autodock-docker

The components necessary to build a docker container running an instance of autodock vina with its own HTTP API. You must have access to an AWS s3 Bucket to successfully run. (This includes your own access key and secret access key)

Contents

• Setup & Run
• API Summary
• API Details

Setup & Run

Docker Desktop

Setting up to use AWS s3 functionality:

1. Obtain your access key and secret access key from your AWS organization.
2. Create a "config.json" file in the top level of this directory to contain your access key and secret access key. This is a json formatted file for example: { "accessKeyId":"[ACCESS KEY]", "secretAccessKey": "[SECRET ACCESS KEY]", "region": "[AWS REGION]" }
3. On your AWS account make sure you have access to your S3 bucket
4. In the index.js file, uncomment AWS.config.loadFromPath('./config.json'); towards the top of the file
5. Set the variable bucket = "<>"
6. Create and Run Docker Image following steps below.

Next, build a docker image from the root directory of the autodock-docker source code.

docker image build -t [NAME OF YOUR IMAGE] [location of the autodock-docker directory]

After the image has been generated, create a container. This container should have port 8000 exposed.

docker container run --publish [PORT ON MACHINE TO EXPOSE]:8000 --detach --name [NAME OF YOUR IMAGE]

Users can now interact with the instance of Autodock in the docker container. The following output should appear:

```
> autodock@0.0.1 start /opt/autodock
> node index.js

Listening on port 8000.
```

When Deploying to AWS ECS Instance: Remove references to "config.json" file

API Summary

This briefly summarizes all API endpoints.

HTTP Method	Endpoint	Function
POST	/v1/autodock	Submits .pdbqt files and parameters and starts an autodock docking job
GET	/v1/autodock	Returns a zip file of finished autodock job, or a "Job still proccessing" if the job has not yet completed

API Details

This outlines the API's endpoints, request types, and expected request parameters or JSON payload.

POST /v1/autodock

Submits .pdbqt files and parameters and starts an autodock docking job

Request body parameters (See http://vina.scripps.edu/manual.html#summary)

Parameter	Type	Function
macromolecule	form data	A macromolecule file to be docked. A .pdbqt file is expected.
ligand	form data	A ligand file to be docked. A .pdbqt file is expected.
center_x	form data	X coordinate of the center.
center_y	form data	Y coordinate of the center.
center_z	form data	Z coordinate of the center.
size_x	form data	size in the X dimension
size_y	form data	size in the Y dimension
size_z	form data	size in the Z dimension
cpu	form data	the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)
seed	form data	explicit random seed
exhaustiveness	form data	exhaustiveness of the global search (roughly proportional to time): 1+
num_modes	form data	maximum number of binding modes to generate
energy_range	form data	maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)

Output

Returns a jobId hash value which is used to retrieve the job once finished. (status: 200) If there is an error, returns an error message.

GET /v1/autodock

Retrieves autodock job file

Path parameters

Parameter	Type	Function
jobId	String	A hash value identifying the autodock job to retrieve

Output

If the job has completed an output.zip file is returned containing the docked macromolecule/ligand and the log.txt (status: 200) If the job is not finished or does not exist, returns the message "Job still processing." (status: 200) If the conversion was a failure an error.txt file is returned containing autodock output (status: 500)