@datagrok-libraries/bio 5.32.3 → 5.32.5
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/.eslintrc.json +17 -12
- package/package.json +1 -1
- package/src/aminoacids.js +3 -4
- package/src/aminoacids.js.map +1 -1
- package/src/monomer-works/consts.d.ts +27 -0
- package/src/monomer-works/consts.d.ts.map +1 -0
- package/src/monomer-works/consts.js +30 -0
- package/src/monomer-works/consts.js.map +1 -0
- package/src/monomer-works/monomer-utils.js +6 -17
- package/src/monomer-works/monomer-utils.js.map +1 -1
- package/src/monomer-works/seq-to-molfile-worker.d.ts +2 -0
- package/src/monomer-works/seq-to-molfile-worker.d.ts.map +1 -0
- package/src/monomer-works/seq-to-molfile-worker.js +19 -0
- package/src/monomer-works/seq-to-molfile-worker.js.map +1 -0
- package/src/monomer-works/seq-to-molfile.d.ts +9 -0
- package/src/monomer-works/seq-to-molfile.d.ts.map +1 -0
- package/src/monomer-works/seq-to-molfile.js +31 -0
- package/src/monomer-works/seq-to-molfile.js.map +1 -0
- package/src/monomer-works/to-atomic-level-utils.d.ts +23 -0
- package/src/monomer-works/to-atomic-level-utils.d.ts.map +1 -0
- package/src/monomer-works/to-atomic-level-utils.js +284 -0
- package/src/monomer-works/to-atomic-level-utils.js.map +1 -0
- package/src/monomer-works/to-atomic-level.d.ts +48 -4
- package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
- package/src/monomer-works/to-atomic-level.js +273 -503
- package/src/monomer-works/to-atomic-level.js.map +1 -1
- package/src/monomer-works/types.d.ts +71 -0
- package/src/monomer-works/types.d.ts.map +1 -0
- package/src/monomer-works/types.js +2 -0
- package/src/monomer-works/types.js.map +1 -0
- package/src/pdb/pdb-helper.js +7 -18
- package/src/pdb/pdb-helper.js.map +1 -1
- package/src/tests/palettes-tests.js +20 -33
- package/src/tests/palettes-tests.js.map +1 -1
- package/src/trees/dendrogram.js +2 -13
- package/src/trees/dendrogram.js.map +1 -1
- package/src/trees/tree-helper.js +7 -18
- package/src/trees/tree-helper.js.map +1 -1
- package/src/utils/cell-renderer.d.ts +1 -1
- package/src/utils/cell-renderer.d.ts.map +1 -1
- package/src/utils/cell-renderer.js +5 -7
- package/src/utils/cell-renderer.js.map +1 -1
- package/src/utils/macromolecule/utils.js +4 -6
- package/src/utils/macromolecule/utils.js.map +1 -1
- package/src/utils/splitter.js +1 -1
- package/src/utils/splitter.js.map +1 -1
- package/src/utils/units-handler.js +26 -38
- package/src/utils/units-handler.js.map +1 -1
- package/src/utils.js +1 -1
- package/src/utils.js.map +1 -1
- package/src/viewers/ngl-gl-viewer.js +6 -17
- package/src/viewers/ngl-gl-viewer.js.map +1 -1
- package/src/viewers/phylocanvas-gl-viewer.js +7 -18
- package/src/viewers/phylocanvas-gl-viewer.js.map +1 -1
- package/tsconfig.json +1 -1
package/.eslintrc.json
CHANGED
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@@ -1,7 +1,7 @@
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{
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"env": {
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"browser": true,
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"
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"es2020": true
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},
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"extends": [
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"google"
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"indent": ["error", 2, {"SwitchCase": 1}],
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"max-len": ["error", 120],
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"no-unused-vars": "off",
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"@typescript-eslint/no-unused-vars": "warn",
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"@typescript-eslint/no-unused-vars": ["warn", { "varsIgnorePattern": "^(_|ui$|grok$|DG$)", "argsIgnorePattern": "^_"}],
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"require-jsdoc": "off",
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"valid-jsdoc": "
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"valid-jsdoc": "warn",
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"spaced-comment": "off",
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"linebreak-style": "off",
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"curly": [
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"curly": [
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"error",
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"multi-or-nest",
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"consistent"
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],
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"brace-style": [
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"error",
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"1tbs",
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{
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"
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"functions": "never",
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"objects": "only-multiline",
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"imports": "only-multiline"
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"allowSingleLine": true
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}
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],
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"
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"block-spacing": [2, "always"],
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"comma-dangle": "off",
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"comma-spacing": "error",
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"comma-style": "error",
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"guard-for-in": "off",
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"space-infix-ops": "error"
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}
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}
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package/package.json
CHANGED
package/src/aminoacids.js
CHANGED
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@@ -101,21 +101,20 @@ export class Aminoacids {
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return !isNaN(parseInt(inner)) ? [outer, ''] : [outer, inner];
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}
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static getColorAAPivot(monomer = '', scheme = 'grok') {
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var _a, _b, _c;
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//const chemPaletteInstance = AAPalettes.GrokGroups();
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const chemPaletteInstance = this.getPalette(scheme);
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let [outerMonomer, innerMonomer] = this.getInnerOuter(monomer);
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outerMonomer = (outerMonomer.length > 6 ? `${outerMonomer.slice(0, 3)}...` : outerMonomer);
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innerMonomer = (innerMonomer.length > 6 ? `${innerMonomer.slice(0, 3)}...` : innerMonomer);
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if (monomer.length == 1 || monomer[1] == '(') {
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const amino =
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const amino = monomer[0]?.toUpperCase();
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return amino in chemPaletteInstance ?
