# Submit Analysis
Source: https://docs.plutus.systems/api-reference/endpoint/analysis

POST /submit/analysis



# Register File
Source: https://docs.plutus.systems/api-reference/endpoint/file

POST /submit/file/



# Get An Analysis
Source: https://docs.plutus.systems/api-reference/endpoint/get-analysis

GET /info/analysis/{analysis_id}



# Get All Files
Source: https://docs.plutus.systems/api-reference/endpoint/get-files

GET /info/files



# Get A Job
Source: https://docs.plutus.systems/api-reference/endpoint/get-job

GET /info/job/{job_id}



# Get All Jobs
Source: https://docs.plutus.systems/api-reference/endpoint/get-jobs

GET /info/jobs



# Get A System
Source: https://docs.plutus.systems/api-reference/endpoint/get-system

GET /info/system/{system_id}



# Get All Systems
Source: https://docs.plutus.systems/api-reference/endpoint/get-systems

GET /info/systems



# Submit Simulation
Source: https://docs.plutus.systems/api-reference/endpoint/job

POST /submit/job



# Retrieve Analysis Data
Source: https://docs.plutus.systems/api-reference/endpoint/retrieve-analysis

GET /retrieve/analysis/{job_id}



# Retrieve Job Data
Source: https://docs.plutus.systems/api-reference/endpoint/retrieve-job

GET /retrieve/job/{job_id}



# Submit System Build
Source: https://docs.plutus.systems/api-reference/endpoint/system

POST /submit/system



# Get Secure Upload URL
Source: https://docs.plutus.systems/api-reference/endpoint/upload-url

GET /submit/upload-url



# Introduction
Source: https://docs.plutus.systems/api-reference/introduction

Overview of the Asclepius API

<Note>
  This section contains the full Asclepius API documentation.\
  If you’re not planning to interact with Asclepius programmatically, you can safely ignore or remove this section.
</Note>

## Welcome

The Asclepius API allows developers and advanced users to interact with the Asclepius engine programmatically.\
Using these endpoints, you can automate workflows, integrate Asclepius into your own tools, or build entirely new applications on top of the platform.

Documentation in this section is generated from the official Asclepius API specification.

<Card title="Asclepius: API Specification" icon="leaf" href="/api-reference/openapi.json">
  View the API specification
</Card>

## Authentication

Access to the Asclepius API requires an API key.\
You can generate and manage your keys within the Asclepius portal.\
Include your key in all requests to authenticate and use the API.


# Examples
Source: https://docs.plutus.systems/examples

View example endpoint calls

<Info>
  **Prerequisites**:

  * A registered Asclepius account
  * A generated API key associated with the account
</Info>

Follow these steps to install and run Mintlify on your operating system.

<Steps>
  <Step title="Request a secure upload URL">
    ```bash theme={null}
    curl --request GET \
      --url 'https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/submit/upload-url?filetype=pdb' \
      --header 'x-api-key: <api-key>'
    ```
  </Step>

  <Step title="Upload your custom simulation files">
    Copy the secure upload link obtained in the previous step and run the following command:

    ```bash theme={null}
    curl --upload-file ./myfile.pdb \
         -H "Content-Type: chemical/x-pdb" \
         "https://your-presigned-url..."
    ```

    A 3d render of your molecules and preview of your files will be available through the [Asclepius UI](https://asclepius.vorticity.xyz).
  </Step>

  <Step title="Register your new files">
    ```bash theme={null}
    curl --request POST \
      --url https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/submit/file/ \
      --header 'Content-Type: application/json' \
      --header 'x-api-key: <api-key>' \
      --data '{
      "name": "<string>",
      "type": "<string>",
      "format": "<string>",
      "file_id": "<string>"
    }'
    ```

    A 3d render of your molecules and preview of your files will be available through the [Asclepius UI](https://asclepius.vorticity.xyz).
  </Step>

  <Step title="Build a system">
    Gather your system requirements including force fields, molecules, and environment before running the next command to build your system.

