diff --git a/ketcher-autotests/tests/Macromolecule-editor/Ambiguous-Monomers/preview-for-ambiguous-monomers.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Ambiguous-Monomers/preview-for-ambiguous-monomers.spec.ts index 7eb2865671..7dde1c488d 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Ambiguous-Monomers/preview-for-ambiguous-monomers.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Ambiguous-Monomers/preview-for-ambiguous-monomers.spec.ts @@ -98,18 +98,21 @@ const ambiguousMonomers: IHELMString[] = [ 'PEPTIDE1{(A,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,Y)}$$$$V2.0', monomerLocatorIndex: 1, monomerLocatorIndexOnMicro: 0, + pageReloadNeeded: true, }, { testDescription: '2. Peptide B (alternatives, from library)', HELMString: 'PEPTIDE2{(D,N)}$$$$V2.0', monomerLocatorIndex: 1, monomerLocatorIndexOnMicro: 0, + pageReloadNeeded: true, }, { testDescription: '3. Alternatives of 10 Peptides (no probabilities)', HELMString: 'PEPTIDE1{(L,K,I,H,G,F,E,D,C,A)}$$$$V2.0', monomerLocatorIndex: 1, monomerLocatorIndexOnMicro: 0, + pageReloadNeeded: true, }, { testDescription: @@ -118,12 +121,14 @@ const ambiguousMonomers: IHELMString[] = [ 'PEPTIDE1{([D-2Pal],[Cys_Bn],[AspOMe],[D-gGlu],[aMePhe],[Chg],[dH],[aIle],[Aad],[Ar5c])}$$$$V2.0', monomerLocatorIndex: 1, monomerLocatorIndexOnMicro: 0, + pageReloadNeeded: true, }, { testDescription: '5. Alternatives of 10 Peptides (with probabilities)', HELMString: 'PEPTIDE1{(L:1,K:3,I:5,H:7,G:9,F:55,E:8,D:6,C:4,A:2)}$$$$V2.0', monomerLocatorIndex: 1, monomerLocatorIndexOnMicro: 0, + pageReloadNeeded: true, }, { testDescription: @@ -132,6 +137,7 @@ const ambiguousMonomers: IHELMString[] = [ 'PEPTIDE1{([D-2Pal]:1,[Cys_Bn]:3,[AspOMe]:5,[D-gGlu]:7,[aMePhe]:9,[Chg]:55,[dH]:8,[aIle]:6,[Aad]:4,[Ar5c]:2)}$$$$V2.0', monomerLocatorIndex: 1, monomerLocatorIndexOnMicro: 0, + pageReloadNeeded: true, }, { testDescription: '7. Peptide X (Mixture, no quantities, from library)', @@ -142,6 +148,7 @@ const ambiguousMonomers: IHELMString[] = [ shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534, https://github.com/epam/ketcher/issues/5566', + pageReloadNeeded: true, }, { testDescription: '8. Peptide B (Mixture, from library)', @@ -151,6 +158,7 @@ const ambiguousMonomers: IHELMString[] = [ shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534, https://github.com/epam/ketcher/issues/5566', + pageReloadNeeded: true, }, { testDescription: '9. Mixture of 10 Peptides (no quantities)', @@ -159,6 +167,7 @@ const ambiguousMonomers: IHELMString[] = [ monomerLocatorIndexOnMicro: 0, shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534', + pageReloadNeeded: true, }, { testDescription: @@ -169,6 +178,7 @@ const ambiguousMonomers: IHELMString[] = [ monomerLocatorIndexOnMicro: 0, shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534', + pageReloadNeeded: true, }, { testDescription: '11. Mixture of 10 Peptides (with quantities)', @@ -177,6 +187,7 @@ const ambiguousMonomers: IHELMString[] = [ monomerLocatorIndexOnMicro: 0, shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534', + pageReloadNeeded: true, }, { testDescription: @@ -187,6 +198,7 @@ const ambiguousMonomers: IHELMString[] = [ monomerLocatorIndexOnMicro: 0, shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534', + pageReloadNeeded: true, }, { testDescription: @@ -210,6 +222,7 @@ const ambiguousMonomers: IHELMString[] = [ HELMString: 'RNA1{[dR](T,G,C,A)P}$$$$V2.0', monomerLocatorIndex: 3, monomerLocatorIndexOnMicro: 1, + pageReloadNeeded: true, }, { testDescription: @@ -217,6 +230,7 @@ const ambiguousMonomers: IHELMString[] = [ HELMString: 'RNA1{[dR](T,G,C)P}$$$$V2.0', monomerLocatorIndex: 3, monomerLocatorIndexOnMicro: 1, + pageReloadNeeded: true, }, { testDescription: @@ -224,6 +238,7 @@ const ambiguousMonomers: IHELMString[] = [ HELMString: 'RNA1{[dR](T:20,G:50,C:30)P}$$$$V2.0', monomerLocatorIndex: 3, monomerLocatorIndexOnMicro: 1, + pageReloadNeeded: true, }, { testDescription: @@ -280,12 +295,14 @@ const ambiguousMonomers: IHELMString[] = [ monomerLocatorIndexOnMicro: 1, shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534', + pageReloadNeeded: true, }, { testDescription: '24. RNA Base B (mixture, with quantities, from library)', HELMString: 'RNA1{R(U:20+G:50+C:30)P}$$$$V2.0', monomerLocatorIndex: 2, monomerLocatorIndexOnMicro: 1, + pageReloadNeeded: true, }, { testDescription: '25. DNA Base N (mixture, no quantities, from library)', @@ -295,6 +312,7 @@ const ambiguousMonomers: IHELMString[] = [ shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534, https://github.com/epam/ketcher/issues/5566', + pageReloadNeeded: true, }, { testDescription: '26. DNA Base B (mixture, no quantities, from library)', @@ -321,6 +339,7 @@ const ambiguousMonomers: IHELMString[] = [ shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534, https://github.com/epam/ketcher/issues/5566', + pageReloadNeeded: true, }, { testDescription: '29. Base R (mixture, no quantities, from library)', @@ -330,6 +349,7 @@ const ambiguousMonomers: IHELMString[] = [ shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534, https://github.com/epam/ketcher/issues/5566', + pageReloadNeeded: true, }, { testDescription: '30. Base R (mixture, with quantities, from library)', @@ -338,6 +358,7 @@ const ambiguousMonomers: IHELMString[] = [ issueNumber: 'https://github.com/epam/ketcher/issues/5566', monomerLocatorIndex: 2, monomerLocatorIndexOnMicro: 1, + pageReloadNeeded: true, }, { testDescription: '31. Mixture of 10 bases (multi-char, no quantities)', @@ -347,6 +368,7 @@ const ambiguousMonomers: IHELMString[] = [ monomerLocatorIndexOnMicro: 1, shouldFail: true, issueNumber: 'https://github.com/epam/ketcher/issues/5534', + pageReloadNeeded: true, }, { testDescription: '32. Mixture of 10 bases (multi-char, with quantities)', @@ -354,6 +376,7 @@ const ambiguousMonomers: IHELMString[] = [ 'RNA1{R([2imen2]:1+[5meC]:3+[4imen2]:5+[cnes4T]:7+[5eU]:9+[dfB]:55+[4ime6A]:8+[ac4C]:6+[allyl9]:4+[cneT]:2)P}$$$$V2.0', monomerLocatorIndex: 2, monomerLocatorIndexOnMicro: 1, + pageReloadNeeded: true, }, ]; diff --git a/ketcher-autotests/tests/Macromolecule-editor/Ambiguous-Monomers/preview-for-ambiguous-monomers.spec.ts-snapshots/Preview-tooltips-checks-10-Mixture-of-10-Pe-41c70--name-no-quantities-in-small-molecules-mode-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Ambiguous-Monomers/preview-for-ambiguous-monomers.spec.ts-snapshots/Preview-tooltips-checks-10-Mixture-of-10-Pe-41c70--name-no-quantities-in-small-molecules-mode-1-chromium-linux.png index bdffb2e669..09260c86e3 100644 Binary files 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a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts-snapshots/Sugar-monomers-on-the-canvas-their-connection-points-and-preview-tooltips-for-14---R2-R3-R4-R5-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts-snapshots/Sugar-monomers-on-the-canvas-their-connection-points-and-preview-tooltips-for-14---R2-R3-R4-R5-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-mol.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-mol.spec.ts index e352e0345e..a2da0586ad 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-mol.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-mol.spec.ts @@ -755,6 +755,7 @@ test.describe('Base monomers on the canvas, their connection points and preview for (const fileName of fileNames) { test(`for ${fileName}`, async () => { + await pageReload(page); await openFileAndAddToCanvasMacro( `Molfiles-V3000/Base-Templates/${fileName}.mol`, page, @@ -815,6 +816,7 @@ test.describe('CHEM monomers on the canvas, their connection points and preview for (const fileName of fileNames) { test(`for ${fileName}`, async () => { + await pageReload(page); await openFileAndAddToCanvasMacro( `Molfiles-V3000/CHEM-Templates/${fileName}.mol`, page, @@ -875,6 +877,7 @@ test.describe('Peptide monomers on the canvas, their connection points and previ for (const fileName of fileNames) { test(`for ${fileName}`, async () => { + await pageReload(page); await openFileAndAddToCanvasMacro( `Molfiles-V3000/Peptide-Templates/${fileName}.mol`, page, @@ -936,6 +939,7 @@ test.describe('Phosphate monomers on the canvas, their connection points and pre for (const fileName of fileNames) { test(`for ${fileName}`, async () => { + await pageReload(page); await openFileAndAddToCanvasMacro( `Molfiles-V3000/Phosphate-Templates/${fileName}.mol`, page, @@ -996,6 +1000,7 @@ test.describe('Sugar monomers on the canvas, their connection points and preview for (const fileName of fileNames) { test(`for ${fileName}`, async () => { + await pageReload(page); await openFileAndAddToCanvasMacro( `Molfiles-V3000/Sugar-Templates/${fileName}.mol`, page, diff --git a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-mol.spec.ts-snapshots/Base-monomers-on-the-canvas-their-connection--07e0b--tooltips-from-mol-file-for-09---R1-R3-R4-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-mol.spec.ts-snapshots/Base-monomers-on-the-canvas-their-connection--07e0b--tooltips-from-mol-file-for-09---R1-R3-R4-1-chromium-linux.png index b060912747..3edb6fbc23 100644 Binary files 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--git a/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-Check-after-zoom-in-on-created-long--6c5ff-ain-of-peptides-you-can-use-scroll-with-Shift-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-Check-after-zoom-in-on-created-long--6c5ff-ain-of-peptides-you-can-use-scroll-with-Shift-1-chromium-linux.png index e1d21e373f..581f8cf200 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-Check-after-zoom-in-on-created-long--6c5ff-ain-of-peptides-you-can-use-scroll-with-Shift-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-Check-after-zoom-in-on-created-long--6c5ff-ain-of-peptides-you-can-use-scroll-with-Shift-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/test-data/Common/Sequence-Mode-Replacement/replacement-expected.ket b/ketcher-autotests/tests/test-data/Common/Sequence-Mode-Replacement/replacement-expected.ket index 2b90a8aa87..8003fce254 100644 --- a/ketcher-autotests/tests/test-data/Common/Sequence-Mode-Replacement/replacement-expected.ket +++ b/ketcher-autotests/tests/test-data/Common/Sequence-Mode-Replacement/replacement-expected.ket @@ -147,72 +147,72 @@ { "label": "C", "location": [ - 1.8617, - 1.3499, + -0.5, + -0.433, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 1.1117, - 2.6489, + 0.5, + -0.433, 0 ] }, { "label": "C", "location": [ - -0.3882, - 2.649, + 1, + 0.433, 0 ] }, { - "label": "N", + "label": "C", "location": [ - -1.1382, - 1.35, + 0.5, + 1.299, 0 ] }, { "label": "C", "location": [ - -0.3883, - 0.0509, + -0.5, + 1.299, 0 ] }, { "label": "N", "location": [ - 1.1117, - 0.0509, + -1, + 0.433, 0 ] }, { "label": "N", "location": [ - 3.0618, - 1.3499, + 2, + 0.433, 0 ] }, { "label": "O", "location": [ - -0.9884, - -0.9883, + -1, + -1.299, 0 ] }, { "label": "H", "location": [ - -2.3383, - 1.35, + -2, + 0.433, 0 ] } @@ -221,22 +221,15 @@ { "type": 1, "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 0, - 5 + 5, + 0 ] }, { "type": 1, "atoms": [ 0, - 6 + 1 ] }, { @@ -254,7 +247,7 @@ ] }, { - "type": 1, + "type": 2, "atoms": [ 3, 4 @@ -263,23 +256,30 @@ { "type": 1, "atoms": [ - 3, - 8 + 4, + 5 ] }, { "type": 1, "atoms": [ - 4, - 5 + 2, + 6 ] }, { "type": 2, "atoms": [ - 4, + 0, 7 ] + }, + { + "type": 1, + "atoms": [ + 5, + 8 + ] } ], "class": "Base", @@ -289,7 +289,7 @@ "alias": "C", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 5, "leavingGroup": { "atoms": [ 8 @@ -313,19 +313,11 @@ "monomerTemplate-R___Ribose": { "type": "monomerTemplate", "atoms": [ - { - "label": "O", - "location": [ - -1.1017, - -1.0663, - 0 - ] - }, { "label": "C", "location": [ - -0.5897, - 0.3436, + 0.294, + -1.026, 0 ], "stereoLabel": "abs" @@ -333,8 +325,8 @@ { "label": "C", "location": [ - 0.0809, - -1.9889, + 1.103, + -0.438, 0 ], "stereoLabel": "abs" @@ -342,8 +334,8 @@ { "label": "C", "location": [ - 0.9095, - 0.2924, + 0.794, + 0.513, 0 ], "stereoLabel": "abs" @@ -351,8 +343,8 @@ { "label": "C", "location": [ - 1.3239, - -1.1493, + -0.206, + 0.513, 0 ], "stereoLabel": "abs" @@ -360,56 +352,64 @@ { "label": "O", "location": [ - 1.8285, - 1.4755, + -0.515, + -0.438, 0 ] }, { "label": "O", "location": [ - 2.4518, - -1.5589, + 0.294, + -2.026, 0 ] }, { - "label": "C", + "label": "O", "location": [ - -1.431, - 1.5834, + 1.382, + 1.322, 0 ] }, { "label": "O", "location": [ - 0.0399, - -3.1881, + 2.054, + -0.747, 0 ] }, { - "label": "O", + "label": "H", "location": [ - -2.9279, - 1.4755, + 2.376, + 1.217, 0 ] }, { - "label": "H", + "label": "C", "location": [ - -3.6017, - 2.4684, + -0.794, + 1.322, + 0 + ] + }, + { + "label": "O", + "location": [ + -1.788, + 1.217, 0 ] }, { "label": "H", "location": [ - 3.0174, - 1.3125, + -2.376, + 2.026, 0 ] } @@ -419,82 +419,75 @@ "type": 1, "atoms": [ 0, - 1 + 4 ] }, { "type": 1, "atoms": [ - 0, - 2 + 4, + 3 ] }, { "type": 1, "atoms": [ - 1, - 3 + 3, + 2 ] }, { "type": 1, "atoms": [ - 1, - 7 - ], - "stereo": 6 + 2, + 1 + ] }, { "type": 1, "atoms": [ - 2, - 4 + 1, + 0 ] }, { "type": 1, "atoms": [ - 2, - 8 + 0, + 5 ], "stereo": 6 }, { "type": 1, "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 5 + 2, + 6 ], "stereo": 1 }, { "type": 1, "atoms": [ - 4, - 6 + 1, + 7 ], "stereo": 1 }, { "type": 1, "atoms": [ - 5, - 11 + 6, + 8 ] }, { "type": 1, "atoms": [ - 7, + 3, 9 - ] + ], + "stereo": 6 }, { "type": 1, @@ -502,6 +495,13 @@ 9, 10 ] + }, + { + "type": 1, + "atoms": [ + 10, + 11 + ] } ], "class": "Sugar", @@ -514,25 +514,25 @@ "attachmentAtom": 9, "leavingGroup": { "atoms": [ - 10 + 11 ] }, "type": "left" }, { - "attachmentAtom": 5, + "attachmentAtom": 6, "leavingGroup": { "atoms": [ - 11 + 8 ] }, "type": "right" }, { - "attachmentAtom": 2, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 8 + 5 ] }, "type": "side" @@ -556,7 +556,7 @@ { "label": "P", "location": [ - -0.2399, + 0, 0, 0 ] @@ -564,23 +564,23 @@ { "label": "O", "location": [ - -1.4399, - 0, + 0.5, + -0.866, 0 ] }, { "label": "O", "location": [ - 0.3598, - -1.0394, + 0.5, + 0.866, 0 ] }, { "label": "O", "location": [ - 0.9601, + -1, 0, 0 ] @@ -588,22 +588,22 @@ { "label": "O", "location": [ - 0.3598, - 1.0394, + 1, + 0, 0 ] } ], "bonds": [ { - "type": 1, + "type": 2, "atoms": [ 0, 1 ] }, { - "type": 2, + "type": 1, "atoms": [ 0, 2 @@ -634,7 +634,7 @@ "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 1 + 3 ] }, "type": "left" @@ -643,7 +643,7 @@ "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 3 + 4 ] }, "type": "right" diff --git a/ketcher-autotests/tests/test-data/Common/Sequence-Mode-Replacement/replacement-expected.mol b/ketcher-autotests/tests/test-data/Common/Sequence-Mode-Replacement/replacement-expected.mol index 211da723a6..499067ef23 100644 --- a/ketcher-autotests/tests/test-data/Common/Sequence-Mode-Replacement/replacement-expected.mol +++ b/ketcher-autotests/tests/test-data/Common/Sequence-Mode-Replacement/replacement-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-08272415002D + -INDIGO-02262514042D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB @@ -31,113 +31,113 @@ M V30 TEMPLATE 1 BASE/Cyt/C NATREPLACE=BASE/C M V30 BEGIN CTAB M V30 COUNTS 9 9 2 0 0 M V30 BEGIN ATOM -M V30 1 C 1.8617 1.3499 0.0 0 -M V30 2 C 1.1117 2.6489 0.0 0 -M V30 3 C -0.3882 2.649 0.0 0 -M V30 4 N -1.1382 1.35 0.0 0 -M V30 5 C -0.3883 0.0509 0.0 0 -M V30 6 N 1.1117 0.0509 0.0 0 -M V30 7 N 3.0618 1.3499 0.0 0 -M V30 8 O -0.9884 -0.9883 0.0 0 -M V30 9 H -2.3383 1.35 0.0 0 +M V30 1 C -0.5 -0.433 0.0 0 +M V30 2 N 0.5 -0.433 0.0 0 +M V30 3 C 1.0 0.433 0.0 0 +M V30 4 C 0.5 1.299 0.0 0 +M V30 5 C -0.5 1.299 0.0 0 +M V30 6 N -1.0 0.433 0.0 0 +M V30 7 N 2.0 0.433 0.0 0 +M V30 8 O -1.0 -1.299 0.0 0 +M V30 9 H -2.0 0.433 0.0 0 M V30 END ATOM M V30 BEGIN BOND -M V30 1 1 1 2 -M V30 2 2 1 6 -M V30 3 1 1 7 -M V30 4 2 2 3 -M V30 5 1 3 4 -M V30 6 1 4 5 -M V30 7 1 4 9 -M V30 8 1 5 6 -M V30 9 2 5 8 +M V30 1 1 6 1 +M V30 2 1 1 2 +M V30 3 2 2 3 +M V30 4 1 3 4 +M V30 5 2 4 5 +M V30 6 1 5 6 +M V30 7 1 3 7 +M V30 8 2 1 8 +M V30 9 1 6 9 M V30 END BOND M V30 BEGIN SGROUP -M V30 1 SUP 1 ATOMS=(1 9) XBONDS=(1 7) BRKXYZ=(9 0.600050 0.000000 0.000000 - +M V30 1 SUP 1 ATOMS=(1 9) XBONDS=(1 9) BRKXYZ=(9 0.500000 0.000000 0.000000 - M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=L- M V30 GRP -M V30 2 SUP 2 ATOMS=(8 1 2 3 4 5 6 7 8) XBONDS=(1 7) BRKXYZ=(9 -0.600050 0.0- +M V30 2 SUP 2 ATOMS=(8 1 2 3 4 5 6 7 8) XBONDS=(1 9) BRKXYZ=(9 -0.500000 0.0- M V30 00000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) - -M V30 LABEL=C CLASS=BASE SAP=(3 4 9 Al) NATREPLACE=BASE/C +M V30 LABEL=C CLASS=BASE SAP=(3 6 9 Al) NATREPLACE=BASE/C M V30 END SGROUP M V30 END CTAB M V30 TEMPLATE 2 SUGAR/Rib/R NATREPLACE=SUGAR/R M V30 BEGIN CTAB M V30 COUNTS 12 12 4 0 0 M V30 BEGIN ATOM -M V30 1 O -1.1017 -1.0663 0.0 0 -M V30 2 C -0.5897 0.3436 0.0 0 CFG=1 -M V30 3 C 0.0809 -1.9889 0.0 0 CFG=2 -M V30 4 C 0.9095 0.2924 0.0 0 CFG=2 -M V30 5 C 1.3239 -1.1493 0.0 0 CFG=1 -M V30 6 O 1.8285 1.4755 0.0 0 -M V30 7 O 2.4518 -1.5589 0.0 0 -M V30 8 C -1.431 1.5834 0.0 0 -M V30 9 O 0.0399 -3.1881 0.0 0 -M V30 10 O -2.9279 1.4755 0.0 0 -M V30 11 H -3.6017 2.4684 0.0 0 -M V30 12 H 3.0174 1.3125 0.0 0 +M V30 1 C 0.294 -1.026 0.0 0 CFG=1 +M V30 2 C 1.103 -0.438 0.0 0 CFG=1 +M V30 3 C 0.794 0.513 0.0 0 CFG=1 +M V30 4 C -0.206 0.513 0.0 0 CFG=2 +M V30 5 O -0.515 -0.438 0.0 0 +M V30 6 O 0.294 -2.026 0.0 0 +M V30 7 O 1.382 1.322 0.0 0 +M V30 8 O 2.054 -0.747 0.0 0 +M V30 9 H 2.376 1.217 0.0 0 +M V30 10 C -0.794 1.322 0.0 0 +M V30 11 O -1.788 1.217 0.0 0 +M V30 12 H -2.376 2.026 0.0 0 M V30 END ATOM M V30 BEGIN BOND -M V30 1 1 1 2 -M V30 2 1 1 3 -M V30 3 1 2 4 -M V30 4 1 2 8 CFG=3 -M V30 5 1 3 5 -M V30 6 1 3 9 CFG=3 -M V30 7 1 4 5 -M V30 8 1 4 6 CFG=1 -M V30 9 1 5 7 CFG=1 -M V30 10 1 6 12 -M V30 11 1 8 10 -M V30 12 1 10 11 +M V30 1 1 1 5 +M V30 2 1 5 4 +M V30 3 1 4 3 +M V30 4 1 3 2 +M V30 5 1 2 1 +M V30 6 1 1 6 CFG=3 +M V30 7 1 3 7 CFG=1 +M V30 8 1 2 8 CFG=1 +M V30 9 1 7 9 +M V30 10 1 4 10 CFG=3 +M V30 11 1 10 11 +M V30 12 1 11 12 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STEABS ATOMS=(4 2 3 4 5) +M V30 MDLV30/STEABS ATOMS=(4 1 2 3 4) M V30 END COLLECTION M V30 BEGIN SGROUP -M V30 1 SUP 1 ATOMS=(1 11) XBONDS=(1 12) BRKXYZ=(9 0.336900 -0.496450 0.0000- +M V30 1 SUP 1 ATOMS=(1 12) XBONDS=(1 12) BRKXYZ=(9 0.294000 -0.404500 0.0000- M V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLAS- M V30 S=LGRP -M V30 2 SUP 2 ATOMS=(1 12) XBONDS=(1 10) BRKXYZ=(9 -0.594450 0.081500 0.0000- -M V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLAS- -M V30 S=LGRP -M V30 3 SUP 3 ATOMS=(1 9) XBONDS=(1 6) BRKXYZ=(9 0.020500 0.599600 0.000000 - +M V30 2 SUP 2 ATOMS=(1 9) XBONDS=(1 9) BRKXYZ=(9 -0.497000 0.052500 0.000000- +M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=- +M V30 LGRP +M V30 3 SUP 3 ATOMS=(1 6) XBONDS=(1 6) BRKXYZ=(9 0.000000 0.500000 0.000000 - M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLASS=- M V30 LGRP -M V30 4 SUP 4 ATOMS=(9 1 2 3 4 5 6 7 8 10) XBONDS=(3 6 10 12) BRKXYZ=(9 -0.0- -M V30 20500 -0.599600 0.000000 0.594450 -0.081500 0.000000 0.000000 0.000000- -M V30 0.000000) BRKXYZ=(9 -0.336900 0.496450 0.000000 0.000000 0.000000 0.0- -M V30 00000 0.000000 0.000000 0.000000) LABEL=R CLASS=SUGAR SAP=(3 10 11 Al)- -M V30 SAP=(3 6 12 Br) SAP=(3 3 9 Cx) NATREPLACE=SUGAR/R +M V30 4 SUP 4 ATOMS=(9 1 2 3 4 5 7 8 10 11) XBONDS=(3 6 9 12) BRKXYZ=(9 0.00- +M V30 0000 -0.500000 0.000000 0.497000 -0.052500 0.000000 0.000000 0.000000 - +M V30 0.000000) BRKXYZ=(9 -0.294000 0.404500 0.000000 0.000000 0.000000 0.00- +M V30 0000 0.000000 0.000000 0.000000) LABEL=R CLASS=SUGAR SAP=(3 10 12 Al) - +M V30 SAP=(3 7 9 Br) SAP=(3 1 6 Cx) NATREPLACE=SUGAR/R M V30 END SGROUP M V30 END CTAB M V30 TEMPLATE 3 PHOSPHATE/P/P NATREPLACE=PHOSPHATE/P M V30 BEGIN CTAB M V30 COUNTS 5 4 3 0 0 M V30 BEGIN ATOM -M V30 1 P -0.2399 0.0 0.0 0 -M V30 2 O -1.4399 0.0 0.0 0 -M V30 3 O 0.3598 -1.0394 0.0 0 -M V30 4 O 0.9601 0.0 0.0 0 -M V30 5 O 0.3598 1.0394 0.0 0 +M V30 1 P 0.0 0.0 0.0 0 +M V30 2 O 0.5 -0.866 0.0 0 +M V30 3 O 0.5 0.866 0.0 0 +M V30 4 O -1.0 0.0 0.0 0 +M V30 5 O 1.0 0.0 0.0 0 M V30 END ATOM M V30 BEGIN BOND -M V30 1 1 1 2 -M V30 2 2 1 3 +M V30 1 2 1 2 +M V30 2 1 1 3 M V30 3 1 1 4 M V30 4 1 1 5 M V30 END BOND M V30 BEGIN SGROUP -M V30 1 SUP 1 ATOMS=(1 2) XBONDS=(1 1) BRKXYZ=(9 0.600000 0.000000 0.000000 - +M V30 1 SUP 1 ATOMS=(1 4) XBONDS=(1 3) BRKXYZ=(9 0.500000 0.000000 0.000000 - M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLASS=- M V30 LGRP -M V30 2 SUP 2 ATOMS=(1 4) XBONDS=(1 3) BRKXYZ=(9 -0.600000 0.000000 0.000000- +M V30 2 SUP 2 ATOMS=(1 5) XBONDS=(1 4) BRKXYZ=(9 -0.500000 0.000000 0.000000- M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLASS- M V30 =LGRP -M V30 3 SUP 3 ATOMS=(3 1 3 5) XBONDS=(2 1 3) BRKXYZ=(9 -0.600000 0.000000 0.