@datagrok-libraries/bio 5.65.4 → 6.0.1
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 +4 -5
- package/src/helm/consts.d.ts +12 -3
- package/src/helm/consts.d.ts.map +1 -1
- package/src/helm/consts.js +22 -2
- package/src/helm/consts.js.map +1 -1
- package/src/helm/helm-helper.d.ts.map +1 -1
- package/src/helm/helm-helper.js +2 -0
- package/src/helm/helm-helper.js.map +1 -1
- package/src/helm/types.d.ts +66 -24
- package/src/helm/types.d.ts.map +1 -1
- package/src/monomer-works/consts.d.ts +3 -4
- package/src/monomer-works/consts.d.ts.map +1 -1
- package/src/monomer-works/consts.js +4 -3
- package/src/monomer-works/consts.js.map +1 -1
- package/src/monomer-works/lib-settings.d.ts.map +1 -1
- package/src/monomer-works/lib-settings.js +14 -4
- package/src/monomer-works/lib-settings.js.map +1 -1
- package/src/monomer-works/monomer-hover.js +2 -1
- package/src/monomer-works/monomer-hover.js.map +1 -1
- package/src/monomer-works/monomer-works.js +6 -6
- package/src/monomer-works/monomer-works.js.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.js +6 -6
- package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
- package/src/monomer-works/to-atomic-level.js +10 -9
- package/src/monomer-works/to-atomic-level.js.map +1 -1
- package/src/monomer-works/utils.d.ts +1 -1
- package/src/monomer-works/utils.d.ts.map +1 -1
- package/src/monomer-works/utils.js +3 -2
- package/src/monomer-works/utils.js.map +1 -1
- package/src/unknown.js +2 -1
- package/src/unknown.js.map +1 -1
- package/src/utils/const.d.ts +15 -3
- package/src/utils/const.d.ts.map +1 -1
- package/src/utils/const.js +7 -0
- package/src/utils/const.js.map +1 -1
- package/src/utils/generator.js +2 -1
- package/src/utils/generator.js.map +1 -1
- package/src/utils/macromolecule/utils.d.ts +1 -2
- package/src/utils/macromolecule/utils.d.ts.map +1 -1
- package/src/utils/macromolecule/utils.js +9 -9
- package/src/utils/macromolecule/utils.js.map +1 -1
- package/src/utils/monomer-ui.js +3 -2
- package/src/utils/monomer-ui.js.map +1 -1
- package/src/utils/sequence-position-scroller.d.ts.map +1 -1
- package/src/utils/sequence-position-scroller.js +1 -1
- package/src/utils/sequence-position-scroller.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": "
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"version": "6.0.1",
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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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@@ -25,18 +25,17 @@
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"mjolnir.js": "^2.7.0",
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"rxjs": "^6.5.5",
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"uuid": "^9.0.1",
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"wu": "^2.1.0"
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"wu": "^2.1.0",
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"@datagrok-libraries/hwe": "^1.0.0"
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},
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"devDependencies": {
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"@datagrok-libraries/helm-web-editor": "^1.1.16",
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"@datagrok-libraries/js-draw-lite": "^0.0.10",
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"@types/signals": "1.0.1",
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"@types/three": "^0.159.0",
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"@types/uuid": "^9.0.1",
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"@types/wu": "^2.1.44",
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"@typescript-eslint/eslint-plugin": "^8.8.1",
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"@typescript-eslint/parser": "^8.8.1",
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"datagrok-tools": "^
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"datagrok-tools": "^6.3.3",
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"eslint": "8.57.1",
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"eslint-config-google": "^0.14.0",
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"eslint-plugin-deprecation": "^3.0.0",
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package/src/helm/consts.d.ts
CHANGED
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@@ -1,4 +1,13 @@
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import { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/
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export
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import { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/hwe';
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export { HelmTypes, MonomerTypes, PolymerTypes };
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export declare enum MonomerNumberingTypes {
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default = 0,
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continuous = 1
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}
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export declare enum HelmTabKeys {
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Sequence = "sequence",
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Helm = "notation",
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Properties = "properties",
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StructureView = "structureview"
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}
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//# sourceMappingURL=consts.d.ts.map
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package/src/helm/consts.d.ts.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"
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{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAC,MAAM,yBAAyB,CAAC;AAE9E,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAC,CAAC;AAM/C,oBAAY,qBAAqB;IAC/B,OAAO,IAAI;IACX,UAAU,IAAI;CACf;AAED,oBAAY,WAAW;IACrB,QAAQ,aAAa;IACrB,IAAI,aAAa;IACjB,UAAU,eAAe;IACzB,aAAa,kBAAkB;CAChC"}
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package/src/helm/consts.js
CHANGED
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@@ -1,3 +1,23 @@
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// HELM type vocabulary is owned by `@datagrok-libraries/hwe` (the standalone
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// HELM editor) and re-exported here as the single source of truth. The string
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// values match the canonical Pistoia HELM Web Editor, except `NUCLEOTIDE` which
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// uses the corrected spelling `HELM_NUCLEOTIDE` (was `HELM_NUCLETIDE`).
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import { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/hwe';
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export { HelmTypes, MonomerTypes, PolymerTypes };
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// hwe migration: these two small enums are not part of the hwe value vocabulary.
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// They are defined here locally (replicating the legacy HELM Web Editor values)
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// so `@datagrok-libraries/bio` no longer depends on
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// `@datagrok-libraries/helm-web-editor`.
