> For the complete documentation index, see [llms.txt](https://docs.pending.ai/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.pending.ai/api-reference/pai-retro.md).

# PAI Retro

Pending AI's Retrosynthesis Engine capability, engineered for high-throughput synthetic feasibility analysis, combines well-curated and diverse datasets to rapidly identify complex multi-step synthetic routes for broad regions of chemical space.

See the **capability** page for more information:

{% content-ref url="/pages/1h5TxpTFc56h802JWFzt" %}
[Retrosynthesis](/capabilities/retrosynthesis.md)
{% endcontent-ref %}

***

## Workflow Summary

Pending AI's Retrosynthesis engine runs behind a queue-based environment for each specific engine. An [**engine**](/api-reference/pai-retro/retrosynthesis-engines.md) and set of [**building block libraries**](/api-reference/pai-retro/building-block-libraries.md), containing molecules used to terminate a synthetic route, must be provided when submitting a query. 

On submission, a [**job**](/api-reference/pai-retro/synthesis-jobs.md) `id` is provided and then used to poll for results until it is completed, at which point results should be retrieved and saved per query. A similar workflow is made available through [**batch-based**](/api-reference/pai-retro/batch-screening.md) submission to provide a faster screening interface on larger collections of query molecules.

{% @mermaid/diagram content="stateDiagram-v2
a: Inspect Retrosynthesis Engines
b: Inspect Building Block Libraries
c: Submit a Retrosynthesis Query Molecule
d: Retrieve a Status for the Query
e: Retrieve Synthesis Routes for the Query
note right of c: Select engines and libraries as configuration parameters.
note right of d: Repeat until status changes to **completed**.
\[*] --> a
\[*] --> b
\[*] --> c
c --> d
d --> e
e --> \[*]: Further Processing
" %}

See the available [Guides](/developer-tools/guides.md) for more implementation possibilities when integrating with existing drug discovery pipelines.

***

## Frequently Asked Questions

<details>

<summary>Q: Why do some molecules take significantly longer than others for retrosynthesis?</summary>

A: The total time until the results of a retrosynthesis job are ready to be retrieved is dependent on the queue wait time and synthesis processing.&#x20;

* Queues are affected by other jobs shared by an engine when too many requests are made in a given time.
* Processing time can be affected by optional parameters such as the number of routes requested or processing timeout.&#x20;

Some molecules may also fail to find any synthetic routes which means the engine will run longer trying to exhaust all reasonable expandable reaction templates.

</details>

<details>

<summary>Q: Why do results contains fewer synthetic routes than requested?</summary>

A: Configuration specifies a *maximum number of routes* to be found during retrosynthesis, results are limited due to a number of facts such as other optional parameters that enforce diversity, the complexity of a structure, the allowed time limit for a job, and the existence of chemically viable synthetic routes.

</details>

<details>

<summary>Q: What happens if one job fails within a batch?</summary>

A: When an individual query molecule fails (due to an invalid SMILES structure or unexpected processing error), the batch will continue processing until all other jobs are completed. A batch summary can be retrieve storing a success flag per job to help screen any unhandled query molecules from within the batch.

</details>

<details>

<summary>Q: What is the maximum size for a batch submission?</summary>

A: Currently Pending AI offers a batch limit of 100,000 which should be created with multiple `POST /batches` and `PUT /batches` requests due to the size of retrosynthesis result data. Use multiple batches if a screening campaign contains more query molecules.

</details>