generate - Biohub Platform

(ESM3) Generates an output track conditioned on inputs

curl --request POST \
  --url https://biohub.ai/api/v1/generate \
  --header 'Authorization: Bearer <token>' \
  --header 'Content-Type: application/json' \
  --data '
{
  "model": "esm3-open-2024-03",
  "track": "<string>",
  "inputs": {
    "sequence": "<string>",
    "secondary_structure": "<string>",
    "sasa": [
      123
    ],
    "function": [
      [
        "<string>",
        123,
        123
      ]
    ],
    "coordinates": [
      [
        [
          123
        ]
      ]
    ],
    "plddt": [
      123
    ],
    "ptm": 123,
    "crmsd": 123,
    "globularity": 123,
    "interface": [
      "<string>"
    ],
    "interface_ptm": 123,
    "pae": [
      [
        123
      ]
    ]
  },
  "potential_sequence_of_concern": false,
  "invalid_ids": [],
  "schedule": "cosine",
  "strategy": "random",
  "num_steps": 20,
  "temperature": 0.5,
  "temperature_annealing": true,
  "top_p": 1,
  "condition_on_coordinates_only": true,
  "only_compute_backbone_rmsd": false,
  "include_pae": false
}
'

import requests

url = "https://biohub.ai/api/v1/generate"

payload = {
    "model": "esm3-open-2024-03",
    "track": "<string>",
    "inputs": {
        "sequence": "<string>",
        "secondary_structure": "<string>",
        "sasa": [123],
        "function": [["<string>", 123, 123]],
        "coordinates": [[[123]]],
        "plddt": [123],
        "ptm": 123,
        "crmsd": 123,
        "globularity": 123,
        "interface": ["<string>"],
        "interface_ptm": 123,
        "pae": [[123]]
    },
    "potential_sequence_of_concern": False,
    "invalid_ids": [],
    "schedule": "cosine",
    "strategy": "random",
    "num_steps": 20,
    "temperature": 0.5,
    "temperature_annealing": True,
    "top_p": 1,
    "condition_on_coordinates_only": True,
    "only_compute_backbone_rmsd": False,
    "include_pae": False
}
headers = {
    "Authorization": "Bearer <token>",
    "Content-Type": "application/json"
}

response = requests.post(url, json=payload, headers=headers)

print(response.text)

const options = {
  method: 'POST',
  headers: {Authorization: 'Bearer <token>', 'Content-Type': 'application/json'},
  body: JSON.stringify({
    model: 'esm3-open-2024-03',
    track: '<string>',
    inputs: {
      sequence: '<string>',
      secondary_structure: '<string>',
      sasa: [123],
      function: [['<string>', 123, 123]],
      coordinates: [[[123]]],
      plddt: [123],
      ptm: 123,
      crmsd: 123,
      globularity: 123,
      interface: ['<string>'],
      interface_ptm: 123,
      pae: [[123]]
    },
    potential_sequence_of_concern: false,
    invalid_ids: [],
    schedule: 'cosine',
    strategy: 'random',
    num_steps: 20,
    temperature: 0.5,
    temperature_annealing: true,
    top_p: 1,
    condition_on_coordinates_only: true,
    only_compute_backbone_rmsd: false,
    include_pae: false
  })
};

fetch('https://biohub.ai/api/v1/generate', options)
  .then(res => res.json())
  .then(res => console.log(res))
  .catch(err => console.error(err));

<?php

$curl = curl_init();

