@datagrok-libraries/bio 5.63.7 → 5.64.1
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.
- package/package.json +1 -1
- package/src/monomer-works/monomer-hover.js +1 -1
- 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 +2 -2
- 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 +7 -5
- package/src/monomer-works/to-atomic-level-utils.d.ts.map +1 -1
- package/src/monomer-works/to-atomic-level-utils.js +195 -46
- package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
- package/src/monomer-works/to-atomic-level.d.ts +7 -5
- package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
- package/src/monomer-works/to-atomic-level.js +156 -36
- package/src/monomer-works/to-atomic-level.js.map +1 -1
- package/src/monomer-works/types.d.ts +10 -0
- package/src/monomer-works/types.d.ts.map +1 -1
- package/src/monomer-works/types.js +7 -0
- package/src/monomer-works/types.js.map +1 -1
- package/src/utils/macromolecule/utils.d.ts +2 -0
- package/src/utils/macromolecule/utils.d.ts.map +1 -1
- package/src/utils/macromolecule/utils.js +17 -3
- package/src/utils/macromolecule/utils.js.map +1 -1
package/package.json
CHANGED
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@@ -8,7 +8,7 @@
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"access": "public"
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},
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"friendlyName": "Datagrok bio library",
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-
"version": "5.
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+
"version": "5.64.1",
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"description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
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"dependencies": {
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"@datagrok-libraries/chem-meta": "^1.2.7",
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@@ -46,7 +46,7 @@ export async function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelpe
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.toArray();
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const alphabet = seqSH.alphabet;
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const polymerType = alphabet == ALPHABET.RNA || alphabet == ALPHABET.DNA ? "RNA" /* PolymerTypes.RNA */ : "PEPTIDE" /* PolymerTypes.PEPTIDE */;
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-
const monomersDict = getMonomersDictFromLib([seqMList], polymerType, alphabet, monomerLib, rdKitModule);
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const monomersDict = getMonomersDictFromLib([seqMList], [undefined], polymerType, alphabet, monomerLib, rdKitModule);
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// Call seq-to-molfile worker core directly
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const molWM = monomerSeqToMolfile(seqMList, monomersDict, alphabet, polymerType);
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return molWM.monomers;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"monomer-hover.js","sourceRoot":"","sources":["monomer-hover.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,MAAM,IAAI,CAAC;AACpB,OAAO,EAAC,QAAQ,EAAC,MAAM,WAAW,CAAC;AAInC,OAAO,EAAC,oBAAoB,EAAE,eAAe,EAAc,eAAe,EAAC,MAAM,yCAAyC,CAAC;AAK3H,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAChD,OAAO,EAAC,sBAAsB,EAAC,MAAM,mBAAmB,CAAC;AACzD,OAAO,EAAC,mBAAmB,EAAC,MAAM,yBAAyB,CAAC;AAE5D,OAAO,EAAC,eAAe,EAAC,MAAM,kBAAkB,CAAC;AAIjD,MAAM,CAAC,MAAM,qBAAqB,GAAG,mBAAmB,CAAC;AAEzD,MAAM,UAAU,mBAAmB,CAAC,UAAe,EAAE,OAAyB;IAC5E,IAAI,OAAO,GAAG,UAAU,CAAC,qBAAqB,CAAC,CAAC;IAChD,IAAI,CAAC,OAAO;QACV,OAAO,GAAG,UAAU,CAAC,qBAAqB,CAAC,GAAG,EAAE,CAAC;IACnD,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACtB,UAAU,CAAC,qBAAqB,CAAC,GAAG,OAAO,CAAC;AAC9C,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,qBAAqB,CACzC,MAAyB,EAAE,MAAyB,EACpD,UAA2B,EAAE,SAAqB,EAAE,WAAqB,EAAE,aAAsB,KAAK;IAEtG,MAAM,KAAK,GAAG,SAAS,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;IAC9C,MAAM,YAAY,GAAG,CAAC,KAAK,CAAC,QAAQ,IAAI,QAAQ,CAAC,GAAG,IAAI,KAAK,CAAC,QAAQ,IAAI,QAAQ,CAAC,GAAG,CAAC,CAAC;IACxF,MAAM,wBAAwB,GAAG,KAAK,CAAC,MAAM,EAAE,IAAI,YAAY,CAAC;IAChE,iIAAiI;IACjI,sFAAsF;IACtF,MAAM,2BAA2B,GAAG,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,YAAY,CAAC;IAEpE,MAAM,8BAA8B,GAAG,CAAC,GAAY,EAAE,EAAE;QACtD,IAAI,GAAG,IAAI,SAAS;YAAE,OAAO,IAAI,CAAC;QAClC,wFAAwF;QACxF,8GAA8G;QAC9G,IAAI,wBAAwB;YAC1B,OAAO,UAAU,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC;QAChD,IAAI,2BAA2B;YAC7B,OAAO,UAAU,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC;QACxC,OAAO,GAAG,CAAC;IACb,CAAC,CAAC;IAEF,MAAM,sBAAsB,GAAmC,UAAU,CAAC,CAAC,CAAC,MAAM,SAAS,CAAC,yBAAyB,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IACzI,SAAS,eAAe,CAAC,MAAyB,EAAE,WAAmB;QACrE,MAAM,KAAK,GAAG,SAAS,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;QAC9C,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,MAAM,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,CAAC;YAC7C,MAAM,OAAO,GAAG,KAAK,CAAC,cAAc,CAAC;YACrC,MAAM,QAAQ,GAAkB,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC;iBAC3D,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE,GAAG,OAAO,EAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,OAAO,EAAgB,CAAC,CAAC,CAAC,CAAC;iBACpH,OAAO,EAAE,CAAC;YAEb,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAoB,CAAC;YAC5C,MAAM,WAAW,GAAG,QAAQ,IAAI,QAAQ,CAAC,GAAG,IAAI,QAAQ,IAAI,QAAQ,CAAC,GAAG,CAAC,CAAC,8BAAkB,CAAC,qCAAqB,CAAC;YACnH,MAAM,YAAY,GAAG,sBAAsB,CAAC,CAAC,QAAQ,CAAC,EAAE,WAAW,EAAE,QAAQ,EAAE,UAAU,EAAE,WAAW,CAAC,CAAC;
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1
