Web API v0.1 - woolfson-group/ccbuilder2 GitHub Wiki

Endpoints

URL: http://coiledcoils.chm.bris.ac.uk/ccbuilder2

Method	URL	Purpose	Details
POST	/builder/api/v0.1/build/coiled-coil	Submits a build job for a single coiled coil.	Link
POST	/builder/api/v0.1/build/collagen	Submits a build job for a single collagen triple helix.	Link
POST	/builder/api/v0.1/optimise/model	Submits a job to optimise the parameters of a model.	Link
GET	/builder/api/v0.1/optimise/check-job-status?opt-job-id=:job-id	Gets the status of an optimisation job.	Link
GET	/builder/api/v0.1/optimise/retrieve-opt-job?opt-job-id=:job-id	Retrieves an optimised model.	Link

---

/builder/api/v0.1/build/coiled-coil Endpoint

Body

The body of the request should be JSON and expects a single field, Parameters, that which contains a list of objects containing the parameters for each helix. Therefore if you have 3 Parameter objects, that equates to a 3-helix coiled coil, 4 would be 4 helix etc.

{
  "Parameters": [
    {
      "Radius": 6.3,
      "Pitch": 194,
      "Interface Angle": 20,
      "Sequence": "EIAAIKQEIAAIKKEIAAIKWEIAAIKQ",
      "Register": "g",
      "Super-Helical Rotation": 0,
      "Orientation": false,
      "Z-Shift": 0,
      "Linked SHR": true
    },
    {
      "Radius": 6.3,
      "Pitch": 194,
      "Interface Angle": 20,
      "Sequence": "EIAAIKQEIAAIKKEIAAIKWEIAAIKQ",
      "Register": "g",
      "Super-Helical Rotation": 0,
      "Orientation": false,
      "Z-Shift": 0,
      "Linked SHR": true
    },
    {
      "Radius": 6.3,
      "Pitch": 194,
      "Interface Angle": 20,
      "Sequence": "EIAAIKQEIAAIKKEIAAIKWEIAAIKQ",
      "Register": "g",
      "Super-Helical Rotation": 0,
      "Orientation": false,
      "Z-Shift": 0,
      "Linked SHR": true
    }
  ]
}

Response

The body of response is JSON and contains the model (pdb, a PDB format string) and various scoring metrics including the BUDE energy (score, a float).

{
  "helix_type": "ALPHA",
  "knob_ids": [
    [
      "A",
      "5"
    ],
    ...
    [
      "C",
      "23"
    ]
  ],
  "mean_rpt_value": 3.6034828742538,
  "model_id": "5ae982e60150dc000caf1021",
  "pdb": "HEADER ISAMBARD Model...",
  "score": -388.61611514213
}

curl Examples

A trimeric coiled coil.

curl --location --request POST "http://coiledcoils.chm.bris.ac.uk/ccbuilder2/builder/api/v0.1/build/coiled-coil" \
         --header "Content-Type: application/json" \
         --data '{
         "Parameters": [
           {
             "Radius": 6.3,
             "Pitch": 194,
             "Interface Angle": 20,
             "Sequence": "EIAAIKQEIAAIKKEIAAIKWEIAAIKQ",
             "Register": "g",
             "Super-Helical Rotation": 0,
             "Orientation": false,
             "Z-Shift": 0,
             "Linked SHR": true
           },
           {
             "Radius": 6.3,
             "Pitch": 194,
             "Interface Angle": 20,
             "Sequence": "EIAAIKQEIAAIKKEIAAIKWEIAAIKQ",
             "Register": "g",
             "Super-Helical Rotation": 0,
             "Orientation": false,
             "Z-Shift": 0,
             "Linked SHR": true
           },
           {
             "Radius": 6.3,
             "Pitch": 194,
             "Interface Angle": 20,
             "Sequence": "EIAAIKQEIAAIKKEIAAIKWEIAAIKQ",
             "Register": "g",
             "Super-Helical Rotation": 0,
             "Orientation": false,
             "Z-Shift": 0,
             "Linked SHR": true
           }
         ]
       }'

A dimeric coiled coil.

