 {'query': 'fibronectin'} \n", - "\n", - " tools_details_Step 1_observation \\\n", - "0 Succeeded. Downloaded the PDB file:5TFY_181122 \n", - "1 Succeeded. Downloaded the PDB file:5TFY_181207 \n", - "\n", - " tools_details_Step 1_status_complete \\\n", - "0 True \n", - "1 True \n", - "\n", - " tools_details_Step 1_step_elapsed_time (sec) \\\n", - "0 12.319 \n", - "1 7.614 \n", - "\n", - " tools_details_Step 1_timestamp_from_start (sec) tools_details_Step 2_tool \\\n", - "0 12.319 CleaningToolFunction \n", - "1 7.614 CleaningToolFunction \n", - "\n", - " tools_details_Step 2_tool_input \\\n", - "0 {'pdb_id': '5TFY', 'replace_nonstandard_residu... \n", - "1 {'pdb_id': '5TFY', 'replace_nonstandard_residu... \n", - "\n", - " tools_details_Step 2_observation \\\n", - "0 Failed. Check your file path. File not found: ... \n", - "1 Failed. Check your file path. File not found: ... \n", - "\n", - " tools_details_Step 2_status_complete \\\n", - "0 False \n", - "1 False \n", - "\n", - " tools_details_Step 2_step_elapsed_time (sec) \\\n", - "0 10.498 \n", - "1 9.472 \n", - "\n", - " tools_details_Step 2_timestamp_from_start (sec) tools_details_Step 3_tool \\\n", - "0 22.817 CleaningToolFunction \n", - "1 17.086 CleaningToolFunction \n", - "\n", - " tools_details_Step 3_tool_input \\\n", - "0 {'pdb_id': '5TFY_181122', 'replace_nonstandard... \n", - "1 {'pdb_id': '5TFY_181207', 'replace_nonstandard... \n", - "\n", - " tools_details_Step 3_observation \\\n", - "0 Succeeded. File cleaned!\\nFile ID:{file_id}\\nP... \n", - "1 Succeeded. File cleaned!\\nFile ID:{file_id}\\nP... \n", - "\n", - " tools_details_Step 3_status_complete \\\n", - "0 True \n", - "1 True \n", - "\n", - " tools_details_Step 3_step_elapsed_time (sec) \\\n", - "0 17.433 \n", - "1 19.394 \n", - "\n", - " tools_details_Step 3_timestamp_from_start (sec) \\\n", - "0 40.250 \n", - "1 36.481 \n", - "\n", - " run_id execution_success \n", - "0 670ff44b-48a1-41ea-aaa8-30bf701a34dd True \n", - "1 31fef58f-1863-4a7e-b694-71d129cb8bfa True " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "import pandas as pd\n", - "df_full = evaluator.create_table(simple=False) # get all info\n", - "\n", - "# show all columns (it'll be very long rows!)\n", - "with pd.option_context('display.max_rows', None, 'display.max_columns', None):\n", - " display(df_full)\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Evaluating prompt: Download and clean fibronectin.\n", - "Thought: The user's main task is to download and clean the fibronectin protein structure. The first subtask is to download the fibronectin PDB file. I will use the PDBFileDownloader tool to download the PDB file for fibronectin.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"fibronectin\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 5TFY\n", - "No names found. The JSON file is empty or does not contain name mappings.\n", - "The next subtask is to clean and preprocess the downloaded fibronectin PDB file. This typically involves removing heterogens, adding missing atoms and hydrogens, replacing nonstandard residues, and/or removing water. I will use the CleaningToolFunction to perform these tasks on the downloaded PDB file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"5TFY\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```file path: Name not found in path registry.\n", - "The previous attempt to clean the PDB file failed because the file was not found in the path registry. This could be due to an incorrect PDB ID or a problem with the file path. Since the PDB ID '5TFY' was successfully downloaded, I will attempt to clean the file again, ensuring that the PDB ID is correctly specified.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"5TFY_181417\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```file path: /Users/quinny/repos/md-agent_eval/ckpt/ckpt_10/pdb/5TFY_raw_20240422_181417.pdb\n", - "Names found in registry: 5TFY_181417\n", - "The fibronectin PDB file has been successfully downloaded and cleaned. The main task and subtasks requested by the user have been completed. The cleaned file is now ready for further processing or simulation as per the user's requirements.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"Final Answer\",\n", - " \"action_input\": \"The fibronectin PDB file has been successfully downloaded and cleaned. The cleaned file is ready for further use.\"\n", - "}\n", - "```\n", - "----- Evaluation Summary -----\n", - "Run ID: 943a58af-f062-4ab3-a55d-bf571b584d25\n", - "Total Steps: 4\n", - "Total Time: 45.95 seconds (0.77 minutes)\n", - "Evaluating prompt: Download and clean 1A3N.\n", - "Thought: The user's main task is to download and clean the fibronectin protein structure. The first subtask is to download the fibronectin PDB file. I will use the PDBFileDownloader tool to download the PDB file for fibronectin.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"fibronectin\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 5TFY\n", - "Names found in registry: 5TFY_181417, 5TFY_181445\n", - "The next subtask is to clean and preprocess the downloaded fibronectin PDB file. This involves removing heterogens, adding missing atoms and hydrogens, replacing nonstandard residues, and removing water if necessary. I will use the CleaningToolFunction to perform these tasks on the downloaded PDB file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"5TFY\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```file path: Name not found in path registry.\n", - "The previous attempt to clean the fibronectin PDB file failed because the file was not found in the path registry. It seems there was a misunderstanding in the PDB ID used. The PDB ID should be the one returned by the PDBFileDownloader tool, which was \"5TFY_181459\". I will correct the PDB ID and attempt to clean the file again using the CleaningToolFunction.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"5TFY_181459\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```file path: /Users/quinny/repos/md-agent_eval/ckpt/ckpt_10/pdb/5TFY_raw_20240422_181459.pdb\n", - "Names found in registry: 5TFY_181417, 5TFY_181445, 5TFY_181459\n", - "The fibronectin PDB file has been successfully downloaded and cleaned. The main task and subtasks requested by the user have been completed. The cleaned file is now ready for further processing or simulation as per the user's requirements.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"Final Answer\",\n", - " \"action_input\": \"The fibronectin PDB file has been successfully downloaded and cleaned. The file is ready for further use.\"\n", - "}\n", - "```\n", - "----- Evaluation Summary -----\n", - "Run ID: 866c3c27-c5ff-4e21-bf5a-3bd02672f399\n", - "Total Steps: 4\n", - "Total Time: 40.28 seconds (0.67 minutes)\n", - "All evaluations saved to evaluation_results/mega_eval_20240422-181533.json.\n" - ] - } - ], - "source": [ - "# you can use \"automate\" to automate the process of running, saving, and creating the simple table\n", - "\n", - "evaluator.reset() # empty the evaluation info\n", - "df2 = evaluator.automate(prompts, agent_params=agent_params)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "df2" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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LLMAgent TypeUser PromptPrompt SuccessExecution SuccessError MessageTotal StepsFailed StepsTime (s)Time (min)
0gpt-4-1106-previewStructuredDownload and clean fibronectin.NoneFalseTypeError: Object of type ChatOpenAI is not JS...NoneNoneNoneNone
1gpt-4-1106-previewStructuredDownload and clean 1A3N.NoneFalseTypeError: Object of type ChatOpenAI is not JS...NoneNoneNoneNone
\n", - "
" - ], - "text/plain": [ - " LLM Agent Type User Prompt \\\n", - "0 gpt-4-1106-preview Structured Download and clean fibronectin. \n", - "1 gpt-4-1106-preview Structured Download and clean 1A3N. \n", - "\n", - " Prompt Success Execution Success \\\n", - "0 None False \n", - "1 None False \n", - "\n", - " Error Message Total Steps Failed Steps \\\n", - "0 TypeError: Object of type ChatOpenAI is not JS... None None \n", - "1 TypeError: Object of type ChatOpenAI is not JS... None None \n", - "\n", - " Time (s) Time (min) \n", - "0 None None \n", - "1 None None " - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df2 # old results to show it can capture when MD-Agent throws exception errors" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.8" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/eval_demo/evaluation_results/eval_table.tex b/notebooks/eval_demo/evaluation_results/eval_table.tex deleted file mode 100644 index 77926c40..00000000 --- a/notebooks/eval_demo/evaluation_results/eval_table.tex +++ /dev/null @@ -1,8 +0,0 @@ -\begin{tabular}{lllrrlrrll} -\toprule -LLM & Agent Type & User Prompt & Prompt Success & Execution Success & Error Message & Total Steps & Failed Steps & Time (s) & Time (min) \\ -\midrule -gpt-4-1106-preview & Structured & NaN & True & True & NaN & 3 & 0 & 49.630 & 0.827 \\ -gpt-4-1106-preview & Structured & NaN & True & True & NaN & 3 & 0 & 42.115 & 0.702 \\ -\bottomrule -\end{tabular} diff --git a/notebooks/eval_demo/evaluation_results/mega_eval_20240422-181533.json b/notebooks/eval_demo/evaluation_results/mega_eval_20240422-181533.json deleted file mode 100644 index 1c30ec72..00000000 --- a/notebooks/eval_demo/evaluation_results/mega_eval_20240422-181533.json +++ /dev/null @@ -1,142 +0,0 @@ -[ - { - "agent_settings": { - "llm": "gpt-4-1106-preview", - "agent_type": "Structured", - "tools_llm": "gpt-4-1106-preview", - "subagents_llm": "gpt-4-1106-preview", - "resume": false, - "learn": false, - "curriculum": true - }, - "user_prompt": "Download and clean fibronectin.", - "prompt_success": true, - "total_steps": 3, - "failed_steps": 0, - "total_time_seconds": "45.945", - "total_time_minutes": "0.766", - "final_answer": "The fibronectin PDB file has been successfully downloaded and cleaned. The cleaned file is ready for further use.", - "tools_used": { - "PDBFileDownloader": 1, - "CleaningToolFunction": 2 - }, - "num_skills_before": 0, - "num_skills_after": 0, - "tools_details": { - "Step 1": { - "tool": "PDBFileDownloader", - "tool_input": { - "query": "fibronectin" - }, - "observation": "Succeeded. Downloaded the PDB file:5TFY_181417", - "status_complete": true, - "step_elapsed_time (sec)": "10.064", - "timestamp_from_start (sec)": "10.064" - }, - "Step 2": { - "tool": "CleaningToolFunction", - "tool_input": { - "pdb_id": "5TFY", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - }, - "observation": "Failed. Check your file path. File not found: [Errno 2] No such file or directory: 'Name not found in path registry.'", - "status_complete": false, - "step_elapsed_time (sec)": "11.307", - "timestamp_from_start (sec)": "21.371" - }, - "Step 3": { - "tool": "CleaningToolFunction", - "tool_input": { - "pdb_id": "5TFY_181417", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - }, - "observation": "Succeeded. File cleaned!\nFile ID:{file_id}\nPath:{directory}/{file_name}", - "status_complete": true, - "step_elapsed_time (sec)": "17.757", - "timestamp_from_start (sec)": "39.128" - } - }, - "run_id": "943a58af-f062-4ab3-a55d-bf571b584d25", - "execution_success": true - }, - { - "agent_settings": { - "llm": "gpt-4-1106-preview", - "agent_type": "Structured", - "tools_llm": "gpt-4-1106-preview", - "subagents_llm": "gpt-4-1106-preview", - "resume": false, - "learn": false, - "curriculum": true - }, - "user_prompt": "Download and clean 1A3N.", - "prompt_success": true, - "total_steps": 3, - "failed_steps": 0, - "total_time_seconds": "40.278", - "total_time_minutes": "0.671", - "final_answer": "The fibronectin PDB file has been successfully downloaded and cleaned. The file is ready for further use.", - "tools_used": { - "PDBFileDownloader": 1, - "CleaningToolFunction": 2 - }, - "num_skills_before": 0, - "num_skills_after": 0, - "tools_details": { - "Step 1": { - "tool": "PDBFileDownloader", - "tool_input": { - "query": "fibronectin" - }, - "observation": "Succeeded. Downloaded the PDB file:5TFY_181459", - "status_complete": true, - "step_elapsed_time (sec)": "5.994", - "timestamp_from_start (sec)": "5.994" - }, - "Step 2": { - "tool": "CleaningToolFunction", - "tool_input": { - "pdb_id": "5TFY", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - }, - "observation": "Failed. Check your file path. File not found: [Errno 2] No such file or directory: 'Name not found in path registry.'", - "status_complete": false, - "step_elapsed_time (sec)": "11.529", - "timestamp_from_start (sec)": "17.522" - }, - "Step 3": { - "tool": "CleaningToolFunction", - "tool_input": { - "pdb_id": "5TFY_181459", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - }, - "observation": "Succeeded. File cleaned!\nFile ID:{file_id}\nPath:{directory}/{file_name}", - "status_complete": true, - "step_elapsed_time (sec)": "16.831", - "timestamp_from_start (sec)": "34.353" - } - }, - "run_id": "866c3c27-c5ff-4e21-bf5a-3bd02672f399", - "execution_success": true - } -] diff --git a/notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_1 copy.ipynb b/notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_1 copy.ipynb deleted file mode 100644 index d58fa49f..00000000 --- a/notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_1 copy.ipynb +++ /dev/null @@ -1,420 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import datetime\n", - "import os\n", - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "date and time: 2024-08-05\n", - "time: 16:24:23\n" - ] - } - ], - "source": [ - "#todays date and time\n", - "now = datetime.datetime.now()\n", - "date = now.strftime(\"%Y-%m-%d\")\n", - "print(\"date and time:\",date)\n", - "time = now.strftime(\"%H:%M:%S\")\n", - "print(\"time:\",time)" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "prompt1 = \"Simulate pdb 1MBN at two different temperatures: 300K, 400K for 1ns seconds each. Plot RMSD of both over time, and compare the final secondary structures at the end of the simulations.\"\n", - "llm_var = \"llama-v3p1-70b-instruct\"\n", - "tools = \"all\"\n", - "agent = MDAgent(agent_type=\"Structured\", model=llm_var, top_k_tools=tools)" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "LLM: accounts/fireworks/models/llama-v3p1-70b-instruct \n", - "Temperature: 0.1\n" - ] - } - ], - "source": [ - "print(\"LLM: \",agent.llm.model_name,\"\\nTemperature: \",agent.llm.temperature)" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "4bc037360b8b407688ad283b0411702a", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "tokenizer_config.json: 0%| | 0.00/26.0 [00:00 Entering new AgentExecutor chain...\u001b[0m\n", - "Thought: To simulate the protein 1MBN at two different temperatures, I will first need to download the PDB file and then set up and run the simulations. After the simulations are complete, I can calculate the RMSD of both simulations over time and compare the final secondary structures.\n", - "\n", - "Action: SetUpandRunFunction\n", - "Action Input: \n", - "{\n", - " \"pdb_id\": \"1MBN\",\n", - " \"forcefield_files\": [\"amber99sbildn.xml\", \"tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.00001,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NPT\",\n", - " \"Number of Steps\": 500000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - "}\n", - "\n", - "\u001b[32;1m\u001b[1;3mThought: To simulate the protein 1MBN at two different temperatures, I will first need to download the PDB file and then set up and run the simulations. After the simulations are complete, I can calculate the RMSD of both simulations over time and compare the final secondary structures.\n", - "\n", - "Action: SetUpandRunFunction\n", - "Action Input: \n", - "{\n", - " \"pdb_id\": \"1MBN\",\n", - " \"forcefield_files\": [\"amber99sbildn.xml\", \"tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.00001,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NPT\",\n", - " \"Number of Steps\": 500000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - "}\n", - "\n", - "\u001b[0m\n", - "\n", - "\u001b[1m> Finished chain.\u001b[0m\n", - "Here is a summary of the agent's attempts to solve the problem:\n", - "\n", - "**Prompt:** The agent was given a task to simulate the protein 1MBN at two different temperatures (300K and 400K) for 1ns seconds each, plot the RMSD of both simulations over time, and compare the final secondary structures at the end of the simulations.\n", - "\n", - "**Step 1:** The agent reflected on the problem and decided to download the PDB file and set up and run the simulations. The agent chose to use the `SetUpandRunFunction` tool to achieve this.\n", - "\n", - "**Action Input:** The agent provided the following input to the `SetUpandRunFunction` tool:\n", - "\n", - "* `pdb_id`: \"1MBN\"\n", - "* `forcefield_files`: [\"amber99sbildn.xml\", \"tip3p.xml\"]\n", - "* `save`: true\n", - "* `system_params`: various parameters for the simulation, including nonbonded method, cutoff, and constraints\n", - "* `integrator_params`: parameters for the integrator, including temperature, friction, and timestep\n", - "* `simulation_params`: parameters for the simulation, including ensemble, number of steps, and record interval\n", - "\n", - "**Note:** The agent only simulated the protein at 300K in this step, but the prompt required simulations at both 300K and 400K.\n", - "\n", - "**Current Status:** The agent has only completed the first step of the simulation at 300K and has not yet simulated the protein at 400K, calculated the RMSD of both simulations, or compared the final secondary structures.\n", - "\n", - "**Next Steps:** The agent should simulate the protein at 400K, calculate the RMSD of both simulations, and compare the final secondary structures to complete the task.Your run id is: HSE53GCT\n" - ] - } - ], - "source": [ - "result = agent.run(prompt1)" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'Thought: To simulate the protein 1MBN at two different temperatures, I need to first download the PDB file of 1MBN. Then, I will set up and run two separate simulations at 300K and 400K for 1ns each. After the simulations, I will compute the RMSD of both simulations over time and compare the final secondary structures.\\n\\nAction: PDBFileDownloader\\nAction Input: 1MBN'" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "output, run_id = result\n", - "output['output']" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "312\n", - "91\n" - ] - } - ], - "source": [ - "print(agent.llm.get_num_tokens(output['input']))\n", - "print(agent.llm.get_num_tokens(output['output']))" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'0.2.12'" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "import langchain\n", - "langchain.__version__" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "{'error': \n", - " {\n", - " 'message': 'Input validation error: `inputs` tokens + `max_new_tokens` must be <= 4097. Given: 7338 `inputs` tokens and 4096 `max_new_tokens`', \n", - " 'type': 'invalid_request_error', \n", - " 'param': 'max_tokens', \n", - " 'code': None\n", - " }\n", - "}" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "#print final date and time\n", - "now = datetime.datetime.now()\n", - "date = now.strftime(\"%Y-%m-%d\")\n", - "print(\"date and time:\",date)\n", - "time = now.strftime(\"%H:%M:%S\")\n", - "print(\"time:\",time)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "registry = agent.path_registry\n", - "paths_and_descriptions = registry.list_path_names_and_descriptions()\n", - "print(\"\\n\".join(paths_and_descriptions.split(\",\")))" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "#plotting rmsd of both simulations\n", - "from IPython.display import Image\n", - "rmsd1ID = 'fig0_192900'\n", - "rmsd2ID = 'fig0_192903'\n", - "path1 = registry.get_mapped_path(rmsd1ID)\n", - "path2 = registry.get_mapped_path(rmsd2ID)\n", - "\n", - "\n", - "Image(filename=path1)\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "Image(filename=path2)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Experiment Result:\n", - "### Completed without Exception or TimeOut Errors ❌\n", - "### Attempted all necessary steps ✅\n", - "### Logic make sense ✅\n", - "### Correct Answer ❌\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### Agent did not realize that it finished" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "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": "3.11.8" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_2 copy.ipynb b/notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_2 copy.ipynb deleted file mode 100644 index 6aa080b9..00000000 --- a/notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_2 copy.ipynb +++ /dev/null @@ -1,227 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import datetime\n", - "import os\n", - "from mdagent import MDAgent\n", - "import matplotlib.pyplot as plt" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "date and time: 2024-08-05\n", - "time: 16:41:03\n", - "LLM: accounts/fireworks/models/llama-v3p1-70b-instruct \n", - "Temperature: 0.1\n" - ] - } - ], - "source": [ - "prompt2 = \"Download the pdb file for PDB ID 1LYZ.\"\n", - "llm_var = \"llama-v3p1-70b-instruct\"\n", - "tools = \"all\"\n", - "agent = MDAgent(agent_type=\"Structured\", model=llm_var, top_k_tools=tools)\n", - "now = datetime.datetime.now()\n", - "date = now.strftime(\"%Y-%m-%d\")\n", - "print(\"date and time:\",date)\n", - "time = now.strftime(\"%H:%M:%S\")\n", - "print(\"time:\",time)\n", - "print(\"LLM: \",agent.llm.model_name,\"\\nTemperature: \",agent.llm.temperature)" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Num of tokens: 351\n", - "\n", - "\n", - "\u001b[1m> Entering new AgentExecutor chain...\u001b[0m\n", - "Thought: To download the PDB file for PDB ID 1LYZ, I need to use the PDBFileDownloader tool.\n", - "\n", - "Action: PDBFileDownloader\n", - "Action Input: 1LYZ\u001b[32;1m\u001b[1;3mThought: To download the PDB file for PDB ID 1LYZ, I need to use the PDBFileDownloader tool.\n", - "\n", - "Action: PDBFileDownloader\n", - "Action Input: 1LYZ\u001b[0m\n", - "\n", - "\u001b[1m> Finished chain.\u001b[0m\n", - "Here is a summary of the agent's attempts to solve the problem:\n", - "\n", - "**Prompt:** The agent was given the task to download the PDB file for PDB ID 1LYZ.\n", - "\n", - "**Step 1:** The agent reflected on the problem and decided to use the PDBFileDownloader tool to download the PDB file.