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guyguy2001guyguy2001
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Refactor/extract scripting api 2 (#840)
## Summary This is part of the process of extracting the script-facing API from PoseEditMode in order to make it usable for non-booster scripts. Replaces #749 ## Implementation Notes I did it like the previous PR, except I didn't implement get_folder/select_folder, since they are behind a "lock", and I didn't want to think yet of whether or not I want the extracted logic to inherit the lock. However, while get_folder is locked, the calculation functions (such as `fold`) which also access the folder, aren't locked (even on `dev`). Is this intended? ## Testing I ran https://eternagame.org/scripts/13774466, and it passed. The script checks that all of the extracted functions (expect folding with binding sites) work and return the same values. This is an unrelated issue, but : For some reason, both on main/master (https://eternagame.org/puzzles/6096060/play) and on my branch, the first time I run it I get the following errors, and on future runs it passes. Reloading the page makes the issue appear again for a single execution. Errors: ![image](https://github.com/user-attachments/assets/1fca8f90-85f4-485c-9ff4-a44fcdb2445a) Successful run: ![image](https://github.com/user-attachments/assets/ecfe8020-2724-44f3-819f-0a6c13182786) (In my branch I just copy pasted the script, since I didn't have it on eternadev.org, and changed `Lib.fold`->`applet.fold`. I shouldn't have Lib in the terminal, right?) ## Related Issues Enables eternagame/eternagame.org#378, #750
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‎src/eterna/eternaScript/FoldingAPI.ts‎

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import EPars from 'eterna/EPars';
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import Folder, {SuboptEnsembleResult} from 'eterna/folding/Folder';
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import DotPlot from 'eterna/rnatypes/DotPlot';
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import SecStruct from 'eterna/rnatypes/SecStruct';
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import Sequence from 'eterna/rnatypes/Sequence';
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import {ExternalInterfaceCtx} from 'eterna/util/ExternalInterface';
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import {Assert} from 'flashbang';
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/**
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* An EternaScript API exposing all functions that handle folding an arbitrary
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* RNA sequence, and aren't dependent on what's the RNA in the puzzle.
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*
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* It adds itself to an existing script API (`ExternalInterfaceCtx`) from
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* `this.registerToScriptInterface`.
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*
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* Note: The API in this class is still affected by the selected folder
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* and the pseudoknot mode of the puzzle - just not the sequence.
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*/
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export default class FoldingAPI {
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private readonly _getFolder: () => Folder | null;
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private readonly _getIsPseudoknot: () => boolean;
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private get _folder(): Folder | null {
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return this._getFolder();
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}
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private get _isPseudoknot(): boolean {
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return this._getIsPseudoknot();
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}
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constructor(params: { getFolder: () => Folder, getIsPseudoknot: () => boolean }) {
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this._getIsPseudoknot = params.getIsPseudoknot;
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this._getFolder = params.getFolder;
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}
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public registerToScriptInterface(scriptInterfaceCtx: ExternalInterfaceCtx) {
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scriptInterfaceCtx.addCallback(
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'fold',
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(seq: string, constraint: string | null = null): string | null => {
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if (this._folder === null) {
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return null;
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}
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if (!this._folder.isSync()) {
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throw new Error('Attempted to use asynchronous folding engine synchronously');
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}
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const seqArr: Sequence = Sequence.fromSequenceString(seq);
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const pseudoknots = this._isPseudoknot;
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const folded: SecStruct | null = this._folder.foldSequence(seqArr, null, constraint, pseudoknots);
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Assert.assertIsDefined(folded);
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return folded.getParenthesis({pseudoknots});
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}
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);
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scriptInterfaceCtx.addCallback(
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'fold_async',
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async (seq: string, constraint: string | null = null): Promise<string | null> => {
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if (this._folder === null) {
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return null;
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}
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const seqArr: Sequence = Sequence.fromSequenceString(seq);
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const pseudoknots = this._isPseudoknot;
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const folded: SecStruct | null = await this._folder.foldSequence(seqArr, null, constraint, pseudoknots);
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Assert.assertIsDefined(folded);
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return folded.getParenthesis({pseudoknots});
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}
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);
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scriptInterfaceCtx.addCallback(
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'fold_with_binding_site',
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(seq: string, site: number[], bonus: number): string | null => {
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if (this._folder === null) {
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return null;
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}
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const seqArr: Sequence = Sequence.fromSequenceString(seq);
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const pseudoknots = this._isPseudoknot;
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const folded: SecStruct | null = this._folder.foldSequenceWithBindingSite(
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seqArr, null, site, Math.floor(bonus * 100), 2.5
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);
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if (folded === null) {
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return null;
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}
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return folded.getParenthesis({pseudoknots});
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}
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);
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scriptInterfaceCtx.addCallback(
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'fold_with_binding_site_async',
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async (seq: string, site: number[], bonus: number): Promise<string | null> => {
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if (this._folder === null) {
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return null;
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}
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const seqArr: Sequence = Sequence.fromSequenceString(seq);
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const pseudoknots = this._isPseudoknot;
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const folded: SecStruct | null = this._folder.foldSequenceWithBindingSite(
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seqArr, null, site, Math.floor(bonus * 100), 2.5
