From 267ac885a97e3a71346b437b61c4913f10a5166e Mon Sep 17 00:00:00 2001 From: qcampbel Date: Wed, 3 Jan 2024 09:21:34 -0500 Subject: [PATCH 1/6] partly combine CreateNewTool and ExecuteSkill --- mdagent/subagents/agents/skill.py | 6 +-- mdagent/subagents/subagent_fxns.py | 5 +-- mdagent/tools/maketools.py | 67 +++++++++++++++++++----------- mdagent/tools/subagent_tools.py | 17 ++++---- 4 files changed, 54 insertions(+), 41 deletions(-) diff --git a/mdagent/subagents/agents/skill.py b/mdagent/subagents/agents/skill.py index 06f08c5d..8eb244db 100644 --- a/mdagent/subagents/agents/skill.py +++ b/mdagent/subagents/agents/skill.py @@ -149,7 +149,7 @@ def update_skill_library(self, function, code_script, description, arguments): ) self.vectordb.persist() - def execute_skill_function(self, tool_name, path_registry, **kwargs): + def execute_skill_function(self, tool_name, **kwargs): code = self.skills.get(tool_name, {}).get("code", None) if not code: raise ValueError( @@ -158,7 +158,7 @@ def execute_skill_function(self, tool_name, path_registry, **kwargs): ) # capture initial state initial_files = set(os.listdir(".")) - initial_registry = path_registry.list_path_names() + initial_registry = self.path_registry.list_path_names() try: self._check_arguments(tool_name, **kwargs) @@ -172,7 +172,7 @@ def execute_skill_function(self, tool_name, path_registry, **kwargs): # capture final state new_files = list(set(os.listdir(".")) - initial_files) new_registry = list( - set(path_registry.list_path_names()) - set(initial_registry) + set(self.path_registry.list_path_names()) - set(initial_registry) ) message = "Successfully executed code." if new_files: diff --git a/mdagent/subagents/subagent_fxns.py b/mdagent/subagents/subagent_fxns.py index a039bcbe..8b1c84ce 100644 --- a/mdagent/subagents/subagent_fxns.py +++ b/mdagent/subagents/subagent_fxns.py @@ -2,22 +2,19 @@ import os from typing import Optional -from mdagent.utils import PathRegistry - from .subagent_setup import SubAgentInitializer, SubAgentSettings class Iterator: def __init__( self, - path_registry: Optional[PathRegistry], subagent_settings: Optional[SubAgentSettings], all_tools_string: Optional[str] = None, current_tools: Optional[dict] = None, ): - self.path_registry = path_registry if subagent_settings is None: raise ValueError("Subagent settings cannot be None") # shouldn't happen + self.path_registry = subagent_settings.path_registry self.ckpt_dir = subagent_settings.ckpt_dir self.all_tools_string = all_tools_string self.current_tools = current_tools diff --git a/mdagent/tools/maketools.py b/mdagent/tools/maketools.py index c9f2891d..a2332c5b 100644 --- a/mdagent/tools/maketools.py +++ b/mdagent/tools/maketools.py @@ -11,7 +11,7 @@ from langchain_experimental.tools import PythonREPLTool from pydantic import BaseModel, Field -from mdagent.subagents import Iterator, SubAgentSettings +from mdagent.subagents import Iterator, SubAgentInitializer, SubAgentSettings from mdagent.utils import PathRegistry, _make_llm from .base_tools import ( @@ -30,7 +30,7 @@ SimulationOutputFigures, VisualizeProtein, ) -from .subagent_tools import ExecuteSkill, SkillRetrieval, WorkflowPlan +from .subagent_tools import RetryExecuteSkill, SkillRetrieval, WorkflowPlan def get_learned_tools(ckpt_dir="ckpt"): @@ -78,7 +78,6 @@ def make_all_tools( base_tools = [ CleaningToolFunction(path_registry=path_instance), CheckDirectoryFiles(), - # InstructionSummary(path_registry=path_instance), ListRegistryPaths(path_registry=path_instance), MapPath2Name(path_registry=path_instance), Name2PDBTool(path_registry=path_instance), @@ -98,7 +97,7 @@ def make_all_tools( if not skip_subagents: subagents_tools = [ CreateNewTool(subagent_settings=subagent_settings), - ExecuteSkill(subagent_settings=subagent_settings), + RetryExecuteSkill(subagent_settings=subagent_settings), SkillRetrieval(subagent_settings=subagent_settings), WorkflowPlan(subagent_settings=subagent_settings), ] @@ -136,7 +135,7 @@ def get_tools( PathRegistry.get_instance() retrieved_tools = [ CreateNewTool(subagent_settings=subagent_settings), - ExecuteSkill(subagent_settings=subagent_settings), + RetryExecuteSkill(subagent_settings=subagent_settings), SkillRetrieval(subagent_settings=subagent_settings), WorkflowPlan(subagent_settings=subagent_settings), ] @@ -149,13 +148,13 @@ def get_tools( llm, subagent_settings, skip_subagents=False, human=human ) - # create vector DB for all tools + # set vector DB for all tools vectordb = Chroma( collection_name="all_tools_vectordb", embedding_function=OpenAIEmbeddings(), persist_directory=f"{ckpt_dir}/all_tools_vectordb", ) - # vectordb.delete_collection() # to clear vectordb directory + # vectordb.delete_collection() #<--- to clear previous vectordb directory for i, tool in enumerate(all_tools): vectordb.add_texts( texts=[tool.description], @@ -186,15 +185,21 @@ class CreateNewToolInputSchema(BaseModel): description="""List of all tools you have access to. Such as this tool, 'ExecuteSkill', 'SkillRetrieval', and maybe `Name2PDBTool`, etc.""" ) + execute: Optional[bool] = Field( + description="Whether to execute the new tool or not. default: True" + ) + args: Optional[dict] = Field( + description="Input variables as a dictionary to pass to the skill" + ) -# move this here to avoid circular import error (since it gets a list of all tools) class CreateNewTool(BaseTool): name: str = "CreateNewTool" description: str = """ Only use if you don't have right tools for sure and need a different tool. - If succeeded, it will return the name of the tool. - You can then use the tool in subsequent steps. + If succeeded, it will return the name of the tool. Unless you set + 'execute' to False, it will also execute the tool and return the result. + Make sure to provide any necessary input arguments for the tool. """ args_schema: Type[BaseModel] = CreateNewToolInputSchema subagent_settings: Optional[SubAgentSettings] @@ -211,30 +216,44 @@ def get_all_tools_string(self): all_tools_string += f"{tool.name}: {tool.description}\n" return all_tools_string - def _run(self, task, orig_prompt, curr_tools): - # def _run(self, task, orig_prompt): + def _run(self, task, orig_prompt, curr_tools, execute=True, args=None): + # run iterator try: - # run iterator - path_registry = self.subagent_settings.path_registry - print("getting all tools info") all_tools_string = self.get_all_tools_string() - print("setting up iterator") newcode_iterator = Iterator( - path_registry, self.subagent_settings, all_tools_string=all_tools_string, current_tools=curr_tools, ) - print("running iterator") + print("running iterator to draft a new tool") tool_name = newcode_iterator.run(task, orig_prompt) - # tool_name = newcode_iterator.run(task, task) - if tool_name: - return f"""Tool created successfully: {tool_name} - You can now use the tool in subsequent steps.""" - else: + if not tool_name: return "The 'CreateNewTool' tool failed to build a new tool." except Exception as e: - return f"Something went wrong. {type(e).__name__}: {e}" + return f"Something went wrong while creating tool. {type(e).__name__}: {e}" + + # execute the new tool code + if execute: + try: + print("executing tool") + agent_initializer = SubAgentInitializer(self.subagent_settings) + skill = agent_initializer.create_skill_manager(resume=True) + if skill is None: + return "SubAgent for this tool not initialized" + if args is not None: + print("input args: ", args) + return skill.execute_skill_function(tool_name, **args) + else: + return skill.execute_skill_function(tool_name) + except TypeError as e: + return f"""{type(e).__name__}: {e}. Executing new tool failed. + Please check your inputs and make sure to use a dictionary.\n""" + except ValueError as e: + return f"{type(e).__name__}: {e}. Provide correct arguments for tool.\n" + except Exception as e: + return f"Something went wrong while executing. {type(e).__name__}:{e}\n" + else: + return f"A new tool is created: {tool_name}. You can use it in next prompt." async def _arun(self, query) -> str: """Use the tool asynchronously.""" diff --git a/mdagent/tools/subagent_tools.py b/mdagent/tools/subagent_tools.py index 0685635d..0c4133a7 100644 --- a/mdagent/tools/subagent_tools.py +++ b/mdagent/tools/subagent_tools.py @@ -15,11 +15,11 @@ class ExecuteSkillInputSchema(BaseModel): ) -class ExecuteSkill(BaseTool): - name = "ExecuteSkill" - description = """Executes the code for a new tool or skill that has - been recently made during the current iteration. Make sure to include - function name and inputs arguments. +class RetryExecuteSkill(BaseTool): + name = "RetryExecuteSkill" + description = """Only use this tool to execute a tool recently created + that previously failed to execute or hasn't been executed yet. + Make sure to include tool name and inputs arguments. """ subagent_settings: Optional[SubAgentSettings] args_schema: Optional[Type[BaseModel]] = ExecuteSkillInputSchema @@ -30,18 +30,15 @@ def __init__(self, subagent_settings: Optional[SubAgentSettings] = None): def _run(self, skill_name, args=None): try: - path_registry = self.subagent_settings.path_registry agent_initializer = SubAgentInitializer(self.subagent_settings) skill = agent_initializer.create_skill_manager(resume=True) if skill is None: return "SubAgent for this tool not initialized" if args is not None: print("args: ", args) - code_result = skill.execute_skill_function( - skill_name, path_registry, **args - ) + code_result = skill.execute_skill_function(skill_name, **args) else: - code_result = skill.execute_skill_function(skill_name, path_registry) + code_result = skill.execute_skill_function(skill_name) return code_result except TypeError as e: return f"""{type(e).__name__}: {e}. Please check your inputs From 1fdd4cf83a02cb0db573e099eaff45e6db41ac56 Mon Sep 17 00:00:00 2001 From: qcampbel Date: Wed, 3 Jan 2024 09:34:42 -0500 Subject: [PATCH 2/6] updated test_agent.py --- tests/test_agent.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/tests/test_agent.py b/tests/test_agent.py index 65130895..b24bc209 100644 --- a/tests/test_agent.py +++ b/tests/test_agent.py @@ -27,8 +27,8 @@ def action(path_registry): @pytest.fixture def iterator(path_registry): - settings = SubAgentSettings(path_registry=None) - return Iterator(path_registry=path_registry, subagent_settings=settings) + settings = SubAgentSettings(path_registry=path_registry) + return Iterator(subagent_settings=settings) def test_exec_code(action): @@ -153,15 +153,13 @@ def test_execute_skill_function(skill_manager): } with patch("os.listdir", return_value=["file1", "file2"]): skill_manager._check_arguments = MagicMock() - message = skill_manager.execute_skill_function( - "sample_tool", path_registry, arg1=5, arg2=3 - ) + message = skill_manager.execute_skill_function("sample_tool", arg1=5, arg2=3) assert "Successfully executed code." in message assert "Code Output: 8" in message skill_manager.skills = {} with pytest.raises(ValueError) as excinfo: - skill_manager.execute_skill_function("nonexistent_tool", path_registry) + skill_manager.execute_skill_function("nonexistent_tool") assert "Code for nonexistent_tool not found" in str(excinfo.value) From 0c9582ec71dd4821a2be901ccb5413af78739e00 Mon Sep 17 00:00:00 2001 From: qcampbel Date: Wed, 3 Jan 2024 09:56:56 -0500 Subject: [PATCH 3/6] test & clean up --- mdagent/tools/maketools.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdagent/tools/maketools.py b/mdagent/tools/maketools.py index a2332c5b..80d3ef11 100644 --- a/mdagent/tools/maketools.py +++ b/mdagent/tools/maketools.py @@ -235,7 +235,7 @@ def _run(self, task, orig_prompt, curr_tools, execute=True, args=None): # execute the new tool code if execute: try: - print("executing tool") + print("\nexecuting tool") agent_initializer = SubAgentInitializer(self.subagent_settings) skill = agent_initializer.create_skill_manager(resume=True) if skill is None: From add148ade35c2fbe9ff4ef2eaaabe7dff640a458 Mon Sep 17 00:00:00 2001 From: qcampbel Date: Thu, 4 Jan 2024 15:30:51 -0500 Subject: [PATCH 4/6] updated pydantic field for createnewtool --- mdagent/tools/maketools.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mdagent/tools/maketools.py b/mdagent/tools/maketools.py index 80d3ef11..0cfc5c52 100644 --- a/mdagent/tools/maketools.py +++ b/mdagent/tools/maketools.py @@ -186,7 +186,8 @@ class CreateNewToolInputSchema(BaseModel): this tool, 'ExecuteSkill', 'SkillRetrieval', and maybe `Name2PDBTool`, etc.""" ) execute: Optional[bool] = Field( - description="Whether to execute the new tool or not. default: True" + True, + description="Whether to execute the new tool or not.", ) args: Optional[dict] = Field( description="Input variables as a dictionary to pass to the skill" From 98ddeeaabfcb3e643c207314ec3a0ad26ffd216e Mon Sep 17 00:00:00 2001 From: qcampbel Date: Thu, 4 Jan 2024 15:38:38 -0500 Subject: [PATCH 5/6] updated createnewtool description & _run args --- mdagent/tools/maketools.