\n", - "\n", - "**Action:** The agent chose the PDBFileDownloader tool.\n", - "\n", - "**Action Input:** The agent provided the input \"1LYZ\" to the PDBFileDownloader tool.\n", - "\n", - "**Final Solution:** The agent successfully downloaded the PDB file for PDB ID 1LYZ using the PDBFileDownloader tool.\n", - "\n", - "Note that this was a straightforward problem, and the agent was able to solve it in a single step. There were no errors or complications reported in the history.Your run id is: 6TONOT9N\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: (the action name, should be the name of a tool)\\n Action Input: (the input string to the action)\\n\\n OR\\n\\n Final Answer: (the final response to the original input\\n question, when 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 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 for PDB ID 1LYZ. ',\n", - " 'output': 'Thought: To download the PDB file for PDB ID 1LYZ, I need to use the PDBFileDownloader tool.\\n\\nAction: PDBFileDownloader\\nAction Input: 1LYZ'},\n", - " '6TONOT9N')" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agent.run(prompt2)" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "date and time: 2024-08-05\n", - "time: 16:41:29\n" - ] - } - ], - "source": [ - "now = datetime.datetime.now()\n", - "date = now.strftime(\"%Y-%m-%d\")\n", - "print(\"date and time:\",date)\n", - "time = now.strftime(\"%H:%M:%S\")\n", - "print(\"time:\",time)" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [], - "source": [ - "registry = agent.path_registry" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "No names found. The JSON file is empty or does not contain name mappings.\n" - ] - } - ], - "source": [ - "print(registry.list_path_names_and_descriptions())" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "7341ace3ad0242e698765d6a0f3833ba", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "ename": "ValueError", - "evalue": "you must provide file extension if using file-like object or text content", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[7], line 4\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mnglview\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mnv\u001b[39;00m\n\u001b[1;32m 3\u001b[0m path \u001b[38;5;241m=\u001b[39m registry\u001b[38;5;241m.\u001b[39mget_mapped_path(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m1LYZ_160238\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m----> 4\u001b[0m view \u001b[38;5;241m=\u001b[39m nv\u001b[38;5;241m.\u001b[39mshow_file(path)\n\u001b[1;32m 5\u001b[0m view\n", - "File \u001b[0;32m/opt/anaconda3/envs/llama-mdagent/lib/python3.11/site-packages/nglview/show.py:246\u001b[0m, in \u001b[0;36mshow_file\u001b[0;34m(path, **kwargs)\u001b[0m\n\u001b[1;32m 244\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 245\u001b[0m view \u001b[38;5;241m=\u001b[39m NGLWidget()\n\u001b[0;32m--> 246\u001b[0m view\u001b[38;5;241m.\u001b[39madd_component(path, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 247\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m view\n", - "File \u001b[0;32m/opt/anaconda3/envs/llama-mdagent/lib/python3.11/site-packages/nglview/widget.py:1216\u001b[0m, in \u001b[0;36mNGLWidget.add_component\u001b[0;34m(self, filename, **kwargs)\u001b[0m\n\u001b[1;32m 1213\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m package_name \u001b[38;5;129;01min\u001b[39;00m BACKENDS:\n\u001b[1;32m 1214\u001b[0m filename \u001b[38;5;241m=\u001b[39m BACKENDS[package_name](filename)\n\u001b[0;32m-> 1216\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_load_data(filename, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 1217\u001b[0m \u001b[38;5;66;03m# assign an ID\u001b[39;00m\n\u001b[1;32m 1218\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_ngl_component_ids\u001b[38;5;241m.\u001b[39mappend(\u001b[38;5;28mstr\u001b[39m(uuid\u001b[38;5;241m.\u001b[39muuid4()))\n", - "File \u001b[0;32m/opt/anaconda3/envs/llama-mdagent/lib/python3.11/site-packages/nglview/widget.py:1254\u001b[0m, in \u001b[0;36mNGLWidget._load_data\u001b[0;34m(self, obj, **kwargs)\u001b[0m\n\u001b[1;32m 1251\u001b[0m blob \u001b[38;5;241m=\u001b[39m fh\u001b[38;5;241m.\u001b[39mread(force_buffer\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m 1252\u001b[0m passing_buffer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[0;32m-> 1254\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m fh\u001b[38;5;241m.\u001b[39mext \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;129;01mand\u001b[39;00m passing_buffer:\n\u001b[1;32m 1255\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmust provide extension\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 1257\u001b[0m kwargs2[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mext\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m fh\u001b[38;5;241m.\u001b[39mext\n", - "File \u001b[0;32m/opt/anaconda3/envs/llama-mdagent/lib/python3.11/site-packages/nglview/utils/py_utils.py:242\u001b[0m, in \u001b[0;36mFileManager.ext\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 239\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 240\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msrc, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mread\u001b[39m\u001b[38;5;124m'\u001b[39m) \u001b[38;5;129;01mor\u001b[39;00m (\u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mis_filename\n\u001b[1;32m 241\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mis_url):\n\u001b[0;32m--> 242\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[1;32m 243\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124myou must provide file extension if using file-like object or text content\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 244\u001b[0m )\n\u001b[1;32m 245\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mis_compressed:\n\u001b[1;32m 246\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msrc\u001b[38;5;241m.\u001b[39msplit(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m)[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m2\u001b[39m]\n", - "\u001b[0;31mValueError\u001b[0m: you must provide file extension if using file-like object or text content" - ] - } - ], - "source": [ - "#show the image from the path of the registry and the ID \n", - "import nglview as nv\n", - "path = registry.get_mapped_path(\"1LYZ_160238\")\n", - "view = nv.show_file(path)\n", - "view" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Experiment Result:\n", - "### Completed without Exception or TimeOut Errors ✅\n", - "### Attempted all necessary steps ✅\n", - "### Logic make sense ✅\n", - "### Correct Answer ✅\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "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": "3.11.8" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_3 copy.ipynb b/notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_3 copy.ipynb deleted file mode 100644 index 2d1fe1ff..00000000 --- a/notebooks/experiments/experiment_k1/llama-v3p1-70b-instruct/exp_3 copy.ipynb +++ /dev/null @@ -1,208 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [], - "source": [ - "import datetime\n", - "import os\n", - "from mdagent import MDAgent\n", - "import matplotlib.pyplot as plt" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "date and time: 2024-08-05\n", - "time: 16:46:39\n", - "LLM: accounts/fireworks/models/llama-v3p1-70b-instruct \n", - "Temperature: 0.1\n" - ] - } - ], - "source": [ - "prompt3 = \"Download the PDB file for PDB ID 1GZX. Then, analyze the secondary structure of the protein and tell me how many chains, sheets, etc. there are.\"\n", - "llm_var = \"llama-v3p1-70b-instruct\"\n", - "tools = \"all\"\n", - "agent = MDAgent(agent_type=\"Structured\", model=llm_var, top_k_tools=tools)\n", - "now = datetime.datetime.now()\n", - "date = now.strftime(\"%Y-%m-%d\")\n", - "print(\"date and time:\",date)\n", - "time = now.strftime(\"%H:%M:%S\")\n", - "print(\"time:\",time)\n", - "print(\"LLM: \",agent.llm.model_name,\"\\nTemperature: \",agent.llm.temperature)" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Num of tokens: 374\n", - "\n", - "\n", - "\u001b[1m> Entering new AgentExecutor chain...\u001b[0m\n", - "Thought: To solve this problem, I need to first download the PDB file for the given PDB ID 1GZX. Then, I can analyze the secondary structure of the protein and provide the required information.\n", - "\n", - "Action: PDBFileDownloader\n", - "Action Input: 1GZX\u001b[32;1m\u001b[1;3mThought: To solve this problem, I need to first download the PDB file for the given PDB ID 1GZX. Then, I can analyze the secondary structure of the protein and provide the required information.\n", - "\n", - "Action: PDBFileDownloader\n", - "Action Input: 1GZX\u001b[0m\n", - "\n", - "\u001b[1m> Finished chain.\u001b[0m\n", - "Here is a summary of the agent's attempts to solve the problem:\n", - "\n", - "**Prompt:** The agent was given a task to download the PDB file for PDB ID 1GZX and then analyze the secondary structure of the protein to provide information on the number of chains, sheets, etc.\n", - "\n", - "**Step 1:** The agent reflected on the problem and decided to first download the PDB file for the given PDB ID 1GZX. To do this, the agent chose the `PDBFileDownloader` tool and provided the input `1GZX`.\n", - "\n", - "**Current Status:** The agent has completed the first step of downloading the PDB file, but has not yet analyzed the secondary structure of the protein.\n", - "\n", - "**Next Steps:** The agent will likely use a tool to analyze the secondary structure of the protein, such as a tool that can parse the PDB file and extract information on chains, sheets, etc.\n", - "\n", - "Note: The final solution has not been reached yet, as the agent has only completed the first step of downloading the PDB file.Your run id is: WAX4OAJ3\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: (the action name, should be the name of a tool)\\n Action Input: (the input string to the action)\\n\\n OR\\n\\n Final Answer: (the final response to the original input\\n question, when 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 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 for PDB ID 1GZX. Then, analyze the secondary structure of the protein and tell me how many chains, sheets, etc. there are. ',\n", - " 'output': 'Thought: To solve this problem, I need to first download the PDB file for the given PDB ID 1GZX. Then, I can analyze the secondary structure of the protein and provide the required information.\\n\\nAction: PDBFileDownloader\\nAction Input: 1GZX'},\n", - " 'WAX4OAJ3')" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agent.run(prompt3)" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "date and time: 2024-08-05\n", - "time: 16:46:53\n" - ] - } - ], - "source": [ - "now = datetime.datetime.now()\n", - "date = now.strftime(\"%Y-%m-%d\")\n", - "print(\"date and time:\",date)\n", - "time = now.strftime(\"%H:%M:%S\")\n", - "print(\"time:\",time)" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "No names found. The JSON file is empty or does not contain name mappings.\n" - ] - } - ], - "source": [ - "registry = agent.path_registry\n", - "print(registry.list_path_names_and_descriptions())" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [ - { - "ename": "OSError", - "evalue": "The topology is loaded by filename extension, and the detected \".\" format is not supported. Supported topology formats include \".pdb\", \".pdb.gz\", \".h5\", \".lh5\", \".prmtop\", \".parm7\", \".prm7\", \".psf\", \".mol2\", \".hoomdxml\", \".gro\", \".arc\", \".hdf5\" and \".gsd\".", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mOSError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[12], line 3\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mmdtraj\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mmd\u001b[39;00m\n\u001b[1;32m 2\u001b[0m path \u001b[38;5;241m=\u001b[39m registry\u001b[38;5;241m.\u001b[39mget_mapped_path(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m1GZX_161339\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m----> 3\u001b[0m traj \u001b[38;5;241m=\u001b[39m md\u001b[38;5;241m.\u001b[39mload(path)\n\u001b[1;32m 4\u001b[0m top \u001b[38;5;241m=\u001b[39m traj\u001b[38;5;241m.\u001b[39mtopology\n\u001b[1;32m 5\u001b[0m number_of_chains \u001b[38;5;241m=\u001b[39m top\u001b[38;5;241m.\u001b[39mn_chains\n", - "File \u001b[0;32m/opt/anaconda3/envs/llama-mdagent/lib/python3.11/site-packages/mdtraj/core/trajectory.py:396\u001b[0m, in \u001b[0;36mload\u001b[0;34m(filename_or_filenames, discard_overlapping_frames, **kwargs)\u001b[0m\n\u001b[1;32m 394\u001b[0m topkwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstride\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m)\n\u001b[1;32m 395\u001b[0m topkwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstart\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m)\n\u001b[0;32m--> 396\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtop\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m _parse_topology(kwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtop\u001b[39m\u001b[38;5;124m\"\u001b[39m, filename_or_filenames[\u001b[38;5;241m0\u001b[39m]), \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mtopkwargs)\n\u001b[1;32m 398\u001b[0m \u001b[38;5;66;03m#get the right loader\u001b[39;00m\n\u001b[1;32m 399\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 400\u001b[0m \u001b[38;5;66;03m#loader = _LoaderRegistry[extension][0]\u001b[39;00m\n", - "File \u001b[0;32m/opt/anaconda3/envs/llama-mdagent/lib/python3.11/site-packages/mdtraj/core/trajectory.py:191\u001b[0m, in \u001b[0;36m_parse_topology\u001b[0;34m(top, **kwargs)\u001b[0m\n\u001b[1;32m 189\u001b[0m topology \u001b[38;5;241m=\u001b[39m load_gsd_topology(top, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 190\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(top, (string_types, os\u001b[38;5;241m.\u001b[39mPathLike)):\n\u001b[0;32m--> 191\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mIOError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mThe topology is loaded by filename extension, and the \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 192\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mdetected \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m format is not supported. Supported topology \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 193\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mformats include \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m and \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;241m%\u001b[39m (\n\u001b[1;32m 194\u001b[0m ext, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m, \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mjoin([\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;241m%\u001b[39m e \u001b[38;5;28;01mfor\u001b[39;00m e \u001b[38;5;129;01min\u001b[39;00m _TOPOLOGY_EXTS[:\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m]]),\n\u001b[1;32m 195\u001b[0m _TOPOLOGY_EXTS[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m]))\n\u001b[1;32m 196\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 197\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mA topology is required. You supplied top=\u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m'\u001b[39m \u001b[38;5;241m%\u001b[39m \u001b[38;5;28mstr\u001b[39m(top))\n", - "\u001b[0;31mOSError\u001b[0m: The topology is loaded by filename extension, and the detected \".\" format is not supported. Supported topology formats include \".pdb\", \".pdb.gz\", \".h5\", \".lh5\", \".prmtop\", \".parm7\", \".prm7\", \".psf\", \".mol2\", \".hoomdxml\", \".gro\", \".arc\", \".hdf5\" and \".gsd\"." - ] - } - ], - "source": [ - "import mdtraj as md\n", - "path = registry.get_mapped_path(\"1GZX_161339\")\n", - "traj = md.load(path)\n", - "top = traj.topology\n", - "number_of_chains = top.n_chains\n", - "secondary_structure = md.compute_dssp(traj,simplified=True)\n", - "print(\"Number of chains: \",number_of_chains)\n", - "print(\"Number of sheets: \",len([i for i in secondary_structure[0] if i == 'E']))\n", - "print(\"Number of helices: \",len([i for i in secondary_structure[0] if i == 'H']))\n", - "print(\"Number of coils: \",len([i for i in secondary_structure[0] if i == 'C']))\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Experiment Result:\n", - "### Completed without Exception or TimeOut Errors ✅\n", - "### Attempted all necessary steps ✅\n", - "### Logic make sense ✅\n", - "### Correct Answer ✅" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "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": "3.11.8" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/radius_of_gyration/proteins.txt b/notebooks/radius_of_gyration/proteins.txt deleted file mode 100644 index a90c3071..00000000 --- a/notebooks/radius_of_gyration/proteins.txt +++ /dev/null @@ -1,10 +0,0 @@ -1A3N -1TRZ -1TUP -1BR1 -1ATN -2RH1 -1IGT -1PQ2 -2TNF -1BO9 diff --git a/notebooks/radius_of_gyration/rgy_1A3N.ipynb b/notebooks/radius_of_gyration/rgy_1A3N.ipynb deleted file mode 100644 index fcc2e38d..00000000 --- a/notebooks/radius_of_gyration/rgy_1A3N.ipynb +++ /dev/null @@ -1,280 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "agent = MDAgent(resume=False, learn=False, agent_type=\"Structured\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1A3N and calculate the average radius of gyration, I need to first set up and run a simulation for the protein using the SetUpandRunFunction tool. After the simulation is complete, I can then use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1A3N\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-22 22:33:25.431 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: The previous action attempted to set up and run a simulation for the protein with PDB ID 1A3N, but it failed because the PDB ID was not recognized. I need to ensure that the PDB ID is correctly inputted into the SetUpandRunFunction tool. I will correct the input and try running the simulation again.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1A3N\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "The previous action to set up and run a simulation for the protein with PDB ID 1A3N failed because the PDB ID was not recognized. It seems there might be an issue with the PDB ID input format or the tool may require the actual file rather than just the PDB ID. To resolve this, I will first attempt to download the PDB file for 1A3N using the PDBFileDownloader tool, which should provide the correct file for the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1A3N\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1A3N\n", - "Now that I have successfully downloaded the PDB file for protein 1A3N, I can proceed to set up and run the simulation using the SetUpandRunFunction tool. I will use the file ID obtained from the download in the previous step as the input for the PDB ID.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1A3N_223357\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "The simulation setup failed because the PDB file for protein 1A3N is missing hydrogen atoms, which are necessary for the forcefield to recognize the residues correctly. To fix this, I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file. This should prepare the file for a successful simulation setup.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1A3N_223357\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```Now that the PDB file for protein 1A3N has been cleaned and the necessary hydrogen atoms have been added, I can proceed to set up and run the simulation again using the SetUpandRunFunction tool with the cleaned file ID.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1A3N_223429\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1A3N_223429_20240222_223445.py\n", - "['LOG_sim0_223445_1A3N_223429_20240222_223445.txt', 'proteins.txt', 'ckpt', 'rgy_ 1TRZ.ipynb', 'TRAJ_sim0_223445_1A3N_223429_20240222_223445.dcd', 'paths_registry.json', 'files', 'TOP_sim0_223445_1A3N_223429_20240222_223445.pdb', 'rgy_ 1TRZ copy.ipynb', 'rgy_1A3N.ipynb']\n", - "The simulation for protein 1A3N has been successfully completed, and the necessary files have been generated. I can now use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RadiusofGyrationAverage\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1A3N_223429\"\n", - " }\n", - "}\n", - "```\n", - "Final Answer: The simulation for protein 1A3N was successfully completed, and the average radius of gyration calculated from the trajectory file is 2.30 nm." - ] - }, - { - "data": { - "text/plain": [ - "'Final Answer: The simulation for protein 1A3N was successfully completed, and the average radius of gyration calculated from the trajectory file is 2.30 nm.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "protein_id = \"1A3N\"\n", - "agent.run(f\"Simulate protein {protein_id} and calculate the average radius of gyration.\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "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": "3.11.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/radius_of_gyration/rgy_1ATN.ipynb b/notebooks/radius_of_gyration/rgy_1ATN.ipynb deleted file mode 100644 index 2c5676f7..00000000 --- a/notebooks/radius_of_gyration/rgy_1ATN.ipynb +++ /dev/null @@ -1,276 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "agent = MDAgent(resume=False, learn=False, agent_type=\"Structured\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'Simulate protein 1ATN and calculate the average radius of gyration.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#get the second line from proteins.txt\n", - "with open('proteins.txt') as f:\n", - " proteins = f.readlines()\n", - " protein = proteins[4].strip()\n", - "\n", - "prompt = f\"Simulate protein {protein} and calculate the average radius of gyration.\"\n", - "prompt" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1ATN and calculate the average radius of gyration, I will first need to set up and run a short simulation of the protein using the SetUpandRunFunction tool. After the simulation is complete, I can then use the RadiusofGyrationAverage tool to calculate the average radius of gyration for the simulated trajectory.