`deeporigin.drug_discovery.constrained_docking`¶

Constrained molecular docking via the served tools API.

Attributes¶

Classes¶

ConstrainedDocking ¶

Bases: Execution, SyncExecutableMixin, NotebookWatchMixin

Harmonic constrained docking via deeporigin.constrained-docking.

Dock exactly one ligand with atom-position constraints. Supply either explicit constraints or a docked reference ligand; MCS alignment derives constraints from the reference pose when reference is used.

Execution is synchronous only: call :meth:run, or :meth:run with quote=True for a cost estimate. There is no async :meth:start path for this tool.

Attributes:

Name	Type	Description
`protein`	`Protein`	Target protein structure.
`ligand`	`Ligand`	Ligand to dock (must have a structure file on the platform).
`pocket`	`Pocket`	Binding pocket defining the docking box.
`constraints`	`list[dict[str, Any]]`	Harmonic constraints sent to the tool.
`effort`	`int`	Docking effort level (1 = fastest, 5 = most thorough).
`name`		Execution label, set automatically unless overridden.

Attributes¶

client `instance-attribute` ¶

client: DeepOriginClient = client

constraints `property` ¶

constraints: list[dict[str, Any]]

Harmonic constraints submitted to the tool.

cost `property` ¶

cost: float | None

Actual cost in dollars, set after execution completes.

This property cannot be set manually.

dto `property` ¶

dto: dict[str, Any] | None

Last tools execution DTO from the platform, if any.

effort `class-attribute` `instance-attribute` ¶

effort: int = effort

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).

ligand `property` ¶

ligand: Ligand

Ligand to dock.

name `instance-attribute` ¶

name = (
    name
    if name is not None
    else _constrained_docking_default_name(protein, ligand)
)

pocket `property` ¶

pocket: Pocket

Binding pocket defining the docking box.

protein `property` ¶

protein: Protein

Target protein structure.

reference `property` ¶

reference: Ligand | None

Reference ligand used to derive constraints, if any.

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.

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

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

tool_version `instance-attribute` ¶

tool_version = tool_version

Functions¶

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

Construct a ConstrainedDocking instance from an execution DTO.

from_id `classmethod` ¶

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

Construct an instance from an existing platform execution ID.

Fetches the execution DTO via client.executions.get and delegates to :meth:from_dto. Concrete subclasses override :meth:from_dto to attach domain state from userInputs.

Parameters:

Name	Type	Description	Default
`id`	`str`	Platform execution ID.	required
`client`	`DeepOriginClient \| None`	Optional API client. Uses the default if not provided.	`None`

Returns:

Type	Description
`Self`	A partially-hydrated instance with common fields populated.

Raises:

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

get_poses ¶

get_poses(*, all_poses: bool = False) -> LigandSet

Download pose SDFs from the platform and return a LigandSet.

get_results ¶

get_results(
    dto: dict[str, Any] | None = None,
    *,
    all_poses: bool = False
) -> LigandSet

Load docked poses for this execution from the data platform or jobOutputs.

get_user_logs ¶

get_user_logs(
    *,
    limit: int | None = None,
    offset: int | None = None,
    select: list[str] | None = None,
    with_total_count: bool = False
) -> dict[str, Any] | 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
`dict[str, Any] \| None`	The search response dict (typically `data` / `meta`), or
`dict[str, Any] \| None`	`None` if this instance has no execution id yet.

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`).

run ¶

run(
    *,
    quote: bool = False,
    approve_amount: int | None = None
) -> LigandSet | None

Execute constrained docking synchronously (blocking).

Parameters:

Name	Type	Description	Default
`quote`	`bool`	Shorthand for `approve_amount=0`.	`False`
`approve_amount`	`int \| None`	Spend cap forwarded to the platform as `approveAmount`.	`None`

Returns:

Type	Description
`LigandSet \| None`	A `LigandSet` of docked poses, or `None` when quoted.

Raises:

Type	Description
`DeepOriginException`	If the execution does not succeed or poses could not be loaded.

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).

show_box ¶

show_box() -> str

Visualize the protein with the docking search box in a Jupyter notebook.

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.constrained_docking¶

Attributes¶

Classes¶

ConstrainedDocking ¶

Attributes¶

client instance-attribute ¶

constraints property ¶

cost property ¶

dto property ¶

effort class-attribute instance-attribute ¶

estimate property ¶

id property ¶

ligand property ¶

name instance-attribute ¶

pocket property ¶

protein property ¶

reference property ¶

runtime property ¶

tool_key class-attribute instance-attribute ¶

tool_version instance-attribute ¶

Functions¶

confirm ¶

duplicate ¶

from_dto classmethod ¶

from_id classmethod ¶

get_poses ¶

get_results ¶

get_user_logs ¶

list classmethod ¶

run ¶

show ¶

show_box ¶

stop_watching ¶

sync ¶

update_from_dto ¶

wait ¶

watch async ¶

Functions¶

`deeporigin.drug_discovery.constrained_docking`¶

client `instance-attribute` ¶

constraints `property` ¶

cost `property` ¶

dto `property` ¶

effort `class-attribute` `instance-attribute` ¶

estimate `property` ¶

id `property` ¶

ligand `property` ¶

name `instance-attribute` ¶

pocket `property` ¶

protein `property` ¶

reference `property` ¶

runtime `property` ¶

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

tool_version `instance-attribute` ¶

from_dto `classmethod` ¶

from_id `classmethod` ¶

list `classmethod` ¶

watch `async` ¶