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{"version":3,"file":"monomer-hover.js","sourceRoot":"","sources":["monomer-hover.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,MAAM,IAAI,CAAC;AACpB,OAAO,EAAC,QAAQ,EAAC,MAAM,WAAW,CAAC;AAInC,OAAO,EAAC,oBAAoB,EAAE,eAAe,EAAc,eAAe,EAAC,MAAM,yCAAyC,CAAC;AAK3H,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAChD,OAAO,EAAC,sBAAsB,EAAC,MAAM,mBAAmB,CAAC;AACzD,OAAO,EAAC,mBAAmB,EAAC,MAAM,yBAAyB,CAAC;AAE5D,OAAO,EAAC,eAAe,EAAC,MAAM,kBAAkB,CAAC;AAIjD,MAAM,CAAC,MAAM,qBAAqB,GAAG,mBAAmB,CAAC;AAEzD,MAAM,UAAU,mBAAmB,CAAC,UAAe,EAAE,OAAyB;IAC5E,IAAI,OAAO,GAAG,UAAU,CAAC,qBAAqB,CAAC,CAAC;IAChD,IAAI,CAAC,OAAO;QACV,OAAO,GAAG,UAAU,CAAC,qBAAqB,CAAC,GAAG,EAAE,CAAC;IACnD,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IACtB,UAAU,CAAC,qBAAqB,CAAC,GAAG,OAAO,CAAC;AAC9C,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,qBAAqB,CACzC,MAAyB,EAAE,MAAyB,EACpD,UAA2B,EAAE,SAAqB,EAAE,WAAqB,EAAE,aAAsB,KAAK;IAEtG,MAAM,KAAK,GAAG,SAAS,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;IAC9C,MAAM,YAAY,GAAG,CAAC,KAAK,CAAC,QAAQ,IAAI,QAAQ,CAAC,GAAG,IAAI,KAAK,CAAC,QAAQ,IAAI,QAAQ,CAAC,GAAG,CAAC,CAAC;IACxF,MAAM,wBAAwB,GAAG,KAAK,CAAC,MAAM,EAAE,IAAI,YAAY,CAAC;IAChE,iIAAiI;IACjI,sFAAsF;IACtF,MAAM,2BAA2B,GAAG,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,YAAY,CAAC;IAEpE,MAAM,8BAA8B,GAAG,CAAC,GAAY,EAAE,EAAE;QACtD,IAAI,GAAG,IAAI,SAAS;YAAE,OAAO,IAAI,CAAC;QAClC,wFAAwF;QACxF,8GAA8G;QAC9G,IAAI,wBAAwB;YAC1B,OAAO,UAAU,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC;QAChD,IAAI,2BAA2B;YAC7B,OAAO,UAAU,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC;QACxC,OAAO,GAAG,CAAC;IACb,CAAC,CAAC;IAEF,MAAM,sBAAsB,GAAmC,UAAU,CAAC,CAAC,CAAC,MAAM,SAAS,CAAC,yBAAyB,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IACzI,SAAS,eAAe,CAAC,MAAyB,EAAE,WAAmB;QACrE,MAAM,KAAK,GAAG,SAAS,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;QAC9C,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,MAAM,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,CAAC;YAC7C,MAAM,OAAO,GAAG,KAAK,CAAC,cAAc,CAAC;YACrC,MAAM,QAAQ,GAAkB,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC;iBAC3D,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE,GAAG,OAAO,EAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,OAAO,EAAgB,CAAC,CAAC,CAAC,CAAC;iBACpH,OAAO,EAAE,CAAC;YAEb,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAoB,CAAC;YAC5C,MAAM,WAAW,GAAG,QAAQ,IAAI,QAAQ,CAAC,GAAG,IAAI,QAAQ,IAAI,QAAQ,CAAC,GAAG,CAAC,CAAC,8BAAkB,CAAC,qCAAqB,CAAC;YACnH,MAAM,YAAY,GAAG,sBAAsB,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,SAAS,CAAC,EAAE,WAAW,EAAE,QAAQ,EAAE,UAAU,EAAE,WAAW,CAAC,CAAC;YACrH,2CAA2C;YAC3C,MAAM,KAAK,GAAG,mBAAmB,CAAC,QAAQ,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,CAAC,CAAC;YACjF,OAAO,KAAK,CAAC,QAAQ,CAAC;QACxB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC;YACxC,MAAM,KAAK,GAAG,SAAS,CAAC,uBAAuB,CAAC,IAAI,EAAE,sBAAuB,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,CAAC,4CAA4C;YAC1I,OAAO,KAAK,CAAC,QAAQ,CAAC;QACxB,CAAC;IACH,CAAC;IAED,MAAM,kBAAkB,GAAG,IAAI,QAAQ,CAAqB,EAAC,GAAG,EAAE,GAAG,EAAC,CAAC,CAAC;IAExE,SAAS,aAAa,CAAC,MAAyB,EAAE,WAAmB;QACnE,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC;QACpC,IAAI,GAAG,IAAI,IAAI;YAAE,OAAO,IAAI,CAAC;QAE7B,IAAI,aAAa,GAAG,kBAAkB,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;QAChD,IAAI,CAAC,aAAa;YAChB,kBAAkB,CAAC,GAAG,CAAC,GAAG,EAAE,aAAa,GAAG,eAAe,CAAC,MAAM,EAAE,WAAW,CAAC,CAAC,CAAC;QAEpF,OAAO,aAAa,CAAC;IACvB,CAAC;IAED,MAAM,OAAO,GAAqB;QAChC,SAAS,EAAE,MAAM;QACjB,OAAO,EAAE,CAAC,WAAwB,EAAE,UAA8B,EAAE,aAA4B,EAAW,EAAE;YAC3G,MAAM,IAAI,GAAG,aAAa,CAAC,IAAI,CAAC;YAChC,MAAM,WAAW,GAAG,WAAW,CAAC,aAAc,CAAC;YAC/C,MAAM,UAAU,GAAG,WAAW,CAAC,OAAO,CAAC;YACvC,MAAM,cAAc,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,IAAI,EAAE,UAAU,CAAC,CAAC;YACjE,MAAM,IAAI,GAAG,eAAe,EAAE,CAAC;YAC/B,IAAI,CAAC,IAAI,IAAI,CAAC,IAAI,IAAI,CAAC,IAAI,CAAC,WAAW,IAAI,MAAM,CAAC,SAAS,CAAC,EAAE,IAAI,IAAI,CAAC,UAAU,IAAI,UAAU;gBAC7F,IAAI,CAAC,UAAU,IAAI,MAAM,CAAC,IAAI,IAAI,IAAI,CAAC,WAAW,IAAI,UAAU,EAAE,QAAQ,CAAC,CAAC,EAC5E,CAAC;gBACD,IAAI,IAAI,EAAE,CAAC;oBACT,eAAe,CAAC,IAAI,CAAC,CAAC;oBACtB,mCAAmC;oBACnC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC;gBACzB,CAAC;gBACD,IAAI,CAAC,UAAU,EAAE,CAAC;oBAChB,eAAe,CAAC,IAAI,CAAC,CAAC;oBACtB,OAAO,IAAI,CAAC;gBACd,CAAC;gBACD,eAAe,CAAC;oBACd,QAAQ,EAAE,cAAc;oBACxB,WAAW,EAAE,MAAM,CAAC,SAAS,CAAC,EAAE;oBAChC,UAAU,EAAE,UAAU;oBACtB,UAAU,EAAE,MAAM,CAAC,IAAI;oBACvB,WAAW,EAAE,8BAA8B,CAAC,UAAU,EAAE,QAAQ,CAAC,IAAI,CAAC,CAAC;oBACvE,YAAY,EAAE,GAA2B,EAAE;wBACzC,IAAI,CAAC,UAAU,IAAI,UAAU,CAAC,MAAM,KAAK,GAAG;4BAC1C,OAAO,SAAS,CAAC;wBAEnB,MAAM,aAAa,GAAG,aAAa,CAAC,MAAM,EAAE,WAAW,CAAC,CAAC;wBACzD,IAAI,CAAC,aAAa;4BAChB,OAAO,SAAS,CAAC;wBAEnB,MAAM,UAAU,GAAG,aAAa,CAAC,GAAG,CAAC,8BAA8B,CAAC,UAAU,EAAE,QAAQ,CAAE,CAAC,CAAC,CAAC,iBAAiB;wBAC9G,IAAI,CAAC,UAAU;4BAAE,OAAO,EAAC,KAAK,EAAE,EAAE,EAAE,KAAK,EAAE,EAAE,EAAE,mBAAmB,EAAE,EAAE,EAAE,mBAAmB,EAAE,EAAE,EAAC,CAAC;wBAEjG,MAAM,GAAG,GAAe,eAAe,CAAC,CAAC,UAAU,CAAC,EAAE,UAAU,CAAC,CAAC;wBAClE,OAAO,GAAG,CAAC;oBACb,CAAC;iBACF,CAAC,CAAC;gBAEH,kCAAkC;gBAClC,oBAAoB;gBACpB,cAAc,CAAC,MAAM,EAAE,CAAC;YAC1B,CAAC;YAED,OAAO,IAAI,CAAC;QACd,CAAC;QACD,wBAAwB,CAAA,YAAY,EAAE,CAAC,WAA0B,EAA2B,EAAE;YAC5F,IAAI,MAAM,CAAC,MAAM,4EAAmC,IAAI,MAAM;gBAAE,OAAO,SAAS,CAAC;YACjF,IAAI,WAAW,IAAI,IAAI;gBAAE,OAAO,SAAS,CAAC;YAC1C,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC;YACpC,IAAI,CAAC,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import { monomerSeqToMolfile } from './to-atomic-level-utils';
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onmessage = (event) => {