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);
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if (folded === null) {
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return null;
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}
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return folded.getParenthesis({pseudoknots});
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}
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);
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scriptInterfaceCtx.addCallback(
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'energy_of_structure',
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(seq: string, secstruct: string): number | null => {
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if (this._folder === null) {
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return null;
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}
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const seqArr: Sequence = Sequence.fromSequenceString(seq);
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const pseudoknots = this._isPseudoknot;
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const structArr: SecStruct = SecStruct.fromParens(secstruct, pseudoknots);
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const freeEnergy = this._isPseudoknot
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? this._folder.scoreStructures(seqArr, structArr, true)
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: this._folder.scoreStructures(seqArr, structArr);
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return 0.01 * freeEnergy;
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}
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);
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scriptInterfaceCtx.addCallback(
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'energy_of_structure_async',
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async (seq: string, secstruct: string): Promise<number | null> => {
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if (this._folder === null) {
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return null;
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}
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const seqArr: Sequence = Sequence.fromSequenceString(seq);
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const pseudoknots = this._isPseudoknot;
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const structArr: SecStruct = SecStruct.fromParens(secstruct, pseudoknots);
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const freeEnergy = this._isPseudoknot
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? this._folder.scoreStructures(seqArr, structArr, true)
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: this._folder.scoreStructures(seqArr, structArr);
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return 0.01 * freeEnergy;
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}
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);
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scriptInterfaceCtx.addCallback(
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'pairing_probabilities',
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(seq: string, secstruct: string | null = null): number[] | null => {
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if (this._folder === null) {
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return null;
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}
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if (!this._folder.isSync()) {
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throw new Error('Attempted to use asynchronous folding engine synchronously');
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}
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const seqArr: Sequence = Sequence.fromSequenceString(seq);
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const pseudoknots = this._isPseudoknot;
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let folded: SecStruct | null;
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if (secstruct) {
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folded = SecStruct.fromParens(secstruct, pseudoknots);
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} else {
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folded = this._folder.foldSequence(seqArr, null, null);
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if (folded === null) {
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return null;
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}
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}
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const pp: DotPlot | null = this._folder.getDotPlot(seqArr, folded);
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Assert.assertIsDefined(pp);
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return pp.data;
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}
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);
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scriptInterfaceCtx.addCallback(
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'pairing_probabilities_async',
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async (seq: string, secstruct: string | null = null): Promise<number[] | null> => {
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if (this._folder === null) {
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return null;
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}
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const seqArr: Sequence = Sequence.fromSequenceString(seq);
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const pseudoknots = this._isPseudoknot;
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let folded: SecStruct | null;
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if (secstruct) {
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folded = SecStruct.fromParens(secstruct, pseudoknots);
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} else {
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folded = await this._folder.foldSequence(seqArr, null, null);
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if (folded === null) {
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return null;
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}
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}
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const pp: DotPlot | null = await this._folder.getDotPlot(seqArr, folded);
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Assert.assertIsDefined(pp);
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return pp.data;
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}
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);
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scriptInterfaceCtx.addCallback(
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'subopt_single_sequence',
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(
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seq: string, kcalDelta: number,
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pseudoknotted: boolean, temp: number = EPars.DEFAULT_TEMPERATURE
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): SuboptEnsembleResult | null => {
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if (this._folder === null) {
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return null;
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}
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// now get subopt stuff
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const seqArr: Sequence = Sequence.fromSequenceString(seq);
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return this._folder.getSuboptEnsembleNoBindingSite(seqArr,
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kcalDelta, pseudoknotted, temp);
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}
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);
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scriptInterfaceCtx.addCallback(
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'subopt_single_sequence_async',
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async (
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seq: string, kcalDelta: number,
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pseudoknotted: boolean, temp: number = EPars.DEFAULT_TEMPERATURE
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): Promise<SuboptEnsembleResult | null> => {
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if (this._folder === null) {
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return null;
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}
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// now get subopt stuff
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const seqArr: Sequence = Sequence.fromSequenceString(seq);
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return this._folder.getSuboptEnsembleNoBindingSite(seqArr,
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kcalDelta, pseudoknotted, temp);
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}
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);
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scriptInterfaceCtx.addCallback(
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'subopt_oligos',
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(
