npm - @datagrok-libraries/bio - Versions diffs - 6.0.1 → 6.0.3 - Mend

@datagrok-libraries/bio 6.0.1 → 6.0.3

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Files changed (24) hide show

package/CHANGELOG.md +5 -0
package/package.json +7 -4
package/src/monomer-works/monomer-hover.d.ts.map +1 -1
package/src/monomer-works/monomer-hover.js +38 -10
package/src/monomer-works/monomer-hover.js.map +1 -1
package/src/monomer-works/seq-to-molfile-worker.js +3 -2
package/src/monomer-works/seq-to-molfile-worker.js.map +1 -1
package/src/monomer-works/seq-to-molfile.d.ts +1 -1
package/src/monomer-works/seq-to-molfile.d.ts.map +1 -1
package/src/monomer-works/seq-to-molfile.js +2 -2
package/src/monomer-works/seq-to-molfile.js.map +1 -1
package/src/monomer-works/to-atomic-level-utils.d.ts +15 -1
package/src/monomer-works/to-atomic-level-utils.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level-utils.js +179 -1
package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
package/src/monomer-works/to-atomic-level.d.ts +1 -0
package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level.js +70 -32
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/monomer-works/types.d.ts +5 -0
package/src/monomer-works/types.d.ts.map +1 -1
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +11 -7
package/src/utils/macromolecule/utils.js.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,10 @@
 # bio changelog
+## 6.0.2 (2026-07-06)
+* To atomic level (linear path): support multi-chain HELM (e.g. `RNA1{...}|RNA2{...}`) — each disjoint chain is assembled independently and stacked vertically into a single molfile instead of being fused into one continuous chain.
+* Monomer hover (linear path): fix the HELM monomer→atom map — infer polymer type from the parsed HELM graph (not the alphabet, which mis-detects modified RNA as UN) and build the map with per-position RNA roles and multi-chain stacking so it matches the rendered molfile.
 ## 5.61.2 (2025-11-03)
 * Split User settings for duplicate monomer preferences into separate entries to avoid length limits.

package/package.json CHANGED Viewed

@@ -8,11 +8,12 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "6.0.1",
+  "version": "6.0.3",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/gridext": "^1.4.0",
+    "@datagrok-libraries/hwe": "^1.0.0",
     "@datagrok-libraries/ml": "^6.7.6",
     "@datagrok-libraries/utils": "^4.5.7",
     "@deck.gl/core": "8.8.12",
@@ -24,9 +25,8 @@
     "lru-cache": "^10.4.3",
     "mjolnir.js": "^2.7.0",
     "rxjs": "^6.5.5",
-    "uuid": "^9.0.1",
-    "wu": "^2.1.0",
-    "@datagrok-libraries/hwe": "^1.0.0"
+    "uuid": "^11.1.1",
+    "wu": "^2.1.0"
   },
   "devDependencies": {
     "@types/signals": "1.0.1",
@@ -52,5 +52,8 @@
     "build-all": "npm --prefix ./../../libraries/chem-meta run build && npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/gridext run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/ml run build && npm run build",
     "lint": "eslint \"./src/**/*.ts\"",
     "lint-fix": "eslint \"./src/**/*.ts\" --fix"
+  },
+  "overrides": {
+    "uuid": "^11.1.1"
   }
 }

package/src/monomer-works/monomer-hover.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/monomer-works/monomer-hover.js CHANGED Viewed