curl_setopt_array($curl, [
  CURLOPT_URL => "https://biohub.ai/api/v1/generate",
  CURLOPT_RETURNTRANSFER => true,
  CURLOPT_ENCODING => "",
  CURLOPT_MAXREDIRS => 10,
  CURLOPT_TIMEOUT => 30,
  CURLOPT_HTTP_VERSION => CURL_HTTP_VERSION_1_1,
  CURLOPT_CUSTOMREQUEST => "POST",
  CURLOPT_POSTFIELDS => json_encode([
    'model' => 'esm3-open-2024-03',
    'track' => '<string>',
    'inputs' => [
        'sequence' => '<string>',
        'secondary_structure' => '<string>',
        'sasa' => [
                123
        ],
        'function' => [
                [
                                '<string>',
                                123,
                                123
                ]
        ],
        'coordinates' => [
                [
                                [
                                                                123
                                ]
                ]
        ],
        'plddt' => [
                123
        ],
        'ptm' => 123,
        'crmsd' => 123,
        'globularity' => 123,
        'interface' => [
                '<string>'
        ],
        'interface_ptm' => 123,
        'pae' => [
                [
                                123
                ]
        ]
    ],
    'potential_sequence_of_concern' => false,
    'invalid_ids' => [
        
    ],
    'schedule' => 'cosine',
    'strategy' => 'random',
    'num_steps' => 20,
    'temperature' => 0.5,
    'temperature_annealing' => true,
    'top_p' => 1,
    'condition_on_coordinates_only' => true,
    'only_compute_backbone_rmsd' => false,
    'include_pae' => false
  ]),
  CURLOPT_HTTPHEADER => [
    "Authorization: Bearer <token>",
    "Content-Type: application/json"
  ],
]);

$response = curl_exec($curl);
$err = curl_error($curl);

curl_close($curl);

if ($err) {
  echo "cURL Error #:" . $err;
} else {
  echo $response;
}

package main

import (
	"fmt"
	"strings"
	"net/http"
	"io"
)

func main() {

	url := "https://biohub.ai/api/v1/generate"

	payload := strings.NewReader("{\n  \"model\": \"esm3-open-2024-03\",\n  \"track\": \"<string>\",\n  \"inputs\": {\n    \"sequence\": \"<string>\",\n    \"secondary_structure\": \"<string>\",\n    \"sasa\": [\n      123\n    ],\n    \"function\": [\n      [\n        \"<string>\",\n        123,\n        123\n      ]\n    ],\n    \"coordinates\": [\n      [\n        [\n          123\n        ]\n      ]\n    ],\n    \"plddt\": [\n      123\n    ],\n    \"ptm\": 123,\n    \"crmsd\": 123,\n    \"globularity\": 123,\n    \"interface\": [\n      \"<string>\"\n    ],\n    \"interface_ptm\": 123,\n    \"pae\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"potential_sequence_of_concern\": false,\n  \"invalid_ids\": [],\n  \"schedule\": \"cosine\",\n  \"strategy\": \"random\",\n  \"num_steps\": 20,\n  \"temperature\": 0.5,\n  \"temperature_annealing\": true,\n  \"top_p\": 1,\n  \"condition_on_coordinates_only\": true,\n  \"only_compute_backbone_rmsd\": false,\n  \"include_pae\": false\n}")

	req, _ := http.NewRequest("POST", url, payload)

	req.Header.Add("Authorization", "Bearer <token>")
	req.Header.Add("Content-Type", "application/json")

	res, _ := http.DefaultClient.Do(req)

	defer res.Body.Close()
	body, _ := io.ReadAll(res.Body)

	fmt.Println(string(body))

}

HttpResponse<String> response = Unirest.post("https://biohub.ai/api/v1/generate")
  .header("Authorization", "Bearer <token>")
  .header("Content-Type", "application/json")
  .body("{\n  \"model\": \"esm3-open-2024-03\",\n  \"track\": \"<string>\",\n  \"inputs\": {\n    \"sequence\": \"<string>\",\n    \"secondary_structure\": \"<string>\",\n    \"sasa\": [\n      123\n    ],\n    \"function\": [\n      [\n        \"<string>\",\n        123,\n        123\n      ]\n    ],\n    \"coordinates\": [\n      [\n        [\n          123\n        ]\n      ]\n    ],\n    \"plddt\": [\n      123\n    ],\n    \"ptm\": 123,\n    \"crmsd\": 123,\n    \"globularity\": 123,\n    \"interface\": [\n      \"<string>\"\n    ],\n    \"interface_ptm\": 123,\n    \"pae\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"potential_sequence_of_concern\": false,\n  \"invalid_ids\": [],\n  \"schedule\": \"cosine\",\n  \"strategy\": \"random\",\n  \"num_steps\": 20,\n  \"temperature\": 0.5,\n  \"temperature_annealing\": true,\n  \"top_p\": 1,\n  \"condition_on_coordinates_only\": true,\n  \"only_compute_backbone_rmsd\": false,\n  \"include_pae\": false\n}")
  .asString();