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export var MonomerNumberingTypes;
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(function (MonomerNumberingTypes) {
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MonomerNumberingTypes[MonomerNumberingTypes["default"] = 0] = "default";
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MonomerNumberingTypes[MonomerNumberingTypes["continuous"] = 1] = "continuous";
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})(MonomerNumberingTypes || (MonomerNumberingTypes = {}));
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export var HelmTabKeys;
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(function (HelmTabKeys) {
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HelmTabKeys["Sequence"] = "sequence";
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HelmTabKeys["Helm"] = "notation";
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HelmTabKeys["Properties"] = "properties";
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HelmTabKeys["StructureView"] = "structureview";
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})(HelmTabKeys || (HelmTabKeys = {}));
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//# sourceMappingURL=consts.js.map
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package/src/helm/consts.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,SAAS,
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{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,6EAA6E;AAC7E,8EAA8E;AAC9E,gFAAgF;AAChF,wEAAwE;AACxE,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAC,MAAM,yBAAyB,CAAC;AAE9E,OAAO,EAAC,SAAS,EAAE,YAAY,EAAE,YAAY,EAAC,CAAC;AAE/C,iFAAiF;AACjF,gFAAgF;AAChF,oDAAoD;AACpD,yCAAyC;AACzC,MAAM,CAAN,IAAY,qBAGX;AAHD,WAAY,qBAAqB;IAC/B,uEAAW,CAAA;IACX,6EAAc,CAAA;AAChB,CAAC,EAHW,qBAAqB,KAArB,qBAAqB,QAGhC;AAED,MAAM,CAAN,IAAY,WAKX;AALD,WAAY,WAAW;IACrB,oCAAqB,CAAA;IACrB,gCAAiB,CAAA;IACjB,wCAAyB,CAAA;IACzB,8CAA+B,CAAA;AACjC,CAAC,EALW,WAAW,KAAX,WAAW,QAKtB"}
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@@ -1 +1 @@
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{"version":3,"file":"helm-helper.d.ts","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAEhC,OAAO,KAAK,EAAC,KAAK,EAAE,GAAG,EAAE,QAAQ,EAAE,kBAAkB,EAAC,MAAM,SAAS,CAAC;AACtE,OAAO,EACW,aAAa,EAAE,OAAO,EAAc,cAAc,EAAE,QAAQ,EAC7E,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,eAAe,EAAC,MAAM,0BAA0B,CAAC;AACzD,OAAO,EAAC,UAAU,EAAC,MAAM,qBAAqB,CAAC;AAC/C,OAAO,EAAC,YAAY,EAAC,MAAM,oCAAoC,CAAC;AAEhE,MAAM,MAAM,qBAAqB,GAAG,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,YAAY,CAAC,GAAG;IAC7E,aAAa,EAAE,OAAO,CAAC,kBAAkB,CAAC,CAAC;IAC3C,QAAQ,EAAE,OAAO,CAAC;CACnB,CAAC;AAEF,8BAAsB,aAAc,SAAQ,EAAE,CAAC,WAAW,CAAC,YAAY,CAAC;IACtE,QAAQ,KAAK,QAAQ,IAAI,OAAO,CAAC;IACjC,QAAQ,KAAK,QAAQ,CAAC,KAAK,EAAE,OAAO,EAAE;IAEtC,QAAQ,KAAK,WAAW,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC;IAEnD,QAAQ,KAAK,OAAO,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC;IAE/C,QAAQ,CAAC,MAAM,IAAI,IAAI;IAEvB,QAAQ,CAAC,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,EAAE,CAAC,EAAE,QAAQ,GAAG,IAAI;CACvE;AAED;;GAEG;AACH,MAAM,MAAM,cAAc,GAAG;IAC3B,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC;CACxC,CAAA;AAED,eAAO,MAAM,yBAAyB,0BAA0B,CAAC;AAEjE,qBAAa,qBAAsB,SAAQ,KAAK;IAC9C,SAAgB,IAAI,2BAA6B;gBAErC,OAAO,CAAC,EAAE,MAAM;CAG7B;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,SAAS,IAAI,UAAU,CAAC;IAE5B,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,qBAAqB,GAAG,aAAa,CAAC;IAE9E,mBAAmB,CAAC,IAAI,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,EAAE,OAAO,CAAC,kBAAkB,CAAC,GAAG,cAAc,CAAC;IAE/F,kBAAkB,CAAC,IAAI,EAAE,cAAc,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,GAAG,CAAC;IAE7D,IAAI,qBAAqB,IAAI,aAAa,GAAG,IAAI,CAAC;IAElD,yBAAyB,CAAC,UAAU,EAAE,eAAe,GAAG,aAAa,CAAC;IAEtE,qBAAqB,CAAC,aAAa,EAAE,aAAa,GAAG,aAAa,CAAC;IACnE,2BAA2B,IAAI,aAAa,CAAC;IAE7C,cAAc,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,QAAQ,GAAG,IAAI,CAAC;IAEpF,kDAAkD;IAClD,WAAW,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,MAAM,EAAE,CAAC;IAE7C,KAAK,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,KAAK,GAAG,OAAO,CAAC;IAC7C,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc,CAAC;CAC1C;AAED,wBAAsB,aAAa,IAAI,OAAO,CAAC,WAAW,CAAC,CAO1D;AAED,OAAO,QAAQ,iBAAiB,CAAC;IAC/B,UAAiB,KAAK,CAAC;QACrB;;WAEG;QACH,SAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,qBAAqB,GAAG,OAAO,CAAC,aAAa,CAAC,CAAC;KAClG;CACF;AAOD,mBAAmB;AACnB,wBAAgB,oBAAoB,CAClC,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,IAAI,CAAC,EAAE,MAAM,GACpC,EAAC,cAAc,AAAd,cAAc,CAAC,QAAQ,EAAE,WAAW,CAAC,MAAM,CAAC,
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{"version":3,"file":"helm-helper.d.ts","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAEhC,OAAO,KAAK,EAAC,KAAK,EAAE,GAAG,EAAE,QAAQ,EAAE,kBAAkB,EAAC,MAAM,SAAS,CAAC;AACtE,OAAO,EACW,aAAa,EAAE,OAAO,EAAc,cAAc,EAAE,QAAQ,EAC7E,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,eAAe,EAAC,MAAM,0BAA0B,CAAC;AACzD,OAAO,EAAC,UAAU,EAAC,MAAM,qBAAqB,CAAC;AAC/C,OAAO,EAAC,YAAY,EAAC,MAAM,oCAAoC,CAAC;AAEhE,MAAM,MAAM,qBAAqB,GAAG,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,YAAY,CAAC,GAAG;IAC7E,aAAa,EAAE,OAAO,CAAC,kBAAkB,CAAC,CAAC;IAC3C,QAAQ,EAAE,OAAO,CAAC;CACnB,CAAC;AAEF,8BAAsB,aAAc,SAAQ,EAAE,CAAC,WAAW,CAAC,YAAY,CAAC;IACtE,QAAQ,KAAK,QAAQ,IAAI,OAAO,CAAC;IACjC,QAAQ,KAAK,QAAQ,CAAC,KAAK,EAAE,OAAO,EAAE;IAEtC,QAAQ,KAAK,WAAW,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC;IAEnD,QAAQ,KAAK,OAAO,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC;IAE/C,QAAQ,CAAC,MAAM,IAAI,IAAI;IAEvB,QAAQ,CAAC,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,EAAE,CAAC,EAAE,QAAQ,GAAG,IAAI;CACvE;AAED;;GAEG;AACH,MAAM,MAAM,cAAc,GAAG;IAC3B,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC;CACxC,CAAA;AAED,eAAO,MAAM,yBAAyB,0BAA0B,CAAC;AAEjE,qBAAa,qBAAsB,SAAQ,KAAK;IAC9C,SAAgB,IAAI,2BAA6B;gBAErC,OAAO,CAAC,EAAE,MAAM;CAG7B;AAED,MAAM,WAAW,WAAW;IAC1B,IAAI,SAAS,IAAI,UAAU,CAAC;IAE5B,eAAe,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,qBAAqB,GAAG,aAAa,CAAC;IAE9E,mBAAmB,CAAC,IAAI,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,EAAE,OAAO,CAAC,kBAAkB,CAAC,GAAG,cAAc,CAAC;IAE/F,kBAAkB,CAAC,IAAI,EAAE,cAAc,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,GAAG,CAAC;IAE7D,IAAI,qBAAqB,IAAI,aAAa,GAAG,IAAI,CAAC;IAElD,yBAAyB,CAAC,UAAU,EAAE,eAAe,GAAG,aAAa,CAAC;IAEtE,qBAAqB,CAAC,aAAa,EAAE,aAAa,GAAG,aAAa,CAAC;IACnE,2BAA2B,IAAI,aAAa,CAAC;IAE7C,cAAc,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,QAAQ,GAAG,IAAI,CAAC;IAEpF,kDAAkD;IAClD,WAAW,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,MAAM,EAAE,CAAC;IAE7C,KAAK,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,KAAK,GAAG,OAAO,CAAC;IAC7C,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc,CAAC;CAC1C;AAED,wBAAsB,aAAa,IAAI,OAAO,CAAC,WAAW,CAAC,CAO1D;AAED,OAAO,QAAQ,iBAAiB,CAAC;IAC/B,UAAiB,KAAK,CAAC;QACrB;;WAEG;QACH,SAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,qBAAqB,GAAG,OAAO,CAAC,aAAa,CAAC,CAAC;KAClG;CACF;AAOD,mBAAmB;AACnB,wBAAgB,oBAAoB,CAClC,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,IAAI,CAAC,EAAE,MAAM,GACpC,EAAC,cAAc,AAAd,cAAc,CAAC,QAAQ,EAAE,WAAW,CAAC,MAAM,CAAC,CAgB/C"}
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package/src/helm/helm-helper.js
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let elem;
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const aa = a;
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if (aa.T === 'ATOM') {
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// Legacy HelmAtom.biotype() returns the js-draw-lite HelmType union (which
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// still carries the `HELM_NUCLETIDE` typo); cast to the hwe-owned HelmType.