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const { seqList, monomersDict, alphabet, polymerType, start, end } = event.data;
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const { seqList, rolesList, monomersDict, alphabet, polymerType, start, end } = event.data;
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const resMolList = new Array(end - start);
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const molfileWarningList = new Array(0);
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for (let rowI = start; rowI < end; ++rowI) {
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try {
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const seq = seqList[rowI];
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const roles = rolesList ? rolesList[rowI] : undefined;
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resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType, roles);
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}
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catch (err) {
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const errMsg = err instanceof Error ? err.message : err.toString();
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{"version":3,"file":"seq-to-molfile-worker.js","sourceRoot":"","sources":["seq-to-molfile-worker.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,mBAAmB,EAAC,MAAM,yBAAyB,CAAC;AAG5D,SAAS,GAAG,CAAC,KAAK,EAAE,EAAE;IACpB,MAAM,EAAC,OAAO,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,EAAC,GAA2B,KAAK,CAAC,IAAI,CAAC;
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+
{"version":3,"file":"seq-to-molfile-worker.js","sourceRoot":"","sources":["seq-to-molfile-worker.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,mBAAmB,EAAC,MAAM,yBAAyB,CAAC;AAG5D,SAAS,GAAG,CAAC,KAAK,EAAE,EAAE;IACpB,MAAM,EAAC,OAAO,EAAE,SAAS,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,EAAC,GAA2B,KAAK,CAAC,IAAI,CAAC;IACjH,MAAM,UAAU,GAAqB,IAAI,KAAK,CAAiB,GAAG,GAAG,KAAK,CAAC,CAAC;IAC5E,MAAM,kBAAkB,GAAG,IAAI,KAAK,CAAS,CAAC,CAAC,CAAC;IAChD,KAAK,IAAI,IAAI,GAAG,KAAK,EAAE,IAAI,GAAG,GAAG,EAAE,EAAE,IAAI,EAAE,CAAC;QAC1C,IAAI,CAAC;YACH,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;YAC1B,MAAM,KAAK,GAAG,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;YACtD,UAAU,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,mBAAmB,CAAC,GAAG,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,CAAC,CAAC;QAClG,CAAC;QAAC,OAAO,GAAQ,EAAE,CAAC;YAClB,MAAM,MAAM,GAAW,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC;YAC3E,MAAM,GAAG,GAAW,8BAA8B,IAAI,KAAK,MAAM,GAAG,CAAC;YACrE,kBAAkB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAC/B,CAAC;IACH,CAAC;IACD,WAAW,CAAC,EAAC,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,kBAAkB,EAA0B,CAAC,CAAC;AAC7F,CAAC,CAAC"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
|
|
3
3
|
import { ALPHABET } from '../utils/macromolecule';
|
|
4
|
-
import { MonomerMap, MonomerMapValue, MonomerMolGraphMap } from './types';
|
|
4
|
+
import { MonomerMap, MonomerMapValue, MonomerMolGraphMap, NucleotideRole } from './types';
|
|
5
5
|
import { ISeqHelper, ToAtomicLevelRes } from '../utils/seq-helper';
|
|
6
6
|
import { IMonomerLib, IMonomerLibBase } from '../types/monomer-library';
|
|
7
7
|
import { PolymerType } from '../helm/types';
|
|
@@ -13,6 +13,6 @@ export type SeqToMolfileResult = {
|
|
|
13
13
|
}[];
|
|
14
14
|
warnings: string[];
|
|
15
15
|
};
|
|
16
|
-
export declare function seqToMolFileWorker(seqCol: DG.Column<string>, monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, monomerLib: IMonomerLib, seqHelper: ISeqHelper, rdKitModule: RDModule): Promise<ToAtomicLevelRes>;
|
|
16
|
+
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>;
|
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17
17
|
export declare function getMolHighlight(monomerMaps: Iterable<MonomerMapValue>, monomerLib: IMonomerLibBase): ISubstruct;
|
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18
18
|
//# sourceMappingURL=seq-to-molfile.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
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,
|
|
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,GAC3C,OAAO,CAAC,gBAAgB,CAAC,CAsD3B;AAED,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,CAAC,eAAe,CAAC,EAAE,UAAU,EAAE,eAAe,GAAG,UAAU,CAuB/G"}
|
|
@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
|
|
|
2
2
|
import wu from 'wu';
|
|
3
3
|
import { getMolColName, hexToPercentRgb } from './utils';
|
|
4
4
|
import { HelmTypes } from '../helm/consts';
|
|
5
|
-
export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymerType, monomerLib, seqHelper, rdKitModule) {
|
|
5
|
+
export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymerType, monomerLib, seqHelper, rdKitModule, rolesList) {
|
|
6
6
|
const srcColLength = seqCol.length;
|
|
7
7
|
const df = seqCol.dataFrame;
|
|
8
8
|
const threadCount = Math.max(navigator.hardwareConcurrency - 2, 1);
|
|
@@ -29,7 +29,7 @@ export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymer
|
|
|
29
29
|
resolve(res.data);
|
|
30
30
|
};
|
|
31
31
|
});
|
|
32
|
-
worker.postMessage({ seqList, monomersDict, alphabet, polymerType, start, end });
|
|
32
|
+
worker.postMessage({ seqList, rolesList, monomersDict, alphabet, polymerType, start, end });
|
|
33
33
|
}
|
|
34
34
|
const molList = [];
|
|
35
35
|
const warnings = [];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"seq-to-molfile.js","sourceRoot":"","sources":["seq-to-molfile.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAWpB,OAAO,EAAC,aAAa,EAAE,eAAe,EAAC,MAAM,SAAS,CAAC;AAGvD,OAAO,EAAC,SAAS,EAAe,MAAM,gBAAgB,CAAC;AAYvD,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,MAAyB,EAAE,YAAgC,EAClG,QAAkB,EAAE,WAAwB,EAC5C,UAAuB,EAAE,SAAqB,EAAE,WAAqB;
