@datagrok/helm 2.0.7 → 2.1.0

package/src/package.ts

@@ -2,32 +2,68 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import * as bio from '@datagrok-libraries/bio';
 
-import {createJsonMonomerLibFromSdf} from './utils';
-import {MONOMER_MANAGER_MAP, RGROUPS, RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
+import {WebEditorMonomer, RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
 import {HelmWebEditor} from './helm-web-editor';
-import {Observable, Subject} from 'rxjs';
+import {NotationConverter, IMonomerLib, Monomer} from '@datagrok-libraries/bio';
+import {HelmCellRenderer} from './cell-renderer';
 
 export const _package = new DG.Package();
-
-const STORAGE_NAME = 'Libraries';
-const LIB_PATH = 'libraries/';
+let monomerLib: IMonomerLib | null = null;
 
 //tags: init
 export async function initHelm(): Promise<void> {
-  return new Promise(async (resolve, reject) => {
+  return Promise.all([new Promise((resolve, reject) => {
     // @ts-ignore
     dojo.ready(function() { resolve(null); });
-    await loadLibraries();
+  }), await grok.functions.call('Bio:getBioLib')]).then(([_, lib]: [void, IMonomerLib]) => {
+    monomerLib = lib;
+    rewriteLibraries();
+    monomerLib.onChanged.subscribe((_) => {
+      rewriteLibraries();
+    })
   });
 }
 
+function rewriteLibraries() {
+  org.helm.webeditor.Monomers.clear();
+  monomerLib.getTypes().forEach(type => {
+    const mms = monomerLib.getMonomerNamesByType(type);
+    mms.forEach(symbol => {
+      let isBroken = false;
+      const monomer: Monomer = monomerLib.getMonomer(type, symbol);
+      const webEditorMonomer: WebEditorMonomer = {
+        id: symbol,
+        m: monomer.molfile,
+        n: monomer.name,
+        na: monomer.naturalAnalog,
+        rs: monomer.rgroups.length,
+        type: monomer.polymerType,
+        mt: monomer.monomerType,
+        at: {}
+      }; 
+
+      if(monomer.rgroups.length > 0) {
+        webEditorMonomer.rs = monomer.rgroups.length;
+        const at = {};
+        monomer.rgroups.forEach(it => {
+          at[it[RGROUP_LABEL]] = it[RGROUP_CAP_GROUP_NAME];
+        });
+        webEditorMonomer.at = at;
+      } else if (monomer.data[SMILES] != null){
+        webEditorMonomer.rs = Object.keys(getRS(monomer.data[SMILES].toString())).length;
+        webEditorMonomer.at = getRS(monomer.data[SMILES].toString());
+      } else
+        isBroken = true;
+
+      if(!isBroken)
+        org.helm.webeditor.Monomers.addOneMonomer(webEditorMonomer);
+    });
+  });
 
-async function loadLibraries() {
-  let uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
-  for (let i = 0; i < uploadedLibraries.length; ++i)
-    await monomerManager(uploadedLibraries[i]);
+  // Obsolete
+  let grid: DG.Grid = grok.shell.tv.grid;
+  grid.invalidate();
 }
 
 //name: helmCellRenderer
@@ -39,57 +75,12 @@ export function helmCellRenderer(): HelmCellRenderer {
   return new HelmCellRenderer();
 }
 