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biotype = aa.biotype();
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elem = aa.elem;
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}
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-
{"version":3,"file":"helm-helper.js","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAkBtC,MAAM,OAAgB,aAAc,SAAQ,EAAE,CAAC,WAAyB;CAWvE;AAWD,MAAM,CAAC,MAAM,yBAAyB,GAAG,uBAAuB,CAAC;AAEjE,MAAM,OAAO,qBAAsB,SAAQ,KAAK;IAG9C,YAAY,OAAgB;QAC1B,KAAK,CAAC,OAAO,CAAC,CAAC;QAHD,SAAI,GAAG,yBAAyB,CAAC;IAIjD,CAAC;CACF;AA2BD,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,MAAM,WAAW,GAAG,MAAM,CAAC;IAC3B,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,eAAe,EAAC,CAAC,CAAC;IAC7E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,qCAAqC,CAAC,CAAC;IAChF,MAAM,GAAG,GAAG,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAiB,CAAC;IACtF,OAAO,GAAG,CAAC;AACb,CAAC;AAWD,EAAE,CAAC,KAAK,CAAC,SAAS,GAAG,KAAK,WACxB,IAAY,EAAE,OAA+B;IAC7C,OAAO,CAAC,MAAM,aAAa,EAAE,CAAC,CAAC,eAAe,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;AAChE,CAAC,CAAC;AAEF,mBAAmB;AACnB,MAAM,UAAU,oBAAoB,CAClC,CAAsB,EAAE,IAAa;IAErC,IAAI,CAAC,CAAC;QACJ,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;IACzE,IAAI,OAAiB,CAAC;IACtB,IAAI,IAAY,CAAC;IACjB,MAAM,EAAE,GAAG,CAAa,CAAC;IACzB,IAAI,EAAE,CAAC,CAAC,KAAK,MAAM,EAAE,CAAC;QACpB,OAAO,GAAG,EAAE,CAAC,OAAO,
|
|
1
|
+
{"version":3,"file":"helm-helper.js","sourceRoot":"","sources":["helm-helper.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAkBtC,MAAM,OAAgB,aAAc,SAAQ,EAAE,CAAC,WAAyB;CAWvE;AAWD,MAAM,CAAC,MAAM,yBAAyB,GAAG,uBAAuB,CAAC;AAEjE,MAAM,OAAO,qBAAsB,SAAQ,KAAK;IAG9C,YAAY,OAAgB;QAC1B,KAAK,CAAC,OAAO,CAAC,CAAC;QAHD,SAAI,GAAG,yBAAyB,CAAC;IAIjD,CAAC;CACF;AA2BD,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,MAAM,WAAW,GAAG,MAAM,CAAC;IAC3B,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,eAAe,EAAC,CAAC,CAAC;IAC7E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,qCAAqC,CAAC,CAAC;IAChF,MAAM,GAAG,GAAG,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAiB,CAAC;IACtF,OAAO,GAAG,CAAC;AACb,CAAC;AAWD,EAAE,CAAC,KAAK,CAAC,SAAS,GAAG,KAAK,WACxB,IAAY,EAAE,OAA+B;IAC7C,OAAO,CAAC,MAAM,aAAa,EAAE,CAAC,CAAC,eAAe,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;AAChE,CAAC,CAAC;AAEF,mBAAmB;AACnB,MAAM,UAAU,oBAAoB,CAClC,CAAsB,EAAE,IAAa;IAErC,IAAI,CAAC,CAAC;QACJ,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;IACzE,IAAI,OAAiB,CAAC;IACtB,IAAI,IAAY,CAAC;IACjB,MAAM,EAAE,GAAG,CAAa,CAAC;IACzB,IAAI,EAAE,CAAC,CAAC,KAAK,MAAM,EAAE,CAAC;QACpB,2EAA2E;QAC3E,4EAA4E;QAC5E,OAAO,GAAG,EAAE,CAAC,OAAO,EAAe,CAAC;QACpC,IAAI,GAAG,EAAE,CAAC,IAAI,CAAC;IACjB,CAAC;SAAM,CAAC;QACN,OAAO,GAAG,CAAa,CAAC;QACxB,IAAI,GAAG,IAAK,CAAC;IACf,CAAC;IACD,OAAO,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;AACzB,CAAC"}
|
package/src/helm/types.d.ts
CHANGED
|
@@ -1,26 +1,69 @@
|
|
|
1
|
-
import type { HelmType, PolymerType, MonomerType,
|
|
2
|
-
import type {
|
|
3
|
-
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
export
|
|
19
|
-
export
|
|
20
|
-
export
|
|
21
|
-
export
|
|
22
|
-
export
|
|
23
|
-
export
|
|
1
|
+
import type { HelmType, PolymerType, MonomerType, HelmAtomLike, HelmBondLike, HelmMolLike, HelmAtomBioLike, AppLike, JSDraw2EditorLike, MonomerExplorerLike, MonomersFuncsLike, IWebEditorMonomerLike } from '@datagrok-libraries/hwe';
|
|
2
|
+
import type { MonomerNumberingTypes } from './consts';
|
|
3
|
+
export type { HelmType, PolymerType, MonomerType };
|
|
4
|
+
/** 2-D point (the legacy JSDraw2 `Point` shape). */
|
|
5
|
+
export interface Point {
|
|
6
|
+
x: number;
|
|
7
|
+
y: number;
|
|
8
|
+
}
|
|
9
|
+
export type IBio<_TBio = unknown> = HelmAtomBioLike;
|
|
10
|
+
export type IHelmBio = HelmAtomBioLike;
|
|
11
|
+
export type Atom<_T = unknown, _TBio = unknown> = HelmAtomLike;
|
|
12
|
+
export type Bond<_T = unknown, _TBio = unknown> = HelmBondLike;
|
|
13
|
+
export type Mol<_T = unknown, _TBio = unknown> = HelmMolLike;
|
|
14
|
+
export type Editor<_T = unknown, _TBio = unknown, _O = unknown> = JSDraw2EditorLike;
|
|
15
|
+
export type IJsAtom = HelmAtomLike;
|
|
16
|
+
export type HelmAtom = HelmAtomLike;
|
|
17
|
+
export type HelmBond = HelmBondLike;
|
|
18
|
+
export type HelmMol = HelmMolLike;
|
|
19
|
+
export type HelmEditor = JSDraw2EditorLike;
|
|
20
|
+
export type HelmString = string;
|
|
21
|
+
export type App = AppLike;
|
|
22
|
+
export type MonomerExplorer = MonomerExplorerLike;
|
|
23
|
+
export type MonomersFuncs = MonomersFuncsLike;
|
|
24
|
+
export type WebEditorRGroups = {
|
|
25
|
+
[group: string]: string;
|
|
26
|
+
};
|
|
27
|
+
export interface IMonomerColors {
|
|
28
|
+
linecolor: string;
|
|
29
|
+
backgroundcolor: string;
|
|
30
|
+
textcolor: string;
|
|
31
|
+
nature?: string;
|
|
32
|
+
}
|
|
33
|
+
export interface IMonomer {
|
|
34
|
+
/** symbol */ id?: string;
|
|
35
|
+
/** name */ n?: string;
|
|
36
|
+
/** natural analog */ na?: string;
|
|
37
|
+
/** polymer type */ type?: PolymerType;
|
|
38
|
+
/** monomer type */ mt?: MonomerType;
|
