@platforma-open/milaboratories.antibody-variant-designer.block 1.0.0 → 1.1.0

package/block-pack/published.json

@@ -3,6 +3,6 @@
   "id": {
     "organization": "milaboratories",
     "name": "antibody-variant-designer",
-    "version": "1.0.0"
+    "version": "1.1.0"
   }
 }

package/dist/AGENTS.d.ts

@@ -5120,6 +5120,31 @@ type PlDataTableStateV2 = {
 } | PlDataTableStateV2V6 | PlDataTableStateV2Normalized | PlDataTableStateV2Normalized$1;
 /** Upgrade PlDataTableStateV2 to the latest version */
 //#endregion
+//#region ../node_modules/.pnpm/@platforma-sdk+model@1.80.13/node_modules/@platforma-sdk/model/dist/components/PlMultiSequenceAlignment.d.ts
+interface PlMultiSequenceAlignmentSettings {
+  sequenceColumnIds?: PObjectId[];
+  labelColumnIds?: PTableColumnId[];
+  colorScheme: PlMultiSequenceAlignmentColorSchemeOption;
+  widgets: PlMultiSequenceAlignmentWidget[];
+  alignmentParams: {
+    gpo: number;
+    gpe: number;
+    tgpe: number;
+  };
+}
+type PlMultiSequenceAlignmentWidget = "consensus" | "seqLogo" | "tree" | "legend";
+interface PlMultiSequenceAlignmentModel extends Partial<PlMultiSequenceAlignmentSettings> {
+  version?: number;
+}
+type PlMultiSequenceAlignmentColorSchemeOption = {
+  type: "no-color";
+} | {
+  type: "chemical-properties";
+} | {
+  type: "markup";
+  columnIds: PObjectId[];
+};
+//#endregion
 //#region ../model/dist/types.d.ts
 //#region src/types.d.ts
 /** A single dataset column reference, derived structurally from
@@ -5127,22 +5152,52 @@ type PlDataTableStateV2 = {
  *  this SDK's public `@platforma-sdk/model` entry point does not re-export
  *  a `PlRef` type. */
 type PlRef = NonNullable<DatasetSelection["primary"]>["column"];
+/** Which objectives a run designs against: liability removal alone, humanization alone, or
+ *  liability removal together with humanization. */
+type RunMode = "liabilities" | "humanization" | "liabilities + humanization";
 /** Unified user-editable state persisted by the model. */
 type BlockData$1 = {
   /** Structures dataset, and its optional Lead Selection subset, picked via
    *  `PlDatasetSelector`. */
   dataset?: DatasetSelection;
+  runMode: RunMode;
   rsasaBuriedCutoff: number;
   actOnFixability: string[];
-  maxEditsPerVariant: number;
-  frConfThresh: number;
-  cdrConfThresh: number;
+  maxLiabilityEdits: number;
+  maxFrameworkEdits: number;
+  frConfidenceThreshold: number;
+  cdrConfidenceThreshold: number;
   variantsPerParent: number;
   candidateResiduesPerPosition: number;
+  structuralWeight: number;
+  objectiveWeight: number;
+  nonHumanPriorMargin: number;
+  maxNewLiabilities: number;
+  /** Taxonomy ids the humanization gate does not count as a liability. Empty
+   *  counts every one of them, so a liability the taxonomy gains later blocks
+   *  humanization until the operator unticks it. */
+  humanizationIgnoredLiabilities: string[];
   lowToleranceFloor: number;
-  epistasisRescoreTopK: number; /** Results-table sort / filter / column state, one per page. */
+  epistasisRescoreTopK: number;
+  /** The spellings these fields carried before they were renamed to say the
+   *  quantity instead of abbreviating it. A project persisted under the old
+   *  names still holds them, and `.args()` reads them when the new key is
+   *  absent. Nothing writes them. */
+  frConfThresh?: number;
+  cdrConfThresh?: number;
+  wStruct?: number;
+  wObj?: number;
+  /** The one cap a project persisted before it split into `maxLiabilityEdits`
+   *  and `maxFrameworkEdits`. `.args()` reads it as the liability cap when the
+   *  new key is absent; the framework cap has no old spelling to fall back to.
+   *  Nothing writes it. */
+  maxEditsPerVariant?: number; /** Results-table sort / filter / column state, one per page. */
   variantsTableState: PlDataTableStateV2;
   liabilitiesTableState: PlDataTableStateV2;
+  /** The comparison view alignment: which sequence and label columns are shown,
+   *  the colour scheme, and which widgets are on. UI-only — the component owns
+   *  every key, and an empty object is what it reads as "the current defaults". */
+  alignmentModel: PlMultiSequenceAlignmentModel;
   /** Advanced Settings → Resource Allocation. Unset means the workflow's
    *  own fixed size for that step; set overrides it. Never data-scaled —
    *  the pipeline itself never derives these from input size, so a value
@@ -5163,13 +5218,20 @@ type BlockData$1 = {
 type BlockArgs = {
   primaryRef: NonNullable<DatasetSelection["primary"]>;
   subsetRef?: PlRef;
+  runMode: RunMode;
   rsasaBuriedCutoff: number;
   actOnFixability: string[];
-  maxEditsPerVariant: number;
-  frConfThresh: number;
-  cdrConfThresh: number;
+  maxLiabilityEdits: number;
+  maxFrameworkEdits: number;
+  frConfidenceThreshold: number;