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mdagent/tools/maketools.py b/mdagent/tools/maketools.py index 0cfc5c52..e7ae1cc6 100644 --- a/mdagent/tools/maketools.py +++ b/mdagent/tools/maketools.py @@ -201,6 +201,7 @@ class CreateNewTool(BaseTool): If succeeded, it will return the name of the tool. Unless you set 'execute' to False, it will also execute the tool and return the result. Make sure to provide any necessary input arguments for the tool. + If execution fails, move on to ReTryExecuteSkill. """ args_schema: Type[BaseModel] = CreateNewToolInputSchema subagent_settings: Optional[SubAgentSettings] @@ -217,7 +218,7 @@ def get_all_tools_string(self): all_tools_string += f"{tool.name}: {tool.description}\n" return all_tools_string - def _run(self, task, orig_prompt, curr_tools, execute=True, args=None): + def _run(self, task, orig_prompt, curr_tools, execute, args=None): # run iterator try: all_tools_string = self.get_all_tools_string() From de72ed4bdfb7a90f292eeb9d554cfc80c92f002d Mon Sep 17 00:00:00 2001 From: qcampbel Date: Wed, 10 Jan 2024 15:14:45 -0500 Subject: [PATCH 6/6] removed old notebook --- notebooks/testing_changes.ipynb | 1891 ------------------------------- 1 file changed, 1891 deletions(-) delete mode 100644 notebooks/testing_changes.ipynb diff --git a/notebooks/testing_changes.ipynb b/notebooks/testing_changes.ipynb deleted file mode 100644 index c945d47e..00000000 --- a/notebooks/testing_changes.ipynb +++ /dev/null @@ -1,1891 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [], - "source": [ - "import ast\n", - "import json\n", - "import os\n", - "from typing import Any, Dict, List, Optional\n", - "\n", - "import langchain\n", - "from langchain import LLMChain, PromptTemplate\n", - "from langchain.base_language import BaseLanguageModel\n", - "from langchain.tools import BaseTool\n", - "from openmm import (\n", - " AndersenThermostat,\n", - " BrownianIntegrator,\n", - " LangevinIntegrator,\n", - " LangevinMiddleIntegrator,\n", - " MonteCarloBarostat,\n", - " VerletIntegrator,\n", - " app,\n", - " Platform,\n", - " OpenMMException,\n", - ")\n", - "from openmm.app import (\n", - " PME,\n", - " CutoffPeriodic,\n", - " DCDReporter,\n", - " ForceField,\n", - " Modeller,\n", - " NoCutoff,\n", - " PDBFile,\n", - " PDBReporter,\n", - " PDBxFile,\n", - " Simulation,\n", - " StateDataReporter,\n", - ")\n", - "from openmm.unit import bar, femtoseconds, kelvin, nanometers, picosecond, picoseconds\n", - "from pydantic import BaseModel, Field, root_validator\n", - "\n", - "\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "True" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "from dotenv import load_dotenv\n", - "import os\n", - "load_dotenv()\n" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/jorgemedina/miniforge3/envs/MDAGENT/lib/python3.11/site-packages/MDAnalysis/topology/TPRParser.py:161: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13\n", - " import xdrlib\n" - ] - } - ], - "source": [ - "from mdagent import MDAgent" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "mrkl = MDAgent(type=\"mrkl\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "mrkl.run(\"Estimate the SASA of fibronectin. Try using mdtraj to load the trajectory and calculate the SASA.\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "print('Thought: Thought: To calculate the SASA (Solvent Accessible Surface Area) of fibronectin, we first need to have the trajectory file of fibronectin. We can use the PDBFileDownloader tool to download the PDB file of fibronectin. After that, we can use the Python_REPL tool to load the trajectory and calculate the SASA using mdtraj.\\n\\nAction:\\n```\\n{\\n \"action\": \"PDBFileDownloader\",\\n \"action_input\": {\\n \"query\": \"fibronectin\"\\n }\\n}\\n```\\nObservation: Name2PDB tool successfully downloaded the PDB file: 1X5Y.pdb\\nThought: Now that we have the PDB file of fibronectin, we can use the Python_REPL tool to load the trajectory and calculate the SASA using mdtraj. \\n\\nAction:\\n```\\n{\\n \"action\": \"Python_REPL\",\\n \"action_input\": {\\n \"query\": \"import mdtraj as md\\\\ntraj = md.load(\\'1X5Y.pdb\\')\\\\nsasa = md.shrake_rupley(traj)\\\\nprint(sasa)\"\\n }\\n}\\n```\\n\\nObservation: [[0.29048446 0.01886919 0.03899633 ... 0.16989732 0.15396945 0.24068788]\\n [0.2965111 0.02140882 0.04156128 ... 0.02492703 0.17091843 0.00640715]\\n [0.3398059 0.03650737 0.02017942 ... 0.14691246 0.2408391 0.15574488]\\n ...\\n [0.3181646 0.03902486 0.03652634 ... 0.16915505 0.13112323 0.25948352]\\n [0.29540354 0.0277239 0.03778433 ... 0.18332024 0.25673175 0.15331419]\\n [0.31588238 0.02645174 0.03275413 ... 0.17979324 0.24976385 0.2284352 ]]\\n\\nThought: The SASA of fibronectin has been calculated using the mdtraj library. The output is a 2D array where each row corresponds to a frame in the trajectory and each column corresponds to an atom in the topology. The values represent the SASA of each atom in each frame. To get the total SASA for each frame, we can sum up the values in each row.\\n\\nAction:\\n```\\n{\\n \"action\": \"Python_REPL\",\\n \"action_input\": {\\n \"query\": \"total_sasa = sasa.sum(axis=1)\\\\nprint(total_sasa)\"\\n }\\n}\\n```\\nObservation: [75.67676 74.52507 75.87748 77.42663 77.3946 73.997116 74.76072\\n 76.645966 76.18153 76.04704 73.347305 76.14905 74.81729 74.481064\\n 75.8655 75.76576 75.239975 76.66776 76.06768 75.27769 ]\\n\\nFinal Answer: The total Solvent Accessible Surface Area (SASA) for each frame in the trajectory of fibronectin has been calculated. The SASA values are in square angstroms and they are as follows: [75.67676, 74.52507, 75.87748, 77.42663, 77.3946, 73.997116, 74.76072, 76.645966, 76.18153, 76.04704, 73.347305, 76.14905, 74.81729, 74.481064, 75.8655, 75.76576, 75.239975, 76.66776, 76.06768, 75.27769].')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "func = MDAgent(type=\"functions\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "func.run(\"Estimate the SASA of fibronectin. Try using mdtraj to load the trajectory and calculate the SASA.\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "func.run(\"Estimate the SASA of fibronectin. Try using mdtraj to load the trajectory and calculate the SASA.\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "result = func.run(\"Estimate the SASA of fibronectin. Try using mdtraj to load the trajectory and calculate the SASA.\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "print(result)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "result = func.run(\"Estimate the SASA of fibronectin. Try using mdtraj to load the trajectory and calculate the SASA.\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "result" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "print(result)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "result[\"intermediate_steps\"][1][1]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "FORCEFIELD_LIST = [\"amber14/DNA.OL15.xml\",\n", - "\"amber14/DNA.bsc1.xml\",\n", - "\"amber14/RNA.OL3.xml\",\n", - "\"amber14/lipid17.xml\",\n", - "\"amber14/protein.ff14SB.xml\",\n", - "\"amber14/protein.ff15ipq.xml\",\n", - "\"amber14/spce.xml\",\n", - "\"amber14/tip3p.xml\",\n", - "\"amber14/tip3pfb.xml\",\n", - "\"amber14/tip4pew.xml\",\n", - "\"amber14/tip4pfb.xml\",\n", - "\"charmm36/spce.xml\",\n", - "\"charmm36/tip3p-pme-b.xml\",\n", - "\"charmm36/tip3p-pme-f.xml\",\n", - "\"charmm36/tip4p2005.xml\",\n", - "\"charmm36/tip4pew.xml\",\n", - "\"charmm36/tip5p.xml\",\n", - "\"charmm36/tip5pew.xml\",\n", - "\"charmm36/water.xml\",\n", - "\"absinth.xml\",\n", - "\"amber03.xml\",\n", - "\"amber03_obc.xml\",\n", - "\"amber10.xml\",\n", - "\"amber10_obc.xml\",\n", - "\"amber14-all\",\n", - "\"amber14-all.xml\",\n", - "\"amber96.xml\",\n", - "\"amber96_obc.xml\",\n", - "\"amber99Test.xml\",\n", - "\"amber99_obc.xml\",\n", - "\"amber99sb.xml\",\n", - "\"amber99sbildn.xml\",\n", - "\"amber99sbnmr.xml\",\n", - "\"amberfb15.xml\",\n", - "\"amoeba2009.xml\",\n", - "\"amoeba2009_gk.xml\",\n", - "\"amoeba2013.xml\",\n", - "\"amoeba2013_gk.xml\",\n", - "\"charmm36.xml\",\n", - "\"charmm_polar_2013.xml\",\n", - "\"hydrogens.xml\",\n", - "\"iamoeba.xml\",\n", - "\"pdbNames.xml\",\n", - "\"residues.xml\",\n", - "\"spce.xml\",\n", - "\"swm4ndp.xml\",\n", - "\"tip3p.xml\",\n", - "\"tip3pfb.xml\",\n", - "\"tip4pew.xml\",\n", - "\"tip4pfb.xml\",\n", - "\"tip5p.xml\"]" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "\n", - "class SetUpAndRunTool(BaseTool):\n", - " name = \"SetUpAndRunTool\"\n", - " description = \"\"\"This tool can only run after InstructionSummary\n", - " This tool will set up the simulation objects\n", - " and run the simulation.\n", - " It will ask for the parameters path.\n", - " input: json file\n", - " \"\"\"\n", - " path_registry: Optional[PathRegistry]\n", - "\n", - " def __init__(\n", - " self,\n", - " path_registry: Optional[PathRegistry],\n", - " ):\n", - " super().__init__()\n", - " self.path_registry = path_registry\n", - "\n", - " def _run(self, query: str) -> str:\n", - " \"\"\"Use the tool\"\"\"\n", - " # find the parameters in the directory\n", - " try:\n", - " if self.path_registry is None: # this should not happen\n", - " return \"Registry not initialized\"\n", - " sim_fxns = SimulationFunctions()\n", - " parameters = sim_fxns._extract_parameters_path()\n", - "\n", - " except ValueError as e:\n", - " return (\n", - " str(e)\n", - " + \"\"\"\\nPlease use the Instruction summary tool with the\n", - " to create a parameters.json file in the directory.\"\"\"\n", - " )\n", - " self.log(\"This are the parameters:\")\n", - " self.log(parameters)\n", - " # print the parameters in json file\n", - " with open(parameters) as f:\n", - " params = json.load(f)\n", - " for key, value in params.items():\n", - " print(key, \":\", value)\n", - " self.log(\"Are you sure you want to run the simulation? (y/n)\")\n", - " response = input(\"yes or no: \")\n", - " if response.lower() in [\"yes\", \"y\"]:\n", - " sim_fxns._setup_and_run_simulation(parameters, self.path_registry)\n", - " else:\n", - " return \"Simulation interrupted due to human input\"\n", - " return \"Simulation Completed, simulation trajectory and data files saved.\"\n", - "\n", - " def log(self, text, color=\"blue\"):\n", - " if color == \"blue\":\n", - " print(\"\\033[1;34m\\t{}\\033[00m\".format(text))\n", - " if color == \"red\":\n", - " print(\"\\033[31m\\t{}\\033[00m\".format(text))\n", - "\n", - " async def _arun(self, query: str) -> str:\n", - " \"\"\"Use the tool asynchronously.\"\"\"\n", - " raise NotImplementedError(\"custom_search does not support async\")\n", - "\n", - "\n", - "class InstructionSummary(BaseTool):\n", - " name = \"Instruction Summary\"\n", - " description = \"\"\"This tool will summarize the instructions\n", - " given by the human. This is the first tool you will\n", - " use, unless you dont have a .cif or .pdb file in\n", - " which case you have to download one first.\n", - " Input: Instructions or original query.\n", - " Output: Summary of instructions\"\"\"\n", - " path_registry: Optional[PathRegistry]\n", - "\n", - " def __init__(\n", - " self,\n", - " path_registry: Optional[PathRegistry],\n", - " ):\n", - " super().__init__()\n", - " self.path_registry = path_registry\n", - "\n", - " def _run(self, query: str) -> str:\n", - " # first check if there is any .cif or .pdb files in the directory\n", - " # if there is, then ask for instructions\n", - " if self.path_registry is None: # this should not happen\n", - " return \"Registry not initialized\"\n", - " files = os.listdir(\".\")\n", - " pdb_cif_files = [f for f in files if f.endswith(\".pdb\") or f.endswith(\".cif\")]\n", - " pdb_cif_files_tidy = [\n", - " f\n", - " for f in files\n", - " if (f.endswith(\".pdb\") or f.endswith(\".cif\")) and \"tidy\" in f\n", - " ]\n", - " if len(pdb_cif_files_tidy) != 0:\n", - " path = pdb_cif_files_tidy[0]\n", - " else:\n", - " path = pdb_cif_files[0]\n", - " sim_fxns = SimulationFunctions()\n", - " summary = sim_fxns._prompt_summary(query + \"the pdbfile is\" + path)\n", - " sim_fxns._save_to_file(\n", - " summary, \"simulation_parameters_summary.json\", self.path_registry\n", - " )\n", - " return summary\n", - "\n", - " async def _arun(self, query: str) -> str:\n", - " \"\"\"Use the tool asynchronously.