@datagrok/helm 2.2.0 → 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-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/utils/dummy-monomer.ts

@@ -1,69 +1,184 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import {_package} from '../package';
 
-/* eslint-disable camelcase */
-export class DummyWebEditorMonomer {
-  public readonly backgroundcolor: string = '#FF4444';
-  public readonly linecolor: string = '#800000';
-  public readonly textcolor: string = '#FFFFFF';
+import * as org from 'org';
+
+import {Monomer} from '@datagrok-libraries/bio/src/types/index';
+import {
+  HELM_REQUIRED_FIELD as REQ, HELM_OPTIONAL_FIELDS as OPT, HELM_RGROUP_FIELDS as RGP,
+} from '@datagrok-libraries/bio/src/utils/const';
+
+export function getRS(smiles: string) {
+  const newS = smiles.match(/(?<=\[)[^\][]*(?=])/gm);
+  const res: { [name: string]: string } = {};
+  let el = '';
+  let digit;
+  if (!!newS) {
+    for (let i = 0; i < newS.length; i++) {
+      if (newS[i] != null) {
+        if (/\d/.test(newS[i])) {
+          digit = newS[i][newS[i].length - 1];
+          newS[i] = newS[i].replace(/[0-9]/g, '');
+          for (let j = 0; j < newS[i].length; j++) {
+            if (newS[i][j] != ':')
+              el += newS[i][j];
+          }
+          res['R' + digit] = el;
+          el = '';
+        }
+      }
+    }
+  }
+  return res;
+}
+
+export class LibraryWebEditorMonomer implements org.helm.WebEditorMonomer {
+  public get rs(): number { return Object.keys(this.at).length; }
 
-  // no effect
-  // public readonly na: string = 'NA';
-  // public readonly nature: string = 'NA';
+  /* eslint-disable max-params */
+  protected constructor(
+    public readonly id: string,
+    public readonly m: string,
+    public readonly n: string,
+    public readonly na: string | undefined,
+    public readonly type: org.helm.PolymerType,
+    public readonly mt: org.helm.MonomerType,
+    public readonly at: org.helm.WebEditorRGroups,
+  ) /* eslint-enable max-params */ {}
+
+  static fromMonomer(biotype: org.helm.HelmType, monomer: Monomer): org.helm.WebEditorMonomer {
+    let at: org.helm.WebEditorRGroups = {};
+    const smiles = monomer[REQ.SMILES];
+    if (monomer.rgroups.length > 0) {
+      monomer.rgroups.forEach((it) => {
+        at[it[RGP.LABEL]] = it[RGP.CAP_GROUP_NAME];
+      });
+    } else if (smiles) {
+      // Generate R-Groups from SMILES
+      at = getRS(smiles);
+    } else {
+      // broken
+      return new BrokenWebEditorMonomer(biotype, monomer[REQ.SYMBOL]);
+    }
+
+    return new LibraryWebEditorMonomer(
+      monomer[REQ.SYMBOL],
+      monomer[REQ.MOLFILE],
+      monomer[REQ.NAME],
+      monomer[OPT.NATURAL_ANALOG],
+      monomer[REQ.POLYMER_TYPE],
+      monomer[REQ.MONOMER_TYPE],
+      at);
+  }
+}
+
+/* eslint-disable camelcase */
+export abstract class DummyWebEditorMonomer implements org.helm.WebEditorMonomer {
+  //@formatter:off
+  public abstract get backgroundcolor(): string | undefined;
+  public abstract get linecolor(): string | undefined;
+  public abstract get textcolor(): string | undefined;
+  //@formatter:on
 
   /** R-Group index os single digit only is allowed in Pistoia code */
-  public readonly at: { [rg: string]: string } = {
+  public readonly at: org.helm.WebEditorRGroups = {
     R1: 'H', R2: 'H', R3: 'H', R4: 'H', R5: 'H', R6: 'H', R7: 'H', R8: 'H', R9: 'H'
   };
 
-  constructor(
+  public get rs(): number { return Object.keys(this.at).length; }
+
+  protected constructor(
     public readonly biotype: string,
-    /** symbol, elem */ public readonly id: string,
-    /** name */ public readonly n: string = 'missing',
-    /** molfile*/ public readonly m?: string,
+    /** symbol */ public readonly id: string,
+    /** name */ public readonly n: string | undefined = 'missing',
+    /** molfile */ public readonly m: string | undefined = undefined,
+    /* Pistoia.HELM deletes .type and .mt in Monomers.addOneMonomer() */
+    /** polymer type */ public readonly type: org.helm.PolymerType | undefined = undefined,
+    /** monomer type */ public readonly mt: org.helm.MonomerType | undefined = undefined,
   ) {
     if (!this.id)
-      throw new Error('Not supported undefined [id].');
-
-    return new Proxy(this, {
-      get: (target: any, prop: string | symbol, _receiver: any) => {
-        const logPrefix = `${this.toLog()}.proxy.get( '${String(prop)}' )`;
-        switch (prop) {
-        case 'id':
-        case 'at':
-        case 'na':
-        case 'nature':
-        case 'backgroundcolor':
-        case 'linecolor':
-        case 'textcolor': {
-          // these attributes are known and handled
-          return target[prop];
-        }
-        case 'rs': {
-          /* R-Group count (?), 2 is default for monomer "?" */
-          throw new Error('Not supported get "rs" attribute.');
-        }
-        default:
-          // Unexpected attribute requested
-          _package.logger.warning(`${logPrefix}`);
-          return target[prop];
-        }
-      },
-      set: (target, prop, value: any, _receiver: any): boolean => {
-        throw new Error(`Not supported set '${String(prop)}' attribute, any.`);
-      },
-      apply: (target: any, thisArg: any, argArray: any[]): any | undefined => {
-        throw new Error(`Not supported call (apply) '${thisArg.toString()}' method, any.`);
-      }
-    });
+      throw new Error('Invalid arg undefined [id].');
+
+    // return new Proxy(this, {
+    //   get: (target: any, prop: string | symbol, _receiver: any) => {
+    //     const logPrefix = `${this.toLog()}.proxy.get( '${String(prop)}' )`;
+    //     switch (prop) {
+    //     case 'id':
+    //     case 'at':
+    //     case 'na':
+    //     case 'nature':
+    //     case 'backgroundcolor':
+    //     case 'linecolor':
+    //     case 'textcolor': {
+    //       // these attributes are known and handled
+    //       return target[prop];
+    //     }
+    //     case 'rs': {
+    //       /* R-Group count (?), 2 is default for monomer "?" */
+    //       throw new Error('Not supported get "rs" attribute.');
+    //     }
+    //     default:
+    //       // Unexpected attribute requested
+    //       _package.logger.warning(`${logPrefix}`);
+    //       return target[prop];
+    //     }
+    //   },
+    //   set: (target, prop, value: any, _receiver: any): boolean => {
+    //     throw new Error(`Not supported set '${String(prop)}' attribute, any.`);
+    //   },
+    //   apply: (target: any, thisArg: any, argArray: any[]): any | undefined => {
+    //     throw new Error(`Not supported call (apply) '${thisArg.toString()}' method, any.`);
+    //   }
+    // });
   }
 