- -M V30 000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=P - -M V30 CLASS=PHOSPHATE SAP=(3 1 2 Al) SAP=(3 1 4 Br) NATREPLACE=PHOSPHATE/P +M V30 3 SUP 3 ATOMS=(3 1 2 3) XBONDS=(2 3 4) BRKXYZ=(9 -0.500000 0.000000 0.- +M V30 000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=P - +M V30 CLASS=PHOSPHATE SAP=(3 1 4 Al) SAP=(3 1 5 Br) NATREPLACE=PHOSPHATE/P M V30 END SGROUP M V30 END CTAB M V30 END TEMPLATE diff --git a/ketcher-autotests/tests/test-data/KET/Antisense-Chains/Antisense-expected.ket b/ketcher-autotests/tests/test-data/KET/Antisense-Chains/Antisense-expected.ket index 378cc1efe4..d29b517bb0 100644 --- a/ketcher-autotests/tests/test-data/KET/Antisense-Chains/Antisense-expected.ket +++ b/ketcher-autotests/tests/test-data/KET/Antisense-Chains/Antisense-expected.ket @@ -389,19 +389,11 @@ "monomerTemplate-R___Ribose": { "type": "monomerTemplate", "atoms": [ - { - "label": "O", - "location": [ - -1.1017, - -1.0663, - 0 - ] - }, { "label": "C", "location": [ - -0.5897, - 0.3436, + 0.294, + -1.026, 0 ], "stereoLabel": "abs" @@ -409,8 +401,8 @@ { "label": "C", "location": [ - 0.0809, - -1.9889, + 1.103, + -0.438, 0 ], "stereoLabel": "abs" @@ -418,8 +410,8 @@ { "label": "C", "location": [ - 0.9095, - 0.2924, + 0.794, + 0.513, 0 ], "stereoLabel": "abs" @@ -427,8 +419,8 @@ { "label": "C", "location": [ - 1.3239, - -1.1493, + -0.206, + 0.513, 0 ], "stereoLabel": "abs" @@ -436,56 +428,64 @@ { "label": "O", "location": [ - 1.8285, - 1.4755, + -0.515, + -0.438, 0 ] }, { "label": "O", "location": [ - 2.4518, - -1.5589, + 0.294, + -2.026, 0 ] }, { - "label": "C", + "label": "O", "location": [ - -1.431, - 1.5834, + 1.382, + 1.322, 0 ] }, { "label": "O", "location": [ - 0.0399, - -3.1881, + 2.054, + -0.747, 0 ] }, { - "label": "O", + "label": "H", "location": [ - -2.9279, - 1.4755, + 2.376, + 1.217, 0 ] }, { - "label": "H", + "label": "C", + "location": [ + -0.794, + 1.322, + 0 + ] + }, + { + "label": "O", "location": [ - -3.6017, - 2.4684, + -1.788, + 1.217, 0 ] }, { "label": "H", "location": [ - 3.0174, - 1.3125, + -2.376, + 2.026, 0 ] } @@ -495,82 +495,75 @@ "type": 1, "atoms": [ 0, - 1 + 4 ] }, { "type": 1, "atoms": [ - 0, - 2 + 4, + 3 ] }, { "type": 1, "atoms": [ - 1, - 3 + 3, + 2 ] }, { "type": 1, "atoms": [ - 1, - 7 - ], - "stereo": 6 + 2, + 1 + ] }, { "type": 1, "atoms": [ - 2, - 4 + 1, + 0 ] }, { "type": 1, "atoms": [ - 2, - 8 + 0, + 5 ], "stereo": 6 }, { "type": 1, "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 5 + 2, + 6 ], "stereo": 1 }, { "type": 1, "atoms": [ - 4, - 6 + 1, + 7 ], "stereo": 1 }, { "type": 1, "atoms": [ - 5, - 11 + 6, + 8 ] }, { "type": 1, "atoms": [ - 7, + 3, 9 - ] + ], + "stereo": 6 }, { "type": 1, @@ -578,6 +571,13 @@ 9, 10 ] + }, + { + "type": 1, + "atoms": [ + 10, + 11 + ] } ], "class": "Sugar", @@ -591,25 +591,25 @@ "type": "left", "leavingGroup": { "atoms": [ - 10 + 11 ] } }, { - "attachmentAtom": 5, + "attachmentAtom": 6, "type": "right", "leavingGroup": { "atoms": [ - 11 + 8 ] } }, { - "attachmentAtom": 2, + "attachmentAtom": 0, "type": "side", "leavingGroup": { "atoms": [ - 8 + 5 ] } } @@ -633,100 +633,93 @@ { "label": "C", "location": [ - 1.8617, - 1.3499, + -0.5, + -1.299, 0 ] }, { "label": "C", "location": [ - 1.1117, - 0.0509, + 0.5, + -1.299, 0 ] }, { "label": "C", "location": [ - -0.3883, - 0.0509, + 1, + -0.433, 0 ] }, { "label": "N", "location": [ - -1.1382, - 1.35, + 0.5, + 0.433, 0 ] }, { "label": "C", "location": [ - -0.3882, - 2.649, + -0.5, + 0.433, 0 ] }, { "label": "N", "location": [ - 1.1117, - 2.6489, + -1, + -0.433, 0 ] }, { "label": "O", "location": [ - 3.0618, - 1.3499, + 2, + -0.433, 0 ] }, { - "label": "O", + "label": "H", "location": [ - -0.9882, - 3.6882, + -2, + -0.433, 0 ] }, { - "label": "H", + "label": "O", "location": [ - -2.3383, - 1.35, + -1, + 1.299, 0 ] } ], "bonds": [ - { - "type": 2, - "atoms": [ - 0, - 6 - ] - }, { "type": 1, "atoms": [ - 0, - 5 + 5, + 0 ] }, { - "type": 1, + "type": 2, "atoms": [ 0, 1 ] }, { - "type": 2, + "type": 1, "atoms": [ 1, 2 @@ -749,22 +742,29 @@ { "type": 1, "atoms": [ - 3, - 8 + 4, + 5 ] }, { "type": 2, "atoms": [ - 4, - 7 + 2, + 6 ] }, { "type": 1, + "atoms": [ + 5, + 7 + ] + }, + { + "type": 2, "atoms": [ 4, - 5 + 8 ] } ], @@ -775,11 +775,11 @@ "alias": "U", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 5, "type": "left", "leavingGroup": { "atoms": [ - 8 + 7 ] } } @@ -803,7 +803,7 @@ { "label": "P", "location": [ - -0.2399, + 0, 0, 0 ] @@ -811,23 +811,23 @@ { "label": "O", "location": [ - -1.4399, - 0, + 0.5, + -0.866, 0 ] }, { "label": "O", "location": [ - 0.3598, - -1.0394, + 0.5, + 0.866, 0 ] }, { "label": "O", "location": [ - 0.9601, + -1, 0, 0 ] @@ -835,22 +835,22 @@ { "label": "O", "location": [ - 0.3598, - 1.0394, + 1, + 0, 0 ] } ], "bonds": [ { - "type": 1, + "type": 2, "atoms": [ 0, 1 ] }, { - "type": 2, + "type": 1, "atoms": [ 0, 2 @@ -882,7 +882,7 @@ "type": "left", "leavingGroup": { "atoms": [ - 1 + 3 ] } }, @@ -891,7 +891,7 @@ "type": "right", "leavingGroup": { "atoms": [ - 3 + 4 ] } } @@ -924,98 +924,98 @@ "type": "monomerTemplate", "atoms": [ { - "label": "C", + "label": "N", "location": [ - 1.0354, - 0.2498, + -0.438, + 0.541, 0 ] }, { "label": "C", "location": [ - -0.0792, - -0.754, + -0.438, + -0.459, 0 ] }, { "label": "C", "location": [ - -1.5057, - -0.2906, + 0.428, + -0.959, 0 ] }, { - "label": "N", + "label": "C", "location": [ - -1.8177, - 1.1766, + 1.294, + -0.459, 0 ] }, { - "label": "C", + "label": "N", "location": [ - -0.7031, - 2.1804, + 1.294, + 0.541, 0 ] }, { - "label": "N", + "label": "C", "location": [ - 0.7235, - 1.717, + 0.428, + 1.041, 0 ] }, { "label": "N", "location": [ - -2.3871, - -1.5034, + 0.22, + -1.937, 0 ] }, { "label": "C", "location": [ - -1.5053, - -2.7168, + -0.775, + -2.041, 0 ] }, { "label": "N", "location": [ - -0.0787, - -2.2532, + -1.182, + -1.128, 0 ] }, { "label": "O", "location": [ - 2.1768, - -0.1209, + 2.16, + -0.959, 0 ] }, { - "label": "N", + "label": "H", "location": [ - -0.9527, - 3.3542, + -2.16, + -0.92, 0 ] }, { - "label": "H", + "label": "N", "location": [ - -3.5871, - -1.5034, + 0.428, + 2.041, 0 ] } @@ -1024,15 +1024,8 @@ { "type": 2, "atoms": [ - 0, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 5 + 5, + 0 ] }, { @@ -1042,13 +1035,6 @@ 1 ] }, - { - "type": 1, - "atoms": [ - 8, - 1 - ] - }, { "type": 2, "atoms": [ @@ -1056,13 +1042,6 @@ 2 ] }, - { - "type": 1, - "atoms": [ - 6, - 2 - ] - }, { "type": 1, "atoms": [ @@ -1071,7 +1050,7 @@ ] }, { - "type": 2, + "type": 1, "atoms": [ 3, 4 @@ -1087,29 +1066,50 @@ { "type": 1, "atoms": [ - 4, - 10 + 1, + 8 ] }, { "type": 1, "atoms": [ - 6, + 8, 7 ] }, + { + "type": 2, + "atoms": [ + 7, + 6 + ] + }, { "type": 1, "atoms": [ 6, - 11 + 2 ] }, { "type": 2, "atoms": [ - 7, - 8 + 3, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 5, + 11 ] } ], @@ -1120,11 +1120,11 @@ "alias": "G", "attachmentPoints": [ { - "attachmentAtom": 6, + "attachmentAtom": 8, "type": "left", "leavingGroup": { "atoms": [ - 11 + 10 ] } } @@ -1170,72 +1170,72 @@ { "label": "C", "location": [ - 1.8617, - 1.3499, + -0.5, + -0.433, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 1.1117, - 2.6489, + 0.5, + -0.433, 0 ] }, { "label": "C", "location": [ - -0.3882, - 2.649, + 1, + 0.433, 0 ] }, { - "label": "N", + "label": "C", "location": [ - -1.1382, - 1.35, + 0.5, + 1.299, 0 ] }, { "label": "C", "location": [ - -0.3883, - 0.0509, + -0.5, + 1.299, 0 ] }, { "label": "N", "location": [ - 1.1117, - 0.0509, + -1, + 0.433, 0 ] }, { "label": "N", "location": [ - 3.0618, - 1.3499, + 2, + 0.433, 0 ] }, { "label": "O", "location": [ - -0.9884, - -0.9883, + -1, + -1.299, 0 ] }, { "label": "H", "location": [ - -2.3383, - 1.35, + -2, + 0.433, 0 ] } @@ -1244,22 +1244,15 @@ { "type": 1, "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 0, - 5 + 5, + 0 ] }, { "type": 1, "atoms": [ 0, - 6 + 1 ] }, { @@ -1277,7 +1270,7 @@ ] }, { - "type": 1, + "type": 2, "atoms": [ 3, 4 @@ -1286,23 +1279,30 @@ { "type": 1, "atoms": [ - 3, - 8 + 4, + 5 ] }, { "type": 1, "atoms": [ - 4, - 5 + 2, + 6 ] }, { "type": 2, "atoms": [ - 4, + 0, 7 ] + }, + { + "type": 1, + "atoms": [ + 5, + 8 + ] } ], "class": "Base", @@ -1312,7 +1312,7 @@ "alias": "C", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 5, "type": "left", "leavingGroup": { "atoms": [ @@ -2131,107 +2131,100 @@ "type": "monomerTemplate", "atoms": [ { - "label": "C", + "label": "N", "location": [ - 1.0354, - 0.2498, + -0.438, + 1.041, 0 ] }, { "label": "C", "location": [ - -0.0792, - -0.754, + -0.438, + 0.041, 0 ] }, { "label": "C", "location": [ - -1.5057, - -0.2906, + 0.428, + -0.459, 0 ] }, { - "label": "N", + "label": "C", "location": [ - -1.8177, - 1.1766, + 1.294, + 0.041, 0 ] }, { - "label": "C", + "label": "N", "location": [ - -0.7031, - 2.1804, + 1.294, + 1.041, 0 ] }, { - "label": "N", + "label": "C", "location": [ - 0.7235, - 1.717, + 0.428, + 1.541, 0 ] }, { "label": "N", "location": [ - -2.3871, - -1.5034, + 0.22, + -1.437, 0 ] }, { "label": "C", "location": [ - -1.5053, - -2.7168, + -0.775, + -1.541, 0 ] }, { "label": "N", "location": [ - -0.0787, - -2.2532, + -1.182, + -0.628, 0 ] }, { "label": "N", "location": [ - 2.1768, - -0.1209, + 2.16, + -0.459, 0 ] }, { "label": "H", "location": [ - -3.5871, - -1.5034, + -2.16, + -0.42, 0 ] } ], "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 9 - ] - }, { "type": 2, "atoms": [ - 0, - 5 + 5, + 0 ] }, { @@ -2241,13 +2234,6 @@ 1 ] }, - { - "type": 1, - "atoms": [ - 8, - 1 - ] - }, { "type": 2, "atoms": [ @@ -2255,13 +2241,6 @@ 2 ] }, - { - "type": 1, - "atoms": [ - 6, - 2 - ] - }, { "type": 1, "atoms": [ @@ -2286,22 +2265,43 @@ { "type": 1, "atoms": [ - 6, - 7 + 1, + 8 ] }, { "type": 1, "atoms": [ - 6, - 10 + 8, + 7 ] }, { "type": 2, "atoms": [ 7, - 8 + 6 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 10 ] } ], @@ -2312,7 +2312,7 @@ "alias": "A", "attachmentPoints": [ { - "attachmentAtom": 6, + "attachmentAtom": 8, "leavingGroup": { "atoms": [ 10 diff --git a/ketcher-autotests/tests/test-data/KET/Antisense-Chains/Antisense-expected.mol b/ketcher-autotests/tests/test-data/KET/Antisense-Chains/Antisense-expected.mol index dea305e268..66365beeab 100644 --- a/ketcher-autotests/tests/test-data/KET/Antisense-Chains/Antisense-expected.mol +++ b/ketcher-autotests/tests/test-data/KET/Antisense-Chains/Antisense-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-12192418172D + -INDIGO-02262513532D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB @@ -65,188 +65,188 @@ M V30 TEMPLATE 1 SUGAR/Rib/R NATREPLACE=SUGAR/R M V30 BEGIN CTAB M V30 COUNTS 12 12 4 0 0 M V30 BEGIN ATOM -M V30 1 O -1.1017 -1.0663 0.0 0 -M V30 2 C -0.5897 0.3436 0.0 0 CFG=1 -M V30 3 C 0.0809 -1.9889 0.0 0 CFG=2 -M V30 4 C 0.9095 0.2924 0.0 0 CFG=2 -M V30 5 C 1.3239 -1.1493 0.0 0 CFG=1 -M V30 6 O 1.8285 1.4755 0.0 0 -M V30 7 O 2.4518 -1.5589 0.0 0 -M V30 8 C -1.431 1.5834 0.0 0 -M V30 9 O 0.0399 -3.1881 0.0 0 -M V30 10 O -2.9279 1.4755 0.0 0 -M V30 11 H -3.6017 2.4684 0.0 0 -M V30 12 H 3.0174 1.3125 0.0 0 +M V30 1 C 0.294 -1.026 0.0 0 CFG=1 +M V30 2 C 1.103 -0.438 0.0 0 CFG=1 +M V30 3 C 0.794 0.513 0.0 0 CFG=1 +M V30 4 C -0.206 0.513 0.0 0 CFG=2 +M V30 5 O -0.515 -0.438 0.0 0 +M V30 6 O 0.294 -2.026 0.0 0 +M V30 7 O 1.382 1.322 0.0 0 +M V30 8 O 2.054 -0.747 0.0 0 +M V30 9 H 2.376 1.217 0.0 0 +M V30 10 C -0.794 1.322 0.0 0 +M V30 11 O -1.788 1.217 0.0 0 +M V30 12 H -2.376 2.026 0.0 0 M V30 END ATOM M V30 BEGIN BOND -M V30 1 1 1 2 -M V30 2 1 1 3 -M V30 3 1 2 4 -M V30 4 1 2 8 CFG=3 -M V30 5 1 3 5 -M V30 6 1 3 9 CFG=3 -M V30 7 1 4 5 -M V30 8 1 4 6 CFG=1 -M V30 9 1 5 7 CFG=1 -M V30 10 1 6 12 -M V30 11 1 8 10 -M V30 12 1 10 11 +M V30 1 1 1 5 +M V30 2 1 5 4 +M V30 3 1 4 3 +M V30 4 1 3 2 +M V30 5 1 2 1 +M V30 6 1 1 6 CFG=3 +M V30 7 1 3 7 CFG=1 +M V30 8 1 2 8 CFG=1 +M V30 9 1 7 9 +M V30 10 1 4 10 CFG=3 +M V30 11 1 10 11 +M V30 12 1 11 12 M V30 END BOND M V30 BEGIN COLLECTION -M V30 MDLV30/STEABS ATOMS=(4 2 3 4 5) +M V30 MDLV30/STEABS ATOMS=(4 1 2 3 4) M V30 END COLLECTION M V30 BEGIN SGROUP -M V30 1 SUP 1 ATOMS=(1 11) XBONDS=(1 12) BRKXYZ=(9 0.336900 -0.496450 0.0000- -M V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLAS- -M V30 S=LGRP -M V30 2 SUP 2 ATOMS=(1 12) XBONDS=(1 10) BRKXYZ=(9 -0.594450 0.081500 0.0000- +M V30 1 SUP 1 ATOMS=(1 12) XBONDS=(1 12) BRKXYZ=(9 0.294000 -0.404500 0.0000- M V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLAS- M V30 S=LGRP -M V30 3 SUP 3 ATOMS=(1 9) XBONDS=(1 6) BRKXYZ=(9 0.020500 0.599600 0.000000 - +M V30 2 SUP 2 ATOMS=(1 9) XBONDS=(1 9) BRKXYZ=(9 -0.497000 0.052500 0.000000- +M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=- +M V30 LGRP +M V30 3 SUP 3 ATOMS=(1 6) XBONDS=(1 6) BRKXYZ=(9 0.000000 0.500000 0.000000 - M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLASS=- M V30 LGRP -M V30 4 SUP 4 ATOMS=(9 1 2 3 4 5 6 7 8 10) XBONDS=(3 6 10 12) BRKXYZ=(9 -0.0- -M V30 20500 -0.599600 0.000000 0.594450 -0.081500 0.000000 0.000000 0.000000- -M V30 0.000000) BRKXYZ=(9 -0.336900 0.496450 0.000000 0.000000 0.000000 0.0- -M V30 00000 0.000000 0.000000 0.000000) LABEL=R CLASS=SUGAR SAP=(3 10 11 Al)- -M V30 SAP=(3 6 12 Br) SAP=(3 3 9 Cx) NATREPLACE=SUGAR/R +M V30 4 SUP 4 ATOMS=(9 1 2 3 4 5 7 8 10 11) XBONDS=(3 6 9 12) BRKXYZ=(9 0.00- +M V30 0000 -0.500000 0.000000 0.497000 -0.052500 0.000000 0.000000 0.000000 - +M V30 0.000000) BRKXYZ=(9 -0.294000 0.404500 0.000000 0.000000 0.000000 0.00- +M V30 0000 0.000000 0.000000 0.000000) LABEL=R CLASS=SUGAR SAP=(3 10 12 Al) - +M V30 SAP=(3 7 9 Br) SAP=(3 1 6 Cx) NATREPLACE=SUGAR/R M V30 END SGROUP M V30 END CTAB M V30 TEMPLATE 2 BASE/Ura/U NATREPLACE=BASE/U M V30 BEGIN CTAB M V30 COUNTS 9 9 2 0 0 M V30 BEGIN ATOM -M V30 1 C 1.8617 1.3499 0.0 0 -M V30 2 C 1.1117 0.0509 0.0 0 -M V30 3 C -0.3883 0.0509 0.0 0 -M V30 4 N -1.1382 1.35 0.0 0 -M V30 5 C -0.3882 2.649 0.0 0 -M V30 6 N 1.1117 2.6489 0.0 0 -M V30 7 O 3.0618 1.3499 0.0 0 -M V30 8 O -0.9882 3.6882 0.0 0 -M V30 9 H -2.3383 1.35 0.0 0 +M V30 1 C -0.5 -1.299 0.0 0 +M V30 2 C 0.5 -1.299 0.0 0 +M V30 3 C 1.0 -0.433 0.0 0 +M V30 4 N 0.5 0.433 0.0 0 +M V30 5 C -0.5 0.433 0.0 0 +M V30 6 N -1.0 -0.433 0.0 0 +M V30 7 O 2.0 -0.433 0.0 0 +M V30 8 H -2.0 -0.433 0.0 0 +M V30 9 O -1.0 1.299 0.0 0 M V30 END ATOM M V30 BEGIN BOND -M V30 1 2 1 7 -M V30 2 1 1 6 -M V30 3 1 1 2 -M V30 4 2 2 3 -M V30 5 1 3 4 -M V30 6 1 4 5 -M V30 7 1 4 9 -M V30 8 2 5 8 -M V30 9 1 5 6 +M V30 1 1 6 1 +M V30 2 2 1 2 +M V30 3 1 2 3 +M V30 4 1 3 4 +M V30 5 1 4 5 +M V30 6 1 5 6 +M V30 7 2 3 7 +M V30 8 1 6 8 +M V30 9 2 5 9 M V30 END BOND M V30 BEGIN SGROUP -M V30 1 SUP 1 ATOMS=(1 9) XBONDS=(1 7) BRKXYZ=(9 0.600050 0.000000 0.000000 - +M V30 1 SUP 1 ATOMS=(1 8) XBONDS=(1 8) BRKXYZ=(9 0.500000 0.000000 0.000000 - M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=L- M V30 GRP -M V30 2 SUP 2 ATOMS=(8 1 2 3 4 5 6 7 8) XBONDS=(1 7) BRKXYZ=(9 -0.600050 0.0- +M V30 2 SUP 2 ATOMS=(8 1 2 3 4 5 6 7 9) XBONDS=(1 8) BRKXYZ=(9 -0.500000 0.0- M V30 00000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) - -M V30 LABEL=U CLASS=BASE SAP=(3 4 9 Al) NATREPLACE=BASE/U +M V30 LABEL=U CLASS=BASE SAP=(3 6 8 Al) NATREPLACE=BASE/U M V30 END SGROUP M V30 END CTAB M V30 TEMPLATE 3 PHOSPHATE/P/P NATREPLACE=PHOSPHATE/P M V30 BEGIN CTAB M V30 COUNTS 5 4 3 0 0 M V30 BEGIN ATOM -M V30 1 P -0.2399 0.0 0.0 0 -M V30 2 O -1.4399 0.0 0.0 0 -M V30 3 O 0.3598 -1.0394 0.0 0 -M V30 4 O 0.9601 0.0 0.0 0 -M V30 5 O 0.3598 1.0394 0.0 0 +M V30 1 P 0.0 0.0 0.0 0 +M V30 2 O 0.5 -0.866 0.0 0 +M V30 3 O 0.5 0.866 0.0 0 +M V30 4 O -1.0 0.0 0.0 0 +M V30 5 O 1.0 0.0 0.0 0 M V30 END ATOM M V30 BEGIN BOND -M V30 1 1 1 2 -M V30 2 2 1 3 +M V30 1 2 1 2 +M V30 2 1 1 3 M V30 3 1 1 4 M V30 4 1 1 5 M V30 END BOND M V30 BEGIN SGROUP -M V30 1 SUP 1 ATOMS=(1 2) XBONDS=(1 1) BRKXYZ=(9 0.600000 0.000000 0.000000 - +M V30 1 SUP 1 ATOMS=(1 4) XBONDS=(1 3) BRKXYZ=(9 0.500000 0.000000 0.000000 - M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLASS=- M V30 LGRP -M V30 2 SUP 2 ATOMS=(1 4) XBONDS=(1 3) BRKXYZ=(9 -0.600000 0.000000 0.000000- +M V30 2 SUP 2 ATOMS=(1 5) XBONDS=(1 4) BRKXYZ=(9 -0.500000 0.000000 0.000000- M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLASS- M V30 =LGRP -M V30 3 SUP 3 ATOMS=(3 1 3 5) XBONDS=(2 1 3) BRKXYZ=(9 -0.600000 0.000000 0.- -M V30 000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=P - -M V30 CLASS=PHOSPHATE SAP=(3 1 2 Al) SAP=(3 1 4 Br) NATREPLACE=PHOSPHATE/P +M V30 3 SUP 3 ATOMS=(3 1 2 3) XBONDS=(2 3 4) BRKXYZ=(9 -0.500000 0.000000 0.- +M V30 000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=P - +M V30 CLASS=PHOSPHATE SAP=(3 1 4 Al) SAP=(3 1 5 Br) NATREPLACE=PHOSPHATE/P M V30 END SGROUP M V30 END CTAB M V30 TEMPLATE 4 BASE/Gua/G NATREPLACE=BASE/G M V30 BEGIN CTAB M V30 COUNTS 12 13 2 0 0 M V30 BEGIN ATOM -M V30 1 C 1.0354 0.2498 0.0 0 -M V30 2 C -0.0792 -0.754 0.0 0 -M V30 3 C -1.5057 -0.2906 0.0 0 -M V30 4 N -1.8177 1.1766 0.0 0 -M V30 5 C -0.7031 2.1804 0.0 0 -M V30 6 N 0.7235 1.717 0.0 0 -M V30 7 N -2.3871 -1.5034 0.0 0 -M V30 8 C -1.5053 -2.7168 0.0 0 -M V30 9 N -0.0787 -2.2532 0.0 0 -M V30 10 O 2.1768 -0.1209 0.0 0 -M V30 11 N -0.9527 3.3542 0.0 0 -M V30 12 H -3.5871 -1.5034 0.0 0 +M V30 1 N -0.438 0.541 0.0 0 +M V30 2 C -0.438 -0.459 0.0 0 +M V30 3 C 0.428 -0.959 0.0 0 +M V30 4 C 1.294 -0.459 0.0 0 +M V30 5 N 1.294 0.541 0.0 0 +M V30 6 C 0.428 1.041 0.0 0 +M V30 7 N 0.22 -1.937 0.0 0 +M V30 8 C -0.775 -2.041 0.0 0 +M V30 9 N -1.182 -1.128 0.0 0 +M V30 10 O 2.16 -0.959 0.0 0 +M V30 11 H -2.16 -0.92 0.0 0 +M V30 12 N 0.428 2.041 0.0 0 M V30 END ATOM M V30 BEGIN BOND -M V30 1 2 1 10 -M V30 2 1 1 6 -M V30 3 1 1 2 -M V30 4 1 9 2 -M V30 5 2 2 3 -M V30 6 1 7 3 -M V30 7 1 3 4 -M V30 8 2 4 5 -M V30 9 1 5 6 -M V30 10 1 5 11 -M V30 11 1 7 8 -M V30 12 1 7 12 -M V30 13 2 8 9 +M V30 1 2 6 1 +M V30 2 1 1 2 +M V30 3 2 2 3 +M V30 4 1 3 4 +M V30 5 1 4 5 +M V30 6 1 5 6 +M V30 7 1 2 9 +M V30 8 1 9 8 +M V30 9 2 8 7 +M V30 10 1 7 3 +M V30 11 2 4 10 +M V30 12 1 9 11 +M V30 13 1 6 12 M V30 END BOND M V30 BEGIN SGROUP -M V30 1 SUP 1 ATOMS=(1 12) XBONDS=(1 12) BRKXYZ=(9 0.600000 0.000000 0.00000- -M V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS- -M V30 =LGRP -M V30 2 SUP 2 ATOMS=(11 1 2 3 4 5 6 7 8 9 10 11) XBONDS=(1 12) BRKXYZ=(9 -0.