\"\"\"\n", - " raise NotImplementedError(\"custom_search does not support async\")\n", - "\n", - "\n", - "#######==================System Congifuration==================########\n", - "# System Configuration\n", - "class SetUpandRunFunctionInput(BaseModel):\n", - " pdb_path: str\n", - " forcefield_files: List[str]\n", - " system_params: Optional[Dict[str, Any]] = Field(\n", - " {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"nonbondedCutoff\": 1*nanometers,\n", - " \"ewaldErrorTolerance\": None,\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": False,\n", - " \"constraintTolerance\": None,\n", - " },\n", - " description=\"\"\"Parameters for the openmm system.\n", - " For nonbondedMethod, you can choose from the following:\n", - " NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME.\n", - " If anything but NoCutoff is chosen,\n", - " you have to include a nonbondedCutoff\n", - " and a constrainTolerance.\n", - " If PME is chosen,\n", - " you have to include an ewaldErrorTolerance too.\n", - " For constraints, you can choose from the following:\n", - " None, HBonds, AllBonds or OnlyWater.\n", - " For rigidWater, you can choose from the following:\n", - " True, False.\n", - " Example1:\n", - " {\"nonbondedMethod\": 'NoCutoff',\n", - " \"constraints\": 'None',\n", - " \"rigidWater\": False}\n", - " Example2:\n", - " {\"nonbondedMethod\": 'CutoffPeriodic',\n", - " \"nonbondedCutoff\": 1.0,\n", - " \"constraints\": 'HBonds',\n", - " \"rigidWater\": True,\n", - " \"constraintTolerance\": 0.00001}\n", - " \"\"\",\n", - " )\n", - " integrator_params: Optional[Dict[str, Any]] = Field(\n", - " {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": 300 * kelvin,\n", - " \"Friction\": 1.0 / picoseconds,\n", - " \"Timestep\": 0.004 * picoseconds,\n", - " \"Pressure\": 1.0 * bar,\n", - " },\n", - " description=\"\"\"Parameters for the openmm integrator.\"\"\",\n", - " )\n", - " simmulation_params: Optional[Dict[str, Any]] = Field(\n", - " {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"],\n", - " },\n", - " \n", - " description=\"\"\"Parameters for the openmm simulation.\n", - " The ensemble can be NPT, NVT or NVE.\n", - " The number of steps is the number of steps the simulation will run for.\n", - " record_interval_steps is the number of steps between each record:\n", - " hould be the number of steps divided by 100.\n", - " The record_params is a list of parameters that will\n", - " be recorded during the simulation The options are:\n", - " [Step,Time,Speed,Progress,RemainingTime,ElapsedTime,\n", - " PotentialEnergy,KineticEnergy,TotalEnergy,\n", - " Temperature,Volume,Density]\"\"\",\n", - " )\n", - "\n", - " @root_validator\n", - " def check_system_params(cls, values):\n", - " \"\"\"Check that the system parameters are valid.\"\"\"\n", - " #lowercase all keys in the dictionary\n", - " values = {k.lower(): v for k, v in values.items()}\n", - " \n", - " system_params = values.get(\"system_params\")\n", - " integrator_params = values.get(\"integrator_params\")\n", - " simmulation_params = values.get(\"simmulation_params\")\n", - " \n", - " nonbondedMethod = system_params.get(\"nonbondedMethod\")\n", - " nonbondedCutoff = system_params.get(\"nonbondedCutoff\")\n", - " ewaldErrorTolerance = system_params.get(\"ewaldErrorTolerance\")\n", - " constraints = system_params.get(\"constraints\")\n", - " rigidWater = system_params.get(\"rigidWater\")\n", - " constraintTolerance = system_params.get(\"constrainTolerance\")\n", - " error_msg = \"\"\n", - " if nonbondedMethod in [\"PME\", \"CutoffNonPeriodic\", \"CutoffPeriodic\"]:\n", - " if nonbondedCutoff is None:\n", - " error_msg += \"\"\"nonbondedCutoff must be specified if\n", - " nonbondedMethod is not NoCutoff\\n\"\"\"\n", - " if nonbondedMethod == \"PME\" and ewaldErrorTolerance is None:\n", - " error_msg += \"\"\"ewaldErrorTolerance must be specified when\n", - " nonbondedMethod is PME\\n\"\"\"\n", - " if constraints in [\"HBonds\", \" AllBonds\", \"OnlyWater\"]:\n", - " if constraintTolerance is None:\n", - " error_msg += \"\"\"constraintTolerance must be specified when\n", - " constraints is HBonds or AllBonds\"\"\"\n", - " if rigidWater and constraintTolerance is None:\n", - " error_msg = \"constraintTolerance must be specified if rigidWater is True\"\n", - " #if no constraints, drop constraintTolerance\n", - " if constraints is None:\n", - " system_params.pop(\"constraintTolerance\")\n", - " print(system_params)\n", - " \"\"\"Checking if the file is in the path\"\"\"\n", - " pdb_path = values.get(\"pdb_path\")\n", - " if not os.path.exists(pdb_path):\n", - " error_msg += \"The pdb file is not present in the file\"\n", - "\n", - " \"\"\"Validating the forcefield files and Integrator\"\"\"\n", - "\n", - " integrator_type = integrator_params.get(\"integrator_type\")\n", - " if integrator_type not in [\"LangevinMiddle\", \"Verlet\", \"Brownian\"]:\n", - " error_msg += \"\"\"integrator_type must be one of the following:\n", - " LangevinMiddle, Verlet, Brownian\\n\"\"\"\n", - " if integrator_type == \"LangevinMiddle\":\n", - " friction = integrator_params.get(\"Friction\")\n", - " if friction is None:\n", - " error_msg += \"\"\"friction must be specified when\n", - " integrator_type is LangevinMiddle\\n\"\"\"\n", - " timestep = integrator_params.get(\"Timestep\")\n", - " if timestep is None:\n", - " error_msg += \"\"\"timestep must be specified when\n", - " integrator_type is LangevinMiddle\\n\"\"\"\n", - " temp = integrator_params.get(\"Temperature\")\n", - " if temp is None:\n", - " error_msg += \"\"\"temperature must be specified when\n", - " integrator_type is LangevinMiddle\\n\"\"\"\n", - "\n", - " if integrator_type == \"Verlet\":\n", - " timestep = integrator_params.get(\"timestep\")\n", - " if timestep is None:\n", - " error_msg += \"\"\"timestep must be specified when\n", - " integrator_type is Verlet\\n\"\"\"\n", - " if integrator_type == \"Brownian\":\n", - " temperature = integrator_params.get(\"temperature\")\n", - " if temperature is None:\n", - " error_msg += \"\"\"temperature must be specified when\n", - " integrator_type is Brownian\\n\"\"\"\n", - "\n", - " # forcefield\n", - " forcefield_files = values.get(\"forcefield_files\")\n", - " if forcefield_files is None:\n", - " error_msg += \"forcefield_files must be specified\\n\"\n", - " else:\n", - " print(forcefield_files)\n", - " for file in forcefield_files:\n", - " if file not in FORCEFIELD_LIST:\n", - " error_msg += \"The forcefield file is not present\"\n", - " \n", - "\n", - " if error_msg != \"\":\n", - " return {\"error\": error_msg + \n", - " \"\\n Correct this and try again. \\n Everthing else is fine\"}\n", - "\n", - " # if no error, return the values with keys in the params in camelCase format\n", - "\n", - " \n", - " values= {\"pdb_path\": pdb_path,\n", - " \"forcefield_files\": forcefield_files,\n", - " \"system_params\": system_params,\n", - " \"integrator_params\": integrator_params,\n", - " \"simmulation_params\": simmulation_params}\n", - " return values\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "test_input = {\"pdb_path\" :\"tidy_1X5Y.pdb\", \n", - " \"forcefield_files\":[\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"system_params\":{\"nonbondedMethod\": \"PME\",\n", - " \"nonbondedCutoff\": 0.001*nanometers,\n", - " \"ewaldErrorTolerance\": None,\n", - " \"constraints\": None,\n", - " \"rigidWater\": False,\n", - " \"constraintTolerance\": None},\n", - " \"integrator_params\":{\"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": 300 * kelvin,\n", - " \"Friction\": 1.0 / picoseconds,\n", - " \"Timestep\": 0.004 * picoseconds,\n", - " \"Pressure\": 1.0 * bar}}" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "input = SetUpandRunFunctionInput(**test_input)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "# TODO finish this class.\n", - "class OpenMMSimulation:\n", - " def __init__(self, input_params: SetUpandRunFunctionInput):\n", - " self.params = input_params\n", - " error = self.params.error if hasattr(self.params, \"error\") else None\n", - " if error:\n", - " raise ValueError(error) \n", - " \n", - " self.int_params = self.params.integrator_params\n", - " self.sys_params = self.params.system_params\n", - " self.sim_params = self.params.simmulation_params\n", - " self.setup_system()\n", - " self.setup_integrator()\n", - " self.create_simulation()\n", - "\n", - " def setup_system(self):\n", - " print(\"Building system...\")\n", - " self.pdb = PDBFile(self.params.pdb_path)\n", - " print(\"forcefield_files\", self.sys_params)\n", - " self.forcefield = ForceField(*self.params.forcefield_files)\n", - " print(\"nonbondingCutoff\", self.sys_params.get(\"nonbondedCutoff\", None))\n", - " self.system = self._create_system(self.pdb, self.forcefield, **self.sys_params)\n", - "\n", - " if self.params.system_params.get(\"nonbondedMethod\", None) in [\n", - " CutoffPeriodic,\n", - " PME,\n", - " ]:\n", - " self.system.addForce(\n", - " MonteCarloBarostat(\n", - " self.int_params[\"Pressure\"],\n", - " self.int_params[\"Temperature\"],\n", - " self.sim_params.get(\"barostatInterval\", 25),\n", - " )\n", - " )\n", - "\n", - " def setup_integrator(self):\n", - " print(\"Setting up integrator...\")\n", - " int_params = self.params.integrator_params\n", - " integrator_type = int_params.get(\"integrator_type\", \"LangevinMiddle\")\n", - " if integrator_type == \"LangevinMiddle\":\n", - " self.integrator = LangevinMiddleIntegrator(\n", - " int_params[\"Temperature\"],\n", - " int_params[\"Friction\"],\n", - " int_params[\"Timestep\"],\n", - " )\n", - " else:\n", - " raise ValueError(\"Invalid integrator type\")\n", - "\n", - " self.integrator.setConstraintTolerance(\n", - " self.params.system_params.get(\"constraintTolerance\", 0.000001)\n", - " )\n", - "\n", - " def create_simulation(self):\n", - " print(\"Creating simulation...\")\n", - " self.simulation = Simulation(\n", - " self.pdb.topology,\n", - " self.system,\n", - " self.integrator,\n", - " Platform.getPlatformByName(\"CPU\"),\n", - " )\n", - " self.simulation.context.setPositions(self.pdb.positions)\n", - "\n", - " # Add reporters for output\n", - " self.simulation.reporters.append(\n", - " DCDReporter(\n", - " \"trajectory.dcd\",\n", - " self.params.simmulation_params[\"record_interval_steps\"],\n", - " )\n", - " )\n", - " self.simulation.reporters.append(\n", - " StateDataReporter(\n", - " \"log.txt\",\n", - " self.params.simmulation_params[\"record_interval_steps\"],\n", - " step=True,\n", - " potentialEnergy=True,\n", - " temperature=True,\n", - " separator=\"\\t\",\n", - " )\n", - " )\n", - "\n", - " def _create_system(self,\n", - " pdb,\n", - " forcefield,\n", - " nonbondedMethod=\"NoCutoff\",\n", - " nonbondedCutoff=None,\n", - " ewaldErrorTolerance=None,\n", - " constraints=\"None\",\n", - " rigidWater=False,\n", - " constraintTolerance=None,\n", - " **kwargs,\n", - " ):\n", - " # Create a dictionary to hold system parameters\n", - " system_params = {\n", - " \"nonbondedMethod\": nonbondedMethod,\n", - " \"constraints\": constraints,\n", - " \"rigidWater\": rigidWater,\n", - " }\n", - "\n", - " # Set nonbondedCutoff if applicable Had to double if pre-commit\n", - " if nonbondedMethod in [\"PME\", \"CutoffNonPeriodic\", \"CutoffPeriodic\"]:\n", - " if nonbondedCutoff is not None:\n", - " system_params[\"nonbondedCutoff\"] = nonbondedCutoff\n", - "\n", - " # Set ewaldErrorTolerance if PME is used\n", - " if nonbondedMethod == \"PME\" and ewaldErrorTolerance is not None:\n", - " system_params[\"ewaldErrorTolerance\"] = ewaldErrorTolerance\n", - "\n", - " # Set constraintTolerance if constraints are used\n", - " if constraints in [\"HBonds\", \" AllBonds\"] and constraintTolerance is not None:\n", - " system_params[\"constraintTolerance\"] = constraintTolerance\n", - " elif system_params[\"rigidWater\"] and constraintTolerance is not None:\n", - " system_params[\"constraintTolerance\"] = constraintTolerance\n", - "\n", - "\n", - " # Update system_params with any additional parameters provided\n", - " system_params.update(kwargs)\n", - " system = forcefield.createSystem(pdb.topology, **system_params)\n", - " return system\n", - "\n", - " def run(self):\n", - " # Minimize and Equilibrate\n", - " print(\"Performing energy minimization...\")\n", - " try:\n", - " self.simulation.minimizeEnergy()\n", - " except OpenMMException as e:\n", - " return \"Minimization failed! Error was:\", e \n", - " print(\"Equilibrating...\")\n", - " _temp = self.params.integrator_params[\"Temperature\"]\n", - " self.simulation.context.setVelocitiesToTemperature(_temp)\n", - " _eq_steps = self.params.simmulation_params.get(\"equilibrationSteps\", 1000)\n", - " self.simulation.step(self.params.simmulation_params.get(_eq_steps))\n", - " # Simulate\n", - " print(\"Simulating...