curl --location --request POST "http://coiledcoils.chm.bris.ac.uk/ccbuilder2/builder/api/v0.1/build/coiled-coil" \
         --header "Content-Type: application/json" \
         --data '{
         "Parameters": [
           {
             "Radius": 5.1,
             "Pitch": 226,
             "Interface Angle": 24,
             "Sequence": "EIAALKQEIAALKKENAALKWEIAALKQ",
             "Register": "g",
             "Super-Helical Rotation": 0,
             "Orientation": false,
             "Z-Shift": 0,
             "Linked SHR": true
           },
           {
             "Radius": 5.1,
             "Pitch": 226,
             "Interface Angle": 24,
             "Sequence": "EIAALKQEIAALKKENAALKWEIAALKQ",
             "Register": "g",
             "Super-Helical Rotation": 0,
             "Orientation": false,
             "Z-Shift": 0,
             "Linked SHR": true
           }
         ]
       }'

/builder/api/v0.1/build/collagen Endpoint

Body

The body of the request should be JSON and expects a single field, Parameters, that which should contain a list of 3 Parameter objects containing the parameters for each helix. Unlike the web app, the API is not restricted to building models with more or less than 3 helices, but this will create non-sense models! The character "O" can be used in the sequence of collagen models, and represents hydroxyproline.

{
  "Parameters": [
    {
      "Radius": 3.34,
      "Pitch": 59.4,
      "Interface Angle": 20.2,
      "Sequence": "GPPGPPGPPGPPGPPGPPGPPGPPGPP",
      "Register": "a",
      "Super-Helical Rotation": 0,
      "Orientation": false,
      "Z-Shift": 0,
      "Linked SHR": true
    },
    {
      "Radius": 3.34,
      "Pitch": 59.4,
      "Interface Angle": 20.2,
      "Sequence": "GPPGPPGPPGPPGPPGPPGPPGPPGPP",
      "Register": "a",
      "Super-Helical Rotation": 0,
      "Orientation": false,
      "Z-Shift": 0,
      "Linked SHR": true
    },
    {
      "Radius": 3.34,
      "Pitch": 59.4,
      "Interface Angle": 20.2,
      "Sequence": "GPPGPPGPPGPPGPPGPPGPPGPPGPP",
      "Register": "a",
      "Super-Helical Rotation": 0,
      "Orientation": false,
      "Z-Shift": 0,
      "Linked SHR": true
    }
  ]
}

Response

The body of response is JSON and contains the model (pdb, a PDB format string) and various scoring metrics including the BUDE energy (score, a float).

{
  "helix_type": "COLLAGEN", 
  "knob_ids": [], 
  "mean_rpt_value": 3.3271884351049152, 
  "model_id": "5af589090150dc0045081ded", 
  "pdb": "HEADER ISAMBARD Model...", 
  "score": -172.4616750283151
}

curl Examples

curl --location --request POST "http://coiledcoils.chm.bris.ac.uk/ccbuilder2/builder/api/v0.1/build/collagen" \
         --header "Content-Type: application/json" \
         --data '{
         "Parameters": [
           {
             "Radius": 3.34,
             "Pitch": 59.4,
             "Interface Angle": 20.2,
             "Sequence": "GPPGPPGPPGPPGPPGPPGPPGPPGPP",
             "Register": "a",
             "Super-Helical Rotation": 0,
             "Orientation": false,
             "Z-Shift": 0,
             "Linked SHR": true
           },
           {
             "Radius": 3.34,
             "Pitch": 59.4,
             "Interface Angle": 20.2,
             "Sequence": "GPPGPPGPPGPPGPPGPPGPPGPPGPP",
             "Register": "a",
             "Super-Helical Rotation": 0,
             "Orientation": false,
             "Z-Shift": 0,
             "Linked SHR": true
           },
           {
             "Radius": 3.34,
             "Pitch": 59.4,
             "Interface Angle": 20.2,
             "Sequence": "GPPGPPGPPGPPGPPGPPGPPGPPGPP",
             "Register": "a",
             "Super-Helical Rotation": 0,
             "Orientation": false,
             "Z-Shift": 0,
             "Linked SHR": true
           }
         ]
       }'