@datagrok/helm 2.2.0 → 2.3.0

package/src/tests/get-monomer-tests.ts

@@ -0,0 +1,279 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import wu from 'wu';
+
+import {
+  after, before, category, delay, expect, test, expectArray, testEvent, expectFloat, timeout
+} from '@datagrok-libraries/utils/src/test';
+import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
+import {Atom, HelmType, IJsAtom, IWebEditorMonomer, GetMonomerFunc} from '@datagrok-libraries/bio/src/helm/types';
+import {IMonomerLib, Monomer, MonomerLibSummaryType} from '@datagrok-libraries/bio/src/types';
+import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
+import {
+  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {defaultMonomerLibSummary, expectMonomerLib} from '@datagrok-libraries/bio/src/tests/monomer-lib-tests';
+
+import {getMonomerHandleArgs} from '../utils/get-monomer';
+import {JSDraw2HelmModule, OrgHelmModule} from '../types';
+
+import {HelmHelper} from '../helm-helper';
+import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from '../constants';
+import {getRS} from '../utils/get-monomer-dummy';
+import {initHelmMainPackage} from './utils';
+
+import {_package} from '../package-test';
+
+declare const org: OrgHelmModule;
+declare const JSDraw2: JSDraw2HelmModule;
+
+type TestDataType = { args: { a: any, name?: string }, tgt: any };
+
+const tests: { [testName: string]: TestDataType } = {
+  /* eslint-disable */
+  //@formatter:off
+  t0:{"args":{"a":"HELM_BASE","name":"A"},"tgt":{"id":"A","m":"HELM Core Monomer library\n  Ketcher 10131612512D 1   1.00000     0.00000     0\n\n 11 12  0     0  0            999 V2000\n    0.9632   -3.5449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0970   -4.0450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0970   -5.0451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.9630   -5.5451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8291   -5.0452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8293   -4.0451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8536   -5.3539    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4413   -4.5449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8535   -3.7357    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    0.9632   -2.5448    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1626   -6.3051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1 10  1  0     0  0\n  1  6  2  0     0  0\n  1  2  1  0     0  0\n  9  2  1  0     0  0\n  2  3  2  0     0  0\n  7  3  1  0     0  0\n  3  4  1  0     0  0\n  4  5  2  0     0  0\n  5  6  1  0     0  0\n  7  8  1  0     0  0\n  7 11  1  0     0  0\n  8  9  2  0     0  0\nA   11\nR1\nM  END\n","n":"Adenine","na":"A","rs":1,"at":{"R1":"H"}}},
+  t1:{"args":{"a":"HELM_BASE","name":"C"},"tgt":{"id":"C","m":"HELM Core Monomer library\nHELMMonomers071816.sdf \n\n  9  9  0  0  0  0  0  0  0  0999 V2000\n   10.7683  -10.8385    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   10.7683  -12.3385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    9.4733  -13.0885    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    8.1683  -12.3385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.1683  -10.8385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    9.4733  -10.0885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    9.4733   -8.5885    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    9.4733  -14.5885    0.0000 R1  0  0  0  0  0  0  0  0  0  0  0  0\n   12.0673  -13.0885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0        0\n  2  3  1  0        0\n  3  4  1  0        0\n  4  5  2  0        0\n  5  6  1  0        0\n  1  6  2  0        0\n  6  7  1  0        0\n  3  8  1  0        0\n  2  9  2  0        0\nA    8\nR1\nM  END\n","n":"Cytosine","na":"C","rs":1,"at":{"R1":"H"}}},
