moltimate-backend

ProMol successor's backend application.

Contents

• Setup & Run
• Wiping Local Database
• API Summary
• API Details

Setup & Run

IntelliJ

To start the application from IntelliJ, import the project as a Maven project, and run the main(...) entrypoint in Application.java.

Maven CLI

To start the application using Maven's CLI, run:

    mvn spring-boot:run

Wiping Local Database

To wipe the database, delete the generated file moltimate.mv.db at the root of the project.

API Summary

This briefly summarizes all API endpoints.

Alignments

HTTP Method	Endpoint	Function
POST	/align/activesite	Aligns protein active sites with motifs
POST	/align/backbone	NOT IMPLEMENTED. Aligns protein backbones with motifs

Motifs

HTTP Method	Endpoint	Function
GET	/motifs	Get a list of motifs
GET	/motifs/{pdbid}	Get a specific motif
GET	/motifs/debug	TEMPORARY. Stores 4 hard-coded Motifs into the database

API Details

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

Alignments

POST /align/activesite

Aligns protein active sites with motifs

Request body parameters

Parameter	Type	Function
pdbIds	String Array	The PDB IDs of the proteins that will be aligned with each motif
ecNumber	String	Filters the set of motifs. This can be partially-qualified ("3", ""3.4", "3.4.21", or "3.4.21.1")
options	String Array	NOT IMPLEMENTED. Additional options available for active site alignments
filters	String Array	NOT IMPLEMENTED. Additional ways to filter the set of motifs

Example JSON request

{
    "pdbIds": ["8gch", "1ezi", "1ma0"],
	"ecNumber": "3.4.21.1",
	"options": ["rmsd"],
	"filters": []
}

POST /align/backbone

Aligns protein backbones with motifs

NOT IMPLEMENTED

Motifs

GET /motifs

Get a list of motifs

Query string parameters

Parameter	Type	Function
ecnumber	String	An optional EC number to filter the list of motifs by

GET /motifs/{pdbid}

Get a specific motif

Path parameters

Parameter	Type	Function
pdbid	String	The unqiue PDB ID of the motif

GET /motifs/debug

TEMPORARY. Stores 4 hard-coded Motifs into the database