-
-function webEditor(cell?: DG.GridCell, value?: string) {
-  let view = ui.div();
-  org.helm.webeditor.MolViewer.molscale = 0.8;
-  let app = new scil.helm.App(view, {
-    showabout: false,
-    mexfontsize: '90%',
-    mexrnapinontab: true,
-    topmargin: 20,
-    mexmonomerstab: true,
-    sequenceviewonly: false,
-    mexfavoritefirst: true,
-    mexfilter: true
-  });
-  var sizes = app.calculateSizes();
-  app.canvas.resize(sizes.rightwidth - 100, sizes.topheight - 210);
-  var s = {width: sizes.rightwidth - 100 + 'px', height: sizes.bottomheight + 'px'};
-  //@ts-ignore
-  scil.apply(app.sequence.style, s);
-  //@ts-ignore
-  scil.apply(app.notation.style, s);
-  s = {width: sizes.rightwidth + 'px', height: (sizes.bottomheight + app.toolbarheight) + 'px'};
-  //@ts-ignore
-  scil.apply(app.properties.parent.style, s);
-  app.structureview.resize(sizes.rightwidth, sizes.bottomheight + app.toolbarheight);
-  app.mex.resize(sizes.topheight - 80);
-  setTimeout(function() {
-    if (typeof cell !== 'undefined') {
-      app.canvas.helm.setSequence(cell.cell.value, 'HELM');
-    } else {
-      app.canvas.helm.setSequence(value, 'HELM');
-    }
-  }, 200);
-  //@ts-ignore
-  ui.dialog({showHeader: false, showFooter: true})
-    .add(view)
-    .onOK(() => {
-      if (typeof cell !== 'undefined') {
-        cell.cell.value = app.canvas.getHelm(true).replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
-      }
-    }).show({modal: true, fullScreen: true});
-}
-
-
 //tags: cellEditor
 //description: Macromolecule
 //input: grid_cell cell
 export function editMoleculeCell(cell: DG.GridCell): void {
-  if (cell.gridColumn.column.tags[DG.TAGS.UNITS] === 'helm') {
+  if (cell.gridColumn.column.tags[DG.TAGS.UNITS] === 'helm')
     webEditor(cell);
-  }
 }
 
 //name: Open Helm Web Editor
@@ -98,7 +89,7 @@ export function editMoleculeCell(cell: DG.GridCell): void {
 //input: string mol { semType: Macromolecule }
 export function openEditor(mol: string): void {
   let df = grok.shell.tv.grid.dataFrame;
-  let converter = new bio.NotationConverter(df.columns.bySemType('Macromolecule'));
+  let converter = new NotationConverter(df.columns.bySemType('Macromolecule'));
   const resStr = converter.convertStringToHelm(mol, '/');
   webEditor(undefined, resStr);
 }
@@ -129,50 +120,48 @@ export async function propertiesPanel(helmString: string) {
   );
 }
 
-
-//name: Manage Libraries
-//tags: panel, widgets
-//input: column helmColumn {semType: Macromolecule}
-//output: widget result
-export async function libraryPanel(helmColumn: DG.Column): Promise<DG.Widget> {
+function webEditor(cell?: DG.GridCell, value?: string) {
+  let view = ui.div();
+  org.helm.webeditor.MolViewer.molscale = 0.8;
+  let app = new scil.helm.App(view, {
+    showabout: false,
+    mexfontsize: '90%',
+    mexrnapinontab: true,
+    topmargin: 20,
+    mexmonomerstab: true,
+    sequenceviewonly: false,
+    mexfavoritefirst: true,
+    mexfilter: true
+  });
+  var sizes = app.calculateSizes();
+  app.canvas.resize(sizes.rightwidth - 100, sizes.topheight - 210);
+  var s = {width: sizes.rightwidth - 100 + 'px', height: sizes.bottomheight + 'px'};
   //@ts-ignore
-  let filesButton: HTMLButtonElement = ui.button('Manage', manageFiles);
-  let divInputs: HTMLDivElement = ui.div();
-  let librariesList: string[] = (await _package.files.list(`${LIB_PATH}`, false, '')).map(it => it.fileName);
-  let uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
-  for (let i = 0; i < uploadedLibraries.length; ++i) {
-    let libraryName: string = uploadedLibraries[i];
-    divInputs.append(ui.boolInput(libraryName, true, async v => {
-      org.helm.webeditor.Monomers.clear();
-      grok.dapi.userDataStorage.remove(STORAGE_NAME, libraryName, true);
-      await loadLibraries();
-      grok.shell.tv.grid.invalidate();
-    }).root);
-  }
-  let unusedLibraries: string[] = librariesList.filter(x => !uploadedLibraries.includes(x));
-  for (let i = 0; i < unusedLibraries.length; ++i) {
-    let libraryName: string = unusedLibraries[i];
-    divInputs.append(ui.boolInput(libraryName, false, v => {
-      monomerManager(libraryName);
-      grok.dapi.userDataStorage.postValue(STORAGE_NAME, libraryName, libraryName, true);
-    }).root);
-  }
-  return new DG.Widget(ui.splitV([
-    divInputs,
-    ui.divV([filesButton])
-  ]));
-}
-
-//name: manageFiles
-export async function manageFiles() {
-  const a = ui.dialog({title: 'Manage files'})
-    //@ts-ignore
-    .add(ui.fileBrowser({path: 'System:AppData/Helm/libraries'}).root)
-    .addButton('OK', () => a.close())
-    .show();
+  scil.apply(app.sequence.style, s);
+  //@ts-ignore
+  scil.apply(app.notation.style, s);
+  s = {width: sizes.rightwidth + 'px', height: (sizes.bottomheight + app.toolbarheight) + 'px'};
+  //@ts-ignore
+  scil.apply(app.properties.parent.style, s);
+  app.structureview.resize(sizes.rightwidth, sizes.bottomheight + app.toolbarheight);
+  app.mex.resize(sizes.topheight - 80);
+  setTimeout(function() {
+    if (typeof cell !== 'undefined') {
+      app.canvas.helm.setSequence(cell.cell.value, 'HELM');
+    } else {
+      app.canvas.helm.setSequence(value, 'HELM');
+    }
+  }, 200);
+  //@ts-ignore
+  ui.dialog({showHeader: false, showFooter: true})
+    .add(view)
+    .onOK(() => {
+      if (typeof cell !== 'undefined') {
+        cell.cell.value = app.canvas.getHelm(true).replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
+      }
+    }).show({modal: true, fullScreen: true});
 }
 
