npm - @datagrok-libraries/bio - Versions diffs - 5.60.0 → 5.61.0 - Mend

@datagrok-libraries/bio 5.60.0 → 5.61.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (13) hide show

package/CHANGELOG.md +4 -0
package/package.json +1 -1
package/src/monomer-works/to-atomic-level-utils.js +1 -1
package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
package/src/utils/composition-table.d.ts.map +1 -1
package/src/utils/composition-table.js +11 -3
package/src/utils/composition-table.js.map +1 -1
package/src/utils/macromolecule/consts.d.ts.map +1 -1
package/src/utils/macromolecule/consts.js.map +1 -1
package/src/utils/macromolecule/utils.d.ts +1 -0
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +11 -3
package/src/utils/macromolecule/utils.js.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,9 @@
 # bio changelog
+## 5.61.0 (2025-10-29)
+* CHEMS and SMILES support in HELM
 ## 5.60.0 (2025-10-28)
 * Monomer library management rework: Transition to library providers, instead of single file based monomer libraries. Support multiple library providers.

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.60.0",
+  "version": "5.61.0",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

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

@@ -25,7 +25,7 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
                 //@ts-ignore
                 monomerObject[field] = it[field];
             });
-            map.set(it["symbol" /* HELM_FIELDS.SYMBOL */], monomerObject);
+            map.set(monomerSymbol, monomerObject);
         }
     }
     return map;

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

	@@ -1 +1 @@
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package/src/utils/composition-table.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"composition-table.d.ts","sourceRoot":"","sources":["composition-table.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,eAAe,EAAC,MAAM,4BAA4B,CAAC;AAC3D,OAAO,EAAC,QAAQ,EAAC,MAAM,iBAAiB,CAAC;~~AAEzC~~,wBAAgB,qBAAqB,CACnC,MAAM,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,eAAe,EAC/E,eAAe,CAAC,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,QAAQ,CAAA;CAAE,GAC1C,gBAAgB,~~CA2ClB~~"}
1	+ {"version":3,"file":"composition-table.d.ts","sourceRoot":"","sources":["composition-table.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,eAAe,EAAC,MAAM,4BAA4B,CAAC;AAC3D,OAAO,EAAC,QAAQ,EAAC,MAAM,iBAAiB,CAAC;AAGzC,wBAAgB,qBAAqB,CACnC,MAAM,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,eAAe,EAC/E,eAAe,CAAC,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,QAAQ,CAAA;CAAE,GAC1C,gBAAgB,CAiDlB"}

package/src/utils/composition-table.js CHANGED Viewed

@@ -1,6 +1,7 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import { GAP_SYMBOL } from './macromolecule/consts';
+import { helmTypeToPolymerType } from '../monomer-works/monomer-works';
 export function buildCompositionTable(counts, biotype, monomerLib, monomerBioTypes) {
     let sumValue = 0;
     let maxValue = null;
@@ -14,8 +15,8 @@ export function buildCompositionTable(counts, biotype, monomerLib, monomerBioTyp
         .map(([cm, value]) => {
         const ratio = value / sumValue;
         let color;
+        const actBioType = monomerBioTypes ? (monomerBioTypes[cm] || biotype) : biotype;
         try {
-            const actBioType = monomerBioTypes ? (monomerBioTypes[cm] || biotype) : biotype;
             const colors = monomerLib.getMonomerColors(actBioType, cm);
             color = colors?.backgroundcolor || '#CCCCCC';
         }
@@ -31,10 +32,17 @@ export function buildCompositionTable(counts, biotype, monomerLib, monomerBioTyp
             barDiv.style.borderStyle = 'solid';
             barDiv.style.borderColor = DG.Color.toHtml(DG.Color.lightGray);
         }
-        const displayMonomer = GAP_SYMBOL === cm ? '-' : cm;
+        let monomerDisplayName = cm;
+        if (cm !== GAP_SYMBOL) {
+            const m = monomerLib.getMonomer(helmTypeToPolymerType(actBioType), cm);
+            if (m && m.symbol !== cm) // for explicit smiles based monomers
+                monomerDisplayName = m.symbol;
+        }
+        else
+            monomerDisplayName = '-';
         const valueDiv = ui.div(`${(100 * ratio).toFixed(2)}%`);
         const el = ui.div([barDiv, valueDiv], { classes: 'macromolecule-cell-comp-analysis-value' });
-        return ({ [displayMonomer]: el });
+        return ({ [monomerDisplayName]: el });
     }));
     const table = ui.tableFromMap(elMap);
     Array.from(table.rows).forEach((row) => {

package/src/utils/composition-table.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/utils.d.ts CHANGED Viewed