- -M V30 600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - -M V30 0.000000) LABEL=G CLASS=BASE SAP=(3 7 12 Al) NATREPLACE=BASE/G +M V30 1 SUP 1 ATOMS=(1 11) XBONDS=(1 12) BRKXYZ=(9 0.489000 -0.104000 0.0000- +M V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLAS- +M V30 S=LGRP +M V30 2 SUP 2 ATOMS=(11 1 2 3 4 5 6 7 8 9 10 12) XBONDS=(1 12) BRKXYZ=(9 -0.- +M V30 489000 0.104000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - +M V30 0.000000) LABEL=G CLASS=BASE SAP=(3 9 11 Al) NATREPLACE=BASE/G M V30 END SGROUP M V30 END CTAB M V30 TEMPLATE 5 BASE/Cyt/C NATREPLACE=BASE/C M V30 BEGIN CTAB M V30 COUNTS 9 9 2 0 0 M V30 BEGIN ATOM -M V30 1 C 1.8617 1.3499 0.0 0 -M V30 2 C 1.1117 2.6489 0.0 0 -M V30 3 C -0.3882 2.649 0.0 0 -M V30 4 N -1.1382 1.35 0.0 0 -M V30 5 C -0.3883 0.0509 0.0 0 -M V30 6 N 1.1117 0.0509 0.0 0 -M V30 7 N 3.0618 1.3499 0.0 0 -M V30 8 O -0.9884 -0.9883 0.0 0 -M V30 9 H -2.3383 1.35 0.0 0 +M V30 1 C -0.5 -0.433 0.0 0 +M V30 2 N 0.5 -0.433 0.0 0 +M V30 3 C 1.0 0.433 0.0 0 +M V30 4 C 0.5 1.299 0.0 0 +M V30 5 C -0.5 1.299 0.0 0 +M V30 6 N -1.0 0.433 0.0 0 +M V30 7 N 2.0 0.433 0.0 0 +M V30 8 O -1.0 -1.299 0.0 0 +M V30 9 H -2.0 0.433 0.0 0 M V30 END ATOM M V30 BEGIN BOND -M V30 1 1 1 2 -M V30 2 2 1 6 -M V30 3 1 1 7 -M V30 4 2 2 3 -M V30 5 1 3 4 -M V30 6 1 4 5 -M V30 7 1 4 9 -M V30 8 1 5 6 -M V30 9 2 5 8 +M V30 1 1 6 1 +M V30 2 1 1 2 +M V30 3 2 2 3 +M V30 4 1 3 4 +M V30 5 2 4 5 +M V30 6 1 5 6 +M V30 7 1 3 7 +M V30 8 2 1 8 +M V30 9 1 6 9 M V30 END BOND M V30 BEGIN SGROUP -M V30 1 SUP 1 ATOMS=(1 9) XBONDS=(1 7) BRKXYZ=(9 0.600050 0.000000 0.000000 - +M V30 1 SUP 1 ATOMS=(1 9) XBONDS=(1 9) BRKXYZ=(9 0.500000 0.000000 0.000000 - M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=L- M V30 GRP -M V30 2 SUP 2 ATOMS=(8 1 2 3 4 5 6 7 8) XBONDS=(1 7) BRKXYZ=(9 -0.600050 0.0- +M V30 2 SUP 2 ATOMS=(8 1 2 3 4 5 6 7 8) XBONDS=(1 9) BRKXYZ=(9 -0.500000 0.0- M V30 00000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) - -M V30 LABEL=C CLASS=BASE SAP=(3 4 9 Al) NATREPLACE=BASE/C +M V30 LABEL=C CLASS=BASE SAP=(3 6 9 Al) NATREPLACE=BASE/C M V30 END SGROUP M V30 END CTAB M V30 TEMPLATE 6 AA/1Nal/1Nal/ NATREPLACE=AA/A @@ -408,39 +408,39 @@ M V30 TEMPLATE 9 BASE/Ade/A NATREPLACE=BASE/A M V30 BEGIN CTAB M V30 COUNTS 11 12 2 0 0 M V30 BEGIN ATOM -M V30 1 C 1.0354 0.2498 0.0 0 -M V30 2 C -0.0792 -0.754 0.0 0 -M V30 3 C -1.5057 -0.2906 0.0 0 -M V30 4 N -1.8177 1.1766 0.0 0 -M V30 5 C -0.7031 2.1804 0.0 0 -M V30 6 N 0.7235 1.717 0.0 0 -M V30 7 N -2.3871 -1.5034 0.0 0 -M V30 8 C -1.5053 -2.7168 0.0 0 -M V30 9 N -0.0787 -2.2532 0.0 0 -M V30 10 N 2.1768 -0.1209 0.0 0 -M V30 11 H -3.5871 -1.5034 0.0 0 +M V30 1 N -0.438 1.041 0.0 0 +M V30 2 C -0.438 0.041 0.0 0 +M V30 3 C 0.428 -0.459 0.0 0 +M V30 4 C 1.294 0.041 0.0 0 +M V30 5 N 1.294 1.041 0.0 0 +M V30 6 C 0.428 1.541 0.0 0 +M V30 7 N 0.22 -1.437 0.0 0 +M V30 8 C -0.775 -1.541 0.0 0 +M V30 9 N -1.182 -0.628 0.0 0 +M V30 10 N 2.16 -0.459 0.0 0 +M V30 11 H -2.16 -0.42 0.0 0 M V30 END ATOM M V30 BEGIN BOND -M V30 1 1 1 10 -M V30 2 2 1 6 -M V30 3 1 1 2 -M V30 4 1 9 2 -M V30 5 2 2 3 -M V30 6 1 7 3 -M V30 7 1 3 4 -M V30 8 2 4 5 -M V30 9 1 5 6 -M V30 10 1 7 8 -M V30 11 1 7 11 -M V30 12 2 8 9 +M V30 1 2 6 1 +M V30 2 1 1 2 +M V30 3 2 2 3 +M V30 4 1 3 4 +M V30 5 2 4 5 +M V30 6 1 5 6 +M V30 7 1 2 9 +M V30 8 1 9 8 +M V30 9 2 8 7 +M V30 10 1 7 3 +M V30 11 1 4 10 +M V30 12 1 9 11 M V30 END BOND M V30 BEGIN SGROUP -M V30 1 SUP 1 ATOMS=(1 11) XBONDS=(1 11) BRKXYZ=(9 0.600000 0.000000 0.00000- -M V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS- -M V30 =LGRP -M V30 2 SUP 2 ATOMS=(10 1 2 3 4 5 6 7 8 9 10) XBONDS=(1 11) BRKXYZ=(9 -0.600- -M V30 000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.0- -M V30 00000) LABEL=A CLASS=BASE SAP=(3 7 11 Al) NATREPLACE=BASE/A +M V30 1 SUP 1 ATOMS=(1 11) XBONDS=(1 12) BRKXYZ=(9 0.489000 -0.104000 0.0000- +M V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLAS- +M V30 S=LGRP +M V30 2 SUP 2 ATOMS=(10 1 2 3 4 5 6 7 8 9 10) XBONDS=(1 12) BRKXYZ=(9 -0.489- +M V30 000 0.104000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.0- +M V30 00000) LABEL=A CLASS=BASE SAP=(3 9 11 Al) NATREPLACE=BASE/A M V30 END SGROUP M V30 END CTAB M V30 END TEMPLATE diff --git a/ketcher-autotests/tests/test-data/KET/micro-macro-structure-expected.ket b/ketcher-autotests/tests/test-data/KET/micro-macro-structure-expected.ket index ce6068faa8..fe83e13a8e 100644 --- a/ketcher-autotests/tests/test-data/KET/micro-macro-structure-expected.ket +++ b/ketcher-autotests/tests/test-data/KET/micro-macro-structure-expected.ket @@ -2,7 +2,7 @@ "root": { "nodes": [ { - "$ref": "monomer7" + "$ref": "monomer0" }, { "$ref": "mol0" @@ -16,7 +16,7 @@ "atomId": "1" }, "endpoint2": { - "monomerId": "monomer7", + "monomerId": "monomer0", "attachmentPointId": "R1" } } @@ -172,9 +172,9 @@ "z": 0 } }, - "monomer7": { + "monomer0": { "type": "monomer", - "id": "7", + "id": "0", "position": { "x": 15.736879933869105, "y": -7.604491937162553 diff --git a/ketcher-autotests/tests/test-data/KET/sequence-with-unresolved-idt-monomers-expected.ket b/ketcher-autotests/tests/test-data/KET/sequence-with-unresolved-idt-monomers-expected.ket index 28a943e46a..764dfc9917 100644 --- a/ketcher-autotests/tests/test-data/KET/sequence-with-unresolved-idt-monomers-expected.ket +++ b/ketcher-autotests/tests/test-data/KET/sequence-with-unresolved-idt-monomers-expected.ket @@ -840,107 +840,100 @@ "type": "monomerTemplate", "atoms": [ { - "label": "C", + "label": "N", "location": [ - 1.0354, - 0.2498, + -0.438, + 1.041, 0 ] }, { "label": "C", "location": [ - -0.0792, - -0.754, + -0.438, + 0.041, 0 ] }, { "label": "C", "location": [ - -1.5057, - -0.2906, + 0.428, + -0.459, 0 ] }, { - "label": "N", + "label": "C", "location": [ - -1.8177, - 1.1766, + 1.294, + 0.041, 0 ] }, { - "label": "C", + "label": "N", "location": [ - -0.7031, - 2.1804, + 1.294, + 1.041, 0 ] }, { - "label": "N", + "label": "C", "location": [ - 0.7235, - 1.717, + 0.428, + 1.541, 0 ] }, { "label": "N", "location": [ - -2.3871, - -1.5034, + 0.22, + -1.437, 0 ] }, { "label": "C", "location": [ - -1.5053, - -2.7168, + -0.775, + -1.541, 0 ] }, { "label": "N", "location": [ - -0.0787, - -2.2532, + -1.182, + -0.628, 0 ] }, { "label": "N", "location": [ - 2.1768, - -0.1209, + 2.16, + -0.459, 0 ] }, { "label": "H", "location": [ - -3.5871, - -1.5034, + -2.16, + -0.42, 0 ] } ], "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 9 - ] - }, { "type": 2, "atoms": [ - 0, - 5 + 5, + 0 ] }, { @@ -950,13 +943,6 @@ 1 ] }, - { - "type": 1, - "atoms": [ - 8, - 1 - ] - }, { "type": 2, "atoms": [ @@ -964,13 +950,6 @@ 2 ] }, - { - "type": 1, - "atoms": [ - 6, - 2 - ] - }, { "type": 1, "atoms": [ @@ -995,22 +974,43 @@ { "type": 1, "atoms": [ - 6, - 7 + 1, + 8 ] }, { "type": 1, "atoms": [ - 6, - 10 + 8, + 7 ] }, { "type": 2, "atoms": [ 7, - 8 + 6 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 10 ] } ], @@ -1021,7 +1021,7 @@ "alias": "A", "attachmentPoints": [ { - "attachmentAtom": 6, + "attachmentAtom": 8, "type": "left", "leavingGroup": { "atoms": [ @@ -1377,98 +1377,98 @@ "type": "monomerTemplate", "atoms": [ { - "label": "C", + "label": "N", "location": [ - 1.0354, - 0.2498, + -0.438, + 0.541, 0 ] }, { "label": "C", "location": [ - -0.0792, - -0.754, + -0.438, + -0.459, 0 ] }, { "label": "C", "location": [ - -1.5057, - -0.2906, + 0.428, + -0.959, 0 ] }, { - "label": "N", + "label": "C", "location": [ - -1.8177, - 1.1766, + 1.294, + -0.459, 0 ] }, { - "label": "C", + "label": "N", "location": [ - -0.7031, - 2.1804, + 1.294, + 0.541, 0 ] }, { - "label": "N", + "label": "C", "location": [ - 0.7235, - 1.717, + 0.428, + 1.041, 0 ] }, { "label": "N", "location": [ - -2.3871, - -1.5034, + 0.22, + -1.937, 0 ] }, { "label": "C", "location": [ - -1.5053, - -2.7168, + -0.775, + -2.041, 0 ] }, { "label": "N", "location": [ - -0.0787, - -2.2532, + -1.182, + -1.128, 0 ] }, { "label": "O", "location": [ - 2.1768, - -0.1209, + 2.16, + -0.959, 0 ] }, { - "label": "N", + "label": "H", "location": [ - -0.9527, - 3.3542, + -2.16, + -0.92, 0 ] }, { - "label": "H", + "label": "N", "location": [ - -3.5871, - -1.5034, + 0.428, + 2.041, 0 ] } @@ -1477,15 +1477,8 @@ { "type": 2, "atoms": [ - 0, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 5 + 5, + 0 ] }, { @@ -1495,13 +1488,6 @@ 1 ] }, - { - "type": 1, - "atoms": [ - 8, - 1 - ] - }, { "type": 2, "atoms": [ @@ -1509,13 +1495,6 @@ 2 ] }, - { - "type": 1, - "atoms": [ - 6, - 2 - ] - }, { "type": 1, "atoms": [ @@ -1524,7 +1503,7 @@ ] }, { - "type": 2, + "type": 1, "atoms": [ 3, 4 @@ -1540,29 +1519,50 @@ { "type": 1, "atoms": [ - 4, - 10 + 1, + 8 ] }, { "type": 1, "atoms": [ - 6, + 8, 7 ] }, + { + "type": 2, + "atoms": [ + 7, + 6 + ] + }, { "type": 1, "atoms": [ 6, - 11 + 2 ] }, { "type": 2, "atoms": [ - 7, - 8 + 3, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 5, + 11 ] } ], @@ -1573,11 +1573,11 @@ "alias": "G", "attachmentPoints": [ { - "attachmentAtom": 6, + "attachmentAtom": 8, "type": "left", "leavingGroup": { "atoms": [ - 11 + 10 ] } } @@ -1789,27 +1789,27 @@ "type": "monomerTemplate", "atoms": [ { - "label": "O", + "label": "C", "location": [ - -0.8788, - -1.208, + 0.294, + -1.026, 0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", "location": [ - -0.3668, - 0.2019, + 1.103, + -0.438, 0 - ], - "stereoLabel": "abs" + ] }, { "label": "C", "location": [ - 0.3038, - -2.1307, + 0.794, + 0.513, 0 ], "stereoLabel": "abs" @@ -1817,65 +1817,65 @@ { "label": "C", "location": [ - 1.1323, - 0.1506, + -0.206, + 0.513, 0 ], "stereoLabel": "abs" }, { - "label": "C", + "label": "O", "location": [ - 1.5468, - -1.291, + -0.515, + -0.438, 0 ] }, { "label": "O", "location": [ - 2.0515, - 1.3338, + 0.294, + -2.026, 0 ] }, { - "label": "C", + "label": "O", "location": [ - -1.2081, - 1.4417, + 1.382, + 1.322, 0 ] }, { - "label": "O", + "label": "H", "location": [ - 0.2628, - -3.3299, + 2.376, + 1.217, 0 ] }, { - "label": "O", + "label": "C", "location": [ - -2.705, - 1.3338, + -0.794, + 1.322, 0 ] }, { - "label": "H", + "label": "O", "location": [ - -3.3788, - 2.3267, + -1.788, + 1.217, 0 ] }, { "label": "H", "location": [ - 3.2403, - 1.1709, + -2.376, + 2.026, 0 ] } @@ -1885,74 +1885,67 @@ "type": 1, "atoms": [ 0, - 1 + 4 ] }, { "type": 1, "atoms": [ - 0, - 2 + 4, + 3 ] }, { "type": 1, "atoms": [ - 1, - 3 + 3, + 2 ] }, { "type": 1, "atoms": [ - 1, - 6 - ], - "stereo": 6 + 2, + 1 + ] }, { "type": 1, "atoms": [ - 2, - 4 + 1, + 0 ] }, { "type": 1, "atoms": [ - 2, - 7 + 0, + 5 ], "stereo": 6 }, { "type": 1, "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 5 + 2, + 6 ], "stereo": 1 }, { "type": 1, "atoms": [ - 5, - 10 + 6, + 7 ] }, { "type": 1, "atoms": [ - 6, + 3, 8 - ] + ], + "stereo": 6 }, { "type": 1, @@ -1960,6 +1953,13 @@ 8, 9 ] + }, + { + "type": 1, + "atoms": [ + 9, + 10 + ] } ], "class": "Sugar", @@ -1969,29 +1969,29 @@ "alias": "dR", "attachmentPoints": [ { - "attachmentAtom": 8, + "attachmentAtom": 9, "type": "left", "leavingGroup": { "atoms": [ - 9 + 10 ] } }, { - "attachmentAtom": 5, + "attachmentAtom": 6, "type": "right", "leavingGroup": { "atoms": [ - 10 + 7 ] } }, { - "attachmentAtom": 2, + "attachmentAtom": 0, "type": "side", "leavingGroup": { "atoms": [ - 7 + 5 ] } } @@ -2092,108 +2092,101 @@ { "label": "C", "location": [ - 1.8617, - 1.3499, + -0.5, + -0.866, 0 ] }, { "label": "C", "location": [ - 1.1117, - 0.0509, + 0.5, + -0.866, 0 ] }, { "label": "C", "location": [ - -0.3883, - 0.0509, + 1, + 0, 0 ] }, { "label": "N", "location": [ - -1.1382, - 1.35, + 0.5, + 0.866, 0 ] }, { "label": "C", "location": [ - -0.3882, - 2.649, + -0.5, + 0.866, 0 ] }, { "label": "N", "location": [ - 1.1117, - 2.6489, + -1, + 0, 0 ] }, { "label": "O", "location": [ - 3.0618, - 1.3499, + 2, + 0, 0 ] }, { - "label": "O", + "label": "H", "location": [ - -0.9882, - 3.6882, + -2, + 0, 0 ] }, { - "label": "H", + "label": "C", "location": [ - -2.3383, - 1.35, + 1, + -1.732, 0 ] }, { - "label": "C", + "label": "O", "location": [ - 1.7117, - -0.9884, + -1, + 1.732, 0 ] } ], "bonds": [ - { - "type": 2, - "atoms": [ - 0, - 6 - ] - }, { "type": 1, "atoms": [ - 0, - 5 + 5, + 0 ] }, { - "type": 1, + "type": 2, "atoms": [ 0, 1 ] }, { - "type": 2, + "type": 1, "atoms": [ 1, 2 @@ -2216,28 +2209,35 @@ { "type": 1, "atoms": [ - 3, - 8 + 4, + 5 ] }, { "type": 2, "atoms": [ - 4, - 7 + 2, + 6 ] }, { "type": 1, "atoms": [ - 4, - 5 + 5, + 7 ] }, { "type": 1, "atoms": [ 1, + 8 + ] + }, + { + "type": 2, + "atoms": [ + 4, 9 ] } @@ -2249,11 +2249,11 @@ "alias": "T", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 5, "type": "left", "leavingGroup": { "atoms": [ - 8 + 7 ] } } diff --git a/ketcher-autotests/tests/test-data/Molfiles-V2000/empty-canvas-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V2000/empty-canvas-expected.mol index 70927b4bf2..497a875f99 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V2000/empty-canvas-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V2000/empty-canvas-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252520382D 0 0 0 0 0 0 0 0 0 0999 V2000 M END diff --git a/ketcher-autotests/tests/test-data/Molfiles-V2000/micro-macro-structure-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V2000/micro-macro-structure-expected.mol index aafa3357f6..faec903afe 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V2000/micro-macro-structure-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V2000/micro-macro-structure-expected.mol @@ -1,5 +1,5 @@ - Ketcher 10 22412 12D 1 1.00000 0.00000 0 + Ketcher 2252519252D 1 1.00000 0.00000 0 14 14 0 0 0 0 0 0 0 0999 V2000 14.6524 -7.9358 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/ketcher-autotests/tests/test-data/Molfiles-V2000/one-attachment-point-added-in-micro-mode-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V2000/one-attachment-point-added-in-micro-mode-expected.mol index ff870f2ba6..035dde4156 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V2000/one-attachment-point-added-in-micro-mode-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V2000/one-attachment-point-added-in-micro-mode-expected.mol @@ -1,5 +1,5 @@ - Ketcher 10 22412 12D 1 1.00000 0.00000 0 + Ketcher 2252519262D 1 1.00000 0.00000 0 7 7 0 0 0 0 0 0 0 0999 V2000 13.8348 -8.0001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/01 - (R1) - Left only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/01 - (R1) - Left only-expected.mol index 63f70dcc35..2e9a45164b 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/01 - (R1) - Left only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/01 - (R1) - Left only-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-02052512442D + -INDIGO-02252522182D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/04 - (R1,R2) - R3 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/04 - (R1,R2) - R3 gap-expected.mol index b78473dfb9..c26cfc2269 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/04 - (R1,R2) - R3 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/04 - (R1,R2) - R3 gap-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252522182D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/05 - (R1,R3) - R2 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/05 - (R1,R3) - R2 gap-expected.mol index e8332d838a..4d53177ed0 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/05 - (R1,R3) - R2 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/05 - (R1,R3) - R2 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522182D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3)_-_R2_gap 11.9 -8.325 0.0 0 CLASS=BASE +M V30 1 (R1,R3)_-_R2_gap 11.025 -7.45 0.0 0 CLASS=BASE M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/08 - (R1,R2,R3)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/08 - (R1,R2,R3)-expected.mol index fb2be4b370..1367cb59a9 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/08 - (R1,R2,R3)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/08 - (R1,R2,R3)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522182D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3) 11.9 -8.325 0.0 0 CLASS=BASE +M V30 1 (R1,R2,R3) 11.025 -7.45 0.0 0 CLASS=BASE M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/09 - (R1,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/09 - (R1,R3,R4)-expected.mol index e17e2bcc4c..1e3a28f5b8 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/09 - (R1,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/09 - (R1,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522182D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3,R4) 11.9 -8.325 0.0 0 CLASS=BASE +M V30 1 (R1,R3,R4) 11.025 -7.45 0.0 0 CLASS=BASE M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/12 - (R1,R2,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/12 - (R1,R2,R3,R4)-expected.mol index 231fb607fa..c86119a878 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/12 - (R1,R2,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/12 - (R1,R2,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522182D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3,R4) 11.9 -8.325 0.0 0 CLASS=BASE +M V30 1 (R1,R2,R3,R4) 11.025 -7.45 0.0 0 CLASS=BASE M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/13 - (R1,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/13 - (R1,R3,R4,R5)-expected.mol index 1a406756a4..31ab769d82 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/13 - (R1,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/13 - (R1,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522182D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=BASE +M V30 1 (R1,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=BASE M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol index a2318051d1..e284ea256a 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522182D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=BASE +M V30 1 (R1,R2,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=BASE M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/01 - (R1) - Left only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/01 - (R1) - Left only-expected.mol index 6b1a1f0789..22c453f098 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/01 - (R1) - Left only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/01 - (R1) - Left only-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/02 - (R2) - Right only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/02 - (R2) - Right only-expected.mol index b034cf4fd5..706d53c62b 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/02 - (R2) - Right only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/02 - (R2) - Right only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2)_-_Right_only 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R2)_-_Right_only 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/03 - (R3) - Side only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/03 - (R3) - Side only-expected.mol index ee516d7f06..ae82d770b3 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/03 - (R3) - Side only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/03 - (R3) - Side only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3)_-_Side_only 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R3)_-_Side_only 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/04 - (R1,R2) - R3 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/04 - (R1,R2) - R3 gap-expected.mol index c6f4bde4fa..9ff90adbd3 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/04 - (R1,R2) - R3 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/04 - (R1,R2) - R3 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2)_-_R3_gap 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R1,R2)_-_R3_gap 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/05 - (R1,R3) - R2 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/05 - (R1,R3) - R2 gap-expected.mol index d8ffb3707b..82f5c124d7 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/05 - (R1,R3) - R2 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/05 - (R1,R3) - R2 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3)_-_R2_gap 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R1,R3)_-_R2_gap 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/06 - (R2,R3) - R1 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/06 - (R2,R3) - R1 gap-expected.mol index 8bfb615248..0ab19e279f 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/06 - (R2,R3) - R1 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/06 - (R2,R3) - R1 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2,R3)_-_R1_gap 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R2,R3)_-_R1_gap 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/07 - (R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/07 - (R3,R4)-expected.mol index 84e9d4ad2e..ad21ae0390 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/07 - (R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/07 - (R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3,R4) 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R3,R4) 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/08 - (R1,R2,R3)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/08 - (R1,R2,R3)-expected.mol index 74c242b810..ec124b9cad 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/08 - (R1,R2,R3)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/08 - (R1,R2,R3)-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/09 - (R1,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/09 - (R1,R3,R4)-expected.mol index 4764104271..136c905497 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/09 - (R1,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/09 - (R1,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3,R4) 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R1,R3,R4) 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/10 - (R2,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/10 - (R2,R3,R4)-expected.mol index 9631e21806..832412e19c 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/10 - (R2,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/10 - (R2,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2,R3,R4) 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R2,R3,R4) 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/11 - (R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/11 - (R3,R4,R5)-expected.mol index 3c42adf858..26268764a3 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/11 - (R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/11 - (R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/12 - (R1,R2,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/12 - (R1,R2,R3,R4)-expected.mol index 0e7725e88c..a7142eb258 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/12 - (R1,R2,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/12 - (R1,R2,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3,R4) 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R1,R2,R3,R4) 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/13 - (R1,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/13 - (R1,R3,R4,R5)-expected.mol index 08c18d36bb..e8809256b1 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/13 - (R1,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/13 - (R1,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R1,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/14 - (R2,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/14 - (R2,R3,R4,R5)-expected.mol index 405e116f56..750abeebb2 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/14 - (R2,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/14 - (R2,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=LINKER +M V30 1 (R2,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=LINKER M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol index 05bb319da6..6abefdd67c 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/CHEM-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252522202D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/01 - (R1) - Left only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/01 - (R1) - Left only-expected.mol index da5e19582a..77ac1c1d15 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/01 - (R1) - Left only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/01 - (R1) - Left only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1)_-_Left_only 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R1)_-_Left_only 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/02 - (R2) - Right only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/02 - (R2) - Right only-expected.mol index 90d5d5ead4..9bf88066b7 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/02 - (R2) - Right only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/02 - (R2) - Right only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2)_-_Right_only 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R2)_-_Right_only 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/03 - (R3) - Side only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/03 - (R3) - Side only-expected.mol index fb4a6aac18..bff146130e 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/03 - (R3) - Side only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/03 - (R3) - Side only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3)_-_Side_only 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R3)_-_Side_only 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/04 - (R1,R2) - R3 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/04 - (R1,R2) - R3 gap-expected.mol index 1f1ec4b1a7..85c5a14679 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/04 - (R1,R2) - R3 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/04 - (R1,R2) - R3 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2)_-_R3_gap 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R1,R2)_-_R3_gap 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/05 - (R1,R3) - R2 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/05 - (R1,R3) - R2 gap-expected.mol index 6fab98e944..dd591462d5 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/05 - (R1,R3) - R2 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/05 - (R1,R3) - R2 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3)_-_R2_gap 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R1,R3)_-_R2_gap 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/06 - (R2,R3) - R1 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/06 - (R2,R3) - R1 gap-expected.mol index 036d8e97e5..785933ae1b 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/06 - (R2,R3) - R1 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/06 - (R2,R3) - R1 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2,R3)_-_R1_gap 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R2,R3)_-_R1_gap 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/07 - (R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/07 - (R3,R4)-expected.mol index 32fe529ef7..b5c8514bde 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/07 - (R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/07 - (R3,R4)-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/08 - (R1,R2,R3)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/08 - (R1,R2,R3)-expected.mol index f1977eb087..34a16fb33d 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/08 - (R1,R2,R3)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/08 - (R1,R2,R3)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3) 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R1,R2,R3) 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/09 - (R1,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/09 - (R1,R3,R4)-expected.mol index 388a034b52..6336a4d8b9 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/09 - (R1,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/09 - (R1,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3,R4) 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R1,R3,R4) 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/10 - (R2,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/10 - (R2,R3,R4)-expected.mol index 979b9705e3..8bedec658d 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/10 - (R2,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/10 - (R2,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2,R3,R4) 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R2,R3,R4) 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/11 - (R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/11 - (R3,R4,R5)-expected.mol index fadf3d5105..8532012396 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/11 - (R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/11 - (R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/12 - (R1,R2,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/12 - (R1,R2,R3,R4)-expected.mol index b87cec6e2b..6118ee6b62 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/12 - (R1,R2,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/12 - (R1,R2,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3,R4) 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R1,R2,R3,R4) 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/13 - (R1,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/13 - (R1,R3,R4,R5)-expected.mol index 13f54b796b..0b3f0cf35f 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/13 - (R1,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/13 - (R1,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R1,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/14 - (R2,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/14 - (R2,R3,R4,R5)-expected.mol index 9b26b93e3d..751ed12657 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/14 - (R2,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/14 - (R2,R3,R4,R5)-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol index 054579501d..9d0fd38283 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Peptide-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522212D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=AA SEQID=1 +M V30 1 (R1,R2,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=AA SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/01 - (R1) - Left only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/01 - (R1) - Left only-expected.mol index c19b632759..a13de8ab37 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/01 - (R1) - Left only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/01 - (R1) - Left only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1)_-_Left_only 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R1)_-_Left_only 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/02 - (R2) - Right only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/02 - (R2) - Right only-expected.mol index 2d6bb8637b..8991e990ea 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/02 - (R2) - Right only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/02 - (R2) - Right only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2)_-_Right_only 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R2)_-_Right_only 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/03 - (R3) - Side only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/03 - (R3) - Side only-expected.mol index fd8cfd4344..8740d1a7ce 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/03 - (R3) - Side only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/03 - (R3) - Side only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3)_-_Side_only 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R3)_-_Side_only 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/04 - (R1,R2) - R3 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/04 - (R1,R2) - R3 gap-expected.mol index 95f154ca41..5c5065d5ac 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/04 - (R1,R2) - R3 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/04 - (R1,R2) - R3 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2)_-_R3_gap 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R1,R2)_-_R3_gap 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/05 - (R1,R3) - R2 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/05 - (R1,R3) - R2 gap-expected.mol index 69a58712d9..a19de32feb 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/05 - (R1,R3) - R2 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/05 - (R1,R3) - R2 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3)_-_R2_gap 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R1,R3)_-_R2_gap 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/06 - (R2,R3) - R1 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/06 - (R2,R3) - R1 gap-expected.mol index bab815bbfc..5c1bd1dde0 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/06 - (R2,R3) - R1 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/06 - (R2,R3) - R1 gap-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/07 - (R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/07 - (R3,R4)-expected.mol index 7d524ec2c0..1ee87d3830 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/07 - (R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/07 - (R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3,R4) 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R3,R4) 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/08 - (R1,R2,R3)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/08 - (R1,R2,R3)-expected.mol index 610e747fa0..f729c74fa9 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/08 - (R1,R2,R3)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/08 - (R1,R2,R3)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3) 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R1,R2,R3) 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/09 - (R1,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/09 - (R1,R3,R4)-expected.mol index c711806e41..0ab7d05972 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/09 - (R1,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/09 - (R1,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3,R4) 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R1,R3,R4) 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/10 - (R2,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/10 - (R2,R3,R4)-expected.mol index ae292d50e3..7bd8d5d06f 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/10 - (R2,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/10 - (R2,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2,R3,R4) 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R2,R3,R4) 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/11 - (R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/11 - (R3,R4,R5)-expected.mol index 7ca56d6163..0124d9e64b 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/11 - (R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/11 - (R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/12 - (R1,R2,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/12 - (R1,R2,R3,R4)-expected.mol index 2e8e8ecf9d..294266c004 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/12 - (R1,R2,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/12 - (R1,R2,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3,R4) 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R1,R2,R3,R4) 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/13 - (R1,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/13 - (R1,R3,R4,R5)-expected.mol index ee51106bbb..42241902a0 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/13 - (R1,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/13 - (R1,R3,R4,R5)-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/14 - (R2,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/14 - (R2,R3,R4,R5)-expected.mol index 64949213e9..9f61c96e85 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/14 - (R2,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/14 - (R2,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R2,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol index 79293659c1..22c6b355fe 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Phosphate-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522222D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=PHOSPHATE SEQID=1 +M V30 1 (R1,R2,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=PHOSPHATE SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/01 - (R1) - Left only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/01 - (R1) - Left only-expected.mol index 97bee9dc2e..bf0f840996 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/01 - (R1) - Left only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/01 - (R1) - Left only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1)_-_Left_only 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R1)_-_Left_only 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/02 - (R2) - Right only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/02 - (R2) - Right only-expected.mol index 15855a884a..798a3bd22f 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/02 - (R2) - Right only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/02 - (R2) - Right only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2)_-_Right_only 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R2)_-_Right_only 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/03 - (R3) - Side