|
|
1
|
+
{"version":3,"file":"seq-to-molfile.js","sourceRoot":"","sources":["seq-to-molfile.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAWpB,OAAO,EAAC,aAAa,EAAE,eAAe,EAAC,MAAM,SAAS,CAAC;AAGvD,OAAO,EAAC,SAAS,EAAe,MAAM,gBAAgB,CAAC;AAYvD,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,MAAyB,EAAE,YAAgC,EAClG,QAAkB,EAAE,WAAwB,EAC5C,UAAuB,EAAE,SAAqB,EAAE,WAAqB,EACrE,SAA4C;IAE5C,MAAM,YAAY,GAAG,MAAM,CAAC,MAAM,CAAC;IACnC,MAAM,EAAE,GAA6B,MAAM,CAAC,SAAS,CAAC;IACtD,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,mBAAmB,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC;IACnE,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;SAC9C,GAAG,CAAC,GAAG,EAAE,CAAC,IAAI,MAAM,CAAC,IAAI,GAAG,CAAC,yBAAyB,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;IAC9E,MAAM,SAAS,GAAG,YAAY,GAAG,WAAW,CAAC;IAC7C,MAAM,QAAQ,GAAG,IAAI,KAAK,CAAiC,WAAW,CAAC,CAAC;IACxE,MAAM,KAAK,GAAG,SAAS,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;IAC9C,MAAM,OAAO,GAAG,WAAW,gCAAoB,CAAC,CAAC,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC;IACtF,MAAM,OAAO,GAAoB,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE;QAC9E,MAAM,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QACxC,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC;aAClC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE;YACd,OAAO,EAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,OAAO,EAAgB,CAAC;QACjG,CAAC,CAAC;aACD,OAAO,EAAE,CAAC;IACf,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC;IACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;QACrC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QAC1B,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,SAAS,CAAC,CAAC;QACxC,MAAM,GAAG,GAAG,CAAC,CAAC,KAAK,WAAW,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,SAAS,CAAC,CAAC;QACrF,QAAQ,CAAC,CAAC,CAAC,GAAG,IAAI,OAAO,CAAwB,CAAC,OAAO,EAAE,EAAE;YAC3D,MAAM,CAAC,SAAS,GAAG,CAAC,GAAoC,EAAQ,EAAE;gBAChE,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;YACpB,CAAC,CAAC;QACJ,CAAC,CAAC,CAAC;QACH,MAAM,CAAC,WAAW,CAAC,EAAC,OAAO,EAAE,SAAS,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,EAA2B,CAAC,CAAC;IACtH,CAAC;IAED,MAAM,OAAO,GAAqB,EAAE,CAAC;IACrC,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,MAAM,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,QAAiC,EAAE,EAAE;QACrE,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;YAC/B,OAAO,CAAC,IAAI,CAAC,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAClC,QAAQ,CAAC,IAAI,CAAC,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;QACrC,CAAC;IACH,CAAC,CAAC,CAAC;IAEH,+GAA+G;IAE/G,UAAU,CAAC,GAAG,EAAE;QACd,OAAO,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,EAAE;YACzB,MAAM,CAAC,SAAS,EAAE,CAAC;QACrB,CAAC,CAAC,CAAC;IACL,CAAC,EAAE,CAAC,CAAC,CAAC;IACN,MAAM,UAAU,GAAG,aAAa,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,CAAC,CAAC;IAClD,MAAM,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC;SAChF,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,OAAO,CAAC,CAAC;IAC9C,MAAM,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,QAAQ,CAAC;IACrC,MAAM,CAAC,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC;IAC/C,MAAM,CAAC,MAAM,sDAA4B,MAAM,CAAC,IAAI,CAAC,CAAC;IAEtD,OAAO,EAAC,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAC,CAAC;AAC9C,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,WAAsC,EAAE,UAA2B;IACjG,MAAM,OAAO,GAAgC,EAAE,CAAC;IAChD,MAAM,OAAO,GAAgC,EAAE,CAAC;IAEhD,KAAK,MAAM,eAAe,IAAI,WAAW,EAAE,CAAC;QAC1C,MAAM,GAAG,GAAG,UAAU,CAAC,mBAAmB,CAAC,eAAe,CAAC,OAAO,EAAE,eAAe,CAAC,MAAM,CAAE,CAAC;QAC7F,MAAM,SAAS,GAAG,GAAG,CAAC,eAAe,CAAC;QACtC,mDAAmD;QACnD,MAAM,OAAO,GAAG,eAAe,CAAC,SAAS,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;QAC7G,KAAK,MAAM,KAAK,IAAI,eAAe,CAAC,KAAK;YACvC,OAAO,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC;QAC3B,KAAK,MAAM,KAAK,IAAI,eAAe,CAAC,KAAK;YACvC,OAAO,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC;IAC7B,CAAC;IAED,MAAM,YAAY,GAAe;QAC/B,KAAK,EAAE,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;QACnD,KAAK,EAAE,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;QACnD,mBAAmB,EAAE,OAAO;QAC5B,mBAAmB,EAAE,OAAO;KAC7B,CAAC;IAEF,OAAO,YAAY,CAAC;AACtB,CAAC"}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { MolfileWithMap, MonomerMolGraphMap } from './types';
|
|
1
|
+
import { MolfileWithMap, MonomerMolGraphMap, NucleotideRole } from './types';
|
|
2
2
|
import { ALPHABET } from '../utils/macromolecule/consts';
|
|
3
3
|
import { IMonomerLibBase } from '../types/monomer-library';
|
|
4
4
|
import { ISeqMonomer, PolymerType } from '../helm/types';
|
|
@@ -9,12 +9,14 @@ import { ISeqMonomer, PolymerType } from '../helm/types';
|
|
|
9
9
|
* @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/
|
|
10
10
|
export declare function getFormattedMonomerLib(monomerLib: IMonomerLibBase, polymerType: PolymerType, alphabet: ALPHABET): Map<string, any>;
|
|
11
11
|
/** Translate a sequence of monomer symbols into Molfile V3000
|
|
12
|
-
* @param {
|
|
13
|
-
* @param {
|
|
12
|
+
* @param {ISeqMonomer[]} monomerSeq - Sequence of monomer symbols (canonical)
|
|
13
|
+
* @param {MonomerMolGraphMap} monomersDict - Mapping of monomer symbols to MolGraph objects
|
|
14
14
|
* @param {ALPHABET} alphabet - Alphabet of the column
|
|
15
15
|
* @param {PolymerType} polymerType - Polymer type
|
|
16
|
-
* @
|
|
17
|
-
|
|
16
|
+
* @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly
|
|
17
|
+
* uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).