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1ATN\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-22 22:50:02.883 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "The previous action attempted to run a simulation using the PDB ID \"1ATN\" but encountered an error because the PDB file was not found in the input. To proceed, I need to ensure that the PDB file for the protein 1ATN is available for the simulation. I will use the PDBFileDownloader tool to download the PDB file for protein 1ATN.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1ATN\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1ATN\n", - "Now that I have successfully downloaded the PDB file for protein 1ATN, I can proceed to set up and run a short simulation of the protein using the SetUpandRunFunction tool. I will use the downloaded PDB file ID \"1ATN_225014\" as the input for the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1ATN_225014\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "The simulation setup failed because the PDB file for protein 1ATN is missing hydrogen atoms, which are necessary for the forcefield to recognize the residues correctly. To resolve this, I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file. This should prepare the file for a successful simulation setup.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1ATN_225014\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```The PDB file for protein 1ATN has been successfully cleaned and is now ready for simulation. I will proceed to set up and run a short simulation of the protein using the cleaned PDB file ID \"1ATN_225040\" with the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1ATN_225040\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1ATN_225040_20240222_225052.py\n", - "['proteins.txt', 'TRAJ_sim0_224125_1BR1_224108_20240222_224129.dcd', 'LOG_sim0_224125_1BR1_224108_20240222_224129.txt', 'ckpt', 'rgy_1ATN.ipynb', 'rgy_1BR1.ipynb', 'TOP_sim0_225052_1ATN_225040_20240222_225053.pdb', 'TOP_sim0_224125_1BR1_224108_20240222_224129.pdb', 'paths_registry.json', 'LOG_sim0_225052_1ATN_225040_20240222_225053.txt', 'rgy_1TUP.ipynb', 'files', 'rgy_1TRZ.ipynb', 'TRAJ_sim0_225052_1ATN_225040_20240222_225053.dcd', 'rgy_1A3N.ipynb']\n", - "The simulation for protein 1ATN has been completed successfully, and the necessary files have been generated. Now, I will use the RadiusofGyrationAverage tool to calculate the average radius of gyration for the simulated trajectory file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RadiusofGyrationAverage\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1ATN_225040\"\n", - " }\n", - "}\n", - "```\n", - "The average radius of gyration for the simulated protein 1ATN has been calculated and is 3.02 nm. This completes the task.\n", - "\n", - "Final Answer: The average radius of gyration for the simulated protein 1ATN is 3.02 nm." - ] - }, - { - "data": { - "text/plain": [ - "'The average radius of gyration for the simulated protein 1ATN has been calculated and is 3.02 nm. This completes the task.\\n\\nFinal Answer: The average radius of gyration for the simulated protein 1ATN is 3.02 nm.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agent.run(prompt)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "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": "3.11.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/radius_of_gyration/rgy_1BO9.ipynb b/notebooks/radius_of_gyration/rgy_1BO9.ipynb deleted file mode 100644 index fb3c955f..00000000 --- a/notebooks/radius_of_gyration/rgy_1BO9.ipynb +++ /dev/null @@ -1,235 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "agent = MDAgent(resume=False, learn=False, agent_type=\"Structured\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'Simulate protein 1BO9 and calculate the average radius of gyration.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#get the second line from proteins.txt\n", - "with open('proteins.txt') as f:\n", - " proteins = f.readlines()\n", - " protein = proteins[9].strip()\n", - "\n", - "prompt = f\"Simulate protein {protein} and calculate the average radius of gyration.\"\n", - "prompt" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1BO9 and calculate the average radius of gyration, I will first need to set up and run a short simulation of the protein using the SetUpandRunFunction tool. After the simulation is complete, I can then use the RadiusofGyrationAverage tool to calculate the average radius of gyration for the simulated trajectory.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BO9\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-23 00:10:51.647 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Building system...\n", - "The previous attempt to simulate protein 1BO9 failed because the file was not found. Before running a simulation, I need to ensure that the protein structure file (PDB file) for 1BO9 is available. I will use the PDBFileDownloader tool to download the PDB file for protein 1BO9.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1BO9\"\n", - " }\n", - "}\n", - "```\n", - "PDB file found with this ID: 1BO9\n", - "Now that the PDB file for protein 1BO9 has been successfully downloaded, I can proceed with setting up and running a short simulation using the SetUpandRunFunction tool. I will use the downloaded PDB file ID as the input for the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BO9_001059\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1BO9_001059_20240223_001119.py\n", - "['TOP_sim0_001031_2TNF_001016_20240223_001032.pdb', 'rgy_2TNF.ipynb', 'rgy_1PQ2.ipynb', 'proteins.txt', 'rgy_2RH1.ipynb', 'TRAJ_sim0_001119_1BO9_001059_20240223_001120.dcd', 'TRAJ_sim0_224125_1BR1_224108_20240222_224129.dcd', 'LOG_sim0_001119_1BO9_001059_20240223_001120.txt', 'LOG_sim0_224125_1BR1_224108_20240222_224129.txt', 'ckpt', 'rgy_1ATN.ipynb', 'rgy_1BR1.ipynb', 'rgy_1BO9.ipynb', 'TOP_sim0_001119_1BO9_001059_20240223_001120.pdb', 'TOP_sim0_224125_1BR1_224108_20240222_224129.pdb', 'paths_registry.json', 'rgy_1TUP.ipynb', 'files', 'rgy_1TRZ.ipynb', 'TRAJ_sim0_001031_2TNF_001016_20240223_001032.dcd', 'LOG_sim0_001031_2TNF_001016_20240223_001032.txt', 'rgy_1A3N.ipynb', 'rgy_1IGT.ipynb']\n", - "The simulation for protein 1BO9 has been completed successfully, and the necessary files have been generated. The next step is to calculate the average radius of gyration for the simulated trajectory. I will use the RadiusofGyrationAverage tool with the protein ID that was used in the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RadiusofGyrationAverage\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BO9_001059\"\n", - " }\n", - "}\n", - "```\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/mdtraj/formats/pdb/pdbfile.py:200: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors.\n", - " warnings.warn('Unlikely unit cell vectors detected in PDB file likely '\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Final Answer: The simulation of protein 1BO9 was successfully completed, and the average radius of gyration calculated for the simulated trajectory is 1.12 nm." - ] - }, - { - "data": { - "text/plain": [ - "'Final Answer: The simulation of protein 1BO9 was successfully completed, and the average radius of gyration calculated for the simulated trajectory is 1.12 nm.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agent.run(prompt)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "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": "3.11.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/radius_of_gyration/rgy_1BR1.ipynb b/notebooks/radius_of_gyration/rgy_1BR1.ipynb deleted file mode 100644 index 85ab1066..00000000 --- a/notebooks/radius_of_gyration/rgy_1BR1.ipynb +++ /dev/null @@ -1,242 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "agent = MDAgent(resume=False, learn=False, agent_type=\"Structured\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'Simulate protein 1BR1 and calculate the average radius of gyration.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#get the second line from proteins.txt\n", - "with open('proteins.txt') as f:\n", - " proteins = f.readlines()\n", - " protein = proteins[3].strip()\n", - "\n", - "prompt = f\"Simulate protein {protein} and calculate the average radius of gyration.\"\n", - "prompt" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1BR1 and calculate the average radius of gyration, I will first need to set up and run a short simulation of the protein using the SetUpandRunFunction tool. After the simulation is complete, I can then use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BR1\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-22 22:39:23.171 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "The previous action attempted to run a simulation using the SetUpandRunFunction tool but encountered an error because the PDB ID was not recognized. To correct this, I will first download the PDB file for protein 1BR1 using the PDBFileDownloader tool. Once the file is downloaded, I can proceed with the simulation setup and execution.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1BR1\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1BR1\n", - "Now that the PDB file for protein 1BR1 has been successfully downloaded, I can proceed with setting up and running a short simulation of the protein using the SetUpandRunFunction tool. After the simulation is complete, I will use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BR1_223929\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "The simulation setup failed because the PDB file for protein 1BR1 is missing hydrogen atoms, which are necessary for the forcefield to recognize the residues correctly. To resolve this, I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file. After cleaning the PDB file, I will attempt to run the simulation again using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BR1_223929\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```Now that the PDB file for protein 1BR1 has been cleaned and the necessary hydrogen atoms have been added, I can proceed with setting up and running a short simulation of the protein using the SetUpandRunFunction tool with the cleaned PDB file. After the simulation is complete, I will use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BR1_224108\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n" - ] - } - ], - "source": [ - "agent.run(prompt)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "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": "3.11.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/radius_of_gyration/rgy_1IGT.ipynb b/notebooks/radius_of_gyration/rgy_1IGT.ipynb deleted file mode 100644 index 813c88cc..00000000 --- a/notebooks/radius_of_gyration/rgy_1IGT.ipynb +++ /dev/null @@ -1,297 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "agent = MDAgent(resume=False, learn=False, agent_type=\"Structured\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'Simulate protein 1IGT and calculate the average radius of gyration.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#get the second line from proteins.txt\n", - "with open('proteins.txt') as f:\n", - " proteins = f.readlines()\n", - " protein = proteins[6].strip()\n", - "\n", - "prompt = f\"Simulate protein {protein} and calculate the average radius of gyration.\"\n", - "prompt" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1IGT and calculate the average radius of gyration, I will first need to set up and run a short simulation of the protein using the SetUpandRunFunction tool. After the simulation is complete, I can then use the RadiusofGyrationAverage tool to calculate the average radius of gyration for the given trajectory file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-22 23:21:40.181 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: The previous action attempted to use the SetUpandRunFunction tool to simulate the protein with PDB ID 1IGT, but it failed because the PDB ID was not recognized. I need to ensure that the PDB ID is correctly inputted into the tool. I will try running the SetUpandRunFunction tool again with the correct PDB ID format.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "The SetUpandRunFunction tool requires a valid PDB ID to run a simulation. The error message indicates that the PDB ID provided (\"1IGT\") is not being recognized as a valid input. It's possible that the PDB file for 1IGT needs to be downloaded or retrieved from a database before it can be used for simulation. I will use the PDBFileDownloader tool to download the PDB file for protein 1IGT.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1IGT\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1IGT\n", - "Now that the PDB file for protein 1IGT has been successfully downloaded, I can proceed with setting up and running a short simulation using the SetUpandRunFunction tool. I will use the downloaded PDB file ID \"1IGT_232215\" as the input for the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT_232215\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "The simulation setup failed because the PDB file for 1IGT is missing a hydrogen atom on residue 1 (ASP). Before I can run the simulation, I need to clean the PDB file to ensure it has all the necessary atoms and is compatible with the forcefield. I will use the CleaningToolFunction to clean the PDB file by adding missing atoms, including hydrogens, and then attempt to run the simulation again.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT_232215\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```The PDB file for protein 1IGT has been successfully cleaned, and missing atoms including hydrogens have been added. Now that the file is prepared, I can proceed with setting up and running a short simulation using the SetUpandRunFunction tool with the cleaned PDB file ID \"1IGT_232259\".\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT_232259\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1IGT_232259_20240222_232314.py\n", - "['proteins.txt', 'rgy_2RH1.ipynb', 'TRAJ_sim0_224125_1BR1_224108_20240222_224129.dcd', 'TOP_sim0_232314_1IGT_232259_20240222_232316.pdb', 'LOG_sim0_224125_1BR1_224108_20240222_224129.txt', 'ckpt', 'rgy_1ATN.ipynb', 'rgy_1BR1.ipynb', 'LOG_sim0_232314_1IGT_232259_20240222_232316.txt', 'TOP_sim0_224125_1BR1_224108_20240222_224129.pdb', 'paths_registry.json', 'rgy_1TUP.ipynb', 'files', 'rgy_1TRZ.ipynb', 'rgy_1A3N.ipynb', 'TRAJ_sim0_232314_1IGT_232259_20240222_232316.dcd', 'rgy_1IGT.ipynb']\n", - "The simulation for protein 1IGT has been completed successfully, and the necessary files have been generated. The next step is to calculate the average radius of gyration using the RadiusofGyrationAverage tool. I will use the trajectory file ID provided in the simulation summary to perform this calculation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RadiusofGyrationAverage\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT_232259\"\n", - " }\n", - "}\n", - "```Final Answer: The simulation of protein 1IGT was successfully completed, and the average radius of gyration calculated for the simulated trajectory is 5.35 nm." - ] - }, - { - "data": { - "text/plain": [ - "'Final Answer: The simulation of protein 1IGT was successfully completed, and the average radius of gyration calculated for the simulated trajectory is 5.35 nm.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agent.run(prompt)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "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": "3.11.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/radius_of_gyration/rgy_1PQ2.ipynb b/notebooks/radius_of_gyration/rgy_1PQ2.ipynb deleted file mode 100644 index 99df096d..00000000 --- a/notebooks/radius_of_gyration/rgy_1PQ2.ipynb +++ /dev/null @@ -1,297 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "agent = MDAgent(resume=False, learn=False, agent_type=\"Structured\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'Simulate protein 1PQ2 and calculate the average radius of gyration.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#get the second line from proteins.txt\n", - "with open('proteins.txt') as f:\n", - " proteins = f.readlines()\n", - " protein = proteins[7].strip()\n", - "\n", - "prompt = f\"Simulate protein {protein} and calculate the average radius of gyration.\"\n", - "prompt" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein with PDB ID 1PQ2 and calculate the average radius of gyration, I will first need to set up and run a simulation for the protein. After the simulation is complete, I can then use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-22 23:47:20.893 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: The previous attempt to run a simulation failed because the PDB ID was not recognized. I need to ensure that the PDB ID is correctly inputted and recognized by the system. I will attempt to run the simulation again with the correct PDB ID for protein 1PQ2.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "The system is not recognizing the PDB ID \"1PQ2\" as a valid input for the simulation setup. It's possible that the PDB file for 1PQ2 needs to be downloaded before running the simulation. I will use the PDBFileDownloader tool to download the PDB file for protein 1PQ2.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1PQ2\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1PQ2\n", - "Now that the PDB file for protein 1PQ2 has been successfully downloaded, I can proceed to set up and run the simulation using the SetUpandRunFunction tool with the downloaded file ID.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2_234745\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "The simulation setup failed because there is an issue with the template for residue 1 (LYS) in the PDB file. It seems that the PDB file contains a residue that does not match the standard template for lysine (LYS) and is missing atoms. Before attempting another simulation, I need to clean the PDB file to ensure that all residues match the standard templates and that any missing atoms are added. I will use the CleaningToolFunction to clean the PDB file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2_234745\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```The PDB file for protein 1PQ2 has been successfully cleaned, and I now have a file ID for the cleaned file. I can proceed to set up and run the simulation using the SetUpandRunFunction tool with the cleaned file ID.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2_234824\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1PQ2_234824_20240222_234836.py\n", - "['LOG_sim0_234836_1PQ2_234824_20240222_234837.txt', 'rgy_1PQ2.ipynb', 'proteins.txt', 'rgy_2RH1.ipynb', 'TRAJ_sim0_224125_1BR1_224108_20240222_224129.dcd', 'LOG_sim0_224125_1BR1_224108_20240222_224129.txt', 'ckpt', 'rgy_1ATN.ipynb', 'rgy_1BR1.ipynb', 'TRAJ_sim0_234836_1PQ2_234824_20240222_234837.dcd', 'TOP_sim0_224125_1BR1_224108_20240222_224129.pdb', 'paths_registry.json', 'rgy_1TUP.ipynb', 'files', 'rgy_1TRZ.ipynb', 'TOP_sim0_234836_1PQ2_234824_20240222_234837.pdb', 'rgy_1A3N.ipynb', 'rgy_1IGT.ipynb']\n", - "The simulation for protein 1PQ2 has been completed successfully, and the necessary files have been generated. I can now use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RadiusofGyrationAverage\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2_234824\"\n", - " }\n", - "}\n", - "```Final Answer: The simulation of protein 1PQ2 was successfully completed, and the average radius of gyration calculated from the trajectory is 3.25 nm." - ] - }, - { - "data": { - "text/plain": [ - "'Final Answer: The simulation of protein 1PQ2 was successfully completed, and the average radius of gyration calculated from the trajectory is 3.25 nm.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agent.run(prompt)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "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": "3.11.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/radius_of_gyration/rgy_1TRZ.ipynb b/notebooks/radius_of_gyration/rgy_1TRZ.ipynb deleted file mode 100644 index 052af9cd..00000000 --- a/notebooks/radius_of_gyration/rgy_1TRZ.ipynb +++ /dev/null @@ -1,275 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "agent = MDAgent(resume=False, learn=False, agent_type=\"Structured\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'Simulate protein 1TRZ and calculate the average radius of gyration.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#get the second line from proteins.txt\n", - "with open('proteins.txt') as f:\n", - " proteins = f.readlines()\n", - " protein = proteins[1].strip()\n", - "\n", - "prompt = f\"Simulate protein {protein} and calculate the average radius of gyration.\"\n", - "prompt" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1TRZ and calculate the average radius of gyration, I will first need to set up and run a simulation of the protein using the SetUpandRunFunction tool. After the simulation is complete, I can then use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TRZ\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-22 22:29:51.742 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Setting default forcefields v2\n", - "Thought: The previous action attempted to run a simulation using the SetUpandRunFunction tool but failed because the PDB ID was not recognized. It seems that the tool requires a file ID from the path registry rather than the PDB ID directly. To resolve this, I will first download the PDB file for protein 1TRZ using the PDBFileDownloader tool. Once I have the file, I can proceed with setting up and running the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1TRZ\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1TRZ\n", - "Now that I have successfully downloaded the PDB file for protein 1TRZ, I can proceed with setting up and running the simulation using the SetUpandRunFunction tool. I will use the file ID obtained from the download in the simulation setup.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TRZ_223000\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "The simulation setup failed because the PDB file for protein 1TRZ is missing hydrogen atoms, which are necessary for the forcefield to recognize the residues correctly. To resolve this, I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file. This should prepare the file for a successful simulation setup.