\")\n", - " self.simulation.currentStep = 0\n", - " self.simulation.step(self.params.simmulation_params[\"Number of Steps\"])\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "SetUpandRunFunctionInput(**test_input)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "sim = OpenMMSimulation(SetUpandRunFunctionInput(**test_input))" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "sim.run()" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/jorgemedina/miniforge3/envs/MDAGENT/lib/python3.11/site-packages/MDAnalysis/topology/TPRParser.py:161: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13\n", - " import xdrlib\n" - ] - } - ], - "source": [ - "from dotenv import load_dotenv\n", - "load_dotenv()\n", - "\n", - "\n", - "from mdagent import MDAgent\n" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "testing_simul = \"Please download 1PGB and clean it for procesing \"\n", - "test = \"Run a basic simulation of 1PGB, using the cleaned file ive already have\"" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "mrkl = MDAgent(agent_type=\"Structured\")\n", - "#mrkl.run(testing_simul)\n" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: The user has a cleaned file of the protein with PDB ID 1PGB and wants to run a basic simulation. The first step is to set up and run the simulation using the SetUpandRunFunction tool. Since the user has not provided specific parameters for the simulation, I will use default parameters for a basic simulation.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PGB\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\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\": \"0.004 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "PDB ID: 1PGB\n", - "PDB Path: Name not found in path registry.\n", - "The previous action attempted to run a simulation using the SetUpandRunFunction tool with the PDB ID 1PGB and default parameters. However, the action failed because the file was not found. Since the user mentioned they already have a cleaned file, it is likely that the file is saved with a different name or path that I need to retrieve before running the simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"ListRegistryPaths\",\n", - " \"action_input\": {\n", - " \"paths\": \"paths\"\n", - " }\n", - "}\n", - "```\n", - "\n", - "The registry contains three paths that include the PDB ID 1PGB. Since the user has a cleaned file, it is necessary to determine which of these paths corresponds to the cleaned file they are referring to. I will use the ListDirectoryFiles tool to list the files in each directory associated with the paths found in the registry to identify the cleaned file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"ListDirectoryFiles\",\n", - " \"action_input\": {\n", - " \"query\": \"1PGB_154902\"\n", - " }\n", - "}\n", - "```The directory for the path `1PGB_154902` does not contain a PDB file, which suggests that this is not the directory containing the cleaned file the user is referring to. I will now check the next path in the registry.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"ListDirectoryFiles\",\n", - " \"action_input\": {\n", - " \"query\": \"1PGB_154959\"\n", - " }\n", - "}\n", - "```\n", - "The directory for the path `1PGB_154959` also does not contain a PDB file, which suggests that this is not the directory containing the cleaned file the user is referring to. I will now check the last path in the registry.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"ListDirectoryFiles\",\n", - " \"action_input\": {\n", - " \"query\": \"1PGB_155636\"\n", - " }\n", - "}\n", - "```None of the directories listed under the registry paths for 1PGB contain a PDB file, which is necessary for running the simulation. It's possible that the cleaned file might be in a different directory or the file might not have been registered correctly. Since I have checked all the paths associated with 1PGB and none contain a PDB file, I will now attempt to retrieve the cleaned PDB file using the PDB ID provided by the user. If the file is not found in the registry, I will need to download it using the PDBFileDownloader tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"1PGB\"\n", - " }\n", - "}\n", - "```\n", - "PDB file found with this ID: 1PGB\n", - "The PDB file for 1PGB has been successfully downloaded and is now available with the name `1PGB_161539`. Since the user has requested a basic simulation using a cleaned file, I will now proceed to set up and run the simulation using the SetUpandRunFunction tool with the downloaded PDB file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PGB_161539\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\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\": \"0.004 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "PDB ID: 1PGB_161539\n", - "PDB Path: /Users/jorgemedina/Desktop/UpdatingSetupandrun/md-agent/notebooks/files/pdb/1PGB_raw_20240103_161539.pdb\n", - "The simulation setup failed because the PDB file is missing hydrogen atoms for residue 1 (MET). This issue can be resolved by adding the missing hydrogen atoms to the PDB file. I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file `1PGB_161539`.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PGB_161539\",\n", - " \"output_path\": \"1PGB_161539_cleaned\",\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\n", - " }\n", - "}\n", - "```pdbfile: /Users/jorgemedina/Desktop/UpdatingSetupandrun/md-agent/notebooks/files/pdb/1PGB_raw_20240103_161539.pdb name: 1PGB end: pdb\n", - "The cleaning process has been completed successfully, and the cleaned PDB file is now available with the name `1PGB_161642`. With the cleaned file, I can now attempt to set up and run the simulation again using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PGB_161642\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\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\": \"0.004 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Building system...\n", - "PDB ID: 1PGB_161642\n", - "PDB Path: /Users/jorgemedina/Desktop/UpdatingSetupandrun/md-agent/notebooks/files/pdb/1PGB_Clean_20240103_161642.pdb\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Equilibrating...\n", - "The simulation setup failed again due to a NaN (Not a Number) error in particle coordinates, which indicates an issue with the initialization of the simulation. This could be due to a variety of factors, such as incorrect nonbonded interactions, constraints, or issues with the cleaned file. To address this, I will adjust the simulation parameters to use a nonbonded method that includes a cutoff and apply constraints to hydrogen bonds, which are common adjustments to stabilize the simulation. I will also ensure that water is treated rigidly, which is a common practice in molecular dynamics simulations.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_id\": \"1PGB_161642\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"CutoffPeriodic\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.004 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```\n", - "Building system...\n", - "PDB ID: 1PGB_161642\n", - "PDB Path: /Users/jorgemedina/Desktop/UpdatingSetupandrun/md-agent/notebooks/files/pdb/1PGB_Clean_20240103_161642.pdb\n", - "Setting up integrator...\n", - "Creating simulation...\n", - "simulation set!\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "1!\n", - "2! NVT_1PGB_161642_20240103_161734.py\n", - "3!\n", - "Standalone simulation script written to files/simulations/NVT_1PGB_161642_20240103_161734.py\n", - "4!\n", - "Eureka!\n", - "The simulation has been successfully completed using the cleaned PDB file for 1PGB with adjusted simulation parameters. The user can now analyze the results of the simulation as needed.\n", - "\n", - "Final Answer: The basic simulation of the protein with PDB ID 1PGB has been successfully run using the cleaned file. The simulation was performed with periodic boundary conditions, constraints on hydrogen bonds, and rigid water molecules. The temperature was set to 300 K, using a Langevin integrator with a friction coefficient of 1.0 ps^-1 and a timestep of 0.004 ps. The simulation was run for 10,000 steps, and data was recorded every 100 steps, including the step number, potential energy, and temperature." - ] - }, - { - "data": { - "text/plain": [ - "'The simulation has been successfully completed using the cleaned PDB file for 1PGB with adjusted simulation parameters. The user can now analyze the results of the simulation as needed.\\n\\nFinal Answer: The basic simulation of the protein with PDB ID 1PGB has been successfully run using the cleaned file. The simulation was performed with periodic boundary conditions, constraints on hydrogen bonds, and rigid water molecules. The temperature was set to 300 K, using a Langevin integrator with a friction coefficient of 1.0 ps^-1 and a timestep of 0.004 ps. The simulation was run for 10,000 steps, and data was recorded every 100 steps, including the step number, potential energy, and temperature.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "mrkl.run(test)" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: Before running an NVT simulation, I need to check if the file 1PGB.pdb is available or needs to be downloaded. If it's not available, I will download it using the PDBFileDownloader tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"ListDirectoryFiles\",\n", - " \"action_input\": {\n", - " \"query\": \"1PGB.pdb\"\n", - " }\n", - "}\n", - "```\n", - "\n", - "The file 1PGB.pdb is available in the directory. I can proceed to set up and run the NVT simulation using the SetUpandRunFunction tool.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_path\": \"1PGB.pdb\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"CutoffPeriodic\",\n", - " \"nonbondedCutoff\": 1.0,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": True,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.004 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_path\": \"1PGB.pdb\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"CutoffPeriodic\",\n", - " \"nonbondedCutoff\": 1.0,\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": True,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.004 * picoseconds\"\n", - " },\n", - " \"simulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```The previous action to set up and run the NVT simulation was not successful due to an invalid or incomplete response. I need to correct the parameters and try running the simulation again. I will adjust the parameters and ensure they are formatted correctly before resubmitting the action.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_path\": \"1PGB.pdb\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"CutoffPeriodic\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.004 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"Step\", \"PotentialEnergy\", \"Temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Using SetUpandRunFunction\n", - "{'pdb_path': '1PGB.pdb', 'forcefield_files': ['amber14-all.xml', 'amber14/tip3pfb.xml'], 'system_params': {'nonbondedMethod': 'CutoffPeriodic', 'nonbondedCutoff': '1.0 * nanometers', 'constraints': 'HBonds', 'rigidWater': True, 'constraintTolerance': 1e-05}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds'}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['Step', 'PotentialEnergy', 'Temperature']}}\n", - "system_params {'nonbondedMethod': 'CutoffPeriodic', 'nonbondedCutoff': '1.0 * nanometers', 'constraints': 'HBonds', 'rigidWater': True, 'constraintTolerance': 1e-05}\n", - "integrator_params {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds'}\n", - "simmulation_params {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['Step', 'PotentialEnergy', 'Temperature']}\n", - "integrator_type LangevinMiddle\n", - "this is the validator ['amber14-all.xml', 'amber14/tip3pfb.xml']\n", - "this is the validator {'pdb_path': '1PGB.pdb', 'forcefield_files': ['amber14-all.xml', 'amber14/tip3pfb.xml'], 'system_params': {'nonbondedMethod': CutoffPeriodic, 'nonbondedCutoff': Quantity(value=1.0, unit=nanometer), 'constraints': HBonds, 'rigidWater': True, 'constraintTolerance': 1e-05}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': Quantity(value=300.0, unit=kelvin), 'Friction': Quantity(value=1, unit=/picosecond), 'Timestep': Quantity(value=0.004, unit=picosecond)}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['Step', 'PotentialEnergy', 'Temperature']}}\n", - "Building system...