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[chemPaletteInstance.get(amino), amino, innerMonomer, 1] :
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[this.undefinedColor, outerMonomer, innerMonomer, 1];
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}
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if (monomer[0] == 'd' && monomer[1] in chemPaletteInstance) {
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if (monomer.length == 2 || monomer[2] == '(') {
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const amino =
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const amino = monomer[1]?.toUpperCase();
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return amino in chemPaletteInstance ?
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[chemPaletteInstance.get(amino), amino, innerMonomer, 2] :
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[this.undefinedColor, outerMonomer, innerMonomer, 2];
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@@ -129,7 +128,7 @@ export class Aminoacids {
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[this.undefinedColor, outerMonomer, innerMonomer, 3];
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}
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}
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if (
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if (monomer[0]?.toLowerCase() == monomer[0]) {
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if (monomer.substring(1, 3) in this.AAFullNames) {
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if (monomer.length == 4 || monomer[4] == '(') {
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const amino = this.AAFullNames[monomer.substring(1, 3)];
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package/src/aminoacids.js.map
CHANGED
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@@ -1 +1 @@
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-
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+
{"version":3,"file":"aminoacids.js","sourceRoot":"","sources":["aminoacids.ts"],"names":[],"mappings":"AAKA,OAAO,EAAa,cAAc,EAAC,MAAM,gBAAgB,CAAC;AAE1D,MAAM,OAAO,kBAAmB,SAAQ,cAAc;IAG7C,MAAM,KAAK,IAAI;QACpB,IAAI,IAAI,CAAC,IAAI,KAAK,KAAK,CAAC,EAAE;YACxB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,WAAW,CAAC;gBAC3B,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,QAAQ,CAAC;gBAChC,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,WAAW,CAAC;gBAC5D,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,SAAS,CAAC;gBAC5B,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,KAAK,CAAC;gBACnB,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,UAAU,CAAC;aACzB,EAAE,KAAK,EAAE,kBAAkB,CAAC,CAAC;SAC/B;QACD,OAAO,IAAI,CAAC,IAAI,CAAC;IACnB,CAAC;IAIM,MAAM,KAAK,UAAU;QAC1B,IAAI,IAAI,CAAC,UAAU,KAAK,KAAK,CAAC,EAAE;YAC9B,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,WAAW,CAAC;gBACjC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,QAAQ,CAAC;gBACtB,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,KAAK,CAAC;gBACnB,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,WAAW,CAAC;gBACvD,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,YAAY,CAAC;gBAC/B,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,WAAW,CAAC;gBACzB,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,QAAQ,CAAC;aACjC,EAAE,KAAK,EAAE,kBAAkB,CAAC,CAAC;SAC/B;QACD,OAAO,IAAI,CAAC,UAAU,CAAC;IACzB,CAAC;IAIM,MAAM,KAAK,MAAM;QACtB,IAAI,IAAI,CAAC,MAAM,KAAK,KAAK,CAAC,EAAE;YAC1B,IAAI,CAAC,MAAM,GAAG,IAAI,kBAAkB,CAAC;gBACnC,yDAAyD;gBACzD,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,GAAG,EAAE,SAAS;gBACd,QAAQ,EAAE,SAAS;aACpB,CAAC,CAAC;SACJ;QACD,OAAO,IAAI,CAAC,MAAM,CAAC;IACrB,CAAC;IAEe,GAAG,CAAC,CAAS;QAC3B,MAAM,IAAI,GAAG,CAAC,IAAI,kBAAkB,CAAC,UAAU,CAAC,CAAC,CAAC,kBAAkB,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACvF,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAC5B,OAAO,GAAG,CAAC;IACb,CAAC;;AAED,8FAA8F;AAC/E,6BAAU,