@datagrok-libraries/bio 5.65.3 → 6.0.0

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.65.3",
+  "version": "6.0.0",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",
@@ -25,18 +25,17 @@
     "mjolnir.js": "^2.7.0",
     "rxjs": "^6.5.5",
     "uuid": "^9.0.1",
-    "wu": "^2.1.0"
+    "wu": "^2.1.0",
+    "@datagrok-libraries/hwe": "^1.0.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.16",
-    "@datagrok-libraries/js-draw-lite": "^0.0.10",
     "@types/signals": "1.0.1",
     "@types/three": "^0.159.0",
     "@types/uuid": "^9.0.1",
     "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^8.8.1",
     "@typescript-eslint/parser": "^8.8.1",
-    "datagrok-tools": "^4.14.20",
+    "datagrok-tools": "^6.3.3",
     "eslint": "8.57.1",
     "eslint-config-google": "^0.14.0",
     "eslint-plugin-deprecation": "^3.0.0",

package/src/helm/consts.d.ts

@@ -1,4 +1,13 @@
-import { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/js-draw-lite/src/types/org';
-import { HelmTabKeys, MonomerNumberingTypes } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
-export { HelmTypes, MonomerTypes, PolymerTypes, MonomerNumberingTypes, HelmTabKeys };
+import { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/hwe';
+export { HelmTypes, MonomerTypes, PolymerTypes };
+export declare enum MonomerNumberingTypes {
+    default = 0,
+    continuous = 1
+}
+export declare enum HelmTabKeys {
+    Sequence = "sequence",
+    Helm = "notation",
+    Properties = "properties",
+    StructureView = "structureview"
+}
 //# sourceMappingURL=consts.d.ts.map

package/src/helm/consts.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAC,MAAM,yBAAyB,CAAC;AAE9E,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAC,CAAC;AAM/C,oBAAY,qBAAqB;IAC/B,OAAO,IAAI;IACX,UAAU,IAAI;CACf;AAED,oBAAY,WAAW;IACrB,QAAQ,aAAa;IACrB,IAAI,aAAa;IACjB,UAAU,eAAe;IACzB,aAAa,kBAAkB;CAChC"}

package/src/helm/consts.js

@@ -1,3 +1,23 @@
-import { HelmTypes } from '@datagrok-libraries/js-draw-lite/src/types/org';
-export { HelmTypes };
+// HELM type vocabulary is owned by `@datagrok-libraries/hwe` (the standalone
+// HELM editor) and re-exported here as the single source of truth. The string
+// values match the canonical Pistoia HELM Web Editor, except `NUCLEOTIDE` which
+// uses the corrected spelling `HELM_NUCLEOTIDE` (was `HELM_NUCLETIDE`).
+import { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/hwe';
+export { HelmTypes, MonomerTypes, PolymerTypes };
+// hwe migration: these two small enums are not part of the hwe value vocabulary.
+// They are defined here locally (replicating the legacy HELM Web Editor values)
+// so `@datagrok-libraries/bio` no longer depends on
+// `@datagrok-libraries/helm-web-editor`.
+export var MonomerNumberingTypes;
+(function (MonomerNumberingTypes) {
+    MonomerNumberingTypes[MonomerNumberingTypes["default"] = 0] = "default";
+    MonomerNumberingTypes[MonomerNumberingTypes["continuous"] = 1] = "continuous";
+})(MonomerNumberingTypes || (MonomerNumberingTypes = {}));
+export var HelmTabKeys;
+(function (HelmTabKeys) {
+    HelmTabKeys["Sequence"] = "sequence";
+    HelmTabKeys["Helm"] = "notation";
+    HelmTabKeys["Properties"] = "properties";
+    HelmTabKeys["StructureView"] = "structureview";
+})(HelmTabKeys || (HelmTabKeys = {}));
 //# sourceMappingURL=consts.js.map

package/src/helm/consts.js.map

@@ -1 +1 @@
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+{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,6EAA6E;AAC7E,8EAA8E;AAC9E,gFAAgF;AAChF,wEAAwE;AACxE,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAC,MAAM,yBAAyB,CAAC;AAE9E,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAC,CAAC;AAE/C,iFAAiF;AACjF,gFAAgF;AAChF,oDAAoD;AACpD,yCAAyC;AACzC,MAAM,CAAN,IAAY,qBAGX;AAHD,WAAY,qBAAqB;IAC/B,uEAAW,CAAA;IACX,6EAAc,CAAA;AAChB,CAAC,EAHW,qBAAqB,KAArB,qBAAqB,QAGhC;AAED,MAAM,CAAN,IAAY,WAKX;AALD,WAAY,WAAW;IACrB,oCAAqB,CAAA;IACrB,gCAAiB,CAAA;IACjB,wCAAyB,CAAA;IACzB,8CAA+B,CAAA;AACjC,CAAC,EALW,WAAW,KAAX,WAAW,QAKtB"}