-
 async function accessServer(url: string, key: string) {
   const params: RequestInit = {
     method: 'GET',
@@ -185,7 +174,6 @@ async function accessServer(url: string, key: string) {
   return json[key];
 }
 
-
 //name: helmToFasta
 //input: string helmString {semType: Macromolecule}
 //output: string res
@@ -203,7 +191,6 @@ export async function helmToRNA(helmString: string) {
   return await accessServer(url, 'Sequence');
 }
 
-
 //name: helmToPeptide
 //description: converts to peptide analogue sequence
 //input: string helmString {semType: Macromolecule}
@@ -244,258 +231,6 @@ function getRS(smiles: string) {
   return res;
 }
 
-//name: monomerManager
-//input: string value
-export async function monomerManager(value: string) {
-  let df: any[];
-  let file;
-  let dfSdf;
-  if (value.endsWith('.sdf')) {
-    const funcList: DG.Func[] = DG.Func.find({package: 'Chem', name: 'importSdf'});
-    console.debug(`Helm: initHelm() funcList.length = ${funcList.length}`);
-    if (funcList.length === 1) {
-      file = await _package.files.readAsBytes(`${LIB_PATH}${value}`);
-      dfSdf = await grok.functions.call('Chem:importSdf', {bytes: file});
-      df = createJsonMonomerLibFromSdf(dfSdf[0]);
-    } else {
-      grok.shell.warning('Chem package is not installed');
-    }
-  } else {
-    const file = await _package.files.readAsText(`${LIB_PATH}${value}`);
-    df = JSON.parse(file);
-  }
-
-  df.forEach(monomer => {
-    const m = {};
-    Object.keys(MONOMER_MANAGER_MAP).forEach(field => {
-      m[field] = monomer[MONOMER_MANAGER_MAP[field]] ?? '';
-    });
-    if (monomer[RGROUPS]) {
-      m['rs'] = monomer[RGROUPS].length;
-      const at = {};
-      monomer[RGROUPS].forEach(it => {
-        at[it[RGROUP_LABEL]] = it[RGROUP_CAP_GROUP_NAME];
-      });
-      m['at'] = at;
-    } else {
-      m['rs'] = Object.keys(getRS(df[SMILES].toString())).length;
-      m['at'] = getRS(df[SMILES].toString());
-    }
-    org.helm.webeditor.Monomers.addOneMonomer(m);
-  });
-
-  // Now after updating org.helm.webeditor.Monomers we update MonomerLib window singleton (fires onChanged event)
-  (getMonomerLibObj() as MonomerLib).update(getAllLibsData());
-  //grok.events.fireCustomEvent('monomersLibChanged', null);
-
-  // Obsolete
-  let grid: DG.Grid = grok.shell.tv.grid;
-  grid.invalidate();
-}
-
-//name: helmColumnToSmiles
-//input: column helmColumn {semType: Macromolecule}
-export function helmColumnToSmiles(helmColumn: DG.Column) {
-  //todo: add column with smiles to col.dataFrame.
-}
-
-
-function split(s: string, sep: string) {
-  var ret = [];
-  var frag = '';
-  var parentheses = 0;
-  var bracket = 0;
-  var braces = 0;
-  var quote = 0;
-  for (var i = 0; i < s.length; ++i) {
-    var c = s.substring(i, i + 1);
-    if (c == sep && bracket == 0 && parentheses == 0 && braces == 0 && quote == 0) {
-      ret.push(frag);
-      frag = '';
-    } else {
-      frag += c;
-      if (quote > 0) {
-        if (c == '\\' && i + 1 < s.length) {
-          ++i;
-          var c2 = s.substring(i, i + 1);
-          frag += c2;
-          c += c2;
-        }
-      }
-      if (c == '\"') {
-        if (!(i > 0 && s.substring(i - 1, i) == '\\'))
-          quote = quote == 0 ? 1 : 0;
-      } else if (c == '[')
-        ++bracket;
-      else if (c == ']')
-        --bracket;
-      else if (c == '(')
-        ++parentheses;
-      else if (c == ')')
-        --parentheses;
-      else if (c == '{')
-        ++braces;
-      else if (c == '}')
-        --braces;
-    }
-  }
-  ret.push(frag);
-  return ret;
-}
-
-function detachAnnotation(s: string) {
-  var ret = _detachAppendix(s, '\"');
-  if (ret.tag != null)
-    return ret;
-
-  var r = _detachAppendix(s, '\'');
-  return {tag: ret.tag, repeat: r.tag, str: r.str};
-}
-
-function _detachAppendix(s: string, c: string) {
-  var tag = null;
-  //@ts-ignore
-  if (scil.Utils.endswith(s, c)) {
-    var p = s.length - 1;
-    while (p > 0) {
-      p = s.lastIndexOf(c, p - 1);