GAA+B;IACtD,OAAO,EAAE,GAAG;IACZ,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;CACX,CAAC;AAGJ,MAAM,OAAO,UAAU;IAqGd,MAAM,CAAC,UAAU,CAAC,SAAiB,MAAM;QAC9C,QAAQ,MAAM,EAAE;YAChB,KAAK,MAAM;gBACT,OAAO,kBAAkB,CAAC,UAAU,CAAC;YACvC,KAAK,MAAM;gBACT,OAAO,kBAAkB,CAAC,IAAI,CAAC;YACjC;gBACE,MAAM,IAAI,KAAK,CAAC,yBAAyB,MAAM,mBAAmB,CAAC,CAAC;SACrE;IACH,CAAC;IAED;;;;;OAKG;IACI,MAAM,CAAC,aAAa,CAAC,CAAS;QACnC,IAAI,OAAO,GAAG,CAAC,CAAC;QAChB,IAAI,KAAK,GAAG,EAAE,CAAC;QACf,IAAI,KAAK,GAAG,EAAE,CAAC;QAEf,KAAK,MAAM,IAAI,IAAI,CAAC,EAAE;YACpB,IAAI,IAAI,IAAI,GAAG;gBACb,OAAO,EAAE,CAAC;iBACP,IAAI,IAAI,IAAI,GAAG;gBAClB,OAAO,EAAE,CAAC;iBACP,IAAI,OAAO;gBACd,KAAK,IAAI,IAAI,CAAC;;gBAEd,KAAK,IAAI,IAAI,CAAC;SACjB;QAED,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;IAChE,CAAC;IAEM,MAAM,CAAC,eAAe,CAAC,UAAkB,EAAE,EAAE,SAAiB,MAAM;QACzE,sDAAsD;QACtD,MAAM,mBAAmB,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC;QACpD,IAAI,CAAC,YAAY,EAAE,YAAY,CAAC,GAAG,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAC;QAC/D,YAAY,GAAG,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC;QAC3F,YAAY,GAAG,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC;QAE3F,IAAI,OAAO,CAAC,MAAM,IAAI,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE;YAC5C,MAAM,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE,WAAW,EAAG,CAAC;YACzC,OAAO,KAAK,IAAI,mBAAmB,CAAC,CAAC;gBACnC,CAAC,mBAAmB,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC,CAAC;gBAC1D,CAAC,IAAI,CAAC,cAAc,EAAE,YAAY,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC;SACxD;QAED,IAAI,OAAO,CAAC,CAAC,CAAC,IAAI,GAAG,IAAI,OAAO,CAAC,CAAC,CAAE,IAAI,mBAAmB,EAAE;YAC3D,IAAI,OAAO,CAAC,MAAM,IAAI,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE;gBAC5C,MAAM,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE,WAAW,EAAG,CAAC;gBACzC,OAAO,KAAK,IAAI,mBAAmB,CAAC,CAAC;oBACnC,CAAC,mBAAmB,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC,CAAC;oBAC1D,CAAC,IAAI,CAAC,cAAc,EAAE,YAAY,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC;aACxD;SACF;QAED,IAAI,OAAO,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,IAAI,CAAC,WAAW,EAAE;YAC/C,IAAI,OAAO,CAAC,MAAM,IAAI,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE;gBAC5C,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;gBACxD,OAAO,KAAK,IAAI,mBAAmB,CAAC,CAAC;oBACnC,CAAC,mBAAmB,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC,CAAC;oBAC1D,CAAC,IAAI,CAAC,cAAc,EAAE,YAAY,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC;aACxD;SACF;QAED,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE;YAC3C,IAAI,OAAO,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,IAAI,CAAC,WAAW,EAAE;gBAC/C,IAAI,OAAO,CAAC,MAAM,IAAI,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE;oBAC5C,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;oBACxD,OAAO,KAAK,IAAI,mBAAmB,CAAC,CAAC;wBACnC,CAAC,mBAAmB,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC,CAAC;wBAC1D,CAAC,IAAI,CAAC,cAAc,EAAE,YAAY,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC;iBACxD;aACF;SACF;QAED,OAAO,CAAC,IAAI,CAAC,cAAc,EAAE,YAAY,EAAE,YAAY,EAAE,CAAC,CAAC,CAAC;IAC9D,CAAC;;AApLe,kBAAO,GAAW,YAAY,CAAC;AAE/B,mCAAwB,GAAW,6BAA6B,CAAC;AAE1E,yBAAc,GAAG,kBAAkB,CAAC;AAE7B,gBAAK,GAAqB;IACtC,GAAG,EAAE,SAAS;IACd,GAAG,EAAE,SAAS;IACd,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,QAAQ;IACb,GAAG,EAAE,eAAe;IACpB,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,eAAe;IACpB,GAAG,EAAE,YAAY;IACjB,GAAG,EAAE,eAAe;IACpB,GAAG,EAAE,SAAS;IACd,GAAG,EAAE,QAAQ;IACb,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,QAAQ;IACb,GAAG,EAAE,SAAS;IACd,GAAG,EAAE,YAAY;IACjB,GAAG,EAAE,YAAY;IACjB,GAAG,EAAE,YAAY;IACjB,GAAG,EAAE,WAAW;CACjB,CAAC;AAEY,mBAAQ,GAAqB;IACzC,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,sBAAsB;IAC3B,GAAG,EAAE,2BAA2B;IAChC,GAAG,EAAE,cAAc;IACnB,GAAG,EAAE,yBAAyB;IAC9B,GAAG,EAAE,yBAAyB;IAC9B,GAAG,EAAE,wBAAwB;IAC7B,GAAG,EAAE,wBAAwB;IAC7B,GAAG,EAAE,wBAAwB;IAC7B,GAAG,EAAE,iBAAiB;IACtB,GAAG,EAAE,iBAAiB;IACtB,GAAG,EAAE,0BAA0B;IAC/B,GAAG,EAAE,wBAAwB;IAC7B,GAAG,EAAE,mBAAmB;IACxB,GAAG,EAAE,iBAAiB;IACtB,GAAG,EAAE,iBAAiB;IACtB,GAAG,EAAE,oCAAoC;IACzC,GAAG,EAAE,0BAA0B;IAC/B,GAAG,EAAE,gBAAgB;IACrB,GAAG,EAAE,iBAAiB;CACvB,CAAC;AAEY,4BAAiB,GAAqB;IAClD,GAAG,EAAE,KAAK;IACV,GAAG,EAAE,iBAAiB;IACtB,GAAG,EAAE,sBAAsB;IAC3B,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,oBAAoB;IACzB,GAAG,EAAE,qBAAqB;IAC1B,GAAG,EAAE,mBAAmB;IACxB,GAAG,EAAE,mBAAmB;IACxB,GAAG,EAAE,qBAAqB;IAC1B,GAAG,EAAE,YAAY;IACjB,GAAG,EAAE,cAAc;IACnB,GAAG,EAAE,qBAAqB;IAC1B,GAAG,EAAE,mBAAmB;IACxB,GAAG,EAAE,gBAAgB;IACrB,GAAG,EAAE,YAAY;IACjB,GAAG,EAAE,aAAa;IAClB,GAAG,EAAE,+BAA+B;IACpC,GAAG,EAAE,qBAAqB;IAC1B,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,YAAY;CAClB,CAAC;AAEF;GACG;AACW,sBAAW,GAAqB;IAC5C,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;IACV,KAAK,EAAE,GAAG;CACX,CAAC"}
|
|
@@ -0,0 +1,27 @@
|
|
|
1
|
+
export declare const monomerWorksConsts: {
|
|
2
|
+
readonly V2K_RGP_SHIFT: 8;
|
|
3
|
+
readonly V2K_RGP_LINE: "M RGP";
|
|
4
|
+
readonly V2K_A_LINE: "A ";
|
|
5
|
+
readonly V3K_COUNTS_SHIFT: 14;
|
|
6
|
+
readonly V3K_IDX_SHIFT: 7;
|
|
7
|
+
readonly V3K_HEADER_FIRST_LINE: "\nDatagrok macromolecule handler\n\n";
|
|
8
|
+
readonly V3K_HEADER_SECOND_LINE: " 0 0 0 0 0 0 999 V3000\n";
|
|
9
|
+
readonly V3K_BEGIN_CTAB_BLOCK: "M V30 BEGIN CTAB\n";
|
|
10
|
+
readonly V3K_END_CTAB_BLOCK: "M V30 END CTAB\n";
|
|
11
|
+
readonly V3K_BEGIN_COUNTS_LINE: "M V30 COUNTS ";
|
|
12
|
+
readonly V3K_COUNTS_LINE_ENDING: " 0 0 0\n";
|
|
13
|
+
readonly V3K_BEGIN_ATOM_BLOCK: "M V30 BEGIN ATOM\n";
|
|
14
|
+
readonly V3K_END_ATOM_BLOCK: "M V30 END ATOM\n";
|
|
15
|
+
readonly V3K_BEGIN_BOND_BLOCK: "M V30 BEGIN BOND\n";
|
|
16
|
+
readonly V3K_END_BOND_BLOCK: "M V30 END BOND\n";
|
|
17
|
+
readonly V3K_BOND_CONFIG: " CFG:";
|
|
18
|
+
readonly V3K_BEGIN_DATA_LINE: "M V30 ";
|
|
19
|
+
readonly V3K_END: "M END";
|
|
20
|
+
readonly PRECISION_FACTOR: 10000;
|
|
21
|
+
readonly DEOXYRIBOSE: "d";
|
|
22
|
+
readonly RIBOSE: "r";
|
|
23
|
+
readonly PHOSPHATE: "p";
|
|
24
|
+
readonly OXYGEN: "O";
|
|
25
|
+
readonly HYDROGEN: "H";
|
|
26
|
+
};
|
|
27
|
+
//# sourceMappingURL=consts.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;CA6BrB,CAAC"}
|
|
@@ -0,0 +1,30 @@
|
|
|
1
|
+
export const monomerWorksConsts = {
|
|
2
|
+
// constants for parsing molfile V2000
|
|
3
|
+
V2K_RGP_SHIFT: 8,
|
|
4
|
+
V2K_RGP_LINE: 'M RGP',
|
|
5
|
+
V2K_A_LINE: 'A ',
|
|
6
|
+
// constants for parsing/reconstruction of molfile V3000
|
|
7
|
+
V3K_COUNTS_SHIFT: 14,
|
|
8
|
+
V3K_IDX_SHIFT: 7,
|
|
9
|
+
V3K_HEADER_FIRST_LINE: '\nDatagrok macromolecule handler\n\n',
|
|
10
|
+
V3K_HEADER_SECOND_LINE: ' 0 0 0 0 0 0 999 V3000\n',
|
|
11
|
+
V3K_BEGIN_CTAB_BLOCK: 'M V30 BEGIN CTAB\n',
|
|
12
|
+
V3K_END_CTAB_BLOCK: 'M V30 END CTAB\n',
|
|
13
|
+
V3K_BEGIN_COUNTS_LINE: 'M V30 COUNTS ',
|
|
14
|
+
V3K_COUNTS_LINE_ENDING: ' 0 0 0\n',
|
|
15
|
+
V3K_BEGIN_ATOM_BLOCK: 'M V30 BEGIN ATOM\n',
|
|
16
|
+
V3K_END_ATOM_BLOCK: 'M V30 END ATOM\n',
|
|
17
|
+
V3K_BEGIN_BOND_BLOCK: 'M V30 BEGIN BOND\n',
|
|
18
|
+
V3K_END_BOND_BLOCK: 'M V30 END BOND\n',
|
|
19
|
+
V3K_BOND_CONFIG: ' CFG:',
|
|
20
|
+
V3K_BEGIN_DATA_LINE: 'M V30 ',
|
|
21
|
+
V3K_END: 'M END',
|
|
22
|
+
PRECISION_FACTOR: 10000,
|
|
23
|
+
// symbols for the corresponding monomers in HELM library
|
|
24
|
+
DEOXYRIBOSE: 'd',
|
|
25
|
+
RIBOSE: 'r',
|
|
26
|
+
PHOSPHATE: 'p',
|
|
27
|
+
OXYGEN: 'O',
|
|
28
|
+
HYDROGEN: 'H',
|
|
29
|
+
};
|
|
30
|
+
//# sourceMappingURL=consts.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAClC,sCAAsC;IACpC,aAAa,EAAE,CAAC;IAChB,YAAY,EAAE,QAAQ;IACtB,UAAU,EAAE,KAAK;IACjB,wDAAwD;IACxD,gBAAgB,EAAE,EAAE;IACpB,aAAa,EAAE,CAAC;IAChB,qBAAqB,EAAE,sCAAsC;IAC7D,sBAAsB,EAAE,2CAA2C;IACnE,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,qBAAqB,EAAE,gBAAgB;IACvC,sBAAsB,EAAE,UAAU;IAClC,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,oBAAoB,EAAE,qBAAqB;IAC3C,kBAAkB,EAAE,mBAAmB;IACvC,eAAe,EAAE,OAAO;IACxB,mBAAmB,EAAE,SAAS;IAC9B,OAAO,EAAE,QAAQ;IACjB,gBAAgB,EAAE,KAAM;IACxB,yDAAyD;IACzD,WAAW,EAAE,GAAG;IAChB,MAAM,EAAE,GAAG;IACX,SAAS,EAAE,GAAG;IAEd,MAAM,EAAE,GAAG;IACX,QAAQ,EAAE,GAAG;CACL,CAAC"}