|
|
18
|
+
* @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */
|
|
19
|
+
export declare function monomerSeqToMolfile(monomerSeq: ISeqMonomer[], monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, roles?: NucleotideRole[]): MolfileWithMap;
|
|
18
20
|
/** Keep precision upon floating point operations over atom coordinates
|
|
19
21
|
* @param {number}x - the floating point number
|
|
20
22
|
* @return {number} - the floating point number with the same precision
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"to-atomic-level-utils.d.ts","sourceRoot":"","sources":["to-atomic-level-utils.ts"],"names":[],"mappings":"AAEA,OAAO,EAA4C,cAAc,EAAwB,kBAAkB,EAAC,MAAM,SAAS,CAAC;
|
|
1
|
+
{"version":3,"file":"to-atomic-level-utils.d.ts","sourceRoot":"","sources":["to-atomic-level-utils.ts"],"names":[],"mappings":"AAEA,OAAO,EAA4C,cAAc,EAAwB,kBAAkB,EACzG,cAAc,EAAC,MAAM,SAAS,CAAC;AAEjC,OAAO,EAAC,QAAQ,EAAa,MAAM,+BAA+B,CAAC;AACnE,OAAO,EAAC,eAAe,EAAU,MAAM,0BAA0B,CAAC;AAClE,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AAIvD;;;;iHAIiH;AACjH,wBAAgB,sBAAsB,CACpC,UAAU,EAAE,eAAe,EAAE,WAAW,EAAE,WAAW,EAAE,QAAQ,EAAE,QAAQ,GACxE,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,CAuBlB;AAED;;;;;;;+EAO+E;AAC/E,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,WAAW,EAAE,EAAE,YAAY,EAAE,kBAAkB,EAC3D,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,EAC5C,KAAK,CAAC,EAAE,cAAc,EAAE,GACvB,cAAc,CA2HhB;AA6YD;;;GAGG;AACH,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE/C"}
|
|
@@ -13,11 +13,13 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
|
|
|
13
13
|
const map = new Map();
|
|
14
14
|
for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {
|
|
15
15
|
const it = monomerLib.getMonomer(polymerType, monomerSymbol);
|
|
16
|
-
if (
|
|
16
|
+
if (
|
|
17
|
+
// RNA: all branch monomers (bases) and all backbone monomers (sugars +
|
|
18
|
+
// phosphates, including modified ones). Modifications are looked up by
|
|
19
|
+
// symbol at assembly time, so they MUST be present in the formatted lib.
|
|
20
|
+
polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ &&
|
|
17
21
|
(it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] === "Branch" /* HELM_MONOMER_TYPE.BRANCH */ ||
|
|
18
|
-
|
|
19
|
-
alphabet === ALPHABET.RNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE.symbol ||
|
|
20
|
-
it["symbol" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE.symbol) ||
|
|
22
|
+
it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] === "Backbone" /* HELM_MONOMER_TYPE.BACKBONE */) ||
|
|
21
23
|
polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */ &&
|
|
22
24
|
it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] !== "Branch" /* HELM_MONOMER_TYPE.BRANCH */) {
|
|
23
25
|
const monomerObject = {};
|
|
@@ -31,19 +33,25 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
|
|
|
31
33
|
return map;
|
|
32
34
|
}
|
|
33
35
|
/** Translate a sequence of monomer symbols into Molfile V3000
|
|
34
|
-
* @param {
|
|
35
|
-
* @param {
|
|
36
|
+
* @param {ISeqMonomer[]} monomerSeq - Sequence of monomer symbols (canonical)
|
|
37
|
+
* @param {MonomerMolGraphMap} monomersDict - Mapping of monomer symbols to MolGraph objects
|
|
36
38
|
* @param {ALPHABET} alphabet - Alphabet of the column
|
|
37
39
|
* @param {PolymerType} polymerType - Polymer type
|
|
38
|
-
* @
|
|
39
|
-
|
|
40
|
+
* @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly
|
|
41
|
+
* uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).
|
|
42
|
+
* @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */
|
|
43
|
+
export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType, roles) {
|
|
40
44
|
if (monomerSeq.length === 0) {
|
|
41
45
|
// throw new Error('monomerSeq is empty');
|
|
42
46
|
return MolfileWithMap.createEmpty();
|
|
43
47
|
}
|
|
48
|
+
// Triples mode is on only when (a) caller flagged the row with roles, and
|
|
49
|
+
// (b) the row's length is a positive multiple of 3 (sugar/base/phosphate triples).
|
|
50
|
+
// in edge cases, terminal phosphate may be missing, so we also allow length % 3 === 2, but only if roles are present to disambiguate the monomers.