-      if (p <= 0 || s.substring(p - 1, p) != '\\')
-        break;
-    }
-
-    if (p > 0 && p < s.length - 1) {
-      tag = s.substring(p + 1, s.length - 1);
-      s = s.substring(0, p);
-    }
-  }
-  if (tag != null)
-    tag = tag.replace(new RegExp('\\' + c, 'g'), c);
-  return {tag: unescape(tag), str: s};
-}
-
-function unescape(s: string) {
-  //@ts-ignore
-  if (scil.Utils.isNullOrEmpty(s))
-    return s;
-
-  return s.replace(/[\\]./g, function(m) {
-    switch (m) {
-    case '\\r':
-      return '\r';
-    case '\\n':
-      return '\n';
-    case '\\t':
-      return '\t';
-    default:
-      return m.substring(1);
-    }
-  });
-}
-
-//name: parseHelm
-//input: string s
-export function parseHelm(s: string) {
-  var sections = split(s, '$');
-  s = sections[0];
-  var monomers = [];
-  //@ts-ignore
-  if (!scil.Utils.isNullOrEmpty(s)) {
-    var seqs = split(s, '|');
-    for (var i = 0; i < seqs.length; ++i) {
-      var e = detachAnnotation(seqs[i]);
-      s = e.str;
-
-      var p = s.indexOf('{');
-
-      s = s.substring(p + 1);
-      p = s.indexOf('}');
-      s = s.substring(0, p);
-
-      var ss = split(s, '.');
-      for (var monomer of ss) {
-        if (monomer.includes('(') && monomer.includes(')')) {
-          var elements = monomer.replace(/[()]/g, '').split('');
-          for (var el of elements) {
-            monomers.push(el);
-          }
-        } else if (monomer.includes('[') && monomer.includes(']')) {
-          var element = monomer.match(/(?<=\[).*?(?=\])/g, '');
-          monomers.push(element[0]);
-        } else {
-          monomers.push(monomer);
-        }
-      }
-    }
-  }
-  return monomers;
-}
-
-//name: findMonomers
-//input: string helmString
-export function findMonomers(helmString: string) {
-  //@ts-ignore
-  const types = Object.keys(org.helm.webeditor.monomerTypeList());
-  const monomers: any = [];
-  const monomer_names: any = [];
-  for (var i = 0; i < types.length; i++) {
-    //@ts-ignore
-    monomers.push(new scil.helm.Monomers.getMonomerSet(types[i]));
-    Object.keys(monomers[i]).forEach(k => {
-      monomer_names.push(monomers[i][k].id);
-    });
-  }
-  const split_string = parseHelm(helmString);
-  return new Set(split_string.filter(val => !monomer_names.includes(val)));
-}
-
-
-class MonomerLib implements bio.IMonomerLib {
-  private _monomers: { [type: string]: { [name: string]: bio.Monomer } };
-  private _onChanged = new Subject<any>();
-
-  get(monomerType: string, monomerName: string): bio.Monomer | null {
-    if (monomerType in this._monomers && monomerName in this._monomers[monomerType])
-      return this._monomers[monomerType][monomerName];
-    else
-      return null;
-  }
-
-  get onChanged(): Observable<any> {
-    return this._onChanged;
-  }
-
-  public update(monomers: { [type: string]: { [name: string]: bio.Monomer } }): void {
-    this._monomers = monomers;
-    this._onChanged.next();
-  }
-}
-
-function getAllLibsData(): { [type: string]: { [name: string]: bio.Monomer } } {
-  //@ts-ignore
-  const types = Object.keys(org.helm.webeditor.monomerTypeList());
-  //const monomers: any = [];
-  const monomers: { [type: string]: { [name: string]: bio.Monomer } } = {};
-  for (let i = 0; i < types.length; i++) {
-    monomers[types[i]] = new scil.helm.Monomers.getMonomerSet(types[i]);
-    //@ts-ignore
-    //monomers.push(new scil.helm.Monomers.getMonomerSet(types[i]));
-  }
-
-  return monomers;
-}
-
-//name: getMonomerLibObj
-//description: Get object of IMonomerLib interface (singleton)
-//output: object result
-export function getMonomerLibObj(): bio.IMonomerLib {
-  if (!('monomerLib' in window)) {
-    window['monomerLib'] = new MonomerLib();
-    window['monomerLib'].update(getAllLibsData()); // TODO: refactor
-  }
-
-  return window['monomerLib'];
-}
-
 //name: getMolfiles
 //input: column col {semType: Macromolecule}
 //output: column res 
@@ -517,132 +252,6 @@ export function getMolfiles(col: DG.Column): DG.Column {
   return res;
 }
 