+  cdrConfidenceThreshold: number;
   variantsPerParent: number;
   candidateResiduesPerPosition: number;
+  structuralWeight: number;
+  objectiveWeight: number;
+  nonHumanPriorMargin: number;
+  maxNewLiabilities: number;
+  humanizationIgnoredLiabilities: string[];
   lowToleranceFloor: number;
   epistasisRescoreTopK: number;
   indexAndScanCpu?: number;
@@ -5179,23 +5241,27 @@ type BlockArgs = {
   buildVariantsCpu?: number;
   buildVariantsMem?: number;
 };
-/** The seven skip reasons the three steps can raise. `no-structure`,
- *  `structure-not-imgt`, `structure-multi-domain-chain` and
- *  `no-researchable-residue` come from index-and-scan's index phase;
- *  `no-liability-survived-triage` from its scan phase; `backend-failed` from
- *  read-tolerance; `no-candidate-cleared-motif` from build-variants. Kept as
- *  seven distinct values rather than folding the two later-added index-phase
- *  reasons into `no-structure`: each already has its own shipped skip TSV
- *  row, and merging them would under-report a structural-numbering failure
- *  as a missing-input one. */
-type SkipReason = "no-structure" | "structure-not-imgt" | "structure-multi-domain-chain" | "no-researchable-residue" | "no-liability-survived-triage" | "backend-failed" | "no-candidate-cleared-motif";
-/** One skipped parent, for the Skipped page.
- *  `detail` is free text and empty for every reason except `backend-failed`:
- *  the other six reasons are named, deterministic conditions already fully
- *  explained by the reason itself. */
+/** The rejection reasons the three steps can raise. Index-and-scan's index phase
+ *  raises `no-structure`, `structure-not-imgt`,
+ *  `structure-multi-domain-chain` and `no-researchable-residue`; its scan
+ *  phase `no-liability-survived-triage`; read-tolerance `backend-failed`;
+ *  build-variants the rest. Each value stays distinct rather than
+ *  folding into a neighbour: each already has its own shipped rejection TSV row,
+ *  and merging two would under-report one failure as another. */
+type RejectionReason = "no-structure" | "structure-not-imgt" | "structure-multi-domain-chain" | "no-researchable-residue" | "no-liability-survived-triage" | "backend-failed" | "no-candidate-cleared-the-gate" | "no-nonhuman-framework-position" | "no-tolerance-at-humanization-position" | "no-humanization-variant-cleared-the-gate";
+/** What was lost, over the two branches that write it. `parent` means the run
+ *  designed nothing for that clonotype — no candidate was ever built.
+ *  `variant` means either a candidate was built and a gate turned it away, or
+ *  the parent shipped a variant carrying no edit from this row's objective.
+ *  A refused candidate therefore writes `variant` even where the parent
+ *  shipped nothing. */
+type RejectedType = "parent" | "variant";
+/** One rejected parent or variant, for the Rejection Causes page.
+ *  `detail` is free text, empty where the reason stands alone and otherwise
+ *  carrying the measurement behind it: the caught exception on
+ *  `backend-failed`, the failed check on a design-gate reason. */
 //#endregion
 //#region ../model/dist/index.d.ts
-//#region src/index.d.ts
 declare const platforma: PlatformaExtended<PlatformaV3<BlockData$1, BlockArgs, InferOutputsFromLambdas<{
   datasetOptions: ConfigRenderLambda<{
     readonly primary: {
@@ -16227,11 +16293,15 @@ declare const platforma: PlatformaExtended<PlatformaV3<BlockData$1, BlockArgs, I
 } & {
   synthesisCsv: ConfigRenderLambda<RemoteBlobHandleAndSize | undefined>;
 } & {
-  skippedClonotypes: ConfigRenderLambda<{
+  rejectedClonotypes: ConfigRenderLambda<{
     clonotypeKey: string;
-    reason: SkipReason;
+    reason: RejectionReason;
     detail: string;
-  }[] | undefined>;
+    rejectedType: RejectedType;
+    objective: string;
+  }[] | undefined> & {
+    withStatus: true;
+  };
 } & {
   clonotypeLabelsPf: ConfigRenderLambda<PFrameHandle | undefined>;
 } & {
@@ -16245,7 +16315,24 @@ declare const platforma: PlatformaExtended<PlatformaV3<BlockData$1, BlockArgs, I
       [x: string]: string;
     } | undefined;
   } | undefined>;
-}>, "/" | "/parents" | "/skipped", {}, BlockDefaultUiServices>>;
+} & {
+  alignmentPf: ConfigRenderLambda<PFrameHandle | undefined>;
+} & {
+  alignmentAxisSpec: ConfigRenderLambda<{
+    readonly type: AxisValueType;
+    readonly name: string;
+    readonly domain?: {
+      [x: string]: string;
+    } | undefined;
+    readonly contextDomain?: {
+      [x: string]: string;
+    } | undefined;
+    readonly annotations?: {
+      [x: string]: string;
+    } | undefined;
+    readonly parentAxes?: number[] | undefined;
+  } | undefined>;
+}>, "/" | "/parents" | "/rejection-causes", {}, BlockDefaultUiServices>>;
 //#endregion
 //#region src/index.d.ts
 type BlockContract = {