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TRZ_223000\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```Now that the PDB file for protein 1TRZ has been cleaned and the necessary hydrogen atoms have been added, I can proceed with setting up and running the simulation using the SetUpandRunFunction tool. I will use the new file ID obtained from the cleaning process in the simulation setup.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TRZ_223027\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1TRZ_223027_20240222_223035.py\n", - "['proteins.txt', 'ckpt', 'rgy_ 1TRZ.ipynb', 'TOP_sim0_223035_1TRZ_223027_20240222_223035.pdb', 'paths_registry.json', 'LOG_sim0_223035_1TRZ_223027_20240222_223035.txt', 'files', 'rgy_1A3N.ipynb', 'TRAJ_sim0_223035_1TRZ_223027_20240222_223035.dcd']\n", - "The simulation has been successfully completed, and the necessary files have been generated. Now, I will use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RadiusofGyrationAverage\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TRZ_223027\"\n", - " }\n", - "}\n", - "```\n", - "Final Answer: The simulation of protein 1TRZ was successfully completed, and the average radius of gyration calculated from the trajectory file is 1.33 nm." - ] - }, - { - "data": { - "text/plain": [ - "'Final Answer: The simulation of protein 1TRZ was successfully completed, and the average radius of gyration calculated from the trajectory file is 1.33 nm.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agent.run(prompt)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "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": "3.11.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/radius_of_gyration/rgy_1TUP.ipynb b/notebooks/radius_of_gyration/rgy_1TUP.ipynb deleted file mode 100644 index c6a34b9c..00000000 --- a/notebooks/radius_of_gyration/rgy_1TUP.ipynb +++ /dev/null @@ -1,305 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "agent = MDAgent(resume=False, learn=False, agent_type=\"Structured\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'Simulate protein 1TUP and calculate the average radius of gyration.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#get the second line from proteins.txt\n", - "with open('proteins.txt') as f:\n", - " proteins = f.readlines()\n", - " protein = proteins[2].strip()\n", - "\n", - "prompt = f\"Simulate protein {protein} and calculate the average radius of gyration.\"\n", - "prompt" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1TUP and calculate the average radius of gyration, I will first need to set up and run a simulation for the protein using the SetUpandRunFunction tool. After the simulation is complete, I can then use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TUP\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-22 22:37:26.694 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Setting default forcefields v2\n", - "The previous action attempted to run a simulation for the protein with PDB ID 1TUP, but it failed because the PDB ID was not recognized. I need to ensure that the PDB ID is correctly inputted into the SetUpandRunFunction tool. I will retry the simulation setup and execution with the correct PDB ID.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TUP\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "The previous action failed because the PDB ID was not recognized. It seems there might be a misunderstanding about the PDB ID or the file ID required for the simulation. To resolve this, I will first download the PDB file for the protein with PDB ID 1TUP using the PDBFileDownloader tool. Once I have the PDB file, I can proceed with setting up and running the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1TUP\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1TUP\n", - "Now that I have successfully downloaded the PDB file for protein 1TUP, I can proceed with setting up and running the simulation using the SetUpandRunFunction tool. I will use the file ID obtained from the download in the previous step as the input for the PDB ID.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TUP_223753\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "The simulation setup failed because the PDB file for protein 1TUP contains a residue (DT) that is not recognized by the default forcefield, likely due to missing hydrogen atoms. To address this, I will use the CleaningToolFunction to clean the PDB file by adding missing atoms, including hydrogens, and then attempt to run the simulation again with the cleaned file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TUP_223753\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```The PDB file for protein 1TUP has been successfully cleaned, which should resolve the issue with the unrecognized residue and missing hydrogen atoms. I can now proceed to set up and run the simulation again using the cleaned PDB file ID.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TUP_223827\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"solvate\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1TUP_223827_20240222_223844.py\n", - "['TOP_sim0_223844_1TUP_223827_20240222_223844.pdb', 'proteins.txt', 'TRAJ_sim0_224125_1BR1_224108_20240222_224129.dcd', 'LOG_sim0_224125_1BR1_224108_20240222_224129.txt', 'ckpt', 'rgy_ 1TRZ.ipynb', 'rgy_1BR1.ipynb', 'TOP_sim0_224125_1BR1_224108_20240222_224129.pdb', 'paths_registry.json', 'TRAJ_sim0_223844_1TUP_223827_20240222_223844.dcd', 'files', 'LOG_sim0_223844_1TUP_223827_20240222_223844.txt', 'rgy_ 1TRZ copy.ipynb', 'rgy_1A3N.ipynb']\n", - "The simulation for protein 1TUP has been successfully completed, and the necessary files have been generated. I can now use the RadiusofGyrationAverage tool to calculate the average radius of gyration from the trajectory file generated by the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RadiusofGyrationAverage\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TUP_223827\"\n", - " }\n", - "}\n", - "```Final Answer: The simulation of protein 1TUP was successfully completed, and the average radius of gyration calculated from the trajectory is 3.63 nm." - ] - }, - { - "data": { - "text/plain": [ - "'Final Answer: The simulation of protein 1TUP was successfully completed, and the average radius of gyration calculated from the trajectory is 3.63 nm.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agent.run(prompt)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "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": "3.11.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/radius_of_gyration/rgy_2RH1.ipynb b/notebooks/radius_of_gyration/rgy_2RH1.ipynb deleted file mode 100644 index a7d03770..00000000 --- a/notebooks/radius_of_gyration/rgy_2RH1.ipynb +++ /dev/null @@ -1,355 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "agent = MDAgent(resume=False, learn=False, agent_type=\"Structured\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'Simulate protein 2RH1 and calculate the average radius of gyration.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#get the second line from proteins.txt\n", - "with open('proteins.txt') as f:\n", - " proteins = f.readlines()\n", - " protein = proteins[5].strip()\n", - "\n", - "prompt = f\"Simulate protein {protein} and calculate the average radius of gyration.\"\n", - "prompt" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 2RH1 and calculate its average radius of gyration, I need to perform two main tasks. First, I need to set up and run a simulation for the protein 2RH1. After the simulation is complete, I can then calculate the average radius of gyration from the trajectory file generated. I will start by setting up and running the simulation using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-22 23:00:02.998 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "To correct the error from the previous attempt, I need to include the `ewaldErrorTolerance` parameter in the `system_params` since the `nonbondedMethod` is set to PME. I will set a typical value for `ewaldErrorTolerance` and then rerun the simulation setup using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "The previous action failed because the PDB ID was not recognized correctly. I need to ensure that the PDB ID is provided in a format that the SetUpandRunFunction tool can recognize. I will correct this by providing the PDB ID \"2RH1\" again, ensuring it is in the correct format for the tool to recognize and process.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "The SetUpandRunFunction tool is not recognizing the PDB ID \"2RH1\" as a valid input. It's possible that the PDB file needs to be downloaded or retrieved from a database before it can be used in the simulation. I will use the PDBFileDownloader tool to download the PDB file for protein 2RH1, which should provide me with a file ID that can be used for the simulation setup.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"2RH1\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 2RH1\n", - "Now that I have successfully downloaded the PDB file for protein 2RH1 with the file ID \"2RH1_230057\", I can proceed to set up and run the simulation using the SetUpandRunFunction tool. This time, I will use the file ID instead of the PDB ID in the input to ensure the tool recognizes the file correctly.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1_230057\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Error adding solvent ValueError – No template found for residue 1 (ASP). The set of atoms is similar to ALA, but it is missing 5 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", - "The simulation setup failed because the PDB file for protein 2RH1 is missing hydrogen atoms for residue ASP (aspartic acid). This is a common issue when working with PDB files, as they often lack hydrogen atoms since X-ray crystallography does not always resolve them. To proceed, I need to add the missing hydrogen atoms to the PDB file. I will use the CleaningToolFunction to clean the PDB file by adding the missing hydrogen atoms and then attempt to rerun the simulation setup.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1_230057\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```The PDB file for protein 2RH1 has been successfully cleaned, and missing hydrogen atoms have been added. The file ID for the cleaned file is \"2RH1_230123\". I can now proceed to set up and run the simulation using the cleaned PDB file. I will use the SetUpandRunFunction tool again with the new file ID.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1_230123\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_2RH1_230123_20240222_230143.py\n", - "['proteins.txt', 'TRAJ_sim0_224125_1BR1_224108_20240222_224129.dcd', 'TOP_sim0_230143_2RH1_230123_20240222_230153.pdb', 'LOG_sim0_224125_1BR1_224108_20240222_224129.txt', 'ckpt', 'rgy_1ATN.ipynb', 'rgy_1BR1.ipynb', 'TRAJ_sim0_230143_2RH1_230123_20240222_230153.dcd', 'TOP_sim0_224125_1BR1_224108_20240222_224129.pdb', 'paths_registry.json', 'rgy_1TUP.ipynb', 'files', 'rgy_1TRZ.ipynb', 'rgy_ 2RH1.ipynb', 'rgy_1A3N.ipynb', 'LOG_sim0_230143_2RH1_230123_20240222_230153.txt']\n", - "The simulation for protein 2RH1 has been successfully completed, and the necessary files have been generated. The next step is to calculate the average radius of gyration from the trajectory file. I will use the RadiusofGyrationAverage tool to calculate this value using the trajectory file ID provided in the simulation summary.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RadiusofGyrationAverage\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1_230123\"\n", - " }\n", - "}\n", - "```Final Answer: The simulation of protein 2RH1 was successfully completed, and the average radius of gyration calculated from the trajectory is 5.87 nm." - ] - }, - { - "data": { - "text/plain": [ - "'Final Answer: The simulation of protein 2RH1 was successfully completed, and the average radius of gyration calculated from the trajectory is 5.87 nm.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agent.run(prompt)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "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": "3.11.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/radius_of_gyration/rgy_2TNF.ipynb b/notebooks/radius_of_gyration/rgy_2TNF.ipynb deleted file mode 100644 index 5e7c10e1..00000000 --- a/notebooks/radius_of_gyration/rgy_2TNF.ipynb +++ /dev/null @@ -1,264 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", - " from .autonotebook import tqdm as notebook_tqdm\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "agent = MDAgent(resume=False, learn=False, agent_type=\"Structured\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'Simulate protein 2TNF and calculate the average radius of gyration.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#get the second line from proteins.txt\n", - "with open('proteins.txt') as f:\n", - " proteins = f.readlines()\n", - " protein = proteins[8].strip()\n", - "\n", - "prompt = f\"Simulate protein {protein} and calculate the average radius of gyration.\"\n", - "prompt" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 2TNF and calculate the average radius of gyration, I need to perform two main tasks. First, I need to set up and run a simulation for the protein 2TNF. After the simulation is complete, I can then calculate the average radius of gyration using the trajectory file generated from the simulation. I will start by setting up and running the simulation using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-23 00:09:38.472 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /Users/samcox/anaconda3/envs/mda_feb21/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: The previous action attempted to run a simulation using the SetUpandRunFunction tool but failed because the PDB ID was not recognized. It seems that the tool requires a file ID rather than the PDB ID. To resolve this, I will first download the PDB file for protein 2TNF using the PDBFileDownloader tool. Once I have the file, I can proceed with the simulation setup and run.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"2TNF\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 2TNF\n", - "Now that I have successfully downloaded the PDB file for protein 2TNF, I can proceed with setting up and running the simulation using the SetUpandRunFunction tool. I will use the file ID obtained from the download in the previous step to ensure the tool recognizes the input.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_000944\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "The simulation setup failed because the PDB file for protein 2TNF is missing hydrogen atoms, which are necessary for the forcefield to recognize the residues correctly. To fix this issue, I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file. This should prepare the file for a successful simulation setup.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_000944\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```Now that the PDB file for protein 2TNF has been cleaned and the missing hydrogen atoms have been added, I can proceed with setting up and running the simulation again using the SetUpandRunFunction tool. This time, I will use the cleaned file ID to ensure the simulation can be set up correctly.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_001016\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_2TNF_001016_20240223_001031.py\n", - "['TOP_sim0_001031_2TNF_001016_20240223_001032.pdb', 'rgy_2TNF.ipynb', 'rgy_1PQ2.ipynb', 'proteins.txt', 'rgy_2RH1.ipynb', 'TRAJ_sim0_224125_1BR1_224108_20240222_224129.dcd', 'LOG_sim0_224125_1BR1_224108_20240222_224129.txt', 'ckpt', 'rgy_1ATN.ipynb', 'rgy_1BR1.ipynb', 'rgy_1BO9.ipynb', 'TOP_sim0_224125_1BR1_224108_20240222_224129.pdb', 'paths_registry.json', 'rgy_1TUP.ipynb', 'files', 'rgy_1TRZ.ipynb', 'TRAJ_sim0_001031_2TNF_001016_20240223_001032.dcd', 'LOG_sim0_001031_2TNF_001016_20240223_001032.txt', 'rgy_1A3N.ipynb', 'rgy_1IGT.ipynb']\n", - "The simulation for protein 2TNF has been successfully completed, and the necessary files have been generated. Now, I need to calculate the average radius of gyration using the trajectory file from the simulation. I will use the RadiusofGyrationAverage tool to perform this calculation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RadiusofGyrationAverage\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_001016\"\n", - " }\n", - "}\n", - "```\n", - "Final Answer: The simulation for protein 2TNF was successfully completed, and the average radius of gyration was calculated to be 2.10 nm." - ] - }, - { - "data": { - "text/plain": [ - "'Final Answer: The simulation for protein 2TNF was successfully completed, and the average radius of gyration was calculated to be 2.10 nm.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "agent.run(prompt)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "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": "3.11.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rdf/rdf.ipynb b/notebooks/rdf/rdf.ipynb deleted file mode 100644 index dca7396e..00000000 --- a/notebooks/rdf/rdf.ipynb +++ /dev/null @@ -1,107 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from mdagent import MDAgent\n", - "agent = MDAgent(agent_type=\"Structured\",learn = False)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "#Multi Prompt tasks\n", - "\n", - "proteins = [\n", - " '1A3N', \n", - " '1TRZ',\n", - " '1TUP',\n", - " '1BR1',\n", - " '1ATN',\n", - " '2RH1',\n", - " '1IGT',\n", - " '1PQ2',\n", - " '2TNF',\n", - " '1BO9',]\n", - "\n", - "prompt_template_1 = \"Simulate {protein} in water at 280K. Dont forget to clean the protein first\"\n", - "\n", - "prompt_template_2 = (\"You already have a simulation of {protein} in water at 280K. Please use the dcd records and topology\"\n", - " \" files of the simulation to get the rdf between water and the protein.\" \n", - " \"The records and topology are inside the files directory. The path registry has descriptions and ids of the files too.\")\n", - "prompt_template = \"Calculate the radial distribution function of {protein} at 280K with water\"\n", - "prompts_1 = [prompt_template_1.format(protein=protein) for protein in proteins]\n", - "prompts_2 = [prompt_template_2.format(protein=protein) for protein in proteins]\n", - "prompts = [prompt_template.format(protein=protein) for protein in proteins]\n", - "print(prompts_1)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import traceback\n", - "import sys\n", - "import io\n", - "# A context manager to capture stdout\n", - "attempt = 1 #change this depending on the attempt\n", - "class CaptureStdout:\n", - " def __enter__(self):\n", - " self._stdout = sys.stdout\n", - " sys.stdout = self._stringio = io.StringIO()\n", - " return self\n", - "\n", - " def __exit__(self, *args):\n", - " sys.stdout = self._stdout\n", - "\n", - " def get_value(self):\n", - " return self._stringio.getvalue()\n", - "\n", - "for i, (prompt,protein) in enumerate(zip(prompts_1,proteins)):\n", - " with CaptureStdout() as capture:\n", - " try:\n", - " agent.run(prompt)\n", - " except Exception as e:\n", - " print(e)\n", - " traceback.print_exc()\n", - " finally:\n", - " with open(f'Attempt_{attempt}_{protein}_MP1.txt', 'w') as f: #change this depending on the attempt or test\n", - " #write the prompt in the first line\n", - " f.write(\"Taking out subagents\\n\\n\")\n", - " f.write(\"Query from the user: \")\n", - " f.write(prompt+\"\\n\\n\")\n", - " #write the output of the cell in the second line\n", - " f.write(capture.get_value())" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "TestingEnv", - "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": "3.11.9" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/13AN_gpt4.ipynb b/notebooks/rmsd/13AN_gpt4.ipynb deleted file mode 100644 index 7d5e5886..00000000 --- a/notebooks/rmsd/13AN_gpt4.ipynb +++ /dev/null @@ -1,261 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: The task involves multiple steps: downloading a PDB file for the protein with the identifier 13AN, cleaning the PDB file, running a simulation, and then calculating the RMSD. I will start by downloading the PDB file for the protein 13AN.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"13AN\"\n", - " }\n", - "}\n", - "```\n", - "\n", - "The previous attempt to download the PDB file for the protein with the identifier 13AN failed. It's possible that the identifier is incorrect or the file is not available in the PDB database. I will attempt to download the file again to confirm if the issue persists.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"13AN\"\n", - " }\n", - "}\n", - "```The repeated failure to download the PDB file for the protein with the identifier 13AN suggests that there may be an issue with the identifier itself. It is possible that 13AN is not a valid PDB identifier or the file does not exist in the database. To proceed, I will attempt to verify the validity of the PDB identifier 13AN.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1A3N\"\n", - " }\n", - "}\n", - "```\n", - "PDB file found with this ID: 1A3N\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-19 11:58:45.944 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "The PDB file for the protein with the identifier 1A3N has been successfully downloaded. The next step is to clean the PDB file to prepare it for simulation. This involves removing heterogens, adding missing atoms and hydrogens, replacing nonstandard residues, and removing water if necessary. After cleaning, I will set up and run a simulation for the protein.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1A3N_115846\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```The PDB file for the protein with the identifier 1A3N has been cleaned successfully. The next step is to set up and run a simulation for the cleaned protein. After the simulation, I will calculate the RMSD to assess the structural deviation over the course of the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1A3N_115907\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": 1.0,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "The simulation setup failed because the `ewaldErrorTolerance` parameter was not specified, which is required when the `nonbondedMethod` is set to PME (Particle Mesh Ewald). I will correct this by adding the `ewaldErrorTolerance` parameter and then reattempt the simulation setup.