|
|
51
|
+
const triplesMode = polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ && !!roles &&
|
|
52
|
+
roles.length === monomerSeq.length && (monomerSeq.length % 3 === 0 || monomerSeq.length % 3 === 2);
|
|
44
53
|
// define atom and bond counts, taking into account the bond type
|
|
45
|
-
const
|
|
46
|
-
const { atomCount, bondCount, needsCapping } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);
|
|
54
|
+
const { atomCount, bondCount, needsCapping } = getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode);
|
|
47
55
|
// create arrays to store lines of the resulting molfile
|
|
48
56
|
const molfileAtomBlock = new Array(atomCount);
|
|
49
57
|
const molfileBondBlock = new Array(bondCount);
|
|
@@ -54,8 +62,12 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
|
|
|
54
62
|
addMonomerToMolblock = addAminoAcidToMolblock;
|
|
55
63
|
else { // nucleotides
|
|
56
64
|
addMonomerToMolblock = addNucleotideToMolblock;
|
|
57
|
-
sugar
|
|
58
|
-
|
|
65
|
+
// Default sugar/phosphate are only consulted in bases-only mode. In
|
|
66
|
+
// triples mode, every nucleotide carries its own.
|
|
67
|
+
if (!triplesMode) {
|
|
68
|
+
sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);
|
|
69
|
+
phosphate = getMolGraph(monomersDict, C.PHOSPHATE);
|
|
70
|
+
}
|
|
59
71
|
}
|
|
60
72
|
const v = {
|
|
61
73
|
i: 0,
|
|
@@ -70,7 +82,8 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
|
|
|
70
82
|
const LC = {
|
|
71
83
|
sugar: sugar,
|
|
72
84
|
phosphate: phosphate,
|
|
73
|
-
|
|
85
|
+
// In triples mode, the "logical" sequence length is the nucleotide count.
|
|
86
|
+
seqLength: triplesMode ? Math.ceil(monomerSeq.length / 3) : monomerSeq.length,
|
|
74
87
|
atomCount: atomCount,
|
|
75
88
|
bondCount: bondCount,
|
|
76
89
|
};
|
|
@@ -78,31 +91,36 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
|
|
|
78
91
|
const steabsCollection = [];
|
|
79
92
|
let nAtoms = 0;
|
|
80
93
|
let lastMonomerCappingAtom = undefined;
|
|
81
|
-
|
|
82
|
-
|
|
83
|
-
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
|
|
101
|
-
|
|
102
|
-
|
|
103
|
-
|
|
104
|
-
|
|
105
|
-
|
|
94
|
+
if (triplesMode) {
|
|
95
|
+
runTriplesAssembly(monomerSeq, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, (a) => { nAtoms += a; }, () => nAtoms);
|
|
96
|
+
}
|
|
97
|
+
else {
|
|
98
|
+
for (v.i = 0; v.i < LC.seqLength; ++v.i) {
|
|
99
|
+
const seqMonomer = monomerSeq[v.i];
|
|
100
|
+
if (seqMonomer.symbol === GAP_SYMBOL)
|
|
101
|
+
continue;
|
|
102
|
+
const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });
|
|
103
|
+
lastMonomerCappingAtom = monomer.terminalR2Atom;
|
|
104
|
+
const mAtomFirst = v.nodeShift;
|
|
105
|
+
const mBondFirst = v.bondShift;
|
|
106
|
+
addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);
|
|
107
|
+
//adding stereo atoms to array for further STEABS block generation
|
|
108
|
+
monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));
|
|
109
|
+
nAtoms += monomer.atoms.x.length;
|
|
110
|
+
const mAtomCount = v.nodeShift - mAtomFirst;
|
|
111
|
+
const mAtomList = new Array(mAtomCount);
|
|
112
|
+
for (let maI = 0; maI < mAtomCount; ++maI)
|
|
113
|
+
mAtomList[maI] = mAtomFirst + maI;
|
|
114
|
+
const mBondCount = v.bondShift - mBondFirst;
|
|
115
|
+
const mBondList = new Array(mBondCount);
|
|
116
|
+
for (let mbI = 0; mbI < mBondCount; ++mbI)
|
|
117
|
+
mBondList[mbI] = mBondFirst + mbI;
|
|
118
|
+
monomers.set(v.i, {
|
|
119
|
+
biotype: seqMonomer.biotype,
|
|
120
|
+
symbol: seqMonomer.symbol,
|
|
121
|
+
atoms: mAtomList, bonds: mBondList
|
|
122
|
+
});
|
|
123
|
+
}
|
|
106
124
|
}
|
|
107
125
|
// if the last monomer needs to be capped, add the terminal OH to the resulting molfile
|
|
108
126
|
if (needsCapping)
|
|
@@ -282,19 +300,22 @@ function fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {
|
|
|
282
300
|
}
|
|
283
301
|
/** Compute the atom/bond counts for the resulting molfile, depending on the
|
|
284
302
|
* type of polymer (peptide/nucleotide)
|
|
285
|
-
* @param {
|
|
286
|
-
* @param {
|
|
287
|
-
* @param {ALPHABET}alphabet - the alphabet of the monomers
|
|
288
|
-
* @param {
|
|
289
|
-
* @
|
|
290
|
-
|
|
303
|
+
* @param {ISeqMonomer[]} monomerSeq - the sequence of monomers
|
|
304
|
+
* @param {MonomerMolGraphMap} monomersDict - the dictionary of monomers
|
|
305
|
+
* @param {ALPHABET} alphabet - the alphabet of the monomers
|
|
306
|
+
* @param {PolymerType} polymerType - the type of polymer
|
|
307
|
+
* @param {boolean} triplesMode - true when monomerSeq is a flat list of HELM RNA triples
|
|
308
|
+
* @return {Object} the atom/bond counts plus needsCapping flag */
|
|
309
|
+
function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode) {
|
|
291
310
|
let atomCount = 0;
|
|
292
311
|
let bondCount = 0;
|
|
293
312
|
let monomerCount = 0;
|
|
294
313
|
let needsCapping = true;
|
|
295
314
|
let lastMonomerGraph = null;
|
|
315
|
+
let lastPhosphateGraph = null;
|
|
296
316
|
// sum up all the atoms/nodes provided by the sequence
|
|
297
|
-
for (
|
|
317
|
+
for (let i = 0; i < monomerSeq.length; ++i) {
|
|
318
|
+
const seqMonomer = monomerSeq[i];
|
|
298
319
|
if (seqMonomer.symbol === GAP_SYMBOL)
|
|
299
320
|
continue; // Skip for gap/empty monomer in MSA
|
|
300
321
|
if (seqMonomer.symbol == '*')
|
|
@@ -303,6 +324,10 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
|
|
|
303
324
|
atomCount += lastMonomerGraph.atoms.x.length;
|
|
304
325
|
bondCount += lastMonomerGraph.bonds.bondTypes.length;
|
|
305
326
|
monomerCount++;
|
|
327
|
+
// In triples mode, every 3rd entry (index 2 mod 3) is a phosphate. Track
|
|
328
|
+
// the LAST one — its atoms/bonds are dropped at the 3'-terminus.
