> ## Documentation Index
> Fetch the complete documentation index at: https://docs.plutus.systems/llms.txt
> Use this file to discover all available pages before exploring further.

# 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>