@datagrok/helm 2.1.34 → 2.2.1

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

@@ -0,0 +1,210 @@
+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 * as org from 'org';
+import * as JSDraw2 from 'JSDraw2';
+import Atom = JSDraw2.Atom;
+import JsAtom = JSDraw2.JsAtom;
+
+import {
+  after, before, category, delay, expect, test, expectArray, testEvent, expectFloat
+} from '@datagrok-libraries/utils/src/test';
+import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
+import {HelmType, MonomerLibSummaryType} from '@datagrok-libraries/bio/src/types';
+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 {defaultMonomerLibSummary, expectMonomerLib} from '@datagrok-libraries/bio/src/tests/monomer-lib-tests';
+
+import {GetMonomerFunc, getMonomerHandleArgs} from '../utils/get-monomer';
+
+import {_package} from '../package-test';
+
+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 monomerLibHelper: IMonomerLibHelper;
+  /** Backup actual user's monomer libraries settings */
+  let userLibSettings: UserLibSettings;
+
+  before(async ()=>{
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = await getUserLibSettings();
+
+    // Tests 'findMonomers' requires default monomer library loaded
+    await setUserLibSettingsForTests();
+    await monomerLibHelper.awaitLoaded();
+    await monomerLibHelper.loadLibraries(true); // load default libraries for tests
+  });
+
+  after(async ()=>{
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadLibraries(true);
+  });
+
+  test('original', async () =>{
+    const helmHelper: IHelmHelper = await getHelmHelper();
+    expect(helmHelper != null, true);
+    // @ts-ignore
+    const mainPkg: HelmPackage = helm._package;
+    const getMonomerFunc = mainPkg.getMonomerOriginal;
+
+    return _testAll('original', getMonomerFunc);
+  }, {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: JsAtom<HelmType> | HelmType): Atom<HelmType> | HelmType {
+  let res: Atom<HelmType> | HelmType;
+  const a = argA as JsAtom<HelmType>;
+  if (a.T === 'ATOM')
+    res = new JSDraw2.Atom<HelmType>(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})`);
+    }
+  }
+}

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

@@ -0,0 +1,97 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {Subject} from 'rxjs';
+
+import {
+  category, expect, test, awaitCheck, delay, testEvent, before, after
+} from '@datagrok-libraries/utils/src/test';
+import {
+  getHelmService, HelmServiceBase, HelmAux, HelmProps
+} from '@datagrok-libraries/bio/src/viewers/helm-service';
+import {RenderTask} from '@datagrok-libraries/bio/src/utils/cell-renderer-async-base';
+
+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 {_package} from '../package-test';
+
+category('HelmService', () => {
+  let monomerLibHelper: IMonomerLibHelper;
+  /** Backup actual user's monomer libraries settings */
+  let userLibSettings: UserLibSettings;
+
+  let helmSvc: HelmServiceBase;
+
+  before(async () => {
+    const logPrefix = `Helm: tests: HelmService: before`;
+    _package.logger.debug(`${logPrefix}, start`);
+    try {
+      monomerLibHelper = await getMonomerLibHelper();
+      userLibSettings = await getUserLibSettings();
+
+      await delay(1000); // for loading monomer libraries files
+      // Test 'helm' requires default monomer library loaded
+      await setUserLibSettingsForTests();
+      await monomerLibHelper.loadLibraries(true); // load default libraries
+      const libSummary = monomerLibHelper.getBioLib().getSummary();
+
+      helmSvc = await getHelmService();
+      await helmSvc.reset();
+
+      _package.logger.debug(`${logPrefix}, end`);
+    } finally {
+      _package.logger.debug(`${logPrefix}, fina`);
+    }
+  });
+
+  after(async () => {
+    const logPrefix = `Helm: tests: HelmService: after`;
+    _package.logger.debug(`${logPrefix}, start`);
+
+    await helmSvc.reset();
+
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadLibraries(true); // load user settings libraries
+    _package.logger.debug(`${logPrefix}, end`);
+  });
+
+  test('helm', async () => {
+    const logPrefix: string = `Helm: tests: HelmService: helm`;
+    _package.logger.debug(`${logPrefix}, start`);
+    const helmStr: string = 'PEPTIDE1{I.H.A.N.T.Thr_PO3H2.Aca.D-Tyr_Et}$$$$';
+    let consumerId: number | null = null;
+    let taskAux: HelmAux | null = null;
+    const event = new Subject<void>();
+    await testEvent(event,
+      () => {
+      },
+      () => {
+        const task: RenderTask<HelmProps, HelmAux> = {
+          name: 'test1',
+          props: {
+            helm: helmStr,
+            backColor: DG.Color.fromHtml('#FFFFFF'),
+            width: 300, height: 100,
+          },
+          onAfterRender: (canvas: HTMLCanvasElement, aux: HelmAux) => {
+            taskAux = aux;
+            event.next();
+          }
+        };
+        helmSvc.reset();
+        consumerId = helmSvc.render(consumerId, task, 0);
+      }, 7000);
+    expect(taskAux !== null, true, 'Helm task aux is null');
+    expect(taskAux!.mol.atoms.length > 0, true, 'Polymer mol atoms empty');
+    expect(taskAux!.mol.atoms.length, 8);
+    expect(taskAux!.mol.bonds.length, 7);
+    expect(helmSvc.errorCount, 0, 'There was errors in NglGlService.');
+    expect(consumerId !== null, true, 'consumerId not assigned');
+    _package.logger.debug(`${logPrefix}, end`);
+  }, {timeout: 10000});
+});