@@ -75,6 +75,7 @@ export declare function getSplitterWithSeparator(separator: string, limit?: numb
 /** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA).
  * Only for linear polymers, does not split RNA for ribose and phosphate monomers.
  * EG byciclic helm: PEPTIDE1{F}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[Cys_Bn].[meG].[Phe_3Cl].[dD].T.[dI].T.[dK].[aG].[3Pal].[xiIle].[meD].[Ala_tBu]}|PEPTIDE3{L.[Pro_4Me3OH].S.[NMe2Abz].Q.[3Pal].[xiIle].[D-Hyp].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].N.[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0
+ * Also should support smiles in monomer names, like: PEPTIDE1{[ac].L.N.[*N[C@H](C(=O)*)Cc1ccc(cc1)OP(=O)(O)O |$_R1;;;;;_R2;;;;;;;;;;;;$|].I.D.L.D.L.V.[am]}$$$$
  * @param {string} seq Source string of HELM notation
  * @param {ISeqSource} src Source of the {@link seq} string
  * @return {string[]}

package/src/utils/macromolecule/utils.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAOtC,OAAO,EAEL,aAAa,EAAE,aAAa,EAAE,YAAY,EAC1C,YAAY,EACZ,WAAW,EAAE,eAAe,EAC5B,YAAY,EACb,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,QAAQ,EAA+E,MAAM,UAAU,CAAC;AAChH,OAAO,EAAC,UAAU,EAAC,MAAM,oBAAoB,CAAC;AAI9C,OAAO,EAAC,UAAU,EAAC,MAAM,eAAe,CAAC;AAIzC,OAAO,EAAY,YAAY,EAAC,MAAM,mBAAmB,CAAC;AAC1D,OAAO,EAAC,QAAQ,EAAE,WAAW,EAAC,MAAM,kBAAkB,CAAC;AAGvD,qBAAa,qBAAsB,YAAW,YAAY;IA4CtD,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,kBAAkB;IA5CrC,IAAI,MAAM,IAAI,MAAM,CAA8B;IAElD,IAAI,SAAS,IAAI,aAAa,GAAG,SAAS,CAEzC;IAED,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO;IAI9B,4DAA4D;IAC5D,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM;IAOpC,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM;IAMnC,kBAAkB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE;IAQxD,iBAAiB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE;IAMvD,IAAI,WAAW,IAAI,MAAM,CAExB;gBAGkB,KAAK,EAAE,eAAe,EACtB,kBAAkB,EAAE,MAAM;CAE9C;AAGD;;GAEG;AACH,qBAAa,YAAa,SAAQ,qBAAqB;IAGnD,SAAS,CAAC,cAAc,EAAE,MAAM,EAAE,EAAE;IACpC,OAAO,CAAC,QAAQ,CAAC,WAAW;IAH9B,OAAO,CAAC,YAAY,CAAiB;gBAEzB,cAAc,EAAE,MAAM,EAAE,EAAE,EAAE,6DAA6D;IAClF,WAAW,EAAE,MAAM,EAAE,4DAA4D;IAClG,YAAY,EAAE,YAAY,EAAE,EAAE,gDAAgD;IAC9E,kBAAkB,EAAE,MAAM;IAK5B,SAAS,CAAC,UAAU,EAAE,aAAa,GAAG,SAAS,CAAa;IAC5D,IAAI,SAAS,IAAI,aAAa,CAG7B;IAED,SAAS,CAAC,gBAAgB,IAAI,aAAa;CAoD5C;AAED,uEAAuE;AACvE,qBAAa,eAAgB,SAAQ,YAAY;IACtC,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM;IAUpC,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM;gBAMhC,YAAY,EAAE,MAAM,EAAE,EAAE,EAAE,kBAAkB,EAAE,MAAM;cAI7C,gBAAgB,IAAI,aAAa;CA8CrD;AAGD,qBAAa,sBAAuB,YAAW,YAAY;IA2CvD,OAAO,CAAC,QAAQ,CAAC,IAAI;IA1CvB,IAAI,MAAM,IAAI,MAAM,CAA6B;IAEjD,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO;IAI9B,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM;IAQpC,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM;IAMnC,kBAAkB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE;IAWxD,iBAAiB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE;IAMvD,IAAI,WAAW,IAAI,MAAM,CAExB;gBAGkB,IAAI,EAAE,MAAM;CAEhC;AAED;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,YAAY,GAAG,WAAW,CAKhH;AAyBD;;;;GAIG;AACH,eAAO,MAAM,eAAe,EAAE,YAc7B,CAAC;AAEF,eAAO,MAAM,qBAAqB,EAAE,YAEnC,CAAC;AAEF;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,SAAS,EAAE,MAAM,EAAE,KAAK,GAAE,MAAM,GAAG,SAAqB,GAAG,YAAY,CAgB/G;AAED;;;;;;;GAOG;AACH,eAAO,MAAM,cAAc,EAAE,YAkB5B,CAAC;AAEF,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,YAAY,CA2BxD;AAGD,4EAA4E;AAC5E,MAAM,MAAM,kBAAkB,GAAG,CAAC,YAAY,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,KAAK,MAAM,CAAC;AAEjF;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,KAAK,GAAE,MAAM,GAAG,SAAqB,GAAG,YAAY,CAajH;AAID,+CAA+C;AAC/C,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,MAAM,CAQhF;AAED,MAAM;AACN,wBAAgB,WAAW,CAAC,QAAQ,EAAE,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAC,CAW3D;AAED;;;;;GAKG;AACH,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,YAAY,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,SAAS,GAAE,MAAY,GAAG,MAAM,CAchH;AAED,+BAA+B;AAC/B,wBAAgB,cAAc,CAAC,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,aAAa,EAAE,EAAE,SAAS,GAAE,MAAY,UAetG;AAED,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,aAAa,EAAE,EAAE,SAAS,GAAE,MAAY,UAe1G;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,SAAS,GAAE,MAAU,GAAG,UAAU,CAYzG;AAED,wBAAgB,gBAAgB,CAAC,WAAW,EAAE,MAAM,GAAG,UAAU,CAWhE;AAED,wBAAgB,YAAY,CAAC,EAAE,EAAE,EAAE,CAAC,SAAS,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,IAAI,CASvE;AAED,wBAAgB,qBAAqB,CAAC,EAAE,EAAE,WAAW,GAAG,QAAQ,CAa/D"}