|
|
@@ -1,12 +1,3 @@
|
|
|
1
|
-
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
|
|
2
|
-
function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
|
|
3
|
-
return new (P || (P = Promise))(function (resolve, reject) {
|
|
4
|
-
function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
|
|
5
|
-
function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
|
|
6
|
-
function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
|
|
7
|
-
step((generator = generator.apply(thisArg, _arguments || [])).next());
|
|
8
|
-
});
|
|
9
|
-
};
|
|
10
1
|
// import * as ui from 'datagrok-api/ui';
|
|
11
2
|
import * as DG from 'datagrok-api/dg';
|
|
12
3
|
import * as grok from 'datagrok-api/grok';
|
|
@@ -128,13 +119,11 @@ export function createJsonMonomerLibFromSdf(table) {
|
|
|
128
119
|
}
|
|
129
120
|
return resultLib;
|
|
130
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|
}
|
|
131
|
-
export function getMonomerLibHelper() {
|
|
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|
-
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
|
|
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|
-
|
|
137
|
-
return res;
|
|
138
|
-
});
|
|
122
|
+
export async function getMonomerLibHelper() {
|
|
123
|
+
const funcList = DG.Func.find({ package: 'Bio', name: 'getMonomerLibHelper' });
|
|
124
|
+
if (funcList.length === 0)
|
|
125
|
+
throw new Error('Package "Bio" must be installer for MonomerLibraryHelper.');
|
|
126
|
+
const res = (await funcList[0].prepare().call()).getOutputParamValue();
|
|
127
|
+
return res;
|
|
139
128
|
}
|
|
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129
|
//# sourceMappingURL=monomer-utils.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"monomer-utils.js","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"monomer-utils.js","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AAAA,yCAAyC;AACzC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAE1C,OAAO,EACQ,gBAAgB,EAAsB,qBAAqB,EACxE,kBAAkB,EAAE,kBAAkB,EAAE,gBAAgB,EACzD,MAAM,gBAAgB,CAAC;AAIxB,OAAO,EAAC,WAAW,EAAC,MAAM,8BAA8B,CAAC;AAEzD,MAAM,UAAU,cAAc,CAAC,GAAc;IAC3C,IAAI,YAAY,GAAG,kBAAkB,CAAC;IACtC,MAAM,iBAAiB,GAA8B,EAAE,CAAC;IACxD,MAAM,KAAK,GAAG,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACtC,MAAM,GAAG,GAAG,GAAG,CAAC,MAAM,kCAAgB,CAAC;IACvC,MAAM,YAAY,GAAiB,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IAC3D,MAAM,kBAAkB,GAAG,EAAE,CAAC;IAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACnC,IAAI,iBAAiB,GAAG,EAAE,CAAC;QAC3B,MAAM,QAAQ,GAAG,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;QAC1C,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAS,EAAE,EAAE;YAC7B,IAAI,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE;gBACzB,IAAI,YAAY,GAAG,kBAAkB,EAAE;oBACrC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,uCAAuC,CAAC,CAAC;oBAC1D,OAAO,IAAI,CAAC;iBACb;gBACD,iBAAiB,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC;gBACpC,YAAY,EAAE,CAAC;aAChB;YACD,iBAAiB,IAAI,MAAM,CAAC,aAAa,CAAC,iBAAiB,CAAC,CAAC,CAAC,CAAC,CAAC;QAClE,CAAC,CAAC,CAAC;QACH,kBAAkB,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;KAC5C;IACD,OAAO,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAC;AACvE,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,GAAc,EAAE,iBAAwB;IACzE,MAAM,KAAK,GAAG,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACtC,MAAM,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC;IACpC,MAAM,YAAY,GAAiB,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IAC3D,MAAM,YAAY,GAAG,qBAAqB,CAAC,iBAAiB,CAAC,CAAC;IAC9D,MAAM,QAAQ,GAAG,EAAE,CAAC;IACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACnC,MAAM,aAAa,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;QACjC,MAAM,QAAQ,GAAG,YAAY,CAAC,aAAa,CAAC,CAAC;QAC7C,MAAM,cAAc,GAAG,EAAE,CAAC;QAC1B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