Synthesis Jobs

Submit target molecules for retrosynthesis and explore novel synthetic routes

For low-throughput screening or synthetic route exploration, a Retrosynthesis job can be submitted for a single query target molecule. The molecule, represented in SMILES format, is provided alongside a set of guiding parameters impacting route diversity and results.

  • Fast synthetic accessibility can be assessed by reducing the time requirement for planning to processing_time=60 and yield only a single route number_of_routes=1.

  • Novel route exploration can be achieved by increasing the time and resource allocation, allowing for multiple routes to be generated and evaluated. Additionally, decreasing building_block_limit and reaction_limit forces the engine to consider more diverse reaction pathways, potentially leading to more novel synthetic routes.

Each job requires specifying a retrosynthesis_engine and building_block_libraries list corresponding to respective resource id fields of the engine and libraries. Our unique representation of synthetic routes provides a detailed reaction tree overview. See our examples for handling results for detailed analysis.

See here for more information on our Retrosynthesis capability.

List jobs

get

Retrieve a list of jobs.

Required scopes
This endpoint requires the following scopes:
Authorizations
OAuth2implicitRequired

OAuth2 authentication.

Authorization URL: Refresh URL:
AuthorizationstringRequired

Provide a valid Pending AI authentication token. Generating tokens can be done through the Pending AI CLI. Ensure you have an existing account or register for a new one.

pending auth login
pendingai auth token
Query parameters
page-numberinteger · min: 1Optional

A page number for retrieving a collection of jobs. Pagination is number-based allowing for arbitrary page lookups. Note that page-size can impact page offset results.

Default: 1Example: 1
page-sizeinteger · min: 1 · max: 100Optional

The number of job resources returned in the response data. There can be fewer jobs returned than requested if the results do not exceed page-size.

Default: 10Example: 10
statusstring · enumOptional

Filter for job statuses to return resources with a matching status value. Use none to skip filtering.

Default: noneExample: nonePossible values:
Responses
200

Returns a list of jobs.

application/json
get
/jobs
GET /retro/v2/jobs HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*

{
  "data": [
    {
      "created": "2000-01-01T00:00:00Z",
      "id": "id_32ALvrkANBUzVixmK2J2BrApeyc",
      "object": "object",
      "parameters": {
        "building_block_libraries": [
          "lib_32ALvrkANBUzVixmK2J2BrApeyc"
        ],
        "building_block_limit": 3,
        "number_of_routes": 25,
        "processing_time": 300,
        "reaction_limit": 3,
        "retrosynthesis_engine": "eng_32ALvrkANBUzVixmK2J2BrApeyc"
      },
      "query": "CC(=O)OCC",
      "routes": [
        {
          "buildingBlocks": [
            {
              "buildingBlockMetadata": [
                {
                  "availability": "in stock",
                  "datasetProvider": "ZINC",
                  "identifier": "fbab3ba39bb8",
                  "price": 2.5
                }
              ],
              "smiles": "OCC"
            }
          ],
          "reactionSmiles": "CC(=O)O.OCC>>CC(=O)OCC",
          "steps": [
            {
              "number": 1,
              "reactionSmiles": "CC(=O)O.OCC>>CC(=O)OCC"
            }
          ]
        }
      ],
      "status": "completed",
      "updated": "2000-01-01T00:00:00Z"
    }
  ],
  "has_more": true,
  "object": "list"
}

Create a job

post

Create a new retrosynthesis job. See the parameters field for options to control the retrosynthesis process.

Required scopes
This endpoint requires the following scopes:
Authorizations
OAuth2implicitRequired

OAuth2 authentication.

Authorization URL: Refresh URL:
AuthorizationstringRequired

Provide a valid Pending AI authentication token. Generating tokens can be done through the Pending AI CLI. Ensure you have an existing account or register for a new one.

pending auth login
pendingai auth token
Body

Request data for creating a new retrosynthesis job.

querystringRequired

A target molecule in a SMILES format to perform retrosynthesis on. If a molecule cannot be processed, the job will return no results.

Example: CC(=O)OCCPattern: ^[a-zA-Z0-9\(\)+-=#%+@\/\\\[\]\*]+$
Responses
200

Returns the job.

application/json
post
/jobs
POST /retro/v2/jobs HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Content-Type: application/json
Accept: */*
Content-Length: 245

