merged from main into 'exp_code_changes' and resolve conflicts

.pre-commit-config.yaml

@@ -14,6 +14,7 @@ repos:
     hooks:
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix ]
+        exclude: ^notebooks/experiments/compare_python_code/llm_only/
   - repo: https://github.com/psf/black
     rev: "24.10.0"
     hooks:
@@ -34,4 +35,4 @@ repos:
     rev: v1.5.0
     hooks:
       - id: detect-secrets
-        args: [--exclude-files, ".github/workflows/"]
+        args: [--exclude-files, ".github/workflows/", --exclude-files, '.*\.ipynb$']

README.md

@@ -1,15 +1,15 @@
-MDCrow is a LLM-agent based toolset for Molecular Dynamics.
+MDCrow is an LLM-agent based toolset for Molecular Dynamics.
 It's built using Langchain and uses a collection of tools to set up and execute molecular dynamics simulations, particularly in OpenMM.
 
 
 ## Environment Setup
-To use the OpenMM features in the agent, please set up a conda environment, following these steps.
+To use the OpenMM features in the agent, please set up a conda environment following these steps.
 ```
 conda env create -n mdcrow -f environment.yaml
 conda activate mdcrow
 ```
 
-If you already have a conda environment, you can install dependencies before you activate it with the following step.
+If you already have a conda environment, you can install dependencies before you activate it with the following steps.
 - Install the necessary conda dependencies: `conda env update -n <YOUR_CONDA_ENV_HERE> -f environment.yaml`
 
 
@@ -20,29 +20,27 @@ pip install git+https://github.com/ur-whitelab/MDCrow.git
 ```
 
 ## Usage
-The next step is to set up your API keys in your environment. An API key for LLM provider is necessary for this project. Supported LLM providers are OpenAI, TogetherAI, Fireworks, and Anthropic.
-We recommend setting up api keys in a .env file. You can use the provided .env.example file as a template.
+The next step is to set up your API keys in your environment. An API key for an LLM provider is necessary for this project. Supported LLM providers are OpenAI, TogetherAI, Fireworks, and Anthropic.
+We recommend setting up the API keys in a .env file. You can use the provided .env.example file as a template.
 1. Copy the `.env.example` file and rename it to `.env`: `cp .env.example .env`
 2. Replace the placeholder values in `.env` with your actual keys
 
-You can ask MDCrow to conduct molecular dynamics tasks using OpenAI's GPT model
+You can ask MDCrow to conduct molecular dynamics tasks using OpenAI's GPT model.
 ```
 from mdcrow import MDCrow
 
 agent = MDCrow(model="gpt-3.5-turbo")
 agent.run("Simulate protein 1ZNI at 300 K for 0.1 ps and calculate the RMSD over time.")
 ```
-Note: to distinguish Together models from the rest, you'll need to add "together\" prefix in model flag, such as `agent = MDCrow(model="together/meta-llama/Meta-Llama-3.1-70B-Instruct-Turbo")`
+Note: To distinguish Together models from the rest, you'll need to add the "together\" prefix in the model flag, such as `agent = MDCrow(model="together/meta-llama/Meta-Llama-3.1-70B-Instruct-Turbo")`
 
 ## LLM Providers
-By default, we support LLMs through OpenAI API. However, feel free to use other LLM providers. Make sure to install the necessary package for it. Here's list of packages required for alternative LLM providers we support:
+By default, we support LLMs through OpenAI API. However, feel free to use other LLM providers. Make sure to install the necessary package for it. Here's a list of packages required for alternative LLM providers we support:
 - `pip install langchain-together` to use models from TogetherAI
 - `pip install langchain-anthropic` to use models from Anthropic
 - `pip install langchain-fireworks` to use models from Fireworks
 
 
 ## Contributing
 
-We welcome contributions to MDCrow! If you're interested in contributing to the project, please check out our [Contributor's Guide](CONTRIBUTING.md) for detailed instructions on getting started, feature development, and the pull request process.
-
 We value and appreciate all contributions to MDCrow.

mdcrow/tools/base_tools/__init__.py

@@ -1,3 +1,4 @@
+from .analysis_tools.bond_angles_dihedrals_tool import ComputeAngles
 from .analysis_tools.distance_tools import ContactsTool, DistanceMatrixTool
 from .analysis_tools.hydrogen_bonding_tools import HydrogenBondTool
 from .analysis_tools.inertia import MomentOfInertia
@@ -63,6 +64,18 @@
     "GetSubunitStructure",
     "GetTurnsBetaSheetsHelices",
     "GetUniprotID",
+    "ComputeAngles",
+    "ComputeChi1",
+    "ComputeChi2",
+    "ComputeChi3",
+    "ComputeChi4",
+    "ComputeDihedrals",
+    "ComputeOmega",
+    "ComputePhi",
+    "ComputePsi",
+    "ListRegistryPaths",
+    "MapPath2Name",
+    "ModifyBaseSimulationScriptTool",
     "ComputeLPRMSD",
     "ComputeRMSD",
     "ComputeRMSF",
@@ -79,6 +92,7 @@
     "PPIDistance",
     "ProteinName2PDBTool",
     "RadiusofGyrationTool",
+    "RamachandranPlot",
     "RDFTool",
     "RMSDCalculator",
     "Scholar2ResultLLM",

mdcrow/tools/base_tools/analysis_tools/__init__.py

@@ -1,3 +1,4 @@
+from .bond_angles_dihedrals_tool import ComputeAngles
 from .distance_tools import ContactsTool, DistanceMatrixTool
 from .hydrogen_bonding_tools import HydrogenBondTool
 from .inertia import MomentOfInertia
@@ -10,6 +11,7 @@
 from .vis_tools import VisFunctions, VisualizeProtein
 
 __all__ = [
+    "ComputeAngles",
     "ComputeLPRMSD",
     "ComputeRMSD",
     "ComputeRMSF",