`deeporigin.drug_discovery.konnektor`¶

Synchronous ligand network generation with the Konnektor platform tool.

Attributes¶

KonnektorNetworkType `module-attribute` ¶

KonnektorNetworkType = Literal['star', 'mst', 'cyclic']

Classes¶

Konnektor ¶

Bases: Execution, SyncExecutableMixin

Generate a ligand network with Konnektor and return a :class:KonnektorResult.

Konnektor accepts at least two ligands. Each ligand is synced before execution so the platform can receive either a ligand entity ID or a remote SDF path. The synchronous :meth:run method returns resolved ligand pairs, connectivity, and inline visualization HTML suitable for :class:~deeporigin.drug_discovery.rbfe.RBFE.

Attributes:

Name	Type	Description
`ligands`	`LigandSet`	Ligands to connect.
`network_type`	`KonnektorNetworkType`	Network topology planner, one of `"star"`, `"mst"`, or `"cyclic"`. Defaults to `"mst"`.

Attributes¶

USER_LOG_COLUMNS `class-attribute` ¶

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

client `instance-attribute` ¶

client: DeepOriginClient = client

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.

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).

ligands `property` ¶

ligands: LigandSet

Ligands to connect.

name `instance-attribute` ¶

name = name

network_type `property` ¶

network_type: KonnektorNetworkType

Network topology planner.

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["konnektor"][
    "tool_key"
]

tool_version `instance-attribute` ¶

tool_version = tool_version

Methods:¶

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 an instance from an execution DTO returned by the platform API.

Creates a bare instance via object.__new__ (bypassing __init__) and populates common tools execution fields (including :attr:name from the DTO name field) via :meth:update_from_dto. If the instance defines _init_after_from_dto (e.g. :class:~deeporigin.drug_discovery.notebook_watch_mixin.NotebookWatchMixin), it is called after common fields are set. Subclasses should call super().from_dto() then rehydrate domain-specific fields from instance._dto["userInputs"].

Parameters:

Name	Type	Description	Default
`dto`	`dict[str, Any]`	Execution payload (same shape as `client.executions.get`).	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`).
`ValueError`	If the DTO `tool.key` does not match `cls.tool_key`.

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`).

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) -> Any

Fetch results for this execution from the data platform.

Thin wrapper around :meth:deeporigin.platform.results.Results.get scoped to this execution's compute_job_id. Subclasses that need result-type-specific filtering (e.g. poses, prepared systems) should override this method and call the appropriate Results wrapper directly rather than teaching this base method about those filters.

Parameters:

Name	Type	Description	Default
`**kwargs`	`Any`	Forwarded verbatim to :meth:`~deeporigin.platform.results.Results.get` (typically `filter_dict`, `limit`, `select`).	`{}`

Returns:

Type	Description
`Any`	Result-explorer response dict with `data` and `meta` keys.

Raises:

Type	Description
`ValueError`	If the execution has no ID yet.

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`).

run ¶

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

Run Konnektor synchronously and return the network result.

Parameters:

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

Returns:

Name	Type	Description
`A`	`KonnektorResult \| None`	class:`KonnektorResult`, or `None` for quote-only responses.

Raises:

Type	Description
`DeepOriginException`	If the execution does not succeed or the response does not contain a valid v0.5 `ligand_network` output.

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.

KonnektorResult `dataclass` ¶

Result of a successful Konnektor synchronous run.

Attributes:

Name	Type	Description
`pairs`	`list[tuple[Ligand, Ligand]]`	Resolved ligand pairs from the planned network edges.
`is_connected`	`bool`	Whether the generated network is fully connected.
`network_html`	`str`	Inline interactive network visualization HTML.

Attributes¶

is_connected `instance-attribute` ¶

is_connected: bool

network_html `instance-attribute` ¶

network_html: str

pairs `instance-attribute` ¶

pairs: list[tuple[Ligand, Ligand]]

Methods:¶

show_network ¶

show_network() -> None

Display the network visualization in IPython.

deeporigin.drug_discovery.konnektor¶

Attributes¶

KonnektorNetworkType module-attribute ¶

Classes¶

Konnektor ¶

Attributes¶

USER_LOG_COLUMNS class-attribute ¶

client instance-attribute ¶

cost property ¶

dto property ¶

estimate property ¶

id property ¶

ligands property ¶

name instance-attribute ¶

network_type property ¶

runtime property ¶

tool_key class-attribute instance-attribute ¶

tool_version instance-attribute ¶

Methods:¶

confirm ¶

duplicate ¶

from_dto classmethod ¶

from_id classmethod ¶

from_last_run classmethod ¶

get_results ¶

get_user_logs ¶

list classmethod ¶

run ¶

sync ¶

update_from_dto ¶

wait ¶

KonnektorResult dataclass ¶

Attributes¶

is_connected instance-attribute ¶

network_html instance-attribute ¶

pairs instance-attribute ¶

Methods:¶

show_network ¶

Functions:¶

`deeporigin.drug_discovery.konnektor`¶

KonnektorNetworkType `module-attribute` ¶

USER_LOG_COLUMNS `class-attribute` ¶

client `instance-attribute` ¶

cost `property` ¶

dto `property` ¶

estimate `property` ¶

id `property` ¶

ligands `property` ¶

name `instance-attribute` ¶

network_type `property` ¶

runtime `property` ¶

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

tool_version `instance-attribute` ¶

from_dto `classmethod` ¶

from_id `classmethod` ¶

from_last_run `classmethod` ¶

list `classmethod` ¶

KonnektorResult `dataclass` ¶

is_connected `instance-attribute` ¶

network_html `instance-attribute` ¶

pairs `instance-attribute` ¶