package/src/tests/helm-tests.ts

@@ -75,6 +75,7 @@ category('Helm', () => {
     'comples-monomer', 'complex-monomer+side-chain', 'complex-monomer+side-chain-RNA',
     'complex-side-chain', 'complex+side-chain+linker'
   ];
+
   test('parseHelm', async () => {
     const expectedResults = [
       ['meI', 'hHis', 'Aca', 'N', 'T', 'dK', 'Thr_PO3H2', 'D-Tyr_Et', 'Aze', 'dV', 'E', 'Phe_4Me'],

package/src/tests/properties-widget-tests.ts

@@ -5,7 +5,9 @@ import * as grok from 'datagrok-api/grok';
 import {after, before, category, expect, expectObject, test} from '@datagrok-libraries/utils/src/test';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
-import {getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {
+  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
 import {getPropertiesDict} from '../widgets/properties-widget';
@@ -88,7 +90,7 @@ category('properties-widget', () => {
 function testPropertiesDict(
   seq: string, units: NOTATION, separator: string | undefined, alphabet: ALPHABET | undefined, expPropDict: {}
 ) {
-  const col = DG.Column.fromList(DG.COLUMN_TYPE.STRING, 'seq', [seq]);
+  const col = DG.Column.fromStrings('seq', [seq]) as DG.Column<string>;
   col.semType = DG.SEMTYPE.MACROMOLECULE;
   col.setTag(DG.TAGS.UNITS, units);
   if (separator) col.setTag(bioTAGS.separator, separator);

package/src/tests/renderers-tests.ts

@@ -3,33 +3,108 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
+import {fromEvent} from 'rxjs';
 
-import {category, expect, test, awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
+import {
+  after, before, category, test, expect, awaitCheck, delay, testEvent
+} from '@datagrok-libraries/utils/src/test';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+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 {awaitGrid} from './utils';
 import {TAGS as helmTAGS} from '../constants';
 
+import {_package} from '../package-test';
+
 category('renderers', () => {
+  let monomerLibHelper: IMonomerLibHelper;
+  /** Backup actual user's monomer libraries settings */
+  let userLibSettings: UserLibSettings;
+
+  before(async () => {
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = await getUserLibSettings();
+
+    // Test 'helm' requires default monomer library loaded
+    await setUserLibSettingsForTests();
+    await monomerLibHelper.loadLibraries(true); // load default libraries
+  });
+
+  after(async () => {
+    // UserDataStorage.put() replaces existing data
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadLibraries(true); // load user settings libraries
+  });
+
+
   test('missedInLib', async () => { await _testMissedInLib(); });
-});
 