|
39
|
+
/** molfile */ m?: string;
|
|
40
|
+
/** molfile compressed */ mz?: any;
|
|
41
|
+
/** substituents */ at?: WebEditorRGroups;
|
|
42
|
+
/** number of substituents */ rs?: number;
|
|
43
|
+
issmiles?: boolean;
|
|
44
|
+
smiles?: string;
|
|
45
|
+
name?: string;
|
|
46
|
+
oldname?: string;
|
|
47
|
+
/** Used by Formula */ stats?: any;
|
|
48
|
+
}
|
|
49
|
+
export interface IWebEditorMonomer extends IMonomer, Partial<IMonomerColors> {
|
|
50
|
+
}
|
|
51
|
+
export type MonomerSetType = {
|
|
52
|
+
[symbol: string]: IMonomer;
|
|
53
|
+
};
|
|
54
|
+
export type GetMonomerResType = IWebEditorMonomerLike | null;
|
|
55
|
+
export type GetMonomerFunc = (a: HelmAtom | HelmType, name?: string) => GetMonomerResType;
|
|
56
|
+
export interface IHelmDrawOptions {
|
|
57
|
+
fontsize?: number;
|
|
58
|
+
monomerNumbering?: MonomerNumberingTypes;
|
|
59
|
+
getMonomer?: GetMonomerFunc;
|
|
60
|
+
}
|
|
61
|
+
export interface IHelmEditorOptions {
|
|
62
|
+
width?: number;
|
|
63
|
+
height?: number;
|
|
64
|
+
viewonly?: boolean;
|
|
65
|
+
drawOptions?: IHelmDrawOptions;
|
|
66
|
+
}
|
|
24
67
|
export interface ISeqMonomer {
|
|
25
68
|
position: number;
|
|
26
69
|
biotype: HelmType;
|
|
@@ -31,5 +74,4 @@ export interface IHelmWebEditor {
|
|
|
31
74
|
get host(): HTMLDivElement;
|
|
32
75
|
resizeEditor(width: number, height: number): void;
|
|
33
76
|
}
|
|
34
|
-
export { MonomerSetType, MonomersFuncs, TabDescType };
|
|
35
77
|
//# sourceMappingURL=types.d.ts.map
|
package/src/helm/types.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EACV,QAAQ,EAAE,WAAW,EAAE,WAAW,EAClC,YAAY,EAAE,YAAY,EAAE,WAAW,EAAE,eAAe,EACxD,OAAO,EAAE,iBAAiB,EAAE,mBAAmB,EAAE,iBAAiB,EAClE,qBAAqB,EACtB,MAAM,yBAAyB,CAAC;AACjC,OAAO,KAAK,EAAC,qBAAqB,EAAC,MAAM,UAAU,CAAC;AAEpD,YAAY,EAAC,QAAQ,EAAE,WAAW,EAAE,WAAW,EAAC,CAAC;AAEjD,oDAAoD;AACpD,MAAM,WAAW,KAAK;IACpB,CAAC,EAAE,MAAM,CAAC;IACV,CAAC,EAAE,MAAM,CAAC;CACX;AAQD,MAAM,MAAM,IAAI,CAAC,KAAK,GAAG,OAAO,IAAI,eAAe,CAAC;AACpD,MAAM,MAAM,QAAQ,GAAG,eAAe,CAAC;AACvC,MAAM,MAAM,IAAI,CAAC,EAAE,GAAG,OAAO,EAAE,KAAK,GAAG,OAAO,IAAI,YAAY,CAAC;AAC/D,MAAM,MAAM,IAAI,CAAC,EAAE,GAAG,OAAO,EAAE,KAAK,GAAG,OAAO,IAAI,YAAY,CAAC;AAC/D,MAAM,MAAM,GAAG,CAAC,EAAE,GAAG,OAAO,EAAE,KAAK,GAAG,OAAO,IAAI,WAAW,CAAC;AAC7D,MAAM,MAAM,MAAM,CAAC,EAAE,GAAG,OAAO,EAAE,KAAK,GAAG,OAAO,EAAE,EAAE,GAAG,OAAO,IAAI,iBAAiB,CAAC;AACpF,MAAM,MAAM,OAAO,GAAG,YAAY,CAAC;AAEnC,MAAM,MAAM,QAAQ,GAAG,YAAY,CAAC;AACpC,MAAM,MAAM,QAAQ,GAAG,YAAY,CAAC;AACpC,MAAM,MAAM,OAAO,GAAG,WAAW,CAAC;AAClC,MAAM,MAAM,UAAU,GAAG,iBAAiB,CAAC;AAC3C,MAAM,MAAM,UAAU,GAAG,MAAM,CAAC;AAEhC,MAAM,MAAM,GAAG,GAAG,OAAO,CAAC;AAC1B,MAAM,MAAM,eAAe,GAAG,mBAAmB,CAAC;AAClD,MAAM,MAAM,aAAa,GAAG,iBAAiB,CAAC;AAG9C,MAAM,MAAM,gBAAgB,GAAG;IAAE,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAE3D,MAAM,WAAW,cAAc;IAC7B,SAAS,EAAE,MAAM,CAAC;IAClB,eAAe,EAAE,MAAM,CAAC;IACxB,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,QAAQ;IACvB,aAAa,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IAC1B,WAAW,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC;IACvB,qBAAqB,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IAClC,mBAAmB,CAAC,IAAI,CAAC,EAAE,WAAW,CAAC;IACvC,mBAAmB,CAAC,EAAE,CAAC,EAAE,WAAW,CAAC;IACrC,cAAc,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC;IAC1B,yBAAyB,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC;IACnC,mBAAmB,CAAC,EAAE,CAAC,EAAE,gBAAgB,CAAC;IAC1C,6BAA6B,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IAC1C,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,sBAAsB,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC;CACpC;AAED,MAAM,WAAW,iBAAkB,SAAQ,QAAQ,EAAE,OAAO,CAAC,cAAc,CAAC;CAAG;AAE/E,MAAM,MAAM,cAAc,GAAG;IAAE,CAAC,MAAM,EAAE,MAAM,GAAG,QAAQ,CAAA;CAAE,CAAC;AAK5D,MAAM,MAAM,iBAAiB,GAAG,qBAAqB,GAAG,IAAI,CAAC;AAC7D,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,IAAI,CAAC,EAAE,MAAM,KAAK,iBAAiB,CAAC;AAE1F,MAAM,WAAW,gBAAgB;IAC/B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,gBAAgB,CAAC,EAAE,qBAAqB,CAAC;IACzC,UAAU,CAAC,EAAE,cAAc,CAAC;CAC7B;AAED,MAAM,WAAW,kBAAkB;IACjC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,WAAW,CAAC,EAAE,gBAAgB,CAAC;CAChC;AAED,MAAM,WAAW,WAAW;IAC1B,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,QAAQ,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,MAAM,IAAI,UAAU,CAAC;IACzB,IAAI,IAAI,IAAI,cAAc,CAAC;IAE3B,YAAY,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;CACnD"}
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
import { PolymerTypes } from '../helm/consts';
|
|
2
1
|
export declare const monomerWorksConsts: {
|
|
3
2
|
readonly V2K_RGP_SHIFT: 8;
|
|
4
3
|
readonly V2K_RGP_LINE: "M RGP";
|
|
@@ -20,15 +19,15 @@ export declare const monomerWorksConsts: {
|
|
|
20
19
|
readonly V3K_END: "M END";
|
|
21
20
|
readonly PRECISION_FACTOR: 10000;
|
|
22
21
|
readonly DEOXYRIBOSE: {
|
|
23
|
-
readonly polymerType:
|
|
22
|
+
readonly polymerType: "RNA";
|
|
24
23
|
readonly symbol: "d";
|
|
25
24
|
};
|
|
26
25
|
readonly RIBOSE: {
|
|
27
|
-
readonly polymerType:
|
|
26
|
+
readonly polymerType: "RNA";
|
|
28
27
|
readonly symbol: "r";