+  t2:{"args":{"a":"HELM_BASE","name":"G"},"tgt":{"id":"G","m":"HELM Core Monomer library\nHELMMonomers071816.sdf \n\n 12 13  0  0  0  0  0  0  0  0999 V2000\n   12.7698  -10.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   12.7698  -11.7854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   11.4733  -12.5380    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   10.1698  -11.7854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   10.1698  -10.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   11.4748   -9.5354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    7.8623  -11.0354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.7448   -9.8154    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   11.4748   -8.0354    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   14.0689  -12.5354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    8.7448  -12.2479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    8.2789  -13.6737    0.0000 R1  0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0        0\n  2  3  2  0        0\n  3  4  1  0        0\n  4  5  2  0        0\n  5  6  1  0        0\n  1  6  1  0        0\n  7  8  2  0        0\n  5  8  1  0        0\n  6  9  2  0        0\n  2 10  1  0        0\n  4 11  1  0        0\n  7 11  1  0        0\n 11 12  1  0        0\nA   12\nR1\nM  END\n","n":"Guanine","na":"G","rs":1,"at":{"R1":"H"}}},
+  t3:{"args":{"a":"HELM_LINKER","name":"p"},"tgt":{"id":"p","m":"HELM Core Monomer library\n  Ketcher 10061618102D 1   1.00000     0.00000     0\n\n  5  4  0     0  0            999 V2000\n   15.7527  -12.0837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   15.7527  -13.0837    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n   16.6188  -13.5837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   15.2527  -13.9496    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   14.7868  -12.8248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0     0  0\n  2  3  1  0     0  0\n  2  4  2  0     0  0\n  2  5  1  0     0  0\nA    1\nR1\nA    3\nR2\nM  END\n","n":"Phosphate","na":"p","rs":2,"at":{"R1":"OH","R2":"OH"}}},
+  t4:{"args":{"a":"HELM_SUGAR","name":"p"},"tgt":null},
+  t5:{"args":{"a":"HELM_SUGAR","name":"r"},"tgt":{"id":"r","m":"HELM Core Monomer library\n  Ketcher 10111608242D 1   1.00000     0.00000     0\n\n 12 12  0     0  0            999 V2000\n  -31.2431   12.8416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -30.9523   11.8849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.9523   11.8659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.6254   12.8108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -30.4231   13.4140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -32.1882   13.1686    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -31.5552   11.0872    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -31.5220   10.0877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.3803   11.0458    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -28.6686   13.1017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -32.3775   14.1506    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -33.2435   14.6506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0     0  0\n  2  3  1  0     0  0\n  3  4  1  0     0  0\n  4  5  1  0     0  0\n  5  1  1  0     0  0\n  1  6  1  1     0  0\n  2  7  1  6     0  0\n  7  8  1  0     0  0\n  3  9  1  6     0  0\n  4 10  1  1     0  0\n  6 11  1  0     0  0\n 11 12  1  0     0  0\nA    8\nR2\nA   10\nR3\nA   12\nR1\nM  END\n","n":"Ribose","na":"r","rs":3,"at":{"R1":"H","R2":"H","R3":"OH"}}},
+  t6:{"args":{"a":{"T":"ATOM","p":{"x":144,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_SUGAR","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"r","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"_parent":"[object Object]","_aaid":4}},"tgt":{"id":"r","m":"HELM Core Monomer library\n  Ketcher 10111608242D 1   1.00000     0.00000     0\n\n 12 12  0     0  0            999 V2000\n  -31.2431   12.8416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -30.9523   11.8849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.9523   11.8659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.6254   12.8108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -30.4231   13.4140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -32.1882   13.1686    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -31.5552   11.0872    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -31.5220   10.0877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.3803   11.0458    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -28.6686   13.1017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -32.3775   14.1506    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -33.2435   14.6506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0     0  0\n  2  3  1  0     0  0\n  3  4  1  0     0  0\n  4  5  1  0     0  0\n  5  1  1  0     0  0\n  1  6  1  1     0  0\n  2  7  1  6     0  0\n  7  8  1  0     0  0\n  3  9  1  6     0  0\n  4 10  1  1     0  0\n  6 11  1  0     0  0\n 11 12  1  0     0  0\nA    8\nR2\nA   10\nR3\nA   12\nR1\nM  END\n","n":"Ribose","na":"r","rs":3,"at":{"R1":"H","R2":"H","R3":"OH"}}},