;YACxC,IAAI,QAAQ,CAAC,CAAC,CAAC,EAAE;gBACf,IAAI,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE;oBAC9B,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,WAAW,QAAQ,CAAC,CAAC,CAAC,0DAA0D,CAAC,CAAC;oBACrG,OAAO,IAAI,CAAC;iBACb;gBACD,2CAA2C;gBAC3C,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;aAC5E;SACF;QACD,QAAQ,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;KAC/B;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,IAAa,EAAE,iBAAwB;IAC9E,MAAM,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAC9C,MAAM,GAAG,GAAG,IAAI,CAAC,MAAO,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC;IAC7C,MAAM,YAAY,GAAiB,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IAC3D,MAAM,YAAY,GAAG,qBAAqB,CAAC,iBAAiB,CAAC,CAAC;IAC9D,MAAM,QAAQ,GAAG,EAAE,CAAC;IACpB,MAAM,aAAa,GAAG,IAAI,CAAC,KAAK,CAAC;IACjC,MAAM,QAAQ,GAAG,YAAY,CAAC,aAAa,CAAC,CAAC;IAC7C,MAAM,cAAc,GAAG,EAAE,CAAC;IAC1B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACxC,IAAI,QAAQ,CAAC,CAAC,CAAC,EAAE;YACf,IAAI,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE;gBAC9B,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,WAAW,QAAQ,CAAC,CAAC,CAAC,0DAA0D,CAAC,CAAC;gBACrG,OAAO,IAAI,CAAC;aACb;YACD,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;SAC5E;KACF;IACD,QAAQ,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;IAC9B,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,GAAU;IAC9C,MAAM,IAAI,GAAoC,EAAE,CAAC;IACjD,GAAG,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,EAAE;QACjB,IAAI,EAAE,CAAC,aAAa,CAAC,KAAK,SAAS,EAAE;YACnC,MAAM,aAAa,GAA2B,EAAE,CAAC;YACjD,gBAAgB,CAAC,OAAO,CAAC,CAAC,KAAK,EAAE,EAAE;gBACjC,aAAa,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC;YACnC,CAAC,CAAC,CAAC;YACH,IAAI,CAAC,EAAE,mCAAoB,CAAC,GAAG,aAAa,CAAC;SAC9C;IACH,CAAC,CAAC,CAAC;IACH,OAAO,IAAI,CAAC;AACd,CAAC;AAED,MAAM,UAAU,2BAA2B,CAAC,KAAmB;IAC7D,MAAM,SAAS,GAAG,EAAE,CAAC;IACrB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,QAAQ,EAAE,CAAC,EAAE,EAAE;QACvC,MAAM,OAAO,GAAoC,EAAE,CAAC;QACpD,MAAM,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,EAAE;YACjD,IAAI,GAAG,sCAAuB,EAAE;gBAC9B,MAAM,aAAa,GAAG,KAAK,CAAC,GAAG,CAAC,qBAAqB,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC;gBAC/D,OAAO,CAAC,GAAG,CAAC,GAAG,aAAa,KAAK,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,gBAAgB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC;aACvF;iBAAM,IAAI,GAAG,wCAAwB,EAAE;gBACtC,MAAM,OAAO,GAAG,KAAK,CAAC,GAAG,CAAC,qBAAqB,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;gBACrE,MAAM,WAAW,GAAU,EAAE,CAAC;gBAC9B,OAAO,CAAC,OAAO,CAAC,CAAC,CAAS,EAAE,EAAE;oBAC5B,MAAM,MAAM,GAAoC,EAAE,CAAC;oBACnD,MAAM,OAAO,GAAG,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC;oBACpD,MAAM,UAAU,GAAG,CAAC,CAAC,KAAK,CAAC,YAAY,CAAE,CAAC,CAAC,CAAC,CAAC;oBAC7C,MAAM,4DAAqC,GAAG,OAAO,KAAK,GAAG,CAAC,CAAC,CAAC,MAAM,UAAU,MAAM,CAAC,CAAC,CAAC,OAAO,UAAU,GAAG,CAAC;oBAC9G,MAAM,qDAAiC,GAAG,OAAO,KAAK,GAAG,CAAC,CAAC,CAAC,IAAI,UAAU,IAAI,CAAC,CAAC,CAAC,IAAI,UAAU,KAAK,CAAC;oBACrG,MAAM,wDAAmC,GAAG,OAAO,KAAK,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC;oBACzE,MAAM,wCAA0B,GAAG,IAAI,UAAU,EAAE,CAAC;oBACpD,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;gBAC3B,CAAC,CAAC,CAAC;gBACH,OAAO,CAAC,GAAG,CAAC,GAAG,WAAW,CAAC;aAC5B;iBAAM;gBACL,IAAK,qBAAyD,CAAC,GAAG,CAAC;oBACjE,OAAO,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,GAAG,CAAE,qBAAyD,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC;aAChG;QACH,CAAC,CAAC,CAAC;QACH,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;KACzB;IACD,OAAO,SAAS,CAAC;AACnB,CAAC;AAeD,MAAM,CAAC,KAAK,UAAU,mBAAmB;IACvC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,qBAAqB,EAAC,CAAC,CAAC;IAC7E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,2DAA2D,CAAC,CAAC;IAE/E,MAAM,GAAG,GAAsB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAuB,CAAC;IAC/G,OAAO,GAAG,CAAC;AACb,CAAC"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"seq-to-molfile-worker.d.ts","sourceRoot":"","sources":["seq-to-molfile-worker.ts"],"names":[],"mappings":""}
