`deeporigin.drug_discovery.patent`¶

Patent drives platform tool deeporigin.draco to extract chemical structures from a PDF document. The workflow is async-only: quote with start(quote=True), confirm(), then wait() and get_results().

Patent -- extract chemical structures from PDF documents via deeporigin.draco.

Attributes¶

Classes¶

Patent ¶

Bases: Execution, AsyncExecutableMixin, NotebookWatchMixin

Extract chemical structures from a patent or chemistry PDF.

Async-only workflow backed by platform tool deeporigin.draco. Upload a local PDF with :meth:start, optionally quote first via start(quote=True) and :meth:confirm, then poll with :meth:wait or :meth:sync and read extracted structures via :meth:get_results.

Attributes¶

USER_LOG_COLUMNS `class-attribute` ¶

USER_LOG_COLUMNS: list[str] = [
    "log_level",
    "tool_key",
    "timestamp",
    "message",
]

app `instance-attribute` ¶

app: str | None = None

approve_amount `instance-attribute` ¶

approve_amount: int | None = None

client `instance-attribute` ¶

client: DeepOriginClient = client

completed_at `instance-attribute` ¶

completed_at: str | None = None

cost `property` ¶

cost: float | None

Actual cost in dollars, set after execution completes.

This property cannot be set manually.

created_at `instance-attribute` ¶

created_at: str | None = None

created_by `instance-attribute` ¶

created_by: str | None = None

dto `property` ¶

dto: dict[str, Any] | None

Last tools execution DTO from the platform, if any.

estimate `property` ¶

estimate: float | None

Cost estimate in dollars, populated when the platform returns a quotation.

Set after run(quote=True), start(quote=True), or any call with approve_amount=0. None until a quotation result is received. This property cannot be set manually.

id `property` ¶

id: str | None

Platform execution ID when set (read-only).

name `instance-attribute` ¶

name = name

pdf `property` ¶

pdf: Path | None

Local PDF path when known (None after :meth:from_dto rehydration).

progress `instance-attribute` ¶

progress: dict | None = None

remote_pdf_path `property` ¶

remote_pdf_path: str | None

UFA key for the uploaded PDF after :meth:start or :meth:from_dto.

runtime `property` ¶

runtime: float | None

Seconds from DTO startedAt to completedAt or current UTC time.

Uses :attr:dto (same shape as client.executions.get). When completedAt is present, it is the end time; otherwise the end time is datetime.now(timezone.utc). Returns None if there is no DTO or startedAt is missing or empty.

session `instance-attribute` ¶

session: str | None = None

started_at `instance-attribute` ¶

started_at: str | None = None

status `instance-attribute` ¶

status: PlatformStatus | None = None

tool_key `class-attribute` `instance-attribute` ¶

tool_key: str = TOOL_KEYS_AND_VERSIONS["patent"]["tool_key"]

tool_version `instance-attribute` ¶

tool_version = tool_version

Methods:¶

cancel ¶

cancel() -> None

Cancel a running or queued execution.

Raises:

Type	Description
`ValueError`	If the job has no execution ID.
`ValueError`	If the job is not in a cancellable state.

confirm ¶

confirm() -> None

Confirm a quoted tools execution on the platform.

Requires :attr:id and status equal to "Quoted". Uses :meth:~deeporigin.platform.executions.Executions.confirm with :data:~deeporigin.utils.constants.TOOL_EXECUTION_POST_TIMEOUT_SECONDS (10 minutes) and retry=False, then applies the returned DTO via :meth:update_from_dto so status, :attr:cost, and :attr:dto reflect the platform response. For direct (blocking) tools the response is typically terminal (Completed); for async tools it may be Created or Running — call :meth:sync until the job finishes.

Raises:

Type	Description
`ValueError`	If there is no platform execution id or status is not `"Quoted"`.

duplicate ¶

duplicate(
    *, client: DeepOriginClient | None = None
) -> Self

Create a fresh copy with the same configuration but no execution state.

Useful after from_id() to re-run the same calculation. The returned instance has no id, status, estimate, or cost — it is ready for run() / start().

Parameters:

Name	Type	Description	Default
`client`	`DeepOriginClient \| None`	Optional API client for the new instance. Falls back to the current instance's client.	`None`

Returns:

Type	Description
`Self`	A new instance sharing the same domain-specific configuration.

from_dto `classmethod` ¶

from_dto(
    dto: dict[str, Any],
    *,
    client: DeepOriginClient | None = None
) -> Self

Construct a Patent instance from an execution DTO.

Parameters:

Name	Type	Description	Default
`dto`	`dict[str, Any]`	Execution payload (same shape as `client.executions.get`).	required
`client`	`DeepOriginClient \| None`	Optional API client.	`None`

Returns:

Type	Description
`Self`	A fully-hydrated Patent instance with status from the DTO.

Raises:

Type	Description
`ValueError`	If `input_file.key` is missing from stored inputs.

from_id `classmethod` ¶

from_id(
    id: str, *, client: DeepOriginClient | None = None
) -> Self

Construct a Patent instance from an existing platform execution ID.

from_last_run `classmethod` ¶

from_last_run(
    *, client: DeepOriginClient | None = None
) -> Self

Construct an instance from the most recently created execution of this tool.