+  t7:{"args":{"a":{"T":"ATOM","p":{"x":144,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_SUGAR","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"r","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":4}},"tgt":{"id":"r","m":"HELM Core Monomer library\n  Ketcher 10111608242D 1   1.00000     0.00000     0\n\n 12 12  0     0  0            999 V2000\n  -31.2431   12.8416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -30.9523   11.8849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.9523   11.8659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.6254   12.8108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -30.4231   13.4140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -32.1882   13.1686    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -31.5552   11.0872    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -31.5220   10.0877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.3803   11.0458    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -28.6686   13.1017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -32.3775   14.1506    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -33.2435   14.6506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0     0  0\n  2  3  1  0     0  0\n  3  4  1  0     0  0\n  4  5  1  0     0  0\n  5  1  1  0     0  0\n  1  6  1  1     0  0\n  2  7  1  6     0  0\n  7  8  1  0     0  0\n  3  9  1  6     0  0\n  4 10  1  1     0  0\n  6 11  1  0     0  0\n 11 12  1  0     0  0\nA    8\nR2\nA   10\nR3\nA   12\nR1\nM  END\n","n":"Ribose","na":"r","rs":3,"at":{"R1":"H","R2":"H","R3":"OH"}}},
+  t8:{"args":{"a":{"T":"ATOM","p":{"x":144,"y":48},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_BASE","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"G","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":5}},"tgt":{"id":"G","m":"HELM Core Monomer library\nHELMMonomers071816.sdf \n\n 12 13  0  0  0  0  0  0  0  0999 V2000\n   12.7698  -10.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   12.7698  -11.7854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   11.4733  -12.5380    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   10.1698  -11.7854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   10.1698  -10.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   11.4748   -9.5354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    7.8623  -11.0354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.7448   -9.8154    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   11.4748   -8.0354    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   14.0689  -12.5354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    8.7448  -12.2479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    8.2789  -13.6737    0.0000 R1  0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0        0\n  2  3  2  0        0\n  3  4  1  0        0\n  4  5  2  0        0\n  5  6  1  0        0\n  1  6  1  0        0\n  7  8  2  0        0\n  5  8  1  0        0\n  6  9  2  0        0\n  2 10  1  0        0\n  4 11  1  0        0\n  7 11  1  0        0\n 11 12  1  0        0\nA   12\nR1\nM  END\n","n":"Guanine","na":"G","rs":1,"at":{"R1":"H"}}},
+  t9:{"args":{"a":{"T":"ATOM","p":{"x":192,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_LINKER","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"p","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"_parent":"[object Object]","_aaid":6}},"tgt":{"id":"p","m":"HELM Core Monomer library\n  Ketcher 10061618102D 1   1.00000     0.00000     0\n\n  5  4  0     0  0            999 V2000\n   15.7527  -12.0837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   15.7527  -13.0837    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n   16.6188  -13.5837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   15.2527  -13.9496    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   14.7868  -12.8248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0     0  0\n  2  3  1  0     0  0\n  2  4  2  0     0  0\n  2  5  1  0     0  0\nA    1\nR1\nA    3\nR2\nM  END\n","n":"Phosphate","na":"p","rs":2,"at":{"R1":"OH","R2":"OH"}}},