require 'uri'
require 'net/http'

url = URI("https://biohub.ai/api/v1/generate")

http = Net::HTTP.new(url.host, url.port)
http.use_ssl = true

request = Net::HTTP::Post.new(url)
request["Authorization"] = 'Bearer <token>'
request["Content-Type"] = 'application/json'
request.body = "{\n  \"model\": \"esm3-open-2024-03\",\n  \"track\": \"<string>\",\n  \"inputs\": {\n    \"sequence\": \"<string>\",\n    \"secondary_structure\": \"<string>\",\n    \"sasa\": [\n      123\n    ],\n    \"function\": [\n      [\n        \"<string>\",\n        123,\n        123\n      ]\n    ],\n    \"coordinates\": [\n      [\n        [\n          123\n        ]\n      ]\n    ],\n    \"plddt\": [\n      123\n    ],\n    \"ptm\": 123,\n    \"crmsd\": 123,\n    \"globularity\": 123,\n    \"interface\": [\n      \"<string>\"\n    ],\n    \"interface_ptm\": 123,\n    \"pae\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"potential_sequence_of_concern\": false,\n  \"invalid_ids\": [],\n  \"schedule\": \"cosine\",\n  \"strategy\": \"random\",\n  \"num_steps\": 20,\n  \"temperature\": 0.5,\n  \"temperature_annealing\": true,\n  \"top_p\": 1,\n  \"condition_on_coordinates_only\": true,\n  \"only_compute_backbone_rmsd\": false,\n  \"include_pae\": false\n}"

response = http.request(request)
puts response.read_body

{
  "model": "esm3-open-2024-03",
  "created": "<string>",
  "potential_sequence_of_concern": false,
  "warning_messages": [
    "<string>"
  ],
  "outputs": {
    "sequence": "<string>",
    "secondary_structure": "<string>",
    "sasa": [
      123
    ],
    "function": [
      [
        "<string>",
        123,
        123
      ]
    ],
    "coordinates": [
      [
        [
          123
        ]
      ]
    ],
    "plddt": [
      123
    ],
    "ptm": 123,
    "crmsd": 123,
    "globularity": 123,
    "interface": [
      "<string>"
    ],
    "interface_ptm": 123,
    "pae": [
      [
        123
      ]
    ]
  }
}

{
  "detail": [
    {
      "loc": [
        "<string>"
      ],
      "msg": "<string>",
      "type": "<string>",
      "input": "<unknown>",
      "ctx": {}
    }
  ]
}

POST

api

generate

(ESM3) Generates an output track conditioned on inputs

curl --request POST \
  --url https://biohub.ai/api/v1/generate \
  --header 'Authorization: Bearer <token>' \
  --header 'Content-Type: application/json' \
  --data '
{
  "model": "esm3-open-2024-03",
  "track": "<string>",
  "inputs": {
    "sequence": "<string>",
    "secondary_structure": "<string>",
    "sasa": [
      123
    ],
    "function": [
      [
        "<string>",
        123,
        123
      ]
    ],
    "coordinates": [
      [
        [
          123
        ]
      ]
    ],
    "plddt": [
      123
    ],
    "ptm": 123,
    "crmsd": 123,
    "globularity": 123,
    "interface": [
      "<string>"
    ],
    "interface_ptm": 123,
    "pae": [
      [
        123
      ]
    ]
  },
  "potential_sequence_of_concern": false,
  "invalid_ids": [],
  "schedule": "cosine",
  "strategy": "random",
  "num_steps": 20,
  "temperature": 0.5,
  "temperature_annealing": true,
  "top_p": 1,
  "condition_on_coordinates_only": true,
  "only_compute_backbone_rmsd": false,
  "include_pae": false
}
'