|
|
@@ -0,0 +1,19 @@
|
|
|
1
|
+
import { monomerSeqToMolfile } from './to-atomic-level-utils';
|
|
2
|
+
onmessage = (event) => {
|
|
3
|
+
const { monomerSequencesArray, monomersDict, alphabet, polymerType, start, end } = event.data;
|
|
4
|
+
const molfileList = new Array(end - start);
|
|
5
|
+
const molfileWarningList = new Array(0);
|
|
6
|
+
for (let rowI = start; rowI < end; ++rowI) {
|
|
7
|
+
try {
|
|
8
|
+
const monomerSeq = monomerSequencesArray[rowI];
|
|
9
|
+
molfileList[rowI - start] = monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType);
|
|
10
|
+
}
|
|
11
|
+
catch (err) {
|
|
12
|
+
const errMsg = err instanceof Error ? err.message : err.toString();
|
|
13
|
+
const msg = `Cannot get molfile of row #${rowI}: ${errMsg}.`;
|
|
14
|
+
molfileWarningList.push(msg);
|
|
15
|
+
}
|
|
16
|
+
}
|
|
17
|
+
postMessage({ molfileList, molfileWarningList });
|
|
18
|
+
};
|
|
19
|
+
//# sourceMappingURL=seq-to-molfile-worker.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"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;AAC5D,SAAS,GAAG,CAAC,KAAK,EAAE,EAAE;IACpB,MAAM,EAAC,qBAAqB,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,EAAC,GAAG,KAAK,CAAC,IAAI,CAAC;IAC5F,MAAM,WAAW,GAAa,IAAI,KAAK,CAAS,GAAG,GAAG,KAAK,CAAC,CAAC;IAC7D,MAAM,kBAAkB,GAAG,IAAI,KAAK,CAAS,CAAC,CAAC,CAAC;IAChD,KAAK,IAAI,IAAI,GAAG,KAAK,EAAE,IAAI,GAAG,GAAG,EAAE,EAAE,IAAI,EAAE;QACzC,IAAI;YACF,MAAM,UAAU,GAAG,qBAAqB,CAAC,IAAI,CAAC,CAAC;YAC/C,WAAW,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,mBAAmB,CAAC,UAAU,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,CAAC,CAAC;SAClG;QAAC,OAAO,GAAQ,EAAE;YACjB,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;SAC9B;KACF;IACD,WAAW,CAAC,EAAC,WAAW,EAAE,kBAAkB,EAAC,CAAC,CAAC;AACjD,CAAC,CAAC"}
|
|
@@ -0,0 +1,9 @@
|
|
|
1
|
+
import { HELM_POLYMER_TYPE } from '../utils/const';
|
|
2
|
+
import { ALPHABET } from '../utils/macromolecule';
|
|
3
|
+
import { MolGraph } from './types';
|
|
4
|
+
export type SeqToMolfileResult = {
|
|
5
|
+
molfileWarningList: string[];
|
|
6
|
+
molfileList: string[];
|
|
7
|
+
};
|
|
8
|
+
export declare function seqToMolFileWorker(monomerSequencesArray: string[][], monomersDict: Map<string, MolGraph>, alphabet: ALPHABET, polymerType: HELM_POLYMER_TYPE, srcColLength: number): Promise<SeqToMolfileResult>;
|
|
9
|
+
//# sourceMappingURL=seq-to-molfile.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"seq-to-molfile.d.ts","sourceRoot":"","sources":["seq-to-molfile.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,iBAAiB,EAAC,MAAM,gBAAgB,CAAC;AACjD,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAChD,OAAO,EAAC,QAAQ,EAAC,MAAM,SAAS,CAAC;AAEjC,MAAM,MAAM,kBAAkB,GAAG;IAC7B,kBAAkB,EAAE,MAAM,EAAE,CAAA;IAC5B,WAAW,EAAE,MAAM,EAAE,CAAA;CACxB,CAAA;AAED,wBAAsB,kBAAkB,CAAC,qBAAqB,EAAE,MAAM,EAAE,EAAE,EAAE,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,EAC7G,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,YAAY,EAAE,MAAM,GACvE,OAAO,CAAC,kBAAkB,CAAC,CA+B7B"}
|
|
@@ -0,0 +1,31 @@
|
|
|
1
|
+
export async function seqToMolFileWorker(monomerSequencesArray, monomersDict, alphabet, polymerType, srcColLength) {
|
|
2
|
+
const threadCount = Math.max(navigator.hardwareConcurrency - 2, 1);
|
|
3
|
+
const workers = new Array(threadCount).fill(null)
|
|
4
|
+
.map(() => new Worker(new URL('./seq-to-molfile-worker', import.meta.url)));
|
|
5
|
+
const chunkSize = srcColLength / threadCount;
|
|
6
|
+
let res = [];
|
|
7
|
+
let warnings = [];
|
|
8
|
+
const promises = new Array(threadCount);
|
|
9
|
+
for (let i = 0; i < threadCount; i++) {
|
|
10
|
+
const start = Math.floor(i * chunkSize);
|
|
11
|
+
const end = (i === threadCount - 1) ? srcColLength : Math.floor((i + 1) * chunkSize);
|
|
12
|
+
workers[i].postMessage({ monomerSequencesArray, monomersDict, alphabet, polymerType, start, end });
|
|
13
|
+
promises[i] = new Promise((resolveWorker) => {
|
|
14
|
+