Calls client.executions.list with tool_key, order set to :data:~deeporigin.utils.constants.EXECUTION_LIST_ORDER_CREATED_DESC, and page_size=1, then delegates to :meth:from_dto. Concrete subclasses inherit this method; domain state is restored via their from_dto overrides.

Parameters:

Name	Type	Description	Default
`client`	`DeepOriginClient \| None`	Optional API client. Uses the default if not provided.	`None`

Returns:

Type	Description
`Self`	A partially-hydrated instance for the newest execution by
`Self`	`createdAt`.

Raises:

Type	Description
`NotImplementedError`	If `cls` has no `tool_key` (bare :class:`Execution`).
`ValueError`	If no executions exist for this tool type.

get_results ¶

get_results(**_kwargs: Any) -> DataFrame | None

Retrieve extracted structures as a ligand-oriented DataFrame.

Returns:

Type	Description
`DataFrame \| None`	A DataFrame with `smiles`, `name`, `page`, and related columns,
`DataFrame \| None`	or `None` if the job has not succeeded or no molecules were found.

Raises:

Type	Description
`ValueError`	If no execution has been started.

get_user_logs ¶

get_user_logs(
    *,
    limit: int | None = None,
    offset: int | None = None,
    select: list[str] | None = None,
    with_total_count: bool = False
) -> DataFrame | None

Search data-platform user_logs rows for this execution.

Uses :meth:deeporigin.platform.user_logs.UserLogs.search with this execution's id (tools executionId), stored as execution_id on user_logs rows — the same string passed to :meth:get_results as compute_job_id.

When no execution id is assigned yet, returns None without calling the API.

Parameters:

Name	Type	Description	Default
`limit`	`int \| None`	Max rows to return (forwarded to `UserLogs.search`).	`None`
`offset`	`int \| None`	Skip offset (forwarded).	`None`
`select`	`list[str] \| None`	Columns to select (forwarded).	`None`
`with_total_count`	`bool`	Request total count from the server (forwarded).	`False`

Returns:

Type	Description
`DataFrame \| None`	A DataFrame with columns `log_level`, `tool_key`, `timestamp`,
`DataFrame \| None`	and `message`. `tool_key` omits the `deeporigin.` prefix;
`DataFrame \| None`	`timestamp` is a compact humanized relative time. Returns `None`
`DataFrame \| None`	if this instance has no execution id yet or the client has no
`DataFrame \| None`	`user_logs` API.

list `classmethod` ¶

list(
    *,
    client: DeepOriginClient | None = None,
    status: list[str] | None = None
) -> list[Self]

List executions of this tool type from the platform.

Calls client.executions.list(fetch_all_pages=True, tool_key=...), then builds instances via :meth:from_dto. Optional status filters hydrated instances by instance.status.

Parameters:

Name	Type	Description	Default
`client`	`DeepOriginClient \| None`	Optional API client. Uses the default if not provided.	`None`
`status`	`list[str] \| None`	Optional list of statuses to keep (membership test).	`None`

Returns:

Type	Description
`list[Self]`	Instances of this class, one per matching execution.

Raises:

Type	Description
`NotImplementedError`	If `cls` has no `tool_key` (bare :class:`Execution`).

show ¶

show() -> None

Display the current execution in Jupyter using the execution card HTML view.

If no platform execution ID exists yet, shows the same card with a short notice instead of raising (see :meth:~deeporigin.platform.execution_display.ExecutionDisplay.from_pending).

start ¶

start(
    *,
    quote: bool = False,
    approve_amount: int | None = None,
    **kwargs
) -> None

Submit a persisted async execution to the platform.

Only valid when status is None (no execution exists yet). All other statuses raise immediately to prevent re-submission.

Pass quote=True or approve_amount=0 to request a cost estimate without running. If the platform returns a Quoted DTO the instance is left in that state — call :meth:~deeporigin.drug_discovery.execution.Execution.confirm explicitly to proceed.

Parameters:

Name	Type	Description	Default
`quote`	`bool`	Shorthand for `approve_amount=0`. Takes precedence when both `quote` and `approve_amount` are provided.	`False`
`approve_amount`	`int \| None`	Spend cap passed to the platform as `approveAmount`. `0` requests a quote only. `None` omits the field (platform runs immediately).	`None`
`**kwargs`		Forwarded verbatim to `_start_impl`.	`{}`

Raises:

Type	Description
`ValueError`	If the current status is not `None`.

stop_watching ¶

stop_watching() -> None

Cancel an in-flight watch loop if one is running.

Safe to call when no watch is active. Does not cancel the caller's current task when invoked from inside the watch loop.

sync ¶

sync() -> None

Fetch the latest tools execution from the platform and refresh fields.