import requests

url = "https://biohub.ai/api/v1/generate"

payload = {
    "model": "esm3-open-2024-03",
    "track": "<string>",
    "inputs": {
        "sequence": "<string>",
        "secondary_structure": "<string>",
        "sasa": [123],
        "function": [["<string>", 123, 123]],
        "coordinates": [[[123]]],
        "plddt": [123],
        "ptm": 123,
        "crmsd": 123,
        "globularity": 123,
        "interface": ["<string>"],
        "interface_ptm": 123,
        "pae": [[123]]
    },
    "potential_sequence_of_concern": False,
    "invalid_ids": [],
    "schedule": "cosine",
    "strategy": "random",
    "num_steps": 20,
    "temperature": 0.5,
    "temperature_annealing": True,
    "top_p": 1,
    "condition_on_coordinates_only": True,
    "only_compute_backbone_rmsd": False,
    "include_pae": False
}
headers = {
    "Authorization": "Bearer <token>",
    "Content-Type": "application/json"
}

response = requests.post(url, json=payload, headers=headers)

print(response.text)

const options = {
  method: 'POST',
  headers: {Authorization: 'Bearer <token>', 'Content-Type': 'application/json'},
  body: JSON.stringify({
    model: 'esm3-open-2024-03',
    track: '<string>',
    inputs: {
      sequence: '<string>',
      secondary_structure: '<string>',
      sasa: [123],
      function: [['<string>', 123, 123]],
      coordinates: [[[123]]],
      plddt: [123],
      ptm: 123,
      crmsd: 123,
      globularity: 123,
      interface: ['<string>'],
      interface_ptm: 123,
      pae: [[123]]
    },
    potential_sequence_of_concern: false,
    invalid_ids: [],
    schedule: 'cosine',
    strategy: 'random',
    num_steps: 20,
    temperature: 0.5,
    temperature_annealing: true,
    top_p: 1,
    condition_on_coordinates_only: true,
    only_compute_backbone_rmsd: false,
    include_pae: false
  })
};

fetch('https://biohub.ai/api/v1/generate', options)
  .then(res => res.json())
  .then(res => console.log(res))
  .catch(err => console.error(err));

<?php

$curl = curl_init();

curl_setopt_array($curl, [
  CURLOPT_URL => "https://biohub.ai/api/v1/generate",
  CURLOPT_RETURNTRANSFER => true,
  CURLOPT_ENCODING => "",
  CURLOPT_MAXREDIRS => 10,
  CURLOPT_TIMEOUT => 30,
  CURLOPT_HTTP_VERSION => CURL_HTTP_VERSION_1_1,
  CURLOPT_CUSTOMREQUEST => "POST",
  CURLOPT_POSTFIELDS => json_encode([
    'model' => 'esm3-open-2024-03',
    'track' => '<string>',
    'inputs' => [
        'sequence' => '<string>',
        'secondary_structure' => '<string>',
        'sasa' => [
                123
        ],
        'function' => [
                [
                                '<string>',
                                123,
                                123
                ]
        ],
        'coordinates' => [
                [
                                [
                                                                123
                                ]
                ]
        ],
        'plddt' => [
                123
        ],
        'ptm' => 123,
        'crmsd' => 123,
        'globularity' => 123,
        'interface' => [
                '<string>'
        ],
        'interface_ptm' => 123,
        'pae' => [
                [
                                123
                ]
        ]
    ],
    'potential_sequence_of_concern' => false,
    'invalid_ids' => [
        
    ],
    'schedule' => 'cosine',
    'strategy' => 'random',
    'num_steps' => 20,
    'temperature' => 0.5,
    'temperature_annealing' => true,
    'top_p' => 1,
    'condition_on_coordinates_only' => true,
    'only_compute_backbone_rmsd' => false,
    'include_pae' => false
  ]),
  CURLOPT_HTTPHEADER => [
    "Authorization: Bearer <token>",
    "Content-Type: application/json"
  ],
]);