@@ -1,9 +1,9 @@
 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 { HelmTypes, PolymerTypes } from '../helm/consts';
 import { ALPHABET } from '../utils/macromolecule';
-import { getMonomersDictFromLib } from './to-atomic-level';
+import { buildRolesForHelmRna, getMonomersDictFromLib } from './to-atomic-level';
 import { monomerSeqToMolfile } from './to-atomic-level-utils';
 import { getMolHighlight } from './seq-to-molfile';
 export const MonomerHoverLinksTemp = 'MonomerHoverLinks';
@@ -28,10 +28,15 @@ export async function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelpe
     const getSeqMonomerCorrectedPosition = (pos) => {
         if (pos == undefined)
             return null;
-        // if its dna or rna, we need to correct position as it will contain sugar and phosphate
-        // toAtomicLevel returns 15 monomers for 15 nucleotides (r(n)p is one monmer), while helm converter returns 45
+        // HELM RNA is split into per-position sugar/base/phosphate monomers, so the
+        // renderer reports a flat monomer index and the monomer map is keyed by that
+        // same flat index — both for the POM converter and (since the map is now
+        // built with roles) for the linear path. No division needed in either case.
         if (isNucleotideHelmSequence)
-            return throughPOM ? pos : Math.floor(pos / 3);
+            return pos;
+        // Non-HELM DNA/RNA: the linear map keys by base position; the POM converter
+        // expands each base into a sugar/base/phosphate triple, so map the base to
+        // its base entry (the middle of its triple).
         if (isNucleotideNonHelmSequence)
             return throughPOM ? pos * 3 + 1 : pos;
         return pos;
@@ -41,15 +46,38 @@ export async function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelpe
         const seqSH = seqHelper.getSeqHandler(seqCol);
         if (!throughPOM) {
             const seqSS = seqSH.getSplitted(tableRowIdx);
-            const biotype = seqSH.defaultBiotype;
+            const gi = seqSS.graphInfo;
+            // Polymer type: for HELM read it from the parsed graph rather than the
+            // alphabet — modified RNA can mis-detect as ALPHABET.UN. The whole row is
+            // assumed to be the first chain's type. Non-HELM falls back to the alphabet.
+            let polymerType;
+            if (seqSH.isHelm() && gi?.polymerTypes && gi.polymerTypes.length > 0)
+                polymerType = gi.polymerTypes[0];
+            else {
+                const a = seqSH.alphabet;
+                polymerType = (a === ALPHABET.RNA || a === ALPHABET.DNA) ? PolymerTypes.RNA : PolymerTypes.PEPTIDE;
+            }
+            // Coerce a UN alphabet to RNA for the RNA polymer path (only used for the
+            // bases-only default sugar/phosphate selection; irrelevant in triples mode).
+            let alphabet = seqSH.alphabet;
+            if (polymerType === PolymerTypes.RNA && alphabet !== ALPHABET.RNA && alphabet !== ALPHABET.DNA)
+                alphabet = ALPHABET.RNA;
+            // HELM RNA is assembled from per-position sugar/base/phosphate triples;
+            // the monomer map must be built with the same roles (and multi-chain
+            // stacking) the real conversion uses, otherwise every monomer is treated
+            // as a base and the atom map does not match the rendered molfile.
+            const isHelmRna = seqSH.isHelm() && polymerType === PolymerTypes.RNA;
+            const biotype = isHelmRna ? HelmTypes.NUCLEOTIDE : seqSH.defaultBiotype;
             const seqMList = wu.count(0).take(seqSS.length)
                 .map((posIdx) => { return { position: posIdx, symbol: seqSS.getCanonical(posIdx), biotype: biotype }; })
                 .toArray();
-            const alphabet = seqSH.alphabet;
-            const polymerType = alphabet == ALPHABET.RNA || alphabet == ALPHABET.DNA ? PolymerTypes.RNA : PolymerTypes.PEPTIDE;
-            const monomersDict = getMonomersDictFromLib([seqMList], [undefined], polymerType, alphabet, monomerLib, rdKitModule);
+            const chainStarts = (gi?.disjointSeqStarts && gi.disjointSeqStarts.length > 0) ?
+                gi.disjointSeqStarts.slice() : [0];
+            const roles = isHelmRna ?
+                buildRolesForHelmRna([seqMList], monomerLib, polymerType, [chainStarts])[0] : undefined;
+            const monomersDict = getMonomersDictFromLib([seqMList], [roles], polymerType, alphabet, monomerLib, rdKitModule);
             // Call seq-to-molfile worker core directly
-            const molWM = monomerSeqToMolfile(seqMList, monomersDict, alphabet, polymerType);
+            const molWM = monomerSeqToMolfile(seqMList, monomersDict, alphabet, polymerType, roles, chainStarts);
             return molWM.monomers;
         }
         else {

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package/src/monomer-works/seq-to-molfile-worker.js CHANGED Viewed

@@ -1,13 +1,14 @@
 import { monomerSeqToMolfile } from './to-atomic-level-utils';
 onmessage = (event) => {
-    const { seqList, rolesList, monomersDict, alphabet, polymerType, start, end } = event.data;
+    const { seqList, rolesList, chainStartsList, monomersDict, alphabet, polymerType, start, end } = event.data;
     const resMolList = new Array(end - start);
     const molfileWarningList = new Array(0);
     for (let rowI = start; rowI < end; ++rowI) {
         try {
             const seq = seqList[rowI];
             const roles = rolesList ? rolesList[rowI] : undefined;
-            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType, roles);
+            const chainStarts = chainStartsList ? chainStartsList[rowI] : undefined;
+            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType, roles, chainStarts);
         }
         catch (err) {
             const errMsg = err instanceof Error ? err.message : err.toString();