+  t10:{"args":{"a":{"T":"ATOM","p":{"x":192,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_LINKER","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"p","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":6}},"tgt":{"id":"p","m":"HELM Core Monomer library\n  Ketcher 10061618102D 1   1.00000     0.00000     0\n\n  5  4  0     0  0            999 V2000\n   15.7527  -12.0837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   15.7527  -13.0837    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n   16.6188  -13.5837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   15.2527  -13.9496    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   14.7868  -12.8248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0     0  0\n  2  3  1  0     0  0\n  2  4  2  0     0  0\n  2  5  1  0     0  0\nA    1\nR1\nA    3\nR2\nM  END\n","n":"Phosphate","na":"p","rs":2,"at":{"R1":"OH","R2":"OH"}}},
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+  t25:{"args":{"a":{"T":"ATOM","p":{"x":48,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_SUGAR","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"r","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":1}},"tgt":{"id":"r","m":"HELM Core Monomer library\n  Ketcher 10111608242D 1   1.00000     0.00000     0\n\n 12 12  0     0  0            999 V2000\n  -31.2431   12.8416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -30.9523   11.8849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.9523   11.8659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.6254   12.8108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -30.4231   13.4140    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -32.1882   13.1686    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -31.5552   11.0872    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -31.5220   10.0877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -29.3803   11.0458    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -28.6686   13.1017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  -32.3775   14.1506    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  -33.2435   14.6506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0     0  0\n  2  3  1  0     0  0\n  3  4  1  0     0  0\n  4  5  1  0     0  0\n  5  1  1  0     0  0\n  1  6  1  1     0  0\n  2  7  1  6     0  0\n  7  8  1  0     0  0\n  3  9  1  6     0  0\n  4 10  1  1     0  0\n  6 11  1  0     0  0\n 11 12  1  0     0  0\nA    8\nR2\nA   10\nR3\nA   12\nR1\nM  END\n","n":"Ribose","na":"r","rs":3,"at":{"R1":"H","R2":"H","R3":"OH"}}},
+  t26:{"args":{"a":{"T":"ATOM","p":{"x":48,"y":48},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_BASE","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"A","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":2}},"tgt":{"id":"A","m":"HELM Core Monomer library\n  Ketcher 10131612512D 1   1.00000     0.00000     0\n\n 11 12  0     0  0            999 V2000\n    0.9632   -3.5449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0970   -4.0450    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0970   -5.0451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.9630   -5.5451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8291   -5.0452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.8293   -4.0451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8536   -5.3539    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4413   -4.5449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8535   -3.7357    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    0.9632   -2.5448    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1626   -6.3051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1 10  1  0     0  0\n  1  6  2  0     0  0\n  1  2  1  0     0  0\n  9  2  1  0     0  0\n  2  3  2  0     0  0\n  7  3  1  0     0  0\n  3  4  1  0     0  0\n  4  5  2  0     0  0\n  5  6  1  0     0  0\n  7  8  1  0     0  0\n  7 11  1  0     0  0\n  8  9  2  0     0  0\nA   11\nR1\nM  END\n","n":"Adenine","na":"A","rs":1,"at":{"R1":"H"}}},