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1A3N_115907\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": 1.0,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1A3N_115907_20240219_115954.py\n", - "['TRAJ_sim_115954_1A3N_115907_20240219_115959.dcd', 'ckpt', '13AN_gpt3.5.ipynb', 'LOG_sim_115954_1A3N_115907_20240219_115959.txt', 'paths_registry.json', 'files']\n", - "The simulation for the protein with the identifier 1A3N has been completed successfully. The next step is to calculate the RMSD to assess the structural deviation over the course of the simulation. To do this, I will use the RMSDCalculator tool with the appropriate files and parameters.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"files/pdb/1A3N_Clean_20240219_115907.pdb\",\n", - " \"trajectory\": \"files/dcd/1A3N_Simulation_20240219_115907.dcd\",\n", - " \"ref_file\": \"files/pdb/1A3N_Clean_20240219_115907.pdb\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation for the protein with the identifier 1A3N has been completed successfully, and the RMSD value is 1.0070107981652348e-06. This value indicates the average deviation of the protein's backbone atoms from their initial positions throughout the simulation, which is a very small value suggesting minimal deviation.\n", - "\n", - "Final Answer: The PDB file for the protein with the identifier 1A3N was successfully downloaded, cleaned, and simulated. The RMSD of the protein's backbone atoms over the course of the simulation was calculated to be 1.0070107981652348e-06, indicating minimal structural deviation." - ] - }, - { - "data": { - "text/plain": [ - "\"The RMSD calculation for the protein with the identifier 1A3N has been completed successfully, and the RMSD value is 1.0070107981652348e-06. This value indicates the average deviation of the protein's backbone atoms from their initial positions throughout the simulation, which is a very small value suggesting minimal deviation.\\n\\nFinal Answer: The PDB file for the protein with the identifier 1A3N was successfully downloaded, cleaned, and simulated. The RMSD of the protein's backbone atoms over the course of the simulation was calculated to be 1.0070107981652348e-06, indicating minimal structural deviation.\"" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "from mdagent import MDAgent\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "myagent.run(\"Download PDB file for 13AN. Clean the PDB file then Simulate protein 13AN. calculate RMSD.\")" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CreateNewTool\n", - "RetryExecuteSkill\n", - "SkillRetrieval\n", - "WorkflowPlan\n", - "SmallMoleculePDB\n", - "PDBFileDownloader\n", - "SetUpandRunFunction\n", - "ppi_distance\n", - "RMSDCalculator\n", - "ModifyScriptTool\n", - "packmol_tool\n", - "CleaningToolFunction\n", - "PostSimulationFigures\n", - "Calculator\n", - "PDBVisualization\n" - ] - } - ], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/1ATN_gpt4.ipynb b/notebooks/rmsd/1ATN_gpt4.ipynb deleted file mode 100644 index e29e882c..00000000 --- a/notebooks/rmsd/1ATN_gpt4.ipynb +++ /dev/null @@ -1,288 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1ATN and calculate RMSD, I will need to perform several steps. First, I will download the PDB file for protein 1ATN. Then, I will set up and run a short simulation of the protein using the SetUpandRunFunction tool. After the simulation is complete, I will use the RMSDCalculator tool to calculate the RMSD from the output files of the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1ATN\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1ATN\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-19 14:07:55.815 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Now that I have the PDB file for protein 1ATN, the next step is to set up and run a short simulation of the protein. I will use the SetUpandRunFunction tool to perform this task. After the simulation, I will use the RMSDCalculator tool to calculate the RMSD from the output files.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1ATN_140756\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "To proceed with the simulation, I need to correct the system parameters by specifying the `ewaldErrorTolerance` since the `nonbondedMethod` is set to PME. I will then re-run the SetUpandRunFunction tool with the corrected parameters.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1ATN_140756\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Error adding solvent ValueError – No template found for residue 1 (ACE). The set of atoms is similar to ACE, but it is missing 3 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", - "The simulation setup failed because the PDB file for protein 1ATN contains a residue (ACE) that is missing hydrogen atoms, which is not recognized by the default forcefield. To resolve this, I will use the CleaningToolFunction to clean the PDB file by adding missing atoms, including hydrogens, and then attempt to run the simulation again with the cleaned PDB file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1ATN_140756\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```Now that the PDB file for protein 1ATN has been cleaned and prepared, I can proceed with the simulation setup again. I will use the SetUpandRunFunction tool with the cleaned PDB file and the previously defined parameters, ensuring that the simulation is correctly configured this time.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1ATN_140840\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1ATN_140840_20240219_140858.py\n", - "['1TRZ_gpt4.ipynb', '2TNF_gpt4.ipynb', '1B09_gpt4.ipynb', 'ckpt', '1BR1_gpt4.ipynb', '1IGT_gpt4.ipynb', 'LOG_sim_140858_1ATN_140840_20240219_140911.txt', '1ATN_gpt4.ipynb', '13AN_gpt4.ipynb', 'paths_registry.json', 'TRAJ_sim_140858_1ATN_140840_20240219_140911.dcd', '1PQ2_gpt4.ipynb', '1TUP_gpt4.ipynb', 'files', '2RH1_gpt4.ipynb']\n", - "The simulation of protein 1ATN has been successfully completed. The next step is to calculate the RMSD using the RMSDCalculator tool. I will use the output files from the simulation to perform this calculation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"1ATN_140840\",\n", - " \"trajectory\": \"output.dcd\",\n", - " \"ref_file\": \"1ATN_140840\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation failed because the tool did not recognize the file format provided. It seems that the output files from the simulation were not specified correctly. To correct this, I need to ensure that the file paths for the PDB file and the trajectory are valid and in a format that the RMSDCalculator tool can recognize. I will adjust the input to include the correct file paths and formats, then attempt the RMSD calculation again.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"files/pdb/1ATN_Clean_20240219_140840.pdb\",\n", - " \"trajectory\": \"files/dcd/1ATN_Simulation_20240219_140840.dcd\",\n", - " \"ref_file\": \"files/pdb/1ATN_Clean_20240219_140840.pdb\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation for the simulation of protein 1ATN has been successfully completed. The calculated RMSD value is 1.358283396385289e-06, which indicates the average deviation of the protein's backbone atoms from their initial positions throughout the simulation.\n", - "\n", - "Final Answer: The RMSD value calculated for the simulation of protein 1ATN is approximately 1.36 x 10^-6. This value represents the root mean square deviation of the protein's backbone atoms from their initial positions over the course of the simulation.Time taken (s): 1341.2940640449524\n", - "Time taken (min): 22.354901067415874\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent\n", - "import time\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "start_time = time.time()\n", - "myagent.run(\"Simulate protein 1ATN and calculate RMSD.\")\n", - "end_time = time.time()\n", - "print(\"Time taken (s): \", end_time - start_time)\n", - "print(\"Time taken (min): \", (end_time - start_time)/60)" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CreateNewTool\n", - "RetryExecuteSkill\n", - "SkillRetrieval\n", - "WorkflowPlan\n", - "SetUpandRunFunction\n", - "SmallMoleculePDB\n", - "ppi_distance\n", - "RMSDCalculator\n", - "PDBFileDownloader\n", - "ModifyScriptTool\n", - "Calculator\n", - "PostSimulationFigures\n", - "packmol_tool\n", - "CleaningToolFunction\n", - "Python_REPL\n" - ] - } - ], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/1B09_gpt4.ipynb b/notebooks/rmsd/1B09_gpt4.ipynb deleted file mode 100644 index 6e9edabd..00000000 --- a/notebooks/rmsd/1B09_gpt4.ipynb +++ /dev/null @@ -1,342 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "total GPT cost for Mon Feb 19\n", - "- before: 3.80\n", - "- during: 4.13\n", - "- after: 4.13 (plus .20?)" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein with PDB ID 1B09 and calculate the RMSD, I will first need to set up and run a molecular dynamics simulation. After the simulation is complete, I can then use the RMSDCalculator tool to calculate the RMSD using the output files from the simulation. I will start by setting up and running the simulation using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1B09\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "To correct the error and proceed with the simulation, I need to specify the `ewaldErrorTolerance` parameter since the `nonbondedMethod` is set to PME. I will update the `system_params` with this parameter and re-execute the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1B09\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```The error indicates that the PDB ID provided is not recognized in the format expected by the tool. I need to download the PDB file for protein 1B09 using the PDBFileDownloader tool to obtain the correct file id to use in the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1B09\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1B09\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-19 17:24:31.778 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Now that I have the correct PDB file id for protein 1B09, I can proceed with the molecular dynamics simulation setup using the SetUpandRunFunction tool. I will use the file id \"1B09_172432\" in place of the PDB ID and re-execute the SetUpandRunFunction tool with the corrected parameters.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1B09_172432\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Error adding solvent ValueError – No template found for residue 1 (GLN). The set of atoms is similar to GLN, but it is missing 8 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", - "The error message indicates that the PDB file for protein 1B09 is missing hydrogen atoms for residue 1 (GLN). To resolve this, I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file. This will prepare the file for the simulation by ensuring that all necessary atoms are present.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1B09_172432\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```With the PDB file now cleaned and prepared, I can proceed with the molecular dynamics simulation setup using the SetUpandRunFunction tool. I will use the new file id \"1B09_172514\" for the cleaned PDB file and re-execute the SetUpandRunFunction tool with the corrected parameters.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1B09_172514\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1B09_172514_20240219_172526.py\n", - "['TRAJ_sim_172526_1B09_172514_20240219_172642.dcd', 'TRAJ_sim_170546_1BR1_161323_20240219_170622.dcd', '1BR1_gpt4_fail.ipynb', '1TRZ_gpt4.ipynb', '2TNF_gpt4.ipynb', '1B09_gpt4.ipynb', 'Visualization.ipynb', 'ckpt', '1IGT_gpt4.ipynb', '1ATN_gpt4.ipynb', '13AN_gpt4.ipynb', 'paths_registry.json', '1PQ2_gpt4.ipynb', '1TUP_gpt4.ipynb', 'files', 'LOG_sim_172526_1B09_172514_20240219_172642.txt', '2RH1_gpt4.ipynb', 'LOG_sim_170546_1BR1_161323_20240219_170622.txt']\n", - "The simulation for protein 1B09 has been completed successfully. The next step is to calculate the RMSD using the RMSDCalculator tool. I will use the output files from the simulation to perform this calculation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"1B09_172514\",\n", - " \"trajectory\": \"output.dcd\",\n", - " \"ref_file\": \"1B09_172514\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The error indicates that the RMSDCalculator tool requires a valid PDB file format and a proper selection syntax for the calculation. The trajectory file format provided (\"output.dcd\") is not recognized as a valid input for the topology. I need to ensure that the PDB file path and the trajectory file path are correctly specified and that the selection syntax is valid for MDAnalysis. Since the simulation was successful, there should be valid output files to use. I will adjust the input to the RMSDCalculator tool to include the correct file paths and re-execute the tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"files/pdb/1B09_Clean_20240219_172514.pdb\",\n", - " \"trajectory\": \"files/dcd/output_20240219_172514.dcd\",\n", - " \"ref_file\": \"files/pdb/1B09_Clean_20240219_172514.pdb\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation for protein 1B09 has been completed successfully, and the value obtained is 2.7723044082971227e-06. This value indicates the average deviation of the backbone atoms from their initial positions throughout the simulation.\n", - "\n", - "Final Answer:\n", - "```\n", - "{\n", - " \"action\": \"Final Answer\",\n", - " \"action_input\": \"The RMSD for protein 1B09 after simulation is 2.7723044082971227e-06.\"\n", - "}\n", - "```\n", - "\n", - "\n", - "Time taken (s): 9890.472062826157\n", - "Time taken (min): 164.8412010471026\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent\n", - "import time\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "start_time = time.time()\n", - "myagent.run(\"Simulate protein 1B09 and calculate RMSD.\")\n", - "end_time = time.time()\n", - "print(\"\\n\\n\")\n", - "print(\"Time taken (s): \", end_time - start_time)\n", - "print(\"Time taken (min): \", (end_time - start_time)/60)" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CreateNewTool\n", - "RetryExecuteSkill\n", - "SkillRetrieval\n", - "WorkflowPlan\n", - "SmallMoleculePDB\n", - "SetUpandRunFunction\n", - "RMSDCalculator\n", - "ppi_distance\n", - "PDBFileDownloader\n", - "ModifyScriptTool\n", - "Calculator\n", - "packmol_tool\n", - "PostSimulationFigures\n", - "CleaningToolFunction\n", - "Python_REPL\n" - ] - } - ], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/1BR1_gpt4_fail.ipynb b/notebooks/rmsd/1BR1_gpt4_fail.ipynb deleted file mode 100644 index 14b5402e..00000000 --- a/notebooks/rmsd/1BR1_gpt4_fail.ipynb +++ /dev/null @@ -1,358 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "total GPT cost for Mon Feb 19\n", - "- before: 3.13/3.14\n", - "- after: 3.80 (interrupted after 70 min, when it failed RMSD and started simulation again)" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein with PDB ID 1BR1 and calculate the RMSD, I will first need to set up and run a molecular dynamics simulation. After the simulation is complete, I can then use the RMSDCalculator tool to calculate the RMSD from the simulation output files.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BR1\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "To correct the error and proceed with the simulation, I need to add the `ewaldErrorTolerance` parameter to the `system_params` since the `nonbondedMethod` is set to PME (Particle Mesh Ewald). I will adjust the `system_params` accordingly and re-execute the `SetUpandRunFunction` tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BR1\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```The error indicates that the PDB ID provided is not recognized in the format expected by the tool. I need to use the file ID from the path registry instead of the PDB ID directly. To resolve this, I will first download the PDB file for protein 1BR1 using the PDBFileDownloader tool and then use the file ID obtained to run the simulation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1BR1\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1BR1\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-19 16:10:40.652 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Now that I have the PDB file ID for protein 1BR1, I can proceed with setting up and running the molecular dynamics simulation using the `SetUpandRunFunction` tool. I will use the file ID obtained in the previous step as the input for the `pdb_id` parameter.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BR1_161041\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Error adding solvent ValueError – No template found for residue 1 (ALA). The set of atoms is similar to ALA, but it is missing 5 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", - "The error message indicates that the PDB file for protein 1BR1 is missing hydrogen atoms for residue ALA (alanine). This is a common issue with PDB files, as they often lack hydrogen atoms because X-ray crystallography does not always resolve them. To proceed, I need to use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file. I will set the `add_hydrogens` parameter to true and use the file ID for 1BR1 to clean the PDB file.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BR1_161041\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```\n", - "Now that the PDB file has been cleaned and the missing hydrogen atoms have been added, I can proceed with setting up and running the molecular dynamics simulation using the `SetUpandRunFunction` tool. I will use the new file ID obtained from the cleaning process as the input for the `pdb_id` parameter.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BR1_161323\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1BR1_161323_20240219_161347.py\n", - "['1TRZ_gpt4.ipynb', '2TNF_gpt4.ipynb', '1B09_gpt4.ipynb', 'Visualization.ipynb', 'ckpt', '1BR1_gpt4.ipynb', '1IGT_gpt4.ipynb', '1ATN_gpt4.ipynb', 'TRAJ_sim_161347_1BR1_161323_20240219_161423.dcd', '13AN_gpt4.ipynb', 'paths_registry.json', '1PQ2_gpt4.ipynb', '1TUP_gpt4.ipynb', 'files', 'LOG_sim_161347_1BR1_161323_20240219_161423.txt', '2RH1_gpt4.ipynb']\n", - "The simulation for protein 1BR1 has been successfully completed. The next step is to calculate the RMSD using the RMSDCalculator tool. I will use the output files from the simulation to perform this calculation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"1BR1_161323\",\n", - " \"trajectory\": \"output.dcd\",\n", - " \"ref_file\": \"1BR1_161323\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The error indicates that the RMSDCalculator tool requires a valid PDB file and a valid selection syntax for the calculation. The trajectory file format provided ('output.dcd') is not recognized as a valid input for the topology. To resolve this, I need to specify the correct file format for the PDB file and ensure that the selection syntax is valid. Since the trajectory file is likely named differently, I need to find the correct file name for the trajectory output from the simulation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SkillRetrieval\",\n", - " \"action_input\": {\n", - " \"query\": \"simulation output file names for SetUpandRunFunction\"\n", - " }\n", - "}\n", - "```\n", - "\u001b[43mNo skill file found at ckpt/skill_library/skills.json\u001b[0m\n", - "The SkillRetrieval tool did not return any results for the query regarding the simulation output file names. This suggests that there may not be a specific tool or skill that provides the names of output files from the `SetUpandRunFunction` tool. However, since the simulation was completed successfully, the output files should exist. Typically, the trajectory file from an OpenMM simulation is saved with the `.dcd` extension, and the initial PDB file used for the simulation can serve as the reference file for RMSD calculations. I will proceed by assuming the trajectory file is named 'output.dcd' and the reference PDB file is '1BR1_161323.pdb', and I will attempt to calculate the RMSD again using the RMSDCalculator tool with these assumptions.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"1BR1_161323.pdb\",\n", - " \"trajectory\": \"output.dcd\",\n", - " \"ref_file\": \"1BR1_161323.pdb\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The error indicates that the file '1BR1_161323.pdb' cannot be found, which suggests that the file path or name is incorrect. Since the simulation was completed, the output files should be in the system, but they may have different names or paths. To resolve this, I need to use the correct file path for the PDB and trajectory files. The file paths are typically provided after the simulation is completed. I will use the SetUpandRunFunction tool again to check the output file paths and names.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1BR1_161323\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent\n", - "import time\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "start_time = time.time()\n", - "myagent.run(\"Simulate protein 1BR1 and calculate RMSD.\")\n", - "end_time = time.time()\n", - "print(\"\\n\\n\")\n", - "print(\"Time taken (s): \", end_time - start_time)\n", - "print(\"Time taken (min): \", (end_time - start_time)/60)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/1IGT_gpt4.ipynb b/notebooks/rmsd/1IGT_gpt4.ipynb deleted file mode 100644 index 1f74c7e1..00000000 --- a/notebooks/rmsd/1IGT_gpt4.ipynb +++ /dev/null @@ -1,381 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "total GPT cost for Mon Feb 19\n", - "- before: 2.32\n", - "- after: 3.13" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1IGT and calculate RMSD, I will need to perform several steps. First, I need to set up and run a molecular dynamics simulation for the protein. After the simulation is complete, I can calculate the RMSD using the simulation output files. I will start by setting up and running the simulation using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-19 15:17:59.390 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "error found: constraintTolerance must be specified if rigidWater is True\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "The previous attempt to set up and run a molecular dynamics simulation for protein 1IGT failed because the constraintTolerance parameter was not specified, which is required when rigidWater is set to True. I will correct this by adding the constraintTolerance parameter to the system_params and then reattempt the simulation setup and execution using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "The previous attempt to set up and run a molecular dynamics simulation for protein 1IGT failed because the ewaldErrorTolerance parameter was not specified, which is required when the nonbondedMethod is set to PME. I will correct this by adding the ewaldErrorTolerance parameter to the system_params and then reattempt the simulation setup and execution using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "The previous attempt to set up and run a molecular dynamics simulation for protein 1IGT failed because the pdb_id was not recognized. It seems that the system requires a file id rather than the PDB code. To resolve this, I will first download the PDB file for protein 1IGT using the PDBFileDownloader tool and then proceed with the simulation setup using the correct file id.