@datagrok-libraries/bio 5.41.8 → 5.41.10

package/CHANGELOG.md

@@ -1,5 +1,13 @@
 # bio changelog
 
+## 5.41.10 (2024-06-10)
+
+NGL typings
+
+## 5.41.9 (2024-05-29)
+
+Fix Monomer type
+
 ## 5.41.8 (2024-05-29)
 
 Fix TAGS, ALPHABET enum

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.41.8",
+  "version": "5.41.10",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.71",
@@ -16,7 +16,7 @@
     "@datagrok-libraries/ml": "^6.6.5",
     "@deck.gl/core": "8.8.12",
     "cash-dom": "latest",
-    "datagrok-api": "^1.17.4",
+    "datagrok-api": "^1.18.6",
     "dayjs": "latest",
     "fastest-levenshtein": "^1.0.16",
     "js-base64": "^3.7.5",

package/src/types/ngl.d.ts

@@ -43,6 +43,8 @@ declare module 'NGL' {
     };
     type StructureRepresentationType = ('angle' | 'axes' | 'backbone' | 'ball+stick' | 'base' | 'cartoon' | 'contact' | 'dihedral' | 'distance' | 'helixorient' | 'hyperball' | 'label' | 'licorice' | 'line' | 'surface' | 'ribbon' | 'rocket' | 'rope' | 'spacefill' | 'trace' | 'tube' | 'unitcell');
     class Component {
+        /** structure, surface, ... */ get type(): string;
+        get object(): Structure | Surface | Volume | any;
         addRepresentation(type: StructureRepresentationType, params?: RepresentationParameters): RepresentationElement;
         autoView(duration?: number): undefined;
         removeAllRepresentations(): undefined;