{
  "parameters": {
    "building_block_libraries": [
      "lib_32ALvrkANBUzVixmK2J2BrApeyc"
    ],
    "building_block_limit": 3,
    "number_of_routes": 25,
    "processing_time": 300,
    "reaction_limit": 3,
    "retrosynthesis_engine": "eng_32ALvrkANBUzVixmK2J2BrApeyc"
  },
  "query": "CC(=O)OCC"
}
{
  "created": "2000-01-01T00:00:00Z",
  "id": "id_32ALvrkANBUzVixmK2J2BrApeyc",
  "object": "object",
  "parameters": {
    "building_block_libraries": [
      "lib_32ALvrkANBUzVixmK2J2BrApeyc"
    ],
    "building_block_limit": 3,
    "number_of_routes": 25,
    "processing_time": 300,
    "reaction_limit": 3,
    "retrosynthesis_engine": "eng_32ALvrkANBUzVixmK2J2BrApeyc"
  },
  "query": "CC(=O)OCC",
  "routes": [
    {
      "buildingBlocks": [
        {
          "buildingBlockMetadata": [
            {
              "availability": "in stock",
              "datasetProvider": "ZINC",
              "identifier": "fbab3ba39bb8",
              "price": 2.5
            }
          ],
          "smiles": "OCC"
        }
      ],
      "reactionSmiles": "CC(=O)O.OCC>>CC(=O)OCC",
      "steps": [
        {
          "number": 1,
          "reactionSmiles": "CC(=O)O.OCC>>CC(=O)OCC"
        }
      ]
    }
  ],
  "status": "completed",
  "updated": "2000-01-01T00:00:00Z"
}

Retrieve a job

get

Retrieve a retrosynthesis job and any generated synthetic routes.

Required scopes
This endpoint requires the following scopes:
Authorizations
OAuth2implicitRequired

OAuth2 authentication.

Authorization URL: Refresh URL:
AuthorizationstringRequired

Provide a valid Pending AI authentication token. Generating tokens can be done through the Pending AI CLI. Ensure you have an existing account or register for a new one.

pending auth login
pendingai auth token
Path parameters
job_idstring · min: 1 · max: 255Required

A unique identifier for a job resource.

Example: job_32ALvrkANBUzVixmK2J2BrApeycPattern: ^\w+$
Responses
200

Returns the job.

application/json
get
/jobs/{job_id}
GET /retro/v2/jobs/{job_id} HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*

{
  "created": "2000-01-01T00:00:00Z",
  "id": "id_32ALvrkANBUzVixmK2J2BrApeyc",
  "object": "object",
  "parameters": {
    "building_block_libraries": [
      "lib_32ALvrkANBUzVixmK2J2BrApeyc"
    ],
    "building_block_limit": 3,
    "number_of_routes": 25,
    "processing_time": 300,
    "reaction_limit": 3,
    "retrosynthesis_engine": "eng_32ALvrkANBUzVixmK2J2BrApeyc"
  },
  "query": "CC(=O)OCC",
  "routes": [
    {
      "buildingBlocks": [
        {
          "buildingBlockMetadata": [
            {
              "availability": "in stock",
              "datasetProvider": "ZINC",
              "identifier": "fbab3ba39bb8",
              "price": 2.5
            }
          ],
          "smiles": "OCC"
        }
      ],
      "reactionSmiles": "CC(=O)O.OCC>>CC(=O)OCC",
      "steps": [
        {
          "number": 1,
          "reactionSmiles": "CC(=O)O.OCC>>CC(=O)OCC"
        }
      ]
    }
  ],
  "status": "completed",
  "updated": "2000-01-01T00:00:00Z"
}

Delete a job

delete

Delete a retrosynthesis job and any generated synthetic routes. The job cannot be deleted while in progress.

Required scopes
This endpoint requires the following scopes:
Authorizations
OAuth2implicitRequired

OAuth2 authentication.

Authorization URL: Refresh URL:
AuthorizationstringRequired

Provide a valid Pending AI authentication token. Generating tokens can be done through the Pending AI CLI. Ensure you have an existing account or register for a new one.

pending auth login
pendingai auth token
Path parameters
job_idstring · min: 1 · max: 255Required

A unique identifier for a job resource.

Example: job_32ALvrkANBUzVixmK2J2BrApeycPattern: ^\w+$
Responses
200

Returns the deleted job.

application/json
delete
/jobs/{job_id}
DELETE /retro/v2/jobs/{job_id} HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*

{
  "created": "2000-01-01T00:00:00Z",
  "id": "id_32ALvrkANBUzVixmK2J2BrApeyc",
  "object": "object",
  "parameters": {
    "building_block_libraries": [
      "lib_32ALvrkANBUzVixmK2J2BrApeyc"
    ],
    "building_block_limit": 3,
    "number_of_routes": 25,
    "processing_time": 300,
    "reaction_limit": 3,
    "retrosynthesis_engine": "eng_32ALvrkANBUzVixmK2J2BrApeyc"
  },
  "query": "CC(=O)OCC",
  "routes": [
    {
      "buildingBlocks": [
        {
          "buildingBlockMetadata": [
            {
              "availability": "in stock",
              "datasetProvider": "ZINC",
              "identifier": "fbab3ba39bb8",
              "price": 2.5
            }
          ],
          "smiles": "OCC"
        }
      ],
      "reactionSmiles": "CC(=O)O.OCC>>CC(=O)OCC",
      "steps": [
        {
          "number": 1,
          "reactionSmiles": "CC(=O)O.OCC>>CC(=O)OCC"
        }
      ]
    }
  ],
  "status": "completed",
  "updated": "2000-01-01T00:00:00Z"
}

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