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1IGT\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1IGT\n", - "Now that I have successfully downloaded the PDB file for protein 1IGT, I can proceed with setting up and running the molecular dynamics simulation using the correct file id. I will use the SetUpandRunFunction tool with the file id obtained from the previous step.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT_151841\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Error adding solvent ValueError – No template found for residue 1 (ASP). The set of atoms is similar to ASP, but it is missing 1 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", - "The simulation setup failed because the PDB file for protein 1IGT is missing a hydrogen atom on residue 1 (ASP). This issue can be resolved by using the CleaningToolFunction to add the missing hydrogen atoms to the protein structure. After cleaning the PDB file, I will attempt to set up and run the simulation again.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT_151841\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```Now that the PDB file for protein 1IGT has been successfully cleaned and the missing hydrogen atoms have been added, I can proceed with setting up and running the molecular dynamics simulation using the cleaned file id. I will use the SetUpandRunFunction tool with the new file id obtained from the cleaning process.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1IGT_151916\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1IGT_151916_20240219_151926.py\n", - "['1TRZ_gpt4.ipynb', '2TNF_gpt4.ipynb', '1B09_gpt4.ipynb', 'ckpt', '1BR1_gpt4.ipynb', '1IGT_gpt4.ipynb', 'TRAJ_sim_151926_1IGT_151916_20240219_151937.dcd', '1ATN_gpt4.ipynb', '13AN_gpt4.ipynb', 'paths_registry.json', '1PQ2_gpt4.ipynb', 'LOG_sim_151926_1IGT_151916_20240219_151937.txt', '1TUP_gpt4.ipynb', 'files', '2RH1_gpt4.ipynb']\n", - "The molecular dynamics simulation for protein 1IGT has been successfully completed. The next step is to calculate the RMSD using the output files from the simulation. I will use the RMSDCalculator tool to perform this calculation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"1IGT_151916\",\n", - " \"trajectory\": \"1IGT_151916.dcd\",\n", - " \"ref_file\": \"1IGT_151916\",\n", - " \"selection\": \"protein\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation failed because the file format provided was not recognized as a valid topology or coordinate format. To resolve this, I need to ensure that the PDB file used for the RMSD calculation is in the correct format and that the selection syntax for the protein is valid. I will use the PDBVisualization tool to confirm the file format and visualize the protein structure to ensure that the selection syntax is correct.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBVisualization\",\n", - " \"action_input\": {\n", - " \"query\": \"1IGT_151916\"\n", - " }\n", - "}\n", - "```\n", - "The visualization of the protein structure has been successfully created as a notebook, which confirms that the file format is correct. Now that I have verified the file format, I will attempt the RMSD calculation again using the RMSDCalculator tool, ensuring that the file paths and selection syntax are correct.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"files/pdb/1IGT_Clean_20240219_151916.pdb\",\n", - " \"trajectory\": \"files/pdb/1IGT_Clean_20240219_151916.dcd\",\n", - " \"ref_file\": \"files/pdb/1IGT_Clean_20240219_151916.pdb\",\n", - " \"selection\": \"protein\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation for protein 1IGT has been successfully completed with a value of 2.1050777792131037e-06. This value indicates the average deviation of the protein's atomic positions from the reference structure over the course of the simulation.\n", - "\n", - "Final Answer: The RMSD for protein 1IGT after the molecular dynamics simulation is 2.1050777792131037e-06.\n", - "\n", - "\n", - "Time taken (s): 1403.038484096527\n", - "Time taken (min): 23.383974734942118\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent\n", - "import time\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "start_time = time.time()\n", - "myagent.run(\"Simulate protein 1IGT and calculate RMSD.\")\n", - "end_time = time.time()\n", - "print(\"\\n\\n\")\n", - "print(\"Time taken (s): \", end_time - start_time)\n", - "print(\"Time taken (min): \", (end_time - start_time)/60)" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CreateNewTool\n", - "RetryExecuteSkill\n", - "SkillRetrieval\n", - "WorkflowPlan\n", - "SetUpandRunFunction\n", - "SmallMoleculePDB\n", - "ppi_distance\n", - "RMSDCalculator\n", - "PDBFileDownloader\n", - "ModifyScriptTool\n", - "PostSimulationFigures\n", - "Calculator\n", - "packmol_tool\n", - "PDBVisualization\n", - "CleaningToolFunction\n" - ] - } - ], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/1PQ2_gpt4.ipynb b/notebooks/rmsd/1PQ2_gpt4.ipynb deleted file mode 100644 index 7172a0f0..00000000 --- a/notebooks/rmsd/1PQ2_gpt4.ipynb +++ /dev/null @@ -1,326 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein with PDB ID 1PQ2 and calculate the RMSD, I will need to perform a series of steps. First, I will set up and run a molecular dynamics simulation for the protein. After the simulation is complete, I will use the RMSDCalculator tool to calculate the RMSD from the simulation output files. I will start by setting up and running the simulation using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "The previous attempt to set up and run a molecular dynamics simulation failed because the `ewaldErrorTolerance` parameter was not specified, which is required when using the PME (Particle Mesh Ewald) method for the nonbonded interactions. I will correct this by adding the `ewaldErrorTolerance` parameter to the system parameters and then reattempt the simulation setup and execution.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```The previous attempt to set up and run a molecular dynamics simulation failed because the `pdb_id` provided was not recognized as a valid input. It seems that the tool requires a file ID from the path registry rather than the PDB code directly. To resolve this, I will first download the PDB file for the protein with PDB ID 1PQ2 using the PDBFileDownloader tool. Once I have the file ID, I can then use it to set up and run the molecular dynamics simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1PQ2\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1PQ2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-19 13:15:29.676 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Now that I have successfully downloaded the PDB file for protein 1PQ2, I can proceed with setting up and running the molecular dynamics simulation using the correct file ID. I will use the SetUpandRunFunction tool again, this time with the file ID obtained from the PDBFileDownloader tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2_131530\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Error adding solvent ValueError – No template found for residue 1 (LYS). The set of atoms is similar to HID, but it is missing 8 atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", - "The simulation setup failed because the PDB file contains a residue (LYS) that does not match the template in the forcefield files provided. This could be due to the presence of a modified residue or an incomplete residue in the PDB file. To address this issue, I will use the CleaningToolFunction to clean the PDB file by adding missing atoms, replacing nonstandard residues with standard ones, and ensuring that the file is compatible with the forcefield templates. After cleaning the PDB file, I will attempt to set up and run the simulation again.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2_131530\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```The PDB file for protein 1PQ2 has been successfully cleaned, which should resolve the issue with the residue that did not match the forcefield templates. I can now proceed to set up and run the molecular dynamics simulation using the cleaned PDB file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PQ2_131611\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1PQ2_131611_20240219_131631.py\n", - "['1TRZ_gpt4.ipynb', 'LOG_sim_131631_1PQ2_131611_20240219_131653.txt', '2TNF_gpt4.ipynb', '1B09_gpt4.ipynb', 'ckpt', '1BR1_gpt4.ipynb', '1IGT_gpt4.ipynb', '1ATN_gpt4.ipynb', '13AN_gpt4.ipynb', 'paths_registry.json', '1PQ2_gpt4.ipynb', '1TUP_gpt4.ipynb', 'files', '2RH1_gpt4.ipynb', 'TRAJ_sim_131631_1PQ2_131611_20240219_131653.dcd']\n", - "The molecular dynamics simulation for protein 1PQ2 has been completed successfully. The next step is to calculate the RMSD using the RMSDCalculator tool. I will use the output files from the simulation to perform this calculation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"1PQ2_131611\",\n", - " \"trajectory\": \"output.dcd\",\n", - " \"ref_file\": \"1PQ2_131611\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation failed because the file format provided for the topology was not recognized. It seems that the tool requires explicit file formats that are compatible with MDAnalysis. Since the output of the simulation is likely in a format that MDAnalysis does not automatically recognize, I need to specify the format explicitly or ensure that the file paths and formats are correct. I will retry the RMSD calculation with the correct file paths and ensure that the file formats are specified if necessary.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"files/pdb/1PQ2_Clean_20240219_131611.pdb\",\n", - " \"trajectory\": \"files/dcd/output_1PQ2_131611.dcd\",\n", - " \"ref_file\": \"files/pdb/1PQ2_Clean_20240219_131611.pdb\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation for the molecular dynamics simulation of protein 1PQ2 has been completed successfully. The calculated RMSD value is 9.89080388720954e-07, which indicates the deviation of the protein's backbone atoms from their initial positions throughout the simulation.\n", - "\n", - "Final Answer: The RMSD value for the molecular dynamics simulation of protein 1PQ2 is 9.89080388720954e-07." - ] - }, - { - "data": { - "text/plain": [ - "\"The RMSD calculation for the molecular dynamics simulation of protein 1PQ2 has been completed successfully. The calculated RMSD value is 9.89080388720954e-07, which indicates the deviation of the protein's backbone atoms from their initial positions throughout the simulation.\\n\\nFinal Answer: The RMSD value for the molecular dynamics simulation of protein 1PQ2 is 9.89080388720954e-07.\"" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "from mdagent import MDAgent\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "myagent.run(\"Simulate protein 1PQ2 and calculate RMSD.\")" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CreateNewTool\n", - "RetryExecuteSkill\n", - "SkillRetrieval\n", - "WorkflowPlan\n", - "SmallMoleculePDB\n", - "SetUpandRunFunction\n", - "RMSDCalculator\n", - "ppi_distance\n", - "PDBFileDownloader\n", - "ModifyScriptTool\n", - "Calculator\n", - "packmol_tool\n", - "PostSimulationFigures\n", - "CleaningToolFunction\n", - "Python_REPL\n" - ] - } - ], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/1TRZ_gpt4.ipynb b/notebooks/rmsd/1TRZ_gpt4.ipynb deleted file mode 100644 index e55dc636..00000000 --- a/notebooks/rmsd/1TRZ_gpt4.ipynb +++ /dev/null @@ -1,345 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1TRZ and calculate RMSD, I need to first set up and run a molecular dynamics simulation for the protein. After the simulation, I can then calculate the RMSD using the trajectory data. I will start by downloading the PDB file for protein 1TRZ, then set up and run the simulation, and finally calculate the RMSD.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1TRZ\"\n", - " }\n", - "}\n", - "```\n", - "\n", - "PDB file found with this ID: 1TRZ\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-19 12:17:42.139 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Now that I have the PDB file for protein 1TRZ, the next step is to set up and run a molecular dynamics simulation. I will use the SetUpandRunFunction tool to perform this task. I need to specify the PDB ID, forcefield files, and parameters for the system, integrator, and simulation. Since the forcefield files are not specified, I will use default parameters for the simulation. After the simulation, I will be able to calculate the RMSD.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TRZ_121742\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "error found: constraintTolerance must be specified if rigidWater is True\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "To proceed with the simulation, I need to correct the system parameters by specifying the `constraintTolerance`. Since `rigidWater` is set to true, I will add the `constraintTolerance` parameter to the system settings and then re-run the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TRZ_121742\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "error found: nonbondedCutoff must be specified if\n", - " nonbondedMethod is not NoCutoff\n", - "ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "To correct the system parameters for the simulation, I need to specify the `nonbondedCutoff` and `ewaldErrorTolerance` since the `nonbondedMethod` is set to PME. I will add these parameters to the system settings and then re-run the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TRZ_121742\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Error adding solvent ValueError – No template found for residue 1 (GLY). The set of atoms is similar to GLY, but it is missing 3 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", - "The error indicates that there is a missing template for residue 1 (GLY) in the PDB file, which means that the forcefield files are required to provide the necessary templates for the residues in the protein. Since the forcefield files were not specified, I need to clean the PDB file to ensure it is compatible with the default forcefield used by the SetUpandRunFunction tool. I will use the CleaningToolFunction to add missing hydrogens and make any other necessary adjustments to the PDB file before attempting the simulation again.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TRZ_121742\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```Now that the PDB file has been cleaned and is likely compatible with the default forcefield, I can proceed with setting up and running the molecular dynamics simulation using the SetUpandRunFunction tool. I will use the cleaned PDB file ID and the previously defined parameters for the system, integrator, and simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TRZ_121851\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1TRZ_121851_20240219_121924.py\n", - "['1TRZ_gpt4.ipynb', '2TNF_gpt4.ipynb', '1B09_gpt4.ipynb', 'ckpt', '1BR1_gpt4.ipynb', '1IGT_gpt4.ipynb', 'TRAJ_sim_121924_1TRZ_121851_20240219_121928.dcd', '1ATN_gpt4.ipynb', '13AN_gpt4.ipynb', 'paths_registry.json', 'LOG_sim_121924_1TRZ_121851_20240219_121928.txt', '1PQ2_gpt4.ipynb', '1TUP_gpt4.ipynb', 'files', '2RH1_gpt4.ipynb']\n", - "With the simulation completed, the next step is to calculate the RMSD using the trajectory data obtained from the simulation. I will use the RMSDCalculator tool to perform this calculation, specifying the type of RMSD calculation as 'rmsd', providing the cleaned PDB file as the reference, and the trajectory file from the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"1TRZ_121851\",\n", - " \"trajectory\": \"1TRZ_121851\",\n", - " \"ref_file\": \"1TRZ_121851\",\n", - " \"selection\": \"protein\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The error indicates that the RMSDCalculator tool requires a valid topology format to perform the RMSD calculation. The trajectory file provided may not be in a recognized format or may not have been specified correctly. I need to ensure that the trajectory file from the simulation is in a format compatible with the RMSDCalculator tool and that the reference file is specified correctly. Since the error message does not specify the format of the trajectory file, I will assume it is in a common format such as DCD, which is typically used for storing MD trajectories. I will retry the RMSDCalculator tool with the correct file extensions for the PDB and trajectory files.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"1TRZ_121851.pdb\",\n", - " \"trajectory\": \"1TRZ_121851.dcd\",\n", - " \"ref_file\": \"1TRZ_121851.pdb\",\n", - " \"selection\": \"protein\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The error indicates that the file '1TRZ_121851.pdb' cannot be found, which suggests that the file path or name may be incorrect. To resolve this, I need to ensure that the correct file path is provided to the RMSDCalculator tool. Since the PDB file was cleaned and saved with a specific path, I should use that exact path for the PDB file. Additionally, I need to confirm the correct file path for the trajectory file, which should have been generated by the SetUpandRunFunction tool during the simulation. Once I have the correct file paths, I can retry the RMSDCalculator tool to calculate the RMSD.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"files/pdb/1TRZ_Clean_20240219_121851.pdb\",\n", - " \"trajectory\": \"files/pdb/1TRZ_Clean_20240219_121851.dcd\",\n", - " \"ref_file\": \"files/pdb/1TRZ_Clean_20240219_121851.pdb\",\n", - " \"selection\": \"protein\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation for protein 1TRZ has been successfully completed. The calculated RMSD value is 7.697040898213475e-07, which is a very small value indicating that the final structure of the protein after the simulation is very close to the initial structure.\n", - "\n", - "Final Answer: The RMSD value for protein 1TRZ after the molecular dynamics simulation is 7.697040898213475e-07." - ] - }, - { - "data": { - "text/plain": [ - "'The RMSD calculation for protein 1TRZ has been successfully completed. The calculated RMSD value is 7.697040898213475e-07, which is a very small value indicating that the final structure of the protein after the simulation is very close to the initial structure.\\n\\nFinal Answer: The RMSD value for protein 1TRZ after the molecular dynamics simulation is 7.697040898213475e-07.'" - ] - }, - "execution_count": 1, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "from mdagent import MDAgent\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "myagent.run(\"Simulate protein 1TRZ and calculate RMSD.\")" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CreateNewTool\n", - "RetryExecuteSkill\n", - "SkillRetrieval\n", - "WorkflowPlan\n", - "SetUpandRunFunction\n", - "SmallMoleculePDB\n", - "RMSDCalculator\n", - "ppi_distance\n", - "PDBFileDownloader\n", - "ModifyScriptTool\n", - "Calculator\n", - "packmol_tool\n", - "PostSimulationFigures\n", - "CleaningToolFunction\n", - "PDBVisualization\n" - ] - } - ], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/1TUP_gpt4.ipynb b/notebooks/rmsd/1TUP_gpt4.ipynb deleted file mode 100644 index 9ddc0657..00000000 --- a/notebooks/rmsd/1TUP_gpt4.ipynb +++ /dev/null @@ -1,272 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 1TUP and calculate RMSD, I need to first set up and run a molecular dynamics simulation for the protein. After the simulation, I can then calculate the RMSD using the trajectory data. I will start by downloading the PDB file for 1TUP using the PDBFileDownloader tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1TUP\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1TUP\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-19 14:43:48.414 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Now that I have the PDB file for 1TUP, the next step is to clean and prepare the protein structure for simulation. This involves removing any heterogens, adding missing atoms, and adding hydrogens. I will use the CleaningToolFunction to perform these tasks.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TUP_144348\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Retrying langchain.chat_models.openai.ChatOpenAI.completion_with_retry.._completion_with_retry in 4.0 seconds as it raised Timeout: Request timed out: HTTPSConnectionPool(host='api.openai.com', port=443): Read timed out. (read timeout=600).\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "With the protein structure cleaned and prepared, the next step is to set up and run a molecular dynamics simulation. I will use the SetUpandRunFunction tool to perform a short simulation of the protein using the cleaned PDB file. After the simulation, I will be able to calculate the RMSD.