workers[i].onmessage = ({ data: { molfileList, molfileWarningList } }) => {
|
|
15
|
+
resolveWorker({ molfileList, molfileWarningList });
|
|
16
|
+
};
|
|
17
|
+
});
|
|
18
|
+
}
|
|
19
|
+
const resArray = await Promise.all(promises);
|
|
20
|
+
resArray.forEach((resItem) => {
|
|
21
|
+
res = res.concat(...resItem.molfileList);
|
|
22
|
+
warnings = warnings.concat(...resItem.molfileWarningList);
|
|
23
|
+
});
|
|
24
|
+
setTimeout(() => {
|
|
25
|
+
workers.forEach((worker) => {
|
|
26
|
+
worker.terminate();
|
|
27
|
+
});
|
|
28
|
+
}, 0);
|
|
29
|
+
return { molfileList: res, molfileWarningList: warnings };
|
|
30
|
+
}
|
|
31
|
+
//# sourceMappingURL=seq-to-molfile.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"seq-to-molfile.js","sourceRoot":"","sources":["seq-to-molfile.ts"],"names":[],"mappings":"AASA,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,qBAAiC,EAAE,YAAmC,EAC7G,QAAkB,EAAE,WAA8B,EAAE,YAAoB;IAExE,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,IAAI,GAAG,GAAa,EAAE,CAAC;IACvB,IAAI,QAAQ,GAAa,EAAE,CAAC;IAC5B,MAAM,QAAQ,GAAG,IAAI,KAAK,CAA8B,WAAW,CAAC,CAAC;IACrE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE;QACpC,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,OAAO,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,EAAC,qBAAqB,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,EAAC,CAAC,CAAC;QACjG,QAAQ,CAAC,CAAC,CAAC,GAAG,IAAI,OAAO,CAAqB,CAAC,aAAa,EAAE,EAAE;YAC9D,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,EAAC,IAAI,EAAE,EAAC,WAAW,EAAE,kBAAkB,EAAC,EAAC,EAAQ,EAAE;gBACzE,aAAa,CAAC,EAAC,WAAW,EAAE,kBAAkB,EAAC,CAAC,CAAC;YACnD,CAAC,CAAC;QACJ,CAAC,CAAC,CAAC;KACJ;IACD,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;IAE7C,QAAQ,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;QAC3B,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;QACzC,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,GAAG,OAAO,CAAC,kBAAkB,CAAC,CAAC;IAC5D,CAAC,CAAC,CAAC;IAEH,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,OAAO,EAAC,WAAW,EAAE,GAAG,EAAE,kBAAkB,EAAE,QAAQ,EAAC,CAAC;AAC1D,CAAC"}
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@@ -0,0 +1,23 @@
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|
1
|
+
import { MolGraph } from './types';
|
|
2
|
+
import { HELM_POLYMER_TYPE } from '../utils/const';
|
|
3
|
+
import { ALPHABET } from '../utils/macromolecule/consts';
|
|
4
|
+
import { IMonomerLib } from '../types';
|
|
5
|
+
/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.
|
|
6
|
+
* @param {IMonomerLib} monomerLib - Monomer library
|
|
7
|
+
* @param {HELM_POLYMER_TYPE} polymerType - Polymer type
|
|
8
|
+
* @param {ALPHABET} alphabet - Alphabet of the column
|
|
9
|
+
* @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/
|
|
10
|
+
export declare function getFormattedMonomerLib(monomerLib: IMonomerLib, polymerType: HELM_POLYMER_TYPE, alphabet: ALPHABET): Map<string, any>;
|
|
11
|
+
/** Translate a sequence of monomer symbols into Molfile V3000
|
|
12
|
+
* @param {string[]} monomerSeq - Sequence of monomer symbols
|
|
13
|
+
* @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects
|
|
14
|
+
* @param {ALPHABET} alphabet - Alphabet of the column
|
|
15
|
+
* @param {HELM_POLYMER_TYPE} polymerType - Polymer type
|
|
16
|
+
* @return {string} - Molfile V3000*/
|
|
17
|
+
export declare function monomerSeqToMolfile(monomerSeq: string[], monomersDict: Map<string, MolGraph>, alphabet: ALPHABET, polymerType: HELM_POLYMER_TYPE): string;
|
|
18
|
+
/** Keep precision upon floating point operations over atom coordinates
|
|
19
|
+
* @param {number}x - the floating point number
|
|
20
|
+
* @return {number} - the floating point number with the same precision
|
|
21
|
+
*/
|
|
22
|
+
export declare function keepPrecision(x: number): number;
|
|
23
|
+
//# sourceMappingURL=to-atomic-level-utils.d.ts.map
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@@ -0,0 +1 @@
|
|
|
1
|
+
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|