-async function _testMissedInLib() {
-  const df: DG.DataFrame = await grok.dapi.files.readCsv('System:AppData/Helm/tests/sample_HELM-missedInLib.csv');
-  const helmCol: DG.Column<string> = df.getCol('HELM');
-
-  const tv: DG.TableView = grok.shell.addTableView(df);
-  await awaitCheck(() => {
-    return $(tv.root).find('.d4-grid canvas').length > 0;
-  }, 'Table view canvas not found', 100);
-
-  expect(helmCol.semType, DG.SEMTYPE.MACROMOLECULE);
-  expect(helmCol.getTag(DG.TAGS.UNITS), NOTATION.HELM);
-  expect(helmCol.getTag(DG.TAGS.CELL_RENDERER), 'helm');
-
-  const cellRendererErrorJson: string = helmCol.getTag(helmTAGS.cellRendererRenderError);
-  if (!!cellRendererErrorJson) {
-    const cellRendererError: any = JSON.parse(cellRendererErrorJson);
-    const err = new Error(cellRendererError['message']);
-    err.stack = cellRendererError['stack'];
-    throw err;
+  test('scatterPlotTooltip', async () => { await _testScatterPlotTooltip(); });
+
+  async function _testMissedInLib() {
+    const df: DG.DataFrame = await grok.dapi.files.readCsv('System:AppData/Helm/tests/sample_HELM-missedInLib.csv');
+    const helmCol: DG.Column<string> = df.getCol('HELM');
+
+    const tv: DG.TableView = grok.shell.addTableView(df);
+    await awaitCheck(() => {
+      return $(tv.root).find('.d4-grid canvas').length > 0;
+    }, 'Table view canvas not found', 100);
+
+    expect(helmCol.semType, DG.SEMTYPE.MACROMOLECULE);
+    expect(helmCol.getTag(DG.TAGS.UNITS), NOTATION.HELM);
+    expect(helmCol.getTag(DG.TAGS.CELL_RENDERER), 'helm');
+
+    const cellRendererErrorJson: string = helmCol.getTag(helmTAGS.cellRendererRenderError);
+    if (!!cellRendererErrorJson) {
+      const cellRendererError: any = JSON.parse(cellRendererErrorJson);
+      const err = new Error(cellRendererError['message']);
+      err.stack = cellRendererError['stack'];
+      throw err;
+    }
+  }
+
+  const helmCoordsCsv = `seq,x,y
+PEPTIDE1{I.H.A.N.T.Thr_PO3H2.Aca.D-Tyr_Et}$$$$,0,0
+RNA1{r(A)p.r(C)p.r(G)p.r(U)p}$$$$,1,0
+RNA1{d(A)p.d(C)p.d(G)p.d(U)p}|PEPTIDE1{I.H.A.N.T.Thr_PO3H2}$$$$,0,1
+`;
+
+  async function _testScatterPlotTooltip(): Promise<void> {
+    const df = DG.DataFrame.fromCsv(helmCoordsCsv);
+    df.currentRowIdx = 0;
+    const view = grok.shell.addTableView(df);
+    const sp: DG.ScatterPlotViewer = df.plot.scatter({x: 'x', y: 'y'});
+    view.dockManager.dock(sp, DG.DOCK_TYPE.RIGHT, null);
+    await Promise.all([
+      testEvent(sp.onAfterDrawScene, () => {}, () => { sp.invalidateCanvas(); }, 1000),
+      awaitGrid(view.grid, 500)
+    ]);
+
+    const spBcr = sp.root.getBoundingClientRect();
+    const wp = sp.worldToScreen(1, 0);
+    const ev = new MouseEvent('mousemove', {
+      cancelable: true, bubbles: true, view: window, button: 0,
+      clientX: spBcr.left + wp.x, clientY: spBcr.top + wp.y
+    });
+    const spCanvas = $(sp.root).find('canvas').get()[0] as HTMLCanvasElement;
+    await testEvent(fromEvent(spCanvas, 'mousemove'), () => {
+      _package.logger.debug(`Test: event, currentRowIdx=${df.currentRowIdx}`);
+      expect($(ui.tooltip.root).find('div table.d4-row-tooltip-table tr td canvas').length, 1);
+      expect(sp.hitTest(wp.x, wp.y), 1);
+    }, () => {
+      spCanvas.dispatchEvent(ev);
+    }, 500);
+    // TODO: Any error occurred become 'Cannot read properties of null (reading 'get$columns')' because of scatter plot
+    //await testEvent(sp.onAfterDrawScene, () => {}, () => { sp.invalidateCanvas(); }, 200);
+    await awaitGrid(view.grid, 500);
   }
-}
+});
+
+
+
+
+

package/src/types/dojo.ts

@@ -0,0 +1,3 @@
+declare module 'dojo' {
+  export function ready(callback: () => void): void;
+}