|
|
329
|
+
if (triplesMode && i % 3 === 2)
|
|
330
|
+
lastPhosphateGraph = lastMonomerGraph;
|
|
306
331
|
}
|
|
307
332
|
// add extra values depending on the polymer type
|
|
308
333
|
if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */) {
|
|
@@ -321,7 +346,19 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
|
|
|
321
346
|
}
|
|
322
347
|
}
|
|
323
348
|
}
|
|
324
|
-
else { // nucleotides
|
|
349
|
+
else if (triplesMode) { // nucleotides — HELM triples (per-position sugar/base/phosphate)
|
|
350
|
+
void lastPhosphateGraph; // kept for symmetry; trailing P is now retained when HELM wrote it
|
|
351
|
+
// Per-monomer-loop already summed sugars + bases + phosphates for every
|
|
352
|
+
// entry in monomerSeq. Reservation: each backbone (sugar/phosphate)
|
|
353
|
+
// reserves +1 bond slot for the chain-extending bond, each branch (base)
|
|
354
|
+
// reserves +1 for its branch bond. Total reservations = monomerCount.
|
|
355
|
+
// length === 3N → trailing P emitted, monomerCount = 3N.
|
|
356
|
+
// length === 3N - 1 → trailing P absent, monomerCount = 3N - 1.
|
|
357
|
+
// Either way, bondCount = sum_bonds + monomerCount.
|
|
358
|
+
atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)
|
|
359
|
+
bondCount += monomerCount;
|
|
360
|
+
}
|
|
361
|
+
else { // nucleotides — bases-only legacy path with default sugar/phosphate
|
|
325
362
|
const sugar = (alphabet === ALPHABET.DNA) ?
|
|
326
363
|
getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);
|
|
327
364
|
const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);
|
|
@@ -342,6 +379,118 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
|
|
|
342
379
|
}
|
|
343
380
|
return { atomCount, bondCount, needsCapping };
|
|
344
381
|
}
|
|
382
|
+
/** Triples-mode RNA assembly. Iterate by NUCLEOTIDE; each nucleotide normally
|
|
383
|
+
* contributes 3 entries from monomerSeq in order [sugar, base, phosphate].
|
|
384
|
+
* The LAST nucleotide may omit its trailing phosphate (length === 3N - 1) —
|
|
385
|
+
* in that case HELM specified an unphosphorylated 3'-end and we cap on the
|
|
386
|
+
* last sugar's R2 instead of on a final phosphate.
|
|
387
|
+
*
|
|
388
|
+
* @param {ISeqMonomer[]} monomerSeq - flat sugar/base/[phosphate] entries
|
|
389
|
+
* @param {MonomerMolGraphMap} monomersDict - monomer dictionary
|
|
390
|
+
* @param {string[]} molfileAtomBlock - output atom block buffer
|
|
391
|
+
* @param {string[]} molfileBondBlock - output bond block buffer
|
|
392
|
+
* @param {LoopVariables} v - mutable loop variables
|
|
393
|
+
* @param {LoopConstants} LC - loop constants (seqLength = nucleotide count)
|
|
394
|
+
* @param {MonomerMap} monomers - per-position monomer index map (filled in)
|
|
395
|
+
* @param {number[]} steabsCollection - stereo atoms collected for STEABS block
|
|
396
|
+
* @param {Function} addAtoms - callback to bump per-row atom counter for stereo offsets
|
|
397
|
+
* @param {Function} getAtoms - callback to read current atom counter */
|
|
398
|
+
function runTriplesAssembly(monomerSeq, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, addAtoms, getAtoms) {
|
|
399
|
+
const N = LC.seqLength;
|
|
400
|
+
// length === 3N → trailing P present. length === 3N-1 → trailing P absent.
|
|
401
|
+
const hasTrailingP = monomerSeq.length === 3 * N;
|
|
402
|
+
for (let n = 0; n < N; ++n) {
|
|
403
|
+
v.i = n;
|
|
404
|
+
const sugarSm = monomerSeq[3 * n];
|
|
405
|
+
const baseSm = monomerSeq[3 * n + 1];
|
|
406
|
+
const sugarG = getMolGraph(monomersDict, { symbol: sugarSm.symbol, polymerType: helmTypeToPolymerType(sugarSm.biotype) });
|
|
407
|
+
const baseG = getMolGraph(monomersDict, { symbol: baseSm.symbol, polymerType: helmTypeToPolymerType(baseSm.biotype) });
|
|
408
|
+
// The previous nucleotide's trailing phosphate is the linker into THIS
|
|
409
|
+
// nucleotide's sugar. It always exists for n >= 1 because only the
|
|
410
|
+
// very LAST nucleotide is permitted to omit its phosphate.
|
|
411
|
+
const prevPhosG = (n === 0) ? null :
|
|
412
|
+
getMolGraph(monomersDict, { symbol: monomerSeq[3 * (n - 1) + 2].symbol,
|
|
413
|
+
polymerType: helmTypeToPolymerType(monomerSeq[3 * (n - 1) + 2].biotype) });
|
|
414
|
+
// emit prevPhosphate (chain linker), then sugar, then base
|
|
415
|
+
const seqStartIdx = 3 * n; // for keying the per-row monomer map by HELM splitter index
|
|
416
|
+
if (prevPhosG) {
|
|
417
|
+
const prevAtomFirst = v.nodeShift;
|
|
418
|
+
const prevBondFirst = v.bondShift;
|
|
419
|
+
addBackboneMonomerToMolblock(prevPhosG, molfileAtomBlock, molfileBondBlock, v);
|
|
420
|
+
prevPhosG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));
|
|
421
|
+
addAtoms(prevPhosG.atoms.x.length);
|
|
422
|
+
// The phosphate "belongs to" nucleotide n-1's HELM index (3*(n-1)+2).