|
|
29
28
|
};
|
|
30
29
|
readonly PHOSPHATE: {
|
|
31
|
-
readonly polymerType:
|
|
30
|
+
readonly polymerType: "RNA";
|
|
32
31
|
readonly symbol: "p";
|
|
33
32
|
};
|
|
34
33
|
readonly OXYGEN: "O";
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAEA,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA8BrB,CAAC"}
|
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
import { PolymerTypes } from '../helm/consts';
|
|
1
2
|
export const monomerWorksConsts = {
|
|
2
3
|
// constants for parsing molfile V2000
|
|
3
4
|
V2K_RGP_SHIFT: 8,
|
|
@@ -21,9 +22,9 @@ export const monomerWorksConsts = {
|
|
|
21
22
|
V3K_END: 'M END',
|
|
22
23
|
PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates
|
|
23
24
|
// symbols for the corresponding monomers in HELM library
|
|
24
|
-
DEOXYRIBOSE: { polymerType:
|
|
25
|
-
RIBOSE: { polymerType:
|
|
26
|
-
PHOSPHATE: { polymerType:
|
|
25
|
+
DEOXYRIBOSE: { polymerType: PolymerTypes.RNA, symbol: 'd' },
|
|
26
|
+
RIBOSE: { polymerType: PolymerTypes.RNA, symbol: 'r' },
|
|
27
|
+
PHOSPHATE: { polymerType: PolymerTypes.RNA, symbol: 'p' },
|
|
27
28
|
OXYGEN: 'O',
|
|
28
29
|
HYDROGEN: 'H',
|
|
29
30
|
};
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAE5C,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,EAAE,mFAAmF;IAC7G,yDAAyD;IAEzD,WAAW,EAAE,EAAC,WAAW,EAAE,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAC;IACzD,MAAM,EAAE,EAAC,WAAW,EAAE,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAC;IACpD,SAAS,EAAE,EAAC,WAAW,EAAE,YAAY,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAC;IAEvD,MAAM,EAAE,GAAG;IACX,QAAQ,EAAE,GAAG;CACL,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lib-settings.d.ts","sourceRoot":"","sources":["lib-settings.ts"],"names":[],"mappings":"AAEA,OAAO,EAAC,eAAe,EAAC,MAAM,SAAS,CAAC;
|
|
1
|
+
{"version":3,"file":"lib-settings.d.ts","sourceRoot":"","sources":["lib-settings.ts"],"names":[],"mappings":"AAEA,OAAO,EAAC,eAAe,EAAC,MAAM,SAAS,CAAC;AA0DxC,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,eAAe,CAAC,CAwBnE;AAED,wBAAsB,kBAAkB,CAAC,KAAK,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAmB9E"}
|
|
@@ -14,12 +14,23 @@ async function getDuplicatePrefsFull() {
|
|
|
14
14
|
if (!resStr)
|
|
15
15
|
return {};
|
|
16
16
|
// chunk will end with special suffix and just before it will have the number of the next chunk key
|
|
17
|
+
let iter = 1;
|
|
17
18
|
while (resStr.endsWith(CHUNK_KEY_SUFFIX)) {
|
|
18
|
-
const
|
|
19
|
+
const nextChunkKeysCount = iter.toString().length;
|
|
20
|
+
const nextChunkIndex = new Array(nextChunkKeysCount).fill(0)
|
|
21
|
+
.reduce((acc, _, i) => acc + resStr.charAt(resStr.length - nextChunkKeysCount + i - CHUNK_KEY_SUFFIX.length), '');
|
|
22
|
+
const nextChunkKey = `${DUPLICATE_MONOMER_PREFERENCES_KEY}${nextChunkIndex}`;
|
|
19
23
|
const nextChunkStr = (await grok.userSettings.getValue(LIB_STORAGE_NAME, nextChunkKey, true)) ?? '';
|
|
20
|
-
resStr = resStr.slice(0, resStr.length - CHUNK_KEY_SUFFIX.length -
|
|
24
|
+
resStr = resStr.slice(0, resStr.length - CHUNK_KEY_SUFFIX.length - nextChunkIndex.length) + nextChunkStr;
|
|
25
|
+
iter++;
|
|
26
|
+
}
|
|
27
|
+
try {
|
|
28
|
+
return JSON.parse(resStr);
|
|
29
|
+
}
|
|
30
|
+
catch (err) {
|
|
31
|
+
console.error(`Failed to parse duplicateMonomerPreferences from user settings: ${err}`);
|
|
32
|
+
return {};
|
|
21
33
|
}
|
|
22
|
-
return JSON.parse(resStr);
|
|
23
34
|
}
|
|
24
35
|
async function setDuplicatePrefsFull(value) {
|
|
25
36
|
const valueStr = JSON.stringify(value);
|
|
@@ -73,7 +84,6 @@ export async function setUserLibSettings(value) {
|
|
|
73
84
|
}
|
|
74
85
|
await setDuplicatePrefsFull(duplicatePrefsShortHand);
|
|
75
86
|
//await grok.userSettings.add(LIB_STORAGE_NAME, DUPLICATE_MONOMER_PREFERENCES_KEY, JSON.stringify(duplicatePrefsShortHand), true);
|
|
76
|
-
value.duplicateMonomerPreferences = {}; // clear to reduce size
|
|
77
87
|
await grok.userSettings.add(LIB_STORAGE_NAME, LIB_SETTINGS_KEY, JSON.stringify(value), true);
|
|
78
88
|
});
|
|
79
89
|
await userLibSettingsPromise;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lib-settings.js","sourceRoot":"","sources":["lib-settings.ts"],"names":[],"mappings":"AAAA,4BAA4B;AAC5B,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAG1C,0BAA0B;AAC1B,MAAM,gBAAgB,GAAG,WAAW,CAAC;AACrC,MAAM,gBAAgB,GAAG,UAAU,CAAC;AACpC,MAAM,iCAAiC,GAAG,6BAA6B,CAAC;AAUxE,2GAA2G;AAC3G,mDAAmD;AACnD,MAAM,+BAA+B,GAAG,IAAI,CAAC;AAC7C,MAAM,gBAAgB,GAAG,WAAW,CAAC;AACrC,KAAK,UAAU,qBAAqB;IACpC,6EAA6E;IAC3E,IAAI,MAAM,GAAW,MAAM,IAAI,CAAC,YAAY,CAAC,QAAQ,CAAC,gBAAgB,EAAE,iCAAiC,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC;IACvH,IAAI,CAAC,MAAM;QACT,OAAO,EAAE,CAAC;IACZ,mGAAmG;IACnG,OAAO,MAAM,CAAC,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC;QACzC,MAAM,
|
|
1
|
+