+  t27:{"args":{"a":{"T":"ATOM","p":{"x":96,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_LINKER","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"p","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"_parent":"[object Object]","_aaid":3}},"tgt":{"id":"p","m":"HELM Core Monomer library\n  Ketcher 10061618102D 1   1.00000     0.00000     0\n\n  5  4  0     0  0            999 V2000\n   15.7527  -12.0837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   15.7527  -13.0837    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n   16.6188  -13.5837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   15.2527  -13.9496    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   14.7868  -12.8248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0     0  0\n  2  3  1  0     0  0\n  2  4  2  0     0  0\n  2  5  1  0     0  0\nA    1\nR1\nA    3\nR2\nM  END\n","n":"Phosphate","na":"p","rs":2,"at":{"R1":"OH","R2":"OH"}}},
+  t28:{"args":{"a":{"T":"ATOM","p":{"x":96,"y":0},"charge":0,"isotope":null,"radical":null,"group":null,"alias":null,"superatom":null,"attachpoints":[],"rgroup":null,"bio":{"type":"HELM_LINKER","id":null,"ambiguity":null},"locked":false,"hidden":null,"_rect":null,"elem":"p","color":null,"hcount":null,"selected":false,"f":null,"bonds":null,"id":null,"atommapid":null,"query":null,"hasError":null,"hs":null,"val":null,"tag":null,"_parent":"[object Object]","_aaid":3}},"tgt":{"id":"p","m":"HELM Core Monomer library\n  Ketcher 10061618102D 1   1.00000     0.00000     0\n\n  5  4  0     0  0            999 V2000\n   15.7527  -12.0837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   15.7527  -13.0837    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n   16.6188  -13.5837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   15.2527  -13.9496    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   14.7868  -12.8248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0     0  0\n  2  3  1  0     0  0\n  2  4  2  0     0  0\n  2  5  1  0     0  0\nA    1\nR1\nA    3\nR2\nM  END\n","n":"Phosphate","na":"p","rs":2,"at":{"R1":"OH","R2":"OH"}}},
+  //@formatter:off
+  /* eslint-enable */
+};
+
+category('getMonomer', ()=>{
+  let libHelper: IMonomerLibHelper;
+  let helmHelper: IHelmHelper;
+
+  let monomerLibHelper: IMonomerLibHelper;
+  /** Backup actual user's monomer libraries settings */
+  let userLibSettings: UserLibSettings;
+
+  before(async ()=>{
+    await initHelmMainPackage();
+
+    [libHelper, helmHelper] = await Promise.all([getMonomerLibHelper(), getHelmHelper()]);
+
+    await timeout(async () => { monomerLibHelper = await getMonomerLibHelper(); }, 5000,
+      'get monomerLibHelper');
+    await timeout(async () => { userLibSettings = await getUserLibSettings(); }, 5000,
+      'get user lib settings for backup');
+
+    // Tests 'findMonomers' requires default monomer library loaded
+    await timeout(async () => { await setUserLibSettingsForTests(); }, 5000,
+      'set user lib settings for tests');
+    await timeout(async ()=> { await monomerLibHelper.awaitLoaded(); }, 5000,
+      'await monomerLib to be loaded');
+    await timeout(async () => { await monomerLibHelper.loadLibraries(true); }, 5000,
+      'reload monomerLib with settings for tests'); // load default libraries for tests
+  });
+
+  after(async ()=>{
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadLibraries(true);
+  });
+
+  test('original', async () =>{
+    const monomerLib = libHelper.getBioLib();
+    rewriteLibraries(monomerLib);
+
+    // const overriddenGetMonomer = helmHelper.revertOriginalGetMonomer();
+    // try {
+    const helmHelper: IHelmHelper = await getHelmHelper();
+    expect(helmHelper != null, true);
+    // @ts-ignore
+    const getMonomerFunc = helmHelper.originalGetMonomer!;
+
+    return _testAll('original', getMonomerFunc);
+    // } finally {
+    //   helmHelper.overrideGetMonomer(overriddenGetMonomer);
+    // }
+  }, {isAggregated: true});
+