\n", - "forcefield_files {'nonbondedMethod': CutoffPeriodic, 'nonbondedCutoff': Quantity(value=1.0, unit=nanometer), 'constraints': HBonds, 'rigidWater': True, 'constraintTolerance': 1e-05}\n", - "nonbondingCutoff 1.0 nm\n", - "nonbondedMethod CutoffPeriodic\n", - "constraints HBonds\n", - "rigidWater True\n", - "The simulation setup failed because the PDB file 1PGB.pdb is missing hydrogen atoms for residue 1 (MET). To resolve this, I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"input_args\": {\n", - " \"input_path\": \"1PGB.pdb\",\n", - " \"operations\": {\n", - " \"add_hydrogens\": true\n", - " }\n", - " }\n", - " }\n", - "}\n", - "```The previous action failed because the input to the CleaningToolFunction was not correctly formatted. I need to provide the input as a dictionary with the key 'pdb_path'. I will correct the input and try again.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"input_args\": {\n", - " \"pdb_path\": \"1PGB.pdb\",\n", - " \"operations\": {\n", - " \"add_hydrogens\": true\n", - " }\n", - " }\n", - " }\n", - "}\n", - "```The file 1PGB.pdb was not found by the CleaningToolFunction, which is unexpected because the file was previously listed in the directory. I will check the list of paths saved in memory to ensure the correct path is used for the PDB file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"ListRegistryPaths\",\n", - " \"action_input\": {\n", - " \"paths\": \"paths\"\n", - " }\n", - "}\n", - "```The file 1PGB.pdb is indeed registered in the system. I will now attempt to add hydrogens to the PDB file again using the correct registered name.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"input_args\": {\n", - " \"pdb_path\": \"1PGB.pdb\",\n", - " \"operations\": {\n", - " \"add_hydrogens\": true\n", - " }\n", - " }\n", - " }\n", - "}\n", - "```The file 1PGB.pdb is still not being found by the CleaningToolFunction despite being listed in the registry. It's possible that the file path might be incorrect or there is an issue with the tool accessing the file. To resolve this, I will map the file name to its path again to ensure that the correct path is being used.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"MapPath2Name\",\n", - " \"action_input\": {\n", - " \"file_and_path\": \"1PGB.pdb, 1PGB.pdb\"\n", - " }\n", - "}\n", - "```Now that the path has been successfully mapped to the name 1PGB.pdb, I will attempt to add hydrogens to the PDB file again using the CleaningToolFunction.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"input_args\": {\n", - " \"pdb_path\": \"1PGB.pdb\",\n", - " \"operations\": {\n", - " \"add_hydrogens\": true\n", - " }\n", - " }\n", - " }\n", - "}\n", - "```The file 1PGB.pdb is still not being found by the CleaningToolFunction despite the path being successfully mapped. There may be an issue with the tool or the file system. To troubleshoot this, I will list the files in the current directory again to confirm the presence of the file.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"ListDirectoryFiles\",\n", - " \"action_input\": {\n", - " \"query\": \"1PGB.pdb\"\n", - " }\n", - "}\n", - "```The file 1PGB.pdb is confirmed to be present in the directory. Since the CleaningToolFunction is not recognizing the file, I will try using the registered name \"1PGB_clean.pdb\" which might be the cleaned version of the PDB file and should be suitable for simulation.\n", - "\n", - "Action:\n", - "```json\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_path\": \"1PGB_clean.pdb\",\n", - " \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"CutoffPeriodic\",\n", - " \"nonbondedCutoff\": \"1.0 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.004 * picoseconds\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"Step\", \"PotentialEnergy\", \"Temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Using SetUpandRunFunction\n", - "{'pdb_path': '1PGB_clean.pdb', 'forcefield_files': ['amber14-all.xml', 'amber14/tip3pfb.xml'], 'system_params': {'nonbondedMethod': 'CutoffPeriodic', 'nonbondedCutoff': '1.0 * nanometers', 'constraints': 'HBonds', 'rigidWater': True, 'constraintTolerance': 1e-05}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds'}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['Step', 'PotentialEnergy', 'Temperature']}}\n", - "system_params {'nonbondedMethod': 'CutoffPeriodic', 'nonbondedCutoff': '1.0 * nanometers', 'constraints': 'HBonds', 'rigidWater': True, 'constraintTolerance': 1e-05}\n", - "integrator_params {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds'}\n", - "simmulation_params {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['Step', 'PotentialEnergy', 'Temperature']}\n", - "integrator_type LangevinMiddle\n", - "this is the validator ['amber14-all.xml', 'amber14/tip3pfb.xml']\n", - "this is the validator {'pdb_path': '1PGB_clean.pdb', 'forcefield_files': ['amber14-all.xml', 'amber14/tip3pfb.xml'], 'system_params': {'nonbondedMethod': CutoffPeriodic, 'nonbondedCutoff': Quantity(value=1.0, unit=nanometer), 'constraints': HBonds, 'rigidWater': True, 'constraintTolerance': 1e-05}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': Quantity(value=300.0, unit=kelvin), 'Friction': Quantity(value=1, unit=/picosecond), 'Timestep': Quantity(value=0.004, unit=picosecond)}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['Step', 'PotentialEnergy', 'Temperature']}}\n", - "Building system...\n", - "forcefield_files {'nonbondedMethod': CutoffPeriodic, 'nonbondedCutoff': Quantity(value=1.0, unit=nanometer), 'constraints': HBonds, 'rigidWater': True, 'constraintTolerance': 1e-05}\n", - "nonbondingCutoff 1.0 nm\n", - "nonbondedMethod CutoffPeriodic\n", - "constraints HBonds\n", - "rigidWater True\n", - "Setting up integrator...\n", - "integrator_type LangevinMiddle\n", - "Creating simulation...\n", - "simulation set!\n", - "running simulation in the tool\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to reproduce_simulation.py\n", - "The NVT simulation for the protein with PDB ID 1PGB has been successfully completed." - ] - }, - { - "data": { - "text/plain": [ - "'Thought: Thought: Before running an NVT simulation, I need to check if the file 1PGB.pdb is available or needs to be downloaded. If it\\'s not available, I will download it using the PDBFileDownloader tool.\\n\\nAction:\\n```\\n{\\n \"action\": \"ListDirectoryFiles\",\\n \"action_input\": {\\n \"query\": \"1PGB.pdb\"\\n }\\n}\\n```\\n\\n\\nObservation: .DS_Store, trajectory.dcd, reproduce_simulation.py, 1PGB_clean.pdb, 1PGB.pdb, log.txt, 1PGB-processed.pdb, paths_registry.json, checkpoint.chk, testing_changes.ipynb, cleaned_1X5Y.pdb, 1X5Y.pdb\\nThought: Could not parse LLM output: The file 1PGB.pdb is available in the directory. I can proceed to set up and run the NVT simulation using the SetUpandRunFunction tool.\\n\\nAction:\\n```\\n{\\n \"action\": \"SetUpandRunFunction\",\\n \"action_input\": {\\n \"pdb_path\": \"1PGB.pdb\",\\n \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3p.xml\"],\\n \"system_params\": {\\n \"nonbondedMethod\": \"CutoffPeriodic\",\\n \"nonbondedCutoff\": 1.0,\\n \"constraints\": \"HBonds\",\\n \"rigidWater\": True,\\n \"constraintTolerance\": 0.00001\\n },\\n \"integrator_params\": {\\n \"integrator_type\": \"LangevinMiddle\",\\n \"Temperature\": \"300 * kelvin\",\\n \"Friction\": \"1.0 / picoseconds\",\\n \"Timestep\": \"0.004 * picoseconds\"\\n },\\n \"simmulation_params\": {\\n \"Ensemble\": \"NVT\",\\n \"Number of Steps\": 10000,\\n \"record_interval_steps\": 100,\\n \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\\n }\\n }\\n}\\n```\\nObservation: Invalid or incomplete response\\nThought: The previous action to set up and run the NVT simulation was not successful due to an invalid or incomplete response. I need to correct the parameters and try running the simulation again. I will adjust the parameters and ensure they are formatted correctly before resubmitting the action.\\n\\nAction:\\n```json\\n{\\n \"action\": \"SetUpandRunFunction\",\\n \"action_input\": {\\n \"pdb_path\": \"1PGB.pdb\",\\n \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\\n \"system_params\": {\\n \"nonbondedMethod\": \"CutoffPeriodic\",\\n \"nonbondedCutoff\": \"1.0 * nanometers\",\\n \"constraints\": \"HBonds\",\\n \"rigidWater\": true,\\n \"constraintTolerance\": 0.00001\\n },\\n \"integrator_params\": {\\n \"integrator_type\": \"LangevinMiddle\",\\n \"Temperature\": \"300 * kelvin\",\\n \"Friction\": \"1.0 / picoseconds\",\\n \"Timestep\": \"0.004 * picoseconds\"\\n },\\n \"simmulation_params\": {\\n \"Ensemble\": \"NVT\",\\n \"Number of Steps\": 10000,\\n \"record_interval_steps\": 100,\\n \"record_params\": [\"Step\", \"PotentialEnergy\", \"Temperature\"]\\n }\\n }\\n}\\n```\\nObservation: No template found for residue 1 (MET). The set of atoms is similar to MET, but it is missing 9 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#templateThis were the inputs {\\'pdb_path\\': \\'1PGB.pdb\\', \\'forcefield_files\\': [\\'amber14-all.xml\\', \\'amber14/tip3pfb.xml\\'], \\'system_params\\': {\\'nonbondedMethod\\': \\'CutoffPeriodic\\', \\'nonbondedCutoff\\': \\'1.0 * nanometers\\', \\'constraints\\': \\'HBonds\\', \\'rigidWater\\': True, \\'constraintTolerance\\': 1e-05}, \\'integrator_params\\': {\\'integrator_type\\': \\'LangevinMiddle\\', \\'Temperature\\': \\'300 * kelvin\\', \\'Friction\\': \\'1.0 / picoseconds\\', \\'Timestep\\': \\'0.004 * picoseconds\\'}, \\'simmulation_params\\': {\\'Ensemble\\': \\'NVT\\', \\'Number of Steps\\': 10000, \\'record_interval_steps\\': 100, \\'record_params\\': [\\'Step\\', \\'PotentialEnergy\\', \\'Temperature\\']}}\\nThought: The simulation setup failed because the PDB file 1PGB.pdb is missing hydrogen atoms for residue 1 (MET). To resolve this, I will use the CleaningToolFunction to add the missing hydrogen atoms to the PDB file.\\n\\nAction:\\n```json\\n{\\n \"action\": \"CleaningToolFunction\",\\n \"action_input\": {\\n \"input_args\": {\\n \"input_path\": \"1PGB.pdb\",\\n \"operations\": {\\n \"add_hydrogens\": true\\n }\\n }\\n }\\n}\\n```\\nObservation: No file path provided.\\n The input has to be a dictionary with the key \\'pdb_path\\'\\nThought: The previous action failed because the input to the CleaningToolFunction was not correctly formatted. I need to provide the input as a dictionary with the key \\'pdb_path\\'. I will correct the input and try again.\\n\\nAction:\\n```json\\n{\\n \"action\": \"CleaningToolFunction\",\\n \"action_input\": {\\n \"input_args\": {\\n \"pdb_path\": \"1PGB.pdb\",\\n \"operations\": {\\n \"add_hydrogens\": true\\n }\\n }\\n }\\n}\\n```\\nObservation: Check your file path. File not found.\\nThought: The file 1PGB.pdb was not found by the CleaningToolFunction, which is unexpected because the file was previously listed in the directory. I will check the list of paths saved in memory to ensure the correct path is used for the PDB file.\\n\\nAction:\\n```json\\n{\\n \"action\": \"ListRegistryPaths\",\\n \"action_input\": {\\n \"paths\": \"paths\"\\n }\\n}\\n```\\nObservation: Names found in registry: 1PGB.pdb, 1PGB_clean.pdb, modified_simul.py, 1X5Y.pdb, cleaned_1X5Y.pdb\\nThought: The file 1PGB.pdb is indeed registered in the system. I will now attempt to add hydrogens to the PDB file again using the correct registered name.\\n\\nAction:\\n```json\\n{\\n \"action\": \"CleaningToolFunction\",\\n \"action_input\": {\\n \"input_args\": {\\n \"pdb_path\": \"1PGB.pdb\",\\n \"operations\": {\\n \"add_hydrogens\": true\\n }\\n }\\n }\\n}\\n```\\nObservation: Check your file path. File not found.\\nThought: The file 1PGB.pdb is still not being found by the CleaningToolFunction despite being listed in the registry. It\\'s possible that the file path might be incorrect or there is an issue with the tool accessing the file. To resolve this, I will map the file name to its path again to ensure that the correct path is being used.\\n\\nAction:\\n```json\\n{\\n \"action\": \"MapPath2Name\",\\n \"action_input\": {\\n \"file_and_path\": \"1PGB.pdb, 1PGB.pdb\"\\n }\\n}\\n```\\nObservation: Path successfully mapped to name: 1PGB.pdb\\nThought: Now that the path has been successfully mapped to the name 1PGB.pdb, I will attempt to add hydrogens to the PDB file again using the CleaningToolFunction.\\n\\nAction:\\n```json\\n{\\n \"action\": \"CleaningToolFunction\",\\n \"action_input\": {\\n \"input_args\": {\\n \"pdb_path\": \"1PGB.pdb\",\\n \"operations\": {\\n \"add_hydrogens\": true\\n }\\n }\\n }\\n}\\n```\\nObservation: Check your file path. File not found.