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seq: string, oligoStrings: string[], kcalDelta: number,
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pseudoknotted: boolean, temp: number = EPars.DEFAULT_TEMPERATURE
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): SuboptEnsembleResult | null => {
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if (this._folder === null) {
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return null;
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}
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// make the sequence string from the oligos
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let newSequence: string = seq;
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for (let oligoIndex = 0; oligoIndex < oligoStrings.length; oligoIndex++) {
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const oligoSequence: string = oligoStrings[oligoIndex];
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newSequence = `${newSequence}&${oligoSequence}`;
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}
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// now get subopt stuff
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const seqArr: Sequence = Sequence.fromSequenceString(newSequence);
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return this._folder.getSuboptEnsembleWithOligos(seqArr,
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oligoStrings, kcalDelta, pseudoknotted, temp);
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}
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);
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scriptInterfaceCtx.addCallback(
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'subopt_oligos_async',
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async (
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seq: string, oligoStrings: string[], kcalDelta: number,
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pseudoknotted: boolean, temp: number = EPars.DEFAULT_TEMPERATURE
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): Promise<SuboptEnsembleResult | null> => {
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if (this._folder === null) {
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return null;
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}
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// make the sequence string from the oligos
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let newSequence: string = seq;
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for (let oligoIndex = 0; oligoIndex < oligoStrings.length; oligoIndex++) {
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const oligoSequence: string = oligoStrings[oligoIndex];
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newSequence = `${newSequence}&${oligoSequence}`;
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}
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// now get subopt stuff
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const seqArr: Sequence = Sequence.fromSequenceString(newSequence);
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return this._folder.getSuboptEnsembleWithOligos(seqArr,
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oligoStrings, kcalDelta, pseudoknotted, temp);
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}
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);
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scriptInterfaceCtx.addCallback(
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'cofold',
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(
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seq: string, oligo: string, malus: number = 0.0, constraint: string | null = null
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): string | null => {
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if (this._folder === null) {
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return null;
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}
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const len: number = seq.length;
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const cseq = `${seq}&${oligo}`;
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const seqArr: Sequence = Sequence.fromSequenceString(cseq);
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const pseudoknots = this._isPseudoknot;
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const folded: SecStruct | null = this._folder.cofoldSequence(
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seqArr, null, Math.floor(malus * 100), constraint
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);
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if (folded === null) {
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return null;
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}
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return `${folded.slice(0, len).getParenthesis({pseudoknots})
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}&${folded.slice(len).getParenthesis({pseudoknots})}`;
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}
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);
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scriptInterfaceCtx.addCallback(
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'cofold_async',
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async (
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seq: string, oligo: string, malus: number = 0.0, constraint: string | null = null
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): Promise<string | null> => {
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if (this._folder === null) {
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return null;
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}
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const len: number = seq.length;
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const cseq = `${seq}&${oligo}`;
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const seqArr: Sequence = Sequence.fromSequenceString(cseq);
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const pseudoknots = this._isPseudoknot;
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const folded: SecStruct | null = this._folder.cofoldSequence(
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seqArr, null, Math.floor(malus * 100), constraint
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);
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if (folded === null) {
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return null;
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}
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return `${folded.slice(0, len).getParenthesis({pseudoknots})
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}&${folded.slice(len).getParenthesis({pseudoknots})}`;
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}
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);
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scriptInterfaceCtx.addCallback(
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'get_defect',
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(
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seq: string, secstruct: string, pseudoknotted: boolean, temp: number = EPars.DEFAULT_TEMPERATURE
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): number | null => {
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if (this._folder === null) {
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return null;
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}
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return this._folder.getDefect(
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Sequence.fromSequenceString(seq),
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SecStruct.fromParens(secstruct, pseudoknotted),
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temp, pseudoknotted
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);
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}
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);
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scriptInterfaceCtx.addCallback(
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'get_defect_async',
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async (
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seq: string, secstruct: string, pseudoknotted: boolean, temp: number = EPars.DEFAULT_TEMPERATURE
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): Promise<number | null> => {
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if (this._folder === null) {
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return null;
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}
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return this._folder.getDefect(
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Sequence.fromSequenceString(seq),
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SecStruct.fromParens(secstruct, pseudoknotted),
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temp, pseudoknotted
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);
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}
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);
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}
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}

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