$response = curl_exec($curl);
$err = curl_error($curl);

curl_close($curl);

if ($err) {
  echo "cURL Error #:" . $err;
} else {
  echo $response;
}

package main

import (
	"fmt"
	"strings"
	"net/http"
	"io"
)

func main() {

	url := "https://biohub.ai/api/v1/generate"

	payload := strings.NewReader("{\n  \"model\": \"esm3-open-2024-03\",\n  \"track\": \"<string>\",\n  \"inputs\": {\n    \"sequence\": \"<string>\",\n    \"secondary_structure\": \"<string>\",\n    \"sasa\": [\n      123\n    ],\n    \"function\": [\n      [\n        \"<string>\",\n        123,\n        123\n      ]\n    ],\n    \"coordinates\": [\n      [\n        [\n          123\n        ]\n      ]\n    ],\n    \"plddt\": [\n      123\n    ],\n    \"ptm\": 123,\n    \"crmsd\": 123,\n    \"globularity\": 123,\n    \"interface\": [\n      \"<string>\"\n    ],\n    \"interface_ptm\": 123,\n    \"pae\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"potential_sequence_of_concern\": false,\n  \"invalid_ids\": [],\n  \"schedule\": \"cosine\",\n  \"strategy\": \"random\",\n  \"num_steps\": 20,\n  \"temperature\": 0.5,\n  \"temperature_annealing\": true,\n  \"top_p\": 1,\n  \"condition_on_coordinates_only\": true,\n  \"only_compute_backbone_rmsd\": false,\n  \"include_pae\": false\n}")

	req, _ := http.NewRequest("POST", url, payload)

	req.Header.Add("Authorization", "Bearer <token>")
	req.Header.Add("Content-Type", "application/json")

	res, _ := http.DefaultClient.Do(req)

	defer res.Body.Close()
	body, _ := io.ReadAll(res.Body)

	fmt.Println(string(body))

}

HttpResponse<String> response = Unirest.post("https://biohub.ai/api/v1/generate")
  .header("Authorization", "Bearer <token>")
  .header("Content-Type", "application/json")
  .body("{\n  \"model\": \"esm3-open-2024-03\",\n  \"track\": \"<string>\",\n  \"inputs\": {\n    \"sequence\": \"<string>\",\n    \"secondary_structure\": \"<string>\",\n    \"sasa\": [\n      123\n    ],\n    \"function\": [\n      [\n        \"<string>\",\n        123,\n        123\n      ]\n    ],\n    \"coordinates\": [\n      [\n        [\n          123\n        ]\n      ]\n    ],\n    \"plddt\": [\n      123\n    ],\n    \"ptm\": 123,\n    \"crmsd\": 123,\n    \"globularity\": 123,\n    \"interface\": [\n      \"<string>\"\n    ],\n    \"interface_ptm\": 123,\n    \"pae\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"potential_sequence_of_concern\": false,\n  \"invalid_ids\": [],\n  \"schedule\": \"cosine\",\n  \"strategy\": \"random\",\n  \"num_steps\": 20,\n  \"temperature\": 0.5,\n  \"temperature_annealing\": true,\n  \"top_p\": 1,\n  \"condition_on_coordinates_only\": true,\n  \"only_compute_backbone_rmsd\": false,\n  \"include_pae\": false\n}")
  .asString();

require 'uri'
require 'net/http'

url = URI("https://biohub.ai/api/v1/generate")

http = Net::HTTP.new(url.host, url.port)
http.use_ssl = true

request = Net::HTTP::Post.new(url)
request["Authorization"] = 'Bearer <token>'
request["Content-Type"] = 'application/json'
request.body = "{\n  \"model\": \"esm3-open-2024-03\",\n  \"track\": \"<string>\",\n  \"inputs\": {\n    \"sequence\": \"<string>\",\n    \"secondary_structure\": \"<string>\",\n    \"sasa\": [\n      123\n    ],\n    \"function\": [\n      [\n        \"<string>\",\n        123,\n        123\n      ]\n    ],\n    \"coordinates\": [\n      [\n        [\n          123\n        ]\n      ]\n    ],\n    \"plddt\": [\n      123\n    ],\n    \"ptm\": 123,\n    \"crmsd\": 123,\n    \"globularity\": 123,\n    \"interface\": [\n      \"<string>\"\n    ],\n    \"interface_ptm\": 123,\n    \"pae\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"potential_sequence_of_concern\": false,\n  \"invalid_ids\": [],\n  \"schedule\": \"cosine\",\n  \"strategy\": \"random\",\n  \"num_steps\": 20,\n  \"temperature\": 0.5,\n  \"temperature_annealing\": true,\n  \"top_p\": 1,\n  \"condition_on_coordinates_only\": true,\n  \"only_compute_backbone_rmsd\": false,\n  \"include_pae\": false\n}"