+  test('monomerLib', async () =>{
+    const monomerLib = monomerLibHelper.getBioLib();
+    expectMonomerLib(monomerLib);
+
+    const getMonomerFunc = org.helm.webeditor.Monomers.getMonomer;
+    return _testAll('monomerLib', getMonomerFunc);
+  }, {isAggregated: true});
+
+  function _testAll(prefix: string, getMonomerFunc: GetMonomerFunc): DG.DataFrame {
+    const resDf = DG.DataFrame.fromColumns([
+      DG.Column.fromStrings('subTest', []),
+      DG.Column.fromList(DG.COLUMN_TYPE.BOOL, 'success', []),
+      DG.Column.fromStrings('res', []),
+      DG.Column.fromStrings('tgt', []),
+      DG.Column.fromStrings('error', []),
+      DG.Column.fromStrings('stack', []),
+    ]);
+
+    // const testCount: number = Object.keys(tests).length + 1;
+    // //* eslint-disable no-array-constructor */
+    // const subTestList: string[] = new Array<string>(testCount);
+    // const successList: boolean[] = new Array<boolean>(testCount);
+    // const resList: string[] = new Array<string>(testCount);
+    // const tgtList:string[] = new Array<string>(testCount);
+    // const errorList: string[] = new Array<string>(testCount);
+    // const stackList: string[] = new Array<string>(testCount);
+    // /* eslint-enable no-array-constructor */
+
+    const resI = resDf.rows.addNew().idx;
+    resDf.set('subTest', resI, 'Monomer lib');
+    resDf.set('res', resI, '');
+    resDf.set('tgt', resI, '');
+    try {
+      const monomerLib = monomerLibHelper.getBioLib();
+      expectMonomerLib(monomerLib);
+      resDf.set('success', resI, true);
+    } catch (err) {
+      const [errMsg, errStack] = errInfo(err);
+      resDf.set('error', resI, errMsg);
+      resDf.set('stack', resI, errStack);
+      resDf.set('success', resI, false);
+    }
+
+    for (const [[testName, testData], testI] of wu.enumerate(Object.entries(tests))) {
+      const a: Atom<HelmType> | HelmType = getAtomFromJson(testData.args.a);
+      const [biotype, elem] = getMonomerHandleArgs(a, testData.args.name);
+      const tgt = testData.tgt;
+
+      const resI = resDf.rows.addNew().idx;
+      resDf.set('subTest', resI, `${prefix}-${testName}-${biotype}-${elem}`);
+      resDf.set('tgt', resI, JSON.stringify(tgt ? {id: tgt.id, n: tgt.n, rs: tgt.rs} : null));
+      try {
+        const res: any = getMonomerFunc(a, testData.args.name);
+        resDf.set('res', resI, JSON.stringify(res ? {id: res.id, n: res.n, rs: res.rs} : null));
+        expectObjectWithNull(res, tgt);
+        resDf.set('success', resI, true);
+      } catch (err) {
+        const [errMsg, errStack] = errInfo(err);
+        resDf.set('error', resI, errMsg);
+        resDf.set('stack', resI, errStack);
+        resDf.set('success', resI, false);
+      }
+    }
+    return resDf;
+  }
+
+  test('missing', async ()=> {
+    /* Tests getMonomer function adding missing monomers. */
+    const helmStr = 'PEPTIDE1{[mis1].R.[mis2].T.C.F}$$$$;';
+
+    expectMonomerLib(monomerLibHelper.getBioLib());
+    const editor = new JSDraw2.Editor(ui.div(), {viewonly: true});
+    editor.setHelm(helmStr);
+    const withMissing = JSON.parse(JSON.stringify(
+      defaultMonomerLibSummary)) as MonomerLibSummaryType;
+    withMissing['PEPTIDE'] += 2;
+    expectMonomerLib(monomerLibHelper.getBioLib(), withMissing);
+  });
+});
+
+function getAtomFromJson(argA: IJsAtom<HelmType> | HelmType): Atom<HelmType> | HelmType {
+  let res: Atom<HelmType> | HelmType;
+  const a = argA as IJsAtom<HelmType>;
+  if (a.T === 'ATOM')
+    res = new JSDraw2.Atom(a.p, a.elem, a.bio);
+  else
+    res = argA as HelmType;
+  return res;
+}
+
+export function expectObjectWithNull(actual: { [key: string]: any }, expected: { [key: string]: any }) {
+  if (actual == null && expected == null)
+    return;
+  else if (actual == null && expected != null)
+    throw new Error('actual is null, but expected is not null');
+  else if (actual!= null && expected == null)
+    throw new Error('actual is not null, but expected is null');
+  else {
+    for (const [expectedKey, expectedValue] of Object.entries(expected)) {
+      if (!(expectedKey in actual || actual.hasOwnProperty(expectedKey)))
+        throw new Error(`Expected property "${expectedKey}" not found`);
+
+      const actualValue = actual[expectedKey];