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

	@@ -1 +1 @@
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package/src/monomer-works/seq-to-molfile.d.ts CHANGED Viewed

@@ -13,6 +13,6 @@ export type SeqToMolfileResult = {
     }[];
     warnings: string[];
 };
-export declare function seqToMolFileWorker(seqCol: DG.Column<string>, monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, monomerLib: IMonomerLib, seqHelper: ISeqHelper, rdKitModule: RDModule, rolesList?: (NucleotideRole[] | undefined)[]): Promise<ToAtomicLevelRes>;
+export declare function seqToMolFileWorker(seqCol: DG.Column<string>, monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, monomerLib: IMonomerLib, seqHelper: ISeqHelper, rdKitModule: RDModule, rolesList?: (NucleotideRole[] | undefined)[], chainStartsList?: number[][]): Promise<ToAtomicLevelRes>;
 export declare function getMolHighlight(monomerMaps: Iterable<MonomerMapValue>, monomerLib: IMonomerLibBase): ISubstruct;
 //# sourceMappingURL=seq-to-molfile.d.ts.map

package/src/monomer-works/seq-to-molfile.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"seq-to-molfile.d.ts","sourceRoot":"","sources":["seq-to-molfile.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,QAAQ,EAAC,MAAM,6CAA6C,CAAC;AAGrE,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAChD,OAAO,EACqB,UAAU,EAAE,eAAe,EAAE,kBAAkB,EAAE,cAAc,EAE1F,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,UAAU,EAAE,gBAAgB,EAAC,MAAM,qBAAqB,CAAC;AAEjE,OAAO,EAAC,WAAW,EAAE,eAAe,EAAC,MAAM,0BAA0B,CAAC;AACtE,OAAO,EAAc,WAAW,EAAC,MAAM,eAAe,CAAC;AAEvD,OAAO,EAAC,UAAU,EAAC,MAAM,yCAAyC,CAAC;AAGnE,MAAM,MAAM,kBAAkB,GAAG;IAC/B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM,CAAC;QAChB,QAAQ,EAAE,UAAU,CAAA;KACrB,EAAE,CAAC;IACJ,QAAQ,EAAE,MAAM,EAAE,CAAA;CACnB,CAAA;AAED,wBAAsB,kBAAkB,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,YAAY,EAAE,kBAAkB,EAClG,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,EAC5C,UAAU,EAAE,WAAW,EAAE,SAAS,EAAE,UAAU,EAAE,WAAW,EAAE,QAAQ,EACrE,SAAS,CAAC,EAAE,CAAC,cAAc,EAAE,GAAG,SAAS,CAAC,EAAE,EAC5C,eAAe,CAAC,EAAE,MAAM,EAAE,EAAE,GAC3B,OAAO,CAAC,gBAAgB,CAAC,CAuD3B;AAED,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,CAAC,eAAe,CAAC,EAAE,UAAU,EAAE,eAAe,GAAG,UAAU,CAuB/G"}

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

@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { getMolColName, hexToPercentRgb } from './utils';
 import { HelmTypes, PolymerTypes } from '../helm/consts';
-export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymerType, monomerLib, seqHelper, rdKitModule, rolesList) {
+export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymerType, monomerLib, seqHelper, rdKitModule, rolesList, chainStartsList) {
     const srcColLength = seqCol.length;
     const df = seqCol.dataFrame;
     const threadCount = Math.max(navigator.hardwareConcurrency - 2, 1);
@@ -29,7 +29,7 @@ export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymer
                 resolve(res.data);
             };
         });
-        worker.postMessage({ seqList, rolesList, monomersDict, alphabet, polymerType, start, end });
+        worker.postMessage({ seqList, rolesList, chainStartsList, monomersDict, alphabet, polymerType, start, end });
     }
     const molList = [];
     const warnings = [];