only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/03 - (R3) - Side only-expected.mol index 274876bc1a..5522d14677 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/03 - (R3) - Side only-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/03 - (R3) - Side only-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3)_-_Side_only 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R3)_-_Side_only 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/04 - (R1,R2) - R3 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/04 - (R1,R2) - R3 gap-expected.mol index 4090ad162d..72cc8ddfb0 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/04 - (R1,R2) - R3 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/04 - (R1,R2) - R3 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522242D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2)_-_R3_gap 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R1,R2)_-_R3_gap 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/05 - (R1,R3) - R2 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/05 - (R1,R3) - R2 gap-expected.mol index 51f7b34ec2..c831710552 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/05 - (R1,R3) - R2 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/05 - (R1,R3) - R2 gap-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/06 - (R2,R3) - R1 gap-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/06 - (R2,R3) - R1 gap-expected.mol index 1bce10d82d..65687f3d6e 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/06 - (R2,R3) - R1 gap-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/06 - (R2,R3) - R1 gap-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2,R3)_-_R1_gap 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R2,R3)_-_R1_gap 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/07 - (R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/07 - (R3,R4)-expected.mol index 9a9f5fed61..9b9edd5eca 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/07 - (R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/07 - (R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3,R4) 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R3,R4) 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/08 - (R1,R2,R3)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/08 - (R1,R2,R3)-expected.mol index 4fe165fe78..75c4f161fc 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/08 - (R1,R2,R3)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/08 - (R1,R2,R3)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522242D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3) 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R1,R2,R3) 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/09 - (R1,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/09 - (R1,R3,R4)-expected.mol index 7d7e8b5cfc..bb05f6daca 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/09 - (R1,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/09 - (R1,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3,R4) 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R1,R3,R4) 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/10 - (R2,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/10 - (R2,R3,R4)-expected.mol index 8db17ed061..4ef3d55893 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/10 - (R2,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/10 - (R2,R3,R4)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2,R3,R4) 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R2,R3,R4) 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/11 - (R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/11 - (R3,R4,R5)-expected.mol index 98d1ed0354..d9176e6001 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/11 - (R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/11 - (R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/12 - (R1,R2,R3,R4)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/12 - (R1,R2,R3,R4)-expected.mol index ab6efbde12..308410507f 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/12 - (R1,R2,R3,R4)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/12 - (R1,R2,R3,R4)-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252522242D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/13 - (R1,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/13 - (R1,R3,R4,R5)-expected.mol index 8c64dddfb2..7293bb5907 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/13 - (R1,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/13 - (R1,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R1,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/14 - (R2,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/14 - (R2,R3,R4,R5)-expected.mol index 023df1fa70..7c08b1f9f8 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/14 - (R2,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/14 - (R2,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R2,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R2,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol index 9cb51d7268..e37b08631b 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Sugar-Templates/15 - (R1,R2,R3,R4,R5)-expected.mol @@ -1,11 +1,11 @@ - -INDIGO-01202510502D + -INDIGO-02252522232D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM -M V30 1 (R1,R2,R3,R4,R5) 11.9 -8.325 0.0 0 CLASS=SUGAR SEQID=1 +M V30 1 (R1,R2,R3,R4,R5) 11.025 -7.45 0.0 0 CLASS=SUGAR SEQID=1 M V30 END ATOM M V30 BEGIN BOND M V30 END BOND diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/fifty-monomers-v3000-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/fifty-monomers-v3000-expected.mol index f91d84bb6c..347f666afc 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/fifty-monomers-v3000-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/fifty-monomers-v3000-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510502D + -INDIGO-02252520382D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/hundred-monomers-v3000-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/hundred-monomers-v3000-expected.mol index c818f294fb..0942fb48d1 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/hundred-monomers-v3000-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/hundred-monomers-v3000-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510502D + -INDIGO-02252520382D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/snake-mode-peptides-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/snake-mode-peptides-expected.mol index f54df71b38..b728f2b680 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/snake-mode-peptides-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/snake-mode-peptides-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510502D + -INDIGO-02252520382D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/two-peptides-connected-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/two-peptides-connected-expected.mol index a02c6bbd27..ed2a4f31e4 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/two-peptides-connected-expected.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/two-peptides-connected-expected.mol @@ -1,5 +1,5 @@ - -INDIGO-12252421332D + -INDIGO-02252519462D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-bases.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-bases.mol index e754de2c41..cc51d422c3 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-bases.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-bases.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510502D + -INDIGO-02252520392D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-chems.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-chems.mol index a3c0766b5b..f1329d707a 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-chems.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-chems.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510502D + -INDIGO-02252520392D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-nucleotides.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-nucleotides.mol index c43473c7df..26e1ada988 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-nucleotides.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-nucleotides.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510502D + -INDIGO-02252520392D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-peptides.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-peptides.mol index 42b03e2197..56b861537b 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-peptides.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-peptides.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510492D + -INDIGO-02252520372D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-phosphates.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-phosphates.mol index 238bb91783..7fb7825001 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-phosphates.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-phosphates.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510502D + -INDIGO-02252520392D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-sugars.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-sugars.mol index 02bfc089e9..d0067442aa 100644 --- a/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-sugars.mol +++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/unsplit-nucleotides-connected-with-sugars.mol @@ -1,5 +1,5 @@ - -INDIGO-01202510502D + -INDIGO-02252520392D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/SDF/micro-macro-structure-v2000-expected.sdf b/ketcher-autotests/tests/test-data/SDF/micro-macro-structure-v2000-expected.sdf index 6069732081..e7c8d82625 100644 --- a/ketcher-autotests/tests/test-data/SDF/micro-macro-structure-v2000-expected.sdf +++ b/ketcher-autotests/tests/test-data/SDF/micro-macro-structure-v2000-expected.sdf @@ -1,5 +1,5 @@ - -INDIGO-10022412012D + -INDIGO-02252519262D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/SDF/micro-macro-structure-v3000-expected.sdf b/ketcher-autotests/tests/test-data/SDF/micro-macro-structure-v3000-expected.sdf index 6069732081..e7c8d82625 100644 --- a/ketcher-autotests/tests/test-data/SDF/micro-macro-structure-v3000-expected.sdf +++ b/ketcher-autotests/tests/test-data/SDF/micro-macro-structure-v3000-expected.sdf @@ -1,5 +1,5 @@ - -INDIGO-10022412012D + -INDIGO-02252519262D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/ketcher-autotests/tests/test-data/SDF/one-attachment-point-added-in-micro-modesdfv2000-expected.sdf b/ketcher-autotests/tests/test-data/SDF/one-attachment-point-added-in-micro-modesdfv2000-expected.sdf index ec428fa14a..77573507e0 100644 --- a/ketcher-autotests/tests/test-data/SDF/one-attachment-point-added-in-micro-modesdfv2000-expected.sdf +++ b/ketcher-autotests/tests/test-data/SDF/one-attachment-point-added-in-micro-modesdfv2000-expected.sdf @@ -1,5 +1,5 @@ - -INDIGO-10022412012D + -INDIGO-02252519262D 7 7 0 0 0 0 0 0 0 0999 V2000 13.8348 -8.0001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/ketcher-autotests/tests/test-data/SDF/one-attachment-point-added-in-micro-modesdfv3000-expected.sdf b/ketcher-autotests/tests/test-data/SDF/one-attachment-point-added-in-micro-modesdfv3000-expected.sdf index dfec18d34f..d7780ec661 100644 --- a/ketcher-autotests/tests/test-data/SDF/one-attachment-point-added-in-micro-modesdfv3000-expected.sdf +++ b/ketcher-autotests/tests/test-data/SDF/one-attachment-point-added-in-micro-modesdfv3000-expected.sdf @@ -1,5 +1,5 @@ - -INDIGO-10022412012D + -INDIGO-02252519262D 0 0 0 0 0 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB diff --git a/package-lock.json b/package-lock.json index 4d098d0f95..abaacd7ca9 100644 --- a/package-lock.json +++ b/package-lock.json @@ -32132,7 +32132,7 @@ } }, "packages/ketcher-core": { - "version": "3.1.0-rc.5", + "version": "3.1.0-rc.6", "license": "Apache-2.0", "dependencies": { "@babel/runtime": "^7.17.9", @@ -32258,7 +32258,7 @@ "dev": true }, "packages/ketcher-macromolecules": { - "version": "3.1.0-rc.5", + "version": "3.1.0-rc.6", "license": "Apache-2.0", "dependencies": { "@babel/runtime": "^7.17.9", @@ -33687,7 +33687,7 @@ } }, "packages/ketcher-react": { - "version": "3.1.0-rc.5", + "version": "3.1.0-rc.6", "license": "Apache-2.0", "dependencies": { "@babel/runtime": "^7.17.9", @@ -35422,7 +35422,7 @@ } }, "packages/ketcher-standalone": { - "version": "3.1.0-rc.5", + "version": "3.1.0-rc.6", "license": "Apache-2.0", "dependencies": { "@babel/runtime": "^7.17.9", diff --git a/packages/ketcher-core/package.json b/packages/ketcher-core/package.json index d56b347c61..5d76594ff2 100644 --- a/packages/ketcher-core/package.json +++ b/packages/ketcher-core/package.json @@ -1,6 +1,6 @@ { "name": "ketcher-core", - "version": "3.1.0-rc.5", + "version": "3.1.0-rc.6", "description": "Web-based molecule sketcher", "license": "Apache-2.0", "homepage": "http://lifescience.opensource.epam.com/ketcher", diff --git a/packages/ketcher-core/src/application/editor/data/monomers.ket b/packages/ketcher-core/src/application/editor/data/monomers.ket index 5e069c4805..ea3487272c 100644 --- a/packages/ketcher-core/src/application/editor/data/monomers.ket +++ b/packages/ketcher-core/src/application/editor/data/monomers.ket @@ -6372,182 +6372,182 @@ }, "monomerTemplate-A___Adenine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.0354, - 0.2498, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.0792, - -0.754, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.5057, - -0.2906, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.8177, - 1.1766, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.7031, - 2.1804, - 0 - ] - }, - { - "label": "N", - "location": [ - 0.7235, - 1.717, - 0 - ] - }, - { - "label": "N", - "location": [ - -2.3871, - -1.5034, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.5053, - -2.7168, - 0 - ] - }, - { - "label": "N", - "location": [ - -0.0787, - -2.2532, - 0 - ] - }, - { - "label": "N", - "location": [ - 2.1768, - -0.1209, - 0 - ] - }, - { - "label": "H", - "location": [ - -3.5871, - -1.5034, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 9 - ] - }, - { - "type": 2, - "atoms": [ - 0, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, "atoms": [ - 6, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 2, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 10 - ] - }, - { - "type": 2, - "atoms": [ - 7, - 8 - ] - } - ], + { + "label": "N", + "location": [ + -0.438, + 1.041, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.438, + 0.041, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.428, + -0.459, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.294, + 0.041, + 0 + ] + }, + { + "label": "N", + "location": [ + 1.294, + 1.041, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.428, + 1.541, + 0 + ] + }, + { + "label": "N", + "location": [ + 0.22, + -1.437, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.775, + -1.541, + 0 + ] + }, + { + "label": "N", + "location": [ + -1.182, + -0.628, + 0 + ] + }, + { + "label": "N", + "location": [ + 2.16, + -0.459, + 0 + ] + }, + { + "label": "H", + "location": [ + -2.16, + -0.42, + 0 + ] + } + ], + "bonds": [ + { + "type": 2, + "atoms": [ + 5, + 0 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 2, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 3 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 7 + ] + }, + { + "type": 2, + "atoms": [ + 7, + 6 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 10 + ] + } + ], "class": "Base", "classHELM": "RNA", "id": "A___Adenine", @@ -6555,7 +6555,7 @@ "alias": "A", "attachmentPoints": [ { - "attachmentAtom": 6, + "attachmentAtom": 8, "leavingGroup": { "atoms": [ 10 @@ -6568,145 +6568,145 @@ }, "monomerTemplate-C___Cytosine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.8617, - 1.3499, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.1117, - 2.6489, - 0 - ] - }, - { - "label": 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{ - "label": "H", + "label": "O", "location": [ - -3.5871, - -1.5034, + 0.0798, + -3.2622, 0 ] } ], "bonds": [ - { - "type": 2, - "atoms": [ - 0, - 9 - ] - }, { "type": 1, "atoms": [ 0, - 5 + 1 ] }, { "type": 1, "atoms": [ 0, - 1 + 2 ] }, { "type": 1, "atoms": [ - 8, - 1 + 1, + 3 ] }, { - "type": 2, + "type": 1, "atoms": [ 1, - 2 - ] + 6 + ], + "stereo": 1 }, { "type": 1, "atoms": [ - 6, - 2 + 2, + 4 ] }, { "type": 1, "atoms": [ 2, - 3 - ] + 7 + ], + "stereo": 6 }, { - "type": 2, + "type": 1, "atoms": [ 3, 4 @@ -7355,453 +7769,39 @@ { "type": 1, "atoms": [ - 4, - 5 + 5, + 10 ] }, { "type": 1, "atoms": [ - 4, - 10 + 6, + 8 ] }, { "type": 1, "atoms": [ - 6, - 7 + 8, + 9 ] }, { "type": 1, "atoms": [ - 6, + 1, 11 - ] + ], + "stereo": 6 }, { - "type": 2, + "type": 1, "atoms": [ - 7, - 8 + 11, + 12 ] - } - ], - "class": "Base", - "classHELM": "RNA", - "id": "G___Guanine", - "fullName": "Guanine", - "alias": "G", - "attachmentPoints": [ - { - "attachmentAtom": 6, - "leavingGroup": { - "atoms": [ - 11 - ] - }, - "type": "left" - } - ], - "naturalAnalogShort": "G" - }, - "monomerTemplate-In___Inosine": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.0354, - 0.2498, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.0792, - -0.754, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.5057, - -0.2906, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.8177, - 1.1766, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.7031, - 2.1804, - 0 - ] - }, - { - "label": "N", - "location": [ - 0.7235, - 1.717, - 0 - ] - }, - { - "label": "N", - "location": [ - -2.3871, - -1.5034, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.5053, - -2.7168, - 0 - ] - }, - { - "label": "N", - "location": [ - -0.0787, - -2.2532, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.1768, - -0.1209, - 0 - ] - }, - { - "label": "H", - "location": [ - -3.5871, - -1.5034, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 0, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 2, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 10 - ] - }, - { - "type": 2, - "atoms": [ - 7, - 8 - ] - } - ], - "class": "Base", - "classHELM": "RNA", - "id": "In___Inosine", - "fullName": "Inosine", - "alias": "In", - "attachmentPoints": [ - { - "attachmentAtom": 6, - "leavingGroup": { - "atoms": [ - 10 - ] - }, - "type": "left" - } - ], - "naturalAnalogShort": "X" - }, - "monomerTemplate-LR___2,'4'-locked-Ribose": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "O", - "location": [ - -0.9702, - 0.0384, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.5413, 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}, - { - "type": 1, - "atoms": [ - 1, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 6 - ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 2, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 7 - ], - "stereo": 6 - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 5, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 11 - ], - "stereo": 6 - }, - { - "type": 1, - "atoms": [ - 11, - 12 - ] - }, + }, { "type": 1, "atoms": [ @@ -8404,78 +8404,78 @@ }, "monomerTemplate-P___Phosphate": { "type": "monomerTemplate", - "atoms": [ - { - "label": "P", - "location": [ - -0.2399, - 0, - 0 - ] - }, - { - "label": "O", - "location": [ - -1.4399, - 0, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.3598, - -1.0394, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.9601, - 0, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.3598, - 1.0394, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 3 - ] - }, - { - "type": 1, "atoms": [ - 0, - 4 - ] - } - ], + { + "label": "P", + "location": [ + 0, + 0, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.5, + -0.866, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.5, + 0.866, + 0 + ] + }, + { + "label": "O", + "location": [ + -1, + 0, + 0 + ] + }, + { + "label": "O", + "location": [ + 1, + 0, + 0 + ] + } + ], + "bonds": [ + { + "type": 2, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 4 + ] + } + ], "class": "Phosphate", "classHELM": "RNA", "id": "P___Phosphate", @@ -8493,7 +8493,7 @@ "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 1 + 3 ] }, "type": "left" @@ -8502,7 +8502,7 @@ "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 3 + 4 ] }, "type": "right" @@ -8667,227 +8667,227 @@ }, "monomerTemplate-R___Ribose": { "type": "monomerTemplate", - "atoms": [ + "atoms": [ + { + "label": "C", + "location": [ + 0.294, + -1.026, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 1.103, + -0.438, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 0.794, + 0.513, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + -0.206, + 0.513, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "O", + "location": [ + -0.515, + -0.438, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.294, + -2.026, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.382, + 1.322, + 0 + ] + }, + { + "label": "O", + "location": [ + 2.054, + -0.747, + 0 + ] + }, + { + "label": "H", + "location": [ + 2.376, + 1.217, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.794, + 1.322, + 0 + ] + }, + { + "label": "O", + "location": [ + -1.788, + 1.217, + 0 + ] + }, + { + "label": "H", + "location": [ + -2.376, + 2.026, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 0 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 5 + ], + "stereo": 6 + }, + { + "type": 1, + "atoms": [ + 2, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 1, + 7 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 9 + ], + "stereo": 6 + }, + { + "type": 1, + "atoms": [ + 9, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 10, + 11 + ] + } + ], + "class": "Sugar", + "classHELM": "RNA", + "id": "R___Ribose", + "fullName": "Ribose", + "alias": "R", + "attachmentPoints": [ { - "label": "O", - "location": [ - -1.1017, - -1.0663, - 0 - ] + "attachmentAtom": 9, + "leavingGroup": { + "atoms": [ + 11 + ] + }, + "type": "left" }, { - "label": "C", - "location": [ - -0.5897, - 0.3436, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 0.0809, - -1.9889, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 0.9095, - 0.2924, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 1.3239, - -1.1493, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "O", - "location": [ - 1.8285, - 1.4755, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.4518, - -1.5589, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.431, - 1.5834, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.0399, - -3.1881, - 0 - ] - }, - { - "label": "O", - "location": [ - -2.9279, - 1.4755, - 0 - ] - }, - { - "label": "H", - "location": [ - -3.6017, - 2.4684, - 0 - ] - }, - { - "label": "H", - "location": [ - 3.0174, - 1.3125, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 7 - ], - "stereo": 6 - }, - { - "type": 1, - "atoms": [ - 2, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 8 - ], - "stereo": 6 - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 5 - ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 4, - 6 - ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 5, - 11 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 9, - 10 - ] - } - ], - "class": "Sugar", - "classHELM": "RNA", - "id": "R___Ribose", - "fullName": "Ribose", - "alias": "R", - "attachmentPoints": [ - { - "attachmentAtom": 9, - "leavingGroup": { - "atoms": [ - 10 - ] - }, - "type": "left" - }, - { - "attachmentAtom": 5, + "attachmentAtom": 6, "leavingGroup": { "atoms": [ - 11 + 8 ] }, "type": "right" }, { - "attachmentAtom": 2, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 8 + 5 ] }, "type": "side" @@ -9211,160 +9211,160 @@ }, "monomerTemplate-T___Thymine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.8617, - 1.3499, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.1117, - 0.0509, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.3883, - 0.0509, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.1382, - 1.35, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.3882, - 2.649, - 0 - ] - }, - { - "label": "N", - "location": [ - 1.1117, - 2.6489, - 0 - ] - }, - { - "label": "O", - "location": [ - 3.0618, - 1.3499, - 0 - ] - }, - { - "label": "O", - "location": [ - -0.9882, - 3.6882, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.3383, - 1.35, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.7117, - -0.9884, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 0, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 5 - ] - }, - { - "type": 1, "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 8 - ] - }, - { - "type": 2, - "atoms": [ - 4, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 9 - ] - } - ], + { + "label": "C", + "location": [ + -0.5, + -0.866, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.5, + -0.866, + 0 + ] + }, + { + "label": "C", + "location": [ + 1, + 0, + 0 + ] + }, + { + "label": "N", + "location": [ + 0.5, + 0.866, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.5, + 0.866, + 0 + ] + }, + { + "label": "N", + "location": [ + -1, + 0, + 0 + ] + }, + { + "label": "O", + "location": [ + 2, + 0, + 0 + ] + }, + { + "label": "H", + "location": [ + -2, + 0, + 0 + ] + }, + { + "label": "C", + "location": [ + 1, + -1.732, + 0 + ] + }, + { + "label": "O", + "location": [ + -1, + 1.732, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 5, + 0 + ] + }, + { + "type": 2, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 5 + ] + }, + { + "type": 2, + "atoms": [ + 2, + 6 + ] + }, + { + "type": 1, + "atoms": [ + 5, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 8 + ] + }, + { + "type": 2, + "atoms": [ + 4, + 9 + ] + } + ], "class": "Base", "classHELM": "RNA", "id": "T___Thymine", @@ -9372,10 +9372,10 @@ "alias": "T", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 5, "leavingGroup": { "atoms": [ - 8 + 7 ] }, "type": "left" @@ -9385,145 +9385,145 @@ }, "monomerTemplate-U___Uracil": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.8617, - 1.3499, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.1117, - 0.0509, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.3883, - 0.0509, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.1382, - 1.35, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.3882, - 2.649, - 0 - ] - }, - { - "label": "N", - "location": [ - 1.1117, - 2.6489, - 0 - ] - }, - { - "label": "O", - "location": [ - 3.0618, - 1.3499, - 0 - ] - }, - { - "label": "O", - "location": [ - -0.9882, - 3.6882, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.3383, - 1.35, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, "atoms": [ - 0, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 8 - ] - }, - { - "type": 2, - "atoms": [ - 4, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - } - ], + { + "label": "C", + "location": [ + -0.5, + -1.299, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.5, + -1.299, + 0 + ] + }, + { + "label": "C", + "location": [ + 1, + -0.433, + 0 + ] + }, + { + "label": "N", + "location": [ + 0.5, + 0.433, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.5, + 0.433, + 0 + ] + }, + { + "label": "N", + "location": [ + -1, + -0.433, + 0 + ] + }, + { + "label": "O", + "location": [ + 2, + -0.433, + 0 + ] + }, + { + "label": "H", + "location": [ + -2, + -0.433, + 0 + ] + }, + { + "label": "O", + "location": [ + -1, + 1.299, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 5, + 0 + ] + }, + { + "type": 2, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 5 + ] + }, + { + "type": 2, + "atoms": [ + 2, + 6 + ] + }, + { + "type": 1, + "atoms": [ + 5, + 7 + ] + }, + { + "type": 2, + "atoms": [ + 4, + 8 + ] + } + ], "class": "Base", "classHELM": "RNA", "id": "U___Uracil", @@ -9531,10 +9531,10 @@ "alias": "U", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 5, "leavingGroup": { "atoms": [ - 8 + 7 ] }, "type": "left" @@ -12345,181 +12345,181 @@ }, "monomerTemplate-dR___Deoxy-Ribose": { "type": "monomerTemplate", - "atoms": [ - { - "label": "O", - "location": [ - -0.8788, - -1.208, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.3668, - 0.2019, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 0.3038, - -2.1307, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 1.1323, - 0.1506, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 1.5468, - -1.291, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.0515, - 1.3338, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.2081, - 1.4417, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.2628, - -3.3299, - 0 - ] - }, - { - "label": "O", - "location": [ - -2.705, - 1.3338, - 0 - ] - }, - { - "label": "H", - "location": [ - -3.3788, - 2.3267, - 0 - ] - }, - { - "label": "H", - "location": [ - 3.2403, - 1.1709, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, "atoms": [ - 1, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 6 + { + "label": "C", + "location": [ + 0.294, + -1.026, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 1.103, + -0.438, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.794, + 0.513, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + -0.206, + 0.513, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "O", + "location": [ + -0.515, + -0.438, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.294, + -2.026, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.382, + 1.322, + 0 + ] + }, + { + "label": "H", + "location": [ + 2.376, + 1.217, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.794, + 1.322, + 0 + ] + }, + { + "label": "O", + "location": [ + -1.788, + 1.217, + 0 + ] + }, + { + "label": "H", + "location": [ + -2.376, + 2.026, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 0 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 5 + ], + "stereo": 6 + }, + { + "type": 1, + "atoms": [ + 2, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 8 + ], + "stereo": 6 + }, + { + "type": 1, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 10 + ] + } ], - "stereo": 6 - }, - { - "type": 1, - "atoms": [ - 2, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 7 - ], - "stereo": 6 - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 5 - ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 5, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 9 - ] - } - ], "class": "Sugar", "classHELM": "RNA", "id": "dR___Deoxy-Ribose", @@ -12527,28 +12527,28 @@ "alias": "dR", "attachmentPoints": [ { - "attachmentAtom": 8, + "attachmentAtom": 9, "leavingGroup": { "atoms": [ - 9 + 10 ] }, "type": "left" }, { - "attachmentAtom": 5, + "attachmentAtom": 6, "leavingGroup": { "atoms": [ - 10 + 7 ] }, "type": "right" }, { - "attachmentAtom": 2, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 7 + 5 ] }, "type": "side" @@ -17257,110 +17257,110 @@ }, "monomerTemplate-A___Alanine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "N", - "location": [ - -1.2549, - -0.392, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.272, - 0.2633, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - -0.3103, - 1.7393, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.0523, - -0.392, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.0829, - -1.5722, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.0353, - 0.2633, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.3334, - 0.0905, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, "atoms": [ - 1, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 2 + { + "label": "N", + "location": [ + -0.866, + -0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0.25, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.732, + 0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -0.25, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + 0.25, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -1.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 1.25, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 1, - 3 - ] - }, - { - "type": 2, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 6 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "A___Alanine", @@ -17371,7 +17371,7 @@ "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 6 + 2 ] }, "type": "left" @@ -17380,7 +17380,7 @@ "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 5 + 4 ] }, "type": "right" @@ -19860,140 +19860,140 @@ }, "monomerTemplate-C___Cysteine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.4457, - -1.1333, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.1453, - -0.384, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 0.143, - 1.1168, - 0 - ] - }, - { - "label": "S", - "location": [ - -1.1573, - 1.8661, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.1551, - -1.1333, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.4475, - -2.3333, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.4842, - -0.532, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.1942, - -0.5331, - 0 - ] - }, - { - "label": "H", - "location": [ - -1.1591, - 3.0661, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, "atoms": [ - 5, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 2 + { + "label": "N", + "location": [ + -0.866, + -1, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -0.5, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.732, + -0.5, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -1, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + -0.5, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -2, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0.5, + 0 + ] + }, + { + "label": "S", + "location": [ + -0.866, + 1, + 0 + ] + }, + { + "label": "H", + "location": [ + -0.866, + 2, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 8 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "C___Cysteine", @@ -20001,25 +20001,25 @@ "alias": "C", "attachmentPoints": [ { - "attachmentAtom": 4, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 7 + 2 ] }, "type": "left" }, { - "attachmentAtom": 0, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 6 + 4 ] }, "type": "right" }, { - "attachmentAtom": 3, + "attachmentAtom": 7, "leavingGroup": { "atoms": [ 8 @@ -20955,170 +20955,170 @@ }, "monomerTemplate-D___Aspartic acid": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.631, - -1.5578, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.6327, - -2.7392, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.3507, - -0.8201, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "N", - "location": [ - -0.9295, - -1.5578, - 0 - ] - }, - { - "label": "H", - "location": [ - -1.9525, - -0.9669, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.3485, - 0.6575, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.9317, - 1.3952, - 0 - ] - }, - { - "label": "O", - "location": [ - -1.9542, - 0.8032, - 0 - ] - }, - { - "label": "O", - "location": [ - -0.9335, - 2.5766, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.6534, - -0.9658, - 0 - ] - }, - { - "label": "H", - "location": [ - 0.0851, - 3.1751, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 1, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 5 + { + "label": "N", + "location": [ + -0.866, + -1.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -0.75, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.732, + -0.75, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -1.25, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + -0.75, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -2.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 0.75, + 0 + ] + }, + { + "label": "O", + "location": [ + -0.866, + 1.75, + 0 + ] + }, + { + "label": "H", + "location": [ + 0, + 2.25, + 0 + ] + }, + { + "label": "O", + "location": [ + -1.732, + 0.25, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 2, + "atoms": [ + 7, + 10 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 2, - "atoms": [ - 6, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 10 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "D___Aspartic acid", @@ -21126,19 +21126,19 @@ "alias": "D", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 4 + 2 ] }, "type": "left" }, { - "attachmentAtom": 0, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 9 + 4 ] }, "type": "right" @@ -21147,7 +21147,7 @@ "attachmentAtom": 8, "leavingGroup": { "atoms": [ - 10 + 9 ] }, "type": "side" @@ -22310,185 +22310,185 @@ }, "monomerTemplate-E___Glutamic acid": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 0.3442, - -1.4777, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 1.6244, - -2.2154, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.6261, - -3.3968, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.6469, - -1.6234, - 0 - ] - }, - { - "label": "N", - "location": [ - -0.9361, - -2.2154, - 0 - ] - }, - { - "label": "H", - "location": [ - -1.9591, - -1.6245, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.3419, - -0.0001, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.9383, - 0.7375, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.9406, - 2.2151, - 0 - ] - }, - { - "label": "O", - "location": [ - -1.9642, - 2.8049, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.0819, - 2.8071, - 0 - ] - }, - { - "label": "H", - "location": [ - 0.0729, - 3.9885, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 1, - 0 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, "atoms": [ - 1, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 6 + { + "label": "N", + "location": [ + -0.866, + -1.75, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -1.25, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.732, + -1.