-function getParts(subParts: string[], s: string): string[] {
-  let j = 0;
-  let allParts: string[] = [];
-  for (let k = 0; k < subParts.length; ++k) {
-    let indexOfMonomer = s.indexOf(subParts[k]);
-    let helmBeforeMonomer = s.slice(j, indexOfMonomer);
-    allParts.push(helmBeforeMonomer);
-    allParts.push(subParts[k]);
-    s = s.substring(indexOfMonomer + subParts[k].length);
-  }
-  allParts.push(s);
-  return allParts;
-}
-
-class HelmCellRenderer extends DG.GridCellRenderer {
-  get name() { return 'helm'; }
-
-  get cellType() { return 'helm'; }
-
-  get defaultWidth(): number | null { return 400; }
-
-  get defaultHeight(): number | null { return 100; }
-
-  onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
-    const maxLengthWordsSum = gridCell.cell.column.temp['helm-sum-maxLengthWords'];
-    const maxIndex = Object.values(gridCell.cell.column.temp['helm-maxLengthWords']).length - 1;
-    const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCell.bounds.x);
-    let left = 0;
-    let right = maxIndex;
-    let found = false;
-    maxLengthWordsSum[maxIndex + 1] = argsX + 1;
-    let mid = 0;
-    if (argsX > maxLengthWordsSum[0]) {
-      while (!found) {
-        mid = Math.floor((right + left) / 2);
-        if (argsX >= maxLengthWordsSum[mid] && argsX <= maxLengthWordsSum[mid + 1]) {
-          left = mid;
-          found = true;
-        } else if (argsX < maxLengthWordsSum[mid]) {
-          right = mid - 1;
-        } else if (argsX > maxLengthWordsSum[mid + 1]) {
-          left = mid + 1;
-        }
-        if (left == right) {
-          found = true;
-        }
-      }
-    }
-    left = (argsX >= maxLengthWordsSum[left]) ? left + 1 : left;
-    const monomers = findMonomers(gridCell.cell.value);
-    let s: string = gridCell.cell.value ?? '';
-    let subParts: string[] = parseHelm(s);
-    let allParts: string[] = getParts(subParts, s);
-    let tooltipMessage: HTMLElement[] = [];
-    for (let i = 0; i < allParts.length; ++i) {
-      if (monomers.has(allParts[i]))
-        tooltipMessage[i] = ui.divV([
-          ui.divText(`Monomer ${allParts[i]} not found.`),
-          ui.divText('Open the Property Panel, then expand Manage Libraries')
-        ]);
-    }
-    (((tooltipMessage[left]?.childNodes.length ?? 0) > 0))
-      ? ui.tooltip.show(ui.div(tooltipMessage[left]), e.x + 16, e.y + 16)
-      : ui.tooltip.hide();
-  }
-
-  render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number,
-    gridCell: DG.GridCell, cellStyle: DG.GridCellStyle
-  ) {
-    const grid = gridCell.gridRow !== -1 ? gridCell.grid : undefined;
-    const undefinedColor = 'rgb(100,100,100)';
-    const grayColor = '#808080';
-    const monomers = findMonomers(gridCell.cell.value);
-    let s: string = gridCell.cell.value ?? '';
-    let subParts: string[] = parseHelm(s);
-    if (monomers.size == 0) {
-      const host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
-      host.setAttribute('dataformat', 'helm');
-      host.setAttribute('data', gridCell.cell.value);
-      gridCell.element = host;
-      //@ts-ignore
-      const canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
-      return;
-    }
-    if (monomers.size > 0) {
-      w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
-      g.save();
-      g.beginPath();
-      g.rect(x, y, w, h);
-      g.clip();
-      g.font = '12px monospace';
-      g.textBaseline = 'top';
-      let x1 = x;
-      let maxLengthWords: any = {};
-      let maxLengthWordSum: any = {};
-      let allParts: string[] = getParts(subParts, s);
-      for (let i = 0; i < allParts.length; ++i) {
-        maxLengthWords[i] = allParts[i].length * 7;
-        let color = monomers.has(allParts[i]) ? 'red' : grayColor;
-        g.fillStyle = undefinedColor;
-        x1 = bio.printLeftOrCentered(x1, y, w, h, g, allParts[i], color, 0, true, 1.0);
-      }
-
-      maxLengthWordSum[0] = maxLengthWords[0];
-      for (let i = 1; i < allParts.length; i++) {
-        maxLengthWordSum[i] = maxLengthWordSum[i - 1] + maxLengthWords[i];
-      }
-      gridCell.cell.column.temp = {
-        'helm-sum-maxLengthWords': maxLengthWordSum,
-        'helm-maxLengthWords': maxLengthWords
-      };
-      g.restore();
-      return;
-    }
-  }
-}
-
-//name: getMonomerLib
-//input: string type
-//output: string monomerSetJSON
-export function getMonomerLib(type: string): string {
-  // TODO: deprecate
-  return JSON.stringify(scil.helm.Monomers.getMonomerSet(type));
-}
-
-
 //name: helmWebEditor
 //output: object
 export function helmWebEditor(): HelmWebEditor {