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

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

@@ -15,11 +15,25 @@ export declare function getFormattedMonomerLib(monomerLib: IMonomerLibBase, poly
  * @param {PolymerType} polymerType - Polymer type
  * @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly
  *   uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).
+ * @param {number[]} chainStarts - Optional 0-based start positions of disjoint HELM chains.
+ *   When more than one chain is present each chain is assembled independently and the
+ *   chains are stacked vertically into a single molfile (multi-strand HELM support).
  * @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */
-export declare function monomerSeqToMolfile(monomerSeq: ISeqMonomer[], monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, roles?: NucleotideRole[]): MolfileWithMap;
+export declare function monomerSeqToMolfile(monomerSeq: ISeqMonomer[], monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, roles?: NucleotideRole[], chainStarts?: number[]): MolfileWithMap;
 /** Keep precision upon floating point operations over atom coordinates
  * @param {number}x - the floating point number
  * @return {number} - the floating point number with the same precision
  */
 export declare function keepPrecision(x: number): number;
+/** Combine several already-assembled single-chain molfiles into one molfile,
+ * stacking them vertically: the first chain keeps its coordinates, every
+ * subsequent chain is shifted straight down so its top-most atom sits just
+ * below the running bottom of everything placed so far. Atom / bond indices
+ * and per-monomer maps are re-based, STEABS collections merged, and the
+ * monomer-map keys offset by each chain's start position so the combined map
+ * still keys by original flat HELM position.
+ * @param {MolfileWithMap[]} parts - per-chain assembled molfiles (chain order)
+ * @param {number[]} chainStarts - flat start position of each chain
+ * @return {MolfileWithMap} - single combined molfile + merged monomer map */
+export declare function combineMolfilesVertically(parts: MolfileWithMap[], chainStarts: number[]): MolfileWithMap;
 //# sourceMappingURL=to-atomic-level-utils.d.ts.map