{"version":3,"file":"lib-settings.js","sourceRoot":"","sources":["lib-settings.ts"],"names":[],"mappings":"AAAA,4BAA4B;AAC5B,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAG1C,0BAA0B;AAC1B,MAAM,gBAAgB,GAAG,WAAW,CAAC;AACrC,MAAM,gBAAgB,GAAG,UAAU,CAAC;AACpC,MAAM,iCAAiC,GAAG,6BAA6B,CAAC;AAUxE,2GAA2G;AAC3G,mDAAmD;AACnD,MAAM,+BAA+B,GAAG,IAAI,CAAC;AAC7C,MAAM,gBAAgB,GAAG,WAAW,CAAC;AACrC,KAAK,UAAU,qBAAqB;IACpC,6EAA6E;IAC3E,IAAI,MAAM,GAAW,MAAM,IAAI,CAAC,YAAY,CAAC,QAAQ,CAAC,gBAAgB,EAAE,iCAAiC,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC;IACvH,IAAI,CAAC,MAAM;QACT,OAAO,EAAE,CAAC;IACZ,mGAAmG;IACnG,IAAI,IAAI,GAAG,CAAC,CAAC;IACb,OAAO,MAAM,CAAC,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC;QACzC,MAAM,kBAAkB,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,MAAM,CAAC;QAClD,MAAM,cAAc,GAAG,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;aACzD,MAAM,CAAC,CAAC,GAAW,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,GAAG,kBAAkB,GAAG,CAAC,GAAG,gBAAgB,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QAC5H,MAAM,YAAY,GAAG,GAAG,iCAAiC,GAAG,cAAc,EAAE,CAAC;QAC7E,MAAM,YAAY,GAAuB,CAAC,MAAM,IAAI,CAAC,YAAY,CAAC,QAAQ,CAAC,gBAAgB,EAAE,YAAY,EAAE,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC;QACxH,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,CAAC,MAAM,GAAG,gBAAgB,CAAC,MAAM,GAAG,cAAc,CAAC,MAAM,CAAC,GAAG,YAAY,CAAC;QACzG,IAAI,EAAE,CAAC;IACT,CAAC;IACD,IAAI,CAAC;QACH,OAAO,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;IAC5B,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,OAAO,CAAC,KAAK,CAAC,mEAAmE,GAAG,EAAE,CAAC,CAAC;QACxF,OAAO,EAAE,CAAC;IACZ,CAAC;AAEH,CAAC;AAED,KAAK,UAAU,qBAAqB,CAAC,KAA2C;IAC9E,MAAM,QAAQ,GAAW,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC;IAC/C,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,GAAG,+BAA+B,CAAC,CAAC;IACjF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;QACrC,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,iCAAiC,CAAC,CAAC,CAAC,GAAG,iCAAiC,GAAG,CAAC,EAAE,CAAC;QACrG,MAAM,OAAO,GAAG,CAAC,GAAG,WAAW,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACtD,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,GAAG,+BAA+B,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,+BAA+B,CAAC,CAAC;QAChH,MAAM,eAAe,GAAG,OAAO,CAAC,CAAC,CAAC,QAAQ,GAAG,OAAO,GAAG,gBAAgB,CAAC,CAAC,CAAC,QAAQ,CAAC;QACnF,MAAM,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,gBAAgB,EAAE,GAAG,EAAE,eAAe,EAAE,IAAI,CAAC,CAAC;IAC5E,CAAC;AACH,CAAC;AAED,IAAI,sBAAsB,GAAkB,OAAO,CAAC,OAAO,EAAE,CAAC;AAE9D,MAAM,CAAC,KAAK,UAAU,kBAAkB;IACtC,IAAI,GAAoB,CAAC;IACzB,sBAAsB,GAAG,sBAAsB,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE;QAC9D,MAAM,MAAM,GAAuB,MAAM,IAAI,CAAC,YAAY,CAAC,QAAQ,CAAC,gBAAgB,EAAE,gBAAgB,EAAE,IAAI,CAAC,CAAC;QAC9G,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAC,OAAO,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,2BAA2B,EAAE,EAAE,EAAC,CAAC;QACjG,MAAM,cAAc,GAAyC,MAAM,qBAAqB,EAAE,CAAC;QAC3F,yEAAyE;QACzE,GAAG,CAAC,OAAO,GAAG,GAAG,CAAC,OAAO,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9D,GAAG,CAAC,QAAQ,GAAG,GAAG,CAAC,QAAQ,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC;QACjE,GAAG,CAAC,2BAA2B,GAAG,GAAG,CAAC,2BAA2B,YAAY,MAAM,CAAC,CAAC;YACnF,GAAG,CAAC,2BAA2B,CAAC,CAAC,CAAC,EAAE,CAAC;QAEvC,oCAAoC;QACpC,KAAK,MAAM,WAAW,IAAI,cAAc,EAAE,CAAC;YACzC,GAAG,CAAC,2BAA2B,CAAC,WAAW,CAAC,GAAG,GAAG,CAAC,2BAA2B,CAAC,WAAW,CAAC,IAAI,EAAE,CAAC;YAClG,KAAK,MAAM,WAAW,IAAI,cAAc,CAAC,WAAW,CAAC,EAAE,CAAC;gBACtD,KAAK,MAAM,aAAa,IAAI,cAAc,CAAC,WAAW,CAAC,CAAC,WAAW,CAAC;oBAClE,GAAG,CAAC,2BAA2B,CAAC,WAAW,CAAC,CAAC,aAAa,CAAC,GAAG,WAAW,CAAC;YAC9E,CAAC;QACH,CAAC;QACD,oFAAoF;IACtF,CAAC,CAAC,CAAC;IACH,MAAM,sBAAsB,CAAC;IAC7B,OAAO,GAAI,CAAC;AACd,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,KAAsB;IAC7D,sBAAsB,GAAG,sBAAsB,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE;QAC9D,KAAK,CAAC,2BAA2B,GAAG,KAAK,CAAC,2BAA2B,IAAI,EAAE,CAAC;QAC5E,sFAAsF;QACtF,qDAAqD;QACrD,MAAM,uBAAuB,GAAyC,EAAE,CAAC;QACzE,KAAK,MAAM,WAAW,IAAI,KAAK,CAAC,2BAA2B,EAAE,CAAC;YAC5D,uBAAuB,CAAC,WAAW,CAAC,GAAG,EAAE,CAAC;YAC1C,KAAK,MAAM,aAAa,IAAI,KAAK,CAAC,2BAA2B,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC3E,MAAM,WAAW,GAAG,KAAK,CAAC,2BAA2B,CAAC,WAAW,CAAC,CAAC,aAAa,CAAC,CAAC;gBAClF,uBAAuB,CAAC,WAAW,CAAC,CAAC,WAAW,CAAC,GAAG,uBAAuB,CAAC,WAAW,CAAC,CAAC,WAAW,CAAC,IAAI,EAAE,CAAC;gBAC5G,uBAAuB,CAAC,WAAW,CAAC,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC;YACxE,CAAC;QACH,CAAC;QACD,MAAM,qBAAqB,CAAC,uBAAuB,CAAC,CAAC;QACrD,kIAAkI;QAClI,MAAM,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,gBAAgB,EAAE,gBAAgB,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC;IAC/F,CAAC,CAAC,CAAC;IACH,MAAM,sBAAsB,CAAC;AAC/B,CAAC"}
|
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import wu from 'wu';
|
|
2
2
|
import { LRUCache } from 'lru-cache';
|
|
3
3
|
import { addSubstructProvider, getMonomerHover, setMonomerHover } from '@datagrok-libraries/chem-meta/src/types';
|
|
4
|
+
import { PolymerTypes } from '../helm/consts';
|
|
4
5
|
import { ALPHABET } from '../utils/macromolecule';
|
|
5
6
|
import { getMonomersDictFromLib } from './to-atomic-level';
|
|
6
7
|
import { monomerSeqToMolfile } from './to-atomic-level-utils';
|
|
@@ -45,7 +46,7 @@ export async function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelpe
|
|
|
45
46
|