\\nThought: The file 1PGB.pdb is still not being found by the CleaningToolFunction despite the path being successfully mapped. There may be an issue with the tool or the file system. To troubleshoot this, I will list the files in the current directory again to confirm the presence of the file.\\n\\nAction:\\n```json\\n{\\n \"action\": \"ListDirectoryFiles\",\\n \"action_input\": {\\n \"query\": \"1PGB.pdb\"\\n }\\n}\\n```\\nObservation: .DS_Store, trajectory.dcd, reproduce_simulation.py, 1PGB_clean.pdb, 1PGB.pdb, log.txt, 1PGB-processed.pdb, paths_registry.json, checkpoint.chk, testing_changes.ipynb, cleaned_1X5Y.pdb, 1X5Y.pdb\\nThought: The file 1PGB.pdb is confirmed to be present in the directory. Since the CleaningToolFunction is not recognizing the file, I will try using the registered name \"1PGB_clean.pdb\" which might be the cleaned version of the PDB file and should be suitable for simulation.\\n\\nAction:\\n```json\\n{\\n \"action\": \"SetUpandRunFunction\",\\n \"action_input\": {\\n \"pdb_path\": \"1PGB_clean.pdb\",\\n \"forcefield_files\": [\"amber14-all.xml\", \"amber14/tip3pfb.xml\"],\\n \"system_params\": {\\n \"nonbondedMethod\": \"CutoffPeriodic\",\\n \"nonbondedCutoff\": \"1.0 * nanometers\",\\n \"constraints\": \"HBonds\",\\n \"rigidWater\": true,\\n \"constraintTolerance\": 0.00001\\n },\\n \"integrator_params\": {\\n \"integrator_type\": \"LangevinMiddle\",\\n \"Temperature\": \"300 * kelvin\",\\n \"Friction\": \"1.0 / picoseconds\",\\n \"Timestep\": \"0.004 * picoseconds\"\\n },\\n \"simmulation_params\": {\\n \"Ensemble\": \"NVT\",\\n \"Number of Steps\": 10000,\\n \"record_interval_steps\": 100,\\n \"record_params\": [\"Step\", \"PotentialEnergy\", \"Temperature\"]\\n }\\n }\\n}\\n```\\nObservation: Simulation done!\\nFinal Answer: The NVT simulation for the protein with PDB ID 1PGB has been successfully completed.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "mrkl = MDAgent(type=\"mrkl\")\n", - "mrkl.run(testing_simul)" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "func = MDAgent(type=\"functions\")\n" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - "\n", - "\u001b[1m> Entering new AgentExecutor chain...\u001b[0m\n", - "\u001b[32;1m\u001b[1;3m\n", - "Invoking: `ListDirectoryFiles` with `.`\n", - "\n", - "\n", - "\u001b[0m\u001b[36;1m\u001b[1;3m.DS_Store, trajectory.dcd, reproduce_simulation.py, 1PGB_clean.pdb, 1PGB.pdb, log.txt, 1PGB-processed.pdb, paths_registry.json, checkpoint.chk, testing_changes.ipynb, cleaned_1X5Y.pdb, 1X5Y.pdb\u001b[0m\u001b[32;1m\u001b[1;3m\n", - "Invoking: `MapPath2Name` with `1PGB,1PGB.pdb`\n", - "\n", - "\n", - "\u001b[0m\u001b[38;5;200m\u001b[1;3mPath successfully mapped to name: 1PGB\u001b[0m\u001b[32;1m\u001b[1;3m\n", - "Invoking: `CleaningToolFunction` with `{'pdb_path': '1PGB.pdb', 'output_path': '1PGB_clean.pdb', 'replace_nonstandard_residues': True, 'add_missing_atoms': True, 'remove_heterogens': True, 'remove_water': True, 'add_hydrogens': True, 'add_hydrogens_ph': 7}`\n", - "\n", - "\n", - "\u001b[0m{'pdb_path': '1PGB.pdb', 'output_path': '1PGB_clean.pdb', 'replace_nonstandard_residues': True, 'add_missing_atoms': True, 'remove_heterogens': True, 'remove_water': True, 'add_hydrogens': True, 'add_hydrogens_ph': 7}\n", - "\u001b[38;5;200m\u001b[1;3mCleaned File: Removed Heterogens, and Water Removed. Added Hydrogens at pH 7. Missing Atoms Added and replaces nonstandard residues. written to 1PGB_clean.pdb\u001b[0m\u001b[32;1m\u001b[1;3m\n", - "Invoking: `MapPath2Name` with `1PGB_clean,1PGB_clean.pdb`\n", - "\n", - "\n", - "\u001b[0m\u001b[38;5;200m\u001b[1;3mPath successfully mapped to name: 1PGB_clean\u001b[0mFinal Answer: The PDB file 1PGB.pdb has been cleaned, resulting in the creation of a new file named 1PGB_clean.pdb. The cleaning process involved removing heterogens and water, adding hydrogens at pH 7, adding any missing atoms, and replacing nonstandard residues. The cleaned file is now mapped with the short name \"1PGB_clean\" for future reference.\u001b[32;1m\u001b[1;3mFinal Answer: The PDB file 1PGB.pdb has been cleaned, resulting in the creation of a new file named 1PGB_clean.pdb. The cleaning process involved removing heterogens and water, adding hydrogens at pH 7, adding any missing atoms, and replacing nonstandard residues. The cleaned file is now mapped with the short name \"1PGB_clean\" for future reference.\u001b[0m\n", - "\n", - "\u001b[1m> Finished chain.\u001b[0m\n" - ] - }, - { - "data": { - "text/plain": [ - "'\\nInvoking: `ListDirectoryFiles` with `.`\\n\\n\\n\\nObservation: .DS_Store, trajectory.dcd, reproduce_simulation.py, 1PGB_clean.pdb, 1PGB.pdb, log.txt, 1PGB-processed.pdb, paths_registry.json, checkpoint.chk, testing_changes.ipynb, cleaned_1X5Y.pdb, 1X5Y.pdb\\n\\nInvoking: `MapPath2Name` with `1PGB,1PGB.pdb`\\n\\n\\n\\nObservation: Path successfully mapped to name: 1PGB\\n\\nInvoking: `CleaningToolFunction` with `{\\'pdb_path\\': \\'1PGB.pdb\\', \\'output_path\\': \\'1PGB_clean.pdb\\', \\'replace_nonstandard_residues\\': True, \\'add_missing_atoms\\': True, \\'remove_heterogens\\': True, \\'remove_water\\': True, \\'add_hydrogens\\': True, \\'add_hydrogens_ph\\': 7}`\\n\\n\\n\\nObservation: Cleaned File: Removed Heterogens, and Water Removed. Added Hydrogens at pH 7. Missing Atoms Added and replaces nonstandard residues. written to 1PGB_clean.pdb\\n\\nInvoking: `MapPath2Name` with `1PGB_clean,1PGB_clean.pdb`\\n\\n\\n\\nObservation: Path successfully mapped to name: 1PGB_clean\\nFinal Answer: Final Answer: The PDB file 1PGB.pdb has been cleaned, resulting in the creation of a new file named 1PGB_clean.pdb. The cleaning process involved removing heterogens and water, adding hydrogens at pH 7, adding any missing atoms, and replacing nonstandard residues. The cleaned file is now mapped with the short name \"1PGB_clean\" for future reference.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "testing_simul = \"Please do a basic cleaning of the PDB file 1PGB.pdb\"\n", - "func.run(testing_simul)" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "testing_simul = \"I made a script called reproduce_simulation.py. Please increase the temperature of the simulation by 10 degrees.\"\n" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: The assistant needs to modify the script to increase the temperature of the simulation by 10 degrees. The ModifyScriptTool can be used for this purpose. The assistant needs to know the current temperature in the script to increase it by 10 degrees. The assistant should first use the ListDirectoryFiles tool to confirm the existence of the script in the current directory. \n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"ListDirectoryFiles\",\n", - " \"action_input\": {\n", - " \"query\": \"\"\n", - " }\n", - "}\n", - "```The file \"reproduce_simulation.py\" exists in the current directory. Now, I need to read the script and find the current temperature setting. I can use the Python_REPL tool to open the file and read its contents. \n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"Python_REPL\",\n", - " \"action_input\": {\n", - " \"query\": \"with open('reproduce_simulation.py', 'r') as file: print(file.read())\"\n", - " }\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 current temperature in the script is set to 300.0 Kelvin. The assistant needs to increase this temperature by 10 degrees. The ModifyScriptTool can be used to make this change. \n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"ModifyScriptTool\",\n", - " \"action_input\": {\n", - " \"base_script\": \"reproduce_simulation.py\",\n", - " \"user_requirement\": \"increase the temperature of the simulation by 10 degrees\"\n", - " }\n", - "}\n", - "```It seems I made a mistake in the input for the ModifyScriptTool. The correct keys for the input are 'query' and 'script'. I will correct this and try again.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"ModifyScriptTool\",\n", - " \"action_input\": {\n", - " \"query\": \"increase the temperature of the simulation by 10 degrees\",\n", - " \"script\": \"reproduce_simulation.py\"\n", - " }\n", - "}\n", - "```The script has been successfully modified to increase the temperature of the simulation by 10 degrees. I can now provide the final answer to the user.\n", - "\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"Final Answer\",\n", - " \"action_input\": \"The script 'reproduce_simulation.py' has been successfully modified to increase the temperature of the simulation by 10 degrees.\"\n", - "}\n", - "```" - ] - }, - { - "data": { - "text/plain": [ - "'Thought: Thought: The assistant needs to modify the script to increase the temperature of the simulation by 10 degrees. The ModifyScriptTool can be used for this purpose. The assistant needs to know the current temperature in the script to increase it by 10 degrees. The assistant should first use the ListDirectoryFiles tool to confirm the existence of the script in the current directory. \\n\\nAction:\\n```\\n{\\n \"action\": \"ListDirectoryFiles\",\\n \"action_input\": {\\n \"query\": \"\"\\n }\\n}\\n```\\nObservation: getpdb_example.ipynb, gitissues.ipynb, .DS_Store, math_example.ipynb, trajectory.dcd, clean_example.ipynb, reproduce_simulation.py, 1PGB_clean.pdb, 1PGB.pdb, log.txt, 1PGB-processed.pdb, modified_simul2.py, paths_registry.json, checkpoint.chk, testing_changes.ipynb, pqa_example.ipynb, set_and_run_example.ipynb, Name2Simulation.ipynb, packmol_example.ipynb, 1X5Y.pdb\\nThought: The file \"reproduce_simulation.py\" exists in the current directory. Now, I need to read the script and find the current temperature setting. I can use the Python_REPL tool to open the file and read its contents. \\n\\nAction:\\n```\\n{\\n \"action\": \"Python_REPL\",\\n \"action_input\": {\\n \"query\": \"with open(\\'reproduce_simulation.py\\', \\'r\\') as file: print(file.read())\"\\n }\\n}\\n```\\n\\nObservation: # This script was generated by MDagent-Setup.\\n\\nfrom openmm import *\\nfrom openmm.app import *\\nfrom openmm.unit import *\\n\\n# Input Files\\npdb = PDBFile(\\'1PGB_clean.pdb\\')\\nforcefield = ForceField(\\'amber14-all.xml\\', \\'amber14/tip3pfb.xml\\')\\n\\n# System Configuration\\nnonbondedMethod = CutoffNonPeriodic\\nconstraints = HBonds\\nrigidWater = True\\nconstraintTolerance = 1e-05\\nnonbondedCutoff = 1.0*nanometer\\n\\n# Integration Options\\ndt = 0.004*picosecond\\ntemperature = 300.0*kelvin\\nfriction = 1/picosecond\\n\\n# Simulation Options\\nsteps = 10000\\nequilibrationSteps = 1000\\nplatform = Platform.getPlatformByName(\\'CPU\\')\\ndcdReporter = DCDReporter(\\'trajectory.dcd\\', 10000)\\ndataReporter = StateDataReporter(\\'log.txt\\', 100,\\ntotalSteps=steps,\\nstep=True, speed=True, progress=True, elapsedTime=True, remainingTime=True,\\npotentialEnergy=True, temperature=True, volume=True, density=True,\\nseparator=\\'\\t\\')\\ncheckpointReporter = CheckpointReporter(\\'checkpoint.chk\\', 10000)\\n\\n# Minimize and Equilibrate\\n# ... code for minimization and equilibration ...\\n\\n# Simulate\\n\\nprint(\\'Building system...\\')\\ntopology = pdb.topology\\npositions = pdb.positions\\n\\nsystem = forcefield.createSystem(topology,\\nnonbondedMethod=nonbondedMethod,\\nnonbondedCutoff=nonbondedCutoff, constraints=constraints,\\nrigidWater=rigidWater)\\n\\nintegrator = LangevinMiddleIntegrator(temperature, friction, dt)\\nintegrator.setConstraintTolerance(constraintTolerance)\\nsimulation = Simulation(topology, system, integrator, platform)\\nsimulation.context.setPositions(positions)\\n\\n# Minimize and Equilibrate\\n\\nprint(\\'Performing energy minimization...\\')\\nsimulation.minimizeEnergy()\\nprint(\\'Equilibrating...\\')\\nsimulation.context.setVelocitiesToTemperature(temperature)\\nsimulation.step(equilibrationSteps)\\n\\n# Simulate\\n\\nprint(\\'Simulating...\\')\\nsimulation.reporters.append(dcdReporter)\\nsimulation.reporters.append(dataReporter)\\nsimulation.reporters.append(checkpointReporter)\\nsimulation.currentStep = 0\\nsimulation.step(steps)\\n\\nThought: The current temperature in the script is set to 300.0 Kelvin. The assistant needs to increase this temperature by 10 degrees. The ModifyScriptTool can be used to make this change. \\n\\nAction:\\n```\\n{\\n \"action\": \"ModifyScriptTool\",\\n \"action_input\": {\\n \"base_script\": \"reproduce_simulation.py\",\\n \"user_requirement\": \"increase the temperature of the simulation by 10 degrees\"\\n }\\n}\\n```\\nObservation: No script provided. The keys for the input are:\\n \\'query\\' and \\'script\\'\\nThought: It seems I made a mistake in the input for the ModifyScriptTool. The correct keys for the input are \\'query\\' and \\'script\\'. I will correct this and try again.