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -1.75, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + -1.25, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -2.75, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 1.25, + 0 + ] + }, + { + "label": "O", + "location": [ + 0, + 1.75, + 0 + ] + }, + { + "label": "O", + "location": [ + -1.732, + 1.75, + 0 + ] + }, + { + "label": "H", + "location": [ + 0, + 2.75, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 2, + "atoms": [ + 8, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 11 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 6, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 8 - ] - }, - { - "type": 2, - "atoms": [ - 8, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 10, - 11 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "E___Glutamic acid", @@ -22496,25 +22496,25 @@ "alias": "E", "attachmentPoints": [ { - "attachmentAtom": 4, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 5 + 2 ] }, "type": "left" }, { - "attachmentAtom": 1, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 3 + 4 ] }, "type": "right" }, { - "attachmentAtom": 10, + "attachmentAtom": 9, "leavingGroup": { "atoms": [ 11 @@ -22720,207 +22720,207 @@ }, "monomerTemplate-F___Phenylalanine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - -0.2052, - 2.5398, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.5064, - 3.286, - 0 - ] - }, - { - "label": "C", - "location": [ - -2.8032, - 2.5322, - 0 - ] - }, - { - "label": "C", - "location": [ - -2.7988, - 1.0322, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.4976, - 0.2861, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.2008, - 1.0398, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.0995, - 0.2905, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.1018, - -1.2103, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "N", - "location": [ - -0.1986, - -1.9596, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.4022, - -1.9596, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.404, - -3.1596, - 0 - ] - }, - { - "label": "O", - "location": [ - 3.4407, - -1.3583, - 0 - ] - }, - { - "label": "H", - "location": [ - -1.2376, - -1.3593, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 0, - 5 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 2, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, "atoms": [ - 5, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 6 + { + "label": "C", + "location": [ + -2.165, + 1.749, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.435, + 1.75, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.298, + 2.249, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.435, + 0.749, + 0 + ] + }, + { + "label": "C", + "location": [ + -2.165, + 0.744, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.296, + 0.249, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.432, + 0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.433, + -0.75, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 1.299, + -1.249, + 0 + ] + }, + { + "label": "N", + "location": [ + -0.433, + -1.251, + 0 + ] + }, + { + "label": "H", + "location": [ + -1.299, + -0.752, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.3, + -2.249, + 0 + ] + }, + { + "label": "O", + "location": [ + 2.165, + -0.749, + 0 + ] + } + ], + "bonds": [ + { + "type": 2, + "atoms": [ + 2, + 0 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 4, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 5, + 3 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 6 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 10 + ] + }, + { + "type": 2, + "atoms": [ + 8, + 11 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 12 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 7, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 9 - ] - }, - { - "type": 2, - "atoms": [ - 9, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 9, - 11 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 12 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "F___Phenylalanine", @@ -22928,19 +22928,19 @@ "alias": "F", "attachmentPoints": [ { - "attachmentAtom": 8, + "attachmentAtom": 9, "leavingGroup": { "atoms": [ - 12 + 10 ] }, "type": "left" }, { - "attachmentAtom": 9, + "attachmentAtom": 8, "leavingGroup": { "atoms": [ - 11 + 12 ] }, "type": "right" @@ -22950,93 +22950,93 @@ }, "monomerTemplate-G___Glycine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - -0.3363, - 0.5346, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.9929, - -0.1107, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.0782, - -1.289, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.9709, - 0.552, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.326, - -0.1107, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.3797, - 0.4238, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - } - ], + { + "label": "N", + "location": [ + -0.866, + 0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0.75, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + 0.25, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + 0.75, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -0.75, + 0 + ] + }, + { + "label": "H", + "location": [ + -1.732, + 0.75, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 3 + ] + }, + { + "type": 2, + "atoms": [ + 2, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 5 + ] + } + ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "G___Glycine", @@ -23044,7 +23044,7 @@ "alias": "G", "attachmentPoints": [ { - "attachmentAtom": 4, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ 5 @@ -23053,7 +23053,7 @@ "type": "left" }, { - "attachmentAtom": 1, + "attachmentAtom": 2, "leavingGroup": { "atoms": [ 3 @@ -23607,207 +23607,207 @@ }, "monomerTemplate-H___Histidine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.8978, - -1.6508, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.8993, - -2.5957, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.8739, - -1.0609, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "N", - "location": [ - -0.15, - -1.6508, - 0 - ] - }, - { - "label": "H", - "location": [ - -0.9683, - -1.1782, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.872, - 0.1209, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.1501, - 0.7098, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.2771, - 1.8841, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.433, - 2.1263, - 0 - ] - }, - { - "label": "C", - "location": [ - -2.0205, - 1.1016, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.2277, - 0.2263, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.7155, - -1.1774, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.0317, - 3.1449, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, "atoms": [ - 1, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 5 + { + "label": "N", + "location": [ + -0.507, + -1.558, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.359, + -1.058, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.373, + -1.058, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.225, + -1.558, + 0 + ] + }, + { + "label": "O", + "location": [ + 2.091, + -1.058, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.225, + -2.558, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.359, + -0.058, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.507, + 0.442, + 0 + ] + }, + { + "label": "C", + "location": [ + -2.091, + 0.778, + 0 + ] + }, + { + "label": "N", + "location": [ + -1.426, + 0.038, + 0 + ] + }, + { + "label": "N", + "location": [ + -1.591, + 1.645, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.617, + 1.44, + 0 + ] + }, + { + "label": "H", + "location": [ + -1.998, + 2.558, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 2, + "atoms": [ + 7, + 11 + ] + }, + { + "type": 1, + "atoms": [ + 11, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 10, + 8 + ] + }, + { + "type": 2, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 10, + 12 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 2, - "atoms": [ - 7, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 9, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 10, - 6 - ] - }, - { - "type": 2, - "atoms": [ - 10, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 11 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 12 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "H___Histidine", @@ -23815,25 +23815,25 @@ "alias": "H", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 4 + 2 ] }, "type": "left" }, { - "attachmentAtom": 0, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 11 + 4 ] }, "type": "right" }, { - "attachmentAtom": 8, + "attachmentAtom": 10, "leavingGroup": { "atoms": [ 12 @@ -25246,157 +25246,157 @@ }, "monomerTemplate-I___Isoleucine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - -1.2557, - 1.6681, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.0245, - 0.9304, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 0.0268, - -0.5472, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "N", - "location": [ - -1.2536, - -1.2849, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.2766, - -0.694, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.3069, - -1.2849, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.3086, - -2.4664, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.3294, - -0.693, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.047, - 1.5223, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.2574, - 2.8495, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 1 + { + "label": "N", + "location": [ + -0.866, + -1, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -0.5, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.732, + -0.5, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -1, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + -0.5, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -2, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0.5, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 0.866, + 1, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 1, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 2, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ], + "stereo": 6 + }, + { + "type": 1, + "atoms": [ + 6, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 9 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 5 - ] - }, - { - "type": 2, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 5, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 8 - ], - "stereo": 6 - }, - { - "type": 1, - "atoms": [ - 0, - 9 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "I___Isoleucine", @@ -25404,19 +25404,19 @@ "alias": "I", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 4 + 2 ] }, "type": "left" }, { - "attachmentAtom": 5, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 7 + 4 ] }, "type": "right" @@ -25589,185 +25589,185 @@ }, "monomerTemplate-K___Lysine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 2.1478, - -2.4874, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.8474, - -1.7382, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 0.8451, - -0.2373, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.4553, - 0.5119, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.4575, - 2.0128, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.7579, - 2.7619, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.7602, - 4.2628, - 0 - ] - }, - { - "label": "N", - "location": [ - -0.453, - -2.4874, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.1495, - -3.6875, - 0 - ] - }, - { - "label": "O", - "location": [ - 3.1863, - -1.8862, - 0 - ] - }, - { - "label": "H", - "location": [ - -1.4921, - -1.8873, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.8, - 4.8619, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 8, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 7 - ] - }, - { - "type": 1, "atoms": [ - 1, - 2 + { + "label": "N", + "location": [ + -0.433, + -2, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.433, + -1.5, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.299, + -1.5, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.299, + -2, + 0 + ] + }, + { + "label": "O", + "location": [ + 2.165, + -1.5, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.299, + -3, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.433, + -0.5, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.433, + 0, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.433, + 1, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.299, + 1.5, + 0 + ] + }, + { + "label": "N", + "location": [ + -1.299, + 2.5, + 0 + ] + }, + { + "label": "H", + "location": [ + -2.165, + 3, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 10, + 11 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 11 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "K___Lysine", @@ -25775,25 +25775,25 @@ "alias": "K", "attachmentPoints": [ { - "attachmentAtom": 7, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 10 + 2 ] }, "type": "left" }, { - "attachmentAtom": 0, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 9 + 4 ] }, "type": "right" }, { - "attachmentAtom": 6, + "attachmentAtom": 10, "leavingGroup": { "atoms": [ 11 @@ -25806,155 +25806,155 @@ }, "monomerTemplate-L___Leucine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 0.3626, - 0.9903, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.9395, - 2.9396, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.9377, - 1.7396, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.9763, - 1.1383, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.3649, - -0.5105, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 1.6653, - -1.2598, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.6671, - -2.4598, - 0 - ] - }, - { - "label": "N", - "location": [ - -0.9355, - -1.2598, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.7038, - -0.6585, - 0 - ] - }, - { - "label": "H", - "location": [ - -1.9746, - -0.6596, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 2, - 0 - ] - }, - { - "type": 1, "atoms": [ - 4, - 0 + { + "label": "C", + "location": [ + -1.732, + 0.5, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 1, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0.5, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 2, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -0.5, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 0.866, + -1, + 0 + ] + }, + { + "label": "N", + "location": [ + -0.866, + -1, + 0 + ] + }, + { + "label": "H", + "location": [ + -1.732, + -0.5, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -2, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + -0.5, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 2 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 4, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 6 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 2, + "atoms": [ + 5, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 5, + 9 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 2, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 2, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 5, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 9 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "L___Leucine", @@ -25962,10 +25962,10 @@ "alias": "L", "attachmentPoints": [ { - "attachmentAtom": 7, + "attachmentAtom": 6, "leavingGroup": { "atoms": [ - 9 + 7 ] }, "type": "left" @@ -25974,7 +25974,7 @@ "attachmentAtom": 5, "leavingGroup": { "atoms": [ - 8 + 9 ] }, "type": "right" @@ -26093,155 +26093,155 @@ }, "monomerTemplate-M___Methionine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.6657, - -1.56, - 0 - ] - }, - { - "label": "N", - "location": [ - -0.9351, - -1.56, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.6675, - -2.76, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.3653, - -0.8107, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 0.363, - 0.6901, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.9373, - 1.4394, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.9794, - 3.5393, - 0 - ] - }, - { - "label": "S", - "location": [ - -0.9396, - 2.9402, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.7042, - -0.9587, - 0 - ] - }, - { - "label": "H", - "location": [ - -1.9742, - -0.9598, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 2, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 3 - ] - }, - { - "type": 1, "atoms": [ - 0, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 + { + "label": "N", + "location": [ + -0.866, + -1.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -0.75, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.732, + -0.75, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -1.25, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + -0.75, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -2.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 0.75, + 0 + ] + }, + { + "label": "S", + "location": [ + -0.866, + 1.75, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.732, + 2.25, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 9 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 5, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 9 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "M___Methionine", @@ -26249,19 +26249,19 @@ "alias": "M", "attachmentPoints": [ { - "attachmentAtom": 1, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 9 + 2 ] }, "type": "left" }, { - "attachmentAtom": 0, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 8 + 4 ] }, "type": "right" @@ -26752,196 +26752,196 @@ }, "monomerTemplate-N___Asparagine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.8929, - -1.4175, - 0 - ] - }, + "atoms": [ + { + "label": "N", + "location": [ + -0.433, + -1, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.433, + -0.5, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.299, + -0.5, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.299, + -1, + 0 + ] + }, + { + "label": "O", + "location": [ + 2.165, + -0.5, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.299, + -2, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.433, + 0.5, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.433, + 1, + 0 + ] + }, + { + "label": "O", + "location": [ + -0.433, + 2, + 0 + ] + }, + { + "label": "N", + "location": [ + -1.299, + 0.5, + 0 + ] + }, + { + "label": "H", + "location": [ + -2.165, + 1, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 2, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 10 + ] + } + ], + "class": "AminoAcid", + "classHELM": "PEPTIDE", + "id": "N___Asparagine", + "fullName": "Asparagine", + "alias": "N", + "attachmentPoints": [ { - "label": "O", - "location": [ - 1.8947, - -2.5989, - 0 - ] + "attachmentAtom": 0, + "leavingGroup": { + "atoms": [ + 2 + ] + }, + "type": "left" }, { - "label": "C", - "location": [ - 0.6127, - -0.6799, - 0 - ], - "stereoLabel": "abs" + "attachmentAtom": 3, + "leavingGroup": { + "atoms": [ + 4 + ] + }, + "type": "right" }, { - "label": "N", - "location": [ - -0.6676, - -1.4175, - 0 - ] - }, - { - "label": "H", - "location": [ - -1.6907, - -0.8266, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.6104, - 0.7978, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.6698, - 1.5354, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.6922, - 0.9434, - 0 - ] - }, - { - "label": "O", - "location": [ - -0.6716, - 2.7168, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.9153, - -0.8255, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.5341, - 1.7724, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 1, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 5 - ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 7 - ] - }, - { - "type": 2, - "atoms": [ - 6, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 