.map((posIdx) => { return { position: posIdx, symbol: seqSS.getCanonical(posIdx), biotype: biotype }; })
|
|
46
47
|
.toArray();
|
|
47
48
|
const alphabet = seqSH.alphabet;
|
|
48
|
-
const polymerType = alphabet == ALPHABET.RNA || alphabet == ALPHABET.DNA ?
|
|
49
|
+
const polymerType = alphabet == ALPHABET.RNA || alphabet == ALPHABET.DNA ? PolymerTypes.RNA : PolymerTypes.PEPTIDE;
|
|
49
50
|
const monomersDict = getMonomersDictFromLib([seqMList], [undefined], polymerType, alphabet, monomerLib, rdKitModule);
|
|
50
51
|
// Call seq-to-molfile worker core directly
|
|
51
52
|
const molWM = monomerSeqToMolfile(seqMList, monomersDict, alphabet, polymerType);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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;
|
|
1
|
+
{"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;AAI3H,OAAO,EAAC,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAC5C,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,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,YAAY,CAAC,OAAO,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,GAAG;gBAAE,OAAO,SAAS,CAAC;YAE3B,MAAM,aAAa,GAAG,aAAa,CAAC,MAAM,EAAE,WAAW,CAAC,CAAC;YACzD,IAAI,CAAC,aAAa;gBAAE,OAAO,SAAS,CAAC;YACrC,MAAM,GAAG,GAAe,eAAe,CAAC,aAAa,CAAC,MAAM,EAAE,EAAE,UAAU,CAAC,CAAC;YAC5E,OAAO,GAAG,CAAC;QACb,CAAC;KACF,CAAC;IAEF,mBAAmB,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;IAC1C,oBAAoB,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;IAE3C,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,MAAM,UAAU,qBAAqB,CACnC,WAAwB,EAAE,UAA8B;IAExD,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,WAAW,CAAC,WAAW,CAAC;QACvC,IAAI,CAAC,MAAM;YAAE,OAAO;QAEpB,MAAM,OAAO,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC;QAC7C,KAAK,IAAI,IAAI,GAAG,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,IAAI,CAAC,EAAE,EAAE,IAAI,EAAE,CAAC;YACtD,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;YAC1B,MAAM,UAAU,GAAG,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;YAC5D,IAAI,UAAU,EAAE,CAAC;gBACf,MAAM,UAAU,GAAG,GAAG,CAAC,OAAO,CAAC,WAAW,EAAE,UAAU,EAAE,UAAU,CAAC,CAAC;gBACpE,IAAI,CAAC,UAAU;oBACb,MAAM;YACV,CAAC;QACH,CAAC;IACH,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IACnB,CAAC;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,MAAyB;IAC5D,OAAO,MAAM,CAAC,IAAI,CAAC,qBAAqB,CAAC,IAAI,EAAE,CAAC;AAClD,CAAC"}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { HelmTypes } from '../helm/consts';
|
|
1
|
+
import { HelmTypes, PolymerTypes } from '../helm/consts';
|
|
2
2
|
export class MonomerWorks {
|
|
3
3
|
//private molfileConverter: IMolfileConverter;
|
|
4
4
|
constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {
|
|
@@ -23,19 +23,19 @@ export function helmTypeToPolymerType(helmType) {
|
|
|
23
23
|
case HelmTypes.NUCLEOTIDE:
|
|
24
24
|
// @ts-ignore
|
|
25
25
|
case 'nucleotide':
|
|
26
|
-
polymerType =
|
|
26
|
+
polymerType = PolymerTypes.RNA;
|
|
27
27
|
break;
|
|
28
28
|
case HelmTypes.AA:
|
|
29
|
-
polymerType =
|
|
29
|
+
polymerType = PolymerTypes.PEPTIDE;
|
|
30
30
|
break;
|
|
31
31
|
case HelmTypes.CHEM:
|
|
32
|
-
polymerType =
|
|
32
|
+
polymerType = PolymerTypes.CHEM;
|
|
33
33
|
break;
|
|
34
34
|
case HelmTypes.BLOB:
|
|
35
|
-
polymerType =
|
|
35
|
+
polymerType = PolymerTypes.BLOB;
|
|
36
36
|
break;
|
|
37
37
|
default:
|
|
38
|
-
polymerType =
|
|
38
|
+
polymerType = PolymerTypes.PEPTIDE;
|
|
39
39
|
console.warn(`Unexpected HelmType '${helmType}'`);
|
|
40
40
|
}
|
|
41
41
|
return polymerType;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"monomer-works.js","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAMA,OAAO,EAAC,SAAS,
|
|
1
|
+
{"version":3,"file":"monomer-works.js","sourceRoot":"","sources":["monomer-works.ts"],"names":[],"mappings":"AAMA,OAAO,EAAC,SAAS,EAAE,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAYvD,MAAM,OAAO,YAAY;IAGvB,8CAA8C;IAE9C,YAAY,UAA2B,CAAA,yCAAyC;QAC9E,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;QAC7B,2CAA2C;IAC7C,CAAC;IAED,qCAAqC;IAC9B,uBAAuB,CAAC,WAAwB,EAAE,WAAmB;QAC1E,sCAAsC;QACtC,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QACrE,IAAI,OAAO;YACT,OAAO,OAAO,CAAC,OAAO,CAAC,CAAC,UAAU;QAEpC,OAAO,IAAI,CAAC;IACd,CAAC;CACF;AAED,MAAM,UAAU,qBAAqB,CAAC,QAAkB;IACtD,IAAI,WAAW,GAA4B,SAAS,CAAC;IACrD,QAAQ,QAAQ,EAAE,CAAC;QACnB,KAAK,SAAS,CAAC,IAAI,CAAC;QACpB,KAAK,SAAS,CAAC,KAAK,CAAC,CAAC,8BAA8B;QACpD,KAAK,SAAS,CAAC,MAAM,CAAC,CAAC,gBAAgB;QACvC,KAAK,SAAS,CAAC,UAAU,CAAC;QACxB,aAAa;QACf,KAAK,YAAY;YACf,WAAW,GAAG,YAAY,CAAC,GAAG,CAAC;YAC/B,MAAM;QACR,KAAK,SAAS,CAAC,EAAE;YACf,WAAW,GAAG,YAAY,CAAC,OAAO,CAAC;YACnC,MAAM;QACR,KAAK,SAAS,CAAC,IAAI;YACjB,WAAW,GAAG,YAAY,CAAC,IAAI,CAAC;YAChC,MAAM;QACR,KAAK,SAAS,CAAC,IAAI;YACjB,WAAW,GAAG,YAAY,CAAC,IAAI,CAAC;YAChC,MAAM;QACR;YACE,WAAW,GAAG,YAAY,CAAC,OAAO,CAAC;YACnC,OAAO,CAAC,IAAI,CAAC,wBAAwB,QAAQ,GAAG,CAAC,CAAC;IACpD,CAAC;IACD,OAAO,WAAW,CAAC;AACrB,CAAC"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import wu from 'wu';
|
|
3
3
|
import { getMolColName, hexToPercentRgb } from './utils';
|
|
4
|
-
import { HelmTypes } from '../helm/consts';