Calls client.executions.get for :attr:id and applies the response with :meth:update_from_dto. Use when the job may have changed outside this process (for example after submission from the web UI), to poll lifecycle state, or to refresh an instance built from an older DTO. Available on sync-only and async execution types alike.

If executions.get returns a falsy value, this instance is left unchanged.

Raises:

Type	Description
`ValueError`	If this instance has no execution id yet.
`NotImplementedError`	If `type(self).tool_key` is empty (bare :class:`Execution`).
`ValueError`	If the returned DTO `tool.key` does not match this class (see :meth:`update_from_dto`).

update_from_dto ¶

update_from_dto(dto: dict[str, Any]) -> None

Apply tools execution fields from dto onto this instance.

Updates id, pricing, lifecycle fields, and _dto the same way as :meth:from_dto for a newly created instance. Use after a live executions.create / sync() response to refresh state without constructing a new object (domain inputs on self are unchanged).

Parameters:

Name	Type	Description	Default
`dto`	`dict[str, Any]`	Execution payload (same shape as `client.executions.get`).	required

Raises:

Type	Description
`NotImplementedError`	If `type(self)` has no `tool_key` (bare :class:`Execution`).
`ValueError`	If the DTO `tool.key` does not match `tool_key`.

wait ¶

wait(
    *,
    poll_interval: float = 5.0,
    timeout: float | None = None
) -> dict[str, Any] | None

Block until this execution reaches a terminal state.

Parameters:

Name	Type	Description	Default
`poll_interval`	`float`	Seconds to sleep between polling cycles.	`5.0`
`timeout`	`float \| None`	Maximum total seconds to wait. If `None`, waits indefinitely.	`None`

Returns:

Type	Description
`dict[str, Any] \| None`	The latest execution DTO, or `None` if the platform returned no DTO.

Raises:

Type	Description
`ValueError`	If this instance has no execution id yet.
`TimeoutError`	If `timeout` elapses before the execution terminates.

watch `async` ¶

watch(
    *, interval: float = 5.0, blocking: bool = False
) -> Task | None

Start live notebook updates; optionally block until the job finishes.

By default, awaiting this coroutine finishes in one event-loop turn, so the cell returns while the display keeps updating in the background. Use this when you need to run other cells while the job runs::

task = await abfe.watch()

Set blocking=True or export JOB_WATCH_BLOCK=1 (truthy values: 1, true, yes, on) to run the poll loop inline so the cell does not return until a terminal state — useful for nbconvert --execute and doc CI (see :data:~deeporigin.utils.constants.JOB_WATCH_BLOCK_ENV)::

await abfe.watch(blocking=True)
# or: export JOB_WATCH_BLOCK=1

Parameters:

Name	Type	Description	Default
`interval`	`float`	Seconds between polls.	`5.0`
`blocking`	`bool`	When True, await the watch loop instead of returning a background task. Also blocks when `JOB_WATCH_BLOCK` is truthy.	`False`

Returns:

Type	Description
`Task \| None`	The background task when not blocking; `None` when blocking.
`Task \| None`	Cancel a background watch with :meth:`stop_watching` or `task.cancel()`.

deeporigin.drug_discovery.patent¶

Attributes¶

Classes¶

Patent ¶

Attributes¶

USER_LOG_COLUMNS class-attribute ¶

app instance-attribute ¶

approve_amount instance-attribute ¶

client instance-attribute ¶

completed_at instance-attribute ¶

cost property ¶

created_at instance-attribute ¶

created_by instance-attribute ¶

dto property ¶

estimate property ¶

id property ¶

name instance-attribute ¶

pdf property ¶

progress instance-attribute ¶

remote_pdf_path property ¶

runtime property ¶

session instance-attribute ¶

started_at instance-attribute ¶

status instance-attribute ¶

tool_key class-attribute instance-attribute ¶

tool_version instance-attribute ¶

Methods:¶

cancel ¶

confirm ¶

duplicate ¶

from_dto classmethod ¶

from_id classmethod ¶

from_last_run classmethod ¶

get_results ¶

get_user_logs ¶

list classmethod ¶

show ¶

start ¶

stop_watching ¶

sync ¶

update_from_dto ¶

wait ¶

watch async ¶

Functions:¶

`deeporigin.drug_discovery.patent`¶

USER_LOG_COLUMNS `class-attribute` ¶

app `instance-attribute` ¶

approve_amount `instance-attribute` ¶

client `instance-attribute` ¶

completed_at `instance-attribute` ¶

cost `property` ¶

created_at `instance-attribute` ¶

created_by `instance-attribute` ¶

dto `property` ¶

estimate `property` ¶

id `property` ¶

name `instance-attribute` ¶

pdf `property` ¶

progress `instance-attribute` ¶

remote_pdf_path `property` ¶

runtime `property` ¶

session `instance-attribute` ¶

started_at `instance-attribute` ¶

status `instance-attribute` ¶

tool_key `class-attribute` `instance-attribute` ¶

tool_version `instance-attribute` ¶

from_dto `classmethod` ¶

from_id `classmethod` ¶

from_last_run `classmethod` ¶

list `classmethod` ¶

watch `async` ¶