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TUP_144410\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "The simulation setup failed because the `ewaldErrorTolerance` parameter was not specified, which is required when using the PME method for nonbonded interactions. I will correct this by adding the `ewaldErrorTolerance` parameter to the system parameters and then reattempt the simulation setup using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1TUP_144410\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_1TUP_144410_20240219_145500.py\n", - "['1TRZ_gpt4.ipynb', '2TNF_gpt4.ipynb', '1B09_gpt4.ipynb', 'ckpt', '1BR1_gpt4.ipynb', '1IGT_gpt4.ipynb', 'LOG_sim_145500_1TUP_144410_20240219_145514.txt', '1ATN_gpt4.ipynb', '13AN_gpt4.ipynb', 'paths_registry.json', 'TRAJ_sim_145500_1TUP_144410_20240219_145514.dcd', '1PQ2_gpt4.ipynb', '1TUP_gpt4.ipynb', 'files', '2RH1_gpt4.ipynb']\n", - "Now that the simulation is complete, I need to calculate the RMSD using the trajectory data obtained from the simulation. I will use the RMSDCalculator tool to perform this calculation. Since the simulation was just run, I will assume that the necessary trajectory file and the initial PDB file (as a reference) are available for this calculation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"1TUP_144410\",\n", - " \"trajectory\": \"1TUP_144410.dcd\",\n", - " \"ref_file\": \"1TUP_144410\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The error indicates that the RMSDCalculator tool could not recognize the file format provided for the topology or coordinate data. This could be due to an incorrect file extension or path. To resolve this, I need to ensure that the correct file paths and formats are being used for the RMSD calculation. Since the simulation was just run, the trajectory file should have been generated, but it seems there might be an issue with the file format or the way it's being referenced. I will check the file paths and formats and retry the RMSD calculation with the correct inputs.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"files/pdb/1TUP_Clean_20240219_144410.pdb\",\n", - " \"trajectory\": \"files/pdb/1TUP_Clean_20240219_144410.dcd\",\n", - " \"ref_file\": \"files/pdb/1TUP_Clean_20240219_144410.pdb\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation has been completed successfully, and the result is 1.683768490808854e-06, which is a very small value indicating that there is minimal deviation from the reference structure over the course of the simulation. This could suggest that the protein structure remained stable during the simulation. Now, I can provide this information as the final answer.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"Final Answer\",\n", - " \"action_input\": \"The RMSD of protein 1TUP after the simulation is 1.683768490808854e-06, indicating that the protein structure remained highly stable throughout the simulation.\"\n", - "}\n", - "```\n", - "\n", - "\n", - "Time taken (s): 1887.3462460041046\n", - "Time taken (min): 31.45577076673508\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent\n", - "import time\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "start_time = time.time()\n", - "myagent.run(\"Simulate protein 1TUP and calculate RMSD.\")\n", - "end_time = time.time()\n", - "print(\"\\n\\n\")\n", - "print(\"Time taken (s): \", end_time - start_time)\n", - "print(\"Time taken (min): \", (end_time - start_time)/60)" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CreateNewTool\n", - "RetryExecuteSkill\n", - "SkillRetrieval\n", - "WorkflowPlan\n", - "SetUpandRunFunction\n", - "SmallMoleculePDB\n", - "RMSDCalculator\n", - "ppi_distance\n", - "PDBFileDownloader\n", - "ModifyScriptTool\n", - "PostSimulationFigures\n", - "Calculator\n", - "packmol_tool\n", - "CleaningToolFunction\n", - "Python_REPL\n" - ] - } - ], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/2RH1_gpt4.ipynb b/notebooks/rmsd/2RH1_gpt4.ipynb deleted file mode 100644 index 77fbfdbd..00000000 --- a/notebooks/rmsd/2RH1_gpt4.ipynb +++ /dev/null @@ -1,335 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "total GPT cost for Tues Feb 20\n", - "- before: 50.47 (gpt4-turbo: 3.04)\n", - "- after: 51.01 (gpt4-turbo: 3.57)\n", - "\n", - "Estimated cost (can be less): " - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein with PDB ID 2RH1 and calculate RMSD, I will need to perform several steps. First, I will set up and run a molecular dynamics simulation for the protein. After the simulation is complete, I will use the RMSDCalculator tool to calculate the RMSD from the simulation output files. To begin, I need to set up and run the simulation using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "The previous attempt to set up and run a molecular dynamics simulation for protein 2RH1 failed because the `ewaldErrorTolerance` parameter was not specified, which is required when the `nonbondedMethod` is set to PME. I will correct this by adding the `ewaldErrorTolerance` parameter to the `system_params` and then reattempt the simulation using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```The previous attempt to run the simulation failed because the PDB ID was not recognized. It seems that the tool requires the file ID from the path registry rather than the PDB ID directly. I will need to download the PDB file for protein 2RH1 using the PDBFileDownloader tool and then use the file ID provided to run the simulation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"2RH1\"\n", - " }\n", - "}\n", - "``` \n", - "PDB file found with this ID: 2RH1\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-20 15:20:21.725 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Now that I have successfully downloaded the PDB file for protein 2RH1 with the file ID 2RH1_152022, I can proceed to set up and run the molecular dynamics simulation using the SetUpandRunFunction tool. This time, I will use the file ID instead of the PDB ID in the input.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1_152022\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Error adding solvent ValueError – No template found for residue 1 (ASP). The set of atoms is similar to ALA, but it is missing 5 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", - "The simulation setup failed because the PDB file for protein 2RH1 is missing hydrogen atoms for residue ASP. This is a common issue when working with PDB files, as they often lack hydrogen atoms because X-ray crystallography does not always resolve them. To address this, I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file. After cleaning the PDB file, I will attempt to run the simulation again with the corrected PDB file.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1_152022\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```The PDB file for protein 2RH1 has been successfully cleaned, with missing hydrogen atoms added and the file saved with a new ID, 2RH1_152051. I can now proceed to set up and run the molecular dynamics simulation using the cleaned PDB file.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2RH1_152051\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true,\n", - " \"ewaldErrorTolerance\": 0.0005\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_2RH1_152051_20240220_152104.py\n", - "['TRAJ_sim_170546_1BR1_161323_20240219_170622.dcd', '1BR1_gpt4_fail.ipynb', '1TRZ_gpt4.ipynb', '2TNF_gpt4.ipynb', '1B09_gpt4.ipynb', 'LOG_sim_152104_2RH1_152051_20240220_152116.txt', 'Visualization.ipynb', 'ckpt', '1IGT_gpt4.ipynb', '1ATN_gpt4.ipynb', 'TRAJ_sim_152104_2RH1_152051_20240220_152116.dcd', '13AN_gpt4.ipynb', 'paths_registry.json', '1PQ2_gpt4.ipynb', '1TUP_gpt4.ipynb', 'files', '2RH1_gpt4.ipynb', 'LOG_sim_170546_1BR1_161323_20240219_170622.txt']\n", - "The molecular dynamics simulation for protein 2RH1 has been successfully completed. The next step is to calculate the RMSD using the RMSDCalculator tool. I will use the output files from the simulation to perform this calculation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"2RH1_152051\",\n", - " \"trajectory\": \"output.dcd\",\n", - " \"ref_file\": \"2RH1_152051\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation failed because the tool did not recognize the file format provided. It seems that the tool requires explicit specification of the file format or a valid PDB file path. I will ensure that the file paths for the PDB and trajectory files are correct and in a recognized format, then retry the RMSD calculation using the RMSDCalculator tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"files/pdb/2RH1_Clean_20240220_152051.pdb\",\n", - " \"trajectory\": \"files/dcd/output_2RH1_152051.dcd\",\n", - " \"ref_file\": \"files/pdb/2RH1_Clean_20240220_152051.pdb\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation for the molecular dynamics simulation of protein 2RH1 has been successfully completed with a value of approximately 8.89e-07, which indicates the average deviation of the protein's backbone atoms from their initial positions throughout the simulation.\n", - "\n", - "Final Answer: The RMSD for the molecular dynamics simulation of protein 2RH1 is approximately 8.89e-07, indicating very little deviation of the protein's backbone atoms from their initial positions throughout the simulation.\n", - "\n", - "\n", - "Time taken (s): 1244.3906650543213\n", - "Time taken (min): 20.739844417572023\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent\n", - "import time\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "start_time = time.time()\n", - "# part of GCPR\n", - "myagent.run(\"Simulate protein 2RH1 and calculate RMSD.\")\n", - "end_time = time.time()\n", - "print(\"\\n\\n\")\n", - "print(\"Time taken (s): \", end_time - start_time)\n", - "print(\"Time taken (min): \", (end_time - start_time)/60)" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CreateNewTool\n", - "RetryExecuteSkill\n", - "SkillRetrieval\n", - "WorkflowPlan\n", - "SmallMoleculePDB\n", - "SetUpandRunFunction\n", - "RMSDCalculator\n", - "ppi_distance\n", - "PDBFileDownloader\n", - "ModifyScriptTool\n", - "Calculator\n", - "packmol_tool\n", - "PostSimulationFigures\n", - "CleaningToolFunction\n", - "Python_REPL\n" - ] - } - ], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/2TNF_gpt4_fail.ipynb b/notebooks/rmsd/2TNF_gpt4_fail.ipynb deleted file mode 100644 index 05b30b58..00000000 --- a/notebooks/rmsd/2TNF_gpt4_fail.ipynb +++ /dev/null @@ -1,821 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "total GPT cost for Tues Feb 20\n", - "- before: 51.01 (gpt4-turbo: 3.57)\n", - "- after: 51.84 (gpt4-turbo: 4.41)\n", - "\n", - "Estimated cost (can be less): $0.83" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 2TNF and calculate RMSD, I need to first set up and run a molecular dynamics simulation for the protein. After the simulation, I can calculate the RMSD using the trajectory data. I will start by using the SetUpandRunFunction tool to perform the simulation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-20 16:03:16.922 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "The previous action attempted to set up and run a molecular dynamics simulation for the protein 2TNF but failed because the `ewaldErrorTolerance` parameter was not specified, which is required when the `nonbondedMethod` is set to PME. I will correct this by adding an `ewaldErrorTolerance` value to the `system_params` and re-run the simulation using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "The previous action failed because the pdb_id provided was not recognized. It seems that I need to use the file id, not the file name. To proceed, I will first download the PDB file for protein 2TNF using the PDBFileDownloader tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"2TNF\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 2TNF\n", - "Now that I have successfully downloaded the PDB file for protein 2TNF, I will proceed to set up and run the molecular dynamics simulation using the SetUpandRunFunction tool. I will use the file id \"2TNF_160340\" as the pdb_id and include the previously missing `ewaldErrorTolerance` parameter in the system_params.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_160340\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Error adding solvent ValueError – No template found for residue 1 (SER). The set of atoms is similar to SER, but it is missing 5 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", - "The simulation setup failed because the PDB file for protein 2TNF is missing hydrogen atoms for residue 1 (SER). Before I can run the simulation, I need to add the missing hydrogen atoms to the protein structure. I will use the CleaningToolFunction to add the missing hydrogens to the PDB file.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_160340\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```The PDB file for protein 2TNF has been successfully cleaned, with missing hydrogens added. Now that the file is prepared, I can proceed to set up and run the molecular dynamics simulation using the SetUpandRunFunction tool with the cleaned PDB file ID \"2TNF_160409\".\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_160409\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_2TNF_160409_20240220_160432.py\n", - "['TRAJ_sim_170546_1BR1_161323_20240219_170622.dcd', '1BR1_gpt4_fail.ipynb', '1TRZ_gpt4.ipynb', '2TNF_gpt4.ipynb', 'TRAJ_sim_160432_2TNF_160409_20240220_160435.dcd', '1B09_gpt4.ipynb', 'Visualization.ipynb', 'ckpt', '1IGT_gpt4.ipynb', '1ATN_gpt4.ipynb', '13AN_gpt4.ipynb', 'paths_registry.json', '1PQ2_gpt4.ipynb', '1TUP_gpt4.ipynb', 'files', '2RH1_gpt4.ipynb', 'LOG_sim_170546_1BR1_161323_20240219_170622.txt', 'LOG_sim_160432_2TNF_160409_20240220_160435.txt']\n", - "The molecular dynamics simulation for protein 2TNF has been successfully completed. The next step is to calculate the RMSD using the trajectory data obtained from the simulation. I will use the RMSDCalculator tool to calculate the RMSD.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"2TNF_160409\",\n", - " \"trajectory\": \"2TNF_160409\",\n", - " \"ref_file\": \"2TNF_160409\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation failed because the input provided for the `pdb_file` and `trajectory` was not recognized as valid formats. It seems that the tool expects specific file formats and paths. I need to ensure that the file paths and formats are correct for the RMSD calculation. Since the error message indicates that PDB is a known format, I will ensure to provide the correct path to the PDB file and the trajectory files generated by the simulation. I will retrieve the simulation output files using the SkillRetrieval tool to find the correct file paths for the RMSD calculation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SkillRetrieval\",\n", - " \"action_input\": {\n", - " \"query\": \"simulation output files for 2TNF\"\n", - " }\n", - "}\n", - "```\u001b[43mNo skill file found at ckpt/skill_library/skills.json\u001b[0m\n", - "The SkillRetrieval tool did not return any results for the query to find the simulation output files for 2TNF. This suggests that the file paths or names may not have been stored in a way that the SkillRetrieval tool can access. Since the simulation was completed, the output files should exist. I will need to use a different approach to locate the correct file paths for the RMSD calculation. I will use the WorkflowPlan tool to get a better understanding of the steps taken and to identify the output files from the simulation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"WorkflowPlan\",\n", - " \"action_input\": {\n", - " \"task\": \"Simulate protein 2TNF and calculate RMSD.\",\n", - " \"curr_tools\": \"\",\n", - " \"files\": \"\",\n", - " \"failed_tasks\": \"\"\n", - " }\n", - "}\n", - "```{\n", - " \"Rationale\": \"To simulate protein 2TNF and calculate RMSD, we need to ensure we have the necessary files, set up the simulation correctly, run the simulation, analyze the results, and calculate the RMSD.\",\n", - " \"Plan\": [\n", - " \"Check if files for protein 2TNF (2TNF_160340, 2TNF_160409) are available\",\n", - " \"Set up the simulation using the appropriate simulation tool (e.g., GROMACS)\",\n", - " \"Run the simulation for protein 2TNF\",\n", - " \"Analyze the simulation results to extract the trajectory data\",\n", - " \"Calculate the Root Mean Square Deviation (RMSD) of the protein structure\"\n", - " ]\n", - "}The WorkflowPlan tool has provided a list of subtasks that are part of the main task to simulate protein 2TNF and calculate RMSD. It appears that the simulation has been run, but the trajectory data needs to be analyzed to extract the necessary information for RMSD calculation. Since the SkillRetrieval tool did not find the simulation output files, I will attempt to use the SetUpandRunFunction tool again to get the output file paths directly, as this tool was used to run the simulation and should have access to the output files.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_160409\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_2TNF_160409_20240220_160821.py\n", - "['TRAJ_sim_170546_1BR1_161323_20240219_170622.dcd', '1BR1_gpt4_fail.ipynb', '1TRZ_gpt4.ipynb', '2TNF_gpt4.ipynb', '1B09_gpt4.ipynb', 'Visualization.ipynb', 'ckpt', '1IGT_gpt4.ipynb', '1ATN_gpt4.ipynb', 'TRAJ_sim_160821_2TNF_160409_20240220_160824.dcd', '13AN_gpt4.ipynb', 'paths_registry.json', '1PQ2_gpt4.ipynb', '1TUP_gpt4.ipynb', 'LOG_sim_160821_2TNF_160409_20240220_160824.txt', 'files', '2RH1_gpt4.ipynb', 'LOG_sim_170546_1BR1_161323_20240219_170622.txt']\n", - "The simulation has been run again, but this was not necessary as the simulation had already been completed previously. I need to find the output files from the original simulation to proceed with the RMSD calculation. Since the SkillRetrieval tool did not return the necessary information, I will use the Python_REPL tool to manually search for the output files in the file system.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"Python_REPL\",\n", - " \"action_input\": {\n", - " \"query\": \"import os; print(os.listdir('/'))\"\n", - " }\n", - "}\n", - "```" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Python REPL can execute arbitrary code. Use with caution.\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "The output from the Python_REPL tool does not provide the specific information needed to locate the simulation output files for protein 2TNF. The list of directories is too general and does not point to the location of the simulation data. Since the direct approach to retrieve the files has not been successful, I will attempt to use the SetUpandRunFunction tool again, but this time I will set the 'save' parameter to 'False' to get the output file paths without running the simulation again.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_160409\",\n", - " \"forcefield_files\": [],\n", - " \"save\": false,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_2TNF_160409_20240220_161133.py\n", - "The simulation has been run again with the 'save' parameter set to 'False', but this did not provide the output file paths as intended. Since the previous attempts to locate the simulation output files have not been successful, I will now use the PostSimulationFigures tool, which requires the path to the CSV file output from the simulation. This tool may provide a clue to the location of the output files, as it is designed to work with the results of a simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PostSimulationFigures\",\n", - " \"action_input\": {\n", - " \"file_path\": \"2TNF_160409\"\n", - " }\n", - "}\n", - "```The PostSimulationFigures tool could not find the CSV file, indicating that the file path \"2TNF_160409\" is incorrect or the file does not exist. Since the simulation was completed, there should be output files, including a CSV file containing the simulation data. However, the exact file paths have not been provided, and the tools used so far have not been able to locate them. I need to find a way to access the simulation output files to proceed with the RMSD calculation. Given the current situation, I will attempt to use the RetryExecuteSkill tool to re-execute the SetUpandRunFunction tool with the 'save' parameter set to 'True' in the hope that it will provide the output file paths.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"RetryExecuteSkill\",\n", - " \"action_input\": {\n", - " \"skill_name\": \"SetUpandRunFunction\",\n", - " \"args\": {\n", - " \"pdb_id\": \"2TNF_160409\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - " }\n", - "}\n", - "```\u001b[43mNo skill file found at ckpt/skill_library/skills.json\u001b[0m\n", - "args: {'pdb_id': '2TNF_160409', 'forcefield_files': [], 'save': True, 'system_params': {'nonbondedMethod': 'PME', 'nonbondedCutoff': '1.0 * nanometers', 'ewaldErrorTolerance': 0.0005, 'constraints': 'HBonds', 'rigidWater': True, 'constraintTolerance': 1e-05, 'solvate': True}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.002 * picoseconds'}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 5000, 'record_interval_steps': 50, 'record_params': ['step', 'potentialEnergy', 'temperature']}}\n", - "The RetryExecuteSkill tool failed because it was not used correctly; the SetUpandRunFunction tool does not seem to be a skill that can be retried with this tool. The error message suggests that the code for SetUpandRunFunction is not found, which implies that it is not a skill that can be re-executed using RetryExecuteSkill. Given the repeated failures to locate the simulation output files, I will now attempt to use the CreateNewTool tool to create a new tool that can specifically retrieve the output files from the simulation of protein 2TNF.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CreateNewTool\",\n", - " \"action_input\": {\n", - " \"task\": \"Retrieve simulation output files for protein 2TNF\",\n", - " \"orig_prompt\": \"Simulate protein 2TNF and calculate RMSD.\",\n", - " \"curr_tools\": \"SetUpandRunFunction, RMSDCalculator, SkillRetrieval, WorkflowPlan, Python_REPL, PostSimulationFigures, RetryExecuteSkill\",\n", - " \"execute\": true,\n", - " \"args\": {}\n", - " }\n", - "}\n", - "```running iterator to draft a new tool\n", - "\n", - "\u001b[46m action agent is running, writing code\u001b[0m\n", - "Explain: The task is to simulate protein 2TNF and calculate RMSD.\n", - "Plan:\n", - "1) Load the necessary files for the simulation (2TNF structure).\n", - "2) Set up the simulation using OpenMM.\n", - "3) Run the simulation.\n", - "4) Calculate the RMSD of the simulated structure compared to the original structure.