    ```bash theme={null}
    curl --request POST \
      --url https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/submit/system \
      --header 'Content-Type: application/json' \
      --header 'x-api-key: <api-key>' \
      --data '{
      "box_name": "<string>",
      "box_shape": "<string>",
      "chain_id": "<string>",
      "concentration": 123,
      "force_field": "<string>",
      "ions": "<string>",
      "keep_Hs": true,
      "ligand_input_formats": [
        "<string>"
      ],
      "ligand_residue_names": [
        "<string>"
      ],
      "ligand_rotations": [
        [
          "<any>"
        ]
      ],
      "ligand_translations": [
        [
          "<any>"
        ]
      ],
      "ligands": [
        "<string>"
      ],
      "membrane": "<string>",
      "minimum_padding": 123,
      "pH": 123,
      "protein": "<string>",
      "water_type": "<string>"
    }'
    ```
  </Step>

  <Step title="Submit a simulation">
    Copy the secure upload link obtained in the previous step and run the following command:

    ```bash theme={null}
    curl --request POST \
      --url https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/submit/job \
      --header 'Content-Type: application/json' \
      --header 'x-api-key: <api-key>' \
      --data '{
      "batch_index": 1,
      "batch_name": "<string>",
      "equilibration": [
        {
          "traj_freq": 1,
          "time": 1,
          "log_freq": 1,
          "type": "<string>",
          "restraint_force": 1,
          "restraint_mask": "<string>"
        }
      ],
      "production": {
        "traj_freq": 1,
        "time": 1,
        "log_freq": 1,
        "type": "<string>"
      },
      "temperature": 1,
      "pressure": 1,
      "surface_tension": 1,
      "friction": 1,
      "integration_timestep": 1,
      "ewald_error_tolerance": 1,
      "non_bonded_cutoff": 1,
      "minimization_steps": 1,
      "trajectory_output_format": "<string>"
    }'
    ```
  </Step>

  <Step title="Analyze your trajectory">
    To run your own analysis on the trajectory that was calculated, run the following command:

    ```bash theme={null}
    curl --request POST \
      --url https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/submit/analysis \
      --header 'Content-Type: application/json' \
      --header 'x-api-key: <api-key>' \
      --data '{
      "downsample_frames": 123,
      "distance_masks": [
        "<string>"
      ],
      "rmsd_masks": [
        [
          "<string>"
        ]
      ],
      "rmsf_masks": [
        "<string>"
      ],
      "hbond_angle": 123,
      "hbond_distance": 123
    }'
    ```
  </Step>

  <Step title="Download results">
    ```bash theme={null}
    curl --request GET \
      --url https://98i2es6mi4.execute-api.us-west-2.amazonaws.com/prod/retrieve/job/{job_id} \
      --header 'x-api-key: <api-key>'
    ```
  </Step>
</Steps>


# Introduction
Source: https://docs.plutus.systems/index

Your gateway to the Asclepius API

# Welcome to the Asclepius API

The Asclepius API gives you full programmatic access to the Asclepius molecular dynamics engine — letting you automate workflows, upload data, build systems, launch simulations, run analyses, and retrieve results entirely from your own applications.

Whether you're integrating Asclepius into a research pipeline, building internal tools, or automating large-scale simulation workloads, this documentation is your starting point.

***

## Get started quickly

Jump in and learn the core concepts of running simulations with Asclepius.

<Card title="Quickstart Guide" icon="rocket" href="/quickstart">
  A simple, five-step walkthrough to submit your first simulation.
</Card>

***

## Explore what you can build

Use the API to tailor Asclepius to your exact needs.

<Columns>
  <Card title="Develop with the API" icon="terminal" href="/api-reference/introduction">
    Learn how to authenticate, upload files, create systems, and launch simulations programmatically.
  </Card>

  <Card title="Upload & Manage Data" icon="cloud-upload" href="/api-reference/endpoint/file">
    Add molecular structures, force fields, and other resources for use in your workflows.
  </Card>

  <Card title="Build & Simulate" icon="beaker" href="/api-reference/endpoint/job">
    Construct molecular systems and submit MD simulations using customizable parameters.
  </Card>

  <Card title="Analyze Results" icon="chart-line" href="/api-reference/endpoint/analysis">
    Retrieve outputs, inspect trajectories, and run analysis pipelines.
  </Card>
</Columns>

***

## Want to see what’s possible?

<Card title="Explore example datasets" icon="stars" href="https://asclepius.vorticity.xyz/databank">
  Browse curated molecular dynamics datasets created using Asclepius.
</Card>

***

## Ready to begin?

Use this documentation as your guide as you integrate Asclepius into your scientific or engineering workflows.