package/src/utils/macromolecule/utils.js CHANGED Viewed

@@ -308,18 +308,26 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
 /** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA).
  * Only for linear polymers, does not split RNA for ribose and phosphate monomers.
  * EG byciclic helm: PEPTIDE1{F}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[Cys_Bn].[meG].[Phe_3Cl].[dD].T.[dI].T.[dK].[aG].[3Pal].[xiIle].[meD].[Ala_tBu]}|PEPTIDE3{L.[Pro_4Me3OH].S.[NMe2Abz].Q.[3Pal].[xiIle].[D-Hyp].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].N.[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0
+ * Also should support smiles in monomer names, like: PEPTIDE1{[ac].L.N.[*N[C@H](C(=O)*)Cc1ccc(cc1)OP(=O)(O)O |$_R1;;;;;_R2;;;;;;;;;;;;$|].I.D.L.D.L.V.[am]}$$$$
  * @param {string} seq Source string of HELM notation
  * @param {ISeqSource} src Source of the {@link seq} string
  * @return {string[]}
  */
 export const splitterAsHelm = (seq) => {
-    const helmParts = seq.split('$');
-    const spList = helmParts[0].split('|');
+    const indexOfSequenceEnd = seq.indexOf('}$');
+    const sequencePart = seq.substring(0, indexOfSequenceEnd + 1);
+    const connectionsEndPart = seq.indexOf('$', indexOfSequenceEnd + 2);
+    const connectionsPart = seq.substring(indexOfSequenceEnd + 2, connectionsEndPart);
+    // const helmParts = seq.split('$');
+    const spList = sequencePart.split('}|');
+    // since we removed }|, need to add } to last part
+    for (let i = 0; i < spList.length - 1; i++)
+        spList[i] = spList[i] + '}';
     const mListSplit = spList
         .map((sp) => (sp.match(/(?<=\{).+(?=})/)?.[0]?.split('.') ?? [])
         .map((m) => cleanupHelmSymbol(m)));
     const polymerTypes = spList.map((sp) => sp.replace(/\d{1,2}\{.+\}/, ''));
-    const res = new HelmSplitted(mListSplit, helmParts[1] ?? '', polymerTypes, GapOriginals[NOTATION.HELM]);
+    const res = new HelmSplitted(mListSplit, connectionsPart ?? '', polymerTypes, GapOriginals[NOTATION.HELM]);
     return res;
 };
 export function splitterAsBiln(seq) {

package/src/utils/macromolecule/utils.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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