Batch Screening
Screen large batches of molecules using our high-throughput retrosynthesis
A high-throughput screening campaign for large-scale chemical libraries can be achieved through submitting batches of Retrosynthesis jobs with shared parameters. Pending AI offers batch sizes of up to 100000 jobs which can be created and then appended to with additional API requests. Batch progress can be tracked with live updates to the number of completed jobs and a high-level screening overview can be retrieved.
Batch synthesis jobs impact the overall queue size for a given engine. Larger batches may lead to a longer wait time for it to complete. Additional metadata data can also be added to the batch submission to help distinguish results beyond an arbitrary batch id field.
See here for more information on our Retrosynthesis capability.
Retrieve a list of batches.
OAuth2 authentication.
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
A pagination field for looking up items in the previous page of results from this resource id. Use the first item in the data field of the previous response.
bat_32ALvrkANBUzVixmK2J2BrApeyc^\w+$A pagination field for looking up items in the next page of results from this resource id. Use the final item in the data field of the previous response.
bat_32ALvrkANBUzVixmK2J2BrApeyc^\w+$Limit the number of results in the data field of the returned list. The number of items in the page can be fewer than the requested value.
50Example: 50Returns a list of batches.
Request validation failed.
GET /retro/v2/batches HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*
{
"data": [
{
"created": "2000-01-01T00:00:00Z",
"description": "Screening of targets for inhibitor 42.",
"filename": "experiment_042_smi",
"id": "id_32ALvrkANBUzVixmK2J2BrApeyc",
"name": "experiment_042",
"number_of_jobs": 100,
"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"
},
"updated": "2000-01-01T00:00:00Z"
}
],
"has_more": true,
"object": "list"
}Create a new batch of retrosynthesis jobs. Individual jobs are provided as a collection of molecules and share a set of parameters options for each.
Provide additional metadata to tag and identify the batch.
The batch size limit is 10000 jobs, although for requests that timeout or fail can be updated with jobs after creation.
OAuth2 authentication.
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
Request data for creating a new batch.
An optional name for the batch. The name provides a human- readable identifier for the batch and is not required to be unique.
An optional filename to help identify the batch and ideal for when a batch is submitted via file.
An optional name for the batch. The name provides a human- readable identifier for the batch and is not required to be unique.
A collection of target molecules in a SMILES format to perform retrosynthesis on. Each structure is submitted as an individual job and queued separately.
NOTE: Duplicate structures are removed automatically.
["CC(=O)OCC","CCN(CC)CC"]Returns the batch.
Payment gateway failed.
Batch resource exceeded size limit.
Request validation failed.
POST /retro/v2/batches HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Content-Type: application/json
Accept: */*
Content-Length: 313
{
"description": "text",
"filename": "text",
"name": "text",
"parameters": {
"building_block_libraries": [
"lib_32ALvrkANBUzVixmK2J2BrApeyc"
],
"building_block_limit": 3,
"number_of_routes": 25,
"processing_time": 300,
"reaction_limit": 3,
"retrosynthesis_engine": "eng_32ALvrkANBUzVixmK2J2BrApeyc"
},
"smiles": [
"CC(=O)OCC",
"CCN(CC)CC"
]
}{
"created": "2000-01-01T00:00:00Z",
"description": "Screening of targets for inhibitor 42.",
"filename": "experiment_042_smi",
"id": "id_32ALvrkANBUzVixmK2J2BrApeyc",
"name": "experiment_042",
"number_of_jobs": 100,
"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"
},
"updated": "2000-01-01T00:00:00Z"
}Retrieve a batch with attached metadata and job parameters.
OAuth2 authentication.
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
A unique identifier for a batch resource.
bat_32ALvrkANBUzVixmK2J2BrApeycPattern: ^\w+$Returns the batch.
Batch resource not found.
Request validation failed.
GET /retro/v2/batches/{batch_id} HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*
{
"created": "2000-01-01T00:00:00Z",
"description": "Screening of targets for inhibitor 42.",
"filename": "experiment_042_smi",
"id": "id_32ALvrkANBUzVixmK2J2BrApeyc",
"name": "experiment_042",
"number_of_jobs": 100,
"object": "object",
"parameters": {
"building_block_libraries": [
"lib_32ALvrkANBUzVixmK2J2BrApeyc"
],
"building_block_limit": 3,
"number_of_routes": 25,
"processing_time": 300,
"reaction_limit": 3,
"retrosynthesis_engine": "eng_32ALvrkANBUzVixmK2J2BrApeyc"
},
"updated": "2000-01-01T00:00:00Z"
}Update a batch resource with more retrosynthesis jobs. The added jobs are queued but must not exceed the total batch limit for a batch resource.