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

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

@@ -36,12 +36,31 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
  * @param {PolymerType} polymerType - Polymer type
  * @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly
  *   uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).
+ * @param {number[]} chainStarts - Optional 0-based start positions of disjoint HELM chains.
+ *   When more than one chain is present each chain is assembled independently and the
+ *   chains are stacked vertically into a single molfile (multi-strand HELM support).
  * @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */
-export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType, roles) {
+export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType, roles, chainStarts) {
     if (monomerSeq.length === 0) {
         // throw new Error('monomerSeq is empty');
         return MolfileWithMap.createEmpty();
     }
+    // Multi-chain HELM (e.g. RNA1{...}|RNA2{...}): assemble each disjoint chain
+    // on its own, then stack them vertically into a single molfile. Each chain
+    // reuses the exact single-chain assembly below, so its geometry, capping and
+    // per-monomer atom/bond map are unchanged; combineMolfilesVertically shifts
+    // the coordinates and re-bases the atom/bond indices and monomer-map keys.
+    if (chainStarts && chainStarts.length > 1) {
+        const parts = new Array(chainStarts.length);
+        for (let c = 0; c < chainStarts.length; ++c) {
+            const s = chainStarts[c];
+            const e = c + 1 < chainStarts.length ? chainStarts[c + 1] : monomerSeq.length;
+            const subSeq = monomerSeq.slice(s, e);
+            const subRoles = roles ? roles.slice(s, e) : undefined;
+            parts[c] = monomerSeqToMolfile(subSeq, monomersDict, alphabet, polymerType, subRoles);
+        }
+        return combineMolfilesVertically(parts, chainStarts);
+    }
     // Triples mode is on only when the caller flagged the row with roles
     // (built and validated by `buildRolesForHelmRna` in to-atomic-level.ts).
     // The roles array carries the per-position semantics — including
@@ -451,4 +470,163 @@ function runTriplesAssembly(monomerSeq, roles, monomersDict, molfileAtomBlock, m
 export function keepPrecision(x) {
     return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;
 }
+// Vertical gap (in molfile coordinate units) inserted between stacked chains
+// of a multi-strand HELM. Roughly two bond lengths — enough to read the strands
+// as separate without pushing them far apart.
+const CHAIN_VERTICAL_GAP = 3.0;
+const STEABS_MARKER = 'M  V30 MDLV30/STEABS ATOMS=(';
+/** Split `body` into its first `n` space-separated tokens plus a trailing
+ * remainder token (so the result has n+1 entries). The remainder keeps any
+ * embedded spaces of the tail verbatim.
+ * @param {string} body - the line body to split
+ * @param {number} n - number of leading tokens to peel off
+ * @return {string[]} - the n tokens followed by the remainder */
+function splitLeadingTokens(body, n) {
+    const out = [];
+    let s = body;
+    for (let i = 0; i < n; ++i) {
+        const sp = s.indexOf(' ');
+        if (sp === -1) {
+            out.push(s);
+            s = '';
+            continue;
+        }
+        out.push(s.substring(0, sp));
+        s = s.substring(sp + 1);
+    }
+    out.push(s);
+    return out;
+}
+/** Extract the data lines (`M  V30 ...`) between a BEGIN/END marker pair.
+ * @param {string} molfile - the V3000 molfile
+ * @param {string} beginMarker - the block BEGIN marker line
+ * @param {string} endMarker - the block END marker line
+ * @return {string[]} - the data lines of the block, newline stripped */
+function extractBlockDataLines(molfile, beginMarker, endMarker) {
+    const begin = molfile.indexOf(beginMarker);
+    if (begin === -1)
+        return [];
+    const start = molfile.indexOf('\n', begin) + 1;
+    const end = molfile.indexOf(endMarker, start);
+    return molfile.substring(start, end === -1 ? molfile.length : end)
+        .split('\n')
+        .filter((l) => l.startsWith(C.V3K_BEGIN_DATA_LINE))
+        .map((l) => l.substring(C.V3K_BEGIN_DATA_LINE.length));
+}
+/** Parse a molfile produced by monomerSeqToMolfile back into atoms / bonds /
+ * stereo-atom indices. Robust because we control the exact serialization
+ * format; only the fields we need to renumber (indices) and shift (y) are
+ * parsed, everything past them is preserved verbatim as an opaque tail.
+ * @param {string} molfile - the V3000 molfile
+ * @return {ParsedMol} - parsed atoms, bonds and STEABS atom indices */
+function parseGeneratedMolfile(molfile) {
+    const atoms = [];
+    for (const body of extractBlockDataLines(molfile, C.V3K_BEGIN_ATOM_BLOCK, C.V3K_END_ATOM_BLOCK)) {
+        // body: "<idx> <type> <x> <y> <z> <...kwargs>"
+        const t = splitLeadingTokens(body, 4); // [idx, type, x, y, tail]
+        atoms.push({ type: t[1], xStr: t[2], y: parseFloat(t[3]), tail: t[4] });
+    }
+    const bonds = [];
+    for (const body of extractBlockDataLines(molfile, C.V3K_BEGIN_BOND_BLOCK, C.V3K_END_BOND_BLOCK)) {
+        // body: "<idx> <btype> <a1> <a2> <...cfg/kwargs>"
+        const t = splitLeadingTokens(body, 4); // [idx, btype, a1, a2, tail]
+        bonds.push({ btype: t[1], a1: parseInt(t[2]), a2: parseInt(t[3]), tail: t[4] });
+    }
+    const steabs = [];
+    let idx = molfile.indexOf(STEABS_MARKER);