+      if (actualValue instanceof Array && expectedValue instanceof Array)
+        expectArray(actualValue, expectedValue);
+      else if (actualValue instanceof Object && expectedValue instanceof Object)
+        expectObjectWithNull(actualValue, expectedValue);
+      else if (Number.isFinite(actualValue) && Number.isFinite(expectedValue))
+        expectFloat(actualValue, expectedValue);
+      else if (actualValue != expectedValue)
+        throw new Error(`Expected (${expectedValue}) for key '${expectedKey}', got (${actualValue})`);
+    }
+  }
+}
+
+/** Fills org.helm.webeditor.Monomers dictionary for WebEditor */
+function rewriteLibraries(monomerLib: IMonomerLib): void {
+  org.helm.webeditor.Monomers.clear();
+  monomerLib!.getPolymerTypes().forEach((polymerType) => {
+    const monomerSymbols = monomerLib!.getMonomerSymbolsByType(polymerType);
+    monomerSymbols.forEach((monomerSymbol) => {
+      let isBroken = false;
+      const monomer: Monomer = monomerLib!.getMonomer(polymerType, monomerSymbol)!;
+      const webEditorMonomer: IWebEditorMonomer = {
+        id: monomerSymbol,
+        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) {
+        // @ts-ignore
+        webEditorMonomer.rs = monomer.rgroups.length;
+        const at: { [prop: string]: any } = {};
+        monomer.rgroups.forEach((it) => {
+          at[it[RGROUP_LABEL]] = it[RGROUP_CAP_GROUP_NAME];
+        });
+        webEditorMonomer.at = at;
+      } else if (monomer[SMILES] != null) {
+        // @ts-ignore
+        webEditorMonomer.rs = Object.keys(getRS(monomer[SMILES].toString())).length;
+        webEditorMonomer.at = getRS(monomer[SMILES].toString());
+      } else
+        isBroken = true;
+
+      if (!isBroken)
+        org.helm.webeditor.Monomers.addOneMonomer(webEditorMonomer);
+    });
+  });
+
+  // Obsolete
+  const grid: DG.Grid = grok.shell.tv?.grid;
+  if (grid) grid.invalidate();
+}

package/src/tests/helm-service-tests.ts

@@ -7,6 +7,7 @@ import {Subject} from 'rxjs';
 import {
   category, expect, test, awaitCheck, delay, testEvent, before, after
 } from '@datagrok-libraries/utils/src/test';
+import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {
   getHelmService, HelmServiceBase, HelmAux, HelmProps
 } from '@datagrok-libraries/bio/src/viewers/helm-service';
@@ -18,6 +19,8 @@ import {
   getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
+import {initHelmMainPackage} from './utils';
+
 import {_package} from '../package-test';
 
 category('HelmService', () => {
@@ -30,6 +33,7 @@ category('HelmService', () => {
   before(async () => {
     const logPrefix = `Helm: tests: HelmService: before`;
     _package.logger.debug(`${logPrefix}, start`);
+    await initHelmMainPackage();
     try {
       monomerLibHelper = await getMonomerLibHelper();
       userLibSettings = await getUserLibSettings();

package/src/tests/helm-tests.ts

@@ -3,8 +3,10 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+
 //import {findMonomers, helmToFasta, helmToPeptide, helmToRNA, initHelm} from '../package';
 import {parseHelm} from '../utils';
+import {initHelmMainPackage} from './utils';
 
 import {_package} from '../package-test';
 
@@ -51,7 +53,7 @@ category('Helm', () => {
   // });
 
   const complexMonomers = [
-    // tests parsing of complex monomemer in square brackets like [L-hArg(Et,Et)]
+    // tests parsing of complex monomer in square brackets like [L-hArg(Et,Et)]
     'PEPTIDE1{[L-hArg(Et,Et)].E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0',
     // tests parsing of complex monomer and one as a side chain as well
     'PEPTIDE1{[L-hArg(Et,Et)]([L-hArg(Et,Et)]).E.F.G}$$$$',
@@ -75,6 +77,11 @@ category('Helm', () => {
     'comples-monomer', 'complex-monomer+side-chain', 'complex-monomer+side-chain-RNA',
     'complex-side-chain', 'complex+side-chain+linker'
   ];
+
+  before(async () => {
+    await initHelmMainPackage();
+  });
+
   test('parseHelm', async () => {
     const expectedResults = [
       ['meI', 'hHis', 'Aca', 'N', 'T', 'dK', 'Thr_PO3H2', 'D-Tyr_Et', 'Aze', 'dV', 'E', 'Phe_4Me'],

package/src/tests/helm-web-editor-tests.ts

@@ -0,0 +1,55 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
+import {
+  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+