<Note>
  If you get stuck, have questions, or want feature guidance, feel free to reach out or explore additional examples in the dataset bank.
</Note>


# Quickstart
Source: https://docs.plutus.systems/quickstart

Start running MD simulations in minutes

## Get started in four steps

Get your first MD simulation running with your customized settings and parameters.

### Step 1: Submit your molecular and simulation files

<AccordionGroup>
  <Accordion icon="upload" title="Request a secure upload-url">
    In order to upload your files, you will first need to request a secure upload URL from us. This URL will give you temporary access to make an upload and has a TTL of 60 minutes.

    Through this URL, you will be able to submit molecular data (e.g., .pdb, .sdf) and custom force field files (e.g., .xml).
  </Accordion>

  <Accordion icon="file-check" title="Register the file to your account">
    Once your file has been successfully uploaded through the secure upload-url, you'll need to register that file with your account to begin using it in your MD simulations.
    Here, you'll use the file\_id obtained from the previous step and assign your file a new name.

    <Tip>Your registered file shows up automatically in your account upon success.</Tip>
  </Accordion>
</AccordionGroup>

### Step 2: Build your simulation box

<AccordionGroup>
  <Accordion icon="sliders" title="Determine your system configuration">
    Before we run an MD simulation, make sure to build the system you'd like to run with first. If you've already built your system before, feel free to skip this step.

    Select the molecules to include in the system. This includes any previously uploaded custom molecule files, or a PDB ID.

    Review the available parameters for customization during the system build. These include force fields, water models, membrane embeddings, and more!
  </Accordion>

  <Accordion icon="rocket" title="Submit the system build ">
    Now, let's hit submit and wait just a few moments for your customized system to build!

    1. Your submitted system build will show up instantly in the System Board.
    2. Make sure to refresh your board periodically to get the latest status updates on your system build.
    3. See your system instantly, once it's built, by viewing its Details.
    4. Make sure to refresh your System View periodically to ge the latest updates on your system build.
    5. Once the build has completed, you'll now be able to submit MD simulations!

    <Tip>Check the simulation logs to see exactly what took place during the system build!</Tip>
  </Accordion>
</AccordionGroup>

### Step 3: Submit your MD simulation

<AccordionGroup>
  <Accordion icon="sliders" title="Determine your simulation configuration">
    Once your system build has complete, you'll now be able to start launching MD simulations.

    Select the system to simulate with via its *system\_id*. Then, review the available parameters for customization during the system build.

    Finally, customize your simulation stages (e.g., energy minimization, equilibration, production), review your selections, and verify the price!
  </Accordion>

  <Accordion icon="play-circle" title="Submit the simulation">
    Now let's hit submit and wait just a few moments for your MD simulation to begin!

    1. Your submitted simulation will show up instantly in the Job Board.
    2. Make sure to refresh your board periodically to get the latest status updates on your simulation.
    3. See your simulation results instantly, as it progresses, by viewing its Details.
    4. Make sure to refresh your Simulation View periodically to ge the latest updates on your simulation.
    5. Once the simulation has completed, you'll now be able to perform analysis on the resulting trajectory!
  </Accordion>
</AccordionGroup>

### Step 4: Run your analysis

<Accordion icon="chart-line" title="Dive Into Your Simulation Trajectory">
  Once your simulation is complete, you can analyze the trajectory to understand its exact molecular interactions.

  Use Amber masking syntax to select residues, atoms, or chains and run analyses tailored to your needs.
</Accordion>

### Step 5: Download your results

<Accordion icon="download" title="Get the Zipped Output Bundle">
  At any point once your simulation has completed, you can download the full set of simulation results in a zipped output bundle.

  This bundle will contain all intermediate structures and trajectories, as well as the final simulated production trajectory at full fidelity.
  All logs, including warnings and error outputs, are included in the bundle.
  You can use these outputs to simply visualize the simulation or even apply your own custom trajectory analysis!
</Accordion>