package/src/helm/helm-helper.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"helm-helper.d.ts","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAEhC,OAAO,KAAK,EAAC,KAAK,EAAE,GAAG,EAAE,QAAQ,EAAE,kBAAkB,EAAC,MAAM,SAAS,CAAC;AACtE,OAAO,EACW,aAAa,EAAE,OAAO,EAAc,cAAc,EAAE,QAAQ,EAC7E,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,eAAe,EAAC,MAAM,0BAA0B,CAAC;AACzD,OAAO,EAAC,UAAU,EAAC,MAAM,qBAAqB,CAAC;AAC/C,OAAO,EAAC,YAAY,EAAC,MAAM,oCAAoC,CAAC;AAEhE,MAAM,MAAM,qBAAqB,GAAG,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,YAAY,CAAC,GAAG;IAC7E,aAAa,EAAE,OAAO,CAAC,kBAAkB,CAAC,CAAC;IAC3C,QAAQ,EAAE,OAAO,CAAC;CACnB,CAAC;AAEF,8BAAsB,aAAc,SAAQ,EAAE,CAAC,WAAW,CAAC,YAAY,CAAC;IACtE,QAAQ,KAAK,QAAQ,IAAI,OAAO,CAAC;IACjC,QAAQ,KAAK,QAAQ,CAAC,KAAK,EAAE,OAAO,EAAE;IAEtC,QAAQ,KAAK,WAAW,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC;IAEnD,QAAQ,KAAK,OAAO,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC;IAE/C,QAAQ,CAAC,MAAM,IAAI,IAAI;IAEvB,QAAQ,CAAC,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,EAAE,CAAC,EAAE,QAAQ,GAAG,IAAI;CACvE;AAED;;GAEG;AACH,MAAM,MAAM,cAAc,GAAG;IAC3B,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC;CACxC,CAAA;AAED,eAAO,MAAM,yBAAyB,0BAA0B,CAAC;AAEjE,qBAAa,qBAAsB,SAAQ,KAAK;IAC9C,SAAgB,IAAI,2BAA6B;gBAErC,OAAO,CAAC,EAAE,MAAM;CAG7B;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,SAAS,IAAI,UAAU,CAAC;IAE5B,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,qBAAqB,GAAG,aAAa,CAAC;IAE9E,mBAAmB,CAAC,IAAI,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,EAAE,OAAO,CAAC,kBAAkB,CAAC,GAAG,cAAc,CAAC;IAE/F,kBAAkB,CAAC,IAAI,EAAE,cAAc,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,GAAG,CAAC;IAE7D,IAAI,qBAAqB,IAAI,aAAa,GAAG,IAAI,CAAC;IAElD,yBAAyB,CAAC,UAAU,EAAE,eAAe,GAAG,aAAa,CAAC;IAEtE,qBAAqB,CAAC,aAAa,EAAE,aAAa,GAAG,aAAa,CAAC;IACnE,2BAA2B,IAAI,aAAa,CAAC;IAE7C,cAAc,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,QAAQ,GAAG,IAAI,CAAC;IAEpF,kDAAkD;IAClD,WAAW,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,MAAM,EAAE,CAAC;IAE7C,KAAK,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,KAAK,GAAG,OAAO,CAAC;IAC7C,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc,CAAC;CAC1C;AAED,wBAAsB,aAAa,IAAI,OAAO,CAAC,WAAW,CAAC,CAO1D;AAED,OAAO,QAAQ,iBAAiB,CAAC;IAC/B,UAAiB,KAAK,CAAC;QACrB;;WAEG;QACH,SAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,qBAAqB,GAAG,OAAO,CAAC,aAAa,CAAC,CAAC;KAClG;CACF;AAOD,mBAAmB;AACnB,wBAAgB,oBAAoB,CAClC,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,IAAI,CAAC,EAAE,MAAM,GACpC,EAAC,cAAc,AAAd,cAAc,CAAC,QAAQ,EAAE,WAAW,CAAC,MAAM,CAAC,CAgB/C"}

package/src/helm/helm-helper.js

@@ -28,6 +28,8 @@ export function getMonomerHandleArgs(a, name) {
     let elem;
     const aa = a;
     if (aa.T === 'ATOM') {
+        // Legacy HelmAtom.biotype() returns the js-draw-lite HelmType union (which
+        // still carries the `HELM_NUCLETIDE` typo); cast to the hwe-owned HelmType.
         biotype = aa.biotype();
         elem = aa.elem;
     }

package/src/helm/helm-helper.js.map

@@ -1 +1 @@
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package/src/helm/types.d.ts

@@ -1,26 +1,69 @@
-import type { HelmType, PolymerType, MonomerType, WebEditorRGroups, MonomerSetType } from '@datagrok-libraries/js-draw-lite/src/types/org';
-import type { Point } from '@datagrok-libraries/js-draw-lite/src/Point';
-import type { Atom } from '@datagrok-libraries/js-draw-lite/src/Atom';
-import type { IBio, IJsAtom } from '@datagrok-libraries/js-draw-lite/src/types/jsdraw2';
-import type { Bond } from '@datagrok-libraries/js-draw-lite/src/Bond';
-import type { Mol } from '@datagrok-libraries/js-draw-lite/src/Mol';
-import type { IMolHandler } from '@datagrok-libraries/js-draw-lite/src/types/mol-handler';
-import type { Editor } from '@datagrok-libraries/js-draw-lite/src/JSDraw.Editor';
-import type { IHelmBio, HelmAtom, HelmBond, HelmMol, HelmEditor, HelmString, IOrgHelmWebEditor, IOrgHelmMonomers, GetMonomerFunc, GetMonomerResType, MonomersFuncs, IHelmEditorOptions, IHelmDrawOptions, IMonomerColors, IWebEditorMonomer } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
-import type { HweWindow } from '@datagrok-libraries/helm-web-editor/src/types';
-import type { MonomerExplorer } from '@datagrok-libraries/helm-web-editor/helm/MonomerExplorer';
-import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
-import type { TabDescType } from '@datagrok-libraries/js-draw-lite/form/Tab';
-import type { JSDraw2ModuleType, ScilModuleType } from '@datagrok-libraries/js-draw-lite/src/types';
-import type { OrgType } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
-import type { Monomers } from '@datagrok-libraries/helm-web-editor/helm/Monomers';
-import type { DojoType, DojoxType } from '@datagrok-libraries/js-draw-lite/src/types/dojo';
-export { HelmType, PolymerType, MonomerType, WebEditorRGroups };
-export { Point, IBio, Atom, IJsAtom, Bond, Mol, Editor, MonomerExplorer };
-export { IHelmBio, HelmAtom, HelmBond, HelmMol, HelmEditor, HelmString };
-export { IWebEditorMonomer, IMonomerColors, IOrgHelmWebEditor, IOrgHelmMonomers, IMolHandler, IHelmEditorOptions, IHelmDrawOptions, GetMonomerFunc, GetMonomerResType, App, Monomers, };
-export { DojoType, DojoxType };
-export { HweWindow, ScilModuleType, JSDraw2ModuleType, OrgType };
+import type { HelmType, PolymerType, MonomerType, HelmAtomLike, HelmBondLike, HelmMolLike, HelmAtomBioLike, AppLike, JSDraw2EditorLike, MonomerExplorerLike, MonomersFuncsLike, IWebEditorMonomerLike } from '@datagrok-libraries/hwe';
+import type { MonomerNumberingTypes } from './consts';
+export type { HelmType, PolymerType, MonomerType };
+/** 2-D point (the legacy JSDraw2 `Point` shape). */
+export interface Point {
+    x: number;
+    y: number;
+}
+export type IBio<_TBio = unknown> = HelmAtomBioLike;
+export type IHelmBio = HelmAtomBioLike;
+export type Atom<_T = unknown, _TBio = unknown> = HelmAtomLike;
+export type Bond<_T = unknown, _TBio = unknown> = HelmBondLike;
+export type Mol<_T = unknown, _TBio = unknown> = HelmMolLike;
+export type Editor<_T = unknown, _TBio = unknown, _O = unknown> = JSDraw2EditorLike;
+export type IJsAtom = HelmAtomLike;
+export type HelmAtom = HelmAtomLike;
+export type HelmBond = HelmBondLike;
+export type HelmMol = HelmMolLike;
+export type HelmEditor = JSDraw2EditorLike;
+export type HelmString = string;
+export type App = AppLike;
+export type MonomerExplorer = MonomerExplorerLike;
+export type MonomersFuncs = MonomersFuncsLike;
+export type WebEditorRGroups = {
+    [group: string]: string;
+};
+export interface IMonomerColors {
+    linecolor: string;
+    backgroundcolor: string;
+    textcolor: string;
+    nature?: string;
+}
+export interface IMonomer {
+    /** symbol */ id?: string;
+    /** name */ n?: string;
+    /** natural analog */ na?: string;
+    /** polymer type */ type?: PolymerType;
+    /** monomer type */ mt?: MonomerType;
+    /** molfile */ m?: string;
+    /** molfile compressed */ mz?: any;
+    /** substituents */ at?: WebEditorRGroups;
+    /** number of substituents */ rs?: number;
+    issmiles?: boolean;
+    smiles?: string;
+    name?: string;
+    oldname?: string;
+    /** Used by Formula */ stats?: any;
+}
+export interface IWebEditorMonomer extends IMonomer, Partial<IMonomerColors> {
+}
+export type MonomerSetType = {
+    [symbol: string]: IMonomer;
+};
+export type GetMonomerResType = IWebEditorMonomerLike | null;
+export type GetMonomerFunc = (a: HelmAtom | HelmType, name?: string) => GetMonomerResType;
+export interface IHelmDrawOptions {
+    fontsize?: number;
+    monomerNumbering?: MonomerNumberingTypes;
+    getMonomer?: GetMonomerFunc;
+}
+export interface IHelmEditorOptions {
+    width?: number;
+    height?: number;
+    viewonly?: boolean;
+    drawOptions?: IHelmDrawOptions;
+}
 export interface ISeqMonomer {
     position: number;
     biotype: HelmType;
@@ -31,5 +74,4 @@ export interface IHelmWebEditor {
     get host(): HTMLDivElement;
     resizeEditor(width: number, height: number): void;
 }
-export { MonomerSetType, MonomersFuncs, TabDescType };
 //# sourceMappingURL=types.d.ts.map

package/src/helm/types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EACV,QAAQ,EAAE,WAAW,EAAE,WAAW,EAClC,YAAY,EAAE,YAAY,EAAE,WAAW,EAAE,eAAe,EACxD,OAAO,EAAE,iBAAiB,EAAE,mBAAmB,EAAE,iBAAiB,EAClE,qBAAqB,EACtB,MAAM,yBAAyB,CAAC;AACjC,OAAO,KAAK,EAAC,qBAAqB,EAAC,MAAM,UAAU,CAAC;AAEpD,YAAY,EAAC,QAAQ,EAAE,WAAW,EAAE,WAAW,EAAC,CAAC;AAEjD,oDAAoD;AACpD,MAAM,WAAW,KAAK;IACpB,CAAC,EAAE,MAAM,CAAC;IACV,CAAC,EAAE,MAAM,CAAC;CACX;AAQD,MAAM,MAAM,IAAI,CAAC,KAAK,GAAG,OAAO,IAAI,eAAe,CAAC;AACpD,MAAM,MAAM,QAAQ,GAAG,eAAe,CAAC;AACvC,MAAM,MAAM,IAAI,CAAC,EAAE,GAAG,OAAO,EAAE,KAAK,GAAG,OAAO,IAAI,YAAY,CAAC;AAC/D,MAAM,MAAM,IAAI,CAAC,EAAE,GAAG,OAAO,EAAE,KAAK,GAAG,OAAO,IAAI,YAAY,CAAC;AAC/D,MAAM,MAAM,GAAG,CAAC,EAAE,GAAG,OAAO,EAAE,KAAK,GAAG,OAAO,IAAI,WAAW,CAAC;AAC7D,MAAM,MAAM,MAAM,CAAC,EAAE,GAAG,OAAO,EAAE,KAAK,GAAG,OAAO,EAAE,EAAE,GAAG,OAAO,IAAI,iBAAiB,CAAC;AACpF,MAAM,MAAM,OAAO,GAAG,YAAY,CAAC;AAEnC,MAAM,MAAM,QAAQ,GAAG,YAAY,CAAC;AACpC,MAAM,MAAM,QAAQ,GAAG,YAAY,CAAC;AACpC,MAAM,MAAM,OAAO,GAAG,WAAW,CAAC;AAClC,MAAM,MAAM,UAAU,GAAG,iBAAiB,CAAC;AAC3C,MAAM,MAAM,UAAU,GAAG,MAAM,CAAC;AAEhC,MAAM,MAAM,GAAG,GAAG,OAAO,CAAC;AAC1B,MAAM,MAAM,eAAe,GAAG,mBAAmB,CAAC;AAClD,MAAM,MAAM,aAAa,GAAG,iBAAiB,CAAC;AAG9C,MAAM,MAAM,gBAAgB,GAAG;IAAE,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAE3D,MAAM,WAAW,cAAc;IAC7B,SAAS,EAAE,MAAM,CAAC;IAClB,eAAe,EAAE,MAAM,CAAC;IACxB,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,QAAQ;IACvB,aAAa,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IAC1B,WAAW,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC;IACvB,qBAAqB,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IAClC,mBAAmB,CAAC,IAAI,CAAC,EAAE,WAAW,CAAC;IACvC,mBAAmB,CAAC,EAAE,CAAC,EAAE,WAAW,CAAC;IACrC,cAAc,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC;IAC1B,yBAAyB,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC;IACnC,mBAAmB,CAAC,EAAE,CAAC,EAAE,gBAAgB,CAAC;IAC1C,6BAA6B,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IAC1C,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,sBAAsB,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC;CACpC;AAED,MAAM,WAAW,iBAAkB,SAAQ,QAAQ,EAAE,OAAO,CAAC,cAAc,CAAC;CAAG;AAE/E,MAAM,MAAM,cAAc,GAAG;IAAE,CAAC,MAAM,EAAE,MAAM,GAAG,QAAQ,CAAA;CAAE,CAAC;AAK5D,MAAM,MAAM,iBAAiB,GAAG,qBAAqB,GAAG,IAAI,CAAC;AAC7D,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,IAAI,CAAC,EAAE,MAAM,KAAK,iBAAiB,CAAC;AAE1F,MAAM,WAAW,gBAAgB;IAC/B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,gBAAgB,CAAC,EAAE,qBAAqB,CAAC;IACzC,UAAU,CAAC,EAAE,cAAc,CAAC;CAC7B;AAED,MAAM,WAAW,kBAAkB;IACjC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,WAAW,CAAC,EAAE,gBAAgB,CAAC;CAChC;AAED,MAAM,WAAW,WAAW;IAC1B,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,QAAQ,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,MAAM,IAAI,UAAU,CAAC;IACzB,IAAI,IAAI,IAAI,cAAc,CAAC;IAE3B,YAAY,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;CACnD"}

package/src/monomer-works/consts.d.ts

@@ -1,4 +1,3 @@
-import { PolymerTypes } from '../helm/consts';
 export declare const monomerWorksConsts: {
     readonly V2K_RGP_SHIFT: 8;
     readonly V2K_RGP_LINE: "M  RGP";
@@ -20,15 +19,15 @@ export declare const monomerWorksConsts: {
     readonly V3K_END: "M  END";
     readonly PRECISION_FACTOR: 10000;
     readonly DEOXYRIBOSE: {
-        readonly polymerType: PolymerTypes.RNA;
+        readonly polymerType: "RNA";
         readonly symbol: "d";
     };
     readonly RIBOSE: {
-        readonly polymerType: PolymerTypes.RNA;
+        readonly polymerType: "RNA";
         readonly symbol: "r";
     };
     readonly PHOSPHATE: {
-        readonly polymerType: PolymerTypes.RNA;
+        readonly polymerType: "RNA";
         readonly symbol: "p";
     };
     readonly OXYGEN: "O";

package/src/monomer-works/consts.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAE5C,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA8BrB,CAAC"}
+{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAEA,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA8BrB,CAAC"}

package/src/monomer-works/consts.js

@@ -1,3 +1,4 @@
+import { PolymerTypes } from '../helm/consts';
 export const monomerWorksConsts = {
     // constants for parsing molfile V2000
     V2K_RGP_SHIFT: 8,
@@ -21,9 +22,9 @@ export const monomerWorksConsts = {
     V3K_END: 'M  END',
     PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates
     // symbols for the corresponding monomers in HELM library
-    DEOXYRIBOSE: { polymerType: "RNA" /* PolymerTypes.RNA */, symbol: 'd' },
-    RIBOSE: { polymerType: "RNA" /* PolymerTypes.RNA */, symbol: 'r' },
-    PHOSPHATE: { polymerType: "RNA" /* PolymerTypes.RNA */, symbol: 'p' },
+    DEOXYRIBOSE: { polymerType: PolymerTypes.RNA, symbol: 'd' },
+    RIBOSE: { polymerType: PolymerTypes.RNA, symbol: 'r' },
+    PHOSPHATE: { polymerType: PolymerTypes.RNA, symbol: 'p' },
     OXYGEN: 'O',
     HYDROGEN: 'H',
 };

package/src/monomer-works/consts.js.map

@@ -1 +1 @@
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+{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAE5C,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAClC,sCAAsC;IACpC,aAAa,EAAE,CAAC;IAChB,YAAY,EAAE,QAAQ;IACtB,UAAU,EAAE,KAAK;IACjB,wDAAwD;IACxD,gBAAgB,EAAE,EAAE;IACpB,aAAa,EAAE,CAAC;IAChB,qBAAqB,EAAE,sCAAsC;IAC7D,sBAAsB,EAAE,2CAA2C;IACnE,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,qBAAqB,EAAE,gBAAgB;IACvC,sBAAsB,EAAE,UAAU;IAClC,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,eAAe,EAAE,OAAO;IACxB,mBAAmB,EAAE,SAAS;IAC9B,OAAO,EAAE,QAAQ;IACjB,gBAAgB,EAAE,KAAM,EAAE,mFAAmF;IAC7G,yDAAyD;IAEzD,WAAW,EAAE,EAAC,WAAW,EAAE,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAC;IACzD,MAAM,EAAE,EAAC,WAAW,EAAE,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAC;IACpD,SAAS,EAAE,EAAC,WAAW,EAAE,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAC;IAEvD,MAAM,EAAE,GAAG;IACX,QAAQ,EAAE,GAAG;CACL,CAAC"}

package/src/monomer-works/monomer-hover.js

@@ -1,6 +1,7 @@
 import wu from 'wu';
 import { LRUCache } from 'lru-cache';
 import { addSubstructProvider, getMonomerHover, setMonomerHover } from '@datagrok-libraries/chem-meta/src/types';
+import { PolymerTypes } from '../helm/consts';
 import { ALPHABET } from '../utils/macromolecule';
 import { getMonomersDictFromLib } from './to-atomic-level';
 import { monomerSeqToMolfile } from './to-atomic-level-utils';
@@ -45,7 +46,7 @@ export async function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelpe
                 .map((posIdx) => { return { position: posIdx, symbol: seqSS.getCanonical(posIdx), biotype: biotype }; })
                 .toArray();
             const alphabet = seqSH.alphabet;
-            const polymerType = alphabet == ALPHABET.RNA || alphabet == ALPHABET.DNA ? "RNA" /* PolymerTypes.RNA */ : "PEPTIDE" /* PolymerTypes.PEPTIDE */;
+            const polymerType = alphabet == ALPHABET.RNA || alphabet == ALPHABET.DNA ? PolymerTypes.RNA : PolymerTypes.PEPTIDE;
             const monomersDict = getMonomersDictFromLib([seqMList], [undefined], polymerType, alphabet, monomerLib, rdKitModule);
             // Call seq-to-molfile worker core directly
             const molWM = monomerSeqToMolfile(seqMList, monomersDict, alphabet, polymerType);

package/src/monomer-works/monomer-hover.js.map

@@ -1 +1 @@
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package/src/monomer-works/monomer-works.js

@@ -1,4 +1,4 @@
-import { HelmTypes } from '../helm/consts';
+import { HelmTypes, PolymerTypes } from '../helm/consts';
 export class MonomerWorks {
     //private molfileConverter: IMolfileConverter;
     constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {
@@ -23,19 +23,19 @@ export function helmTypeToPolymerType(helmType) {
         case HelmTypes.NUCLEOTIDE:
         // @ts-ignore
         case 'nucleotide':
-            polymerType = "RNA" /* PolymerTypes.RNA */;
+            polymerType = PolymerTypes.RNA;
             break;
         case HelmTypes.AA:
-            polymerType = "PEPTIDE" /* PolymerTypes.PEPTIDE */;
+            polymerType = PolymerTypes.PEPTIDE;
             break;
         case HelmTypes.CHEM:
-            polymerType = "CHEM" /* PolymerTypes.CHEM */;
+            polymerType = PolymerTypes.CHEM;
             break;
         case HelmTypes.BLOB:
-            polymerType = "BLOB" /* PolymerTypes.BLOB */;
+            polymerType = PolymerTypes.BLOB;
             break;
         default:
-            polymerType = "PEPTIDE" /* PolymerTypes.PEPTIDE */;
+            polymerType = PolymerTypes.PEPTIDE;
             console.warn(`Unexpected HelmType '${helmType}'`);
     }
     return polymerType;

package/src/monomer-works/monomer-works.js.map

@@ -1 +1 @@
-{"version":3,"file":"monomer-works.js","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAMA,OAAO,EAAC,SAAS,EAAe,MAAM,gBAAgB,CAAC;AAYvD,MAAM,OAAO,YAAY;IAGvB,8CAA8C;IAE9C,YAAY,UAA2B,CAAA,yCAAyC;QAC9E,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;QAC7B,2CAA2C;IAC7C,CAAC;IAED,qCAAqC;IAC9B,uBAAuB,CAAC,WAAwB,EAAE,WAAmB;QAC1E,sCAAsC;QACtC,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QACrE,IAAI,OAAO;YACT,OAAO,OAAO,CAAC,OAAO,CAAC,CAAC,UAAU;QAEpC,OAAO,IAAI,CAAC;IACd,CAAC;CACF;AAED,MAAM,UAAU,qBAAqB,CAAC,QAAkB;IACtD,IAAI,WAAW,GAA4B,SAAS,CAAC;IACrD,QAAQ,QAAQ,EAAE,CAAC;QACnB,KAAK,SAAS,CAAC,IAAI,CAAC;QACpB,KAAK,SAAS,CAAC,KAAK,CAAC,CAAC,8BAA8B;QACpD,KAAK,SAAS,CAAC,MAAM,CAAC,CAAC,gBAAgB;QACvC,KAAK,SAAS,CAAC,UAAU,CAAC;QACxB,aAAa;QACf,KAAK,YAAY;YACf,WAAW,+BAAmB,CAAC;YAC/B,MAAM;QACR,KAAK,SAAS,CAAC,EAAE;YACf,WAAW,uCAAuB,CAAC;YACnC,MAAM;QACR,KAAK,SAAS,CAAC,IAAI;YACjB,WAAW,iCAAoB,CAAC;YAChC,MAAM;QACR,KAAK,SAAS,CAAC,IAAI;YACjB,WAAW,iCAAoB,CAAC;YAChC,MAAM;QACR;YACE,WAAW,uCAAuB,CAAC;YACnC,OAAO,CAAC,IAAI,CAAC,wBAAwB,QAAQ,GAAG,CAAC,CAAC;IACpD,CAAC;IACD,OAAO,WAAW,CAAC;AACrB,CAAC"}
+{"version":3,"file":"monomer-works.js","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAMA,OAAO,EAAC,SAAS,EAAE,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAYvD,MAAM,OAAO,YAAY;IAGvB,8CAA8C;IAE9C,YAAY,UAA2B,CAAA,yCAAyC;QAC9E,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;QAC7B,2CAA2C;IAC7C,CAAC;IAED,qCAAqC;IAC9B,uBAAuB,CAAC,WAAwB,EAAE,WAAmB;QAC1E,sCAAsC;QACtC,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QACrE,IAAI,OAAO;YACT,OAAO,OAAO,CAAC,OAAO,CAAC,CAAC,UAAU;QAEpC,OAAO,IAAI,CAAC;IACd,CAAC;CACF;AAED,MAAM,UAAU,qBAAqB,CAAC,QAAkB;IACtD,IAAI,WAAW,GAA4B,SAAS,CAAC;IACrD,QAAQ,QAAQ,EAAE,CAAC;QACnB,KAAK,SAAS,CAAC,IAAI,CAAC;QACpB,KAAK,SAAS,CAAC,KAAK,CAAC,CAAC,8BAA8B;QACpD,KAAK,SAAS,CAAC,MAAM,CAAC,CAAC,gBAAgB;QACvC,KAAK,SAAS,CAAC,UAAU,CAAC;QACxB,aAAa;QACf,KAAK,YAAY;YACf,WAAW,GAAG,YAAY,CAAC,GAAG,CAAC;YAC/B,MAAM;QACR,KAAK,SAAS,CAAC,EAAE;YACf,WAAW,GAAG,YAAY,CAAC,OAAO,CAAC;YACnC,MAAM;QACR,KAAK,SAAS,CAAC,IAAI;YACjB,WAAW,GAAG,YAAY,CAAC,IAAI,CAAC;YAChC,MAAM;QACR,KAAK,SAAS,CAAC,IAAI;YACjB,WAAW,GAAG,YAAY,CAAC,IAAI,CAAC;YAChC,MAAM;QACR;YACE,WAAW,GAAG,YAAY,CAAC,OAAO,CAAC;YACnC,OAAO,CAAC,IAAI,CAAC,wBAAwB,QAAQ,GAAG,CAAC,CAAC;IACpD,CAAC;IACD,OAAO,WAAW,CAAC;AACrB,CAAC"}

package/src/monomer-works/seq-to-molfile.js

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { getMolColName, hexToPercentRgb } from './utils';
-import { HelmTypes } from '../helm/consts';
+import { HelmTypes, PolymerTypes } from '../helm/consts';
 export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymerType, monomerLib, seqHelper, rdKitModule, rolesList) {
     const srcColLength = seqCol.length;
     const df = seqCol.dataFrame;
@@ -11,7 +11,7 @@ export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymer
     const chunkSize = srcColLength / threadCount;
     const promises = new Array(threadCount);
     const seqSH = seqHelper.getSeqHandler(seqCol);
-    const biotype = polymerType == "RNA" /* PolymerTypes.RNA */ ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
+    const biotype = polymerType == PolymerTypes.RNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
     const seqList = wu.count(0).take(seqCol.length).map((rowIdx) => {
         const seqSS = seqSH.getSplitted(rowIdx);
         return wu.count(0).take(seqSS.length)

package/src/monomer-works/seq-to-molfile.js.map

@@ -1 +1 @@
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package/src/monomer-works/to-atomic-level-utils.d.ts.map

@@ -1 +1 @@
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package/src/monomer-works/to-atomic-level-utils.js

@@ -1,7 +1,7 @@
 /* eslint-disable max-len */
 import { monomerWorksConsts as C } from './consts';
 import { getMolGraph, MolfileWithMap, MonomerMap, NucleotideRole } from './types';
-import { HELM_CORE_FIELDS, } from '../utils/const';
+import { HELM_CORE_FIELDS, HELM_POLYMER_TYPE, HELM_MONOMER_TYPE, } from '../utils/const';
 import { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';
 import { helmTypeToPolymerType } from './monomer-works';
 /** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.
@@ -17,8 +17,8 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
         // RNA: all branch monomers (bases) and all backbone monomers (sugars +
         // phosphates, including modified ones). Modifications are looked up by
         // symbol at assembly time, so they MUST be present in the formatted lib.
-        polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ || (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */ &&
-            it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] !== "Branch" /* HELM_MONOMER_TYPE.BRANCH */)) {
+        polymerType === HELM_POLYMER_TYPE.RNA || (polymerType === HELM_POLYMER_TYPE.PEPTIDE &&
+            it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] !== HELM_MONOMER_TYPE.BRANCH)) {
             const monomerObject = {};
             HELM_CORE_FIELDS.forEach((field) => {
                 //@ts-ignore
@@ -47,7 +47,7 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
     // The roles array carries the per-position semantics — including
     // TERMINAL_5P / TERMINAL_3P for non-canonical chain ends — so we don't
     // re-validate the length here.
-    const triplesMode = polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ && !!roles &&
+    const triplesMode = polymerType === HELM_POLYMER_TYPE.RNA && !!roles &&
         roles.length === monomerSeq.length;
     // define atom and bond counts, taking into account the bond type
     const { atomCount, bondCount, needsCapping } = getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode, roles);
@@ -57,7 +57,7 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
     let addMonomerToMolblock;
     let sugar = null;
     let phosphate = null;
-    if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */)
+    if (polymerType === HELM_POLYMER_TYPE.PEPTIDE)
         addMonomerToMolblock = addAminoAcidToMolblock;
     else { // nucleotides
         addMonomerToMolblock = addNucleotideToMolblock;
@@ -330,7 +330,7 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
             lastPhosphateGraph = lastMonomerGraph;
     }
     // add extra values depending on the polymer type
-    if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */) {
+    if (polymerType === HELM_POLYMER_TYPE.PEPTIDE) {
         // add the rightmost/terminating cap group 'OH' (i.e. 'O')
         atomCount += 1;
         // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)
@@ -358,8 +358,19 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
         // 3'-terminal modifier (e.g. GalNAc) that IS the chain end.
         const has3pTerm = !!roles && roles.length > 0 &&
             roles[roles.length - 1] === NucleotideRole.TERMINAL_3P;
-        if (has3pTerm)
+        if (has3pTerm) {
             needsCapping = false;
+            // Mirror the peptide branch (which does both atomCount-- and bondCount--
+            // when it skips the terminal cap). `bondCount += monomerCount` above
+            // reserves one chain-extending slot per monomer; the LAST monomer's slot
+            // is normally filled by the terminal OH cap bond. With a 3'-terminal
+            // modifier there is no cap, so that last reserved slot stays empty —
+            // leaving the declared bond count one higher than the emitted bond
+            // lines. Drop it so the V3000 COUNTS line matches the bond block exactly
+            // (otherwise the pre-OCL molfile is malformed and only survives because
+            // the OCL chirality pass re-derives the counts).
+            bondCount -= 1;
+        }
         else
             atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)
     }

package/src/monomer-works/to-atomic-level-utils.js.map

@@ -1 +1 @@
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