|
|
423
|
+
const prevPhosKey = 3 * (n - 1) + 2;
|
|
424
|
+
const aList = [];
|
|
425
|
+
for (let a = prevAtomFirst; a < v.nodeShift; ++a)
|
|
426
|
+
aList.push(a);
|
|
427
|
+
const bList = [];
|
|
428
|
+
for (let b = prevBondFirst; b < v.bondShift; ++b)
|
|
429
|
+
bList.push(b);
|
|
430
|
+
monomers.set(prevPhosKey, {
|
|
431
|
+
biotype: monomerSeq[prevPhosKey].biotype,
|
|
432
|
+
symbol: monomerSeq[prevPhosKey].symbol,
|
|
433
|
+
atoms: aList, bonds: bList,
|
|
434
|
+
});
|
|
435
|
+
}
|
|
436
|
+
const sugarAtomFirst = v.nodeShift;
|
|
437
|
+
const sugarBondFirst = v.bondShift;
|
|
438
|
+
addBackboneMonomerToMolblock(sugarG, molfileAtomBlock, molfileBondBlock, v);
|
|
439
|
+
sugarG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));
|
|
440
|
+
addAtoms(sugarG.atoms.x.length);
|
|
441
|
+
const sAList = [];
|
|
442
|
+
for (let a = sugarAtomFirst; a < v.nodeShift; ++a)
|
|
443
|
+
sAList.push(a);
|
|
444
|
+
const sBList = [];
|
|
445
|
+
for (let b = sugarBondFirst; b < v.bondShift; ++b)
|
|
446
|
+
sBList.push(b);
|
|
447
|
+
monomers.set(seqStartIdx, {
|
|
448
|
+
biotype: sugarSm.biotype, symbol: sugarSm.symbol,
|
|
449
|
+
atoms: sAList, bonds: sBList,
|
|
450
|
+
});
|
|
451
|
+
const baseAtomFirst = v.nodeShift;
|
|
452
|
+
const baseBondFirst = v.bondShift;
|
|
453
|
+
addBranchMonomerToMolblock(baseG, molfileAtomBlock, molfileBondBlock, v);
|
|
454
|
+
baseG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));
|
|
455
|
+
addAtoms(baseG.atoms.x.length);
|
|
456
|
+
const bAList = [];
|
|
457
|
+
for (let a = baseAtomFirst; a < v.nodeShift; ++a)
|
|
458
|
+
bAList.push(a);
|
|
459
|
+
const bBList = [];
|
|
460
|
+
for (let b = baseBondFirst; b < v.bondShift; ++b)
|
|
461
|
+
bBList.push(b);
|
|
462
|
+
monomers.set(seqStartIdx + 1, {
|
|
463
|
+
biotype: baseSm.biotype, symbol: baseSm.symbol,
|
|
464
|
+
atoms: bAList, bonds: bBList,
|
|
465
|
+
});
|
|
466
|
+
}
|
|
467
|
+
// Emit the trailing phosphate (the LAST nucleotide's P) as the final
|
|
468
|
+
// backbone monomer ONLY if HELM explicitly wrote it. The OH cap then
|
|
469
|
+
// rides on its free oxygen (3'-phosphate-OH terminus). If HELM omitted
|
|
470
|
+
// the trailing phosphate, the cap rides on the last sugar's R2 — that
|
|
471
|
+
// requires no extra emission here, since v.backboneAttachNode already
|
|
472
|
+
// points at the last sugar's R2 attach.
|
|
473
|
+
if (hasTrailingP) {
|
|
474
|
+
const lastPhosKey = 3 * (N - 1) + 2;
|
|
475
|
+
const lastPhosSm = monomerSeq[lastPhosKey];
|
|
476
|
+
const lastPhosG = getMolGraph(monomersDict, { symbol: lastPhosSm.symbol, polymerType: helmTypeToPolymerType(lastPhosSm.biotype) });
|
|
477
|
+
const trailAtomFirst = v.nodeShift;
|
|
478
|
+
const trailBondFirst = v.bondShift;
|
|
479
|
+
addBackboneMonomerToMolblock(lastPhosG, molfileAtomBlock, molfileBondBlock, v);
|
|
480
|
+
lastPhosG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));
|
|
481
|
+
addAtoms(lastPhosG.atoms.x.length);
|
|
482
|
+
const tAList = [];
|
|
483
|
+
for (let a = trailAtomFirst; a < v.nodeShift; ++a)
|
|
484
|
+
tAList.push(a);
|
|
485
|
+
const tBList = [];
|
|
486
|
+
for (let b = trailBondFirst; b < v.bondShift; ++b)
|
|
487
|
+
tBList.push(b);
|
|
488
|
+
monomers.set(lastPhosKey, {
|
|
489
|
+
biotype: lastPhosSm.biotype, symbol: lastPhosSm.symbol,
|
|
490
|
+
atoms: tAList, bonds: tBList,
|
|
491
|
+
});
|
|
492
|
+
}
|
|
493
|
+
}
|
|
345
494
|
/** Keep precision upon floating point operations over atom coordinates
|
|
346
495
|
* @param {number}x - the floating point number
|
|
347
496
|
* @return {number} - the floating point number with the same precision
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
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2
2
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import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
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3
3
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import { ALPHABET } from '../utils/macromolecule/consts';
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4
4
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import { IMonomerLib, IMonomerLibBase, Monomer } from '../types/monomer-library';
|
|
5
|
-
import { Bonds, MolGraph, MonomerMolGraphMap } from './types';
|
|
5
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+
import { Bonds, MolGraph, MonomerMolGraphMap, NucleotideRole } from './types';
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|
6
6
|
import { ISeqHelper, ToAtomicLevelRes } from '../utils/seq-helper';
|
|
7
7
|
import { ISeqMonomer, PolymerType } from '../helm/types';
|
|
8
8
|
/** Convert Macromolecule column into Molecule column storing molfile V3000 with the help of a monomer library
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@@ -18,12 +18,14 @@ export declare function getMonomerSequencesArray(macroMolCol: DG.Column<string>,
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|
18
18
|
/** Get a mapping of monomer symbols to MolGraph objects. Notice, the
|
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19
19
|
* transformation from molfile V2000 to V3000 takes place,
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20
20
|
* with the help of async function call from Chem (RdKit module)
|
|
21
|
-
* @param {
|
|
22
|
-
* @param {
|
|
21
|
+
* @param {ISeqMonomer[][]} monomerSequencesArray - Jagged array of monomer symbols for the dataframe
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|
22
|
+
* @param {Array} rolesArray - Per-row NucleotideRole tags (undefined for legacy bases-only rows)
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23
23
|
* @param {PolymerType} polymerType - Polymer type
|
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24
24
|
* @param {ALPHABET} alphabet - Alphabet
|
|
25
|
-
* @
|
|
26
|
-
|
|
25
|
+
* @param {IMonomerLibBase} monomerLib - Monomer library
|
|
26
|
+
* @param {RDModule} rdKitModule - RDKit module
|
|
27
|
+
* @return {MonomerMolGraphMap} - Mapping of monomer symbols to MolGraph objects */
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|
28
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+
export declare function getMonomersDictFromLib(monomerSequencesArray: ISeqMonomer[][], rolesArray: (NucleotideRole[] | undefined)[], polymerType: PolymerType, alphabet: ALPHABET, monomerLib: IMonomerLibBase, rdKitModule: RDModule): MonomerMolGraphMap;
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/** Parse element symbols for R-groups from the HELM monomer library R-group field
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* @param {any[]} rGroupObjList - R-group object list
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* @return {Map<number, number>} - Cap group index map*/
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