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

@@ -1 +1 @@
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+{"version":3,"file":"ngl.d.ts","sourceRoot":"","sources":["ngl.ts"],"names":[],"mappings":";AAAA,OAAO,QAAQ,KAAK,CAAC;IACnB,OAAO,EAAC,MAAM,EAAC,MAAM,SAAS,CAAC;IAC/B,OAAO,EAAC,IAAI,EAAE,KAAK,EAAE,aAAa,EAAC,MAAM,OAAO,CAAC;IAEjD,UAAiB,SAAS;QACxB,IAAI,SAAS,IAAI,MAAM,CAAC;QACxB,IAAI,SAAS,IAAI,MAAM,CAAC;QACxB,IAAI,UAAU,IAAI,GAAG,CAAC;QACtB,OAAO,CAAC,SAAS,EAAE,SAAS,GAAG,SAAS,CAAC;KAC1C;IAED,KAAY,MAAM,GAAG,GAAG,CAAC;IACzB,KAAY,OAAO,GAAG,GAAG,CAAC;IAE1B,UAAiB,SAAS;QACxB,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;QACpB,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAA;KACpB;IAED,KAAY,gBAAgB,GAAG;QAC7B,GAAG,EAAE,MAAM,CAAC;QACZ,UAAU,EAAE,OAAO,CAAC;QACpB,MAAM,EAAE,OAAO,CAAC;QAChB,IAAI,EAAE,MAAM,CAAC;QACb,qBAAqB,EAAE,OAAO,CAAA;KAC/B,CAAC;IAEF,KAAY,SAAS,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,CAAA;IACrE,KAAY,UAAU,GAAG,MAAM,GAAG,QAAQ,CAAA;IAE1C,KAAY,eAAe,GAAG,GAAG,CAAC;IAElC,UAAiB,oBAAqB,SAAQ,eAAe;QAC3D,SAAS,CAAC,EAAE,SAAS,CAAC;QACtB,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,OAAO,CAAC,EAAE,OAAO,CAAC;QAClB,IAAI,CAAC,EAAE,SAAS,CAAC;KAClB;IAED,KAAY,mBAAmB,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,oBAAoB,GAAG,SAAS,CAAC,CAAA;IAEpF,KAAY,UAAU,GAAG,EAAE,CAAC;IAE5B,MAAa,uBAAuB;QAClC,GAAG,CAAC,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,UAAU,GAAG,SAAS;QAE9C,SAAS,CAAC,MAAM,EAAE,QAAQ,GAAG,UAAU,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM;QAE/D,kBAAkB,CAAC,QAAQ,EAAE,mBAAmB,EAAE,EAAE,KAAK,CAAC,EAAE,MAAM,GAAG,MAAM;KAC5E;IAEM,MAAM,kBAAkB,EAAE,uBAAuB,CAAC;IAEzD,KAAY,wBAAwB,GAAG;QAAE,CAAC,CAAC,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,CAAA;IAE3D,KAAY,2BAA2B,GAAG,CACxC,OAAO,GAAG,MAAM,GAAG,UAAU,GAAG,YAAY,GAAG,MAAM,GAAG,SAAS,GAAG,SAAS,GAAG,UAAU,GAC1F,UAAU,GAAG,aAAa,GAAG,WAAW,GAAG,OAAO,GAAG,UAAU,GAAG,MAAM,GAAG,SAAS,GACpF,QAAQ,GAAG,QAAQ,GAAG,MAAM,GAAG,WAAW,GAAG,OAAO,GAAG,MAAM,GAAG,UAAU,CACzE,CAAA;IAEH,MAAa,SAAS;QACpB,8BAA8B,CAAC,IAAI,IAAI,IAAI,MAAM,CAAC;QAElD,IAAI,MAAM,IAAI,SAAS,GAAG,OAAO,GAAG,MAAM,GAAG,GAAG,CAAC;QAEjD,iBAAiB,CAAC,IAAI,EAAE,2BAA2B,EAAE,MAAM,CAAC,EAAE,wBAAwB,GAAG,qBAAqB;QAE9G,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,SAAS;QAEtC,wBAAwB,IAAI,SAAS;KACtC;IAED,MAAa,qBAAsB,SAAQ,SAAS;KAEnD;IAED,MAAa,KAAK;QAChB,MAAM,EAAE,MAAM,CAAC;QAEf,IAAI,QAAQ,IAAI,SAAS,EAAE,CAAC;oBAGhB,IAAI,EAAE,WAAW;QAE7B,YAAY,IAAI,SAAS;QAEzB,eAAe,CAAC,SAAS,EAAE,SAAS,GAAG,SAAS;QAEhD,mBAAmB,CAAC,IAAI,CAAC,EAAE,MAAM,GAAG,SAAS;QAE7C,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,GAAG,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,gBAAgB,CAAC,GAAG,OAAO,CAAC,IAAI,CAAC;QAEtF,OAAO,IAAI,SAAS;KACrB;IAED,MAAa,MAAM;QACjB,OAAO,EAAE,aAAa,CAAC;QAEvB,SAAS,EAAE,WAAW,CAAC;QACvB,OAAO,EAAE,WAAW,CAAC;QAErB,WAAW,EAAE,MAAM,CAAC;QAEpB,KAAK,EAAE,KAAK,CAAC;QAEb,KAAK,EAAE,MAAM,CAAC;QACd,MAAM,EAAE,MAAM,CAAC;QAEf,KAAK,EAAE,KAAK,CAAC;QAEb,QAAQ,EAAE,aAAa,CAAC;QACxB,WAAW,EAAE,IAAI,CAAC;QAElB,SAAS,EAAE,OAAO,CAAC;QACnB,aAAa,EAAE,OAAO,CAAC;QAEvB,MAAM,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI;QAE9B,aAAa,IAAI,IAAI;QAErB,OAAO,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI;KAC7C;IAED,MAAa,KAAK;QAChB,OAAO,EAAE;YACP,OAAO,EAAE,MAAM,CAAA;SAChB,CAAC;QAEF,WAAW,EAAE,MAAM,CAAC;QACpB,WAAW,EAAE,MAAM,CAAC;QACpB,WAAW,EAAE,MAAM,CAAC;QACpB,YAAY,EAAE,MAAM,CAAC;QAErB,WAAW,EAAE,MAAM,CAAC;QACpB,OAAO,EAAE,MAAM,CAAC;QAChB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,CAAC;QACf,KAAK,EAAE,MAAM,CAAC;QAEd,SAAS,EAAE,MAAM,CAAC;QAClB,WAAW,EAAE,MAAM,CAAC;KACrB;IAED,UAAiB,aAAa;QAC5B,MAAM,EAAE,MAAM,CAAC;QACf,QAAQ,EAAE,MAAM,CAAA;KACjB;IAED,KAAY,WAAW,GAAG,IAAI,GAAG,IAAI,GAAG,MAAM,CAAA;IAE9C,KAAY,iBAAiB,GAAG,KAAK,GAAG,MAAM,GAAG,MAAM,CAAA;IAEvD,UAAiB,YAAY;QAC3B,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,cAAc,CAAC,EAAE,OAAO,CAAC;QACzB,YAAY,CAAC,EAAE,OAAO,CAAC;QACvB,UAAU,CAAC,EAAE,OAAO,CAAC;QACrB,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,WAAW,CAAC,EAAE,MAAM,CAAC;QACrB,UAAU,CAAC,EAAE,iBAAiB,CAAC;KAChC;IAED,SAAgB,QAAQ,CAAC,IAAI,EAAE,WAAW,EAAE,MAAM,CAAC,EAAE,OAAO,CAAC,gBAAgB,GAAG,YAAY,CAAC,GAAG,OAAO,CAAC,SAAS,CAAC,CAAC;IAEnH,MAAa,SAAS;oBACR,KAAK,EAAE,MAAM;KAC1B;IAED,MAAa,SAAS;oBACR,GAAG,EAAE,SAAS,EAAE,MAAM,CAAC,EAAE,GAAG;QAExC,SAAS,IAAI,MAAM;KACpB;IAED,MAAa,SAAS;oBACR,GAAG,EAAE,SAAS,EAAE,MAAM,CAAC,EAAE,GAAG;QAExC,OAAO,IAAI,MAAM;KAClB;CACF"}

package/src/utils/const.d.ts

@@ -6,6 +6,7 @@ import MonomerTypes = org.helm.MonomerTypes;
 export { PolymerTypes, HelmTypes, MonomerTypes };
 import HELM_POLYMER_TYPE = org.helm.PolymerTypes;
 import HELM_MONOMER_TYPE = org.helm.MonomerTypes;
+import { RGroup } from '../types';
 export { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };
 /** Required HELM library monomer fields:
  * https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */
@@ -61,16 +62,16 @@ export declare const jsonSdfMonomerLibDict: {
     symbol: string;
 };
 export declare const DUMMY_MONOMER: {
-    monomerType: string;
+    monomerType: "Backbone" | "Branch" | "Terminal";
     smiles: string;
     name: string;
     author: string;
     molfile: string;
     naturalAnalog: string;
-    rgroups: never[];
+    rgroups: RGroup[];
     createDate: null;
     id: number;
-    polymerType: string;
+    polymerType: "G" | "RNA" | "PEPTIDE" | "CHEM" | "BLOB";
     symbol: string;
 };
 export declare const MONOMER_ENCODE_MIN = 256;

package/src/utils/const.d.ts.map

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