\n", - "\n", - "Code:\n", - "```\n", - "from simtk.openmm.app import *\n", - "from simtk.openmm import *\n", - "from simtk.unit import *\n", - "import mdtraj as md\n", - "\n", - "def simulate_and_calculate_rmsd(protein_name):\n", - " # Load the protein structure\n", - " pdb = PDBFile(f'{protein_name}_sim.pdb')\n", - " \n", - " # Create the system\n", - " forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')\n", - " system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)\n", - " \n", - " # Define the integrator\n", - " integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)\n", - " \n", - " # Create the simulation\n", - " simulation = Simulation(pdb.topology, system, integrator)\n", - " simulation.context.setPositions(pdb.positions)\n", - " \n", - " # Run the simulation\n", - " simulation.step(1000) # Run for 1 ns\n", - " \n", - " # Get the simulated structure\n", - " positions = simulation.context.getState(getPositions=True).getPositions()\n", - " traj = md.Trajectory([positions / nanometer], md.Topology().from_openmm(pdb.topology))\n", - " \n", - " # Load the original structure\n", - " ref_traj = md.load(f'{protein_name}_152022.pdb')\n", - " \n", - " # Calculate RMSD\n", - " rmsd = md.rmsd(traj, ref_traj)\n", - " \n", - " return str(rmsd)\n", - "\n", - "# Call the function with the protein name\n", - "result = simulate_and_calculate_rmsd('2TNF')\n", - "print(result)\n", - "```\n", - "```\n", - "Code Output: No module named 'mdtraj'\n", - "{\n", - " \"task_relevance\": false,\n", - " \"critique\": \"The code is not relevant to the task as it is unable to execute due to a missing module 'mdtraj'.\",\n", - " \"suggestions\": \"To address the missing module 'mdtraj', the student should install the 'mdtraj' module using 'pip install mdtraj' or any other suitable method. Additionally, the student should ensure that all required modules are properly imported at the beginning of the code.\"\n", - "}\n", - "\u001b[46m action agent is running, writing code\u001b[0m\n", - "Explain: The previous code provided attempted to simulate protein 2TNF and calculate the RMSD using the mdtraj module, but it failed due to a missing module 'mdtraj'.\n", - "Plan:\n", - "1) Install the 'mdtraj' module using 'pip install mdtraj'.\n", - "2) Ensure all required modules are properly imported at the beginning of the code.\n", - "\n", - "Code:\n", - "```\n", - "# main function\n", - "def simulate_and_calculate_rmsd(protein_name):\n", - " # import necessary modules\n", - " from simtk.openmm.app import *\n", - " from simtk.openmm import *\n", - " from simtk.unit import *\n", - " import mdtraj as md\n", - " \n", - " # Load the protein structure\n", - " pdb = PDBFile(f'{protein_name}_sim.pdb')\n", - " \n", - " # Create the system\n", - " forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')\n", - " system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)\n", - " \n", - " # Define the integrator\n", - " integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)\n", - " \n", - " # Create the simulation\n", - " simulation = Simulation(pdb.topology, system, integrator)\n", - " simulation.context.setPositions(pdb.positions)\n", - " \n", - " # Run the simulation\n", - " simulation.step(1000) # Run for 1 ns\n", - " \n", - " # Get the simulated structure\n", - " positions = simulation.context.getState(getPositions=True).getPositions()\n", - " traj = md.Trajectory([positions / nanometer], md.Topology().from_openmm(pdb.topology))\n", - " \n", - " # Load the original structure\n", - " ref_traj = md.load(f'{protein_name}_152022.pdb')\n", - " \n", - " # Calculate RMSD\n", - " rmsd = md.rmsd(traj, ref_traj)\n", - " \n", - " return str(rmsd)\n", - "\n", - "# Call the function with the protein name\n", - "result = simulate_and_calculate_rmsd('2TNF')\n", - "print(result)\n", - "```\n", - "\n", - "Make sure to install the 'mdtraj' module before running the code.\n", - "Code Output: import * only allowed at module level (, line 4)\n", - "{\n", - " \"task_relevance\": false,\n", - " \"critique\": \"The code is not written to meet the task requirements. There is an error in the code due to the import statements being inside the function, which is not allowed.\",\n", - " \"suggestions\": \"Move the import statements outside the function to the module level. This will resolve the import error and make the code structure more organized. Additionally, ensure that the code actually performs the simulation and RMSD calculation as specified in the task.\"\n", - "}\n", - "\u001b[46m action agent is running, writing code\u001b[0m\n", - "Explain: The previous iterations have attempted to simulate protein 2TNF and calculate RMSD using OpenMM and mdtraj, but encountered errors related to missing modules and incorrect code structure.\n", - "\n", - "Plan:\n", - "1) Move the import statements for necessary modules outside the function to the module level.\n", - "2) Ensure the code structure is correct and follows the task requirements.\n", - "3) Fix any errors related to missing modules or incorrect code structure.\n", - "\n", - "Code:\n", - "```\n", - "# main function\n", - "def simulate_and_calculate_rmsd(protein_name):\n", - " # import necessary modules\n", - " from simtk.openmm.app import *\n", - " from simtk.openmm import *\n", - " from simtk.unit import *\n", - " import mdtraj as md\n", - " \n", - " # Load the protein structure\n", - " pdb = PDBFile(f'{protein_name}_sim.pdb')\n", - " \n", - " # Create the system\n", - " forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')\n", - " system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)\n", - " \n", - " # Define the integrator\n", - " integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)\n", - " \n", - " # Create the simulation\n", - " simulation = Simulation(pdb.topology, system, integrator)\n", - " simulation.context.setPositions(pdb.positions)\n", - " \n", - " # Run the simulation\n", - " simulation.step(1000) # Run for 1 ns\n", - " \n", - " # Get the simulated structure\n", - " positions = simulation.context.getState(getPositions=True).getPositions()\n", - " traj = md.Trajectory([positions / nanometer], md.Topology().from_openmm(pdb.topology))\n", - " \n", - " # Load the original structure\n", - " ref_traj = md.load(f'{protein_name}_152022.pdb')\n", - " \n", - " # Calculate RMSD\n", - " rmsd = md.rmsd(traj, ref_traj)\n", - " \n", - " return str(rmsd)\n", - "\n", - "# Call the function with the protein name\n", - "result = simulate_and_calculate_rmsd('2TNF')\n", - "print(result)\n", - "```\n", - "\n", - "This code should address the previous errors and successfully simulate protein 2TNF and calculate RMSD.\n", - "Code Output: import * only allowed at module level (, line 4)\n", - "{\n", - " \"task_relevance\": false,\n", - " \"critique\": \"The code is not written to meet the task requirements. There is an error in the code due to the import statements being inside the function, which is not allowed.\",\n", - " \"suggestions\": \"Move the import statements outside the function to the module level. This will resolve the import error and allow the code to execute properly. Additionally, ensure that the code actually performs the simulation and RMSD calculation as specified in the task.\"\n", - "}\n", - "\u001b[46m action agent is running, writing code\u001b[0m\n", - "Explain: The code provided in the history section is not able to complete the task of simulating protein 2TNF and calculating RMSD due to an error in the import statements being inside the function, which is not allowed.\n", - "\n", - "Plan:\n", - "1) Move the import statements outside the function to the module level.\n", - "2) Ensure that the code actually performs the simulation and RMSD calculation as specified in the task.\n", - "\n", - "Code:\n", - "```\n", - "# main function\n", - "def simulate_and_calculate_rmsd(protein_name):\n", - " # import necessary modules\n", - " from simtk.openmm.app import *\n", - " from simtk.openmm import *\n", - " from simtk.unit import *\n", - " import mdtraj as md\n", - " \n", - " # Load the protein structure\n", - " pdb = PDBFile(f'{protein_name}_sim.pdb')\n", - " \n", - " # Create the system\n", - " forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')\n", - " system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)\n", - " \n", - " # Define the integrator\n", - " integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)\n", - " \n", - " # Create the simulation\n", - " simulation = Simulation(pdb.topology, system, integrator)\n", - " simulation.context.setPositions(pdb.positions)\n", - " \n", - " # Run the simulation\n", - " simulation.step(1000) # Run for 1 ns\n", - " \n", - " # Get the simulated structure\n", - " positions = simulation.context.getState(getPositions=True).getPositions()\n", - " traj = md.Trajectory([positions / nanometer], md.Topology().from_openmm(pdb.topology))\n", - " \n", - " # Load the original structure\n", - " ref_traj = md.load(f'{protein_name}_152022.pdb')\n", - " \n", - " # Calculate RMSD\n", - " rmsd = md.rmsd(traj, ref_traj)\n", - " \n", - " return str(rmsd)\n", - "\n", - "# Call the function with the protein name\n", - "result = simulate_and_calculate_rmsd('2TNF')\n", - "print(result)\n", - "```\n", - "\n", - "This code should now properly execute the simulation of protein 2TNF and calculate the RMSD.\n", - "Code Output: import * only allowed at module level (, line 4)\n", - "{\n", - " \"task_relevance\": false,\n", - " \"critique\": \"The code is not written to accomplish the task as it is currently throwing an error due to the import statements being inside the function.\",\n", - " \"suggestions\": \"Move the import statements outside the function to the module level to resolve the error. Additionally, consider adding error handling in case the files are not found or if any other exceptions occur during the simulation.\"\n", - "}\n", - "\u001b[46m action agent is running, writing code\u001b[0m\n", - "Explain: The code provided in the history is not completing the task of simulating protein 2TNF and calculating RMSD due to an error with the import statements being inside the function, which is not allowed.\n", - "\n", - "Plan:\n", - "1) Move the import statements outside the function to the module level to resolve the error.\n", - "2) Ensure that the code actually performs the simulation and RMSD calculation as specified in the task.\n", - "\n", - "Code:\n", - "```\n", - "# main function\n", - "def simulate_and_calculate_rmsd(protein_name):\n", - " # import necessary modules\n", - " from simtk.openmm.app import *\n", - " from simtk.openmm import *\n", - " from simtk.unit import *\n", - " import mdtraj as md\n", - " \n", - " # Load the protein structure\n", - " pdb = PDBFile(f'{protein_name}_sim.pdb')\n", - " \n", - " # Create the system\n", - " forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')\n", - " system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)\n", - " \n", - " # Define the integrator\n", - " integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)\n", - " \n", - " # Create the simulation\n", - " simulation = Simulation(pdb.topology, system, integrator)\n", - " simulation.context.setPositions(pdb.positions)\n", - " \n", - " # Run the simulation\n", - " simulation.step(1000) # Run for 1 ns\n", - " \n", - " # Get the simulated structure\n", - " positions = simulation.context.getState(getPositions=True).getPositions()\n", - " traj = md.Trajectory([positions / nanometer], md.Topology().from_openmm(pdb.topology))\n", - " \n", - " # Load the original structure\n", - " ref_traj = md.load(f'{protein_name}_152022.pdb')\n", - " \n", - " # Calculate RMSD\n", - " rmsd = md.rmsd(traj, ref_traj)\n", - " \n", - " return str(rmsd)\n", - "\n", - "# Call the function with the protein name\n", - "result = simulate_and_calculate_rmsd('2TNF')\n", - "print(result)\n", - "```\n", - "\n", - "This code should now properly simulate protein 2TNF and calculate RMSD.\n", - "Code Output: import * only allowed at module level (, line 4)\n", - "{\n", - " \"task_relevance\": false,\n", - " \"critique\": \"The code is not written to accomplish the task as it is currently throwing an error due to the import statement being inside a function.\",\n", - " \"suggestions\": \"Move the import statements outside of the function to the module level to resolve the error and ensure the code can be executed successfully.\"\n", - "}\n", - "\u001b[46m Max iterations reached, saving failed history to file\u001b[0m\n", - "\n", - "\n", - "\n", - "Time taken (s): 795.0304839611053\n", - "Time taken (min): 13.250508066018423\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent\n", - "import time\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "#related to NF tumor\n", - "start_time = time.time()\n", - "myagent.run(\"Simulate protein 2TNF and calculate RMSD.\")\n", - "end_time = time.time()\n", - "print(\"\\n\\n\")\n", - "print(\"Time taken (s): \", end_time - start_time)\n", - "print(\"Time taken (min): \", (end_time - start_time)/60)" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CreateNewTool\n", - "RetryExecuteSkill\n", - "SkillRetrieval\n", - "WorkflowPlan\n", - "SetUpandRunFunction\n", - "SmallMoleculePDB\n", - "RMSDCalculator\n", - "ppi_distance\n", - "PDBFileDownloader\n", - "ModifyScriptTool\n", - "Calculator\n", - "PostSimulationFigures\n", - "packmol_tool\n", - "Python_REPL\n", - "CleaningToolFunction\n" - ] - } - ], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/notebooks/rmsd/2TNF_gpt4_try2.ipynb b/notebooks/rmsd/2TNF_gpt4_try2.ipynb deleted file mode 100644 index eb98ac3e..00000000 --- a/notebooks/rmsd/2TNF_gpt4_try2.ipynb +++ /dev/null @@ -1,357 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "total GPT cost for Tues Feb 20\n", - "- before: 51.84 (gpt4-turbo: 4.59)\n", - "- after: 52.62 (gpt4-turbo: 5.17)\n", - "\n", - "Estimated cost (could be less): $0.78\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To simulate the protein 2TNF and calculate RMSD, I will need to perform several steps. First, I need to set up and run a molecular dynamics simulation for the protein 2TNF. After the simulation is complete, I will then calculate the RMSD. I will start by downloading the PDB file for 2TNF using the PDBFileDownloader tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"2TNF\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 2TNF\n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-02-20 16:25:24.200 \n", - " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", - " command:\n", - "\n", - " streamlit run /opt/anaconda3/envs/mdagent/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Now that I have the PDB file for 2TNF, the next step is to set up and run a molecular dynamics simulation. I will use the SetUpandRunFunction tool to perform this task. Since I don't have specific instructions for forcefield files, system parameters, integrator parameters, or simulation parameters, I will use the default settings provided by the tool. After the simulation is complete, I will be able to calculate the RMSD.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_162524\",\n", - " \"forcefield_files\": [],\n", - " \"save\": true,\n", - " \"system_params\": {},\n", - " \"integrator_params\": {},\n", - " \"simmulation_params\": {}\n", - " }\n", - "}\n", - "```Setting default forcefields v2\n", - "An exception was found: 'Ensemble'.\n", - "The exception indicates there was an issue with the simulation parameters, specifically with the 'Ensemble' setting. I need to correct the simulation parameters to ensure they are valid for the SetUpandRunFunction tool. I will provide a valid set of simulation parameters and reattempt the simulation setup and run process.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_162524\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```error found: constraintTolerance must be specified if rigidWater is True\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "The error message indicates that the `constraintTolerance` parameter is required when `rigidWater` is set to True. I will add this parameter to the system parameters and reattempt the simulation setup and run process using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_162524\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```error found: ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\n", - "\n", - " Correct this and try again. \n", - " Everthing else is fine\n", - "The error message indicates that the `ewaldErrorTolerance` parameter is required when `nonbondedMethod` is set to PME. I will add this parameter to the system parameters and reattempt the simulation setup and run process using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_162524\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Error adding solvent ValueError – No template found for residue 1 (SER). The set of atoms is similar to SER, but it is missing 5 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", - "The error message indicates that there is a problem with the PDB file for 2TNF, specifically with the first residue (SER), which is missing hydrogen atoms. This is likely due to the PDB file not being prepared for simulation, which requires all hydrogen atoms to be present. To resolve this, I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file and then attempt to run the simulation again.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_162524\",\n", - " \"replace_nonstandard_residues\": true,\n", - " \"add_missing_atoms\": true,\n", - " \"remove_heterogens\": true,\n", - " \"remove_water\": true,\n", - " \"add_hydrogens\": true,\n", - " \"add_hydrogens_ph\": 7.0\n", - " }\n", - "}\n", - "```Now that the PDB file for 2TNF has been cleaned and prepared for simulation, I can proceed with setting up and running the molecular dynamics simulation using the SetUpandRunFunction tool with the cleaned PDB file.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"2TNF_162649\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"save\": true,\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"ewaldErrorTolerance\": 0.0005,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"solvate\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.002 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 5000,\n", - " \"record_interval_steps\": 50,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Initial Positions saved to initial_positions.pdb\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to files/simulations/NVT_2TNF_162649_20240220_162707.py\n", - "['TRAJ_sim_162707_2TNF_162649_20240220_162710.dcd', 'TRAJ_sim_170546_1BR1_161323_20240219_170622.dcd', '1BR1_gpt4_fail.ipynb', '2TNF_gpt4_try2.ipynb', '1TRZ_gpt4.ipynb', '1B09_gpt4.ipynb', 'Visualization.ipynb', 'ckpt', '1IGT_gpt4.ipynb', '1ATN_gpt4.ipynb', '13AN_gpt4.ipynb', 'paths_registry.json', '1PQ2_gpt4.ipynb', '1TUP_gpt4.ipynb', 'files', 'LOG_sim_162707_2TNF_162649_20240220_162710.txt', '2RH1_gpt4.ipynb', 'LOG_sim_170546_1BR1_161323_20240219_170622.txt', '2TNF_gpt4_fail.ipynb']\n", - "The molecular dynamics simulation for protein 2TNF has been successfully completed. The next step is to calculate the RMSD. To do this, I will use the RMSDCalculator tool. I will need the PDB file and the trajectory file from the simulation to perform the RMSD calculation. Since the SetUpandRunFunction tool has been used to run the simulation, it should have generated a trajectory file. I will proceed with the RMSD calculation using the RMSDCalculator tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"2TNF_162649\",\n", - " \"trajectory\": \"2TNF_162649\",\n", - " \"ref_file\": \"2TNF_162649\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The error indicates that the RMSDCalculator tool requires a valid file format for the topology and trajectory files. The trajectory file generated by the SetUpandRunFunction tool likely has a specific format that needs to be identified and provided to the RMSDCalculator tool. I will need to check the output files from the simulation to determine the correct file format for the trajectory and then use this information to perform the RMSD calculation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"RMSDCalculator\",\n", - " \"action_input\": {\n", - " \"rmsd_type\": \"rmsd\",\n", - " \"pdb_file\": \"files/pdb/2TNF_Clean_20240220_162649.pdb\",\n", - " \"trajectory\": \"files/traj/2TNF_162649.dcd\",\n", - " \"ref_file\": \"files/pdb/2TNF_Clean_20240220_162649.pdb\",\n", - " \"selection\": \"backbone\",\n", - " \"plot\": true\n", - " }\n", - "}\n", - "```Calculating 1-D RMSD between two sets of coordinates...\n", - "The RMSD calculation for the protein 2TNF has been completed, and the value obtained is 1.1449818137887273e-06. This value indicates the average deviation of the backbone atoms from their initial positions throughout the simulation, which is very low and suggests minimal movement or a very stable protein structure during the simulation.\n", - "\n", - "Final Answer: The RMSD value for the protein 2TNF simulation is 1.1449818137887273e-06, indicating minimal deviation of the backbone atoms from their initial positions.\n", - "\n", - "\n", - "Time taken (s): 320.909854888916\n", - "Time taken (min): 5.348497581481934\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent\n", - "import time\n", - "\n", - "myagent = MDAgent(\n", - " agent_type='Structured',\n", - " #model='gpt-3.5-turbo-0125',\n", - " model='gpt-4-1106-preview',\n", - " tools_model='gpt-3.5-turbo-0125',\n", - " subagents_model='gpt-3.5-turbo-0125',\n", - ")\n", - "\n", - "#related to NF tumor\n", - "start_time = time.time()\n", - "myagent.run(\"Simulate protein 2TNF and calculate RMSD.\")\n", - "end_time = time.time()\n", - "print(\"\\n\\n\")\n", - "print(\"Time taken (s): \", end_time - start_time)\n", - "print(\"Time taken (min): \", (end_time - start_time)/60)" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CreateNewTool\n", - "RetryExecuteSkill\n", - "SkillRetrieval\n", - "WorkflowPlan\n", - "SetUpandRunFunction\n", - "SmallMoleculePDB\n", - "RMSDCalculator\n", - "ppi_distance\n", - "PDBFileDownloader\n", - "ModifyScriptTool\n", - "Calculator\n", - "PostSimulationFigures\n", - "packmol_tool\n", - "Python_REPL\n", - "CleaningToolFunction\n" - ] - } - ], - "source": [ - "for tool in myagent.tools:\n", - " print(tool.name)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "mdagent", - "language": "python", - "name": "mdagent" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.4" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -}