@datagrok-libraries/bio 5.11.0 → 5.12.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.eslintrc.json +50 -49
- package/package.json +1 -1
- package/src/monomer-works/monomer-utils.d.ts +2 -2
- package/src/monomer-works/monomer-utils.d.ts.map +1 -1
- package/src/monomer-works/monomer-utils.js +1 -1
- package/src/monomer-works/monomer-works.d.ts +11 -1
- package/src/monomer-works/monomer-works.d.ts.map +1 -1
- package/src/monomer-works/monomer-works.js +10 -3
- package/src/monomer-works/to-atomic-level.d.ts +10 -0
- package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
- package/src/monomer-works/to-atomic-level.js +203 -81
- package/src/utils/const.d.ts +4 -0
- package/src/utils/const.d.ts.map +1 -1
- package/src/utils/const.js +1 -1
- package/src/utils/tree-helper.d.ts +5 -3
- package/src/utils/tree-helper.d.ts.map +1 -1
- package/src/utils/tree-helper.js +1 -1
package/src/utils/const.d.ts
CHANGED
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@@ -12,6 +12,10 @@ export declare const enum HELM_FIELDS {
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POLYMER_TYPE = "polymerType",
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SYMBOL = "symbol"
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}
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+
export declare const enum MODE {
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STANDARD = 0,
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SEQ_TRAN = 1
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}
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export declare const enum RGROUP_FIELDS {
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CAP_GROUP_SMILES = "capGroupSmiles",
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CAP_GROUP_SMILES_UPPERCASE = "capGroupSMILES",
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package/src/utils/const.d.ts.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"const.d.ts","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAIA,eAAO,MAAM,sBAAsB,+BAA+B,CAAC;AAEnE,0BAAkB,WAAW;IAC3B,YAAY,gBAAgB;IAC5B,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,MAAM,WAAW;IACjB,OAAO,YAAY;IACnB,cAAc,kBAAkB;IAChC,OAAO,YAAY;IACnB,WAAW,eAAe;IAC1B,EAAE,OAAO;IACT,YAAY,gBAAgB;IAC5B,MAAM,WAAW;CAClB;AAGD,0BAAkB,aAAa;IAC7B,gBAAgB,mBAAmB;IACnC,0BAA0B,mBAAmB;IAC7C,QAAQ,gBAAgB;IACxB,cAAc,iBAAiB;IAC/B,KAAK,UAAU;CAChB;AAGD,0BAAkB,iBAAiB;IACjC,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,iBAAiB;IACjC,QAAQ,aAAa;IACrB,QAAQ,aAAa;IACrB,MAAM,WAAW;CAClB;AAGD,eAAO,MAAM,gBAAgB,eAO5B,CAAC;AAEF,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;AAG9C,eAAO,MAAM,qBAAqB;;;;;;;;;;;;CAYjC,CAAC;AAGF,eAAO,MAAM,kBAAkB,MAAQ,CAAC;AACxC,eAAO,MAAM,kBAAkB,OAAQ,CAAC"}
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1
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+
{"version":3,"file":"const.d.ts","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAIA,eAAO,MAAM,sBAAsB,+BAA+B,CAAC;AAEnE,0BAAkB,WAAW;IAC3B,YAAY,gBAAgB;IAC5B,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,MAAM,WAAW;IACjB,OAAO,YAAY;IACnB,cAAc,kBAAkB;IAChC,OAAO,YAAY;IACnB,WAAW,eAAe;IAC1B,EAAE,OAAO;IACT,YAAY,gBAAgB;IAC5B,MAAM,WAAW;CAClB;AAGD,0BAAkB,IAAI;IACpB,QAAQ,IAAA;IACR,QAAQ,IAAA;CACT;AAGD,0BAAkB,aAAa;IAC7B,gBAAgB,mBAAmB;IACnC,0BAA0B,mBAAmB;IAC7C,QAAQ,gBAAgB;IACxB,cAAc,iBAAiB;IAC/B,KAAK,UAAU;CAChB;AAGD,0BAAkB,iBAAiB;IACjC,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,iBAAiB;IACjC,QAAQ,aAAa;IACrB,QAAQ,aAAa;IACrB,MAAM,WAAW;CAClB;AAGD,eAAO,MAAM,gBAAgB,eAO5B,CAAC;AAEF,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;AAG9C,eAAO,MAAM,qBAAqB;;;;;;;;;;;;CAYjC,CAAC;AAGF,eAAO,MAAM,kBAAkB,MAAQ,CAAC;AACxC,eAAO,MAAM,kBAAkB,OAAQ,CAAC"}
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package/src/utils/const.js
CHANGED
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@@ -26,4 +26,4 @@ export const jsonSdfMonomerLibDict = {
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// range of hex nubers used in PepSea library to endode monomers
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export const MONOMER_ENCODE_MIN = 0x100;
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export const MONOMER_ENCODE_MAX = 0x40A;
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-
//# sourceMappingURL=data:application/json;base64,
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+
//# sourceMappingURL=data:application/json;base64,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@@ -1,5 +1,5 @@
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import * as DG from 'datagrok-api/dg';
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-
import { NodeType } from '../types';
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import { NodeCuttedType, NodeType } from '../types';
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export interface ITreeHelper {
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toNewick(node: NodeType | null): string;
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getLeafList(node: NodeType): NodeType[];
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@@ -8,9 +8,11 @@ export interface ITreeHelper {
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[name: string]: any;
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}): NodeType | null;
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treeCutAsLeaves(node: NodeType, cutHeight: number, currentHeight?: number): NodeType[];
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treeCutAsTree(node: NodeType, cutHeight: number, currentHeight?: number): NodeType | null;
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treeCutAsTree(node: NodeType, cutHeight: number, keepShorts?: boolean, currentHeight?: number): NodeType | null;
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setGridOrder(node: NodeType, grid: DG.Grid, leafColName: string): [NodeType, string[]];
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markClusters(tree: NodeCuttedType, dataDf: DG.DataFrame, leafColName: string, clusterColName: string, na?: any): void;
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buildClusters(tree: NodeCuttedType, clusterDf: DG.DataFrame, clusterColName: string, leafColName: string): void;
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cutTreeToGrid(node: NodeType, cutHeight: number, dataDf: DG.DataFrame, leafColName: string, clusterColName: string, na?: any): void;
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}
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export declare function getTreeHelper(): Promise<ITreeHelper>;
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//# sourceMappingURL=tree-helper.d.ts.map
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@@ -1 +1 @@
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{"version":3,"file":"tree-helper.d.ts","sourceRoot":"","sources":["tree-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,QAAQ,EAAC,MAAM,UAAU,CAAC;
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{"version":3,"file":"tree-helper.d.ts","sourceRoot":"","sources":["tree-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,cAAc,EAAE,QAAQ,EAAC,MAAM,UAAU,CAAC;AAGlD,MAAM,WAAW,WAAW;IAC1B,QAAQ,CAAC,IAAI,EAAE,QAAQ,GAAG,IAAI,GAAG,MAAM,CAAC;IAExC,WAAW,CAAC,IAAI,EAAE,QAAQ,GAAG,QAAQ,EAAE,CAAC;IAExC,WAAW,CAAC,IAAI,EAAE,QAAQ,GAAG,QAAQ,EAAE,CAAC;IAExC,kBAAkB,CAAC,IAAI,EAAE,QAAQ,EAAE,MAAM,EAAE;QAAE,CAAC,IAAI,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,GAAG,QAAQ,GAAG,IAAI,CAAC;IAErF,eAAe,CAAC,IAAI,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,EAAE,aAAa,CAAC,EAAE,MAAM,GAAG,QAAQ,EAAE,CAAC;IAEvF,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,OAAO,EAAE,aAAa,CAAC,EAAE,MAAM,GAAG,QAAQ,GAAG,IAAI,CAAC;IAEhH,YAAY,CAAC,IAAI,EAAE,QAAQ,EAAE,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,WAAW,EAAE,MAAM,GAAG,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC;IAEvF,YAAY,CAAC,IAAI,EAAE,cAAc,EAAE,MAAM,EAAE,EAAE,CAAC,SAAS,EAAE,WAAW,EAAE,MAAM,EAAE,cAAc,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,GAAG,GAAG,IAAI,CAAC;IAEtH,aAAa,CAAC,IAAI,EAAE,cAAc,EAAE,SAAS,EAAE,EAAE,CAAC,SAAS,EAAE,cAAc,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAEhH,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,SAAS,EACnE,WAAW,EAAE,MAAM,EAAE,cAAc,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,GAAG,GAAG,IAAI,CAAC;CAChE;AAED,wBAAsB,aAAa,IAAI,OAAO,CAAC,WAAW,CAAC,CAO1D"}
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package/src/utils/tree-helper.js
CHANGED
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@@ -17,4 +17,4 @@ export function getTreeHelper() {
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return res;
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});
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}
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//# sourceMappingURL=data:application/json;base64,
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