OAuth2 authentication.
Provide a valid Pending AI authentication token. Generating tokens can be done through the Pending AI CLI. Ensure you have an existing account or register for a new one.
pending auth login
pendingai auth token
A unique identifier for a batch resource.
bat_32ALvrkANBUzVixmK2J2BrApeycPattern: ^\w+$Request data for updating an existing batch.
A collection of target molecules in a SMILES format to perform retrosynthesis on. Each structure is submitted as an individual job and queued separately.
NOTE: Duplicate structures are removed automatically.
["CC(=O)OCC","CCN(CC)CC"]Returns the updated batch.
Payment gateway failed.
Batch resource not found.
Batch resource exceeded size limit.
Request validation failed.
PUT /retro/v2/batches/{batch_id} HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Content-Type: application/json
Accept: */*
Content-Length: 36
{
"smiles": [
"CC(=O)OCC",
"CCN(CC)CC"
]
}{
"created": "2000-01-01T00:00:00Z",
"description": "Screening of targets for inhibitor 42.",
"filename": "experiment_042_smi",
"id": "id_32ALvrkANBUzVixmK2J2BrApeyc",
"name": "experiment_042",
"number_of_jobs": 100,
"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"
},
"updated": "2000-01-01T00:00:00Z"
}Delete a batch resource and all attached retrosynthesis jobs. When the request is made for a batch currently being processed, all queued jobs are cancelled.
OAuth2 authentication.
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
A unique identifier for a batch resource.
bat_32ALvrkANBUzVixmK2J2BrApeycPattern: ^\w+$Returns the deleted batch.
Payment gateway failed.
Batch resource not found.
Request validation failed.
DELETE /retro/v2/batches/{batch_id} HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*
{
"created": "2000-01-01T00:00:00Z",
"description": "Screening of targets for inhibitor 42.",
"filename": "experiment_042_smi",
"id": "id_32ALvrkANBUzVixmK2J2BrApeyc",
"name": "experiment_042",
"number_of_jobs": 100,
"object": "object",
"parameters": {
"building_block_libraries": [
"lib_32ALvrkANBUzVixmK2J2BrApeyc"
],
"building_block_limit": 3,
"number_of_routes": 25,
"processing_time": 300,
"reaction_limit": 3,
"retrosynthesis_engine": "eng_32ALvrkANBUzVixmK2J2BrApeyc"
},
"updated": "2000-01-01T00:00:00Z"
}Retrieve the collection of results from retrosynthesis jobs in the batch. The list contains information about the individual job ids used for retrieving synthetic routes and whether the molecules were synthesizable.
OAuth2 authentication.
Provide a valid Pending AI authentication token. Generating tokens can be done through the Pending AI CLI. Ensure you have an existing account or register for a new one.
pending auth login
pendingai auth token
A unique identifier for a batch resource.
bat_32ALvrkANBUzVixmK2J2BrApeycPattern: ^\w+$Providing this header and the value gzip yields results from the endpoint as gzipped plaintext with a base64 encoding.
Returns the batch result.
Batch resource not found.
Request validation failed.
GET /retro/v2/batches/{batch_id}/result HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*
[
{
"completed": true,
"job_id": "job_32ALvrkANBUzVixmK2J2BrApeyc",
"smiles": "CC(=O)OCC",
"synthesizable": true
}
]Retrieve the current status of a batch. The batch status relies on the individual status of all retrosynthesis jobs and can take longer to process. Poll the route with spaced requests compared to the individual retrosynthesis jobs.
OAuth2 authentication.
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
A unique identifier for a batch resource.
bat_32ALvrkANBUzVixmK2J2BrApeycPattern: ^\w+$Returns the batch status.
Batch resource not found.
Request validation failed.
GET /retro/v2/batches/{batch_id}/status HTTP/1.1
Host: api.pending.ai
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*
{
"completed_jobs": 1,
"number_of_jobs": 1,
"status": "submitted"
}Was this helpful?