10 - ] - } - ], - "class": "AminoAcid", - "classHELM": "PEPTIDE", - "id": "N___Asparagine", - "fullName": "Asparagine", - "alias": "N", - "attachmentPoints": [ - { - "attachmentAtom": 3, - "leavingGroup": { - "atoms": [ - 4 - ] - }, - "type": "left" - }, - { - "attachmentAtom": 0, - "leavingGroup": { - "atoms": [ - 9 - ] - }, - "type": "right" - }, - { - "attachmentAtom": 7, + "attachmentAtom": 9, "leavingGroup": { "atoms": [ 10 @@ -28031,147 +28031,147 @@ }, "monomerTemplate-P___Proline": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 0.0018, - 1.6555, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.4799, - 1.889, - 0 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-0.866, + -1, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -0.5, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.732, + -0.5, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -1, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + -0.5, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -2, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0.5, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "O", + "location": [ + 0.866, + 1, + 0 + ] + }, + { + "label": "H", + "location": [ + 0.866, + 2, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 1, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 9 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 5, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 9 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "T___Threonine", @@ -30328,28 +30328,28 @@ "alias": "T", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 4 + 2 ] }, "type": "left" }, { - "attachmentAtom": 0, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 8 + 4 ] }, "type": "right" }, { - "attachmentAtom": 6, + "attachmentAtom": 7, "leavingGroup": { "atoms": [ - 9 + 8 ] }, "type": "side" @@ -31458,140 +31458,140 @@ }, "monomerTemplate-V___Valine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.1543, - -0.9675, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.1446, - -0.2156, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - -1.1823, - 1.8865, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.1438, - 1.2853, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.896, - 1.8843, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.1536, - -2.1676, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.4435, - -0.9675, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.1941, - -0.3685, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.4838, - -0.3695, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 5, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 6 - ] - }, - { - "type": 1, "atoms": [ - 1, - 3 + { + "label": "N", + "location": [ + -0.866, + -0.5, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.732, + 0, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -0.5, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + 0, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -1.5, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 1, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + 1.5, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 1.5, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 8 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 3, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 8 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "V___Valine", @@ -31599,19 +31599,19 @@ "alias": "V", "attachmentPoints": [ { - "attachmentAtom": 6, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 8 + 2 ] }, "type": "left" }, { - "attachmentAtom": 0, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 7 + 4 ] }, "type": "right" @@ -31621,274 +31621,272 @@ }, "monomerTemplate-W___Tryptophan": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 2.0938, - -2.3551, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.0952, - -3.3, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.0698, - -1.7652, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "N", - "location": [ - 0.0459, - -2.3551, - 0 - ] - }, - { - "label": "H", - "location": [ - -0.7723, - -1.8826, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.068, - -0.5835, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.0458, - 0.0055, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.0319, - -0.4779, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.8246, - 0.3978, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.237, - 1.4216, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.081, - 1.1793, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.7068, - 2.0591, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.3387, - 3.1814, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.8173, - 3.4238, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.6051, - 2.5438, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.9114, - -1.8818, - 0 - ] - }, - { - "label": "H", - "location": [ - -3.0061, - 0.3887, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 1, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 5 + { + "label": "N", + "location": [ + -0.01, + -1.948, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.857, + -1.447, + 0 + ] + }, + { + "label": "H", + "location": [ + -0.877, + -1.447, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.724, + -1.948, + 0 + ] + }, + { + "label": "O", + "location": [ + 2.592, + -1.447, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.724, + -2.949, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.857, + -0.446, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.01, + 0.055, + 0 + ] + }, + { + "label": "N", + "location": [ + -1.596, + 0.392, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.93, + -0.35, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.095, + 1.26, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.119, + 1.054, + 0 + ] + }, + { + "label": "H", + "location": [ + -2.592, + 0.288, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.546, + 1.796, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.237, + 2.744, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.739, + 2.949, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.404, + 2.207, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 11 + ] + }, + { + "type": 1, + "atoms": [ + 11, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 10, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 12 + ] + }, + { + "type": 1, + "atoms": [ + 11, + 13 + ] + }, + { + "type": 1, + "atoms": [ + 13, + 14 + ] + }, + { + "type": 1, + "atoms": [ + 14, + 15 + ] + }, + { + "type": 1, + "atoms": [ + 15, + 16 + ] + }, + { + "type": 1, + "atoms": [ + 16, + 10 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 2, - "atoms": [ - 7, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 9, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 10, - 6 - ] - }, - { - "type": 2, - "atoms": [ - 10, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 10, - 11 - ] - }, - { - "type": 2, - "atoms": [ - 11, - 12 - ] - }, - { - "type": 1, - "atoms": [ - 12, - 13 - ] - }, - { - "type": 1, - "atoms": [ - 14, - 9 - ] - }, - { - "type": 2, - "atoms": [ - 13, - 14 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 15 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 16 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "W___Tryptophan", @@ -31896,19 +31894,19 @@ "alias": "W", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 4 + 2 ] }, "type": "left" }, { - "attachmentAtom": 0, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 15 + 4 ] }, "type": "right" @@ -31917,7 +31915,7 @@ "attachmentAtom": 8, "leavingGroup": { "atoms": [ - 16 + 12 ] }, "type": "side" @@ -32187,237 +32185,237 @@ }, "monomerTemplate-Y___Tyrosine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 2.2957, - -1.9502, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.2972, - -2.8951, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.2718, - -1.3602, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "N", - "location": [ - 0.2479, - -1.9502, - 0 - ] - }, - { - "label": "H", - "location": [ - -0.5703, - -1.4776, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.2701, - -0.1785, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.2461, - 0.4114, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.2426, - 1.5925, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.782, - 2.1801, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.8031, - 1.5866, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.7996, - 0.4055, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.7751, - -0.182, - 0 - ] - }, - { - "label": "O", - "location": [ - -2.6228, - 2.0566, - 0 - ] - }, - { - "label": "O", - "location": [ - 3.1134, - -1.4768, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.6319, - 3.2381, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 1, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 5 + { + "label": "N", + "location": [ + 0, + -1.75, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -1.25, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -0.866, + -1.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.732, + -1.75, + 0 + ] + }, + { + "label": "O", + "location": [ + 2.598, + -1.25, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + -2.75, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 1.25, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + 1.75, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.732, + 1.25, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.732, + 0.25, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + -0.25, + 0 + ] + }, + { + "label": "O", + "location": [ + -2.598, + 1.75, + 0 + ] + }, + { + "label": "H", + "location": [ + -2.598, + 2.75, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 2, + "atoms": [ + 12, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 2, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 10 + ] + }, + { + "type": 2, + "atoms": [ + 10, + 11 + ] + }, + { + "type": 1, + "atoms": [ + 11, + 12 + ] + }, + { + "type": 1, + "atoms": [ + 10, + 13 + ] + }, + { + "type": 1, + "atoms": [ + 13, + 14 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 6 - ] - }, - { - "type": 2, - "atoms": [ - 8, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 9, - 8 - ] - }, - { - "type": 2, - "atoms": [ - 10, - 9 - ] - }, - { - "type": 2, - "atoms": [ - 11, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 11, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 9, - 12 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 13 - ] - }, - { - "type": 1, - "atoms": [ - 12, - 14 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "Y___Tyrosine", @@ -32425,25 +32423,25 @@ "alias": "Y", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 4 + 2 ] }, "type": "left" }, { - "attachmentAtom": 0, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 13 + 4 ] }, "type": "right" }, { - "attachmentAtom": 12, + "attachmentAtom": 13, "leavingGroup": { "atoms": [ 14 @@ -41964,140 +41962,140 @@ }, "monomerTemplate-U___Selenocysteine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "N", - "location": [ - -0.4339745962155608, - -1.0000000000000009, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.4320508075688785, - -0.5000000000000009, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 1.298076211353316, - -1.0000000000000027, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.1641016151377572, - -0.5000000000000027, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.298076211353316, - -2.0000000000000027, - 0 - ] - }, - { - "label": "H", - "location": [ - -1.3, - -0.5000000000000009, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.4320508075688785, - 0.4999999999999991, - 0 - ] - }, - { - "label": "Se", - "location": [ - -0.433974596215559, - 1.0000000000000009, - 0 - ] - }, - { - "label": "H", - "location": [ - -0.433974596215559, - 2, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 2, - "atoms": [ - 2, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 6 + { + "label": "N", + "location": [ + -0.866, + -1, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -0.5, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -1.732, + -0.5, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + -1, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.732, + -0.5, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -2, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + 0.5, + 0 + ] + }, + { + "label": "Se", + "location": [ + -0.866, + 1, + 0 + ] + }, + { + "label": "H", + "location": [ + -0.866, + 2, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 6, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 8 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "U___Selenocysteine", @@ -42108,16 +42106,16 @@ "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 5 + 2 ] }, "type": "left" }, { - "attachmentAtom": 2, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 3 + 4 ] }, "type": "right" @@ -45321,299 +45319,299 @@ }, "monomerTemplate-O___Pyrrolysine": { "type": "monomerTemplate", - "atoms": [ - { - "label": "H", - "location": [ - -2.0487, - -3.86, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.0256, - -4.4508, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.0024, - -3.86, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 1.0208, - -4.4508, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.0439, - -3.86, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.0208, - -5.6322, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.0024, - -2.6786, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.5883, - -1.6554, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.0024, - -0.6322, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.5883, - 0.3909, - 0 - ] - }, - { - "label": "N", - "location": [ - -0.0024, - 1.4141, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.5883, - 2.4373, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.0024, - 3.4604, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "O", - "location": [ - 1.7698, - 2.4373, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.1768, - 3.5839, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.4223, - 4.739, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.3997, - 5.3294, - 0 - ] - }, - { - "label": "N", - "location": [ - 0.4779, - 4.5392, - 0 - ] - }, - { - "label": "C", - "location": [ - -2.0122, - 2.7484, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 2, - "atoms": [ - 3, - 5 - ] - }, - { - "type": 1, "atoms": [ - 2, - 6 + { + "label": "N", + "location": [ + -1.732, + -3.269, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + -2.769, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "H", + "location": [ + -2.598, + -2.769, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -3.269, + 0 + ] + }, + { + "label": "O", + "location": [ + 0.866, + -2.769, + 0 + ] + }, + { + "label": "O", + "location": [ + 0, + -4.269, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.866, + -1.769, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -1.269, + 0 + ] + }, + { + "label": "C", + "location": [ + 0, + -0.269, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.866, + 0.231, + 0 + ] + }, + { + "label": "N", + "location": [ + 0.866, + 1.231, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.732, + 1.731, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.732, + 2.731, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "O", + "location": [ + 2.598, + 1.231, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.923, + 3.318, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.232, + 4.269, + 0 + ] + }, + { + "label": "C", + "location": [ + 2.232, + 4.269, + 0 + ] + }, + { + "label": "N", + "location": [ + 2.541, + 3.318, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.028, + 3.009, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 10, + 11 + ] + }, + { + "type": 1, + "atoms": [ + 11, + 12 + ] + }, + { + "type": 2, + "atoms": [ + 11, + 13 + ] + }, + { + "type": 1, + "atoms": [ + 12, + 17 + ] + }, + { + "type": 2, + "atoms": [ + 17, + 16 + ] + }, + { + "type": 1, + "atoms": [ + 16, + 15 + ] + }, + { + "type": 1, + "atoms": [ + 15, + 14 + ] + }, + { + "type": 1, + "atoms": [ + 14, + 18 + ] + }, + { + "type": 1, + "atoms": [ + 12, + 14 + ], + "stereo": 1 + } ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 6, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 9, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 10, - 11 - ] - }, - { - "type": 1, - "atoms": [ - 11, - 12 - ] - }, - { - "type": 2, - "atoms": [ - 11, - 13 - ] - }, - { - "type": 2, - "atoms": [ - 16, - 17 - ] - }, - { - "type": 1, - "atoms": [ - 15, - 16 - ] - }, - { - "type": 1, - "atoms": [ - 14, - 15 - ] - }, - { - "type": 1, - "atoms": [ - 12, - 14 - ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 17, - 12 - ] - }, - { - "type": 1, - "atoms": [ - 14, - 18 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "O___Pyrrolysine", @@ -45621,10 +45619,10 @@ "alias": "O", "attachmentPoints": [ { - "attachmentAtom": 1, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 0 + 2 ] }, "type": "left" diff --git a/packages/ketcher-core/src/application/render/renderStruct.ts b/packages/ketcher-core/src/application/render/renderStruct.ts index 6cd385b5f4..a9d0ca431e 100644 --- a/packages/ketcher-core/src/application/render/renderStruct.ts +++ b/packages/ketcher-core/src/application/render/renderStruct.ts @@ -110,8 +110,8 @@ export class RenderStruct { }; if (window.isPolymerEditorTurnedOn) { - extendedOptions.fontsz = 40; - extendedOptions.fontszsub = 30; + extendedOptions.fontsz = 30; + extendedOptions.fontszsub = 20; extendedOptions.width = svgSize; extendedOptions.height = svgSize; } diff --git a/packages/ketcher-macromolecules/package.json b/packages/ketcher-macromolecules/package.json index 6cc8cbd740..d65cff9134 100644 --- a/packages/ketcher-macromolecules/package.json +++ b/packages/ketcher-macromolecules/package.json @@ -1,6 +1,6 @@ { "name": "ketcher-macromolecules", - "version": "3.1.0-rc.5", + "version": "3.1.0-rc.6", "description": "Web-based molecule sketcher", "license": "Apache-2.0", "homepage": "http://lifescience.opensource.epam.com/ketcher", diff --git a/packages/ketcher-react/package.json b/packages/ketcher-react/package.json index d00a2a16fc..7475d6d839 100644 --- a/packages/ketcher-react/package.json +++ b/packages/ketcher-react/package.json @@ -1,6 +1,6 @@ { "name": "ketcher-react", - "version": "3.1.0-rc.5", + "version": "3.1.0-rc.6", "description": "Web-based molecule sketcher", "license": "Apache-2.0", "homepage": "http://lifescience.opensource.epam.com/ketcher", diff --git a/packages/ketcher-standalone/package.json b/packages/ketcher-standalone/package.json index 8f2f06e735..24433f26b4 100644 --- a/packages/ketcher-standalone/package.json +++ b/packages/ketcher-standalone/package.json @@ -1,6 +1,6 @@ { "name": "ketcher-standalone", - "version": "3.1.0-rc.5", + "version": "3.1.0-rc.6", "description": "Web-based molecule sketcher", "license": "Apache-2.0", "homepage": "http://lifescience.opensource.epam.com/ketcher",