+import {initHelmMainPackage} from './utils';
+
+category('helm-web-editor', async () => {
+  let monomerLibHelper: IMonomerLibHelper;
+  let userLibSettings: UserLibSettings;
+
+  let hh: IHelmHelper;
+
+  before(async () => {
+    await initHelmMainPackage();
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = await getUserLibSettings();
+    await setUserLibSettingsForTests();
+    await monomerLibHelper.awaitLoaded();
+    await monomerLibHelper.loadLibraries(true);
+
+    hh = await getHelmHelper();
+  });
+
+  after(async () => {
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadLibraries(true);
+  });
+
+  test('helm-web-editor', async () => {
+    const editor = hh.createHelmWebEditor();
+  });
+
+  test('web-editor-app', async () => {
+    const helmStr: string = 'PEPTIDE1{I.H.A.N.T.Thr_PO3H2.Aca.D-Tyr_Et}$$$$';
+
+    const appHost = ui.div([],
+      {style: {width: '700px', height: '432px'}});
+    const app = hh.createWebEditorApp(appHost, helmStr);
+
+    const dlg = ui.dialog().add(appHost).show();
+    try {
+
+    } finally {
+      dlg.close();
+    }
+  });
+});

package/src/tests/parse-helm-tests.ts

@@ -0,0 +1,98 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+
+import {after, before, category, delay, expect, test, expectArray, timeout} from '@datagrok-libraries/utils/src/test';
+import {HelmType, Mol, OrgType} from '@datagrok-libraries/bio/src/helm/types';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
+import {
+  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+
+import {JSDraw2HelmModule} from '../types';
+import {initHelmMainPackage} from './utils';
+
+declare const org: OrgType;
+declare const JSDraw2: JSDraw2HelmModule;
+
+type TestTgtType = { atomCount: number, bondCount: number };
+
+category('parseHelm', () => {
+  const testData: { [testName: string]: { src: string, tgt: TestTgtType } } = {
+    'PT': {
+      src: 'PEPTIDE1{[L-hArg(Et,Et)].E.F.G}|PEPTIDE2{C.E}$PEPTIDE1,PEPTIDE2,2:R3-1:R1$$$V2.0',
+      tgt: {atomCount: 6, bondCount: 5}
+    },
+    'RNA': {
+      src: 'RNA1{[dhp]([m1A])p.r(T)p.r(T)p.r(G)p}$$$$V2.0',
+      tgt: {atomCount: 12, bondCount: 11}
+    }
+  };
+
+  let libHelper: IMonomerLibHelper;
+  /** Backup actual user's monomer libraries settings */
+  let userLibSettings: UserLibSettings;
+
+  before(async () => {
+    await initHelmMainPackage();
+
+    libHelper = await getMonomerLibHelper();
+
+    await timeout(async () => { userLibSettings = await getUserLibSettings(); }, 5000,
+      'get user lib settings for backup');
+
+    // parseHelm is dependent on monomers RGroups available, test requires default monomer library
+    await setUserLibSettingsForTests();
+    await timeout(async () => { await libHelper.awaitLoaded(); }, 5000,
+      'await monomerLib to be loaded');
+    await libHelper.loadLibraries(true);
+  });
+
+  after(async () => {
+    await setUserLibSettings(userLibSettings);
+    await libHelper.loadLibraries(true);
+  });
+
+  for (const [testName, {src, tgt}] of Object.entries(testData)) {
+    test(`Editor-${testName}`, async () => {
+      _testParseHelmWithEditor(src, tgt);
+    });
+  }
+
+  for (const [testName, {src, tgt}] of Object.entries(testData)) {
+    test(`woDOM-${testName}`, async () => {
+      _testParseHelmWithoutDOM(src, tgt);
+    });
+  }
+});
+
+function _testParseHelmWithEditor(src: string, tgt: TestTgtType): void {
+  const io = org.helm.webeditor.IO;
+
+  const editorHost = ui.div();
+  const editor = new JSDraw2.Editor(editorHost, {viewonly: true});
+
+  const plugin = new org.helm.webeditor.Plugin(editor);
+  const origin = new JSDraw2.Point(0, 0);
+  io.parseHelm(plugin, src, origin, null);
+
+  const m: Mol<HelmType> = plugin.jsd.m;
+  expect(m.atoms.length, tgt.atomCount);
+  expect(m.bonds.length, tgt.bondCount);
+}
+
+function _testParseHelmWithoutDOM(src: string, tgt: TestTgtType): void {
+  const io = org.helm.webeditor.IO;
+
+  const molHandler = new JSDraw2.MolHandler();
+
+  const plugin = new org.helm.webeditor.Plugin(molHandler);
+  const origin = new JSDraw2.Point(0, 0);
+  io.parseHelm(plugin, src, origin, null);
+
+  const m: Mol<HelmType> = plugin.jsd.m;
+  expect(m.atoms.length, tgt.atomCount);
+  expect(m.bonds.length, tgt.bondCount);
+}