package/src/tests/helm-tests.ts

@@ -1,7 +1,7 @@
 import {after, before, category, delay, expect, test} from '@datagrok-libraries/utils/src/test';
 //import {findMonomers, helmToFasta, helmToPeptide, helmToRNA, initHelm} from '../package';
 import {_package} from '../package-test';
-import {manageFiles, parseHelm} from '../package';
+import {parseHelm} from '../utils';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
@@ -46,31 +46,6 @@ category('Helm', () => {
   //   expect(col.tags[DG.TAGS.UNITS], 'HELM');
   // });
 
-  test('manageFiles', async () => {
-    return await manageFiles();
-  });
-
-  
-  test('monomerManager', async() => {
-    const df: DG.DataFrame = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/test.csv'));
-    grok.shell.addTableView(df);
-    await grok.functions.call('Helm:monomerManager', {value: 'HELMCoreLibrary.json'});
-    const checkName = '2-Chloroadenine';
-    let flag = false;
-    const types = Object.keys(org.helm.webeditor.monomerTypeList());
-    const monomers: any = [];
-    for (var i = 0; i < types.length; i++) {
-      //@ts-ignore
-      monomers.push(new scil.helm.Monomers.getMonomerSet(types[i]));
-      Object.keys(monomers[i]).forEach(k => {
-        if (monomers[i][k].n == checkName){
-          flag = true;
-        }
-      });
-    }
-    expect(flag, true);
-  });
-
   test('parseHelm', async() => {
     const expectedResults = [
       ['meI', 'hHis', 'Aca', 'N', 'T', 'dK', 'Thr_PO3H2', 'D-Tyr_Et', 'Aze', 'dV', 'E', 'Phe_4Me'],
@@ -90,5 +65,4 @@ category('Helm', () => {
       expect(JSON.stringify(monomerArray), JSON.stringify(expectedResults[idx]));
     }
   });
-
 });