|
|
4
|
+
import { HelmTypes, PolymerTypes } from '../helm/consts';
|
|
5
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;
|
|
@@ -11,7 +11,7 @@ export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymer
|
|
|
11
11
|
const chunkSize = srcColLength / threadCount;
|
|
12
12
|
const promises = new Array(threadCount);
|
|
13
13
|
const seqSH = seqHelper.getSeqHandler(seqCol);
|
|
14
|
-
const biotype = polymerType ==
|
|
14
|
+
const biotype = polymerType == PolymerTypes.RNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
|
|
15
15
|
const seqList = wu.count(0).take(seqCol.length).map((rowIdx) => {
|
|
16
16
|
const seqSS = seqSH.getSplitted(rowIdx);
|
|
17
17
|
return wu.count(0).take(seqSS.length)
|
|
@@ -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,
|
|
1
|
+
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@@ -1,7 +1,7 @@
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1
1
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/* eslint-disable max-len */
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2
2
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import { monomerWorksConsts as C } from './consts';
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3
3
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import { getMolGraph, MolfileWithMap, MonomerMap, NucleotideRole } from './types';
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4
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-
import { HELM_CORE_FIELDS, } from '../utils/const';
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4
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+
import { HELM_CORE_FIELDS, HELM_POLYMER_TYPE, HELM_MONOMER_TYPE, } from '../utils/const';
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5
5
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import { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';
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6
6
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import { helmTypeToPolymerType } from './monomer-works';
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7
7
|
/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.
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@@ -17,8 +17,8 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
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17
17
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// RNA: all branch monomers (bases) and all backbone monomers (sugars +
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18
18
|
// phosphates, including modified ones). Modifications are looked up by
|
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19
19
|
// symbol at assembly time, so they MUST be present in the formatted lib.
|
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20
|
-
polymerType ===
|
|
21
|
-
it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] !==
|
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20
|
+
polymerType === HELM_POLYMER_TYPE.RNA || (polymerType === HELM_POLYMER_TYPE.PEPTIDE &&
|
|
21
|
+
it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] !== HELM_MONOMER_TYPE.BRANCH)) {
|
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22
22
|
const monomerObject = {};
|
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23
23
|
HELM_CORE_FIELDS.forEach((field) => {
|
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24
24
|
//@ts-ignore
|
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@@ -47,7 +47,7 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
|
|
|
47
47
|
// The roles array carries the per-position semantics — including
|
|
48
48
|
// TERMINAL_5P / TERMINAL_3P for non-canonical chain ends — so we don't
|
|
49
49
|
// re-validate the length here.
|
|
50
|
-
const triplesMode = polymerType ===
|
|
50
|
+
const triplesMode = polymerType === HELM_POLYMER_TYPE.RNA && !!roles &&
|
|
51
51
|
roles.length === monomerSeq.length;
|
|
52
52
|
// define atom and bond counts, taking into account the bond type
|
|
53
53
|
const { atomCount, bondCount, needsCapping } = getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode, roles);
|
|
@@ -57,7 +57,7 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
|
|
|
57
57
|
let addMonomerToMolblock;
|
|
58
58
|
let sugar = null;
|
|
59
59
|
let phosphate = null;
|
|
60
|
-
if (polymerType ===
|
|
60
|
+
if (polymerType === HELM_POLYMER_TYPE.PEPTIDE)
|
|
61
61
|
addMonomerToMolblock = addAminoAcidToMolblock;
|
|
62
62
|
else { // nucleotides
|
|
63
63
|
addMonomerToMolblock = addNucleotideToMolblock;
|
|
@@ -330,7 +330,7 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
|
|
|
330
330
|
lastPhosphateGraph = lastMonomerGraph;
|
|
331
331
|
}
|
|
332
332
|
// add extra values depending on the polymer type
|
|
333
|
-
if (polymerType ===
|
|
333
|
+
if (polymerType === HELM_POLYMER_TYPE.PEPTIDE) {
|
|
334
334
|
// add the rightmost/terminating cap group 'OH' (i.e. 'O')
|
|
335
335
|
atomCount += 1;
|
|
336
336
|
// add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)
|