   private static objCounter: number = -1;
   private readonly objId: number = ++DummyWebEditorMonomer.objCounter;
 
+  private readonly className: string = 'DummyWebEditorMonomer';
+
   protected toLog(): string {
-    return `Helm: DummyWebEditorMonomer<${this.objId}>`;
+    return `Helm: ${this.className}<${this.objId}>`;
+  }
+}
+
+export class GapWebEditorMonomer extends DummyWebEditorMonomer {
+  public readonly backgroundcolor: string = '#FFFFFF';
+  public readonly linecolor: string = '#808080';
+  public readonly textcolor: string = '#808080';
+
+  constructor(biotype: string, id: string) {
+    super(biotype, id, 'gap');
+  }
+}
+
+export class AmbiguousWebEditorMonomer extends DummyWebEditorMonomer {
+  public readonly backgroundcolor: string = '#808080';
+  public readonly linecolor: string = '#000000';
+  public readonly textcolor: string = '#000000';
+
+  constructor(biotype: string, id: string) {
+    super(biotype, id, 'ambiguous');
+  }
+}
+
+export class MissingWebEditorMonomer extends DummyWebEditorMonomer {
+  public readonly backgroundcolor: string = '#FF4444';
+  public readonly linecolor: string = '#800000';
+  public readonly textcolor: string = '#FFFFFF';
+
+  constructor(biotype: string, id: string) {
+    super(biotype, id, 'missing');
+  }
+}
+
+export class BrokenWebEditorMonomer extends DummyWebEditorMonomer {
+  public readonly backgroundcolor: string = '#FFFF44';
+  public readonly linecolor: string = '#800000';
+  public readonly textcolor: string = '#000000';
+
+  constructor(biotype: string, id: string) {
+    super(biotype, id, 'broken');
   }
 }

package/src/utils/get-hovered.ts

@@ -2,10 +2,10 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
-import * as org from 'org';
 import * as JSDraw2 from 'JSDraw2';
 
-import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+import {helmTypeToPolymerType} from '@datagrok-libraries/bio/src/monomer-works/monomer-works';
+import {PolymerType} from '@datagrok-libraries/bio/src/types';
 
 import {HelmMonomerPlacer, ISeqMonomer} from '../helm-monomer-placer';
 
@@ -80,32 +80,21 @@ export function getHoveredMonomerFallback(
   }
   left = (argsX >= sumLengths[left]) ? left : left - 1; // correct left to between sumLengths
   if (left >= 0)
-    hoveredSeqMonomer = getSeqMonomerFromHelm(allParts[0], allParts[left], helmPlacer.monomerLib);
+    hoveredSeqMonomer = getSeqMonomerFromHelm(allParts[0], allParts[left]);
   return hoveredSeqMonomer;
 }
 
 function getSeqMonomerFromHelmAtom(atom: JSDraw2.IEditorMolAtom): ISeqMonomer {
-  let polymerType: string | undefined = undefined;
-  switch (atom.bio.type) {
-  case 'HELM_BASE':
-  case 'HELM_SUGAR': // r - ribose, d - deoxyribose
-  case 'HELM_LINKER': // p - phosphate
-    polymerType = 'RNA';
-    break;
-  case 'HELM_AA':
-    polymerType = 'PEPTIDE';
-    break;
-  default:
-    polymerType = 'PEPTIDE';
-  }
+  const polymerType = helmTypeToPolymerType(atom.bio.type);
   return {symbol: atom.elem, polymerType: polymerType};
 }
 
 function getSeqMonomerFromHelm(
-  helmPrefix: string, symbol: string, monomerLib: IMonomerLib
+  helmPrefix: string, symbol: string
 ): ISeqMonomer {
   let resSeqMonomer: ISeqMonomer | undefined = undefined;
-  for (const polymerType of monomerLib.getPolymerTypes()) {
+  const polymerTypeList: PolymerType[] = ['RNA', 'PEPTIDE', 'CHEM', 'BLOB', 'G'];
+  for (const polymerType of polymerTypeList) {
     if (helmPrefix.startsWith(polymerType))
       resSeqMonomer = {symbol: symbol, polymerType: polymerType};
   }