\\n\\nAction:\\n```\\n{\\n \"action\": \"ModifyScriptTool\",\\n \"action_input\": {\\n \"query\": \"increase the temperature of the simulation by 10 degrees\",\\n \"script\": \"reproduce_simulation.py\"\\n }\\n}\\n```\\nObservation: Script modified successfully\\nFinal Answer: The script \\'reproduce_simulation.py\\' has been successfully modified to increase the temperature of the simulation by 10 degrees.'" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "mrkl = MDAgent(type=\"mrkl\")\n", - "mrkl.run(testing_simul)\n" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Thought: To run a simulation of fibronectin, we first need to download the PDB file for fibronectin. After that, we can use the SetUpandRunFunction tool to run the simulation. Finally, we can calculate the average surface area of the protein using Python_REPL tool. Let's start by downloading the PDB file for fibronectin.\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"PDBFileDownloader\",\n", - " \"action_input\": {\n", - " \"query\": \"fibronectin\"\n", - " }\n", - "}\n", - "```PDB file found with this ID: 1X5Y\n", - "1X5Y.pdb is created.\n", - "Now that we have the PDB file for fibronectin, we can proceed to run a simulation. For this, we will use the SetUpandRunFunction tool. We will use the default parameters for the simulation. The PDB file path is required as an input for this tool. Let's run the simulation.\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_path\": \"1X5Y.pdb\",\n", - " \"forcefield_files\": [],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"ewaldErrorTolerance\": null,\n", - " \"constraints\": \"None\",\n", - " \"rigidWater\": false,\n", - " \"constraintTolerance\": null\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.004 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```\n", - "Using SetUpandRunFunction\n", - "{'pdb_path': '1X5Y.pdb', 'forcefield_files': [], 'system_params': {'nonbondedMethod': 'NoCutoff', 'nonbondedCutoff': '1 * nanometers', 'ewaldErrorTolerance': None, 'constraints': 'None', 'rigidWater': False, 'constraintTolerance': None}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds', 'Pressure': '1.0 * bar'}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}}\n", - "system_params {'nonbondedMethod': 'NoCutoff', 'nonbondedCutoff': '1 * nanometers', 'ewaldErrorTolerance': None, 'constraints': 'None', 'rigidWater': False, 'constraintTolerance': None}\n", - "integrator_params {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds', 'Pressure': '1.0 * bar'}\n", - "simmulation_params {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}\n", - "integrator_type LangevinMiddle\n", - "Setting default forcefields v2\n", - "this is the validator error message Invalid ewaldErrorTolerance: float() argument must be a string or a real number, not 'NoneType'.\n", - " If you are using null or None, just dont include\n", - " as part of the parameters.\n", - "Invalid constraintTolerance. float() argument must be a string or a real number, not 'NoneType'. If\n", - " constraintTolerance is null or None,\n", - " just dont include as part of the parameters.\n", - "\n", - "It seems that the simulation failed because of invalid parameters. The error messages suggest that the parameters \"ewaldErrorTolerance\" and \"constraintTolerance\" should not be included if they are null or None. Let's correct this and try again.\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_path\": \"1X5Y.pdb\",\n", - " \"forcefield_files\": [],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\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\": \"0.004 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Using SetUpandRunFunction\n", - "{'pdb_path': '1X5Y.pdb', 'forcefield_files': [], 'system_params': {'nonbondedMethod': 'NoCutoff', 'nonbondedCutoff': '1 * nanometers', 'constraints': 'None', 'rigidWater': False}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds', 'Pressure': '1.0 * bar'}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}}\n", - "system_params {'nonbondedMethod': 'NoCutoff', 'nonbondedCutoff': '1 * nanometers', 'constraints': 'None', 'rigidWater': False}\n", - "integrator_params {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds', 'Pressure': '1.0 * bar'}\n", - "simmulation_params {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}\n", - "integrator_type LangevinMiddle\n", - "Setting default forcefields v2\n", - "this is the validator {'pdb_path': '1X5Y.pdb', 'forcefield_files': ['amber14-all.xml', 'amber14/tip3pfb.xml'], 'system_params': {'nonbondedMethod': NoCutoff, 'nonbondedCutoff': Quantity(value=1.0, unit=nanometer), 'constraints': None, 'rigidWater': False}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': Quantity(value=300.0, unit=kelvin), 'Friction': Quantity(value=1, unit=/picosecond), 'Timestep': Quantity(value=0.004, unit=picosecond), 'Pressure': Quantity(value=1.0, unit=bar)}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}}\n", - "Building system...\n", - "forcefield_files {'nonbondedMethod': NoCutoff, 'nonbondedCutoff': Quantity(value=1.0, unit=nanometer), 'constraints': None, 'rigidWater': False}\n", - "nonbondingCutoff 1.0 nm\n", - "nonbondedMethod NoCutoff\n", - "constraints None\n", - "rigidWater False\n", - "The simulation failed because no template was found for residue 1 (GLY). This could be due to the chain missing a terminal group. To resolve this, we can use the CleaningToolFunction to perform various cleaning operations on the PDB file, such as adding missing atoms and hydrogens, replacing nonstandard residues, and/or removing water. Let's clean the PDB file and try running the simulation again.\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"CleaningToolFunction\",\n", - " \"action_input\": {\n", - " \"input_args\": {\n", - " \"pdb_path\": \"1X5Y.pdb\",\n", - " \"output_path\": \"cleaned_1X5Y.pdb\",\n", - " \"remove_heterogens\": false,\n", - " \"add_hydrogens\": true,\n", - " \"replace_nonstandard_residues\": true,\n", - " \"remove_water\": false\n", - " }\n", - " }\n", - "}\n", - "```Now that we have cleaned the PDB file, let's try running the simulation again using the cleaned PDB file.\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_path\": \"cleaned_1X5Y.pdb\",\n", - " \"forcefield_files\": [],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"NoCutoff\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\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\": \"0.004 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Using SetUpandRunFunction\n", - "{'pdb_path': 'cleaned_1X5Y.pdb', 'forcefield_files': [], 'system_params': {'nonbondedMethod': 'NoCutoff', 'nonbondedCutoff': '1 * nanometers', 'constraints': 'None', 'rigidWater': False}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds', 'Pressure': '1.0 * bar'}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}}\n", - "system_params {'nonbondedMethod': 'NoCutoff', 'nonbondedCutoff': '1 * nanometers', 'constraints': 'None', 'rigidWater': False}\n", - "integrator_params {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds', 'Pressure': '1.0 * bar'}\n", - "simmulation_params {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}\n", - "integrator_type LangevinMiddle\n", - "Setting default forcefields v2\n", - "this is the validator {'pdb_path': 'cleaned_1X5Y.pdb', 'forcefield_files': ['amber14-all.xml', 'amber14/tip3pfb.xml'], 'system_params': {'nonbondedMethod': NoCutoff, 'nonbondedCutoff': Quantity(value=1.0, unit=nanometer), 'constraints': None, 'rigidWater': False}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': Quantity(value=300.0, unit=kelvin), 'Friction': Quantity(value=1, unit=/picosecond), 'Timestep': Quantity(value=0.004, unit=picosecond), 'Pressure': Quantity(value=1.0, unit=bar)}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}}\n", - "Building system...\n", - "forcefield_files {'nonbondedMethod': NoCutoff, 'nonbondedCutoff': Quantity(value=1.0, unit=nanometer), 'constraints': None, 'rigidWater': False}\n", - "nonbondingCutoff 1.0 nm\n", - "nonbondedMethod NoCutoff\n", - "constraints None\n", - "rigidWater False\n", - "Setting up integrator...\n", - "integrator_type LangevinMiddle\n", - "Creating simulation...\n", - "simulation set!\n", - "running simulation in the tool\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Equilibrating...\n", - "The simulation failed again due to a NaN error in the particle coordinates. This could be due to a problem with the initial configuration of the system. We can try to resolve this by changing the parameters of the simulation, such as the nonbondedMethod and constraints. Let's try running the simulation again with different parameters.\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_path\": \"cleaned_1X5Y.pdb\",\n", - " \"forcefield_files\": [],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"CutoffNonPeriodic\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.004 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Using SetUpandRunFunction\n", - "{'pdb_path': 'cleaned_1X5Y.pdb', 'forcefield_files': [], 'system_params': {'nonbondedMethod': 'CutoffNonPeriodic', 'nonbondedCutoff': '1 * nanometers', 'constraints': 'HBonds', 'rigidWater': True}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds', 'Pressure': '1.0 * bar'}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}}\n", - "system_params {'nonbondedMethod': 'CutoffNonPeriodic', 'nonbondedCutoff': '1 * nanometers', 'constraints': 'HBonds', 'rigidWater': True}\n", - "integrator_params {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds', 'Pressure': '1.0 * bar'}\n", - "simmulation_params {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}\n", - "integrator_type LangevinMiddle\n", - "Setting default forcefields v2\n", - "this is the validator error message constraintTolerance must be specified if rigidWater is True\n", - "The simulation failed because the \"constraintTolerance\" parameter must be specified if \"rigidWater\" is set to true. Let's correct this and try running the simulation again.\n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"SetUpandRunFunction\",\n", - " \"action_input\": {\n", - " \"pdb_path\": \"cleaned_1X5Y.pdb\",\n", - " \"forcefield_files\": [],\n", - " \"system_params\": {\n", - " \"nonbondedMethod\": \"CutoffNonPeriodic\",\n", - " \"nonbondedCutoff\": \"1 * nanometers\",\n", - " \"constraints\": \"HBonds\",\n", - " \"rigidWater\": true,\n", - " \"constraintTolerance\": 0.00001\n", - " },\n", - " \"integrator_params\": {\n", - " \"integrator_type\": \"LangevinMiddle\",\n", - " \"Temperature\": \"300 * kelvin\",\n", - " \"Friction\": \"1.0 / picoseconds\",\n", - " \"Timestep\": \"0.004 * picoseconds\",\n", - " \"Pressure\": \"1.0 * bar\"\n", - " },\n", - " \"simmulation_params\": {\n", - " \"Ensemble\": \"NVT\",\n", - " \"Number of Steps\": 10000,\n", - " \"record_interval_steps\": 100,\n", - " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", - " }\n", - " }\n", - "}\n", - "```Using SetUpandRunFunction\n", - "{'pdb_path': 'cleaned_1X5Y.pdb', 'forcefield_files': [], 'system_params': {'nonbondedMethod': 'CutoffNonPeriodic', 'nonbondedCutoff': '1 * nanometers', 'constraints': 'HBonds', 'rigidWater': True, 'constraintTolerance': 1e-05}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds', 'Pressure': '1.0 * bar'}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}}\n", - "system_params {'nonbondedMethod': 'CutoffNonPeriodic', 'nonbondedCutoff': '1 * nanometers', 'constraints': 'HBonds', 'rigidWater': True, 'constraintTolerance': 1e-05}\n", - "integrator_params {'integrator_type': 'LangevinMiddle', 'Temperature': '300 * kelvin', 'Friction': '1.0 / picoseconds', 'Timestep': '0.004 * picoseconds', 'Pressure': '1.0 * bar'}\n", - "simmulation_params {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}\n", - "integrator_type LangevinMiddle\n", - "Setting default forcefields v2\n", - "this is the validator {'pdb_path': 'cleaned_1X5Y.pdb', 'forcefield_files': ['amber14-all.xml', 'amber14/tip3pfb.xml'], 'system_params': {'nonbondedMethod': CutoffNonPeriodic, 'nonbondedCutoff': Quantity(value=1.0, unit=nanometer), 'constraints': HBonds, 'rigidWater': True, 'constraintTolerance': 1e-05}, 'integrator_params': {'integrator_type': 'LangevinMiddle', 'Temperature': Quantity(value=300.0, unit=kelvin), 'Friction': Quantity(value=1, unit=/picosecond), 'Timestep': Quantity(value=0.004, unit=picosecond), 'Pressure': Quantity(value=1.0, unit=bar)}, 'simmulation_params': {'Ensemble': 'NVT', 'Number of Steps': 10000, 'record_interval_steps': 100, 'record_params': ['step', 'potentialEnergy', 'temperature']}}\n", - "Building system...