+    while (idx !== -1) {
+        idx += STEABS_MARKER.length;
+        const closeIdx = molfile.indexOf(')', idx);
+        // first entry inside the parens is the atom count, not an atom index
+        steabs.push(...molfile.substring(idx, closeIdx).split(' ').slice(1)
+            .map((s) => parseInt(s)).filter((n) => !Number.isNaN(n)));
+        idx = molfile.indexOf(STEABS_MARKER, closeIdx);
+    }
+    return { atoms, bonds, steabs };
+}
+/** Combine several already-assembled single-chain molfiles into one molfile,
+ * stacking them vertically: the first chain keeps its coordinates, every
+ * subsequent chain is shifted straight down so its top-most atom sits just
+ * below the running bottom of everything placed so far. Atom / bond indices
+ * and per-monomer maps are re-based, STEABS collections merged, and the
+ * monomer-map keys offset by each chain's start position so the combined map
+ * still keys by original flat HELM position.
+ * @param {MolfileWithMap[]} parts - per-chain assembled molfiles (chain order)
+ * @param {number[]} chainStarts - flat start position of each chain
+ * @return {MolfileWithMap} - single combined molfile + merged monomer map */
+export function combineMolfilesVertically(parts, chainStarts) {
+    const combinedAtomLines = [];
+    const combinedBondLines = [];
+    const combinedSteabs = [];
+    const combinedMap = new MonomerMap();
+    let atomOffset = 0;
+    let bondOffset = 0;
+    let runningBottom = Number.POSITIVE_INFINITY; // lowest y placed so far
+    let anyPlaced = false;
+    for (let c = 0; c < parts.length; ++c) {
+        const part = parts[c];
+        if (!part || !part.molfile)
+            continue;
+        const pm = parseGeneratedMolfile(part.molfile);
+        if (pm.atoms.length === 0)
+            continue;
+        let minY = Number.POSITIVE_INFINITY;
+        let maxY = Number.NEGATIVE_INFINITY;
+        for (const a of pm.atoms) {
+            if (a.y < minY)
+                minY = a.y;
+            if (a.y > maxY)
+                maxY = a.y;
+        }
+        // First placed chain keeps its coordinates; later chains drop below the
+        // current bottom, leaving CHAIN_VERTICAL_GAP between the strands.
+        const yShift = anyPlaced ? keepPrecision(runningBottom - CHAIN_VERTICAL_GAP - maxY) : 0;
+        for (let ai = 0; ai < pm.atoms.length; ++ai) {
+            const a = pm.atoms[ai];
+            const newIdx = atomOffset + ai + 1;
+            const newY = keepPrecision(a.y + yShift);
+            combinedAtomLines.push(C.V3K_BEGIN_DATA_LINE + newIdx + ' ' + a.type + ' ' + a.xStr + ' ' + newY + ' ' + a.tail + '\n');
+        }
+        for (let bi = 0; bi < pm.bonds.length; ++bi) {
+            const b = pm.bonds[bi];
+            const newIdx = bondOffset + bi + 1;
+            const tail = b.tail ? ' ' + b.tail : '';
+            combinedBondLines.push(C.V3K_BEGIN_DATA_LINE + newIdx + ' ' + b.btype + ' ' + (b.a1 + atomOffset) + ' ' + (b.a2 + atomOffset) + tail + '\n');
+        }
+        for (const s of pm.steabs)
+            combinedSteabs.push(s + atomOffset);
+        const posOffset = chainStarts[c] ?? 0;
+        for (const [pos, val] of part.monomers) {
+            combinedMap.set(posOffset + pos, {
+                biotype: val.biotype,
+                symbol: val.symbol,
+                atoms: val.atoms.map((x) => x + atomOffset),
+                bonds: val.bonds.map((x) => x + bondOffset),
+            });
+        }
+        const newBottom = keepPrecision(minY + yShift);
+        runningBottom = anyPlaced ? Math.min(runningBottom, newBottom) : newBottom;
+        anyPlaced = true;
+        atomOffset += pm.atoms.length;
+        bondOffset += pm.bonds.length;
+    }
+    if (!anyPlaced)
+        return MolfileWithMap.createEmpty();
+    let result = '';
+    result += C.V3K_HEADER_FIRST_LINE;
+    result += C.V3K_HEADER_SECOND_LINE;
+    result += C.V3K_BEGIN_CTAB_BLOCK;
+    result += C.V3K_BEGIN_COUNTS_LINE + atomOffset + ' ' + bondOffset + C.V3K_COUNTS_LINE_ENDING;
+    result += C.V3K_BEGIN_ATOM_BLOCK;
+    result += combinedAtomLines.join('');
+    result += C.V3K_END_ATOM_BLOCK;
+    result += C.V3K_BEGIN_BOND_BLOCK;
+    result += combinedBondLines.join('');
+    result += C.V3K_END_BOND_BLOCK;
+    if (combinedSteabs.length > 0)
+        result += getCollectionBlock(combinedSteabs);
+    result += C.V3K_END_CTAB_BLOCK;
+    result += C.V3K_END;
+    return { molfile: result, monomers: combinedMap };
+}
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package/src/monomer-works/to-atomic-level.d.ts CHANGED Viewed

@@ -11,6 +11,7 @@ import { ISeqMonomer, PolymerType } from '../helm/types';
  * @param {IMonomerLib} monomerLib - Monomer library
  */
 export declare function _toAtomicLevel(df: DG.DataFrame, seqCol: DG.Column<string>, monomerLib: IMonomerLib, seqHelper: ISeqHelper, rdKitModule: RDModule): Promise<ToAtomicLevelRes>;
+export declare function buildRolesForHelmRna(monomerSequencesArray: ISeqMonomer[][], monomerLib: IMonomerLibBase, polymerType: PolymerType, chainStartsArray?: number[][]): (NucleotideRole[] | undefined)[];
 /** Get jagged array of monomer symbols for the dataframe
  * @param {DG.Column} macroMolCol - Column with macro-molecules
  * @return {string[]} - Jagged array of monomer symbols for the dataframe */

package/src/monomer-works/to-atomic-level.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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