response = http.request(request)
puts response.read_body

{
  "model": "esm3-open-2024-03",
  "created": "<string>",
  "potential_sequence_of_concern": false,
  "warning_messages": [
    "<string>"
  ],
  "outputs": {
    "sequence": "<string>",
    "secondary_structure": "<string>",
    "sasa": [
      123
    ],
    "function": [
      [
        "<string>",
        123,
        123
      ]
    ],
    "coordinates": [
      [
        [
          123
        ]
      ]
    ],
    "plddt": [
      123
    ],
    "ptm": 123,
    "crmsd": 123,
    "globularity": 123,
    "interface": [
      "<string>"
    ],
    "interface_ptm": 123,
    "pae": [
      [
        123
      ]
    ]
  }
}

{
  "detail": [
    {
      "loc": [
        "<string>"
      ],
      "msg": "<string>",
      "type": "<string>",
      "input": "<unknown>",
      "ctx": {}
    }
  ]
}

Authorizations

Authorization

string

header

required

Bearer authentication header of the form Bearer <token>, where <token> is your auth token.

Headers

string | null

Body

application/json

model

enum<string>

required

You may have access to additional, private models as well. These will be visible on the Rate Limits page under the Developer Console

Available options:

esm3-open-2024-03

track

string

required

Track to generate: sequence, structure, secondary_structure, sasa, or function.

inputs

object

required

Show child attributes

potential_sequence_of_concern

boolean

default:false

Disclose potential sequences of concern. For approved users, such sequences will not go through additional safety filtering. Reach out if you are interested in using this.

invalid_ids

integer[]

Token indices that should not be sampled.

schedule

enum<string>

default:cosine

Unmasking schedule for generation. Controls the number of tokens to unmask during each round of iterative generation.

Available options:

cosine,

linear

strategy

enum<string>

default:random

Unmasking strategy to use. Controls which tokens to unmask during each round of iterative generation. 'random' will unmask a correct number of tokens randomly. 'entropy' will unmask the tokens with the lowest logit entropy first. Default was random. Updated on 02/14/2025.

Available options:

random,

entropy

num_steps

integer

default:20

Number of steps for generation. There is diminishing return for decoding steps more than 20. Note that this needs to be less than or equal to the sequence length. Default was 8. Updated on 02/14/2025.

Required range: 1 <= x <= 100

temperature

number

default:0.5

Temperature for sampling. Default was 1.0. Updated on 02/14/2025.

Required range: x >= 0

temperature_annealing

boolean

default:true

Whether temperature should be annealed during generation. Default was False. Updated on 02/14/2025.

top_p

number

default:1

Top-p sampling.

Required range: x <= 1

condition_on_coordinates_only

boolean

default:true

Use coordinates instead of structure tokens as generation conditioning.

only_compute_backbone_rmsd

boolean

default:false

Only compute the RMSD of the backbone atoms. Affects the returned crmsd.

include_pae

boolean

default:false

Whether to include Predicted Aligned Error (PAE) matrix in the response. Local inference ignores this flag.

Response

Successful Response

model

enum<string>

required

You may have access to additional, private models as well. These will be visible on the Rate Limits page under the Developer Console

Available options:

esm3-open-2024-03

created

string

required

ISO formatted date time

potential_sequence_of_concern

boolean

default:false

Indicate that the returned sequence may be of potential concerns.

warning_messages

string[] | null

Warning messages returned by FastAPI.

outputs

object | null

Show child attributes