openprotein.prompt#

Create prompts to be used with PoET models, along with queries which opens up use-cases like inverse folding with PoET-2.

class openprotein.prompt.PromptAPI[source]#

Prompt API providing the interface to create prompts for use with PoET models.

__init__(session)[source]#
Parameters:

session (APISession)

create_prompt(context, name=None, description=None)[source]#

Create a prompt.

Parameters:

  • context (Context | Sequence[Context]) – context or list of contexts, where each context is a Sequence of str, bytes, and/or Protein

  • query (Optional[bytes | str | Protein]) – Optional query provided as sequence/structure

  • name (str) – Name of the prompt.

  • description (Optional[str]) – Description of the prompt.

Returns:

Metadata of the created prompt.

Return type:

PromptMetadata

get_prompt(prompt_id)[source]#

Get the prompt for a given prompt ID.

Parameters:

prompt_id (str) – The prompt ID.

Returns:

The prompt data in binary format.

Return type:

BinaryIO

list_prompts()[source]#

List all prompts.

Returns:

List of prompt metadata.

Return type:

List[PromptMetadata]

create_query(query)[source]#

Create a query.

Parameters:

query (Optional[bytes | str | Protein]) – Optional query provided as sequence/structure

Returns:

Metadata of the created query.

Return type:

QueryMetadata

get_query(query_id)[source]#

Get the query for a given query ID.

Parameters:

query_id (str) – The query ID.

Returns:

The query data in binary format.

Return type:

BinaryIO

class openprotein.prompt.Prompt[source]#

Prompt which contains a set of sequences and/or structures used to condition the PoET models.

__init__(session, job=None, metadata=None, num_replicates=None)[source]#

Initialize a new Prompt instance.

Parameters:

  • session (APISession) – An APISession object used for interacting with the API.

  • job (PromptJob | None) – A PromptJob containing information about the optional prompt job.

  • metadata (PromptMetadata) – A PromptMetadata object containing metadata for the prompt.

  • num_replicates (int | None)

get()[source]#

Return the results from this job.

Return type:

list[list[Protein]]

cancelled()#

check if job is cancelled

Return type:

bool

done()#

Check if job is complete

Return type:

bool

refresh()#

Refresh job status.

wait(interval=5, timeout=None, verbose=False)#

Wait for job to complete, then fetch results.

Parameters:

  • interval (int, optional) – time between polling. Defaults to config.POLLING_INTERVAL.

  • timeout (int, optional) – max time to wait. Defaults to None.

  • verbose (bool, optional) – verbosity flag. Defaults to False.

Returns:

results of job

Return type:

results

wait_until_done(interval=5, timeout=None, verbose=False)#

Wait for job to complete. Do not fetch results (unlike wait())

Parameters:

  • interval (int, optional) – time between polling. Defaults to config.POLLING_INTERVAL.

  • timeout (int, optional) – max time to wait. Defaults to None.

  • verbose (bool, optional) – verbosity flag. Defaults to False.

Returns:

results of job

Return type:

results

class openprotein.prompt.Query[source]#

Query containing a sequence/structure used to query the PoET-2 model which opens up new workflows.

__init__(session, metadata)[source]#

Initialize a new Query instance.

Parameters:

  • session (APISession) – An APISession object used for interacting with the API.

  • metadata (QueryMetadata) – A QueryMetadata object containing metadata for the query.