\n", - "forcefield_files {'nonbondedMethod': CutoffNonPeriodic, 'nonbondedCutoff': Quantity(value=1.0, unit=nanometer), 'constraints': HBonds, 'rigidWater': True, 'constraintTolerance': 1e-05}\n", - "nonbondingCutoff 1.0 nm\n", - "nonbondedMethod CutoffNonPeriodic\n", - "constraints HBonds\n", - "rigidWater True\n", - "Setting up integrator...\n", - "integrator_type LangevinMiddle\n", - "Creating simulation...\n", - "simulation set!\n", - "running simulation in the tool\n", - "Performing energy minimization...\n", - "Minimization complete!\n", - "Equilibrating...\n", - "Simulating...\n", - "Done!\n", - "Standalone simulation script written to reproduce_simulation.py\n", - "Now that the simulation has been successfully completed, we can proceed to calculate the average surface area of the protein. For this, we can use the Python_REPL tool to execute a Python command that calculates the surface area. However, calculating the surface area of a protein is a complex task that requires specialized algorithms and is typically done using specialized software or libraries, such as DSSP or MSMS. Unfortunately, I don't have the capability to perform such a calculation. I recommend using a specialized tool or software for this task. \n", - "Action:\n", - "```\n", - "{\n", - " \"action\": \"Final Answer\",\n", - " \"action_input\": \"The simulation of fibronectin has been successfully completed. However, calculating the average surface area of a protein is a complex task that requires specialized algorithms and is typically done using specialized software or libraries, such as DSSP or MSMS. Unfortunately, I don't have the capability to perform such a calculation. I recommend using a specialized tool or software for this task.\"\n", - "}\n", - "```" - ] - }, - { - "data": { - "text/plain": [ - "'Thought: Thought: To run a simulation of fibronectin, we first need to download the PDB file for fibronectin. After that, we can use the SetUpandRunFunction tool to run the simulation. Finally, we can calculate the average surface area of the protein using Python_REPL tool. Let\\'s start by downloading the PDB file for fibronectin.\\nAction:\\n```\\n{\\n \"action\": \"PDBFileDownloader\",\\n \"action_input\": {\\n \"query\": \"fibronectin\"\\n }\\n}\\n```\\nObservation: Name2PDB tool successfully downloaded the PDB file: 1X5Y.pdb\\nThought: Now that we have the PDB file for fibronectin, we can proceed to run a simulation. For this, we will use the SetUpandRunFunction tool. We will use the default parameters for the simulation. The PDB file path is required as an input for this tool. Let\\'s run the simulation.\\nAction:\\n```\\n{\\n \"action\": \"SetUpandRunFunction\",\\n \"action_input\": {\\n \"pdb_path\": \"1X5Y.pdb\",\\n \"forcefield_files\": [],\\n \"system_params\": {\\n \"nonbondedMethod\": \"NoCutoff\",\\n \"nonbondedCutoff\": \"1 * nanometers\",\\n \"ewaldErrorTolerance\": null,\\n \"constraints\": \"None\",\\n \"rigidWater\": false,\\n \"constraintTolerance\": null\\n },\\n \"integrator_params\": {\\n \"integrator_type\": \"LangevinMiddle\",\\n \"Temperature\": \"300 * kelvin\",\\n \"Friction\": \"1.0 / picoseconds\",\\n \"Timestep\": \"0.004 * picoseconds\",\\n \"Pressure\": \"1.0 * bar\"\\n },\\n \"simmulation_params\": {\\n \"Ensemble\": \"NVT\",\\n \"Number of Steps\": 10000,\\n \"record_interval_steps\": 100,\\n \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\\n }\\n }\\n}\\n```\\n\\nObservation: Invalid ewaldErrorTolerance: float() argument must be a string or a real number, not \\'NoneType\\'.\\n If you are using null or None, just dont include\\n as part of the parameters.\\nInvalid constraintTolerance. float() argument must be a string or a real number, not \\'NoneType\\'. If\\n constraintTolerance is null or None,\\n just dont include as part of the parameters.\\n\\n Correct this and try again. \\n Everthing else is fine\\nThought: It seems that the simulation failed because of invalid parameters. The error messages suggest that the parameters \"ewaldErrorTolerance\" and \"constraintTolerance\" should not be included if they are null or None. Let\\'s correct this and try again.\\nAction:\\n```\\n{\\n \"action\": \"SetUpandRunFunction\",\\n \"action_input\": {\\n \"pdb_path\": \"1X5Y.pdb\",\\n \"forcefield_files\": [],\\n \"system_params\": {\\n \"nonbondedMethod\": \"NoCutoff\",\\n \"nonbondedCutoff\": \"1 * nanometers\",\\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\": \"0.004 * picoseconds\",\\n \"Pressure\": \"1.0 * bar\"\\n },\\n \"simmulation_params\": {\\n \"Ensemble\": \"NVT\",\\n \"Number of Steps\": 10000,\\n \"record_interval_steps\": 100,\\n \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\\n }\\n }\\n}\\n```\\nObservation: No template found for residue 1 (GLY). The set of atoms matches GLY, but the bonds are different. Perhaps the chain is missing a terminal group? For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#templateThis were the inputs {\\'pdb_path\\': \\'1X5Y.pdb\\', \\'forcefield_files\\': [], \\'system_params\\': {\\'nonbondedMethod\\': \\'NoCutoff\\', \\'nonbondedCutoff\\': \\'1 * nanometers\\', \\'constraints\\': \\'None\\', \\'rigidWater\\': False}, \\'integrator_params\\': {\\'integrator_type\\': \\'LangevinMiddle\\', \\'Temperature\\': \\'300 * kelvin\\', \\'Friction\\': \\'1.0 / picoseconds\\', \\'Timestep\\': \\'0.004 * picoseconds\\', \\'Pressure\\': \\'1.0 * bar\\'}, \\'simmulation_params\\': {\\'Ensemble\\': \\'NVT\\', \\'Number of Steps\\': 10000, \\'record_interval_steps\\': 100, \\'record_params\\': [\\'step\\', \\'potentialEnergy\\', \\'temperature\\']}}\\nThought: The simulation failed because no template was found for residue 1 (GLY). This could be due to the chain missing a terminal group. To resolve this, we can use the CleaningToolFunction to perform various cleaning operations on the PDB file, such as adding missing atoms and hydrogens, replacing nonstandard residues, and/or removing water. Let\\'s clean the PDB file and try running the simulation again.\\nAction:\\n```\\n{\\n \"action\": \"CleaningToolFunction\",\\n \"action_input\": {\\n \"input_args\": {\\n \"pdb_path\": \"1X5Y.pdb\",\\n \"output_path\": \"cleaned_1X5Y.pdb\",\\n \"remove_heterogens\": false,\\n \"add_hydrogens\": true,\\n \"replace_nonstandard_residues\": true,\\n \"remove_water\": false\\n }\\n }\\n}\\n```\\nObservation: Cleaned File: Added Hydrogens at pH 7.0. Missing Atoms Added and replaces nonstandard residues. written to cleaned_1X5Y.pdb\\nThought: Now that we have cleaned the PDB file, let\\'s try running the simulation again using the cleaned PDB file.\\nAction:\\n```\\n{\\n \"action\": \"SetUpandRunFunction\",\\n \"action_input\": {\\n \"pdb_path\": \"cleaned_1X5Y.pdb\",\\n \"forcefield_files\": [],\\n \"system_params\": {\\n \"nonbondedMethod\": \"NoCutoff\",\\n \"nonbondedCutoff\": \"1 * nanometers\",\\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\": \"0.004 * picoseconds\",\\n \"Pressure\": \"1.0 * bar\"\\n },\\n \"simmulation_params\": {\\n \"Ensemble\": \"NVT\",\\n \"Number of Steps\": 10000,\\n \"record_interval_steps\": 100,\\n \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\\n }\\n }\\n}\\n```\\nObservation: An exception was found: Particle coordinate is NaN. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan. Not a problem, thats one\\n purpose of this tool: to run a short simulation to check for correct\\n initialization. \\n\\n Try a) with different parameters like\\n nonbondedMethod, constraints, etc or b) clean file inputs depending on error\\n \\nThought: The simulation failed again due to a NaN error in the particle coordinates. This could be due to a problem with the initial configuration of the system. We can try to resolve this by changing the parameters of the simulation, such as the nonbondedMethod and constraints. Let\\'s try running the simulation again with different parameters.\\nAction:\\n```\\n{\\n \"action\": \"SetUpandRunFunction\",\\n \"action_input\": {\\n \"pdb_path\": \"cleaned_1X5Y.pdb\",\\n \"forcefield_files\": [],\\n \"system_params\": {\\n \"nonbondedMethod\": \"CutoffNonPeriodic\",\\n \"nonbondedCutoff\": \"1 * nanometers\",\\n \"constraints\": \"HBonds\",\\n \"rigidWater\": true\\n },\\n \"integrator_params\": {\\n \"integrator_type\": \"LangevinMiddle\",\\n \"Temperature\": \"300 * kelvin\",\\n \"Friction\": \"1.0 / picoseconds\",\\n \"Timestep\": \"0.004 * picoseconds\",\\n \"Pressure\": \"1.0 * bar\"\\n },\\n \"simmulation_params\": {\\n \"Ensemble\": \"NVT\",\\n \"Number of Steps\": 10000,\\n \"record_interval_steps\": 100,\\n \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\\n }\\n }\\n}\\n```\\nObservation: constraintTolerance must be specified if rigidWater is True\\n Correct this and try again. \\n Everthing else is fine\\nThought: The simulation failed because the \"constraintTolerance\" parameter must be specified if \"rigidWater\" is set to true. Let\\'s correct this and try running the simulation again.\\nAction:\\n```\\n{\\n \"action\": \"SetUpandRunFunction\",\\n \"action_input\": {\\n \"pdb_path\": \"cleaned_1X5Y.pdb\",\\n \"forcefield_files\": [],\\n \"system_params\": {\\n \"nonbondedMethod\": \"CutoffNonPeriodic\",\\n \"nonbondedCutoff\": \"1 * nanometers\",\\n \"constraints\": \"HBonds\",\\n \"rigidWater\": true,\\n \"constraintTolerance\": 0.00001\\n },\\n \"integrator_params\": {\\n \"integrator_type\": \"LangevinMiddle\",\\n \"Temperature\": \"300 * kelvin\",\\n \"Friction\": \"1.0 / picoseconds\",\\n \"Timestep\": \"0.004 * picoseconds\",\\n \"Pressure\": \"1.0 * bar\"\\n },\\n \"simmulation_params\": {\\n \"Ensemble\": \"NVT\",\\n \"Number of Steps\": 10000,\\n \"record_interval_steps\": 100,\\n \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\\n }\\n }\\n}\\n```\\nObservation: Simulation done!\\nFinal Answer: The simulation of fibronectin has been successfully completed. However, calculating the average surface area of a protein is a complex task that requires specialized algorithms and is typically done using specialized software or libraries, such as DSSP or MSMS. Unfortunately, I don\\'t have the capability to perform such a calculation. I recommend using a specialized tool or software for this task.'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "test = \"Run a simple simulation of fibronectin\"\n", - "mrkl.run(test)" - ] - }, - { - "cell_type": "code", - "execution_count": 23, - "metadata": {}, - "outputs": [], - "source": [ - "from datetime import datetime\n", - "\n", - "def get_timestamp():\n", - " # Get the current date and time\n", - " now = datetime.now()\n", - " # Format the date and time as \"YYYYMMDD_HHMMSS\"\n", - " timestamp = now.strftime(\"%Y%m%d_%H%M%S\")\n", - "\n", - " return timestamp\n", - "\n", - " #File Name/ID in Path Registry JSON\n", - "def _get_fileid(file_name, type):\n", - " # Split the filename on underscores\n", - " parts, ending = file_name.split('.')\n", - " parts = parts.split('_')\n", - " print(parts)\n", - "\n", - " # Extract the timestamp (assuming it's always in the second to last part)\n", - " timestamp_part = parts[-1]\n", - " # Get the last 6 digits of the timestamp\n", - " timestamp_digits = timestamp_part[-6:]\n", - " print(timestamp_digits)\n", - "\n", - " if type == 'protein':\n", - " # Extract the PDB ID (assuming it's always the first part)\n", - " pdb_id = parts[0]\n", - " return pdb_id + timestamp_digits\n", - " if type == 'simulation':\n", - " return \"sim\" + timestamp_digits\n", - " if type == 'record':\n", - " return \"rec\" + timestamp_digits\n", - "\n", - "\n", - "def write_file_name( type:str, **kwargs):\n", - " time_stamp = get_timestamp()\n", - " if type == 'protein':\n", - " file_name = f\"{kwargs['protein_name']}_{kwargs['description']}_{time_stamp}.{kwargs['file_format']}\"\n", - " if type == 'simulation':\n", - " file_name = f\"{kwargs['type_of_sim']}_{kwargs['protein_file_id']}_{kwargs['conditions']}_{time_stamp}\"\n", - " if type == 'record':\n", - " file_name = f\"{kwargs['protein_file_id']}_{kwargs['Sim_id']}_{time_stamp}\"\n", - "\n", - " return file_name\n", - " " - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['AHH', 'raw', '20231220', '151938']\n", - "151938\n" - ] - } - ], - "source": [ - "filename = write_file_name(type='protein', protein_name=\"AHH\", description = 'raw', file_format=\"pdb\")\n", - "file_id = _get_fileid(filename,'protein')" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "AHH_raw_20231220_151938.pdb\n", - "AHH151938\n" - ] - } - ], - "source": [ - "print(filename)\n", - "print(file_id)" - ] - }, - { - "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": "3.11.5" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -}