diff --git a/ketcher-autotests/tests/Macromolecule-editor/API-Macro/set-mode.spec.ts-snapshots/setMode-Should-set-sequence-mode-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/API-Macro/set-mode.spec.ts-snapshots/setMode-Should-set-sequence-mode-1-chromium-linux.png index 9788797494..126b02daf5 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/API-Macro/set-mode.spec.ts-snapshots/setMode-Should-set-sequence-mode-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/API-Macro/set-mode.spec.ts-snapshots/setMode-Should-set-sequence-mode-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/API-Macro/set-mode.spec.ts-snapshots/setMode-Should-set-sequence-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/API-Macro/set-mode.spec.ts-snapshots/setMode-Should-set-sequence-mode-2-chromium-linux.png index a0dfb9807f..979c989a87 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/API-Macro/set-mode.spec.ts-snapshots/setMode-Should-set-sequence-mode-2-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/API-Macro/set-mode.spec.ts-snapshots/setMode-Should-set-sequence-mode-2-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Clear-Tool/clear-tool.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Clear-Tool/clear-tool.spec.ts index 0e2f91fdd2..6ebb5ac69f 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Clear-Tool/clear-tool.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Clear-Tool/clear-tool.spec.ts @@ -13,6 +13,7 @@ import { turnOnMicromoleculesEditor, } from '@utils/macromolecules'; import { bondTwoMonomers } from '@utils/macromolecules/polymerBond'; +import { Peptides } from '@utils/selectors/macromoleculeEditor'; /* eslint-disable no-magic-numbers */ test.describe('Clear Canvas Tool', () => { @@ -29,7 +30,7 @@ test.describe('Clear Canvas Tool', () => { */ // Create 4 peptides on canvas - const MONOMER_NAME = 'Tza___3-thiazolylalanine'; + const MONOMER_NAME = Peptides.Tza; const MONOMER_ALIAS = 'Tza'; const peptide1 = await addSingleMonomerToCanvas( diff --git a/ketcher-autotests/tests/Macromolecule-editor/Erase-Tool/erase-tool.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Erase-Tool/erase-tool.spec.ts index ab686b59ac..1d4a1a1643 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Erase-Tool/erase-tool.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Erase-Tool/erase-tool.spec.ts @@ -22,6 +22,7 @@ import { turnOnMacromoleculesEditor, } from '@utils/macromolecules'; import { bondTwoMonomers } from '@utils/macromolecules/polymerBond'; +import { Peptides } from '@utils/selectors/macromoleculeEditor'; /* eslint-disable no-magic-numbers */ test.describe('Erase Tool', () => { @@ -37,7 +38,7 @@ test.describe('Erase Tool', () => { */ // Create 4 peptides on canvas - const MONOMER_NAME = 'Tza___3-thiazolylalanine'; + const MONOMER_NAME = Peptides.Tza; const MONOMER_ALIAS = 'Tza'; const peptide1 = await addSingleMonomerToCanvas( diff --git a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts index 3a62fe8a41..16a90bc991 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts @@ -22,6 +22,7 @@ import { dragMouseTo, } from '@utils'; import { turnOnMacromoleculesEditor } from '@utils/macromolecules'; +import { Peptides } from '@utils/selectors/macromoleculeEditor'; test.describe('Import-Saving .ket Files', () => { test.beforeEach(async ({ page }) => { @@ -124,7 +125,7 @@ test.describe('Import-Saving .ket Files', () => { Test case: Import/Saving files #3827 #3757 Description: The monomer name is present in the preview after opening the saved file. */ - await page.getByTestId('Bal___beta-Alanine').click(); + await page.getByTestId(Peptides.BetaAlanine).click(); await clickInTheMiddleOfTheScreen(page); const expectedFile = await getKet(page); await saveToFile('KET/monomer-expected.ket', expectedFile); @@ -196,7 +197,7 @@ test.describe('Import-Saving .ket Files', () => { Test case: Import/Saving files #4172 Description: "leavingGroup" section contain information about number of atoms. */ - await page.getByTestId('D-2Nal___D-3-naphthylalanine').click(); + await page.getByTestId(Peptides.D2Nal).click(); await clickInTheMiddleOfTheScreen(page); const expectedFile = await getKet(page); await saveToFile('KET/D-2Nal-expected.ket', expectedFile); diff --git a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts-snapshots/Import-Saving-ket-Files-Validate-that-saving--0540b-fter-loading-it-back-from-ket-file-to-canvas-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts-snapshots/Import-Saving-ket-Files-Validate-that-saving--0540b-fter-loading-it-back-from-ket-file-to-canvas-1-chromium-linux.png index 5771a59db0..2092b311b3 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts-snapshots/Import-Saving-ket-Files-Validate-that-saving--0540b-fter-loading-it-back-from-ket-file-to-canvas-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts-snapshots/Import-Saving-ket-Files-Validate-that-saving--0540b-fter-loading-it-back-from-ket-file-to-canvas-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts index 9c857975c6..be58a68238 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts @@ -65,6 +65,7 @@ import { import { bondTwoMonomersPointToPoint } from '@utils/macromolecules/polymerBond'; import { clickOnSequenceSymbol } from '@utils/macromolecules/sequence'; import { miewApplyButtonIsEnabled } from '@utils/common/loaders/waitForMiewApplyButtonIsEnabled'; +import { Peptides } from '@utils/selectors/macromoleculeEditor'; const topLeftCorner = { x: -325, @@ -101,7 +102,7 @@ async function pasteFromClipboard( } async function addToFavoritesMonomers(page: Page) { - await page.getByTestId('Bal___beta-Alanine').getByText('★').click(); + await page.getByTestId(Peptides.BetaAlanine).getByText('★').click(); await page .getByTestId('Phe4Me___p-Methylphenylalanine') .getByText('★') @@ -582,7 +583,7 @@ test.describe('Macro-Micro-Switcher', () => { After closing the ticket, should update the screenshots. */ - await page.getByTestId('Bal___beta-Alanine').click(); + await page.getByTestId(Peptides.BetaAlanine).click(); await clickInTheMiddleOfTheScreen(page); await turnOnMicromoleculesEditor(page); await selectRing(RingButton.Benzene, page); @@ -608,7 +609,7 @@ test.describe('Macro-Micro-Switcher', () => { ); } }); - await page.getByTestId('Bal___beta-Alanine').click(); + await page.getByTestId(Peptides.BetaAlanine).click(); await clickInTheMiddleOfTheScreen(page); await turnOnMicromoleculesEditor(page); await turnOnMacromoleculesEditor(page); diff --git a/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Add-to-Favorites-section--a53db--and-CHEMs-then-switch-to-Micro-mode-and-back-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Add-to-Favorites-section--a53db--and-CHEMs-then-switch-to-Micro-mode-and-back-1-chromium-linux.png index 7371dd607b..3ee9980403 100755 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Add-to-Favorites-section--a53db--and-CHEMs-then-switch-to-Micro-mode-and-back-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Add-to-Favorites-section--a53db--and-CHEMs-then-switch-to-Micro-mode-and-back-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Add-to-Favorites-section--afd6d-ide-Library-and-switch-to-Micro-mode-and-back-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Add-to-Favorites-section--afd6d-ide-Library-and-switch-to-Micro-mode-and-back-1-chromium-linux.png index de9045bc46..95ecb7933b 100755 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Add-to-Favorites-section--afd6d-ide-Library-and-switch-to-Micro-mode-and-back-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts-snapshots/Macro-Micro-Switcher-Add-to-Favorites-section--afd6d-ide-Library-and-switch-to-Micro-mode-and-back-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts index fa5b61b861..e8efcbccff 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts @@ -13,6 +13,7 @@ import { waitForPageInit, } from '@utils'; import { turnOnMacromoleculesEditor } from '@utils/macromolecules'; +import { Chems } from '@utils/selectors/macromoleculeEditor'; test.describe('Peptide library testing', () => { test.beforeEach(async ({ page }) => { @@ -33,7 +34,7 @@ test.describe('Peptide library testing', () => { test('Placing betaAlanine on canvas', async ({ page }) => { // placing molecule on canvas and molecule selected state check - await addPeptideOnCanvas(page, 'Bal___beta-Alanine'); + await addPeptideOnCanvas(page, 'bAla___beta-Alanine'); await takeEditorScreenshot(page); }); @@ -208,7 +209,7 @@ test.describe('Peptide library testing', () => { Description: A tooltip appears when hovering over a CHEM on canvas while Selection tool is selected. */ await page.getByTestId('CHEM-TAB').click(); - await page.getByTestId('SMPEG2___SM(PEG)2 linker from Pierce').click(); + await page.getByTestId(Chems.SMPEG2).click(); await clickInTheMiddleOfTheScreen(page); await selectRectangleSelectionTool(page); await page.getByText('SMPEG2').locator('..').first().hover(); diff --git a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-A-tooltip-appears-when-c6566-EM-on-canvas-while-Selection-tool-is-selected-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-A-tooltip-appears-when-c6566-EM-on-canvas-while-Selection-tool-is-selected-1-chromium-linux.png index 1b8ed85d00..342d4a1290 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-A-tooltip-appears-when-c6566-EM-on-canvas-while-Selection-tool-is-selected-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-A-tooltip-appears-when-c6566-EM-on-canvas-while-Selection-tool-is-selected-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Monomer-library-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Monomer-library-1-chromium-linux.png index 14d904bb7e..8456b7f874 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Monomer-library-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Monomer-library-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Placing-betaAlanine-on-canvas-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Placing-betaAlanine-on-canvas-1-chromium-linux.png index 7b1ea8c7ba..bc682e259c 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Placing-betaAlanine-on-canvas-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Placing-betaAlanine-on-canvas-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Structure-displaying-in-library-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Structure-displaying-in-library-1-chromium-linux.png index 4c571cb99a..5dcf5272e1 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Structure-displaying-in-library-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-Structure-displaying-in-library-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-add-molecule-in-favourites-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-add-molecule-in-favourites-1-chromium-linux.png index 0e3008e894..2a32297260 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-add-molecule-in-favourites-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Peptides/peptide-monomer-library.spec.ts-snapshots/Peptide-library-testing-add-molecule-in-favourites-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-hover.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-hover.spec.ts index 602f1040db..7b701ac7cd 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-hover.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-hover.spec.ts @@ -7,6 +7,7 @@ import { } from '@utils'; import { turnOnMacromoleculesEditor } from '@utils/macromolecules'; import { bondTwoMonomers } from '@utils/macromolecules/polymerBond'; +import { Peptides } from '@utils/selectors/macromoleculeEditor'; test.describe('Check attachment point hover', () => { test.beforeEach(async ({ page }) => { @@ -17,7 +18,7 @@ test.describe('Check attachment point hover', () => { test('Move monomer bonded with another monomers and hover attachment points', async ({ page, }) => { - const MONOMER_NAME = 'Tza___3-thiazolylalanine'; + const MONOMER_NAME = Peptides.Tza; const MONOMER_ALIAS = 'Tza'; const coordinatesStart = { x: 300, y: 300 }; const peptide1 = await addSingleMonomerToCanvas( diff --git a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts index c681e164b8..09067a376c 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts @@ -9,6 +9,7 @@ import { } from '@utils'; import { turnOnMacromoleculesEditor } from '@utils/macromolecules'; import { bondTwoMonomers } from '@utils/macromolecules/polymerBond'; +import { Peptides } from '@utils/selectors/macromoleculeEditor'; /* eslint-disable no-magic-numbers */ test.describe('Check attachment point rotation', () => { @@ -24,7 +25,7 @@ test.describe('Check attachment point rotation', () => { */ // Create 4 peptides on canvas - const MONOMER_NAME = 'Tza___3-thiazolylalanine'; + const MONOMER_NAME = Peptides.Tza; const MONOMER_ALIAS = 'Tza'; // Get 4 peptides locators @@ -94,7 +95,7 @@ test.describe('Check attachment point rotation', () => { Description: when monomers are moved, attachment points move also */ - const MONOMER_NAME = 'Tza___3-thiazolylalanine'; + const MONOMER_NAME = Peptides.Tza; const MONOMER_ALIAS = 'Tza'; // Get 4 peptides locators diff --git a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Move-monomer-b-29ea5--another-monomers-and-check-attachment-points-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Move-monomer-b-29ea5--another-monomers-and-check-attachment-points-2-chromium-linux.png index 4648360581..02c2d5d29c 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Move-monomer-b-29ea5--another-monomers-and-check-attachment-points-2-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Move-monomer-b-29ea5--another-monomers-and-check-attachment-points-2-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Move-monomer-b-c144d--another-monomers-and-check-attachment-points-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Move-monomer-b-c144d--another-monomers-and-check-attachment-points-1-chromium-linux.png index bfc3258e5e..9262cec2ec 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Move-monomer-b-c144d--another-monomers-and-check-attachment-points-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Move-monomer-b-c144d--another-monomers-and-check-attachment-points-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Select-monomer-and-bonds-and-then-hover-monomer-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Select-monomer-and-bonds-and-then-hover-monomer-1-chromium-linux.png index e7a7716133..363967947c 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Select-monomer-and-bonds-and-then-hover-monomer-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Select-monomer-and-bonds-and-then-hover-monomer-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Select-monomer-and-bonds-and-then-hover-monomer-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Select-monomer-and-bonds-and-then-hover-monomer-2-chromium-linux.png index 8391a654be..e9d375b1de 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Select-monomer-and-bonds-and-then-hover-monomer-2-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/attachment-point-rotation.spec.ts-snapshots/Check-attachment-point-rotation-Select-monomer-and-bonds-and-then-hover-monomer-2-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts index e3c7dfb5c5..a10c2ff9de 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts @@ -12,6 +12,7 @@ import { } from '@utils/macromolecules'; import { connectMonomersWithBonds } from '@utils/macromolecules/monomer'; import { bondTwoMonomers } from '@utils/macromolecules/polymerBond'; +import { Chems, Peptides } from '@utils/selectors/macromoleculeEditor'; /* eslint-disable no-magic-numbers */ test.describe('Polymer Bond Tool', () => { @@ -30,7 +31,7 @@ test.describe('Polymer Bond Tool', () => { Description: Polymer bond tool */ // Choose peptide - const MONOMER_NAME = 'Tza___3-thiazolylalanine'; + const MONOMER_NAME = Peptides.Tza; const MONOMER_ALIAS = 'Tza'; const peptide1 = await addSingleMonomerToCanvas( @@ -88,7 +89,7 @@ test.describe('Polymer Bond Tool', () => { */ // Choose chems await page.getByText('CHEM').click(); - await page.getByTestId('hxy___Hexynyl alcohol').click(); + await page.getByTestId(Chems.hxy).click(); // Create 2 chems on canvas await page.mouse.click(300, 300); @@ -126,7 +127,7 @@ test.describe('Signle Bond Tool', () => { Description: The system shall unable user to create more than 1 bond between the first and the second monomer */ - const MONOMER_NAME = 'Tza___3-thiazolylalanine'; + const MONOMER_NAME = Peptides.Tza; const MONOMER_ALIAS = 'Tza'; const peptide1 = await addSingleMonomerToCanvas( page, @@ -165,9 +166,9 @@ test.describe('Signle Bond Tool', () => { const x = 800; const y = 350; await page.locator('.css-1kbfai8').click(); - await page.getByTestId('Bal___beta-Alanine').click(); + await page.getByTestId(Peptides.BetaAlanine).click(); await clickInTheMiddleOfTheScreen(page); - await page.getByTestId('Edc___S-ethylthiocysteine').click(); + await page.getByTestId(Peptides.Ethylthiocysteine).click(); await page.mouse.click(x, y); await connectMonomersWithBonds(page, ['Bal', 'Edc']); await takeEditorScreenshot(page); diff --git a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts-snapshots/Polymer-Bond-Tool-Create-bond-between-two-chems-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts-snapshots/Polymer-Bond-Tool-Create-bond-between-two-chems-1-chromium-linux.png index 9c4577f46c..a3514bfab4 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts-snapshots/Polymer-Bond-Tool-Create-bond-between-two-chems-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts-snapshots/Polymer-Bond-Tool-Create-bond-between-two-chems-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts-snapshots/Signle-Bond-Tool-Check-in-full-screen-mode-it--0f0a2-pulled-not-from-a-specific-attachment-point-R-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts-snapshots/Signle-Bond-Tool-Check-in-full-screen-mode-it--0f0a2-pulled-not-from-a-specific-attachment-point-R-1-chromium-linux.png index 354782e69e..e8b5b84487 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts-snapshots/Signle-Bond-Tool-Check-in-full-screen-mode-it--0f0a2-pulled-not-from-a-specific-attachment-point-R-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/polymer-bond-tool.spec.ts-snapshots/Signle-Bond-Tool-Check-in-full-screen-mode-it--0f0a2-pulled-not-from-a-specific-attachment-point-R-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/rna-library.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/rna-library.spec.ts index ca99b3114d..d0595f089f 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/rna-library.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/rna-library.spec.ts @@ -44,6 +44,7 @@ import { toggleRnaBuilderAccordion, toggleSugarsAccordion, } from '@utils/macromolecules/rnaBuilder'; +import { Chems } from '@utils/selectors/macromoleculeEditor'; async function expandCollapseRnaBuilder(page: Page) { await page @@ -1349,7 +1350,7 @@ test.describe('RNA Library', () => { await moveMouseAway(page); // Case 24 - await page.getByTestId('SMPEG2___SM(PEG)2 linker from Pierce').hover(); + await page.getByTestId(Chems.SMPEG2).hover(); await delay(1); await takeMonomerLibraryScreenshot(page); await moveMouseAway(page); diff --git a/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/rna-library.spec.ts-snapshots/RNA-Library-CHEM-tab-check-at-Library-3-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/rna-library.spec.ts-snapshots/RNA-Library-CHEM-tab-check-at-Library-3-chromium-linux.png index 57f2a65a91..54b62774b6 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/rna-library.spec.ts-snapshots/RNA-Library-CHEM-tab-check-at-Library-3-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/rna-library.spec.ts-snapshots/RNA-Library-CHEM-tab-check-at-Library-3-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts index 47635360b6..ebc4045b2d 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts @@ -48,7 +48,7 @@ test.describe('Rectangle Selection Tool', () => { */ // Create 4 peptides on canvas - const MONOMER_NAME = 'Tza___3-thiazolylalanine'; + const MONOMER_NAME = Peptides.Tza; const MONOMER_ALIAS = 'Tza'; const peptide1 = await addSingleMonomerToCanvas( @@ -191,7 +191,7 @@ test.describe('Rectangle Selection Tool', () => { */ // Create 4 peptides on canvas - const MONOMER_NAME = 'Tza___3-thiazolylalanine'; + const MONOMER_NAME = 'Tza___3-(4-Thiazolyl)-alanine'; const MONOMER_ALIAS = 'Tza'; const peptide1 = await addSingleMonomerToCanvas( @@ -385,9 +385,9 @@ test.describe('Rectangle Selection Tool', () => { */ const x = 200; const y = 200; - await addPeptideOnCanvas(page, 'Nal___3-naphthylalanine'); + await addPeptideOnCanvas(page, '2Nal___3-(2-naphthyl)-alanine'); await selectRectangleSelectionTool(page); - await page.getByText('Nal').locator('..').first().hover(); + await page.getByText('2Nal').locator('..').first().hover(); await dragMouseTo(x, y, page); await page.getByTestId('undo').click(); await takeEditorScreenshot(page); diff --git a/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Monomer-appears-above-other-monomers-when-selected-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Monomer-appears-above-other-monomers-when-selected-1-chromium-linux.png index 2664a63ec8..d4cd1ae931 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Monomer-appears-above-other-monomers-when-selected-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Monomer-appears-above-other-monomers-when-selected-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-a-monomer-then-use-the-Undo-Redo-function-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-a-monomer-then-use-the-Undo-Redo-function-1-chromium-linux.png index f5d3b42ec9..7f91969d8b 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-a-monomer-then-use-the-Undo-Redo-function-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-a-monomer-then-use-the-Undo-Redo-function-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-a-monomer-then-use-the-Undo-Redo-function-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-a-monomer-then-use-the-Undo-Redo-function-2-chromium-linux.png index 676cd75d8d..4daacdcc52 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-a-monomer-then-use-the-Undo-Redo-function-2-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-a-monomer-then-use-the-Undo-Redo-function-2-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-monomer-bonded-with-another-monomers-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-monomer-bonded-with-another-monomers-2-chromium-linux.png index 751c9a4497..ce233da175 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-monomer-bonded-with-another-monomers-2-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Rectangle-Selection-Tool/rectangle-selection-tool.spec.ts-snapshots/Rectangle-Selection-Tool-Move-monomer-bonded-with-another-monomers-2-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode.spec.ts-snapshots/Sequence-Mode-Select-drop-down-menu-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode.spec.ts-snapshots/Sequence-Mode-Select-drop-down-menu-1-chromium-linux.png index 500a2d32c9..eafb7b0838 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode.spec.ts-snapshots/Sequence-Mode-Select-drop-down-menu-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode.spec.ts-snapshots/Sequence-Mode-Select-drop-down-menu-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts index ea58fec755..137991ca86 100755 --- a/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts @@ -28,14 +28,15 @@ import { turnOnMicromoleculesEditor, } from '@utils/macromolecules'; import { bondTwoMonomers } from '@utils/macromolecules/polymerBond'; +import { Peptides } from '@utils/selectors/macromoleculeEditor'; /* eslint-disable no-magic-numbers */ -const MONOMER_NAME_TZA = 'Tza___3-thiazolylalanine'; +const MONOMER_NAME_TZA = Peptides.Tza; const MONOMER_ALIAS_TZA = 'Tza'; async function createBondedMonomers(page: Page) { - const MONOMER_NAME_DSEC = 'dSec___D-SelenoCysteine'; - const MONOMER_ALIAS_DSEC = 'dSec'; + const MONOMER_NAME_DSEC = 'dU___D-selenocysteine'; + const MONOMER_ALIAS_DSEC = 'dU'; const MONOMER_NAME_MEC = 'meC___N-Methyl-Cysteine'; const MONOMER_ALIAS_MEC = 'meC'; @@ -365,8 +366,8 @@ test.describe('Snake Bond Tool', () => { await page.getByTestId('PEPTIDES-TAB').click(); await addBondedMonomersToCanvas( page, - 'Bal___beta-Alanine', - 'Bal', + Peptides.BetaAlanine, + 'bAla', 700, 500, 50, @@ -541,8 +542,8 @@ test.describe('Snake Bond Tool', () => { const [balPeptide] = await addBondedMonomersToCanvas( page, - 'Bal___beta-Alanine', - 'Bal', + Peptides.BetaAlanine, + 'bAla', 700, 700, 50, @@ -551,8 +552,8 @@ test.describe('Snake Bond Tool', () => { ); const balPeptide1 = await addSingleMonomerToCanvas( page, - 'Bal___beta-Alanine', - 'Bal', + Peptides.BetaAlanine, + 'bAla', 850, 650, 2, @@ -577,8 +578,8 @@ test.describe('Snake Bond Tool', () => { test('Create snake mode for single monomer and nucleoside', async () => { await addSingleMonomerToCanvas( page, - 'Bal___beta-Alanine', - 'Bal', + Peptides.BetaAlanine, + 'bAla', 300, 300, 0, diff --git a/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Check-finding-right-chain-sequence-using-snake-mode-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Check-finding-right-chain-sequence-using-snake-mode-1-chromium-linux.png index 4d62ad463a..3489a8f6f2 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Check-finding-right-chain-sequence-using-snake-mode-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Check-finding-right-chain-sequence-using-snake-mode-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Check-finding-right-chain-sequence-using-snake-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Check-finding-right-chain-sequence-using-snake-mode-2-chromium-linux.png index 9ea9e95753..f12c703b9b 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Check-finding-right-chain-sequence-using-snake-mode-2-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Check-finding-right-chain-sequence-using-snake-mode-2-chromium-linux.png differ diff --git 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and b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Create-snake-mode-for-single-monomer-and-nucleoside-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Create-snake-mode-for-single-monomer-and-nucleoside-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Create-snake-mode-for-single-monomer-and-nucleoside-2-chromium-linux.png index 7a4806ad81..c00762142f 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Create-snake-mode-for-single-monomer-and-nucleoside-2-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Create-snake-mode-for-single-monomer-and-nucleoside-2-chromium-linux.png differ diff --git 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a/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Pressing-snake-layout-button-f0566-rming-chain-on-screen-in-a-snake-like-pattern-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Pressing-snake-layout-button-f0566-rming-chain-on-screen-in-a-snake-like-pattern-1-chromium-linux.png index 22c2b449e6..38d343d627 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Pressing-snake-layout-button-f0566-rming-chain-on-screen-in-a-snake-like-pattern-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Snake-Mode/snake-bond-tool.spec.ts-snapshots/Snake-Bond-Tool-Pressing-snake-layout-button-f0566-rming-chain-on-screen-in-a-snake-like-pattern-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts index 027800a9fa..3d74cdb6d9 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts @@ -21,6 +21,7 @@ import { moveMonomer, } from '@utils/macromolecules/monomer'; import { bondTwoMonomers } from '@utils/macromolecules/polymerBond'; +import { Peptides } from '@utils/selectors/macromoleculeEditor'; /* eslint-disable no-magic-numbers */ test.describe('Undo Redo', () => { @@ -29,7 +30,7 @@ test.describe('Undo Redo', () => { test.beforeEach(async ({ page }) => { await waitForPageInit(page); await turnOnMacromoleculesEditor(page); - const MONOMER_NAME = 'Tza___3-thiazolylalanine'; + const MONOMER_NAME = Peptides.Tza; const MONOMER_ALIAS = 'Tza'; peptide1 = await addSingleMonomerToCanvas( @@ -195,7 +196,7 @@ test.describe('Undo-Redo tests', () => { */ const addMonomers = async (x: number, y: number) => { - await page.getByTestId('Bal___beta-Alanine').click(); + await page.getByTestId(Peptides.BetaAlanine).click(); await page.mouse.click(x, y); }; @@ -235,7 +236,7 @@ test.describe('Undo-Redo tests', () => { const addMonomers = async (x: number, y: number) => { await page.getByTestId('CHEM-TAB').click(); - await page.getByTestId('SMPEG2___SM(PEG)2 linker from Pierce').click(); + await page.getByTestId('SMPEG2___SM(PEG)2').click(); await page.mouse.click(x, y); }; diff --git a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-1-chromium-linux.png index 1c1566efe5..3e99064132 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-2-chromium-linux.png index b7711e5d25..c94d3bfe37 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-2-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-2-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-3-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-3-chromium-linux.png index 87d9f4e92a..4bd48b9e9c 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-3-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-after-undoing-and-redoing-all-steps-Undo-and-Redo-buttons-turn-gray-3-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-undo-redo-toggle-snake-mode-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-undo-redo-toggle-snake-mode-1-chromium-linux.png index bd326d1d25..bd5abed593 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-undo-redo-toggle-snake-mode-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-undo-redo-toggle-snake-mode-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-undo-redo-toggle-snake-mode-3-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-undo-redo-toggle-snake-mode-3-chromium-linux.png index 2c296309d3..8ae675e85a 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-undo-redo-toggle-snake-mode-3-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Check-that-undo-redo-toggle-snake-mode-3-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Track-32-steps-Undo-Redo-action-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Track-32-steps-Undo-Redo-action-1-chromium-linux.png index 180a403b0d..ea977e8dc7 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Track-32-steps-Undo-Redo-action-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Track-32-steps-Undo-Redo-action-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Track-32-steps-Undo-Redo-action-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Track-32-steps-Undo-Redo-action-2-chromium-linux.png index f42e5cf0e5..3d4d88b401 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Track-32-steps-Undo-Redo-action-2-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-tests-Track-32-steps-Undo-Redo-action-2-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts index b488e542ce..c2fc8e913e 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts @@ -16,6 +16,7 @@ import { } from '@utils'; import { turnOnMacromoleculesEditor } from '@utils/macromolecules'; import { connectMonomersWithBonds } from '@utils/macromolecules/monomer'; +import { Chems, Peptides } from '@utils/selectors/macromoleculeEditor'; async function zoomWithMouseScrollAndTakeScreenshot(page: Page) { const zoomLevelDelta = 600; @@ -299,7 +300,7 @@ test.describe('Zoom Tool', () => { const y = 350; const x1 = 650; const y1 = 150; - await page.getByTestId('Bal___beta-Alanine').click(); + await page.getByTestId(Peptides.BetaAlanine).click(); await clickInTheMiddleOfTheScreen(page); for (let i = 0; i < 3; i++) { await waitForRender(page, async () => { @@ -308,7 +309,7 @@ test.describe('Zoom Tool', () => { } await page.getByTestId('Edc___S-ethylthiocysteine').click(); await page.mouse.click(x, y); - await connectMonomersWithBonds(page, ['Bal', 'Edc']); + await connectMonomersWithBonds(page, ['bAla', 'Edc']); for (let i = 0; i < 5; i++) { await waitForRender(page, async () => { await page.keyboard.press('Control+-'); @@ -328,11 +329,11 @@ test.describe('Zoom Tool', () => { */ const x = 800; const y = 350; - await page.getByTestId('Bal___beta-Alanine').click(); + await page.getByTestId(Peptides.BetaAlanine).click(); await clickInTheMiddleOfTheScreen(page); await page.getByTestId('Edc___S-ethylthiocysteine').click(); await page.mouse.click(x, y); - await connectMonomersWithBonds(page, ['Bal', 'Edc']); + await connectMonomersWithBonds(page, ['bAla', 'Edc']); await takeEditorScreenshot(page); for (let i = 0; i < 5; i++) { await waitForRender(page, async () => { @@ -356,7 +357,7 @@ test.describe('Zoom Tool', () => { await page.keyboard.press('Control+-'); }); } - await page.getByTestId('Bal___beta-Alanine').click(); + await page.getByTestId(Peptides.BetaAlanine).click(); await moveMouseToTheMiddleOfTheScreen(page); await takeEditorScreenshot(page); await page.getByTestId('RNA-TAB').click(); @@ -364,7 +365,7 @@ test.describe('Zoom Tool', () => { await moveMouseToTheMiddleOfTheScreen(page); await takeEditorScreenshot(page); await page.getByTestId('CHEM-TAB').click(); - await page.getByTestId('SMPEG2___SM(PEG)2 linker from Pierce').click(); + await page.getByTestId(Chems.SMPEG2).click(); await moveMouseToTheMiddleOfTheScreen(page); await takeEditorScreenshot(page); }); diff --git a/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-After-zooming-out-to-maximum-canvas--6b8e8-omer-entities-remains-same-as-before-zoom-out-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-After-zooming-out-to-maximum-canvas--6b8e8-omer-entities-remains-same-as-before-zoom-out-1-chromium-linux.png index 04f3a0623f..57c5479712 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-After-zooming-out-to-maximum-canvas--6b8e8-omer-entities-remains-same-as-before-zoom-out-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-After-zooming-out-to-maximum-canvas--6b8e8-omer-entities-remains-same-as-before-zoom-out-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-Check-if-you-create-a-peptide-chain--2270f--chain-then-zoom-out-and-add-another-elements-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-Check-if-you-create-a-peptide-chain--2270f--chain-then-zoom-out-and-add-another-elements-1-chromium-linux.png index fc646e9082..12c6aa1002 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-Check-if-you-create-a-peptide-chain--2270f--chain-then-zoom-out-and-add-another-elements-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-Check-if-you-create-a-peptide-chain--2270f--chain-then-zoom-out-and-add-another-elements-1-chromium-linux.png differ diff --git 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b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-Undo-not-undoing-zoom-3-chromium-linux.png differ diff --git a/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-When-zoomed-to-175-and-more-button-32d07-nge-their-position-and-not-overlap-each-other-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-When-zoomed-to-175-and-more-button-32d07-nge-their-position-and-not-overlap-each-other-1-chromium-linux.png index f8d9038e0a..81a4992295 100644 Binary files a/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-When-zoomed-to-175-and-more-button-32d07-nge-their-position-and-not-overlap-each-other-1-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Zoom-Tool/zoom.spec.ts-snapshots/Zoom-Tool-When-zoomed-to-175-and-more-button-32d07-nge-their-position-and-not-overlap-each-other-1-chromium-linux.png differ diff --git a/ketcher-autotests/tests/test-data/KET/D-2Nal-expected.ket b/ketcher-autotests/tests/test-data/KET/D-2Nal-expected.ket index 2244beb094..51029ebbef 100644 --- a/ketcher-autotests/tests/test-data/KET/D-2Nal-expected.ket +++ b/ketcher-autotests/tests/test-data/KET/D-2Nal-expected.ket @@ -8,7 +8,7 @@ "connections": [], "templates": [ { - "$ref": "monomerTemplate-D-2Nal___D-3-naphthylalanine" + "$ref": "monomerTemplate-D-2Nal___D-3-(2-naphtyl)-alanine" } ] }, @@ -20,9 +20,9 @@ "y": -7.65 }, "alias": "D-2Nal", - "templateId": "D-2Nal___D-3-naphthylalanine" + "templateId": "D-2Nal___D-3-(2-naphtyl)-alanine" }, - "monomerTemplate-D-2Nal___D-3-naphthylalanine": { + "monomerTemplate-D-2Nal___D-3-(2-naphtyl)-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -294,8 +294,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-2Nal___D-3-naphthylalanine", - "fullName": "D-3-naphthylalanine", + "id": "D-2Nal___D-3-(2-naphtyl)-alanine", + "fullName": "D-3-(2-naphtyl)-alanine", "alias": "D-2Nal", "attachmentPoints": [ { diff --git a/ketcher-autotests/tests/test-data/KET/monomer-expected.ket b/ketcher-autotests/tests/test-data/KET/monomer-expected.ket index 737f83b9f4..720ee0bf9e 100644 --- a/ketcher-autotests/tests/test-data/KET/monomer-expected.ket +++ b/ketcher-autotests/tests/test-data/KET/monomer-expected.ket @@ -8,7 +8,7 @@ "connections": [], "templates": [ { - "$ref": "monomerTemplate-Bal___beta-Alanine" + "$ref": "monomerTemplate-bAla___beta-Alanine" } ] }, @@ -19,10 +19,10 @@ "x": 14.75, "y": -7.65 }, - "alias": "Bal", - "templateId": "Bal___beta-Alanine" + "alias": "bAla", + "templateId": "bAla___beta-Alanine" }, - "monomerTemplate-Bal___beta-Alanine": { + "monomerTemplate-bAla___beta-Alanine": { "type": "monomerTemplate", "atoms": [ { @@ -128,9 +128,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Bal___beta-Alanine", + "id": "bAla___beta-Alanine", "fullName": "beta-Alanine", - "alias": "Bal", + "alias": "bAla", "attachmentPoints": [ { "attachmentAtom": 5, diff --git a/ketcher-autotests/tests/utils/selectors/macromoleculeEditor.ts b/ketcher-autotests/tests/utils/selectors/macromoleculeEditor.ts index 6debd297d9..a4ee40ce78 100644 --- a/ketcher-autotests/tests/utils/selectors/macromoleculeEditor.ts +++ b/ketcher-autotests/tests/utils/selectors/macromoleculeEditor.ts @@ -1,7 +1,14 @@ export const ALANINE = "[data-testid='A___Alanine']"; export const Peptides = { - BetaAlanine: 'Bal___beta-Alanine', + BetaAlanine: 'bAla___beta-Alanine', Ethylthiocysteine: 'Edc___S-ethylthiocysteine', + Tza: 'Tza___3-(4-Thiazolyl)-alanine', + D2Nal: 'D-2Nal___D-3-(2-naphtyl)-alanine', +}; + +export const Chems = { + SMPEG2: 'SMPEG2___SM(PEG)2', + hxy: 'hxy___5-hexyn-1-ol', }; export function getFavoriteButtonSelector(molecule: string): string { diff --git a/packages/ketcher-core/src/application/editor/data/monomers.ket b/packages/ketcher-core/src/application/editor/data/monomers.ket index 1860d96ade..18cb9160ac 100644 --- a/packages/ketcher-core/src/application/editor/data/monomers.ket +++ b/packages/ketcher-core/src/application/editor/data/monomers.ket @@ -199,73 +199,73 @@ "$ref": "monomerTemplate-Test-6-P___Test-6-AP-Peptide" }, { - "$ref": "monomerTemplate-Aad___2-aminoadipic acid" + "$ref": "monomerTemplate-Aad___L-2-aminoadipic acid" }, { - "$ref": "monomerTemplate-Abu___2-aminobutanoic acid" + "$ref": "monomerTemplate-Abu___L-2-aminobutyric acid" }, { - "$ref": "monomerTemplate-Aca___2-aminocapric acid" + "$ref": "monomerTemplate-Aca___L-decyline" }, { - "$ref": "monomerTemplate-Aib___alpha-aminoisobutyric acid (2-aminoalanine)" + "$ref": "monomerTemplate-Aib___2-aminoisobutyric acid" }, { - "$ref": "monomerTemplate-Apm___2-aminopimelic acid" + "$ref": "monomerTemplate-Apm___L-2-aminopimelic acid" }, { - "$ref": "monomerTemplate-App___gamma-amino-beta-hydroxybenzenepentanoic acid" + "$ref": "monomerTemplate-App___(3R,4S)-4-amino-3-hydroxy-5-phenylpentanoic acid" }, { - "$ref": "monomerTemplate-Asu___2-aminosuberic acid" + "$ref": "monomerTemplate-Asu___(R)-2-aminooctanedioic acid" }, { - "$ref": "monomerTemplate-Aze___2-carboxyazetidine" + "$ref": "monomerTemplate-Aze___L-azetidine-2-carboxylic acid" }, { - "$ref": "monomerTemplate-Bal___beta-Alanine" + "$ref": "monomerTemplate-bAla___beta-Alanine" }, { - "$ref": "monomerTemplate-Bua___butanoic acid" + "$ref": "monomerTemplate-Bua-___N-Terminal butanoyl" }, { - "$ref": "monomerTemplate-Bux___4-amino-3-hydroxybutanoic acid" + "$ref": "monomerTemplate-Bux___(3S)-4-amino-3-hydroxybutanoic acid" }, { "$ref": "monomerTemplate-C___Cysteine" }, { - "$ref": "monomerTemplate-Cap___gamma-amino-beta-hydroxycyclohexanepentanoic acid" + "$ref": "monomerTemplate-Cap___(2R,3S)-3-amino-2-hydroxy-5-cyclohexylpentanoic acid" }, { "$ref": "monomerTemplate-Cha___3-cyclohexylalanine" }, { - "$ref": "monomerTemplate-Cit___citrullin" + "$ref": "monomerTemplate-Cit___Citrulline" }, { - "$ref": "monomerTemplate-Cya___3-sulfoalanine" + "$ref": "monomerTemplate-Cya___Cysteic acid" }, { "$ref": "monomerTemplate-D___Aspartic acid" }, { - "$ref": "monomerTemplate-AspOH___Aspartic acid (OH)" + "$ref": "monomerTemplate-D*___Aspartic acid*" }, { "$ref": "monomerTemplate-Pyrro___Pyrrolidine" }, { - "$ref": "monomerTemplate-Dab___2,4-diaminobutanoic acid" + "$ref": "monomerTemplate-Dab___L-2,4-diaminobutanoic acid" }, { "$ref": "monomerTemplate-Dpm___diaminopimelic acid" }, { - "$ref": "monomerTemplate-Dpr___2,3-diaminopropanoic acid" + "$ref": "monomerTemplate-Dap___3-aminoalanine" }, { - "$ref": "monomerTemplate-Dsu___2,7-diaminosuberic acid (2,7-diaminooctanedioic acid)" + "$ref": "monomerTemplate-Dsu___2,7-diaminosuberic acid" }, { "$ref": "monomerTemplate-E___Glutamic acid" @@ -280,7 +280,7 @@ "$ref": "monomerTemplate-G___Glycine" }, { - "$ref": "monomerTemplate-Ggu___gamma-glutamic acid" + "$ref": "monomerTemplate-gGlu___gamma-glutamic acid" }, { "$ref": "monomerTemplate-Gla___gamma-carboxyglutamic acid" @@ -288,9 +288,6 @@ { "$ref": "monomerTemplate-Glc___glycolic acid" }, - { - "$ref": "monomerTemplate-Glp___pyroglutamic acid" - }, { "$ref": "monomerTemplate-H___Histidine" }, @@ -303,20 +300,17 @@ { "$ref": "monomerTemplate-Hhs___homohistidine" }, - { - "$ref": "monomerTemplate-Hiv___2-hydroxyisovaleric acid" - }, { "$ref": "monomerTemplate-Hse___homoserine" }, { - "$ref": "monomerTemplate-Hva___2-hydroxypentanoic acid" + "$ref": "monomerTemplate-Hva___(2S)-2-hydroxypentanoic acid" }, { - "$ref": "monomerTemplate-Hyl___5-hydroxylysine" + "$ref": "monomerTemplate-Hyl5xi___5-hydroxylysine" }, { - "$ref": "monomerTemplate-Hyp___4-hydroxyproline" + "$ref": "monomerTemplate-Hyp___trans-4-hydroxy-L-proline" }, { "$ref": "monomerTemplate-I___Isoleucine" @@ -331,40 +325,34 @@ "$ref": "monomerTemplate-L___Leucine" }, { - "$ref": "monomerTemplate-Lac___lactic acid" + "$ref": "monomerTemplate-L-OAla___lactic acid" }, { "$ref": "monomerTemplate-M___Methionine" }, { - "$ref": "monomerTemplate-Maa___mercaptoacetic acid" + "$ref": "monomerTemplate-Mba___(2S)-2-mercaptobutyric acid" }, { - "$ref": "monomerTemplate-Mba___mercaptobutanoic acid (GMBA)" + "$ref": "monomerTemplate-Mhp___3-hydroxy-4-methylproline" }, { - "$ref": "monomerTemplate-Mhp___4-methyl-3-hydroxyproline" - }, - { - "$ref": "monomerTemplate-Mpa___mercaptopropanoic acid" + "$ref": "monomerTemplate-Mpa___Thiolactic acid" }, { "$ref": "monomerTemplate-N___Asparagine" }, { - "$ref": "monomerTemplate-Nal___3-naphthylalanine" + "$ref": "monomerTemplate-2Nal___3-(2-naphthyl)-alanine" }, { "$ref": "monomerTemplate-Nle___norleucine" }, - { - "$ref": "monomerTemplate-Nty___nitrotyrosine" - }, { "$ref": "monomerTemplate-Nva___norvaline" }, { - "$ref": "monomerTemplate-Oic___2-carboxyocthydroindole" + "$ref": "monomerTemplate-Oic___(2S)-perhydroindolic acid" }, { "$ref": "monomerTemplate-Orn___L-ornithine" @@ -373,13 +361,13 @@ "$ref": "monomerTemplate-P___Proline" }, { - "$ref": "monomerTemplate-Pen___penicillamine (3-mercaptovaline)" + "$ref": "monomerTemplate-Pen___Penicillamine" }, { - "$ref": "monomerTemplate-Phg___2-phenylglycine" + "$ref": "monomerTemplate-Phg___L-phenylglycine" }, { - "$ref": "monomerTemplate-Pqa___Piperazine quinazolinone acetic acid, 2-(4-oxo-6-piperazin-1-yl-quinazolin-3-yl)acetic acid" + "$ref": "monomerTemplate-Pqa___2-(4-xxo-6-(piperazin-1-yl)quinazolin-3(4H)-yl)acetic acid" }, { "$ref": "monomerTemplate-Q___Glutamine" @@ -391,31 +379,31 @@ "$ref": "monomerTemplate-S___Serine" }, { - "$ref": "monomerTemplate-Sar___sarcosine (N-methylglycine)" + "$ref": "monomerTemplate-meG___Sarcosine" }, { - "$ref": "monomerTemplate-Spg___1-amino-1-carboxycyclopentane" + "$ref": "monomerTemplate-Ar5c___Cycloleucine" }, { - "$ref": "monomerTemplate-Sta___statin (4-amino-3-hydroxy-6-methylheptanoic acid)" + "$ref": "monomerTemplate-Sta___Statine" }, { "$ref": "monomerTemplate-T___Threonine" }, { - "$ref": "monomerTemplate-Thi___3-thienylalanine" + "$ref": "monomerTemplate-Thi___3-(2-thienyl)-alanine" }, { "$ref": "monomerTemplate-Tic___1,2,3,4-tetrahydro-3-isoquinolinecarboxylic acid" }, { - "$ref": "monomerTemplate-Tle___3-methylvaline" + "$ref": "monomerTemplate-tLeu___L-tert-leucine" }, { - "$ref": "monomerTemplate-Tml___epsilon-N-trimethyllysine" + "$ref": "monomerTemplate-LysMe3___epsilon-N-trimethyllysine" }, { - "$ref": "monomerTemplate-Tza___3-thiazolylalanine" + "$ref": "monomerTemplate-Tza___3-(4-Thiazolyl)-alanine" }, { "$ref": "monomerTemplate-V___Valine" @@ -424,16 +412,16 @@ "$ref": "monomerTemplate-W___Tryptophan" }, { - "$ref": "monomerTemplate-Wil___alpha-amino-2,4-dioxopyrimidinepropanoic acid" + "$ref": "monomerTemplate-Wil___Willardiine" }, { "$ref": "monomerTemplate-Y___Tyrosine" }, { - "$ref": "monomerTemplate-ac___N-Terminal Acetic Acid" + "$ref": "monomerTemplate-Ac-___N-Terminal acetyl" }, { - "$ref": "monomerTemplate-am___C-Terminal amine" + "$ref": "monomerTemplate-Am-___C-Terminal amino" }, { "$ref": "monomerTemplate-dA___D-Alanine" @@ -493,7 +481,7 @@ "$ref": "monomerTemplate-dY___D-Tyrosine" }, { - "$ref": "monomerTemplate-fmoc___fmoc N-Terminal Protection Group" + "$ref": "monomerTemplate-fmoc-___N-Terminal fluorenylmethoxycarbonyl" }, { "$ref": "monomerTemplate-meA___N-Methyl-Alanine" @@ -562,7 +550,7 @@ "$ref": "monomerTemplate-pnT___PNA Thymine" }, { - "$ref": "monomerTemplate-seC___SelenoCysteine" + "$ref": "monomerTemplate-U___Selenocysteine" }, { "$ref": "monomerTemplate-Test-6-Ch___Test-6-AP-Chem" @@ -571,7 +559,7 @@ "$ref": "monomerTemplate-A6OH___6-amino-hexanol" }, { - "$ref": "monomerTemplate-Az___Azide" + "$ref": "monomerTemplate-Az___4-azidobutyric acid" }, { "$ref": "monomerTemplate-EG___Ethylene Glycol" @@ -583,43 +571,43 @@ "$ref": "monomerTemplate-PEG-2___Diethylene Glycol" }, { - "$ref": "monomerTemplate-SMCC___SMCC linker from Pierce" + "$ref": "monomerTemplate-SMCC___SMCC" }, { - "$ref": "monomerTemplate-SMPEG2___SM(PEG)2 linker from Pierce" + "$ref": "monomerTemplate-SMPEG2___SM(PEG)2" }, { "$ref": "monomerTemplate-SS3___Dipropanol-disulfide" }, { - "$ref": "monomerTemplate-hxy___Hexynyl alcohol" + "$ref": "monomerTemplate-hxy___5-hexyn-1-ol" }, { "$ref": "monomerTemplate-sDBL___Symmetric Doubler" }, { - "$ref": "monomerTemplate-dPyl___D-Pyl" + "$ref": "monomerTemplate-dO___D-pyrrolysine" }, { - "$ref": "monomerTemplate-dSec___D-SelenoCysteine" + "$ref": "monomerTemplate-dU___D-selenocysteine" }, { - "$ref": "monomerTemplate-Pyl___Pyl" + "$ref": "monomerTemplate-O___Pyrrolysine" }, { - "$ref": "monomerTemplate-NMe___C-Terminal NMe" + "$ref": "monomerTemplate--NMe___C-Terminal methylamino" }, { - "$ref": "monomerTemplate-OMe___C-Terminal OMe" + "$ref": "monomerTemplate--OMe___C-Terminal methoxy" }, { - "$ref": "monomerTemplate-OtBu___C-Terminal OtBu" + "$ref": "monomerTemplate--OtBu___C-Terminal tert-butoxy" }, { - "$ref": "monomerTemplate-Oxa___C-Terminal Oxa" + "$ref": "monomerTemplate-Oxa___2‑oxazoline" }, { - "$ref": "monomerTemplate-OBz___C-Terminal OBz" + "$ref": "monomerTemplate--OBn___C-Terminal benzyloxy" }, { "$ref": "monomerTemplate--Me___C-Terminal methyl" @@ -637,7 +625,7 @@ "$ref": "monomerTemplate-D-hPhe___D-Homophenylalanine" }, { - "$ref": "monomerTemplate-D-Hyp___D-4-Hydroxyproline" + "$ref": "monomerTemplate-D-Hyp___trans-4-hydroxy-D-proline" }, { "$ref": "monomerTemplate-D-Nva___D-Norvaline" @@ -676,19 +664,19 @@ "$ref": "monomerTemplate-aThr___L-allo-Threonine" }, { - "$ref": "monomerTemplate-D-2Nal___D-3-naphthylalanine" + "$ref": "monomerTemplate-D-2Nal___D-3-(2-naphtyl)-alanine" }, { - "$ref": "monomerTemplate-D-2Thi___D-3-thienylalanine" + "$ref": "monomerTemplate-D-2Thi___3-(2-thienyl)-D-alanine" }, { - "$ref": "monomerTemplate-D-aHyp___D-allo-4-hydroxyproline" + "$ref": "monomerTemplate-D-aHyp___cis-4-hydroxy-D-proline" }, { "$ref": "monomerTemplate-D-aIle___D-allo-Isoleucine" }, { - "$ref": "monomerTemplate-D-Phg___D-2-phenylglycine" + "$ref": "monomerTemplate-D-Phg___D-phenylglycine" }, { "$ref": "monomerTemplate-DSertB___O-tert-Butyl-D-serine" @@ -703,7 +691,7 @@ "$ref": "monomerTemplate-TyrtBu___O-tert-Butyl-L-tyrosine" }, { - "$ref": "monomerTemplate-aHyp___L-allo-4-hydroxyproline" + "$ref": "monomerTemplate-aHyp___cis-4-hydroxy-L-proline" }, { "$ref": "monomerTemplate-hPhe___Homophenylalanine" @@ -715,10 +703,10 @@ "$ref": "monomerTemplate-D-aThr___D-allo-Threonine" }, { - "$ref": "monomerTemplate-D-Cha___D-2-Amino-3-cyclohexyl-propionic acid" + "$ref": "monomerTemplate-D-Cha___3-cyclohexyl-D-alanine" }, { - "$ref": "monomerTemplate-D-Pen___D-penicillamine (3-mercaptovaline)" + "$ref": "monomerTemplate-D-Pen___D-penicillamine" }, { "$ref": "monomerTemplate-DPhe4C___4-Chloro-D-phenylalanine" @@ -727,10 +715,10 @@ "$ref": "monomerTemplate-DSerBn___O-Benzyl-D-serine" }, { - "$ref": "monomerTemplate-MsO___Mesylate" + "$ref": "monomerTemplate-MsO-___N-Terminal methanesulfonyl" }, { - "$ref": "monomerTemplate-Oic3aS___Perhydroindolic acid" + "$ref": "monomerTemplate-Oic3aS___(2S,3aS,7aS)-perhydroindolic acid" }, { "$ref": "monomerTemplate-Pip___Pipecolic acid" @@ -745,7 +733,7 @@ "$ref": "monomerTemplate-Chg___Alpha-cyclohexylglycine" }, { - "$ref": "monomerTemplate-D-3Pal___D-3-(2-pyridyl)-alanine" + "$ref": "monomerTemplate-D-3Pal___D-3-(3-pyridyl)-alanine" }, { "$ref": "monomerTemplate-DaMeAb___D-Isovaline" @@ -754,7 +742,7 @@ "$ref": "monomerTemplate-D-Chg___D-Alpha-cyclohexylglycine" }, { - "$ref": "monomerTemplate-D-Cit___D-Citrullin" + "$ref": "monomerTemplate-D-Cit___D-citrulline" }, { "$ref": "monomerTemplate-D-Dab___D-2,4-diaminobutanoic acid" @@ -772,25 +760,25 @@ "$ref": "monomerTemplate-D-Abu___D-2-aminobutanoic acid" }, { - "$ref": "monomerTemplate-D-Dap___D-2,3-diaminopropanoic acid" + "$ref": "monomerTemplate-D-Dap___3-amino-D-alanine" }, { - "$ref": "monomerTemplate-Cbz___Carboxybenzyl" + "$ref": "monomerTemplate-Cbz-___N-Terminal carboxybenzyl" }, { "$ref": "monomerTemplate--Et___C-Terminal ethyl" }, { - "$ref": "monomerTemplate-NHEt___Ethanamine" + "$ref": "monomerTemplate--NHEt___C-Terminal ethylamino" }, { - "$ref": "monomerTemplate-OEt___Ethanol" + "$ref": "monomerTemplate--OEt___C-terminal ethoxy" }, { - "$ref": "monomerTemplate-Tos___Tosyl" + "$ref": "monomerTemplate-Tos-___N-Terminal tosyl" }, { - "$ref": "monomerTemplate-D-Thz___(4S)-1,3-thiazolidine-4-carboxylic acid" + "$ref": "monomerTemplate-D-Thz___D-thioproline" }, { "$ref": "monomerTemplate-DACys___Deamino-Cysteine" @@ -808,34 +796,34 @@ "$ref": "monomerTemplate-DAGlyO___2-hydroxyacetic acid" }, { - "$ref": "monomerTemplate-DAGlyT___2-(thiophen-2-yl)acetic acid" + "$ref": "monomerTemplate-DAGlyT___2-thiopheneacetic acid" }, { - "$ref": "monomerTemplate-DTrpFo___(2R)-2-amino-3-(1-formyl-1H-indol-3-yl)propanoic acid" + "$ref": "monomerTemplate-DTrpFo___1-formyl-D-tryptophan" }, { - "$ref": "monomerTemplate-DANcy___2-sulfanylacetic acid" + "$ref": "monomerTemplate-DANcy___Thioglycolic acid" }, { - "$ref": "monomerTemplate-DAPhe___Deamino-Phenylalanine" + "$ref": "monomerTemplate-PhLA___3-phenyllactic acid" }, { "$ref": "monomerTemplate-DAPhg3___2-(3,5-dimethylphenyl)acetic acid" }, { - "$ref": "monomerTemplate-DALeu___Deamino-Leucine" + "$ref": "monomerTemplate-DALeu___4-methylpentanoic acid" }, { - "$ref": "monomerTemplate-D-OAla___(2R)-2-hydroxypropanoic acid" + "$ref": "monomerTemplate-D-OAla___D-lactic acid" }, { - "$ref": "monomerTemplate-L-OVal___(2S)-2-hydroxy-3-methylbutanoic acid" + "$ref": "monomerTemplate-L-OVal___2-hydroxyisovaleric acid" }, { - "$ref": "monomerTemplate-NHBn-___N-Terminal 1-phenylmethanamine" + "$ref": "monomerTemplate-NHBn-___N-Terminal benzylamino" }, { - "$ref": "monomerTemplate-Bz___Benzaldehyde" + "$ref": "monomerTemplate-Bz-___N-Terminal benzoyl" }, { "$ref": "monomerTemplate-Et-___N-Terminal ethyl" @@ -844,13 +832,13 @@ "$ref": "monomerTemplate-Me-___N-Terminal methyl" }, { - "$ref": "monomerTemplate-DTyrEt___(2R)-2-amino-3-(4-ethoxyphenyl)propanoic acid" + "$ref": "monomerTemplate-DTyrEt___O-ethyl-D-tyrosine" }, { - "$ref": "monomerTemplate-Lys_Ac___(2S)-2-amino-6-acetamidohexanoic acid" + "$ref": "monomerTemplate-Lys_Ac___N-epsilon-acetyl-L-lysine" }, { - "$ref": "monomerTemplate-OMe-___N-Terminal methanol" + "$ref": "monomerTemplate-OMe-___N-Terminal methoxy" }, { "$ref": "monomerTemplate-AspOMe___(2S)-2-amino-4-methoxy-4-oxobutanoic acid" @@ -859,46 +847,46 @@ "$ref": "monomerTemplate-NMe23A___3-(dimethylamino)benzoic acid" }, { - "$ref": "monomerTemplate-PheaDH___2-amino-3-phenylprop-2-enoic acid" + "$ref": "monomerTemplate-PheaDH___Dehydrophenylalanine" }, { "$ref": "monomerTemplate-Sta3xi___4-amino-3-hydroxy-6-methylheptanoic acid" }, { - "$ref": "monomerTemplate-TyrabD___2-amino-3-(4-methoxyphenyl)prop-2-enoic acid" + "$ref": "monomerTemplate-TyrabD___(2E)-2-amino-3-(4-methoxyphenyl)prop-2-enoic acid" }, { - "$ref": "monomerTemplate-DAlaol___(2R)-2-aminopropan-1-ol" + "$ref": "monomerTemplate-DAlaol___D-alaninol" }, { - "$ref": "monomerTemplate-DPhgol___2-amino-2-methylpropan-1-ol" + "$ref": "monomerTemplate-DPhgol___D-phenylglycinol" }, { - "$ref": "monomerTemplate-DThrol___(2R,3R)-2-aminobutane-1,3-diol" + "$ref": "monomerTemplate-DThrol___L-threoninol" }, { "$ref": "monomerTemplate-Gly-ol___aminomethanol" }, { - "$ref": "monomerTemplate-Ala-ol___(2S)-2-aminopropan-1-ol" + "$ref": "monomerTemplate-Ala-ol___L-Alaninol" }, { "$ref": "monomerTemplate-Lys-ol___(2S)-2,6-diaminohexan-1-ol" }, { - "$ref": "monomerTemplate-Phg-ol___(2S)-2-amino-2-phenylethan-1-ol" + "$ref": "monomerTemplate-Phg-ol___L-phenylglycinol" }, { - "$ref": "monomerTemplate-Pro-ol___[(2S)-pyrrolidin-2-yl]methanol" + "$ref": "monomerTemplate-Pro-ol___L-prolinol" }, { - "$ref": "monomerTemplate-Val-ol___(2S)-2-amino-3-methylbutan-1-ol" + "$ref": "monomerTemplate-Val-ol___L-valinol" }, { "$ref": "monomerTemplate-Ala-al___(2S)-2-aminopropanal" }, { - "$ref": "monomerTemplate-Arg-al___N''-[(4S)-4-amino-5-oxopentyl]guanidine" + "$ref": "monomerTemplate-Arg-al___Argininal" }, { "$ref": "monomerTemplate-Asp-al___(3S)-3-amino-4-oxobutanoic acid" @@ -910,55 +898,55 @@ "$ref": "monomerTemplate-Pro-al___(2S)-pyrrolidine-2-carbaldehyde" }, { - "$ref": "monomerTemplate--NHBn___C-Terminal 1-phenylmethanamine" + "$ref": "monomerTemplate--NHBn___C-Terminal benzylamino" }, { - "$ref": "monomerTemplate-Met_O2___(2S)-2-amino-4-methanesulfonylbutanoic acid" + "$ref": "monomerTemplate-Met_O2___L-methionine sulfone" }, { - "$ref": "monomerTemplate-Phe2Me___(2S)-2-amino-3-(2-methylphenyl)propanoic acid" + "$ref": "monomerTemplate-Phe2Me___2-methyl-L-phenylalanine" }, { - "$ref": "monomerTemplate-Phe34d___(2S)-2-amino-3-(3,4-dichlorophenyl)propanoic acid" + "$ref": "monomerTemplate-Phe34d___3,4-dichloro-L-phenylalanine" }, { - "$ref": "monomerTemplate-Phe4Br___(2S)-2-amino-3-(4-bromophenyl)propanoic acid" + "$ref": "monomerTemplate-Phe4Br___4-bromo-L-phenylalanine" }, { - "$ref": "monomerTemplate-Phe_4I___(2S)-2-amino-3-(4-iodophenyl)propanoic acid" + "$ref": "monomerTemplate-Phe_4I___4-iodo-L-phenylalanine" }, { "$ref": "monomerTemplate-Phe4SD___(2S)-2-amino-3-{4-[(4S)-2,6-dioxo-1,3-diazinane-4-amido]phenyl}propanoic acid" }, { - "$ref": "monomerTemplate-SerPO3___(2S)-2-amino-3-(phosphonooxy)propanoic acid" + "$ref": "monomerTemplate-SerPO3___O-phospho-L-serine" }, { - "$ref": "monomerTemplate-ThrPO3___(2S,3R)-2-amino-3-(phosphonooxy)butanoic acid" + "$ref": "monomerTemplate-ThrPO3___O-phospho-L-threonine" }, { - "$ref": "monomerTemplate-Thz___(4R)-1,3-thiazolidine-4-carboxylic acid" + "$ref": "monomerTemplate-Thz___L-thioproline" }, { - "$ref": "monomerTemplate-Trp_Me___(2S)-2-amino-3-(1-methyl-1H-indol-3-yl)propanoic acid" + "$ref": "monomerTemplate-Trp_Me___1-methyl-L-tryptophan" }, { - "$ref": "monomerTemplate-Tyr26d___(2S)-2-amino-3-(4-hydroxy-2,6-dimethylphenyl)propanoic acid" + "$ref": "monomerTemplate-Tyr26d___2,6-dimethyl-L-tyrosine" }, { - "$ref": "monomerTemplate-Tyr_3I___(2S)-2-amino-3-(4-hydroxy-3-iodophenyl)propanoic acid" + "$ref": "monomerTemplate-Tyr_3I___3-iodo-L-tyrosine" }, { - "$ref": "monomerTemplate-Tyr3NO___(2S)-2-amino-3-(4-hydroxy-3-nitrophenyl)propanoic acid" + "$ref": "monomerTemplate-Tyr3NO___3-nitro-L-tyrosine" }, { "$ref": "monomerTemplate-TyrPh4___(2S)-2-amino-3-[4-(4-hydroxyphenoxy)phenyl]propanoic acid" }, { - "$ref": "monomerTemplate-TyrSO3___(2S)-2-amino-3-[4-(sulfooxy)phenyl]propanoic acid" + "$ref": "monomerTemplate-TyrSO3___O-sulfo-L-tyrosine" }, { - "$ref": "monomerTemplate-Val3OH___(2S)-2-amino-3-hydroxy-3-methylbutanoic acid" + "$ref": "monomerTemplate-Val3OH___3-hydroxy-L-valine" }, { "$ref": "monomerTemplate-xiIle___(2S)-2-amino-3-methylpentanoic acid" @@ -970,22 +958,22 @@ "$ref": "monomerTemplate-NMebAl___3-(methylamino)propanoic acid" }, { - "$ref": "monomerTemplate-aMePhe___(2S)-2-amino-2-methyl-3-phenylpropanoic acid" + "$ref": "monomerTemplate-aMePhe___alpha-methyl-L-phenylalanine" }, { - "$ref": "monomerTemplate-aMePro___(2S)-2-methylpyrrolidine-2-carboxylic acid" + "$ref": "monomerTemplate-aMePro___alpha-methyl-L-proline" }, { - "$ref": "monomerTemplate-aMeTy3___(2S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid" + "$ref": "monomerTemplate-aMeTy3___L-methyldopa" }, { - "$ref": "monomerTemplate-Bmt___(2S,3R,4R)-2-amino-3-hydroxy-4-methyloct-6-enoic acid" + "$ref": "monomerTemplate-Bmt___(2S,3R,4R,6E)-2-amino-3-hydroxy-4-methyloct-6-enoic acid" }, { - "$ref": "monomerTemplate-Cys_Bn___(2R)-2-amino-3-(benzylsulfanyl)propanoic acid" + "$ref": "monomerTemplate-Cys_Bn___S-benzylcysteine" }, { - "$ref": "monomerTemplate-His1Me___(2S)-2-amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acid" + "$ref": "monomerTemplate-His1Me___1-methyl-L-histidine" }, { "$ref": "monomerTemplate-Glyall___(2S)-2-aminopent-4-enoic acid" @@ -994,16 +982,16 @@ "$ref": "monomerTemplate-GlycPr___(2S)-2-amino-2-cyclopropylacetic acid" }, { - "$ref": "monomerTemplate-Hsl___(3S)-3-aminooxolan-2-one" + "$ref": "monomerTemplate-Hsl___L-homoserine lactone" }, { - "$ref": "monomerTemplate-AspPh2___(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid" + "$ref": "monomerTemplate-Kyn___Kynurenine" }, { "$ref": "monomerTemplate-Azi___(2S)-aziridine-2-carboxylic acid" }, { - "$ref": "monomerTemplate-2Abz___2-Aminobenzoic acid" + "$ref": "monomerTemplate-2Abz___Anthranilic acid" }, { "$ref": "monomerTemplate-3Abz___3-Aminobenzoic acid" @@ -1015,25 +1003,25 @@ "$ref": "monomerTemplate-Ac3c___1-aminocyclopropane-1-carboxylic acid" }, { - "$ref": "monomerTemplate-Ac6c___1-aminocyclohexane-1-carboxylic acid" + "$ref": "monomerTemplate-Ac6c___Homocycloleucine" }, { - "$ref": "monomerTemplate-D-Bmt___(2R,3S,4S)-2-amino-3-hydroxy-4-methyloct-6-enoic acid" + "$ref": "monomerTemplate-D-Bmt___(2R,3S,4S,6E)-2-amino-3-hydroxy-4-methyloct-6-enoic acid" }, { - "$ref": "monomerTemplate-D-hArg___(2R)-2-amino-6-[(diaminomethylidene)amino]hexanoic acid" + "$ref": "monomerTemplate-D-hArg___D-homoarginine" }, { - "$ref": "monomerTemplate-DPhe4F___(2R)-2-amino-3-(4-fluorophenyl)propanoic acid" + "$ref": "monomerTemplate-DPhe4F___4-fluoro-D-phenylalanine" }, { - "$ref": "monomerTemplate-DTrp2M___(2R)-2-amino-3-(2-methyl-1H-indol-3-yl)propanoic acid" + "$ref": "monomerTemplate-DTrp2M___2-methyl-D-tryptophan" }, { - "$ref": "monomerTemplate-DTyr3O___(2R)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid" + "$ref": "monomerTemplate-DTyr3O___D-methyldopa" }, { - "$ref": "monomerTemplate-DTyrMe___(2R)-2-amino-3-(4-methoxyphenyl)propanoic acid" + "$ref": "monomerTemplate-DTyrMe___O-methyl-D-tyrosine" }, { "$ref": "monomerTemplate-DxiIle___(2R)-2-amino-3-methylpentanoic acid" @@ -1042,13 +1030,13 @@ "$ref": "monomerTemplate-LysiPr___(2S)-2-amino-6-[(propan-2-yl)amino]hexanoic acid" }, { - "$ref": "monomerTemplate--Bn___C-Terminal toluene" + "$ref": "monomerTemplate--Bn___C-Terminal benzyl" }, { - "$ref": "monomerTemplate-Ph___Phenyl" + "$ref": "monomerTemplate--Ph___C-terminal phenyl" }, { - "$ref": "monomerTemplate-Boc___Tert-butyloxycarbonyl" + "$ref": "monomerTemplate-Boc-___N-Terminal tert-butyloxycarbonyl" }, { "$ref": "monomerTemplate-DAChg___2-cyclohexylacetic acid" @@ -1063,25 +1051,25 @@ "$ref": "monomerTemplate-DAhPhe___4-phenylbutanoic acid" }, { - "$ref": "monomerTemplate-DAnTyr___2-(4-methoxyphenyl)acetic acid" + "$ref": "monomerTemplate-DAnTyr___4-methoxyphenylacetic acid" }, { - "$ref": "monomerTemplate-DAPhg4___2-(4-chlorophenyl)acetic acid" + "$ref": "monomerTemplate-DAPhg4___4-chlorophenylacetic acid" }, { - "$ref": "monomerTemplate-D-OVal___(2R)-2-hydroxy-3-methylbutanoic acid" + "$ref": "monomerTemplate-D-OVal___D-2-hydroxyisovaleric acid" }, { - "$ref": "monomerTemplate-OLeu___(2S)-2-hydroxy-4-methylpentanoic acid" + "$ref": "monomerTemplate-OLeu___L-leucic acid" }, { - "$ref": "monomerTemplate-Bn-___N-Terminal toluene" + "$ref": "monomerTemplate-Bn-___N-Terminal benzyl" }, { - "$ref": "monomerTemplate-OBn-___N-Terminal phenylmethanol" + "$ref": "monomerTemplate-OBn-___N-Terminal benzyloxy" }, { - "$ref": "monomerTemplate-DALys___Deamino-Lysine" + "$ref": "monomerTemplate-DALys___6-amino-2-hydroxyhexanoic acid" }, { "$ref": "monomerTemplate-NMe24A___4-(dimethylamino)benzoic acid" @@ -1093,16 +1081,16 @@ "$ref": "monomerTemplate-Aib-ol___2-amino-2-methylpropan-1-ol" }, { - "$ref": "monomerTemplate-DProol___[(2R)-pyrrolidin-2-yl]methanol" + "$ref": "monomerTemplate-DProol___D-prolinol" }, { - "$ref": "monomerTemplate-Leu-ol___(2S)-2-amino-4-methylpentan-1-ol" + "$ref": "monomerTemplate-Leu-ol___L-leucinol" }, { - "$ref": "monomerTemplate-Phe-ol___(2S)-2-amino-3-phenylpropan-1-ol" + "$ref": "monomerTemplate-Phe-ol___L-phenylalaninol" }, { - "$ref": "monomerTemplate-Thr-ol___(2S,3S)-2-aminobutane-1,3-diol" + "$ref": "monomerTemplate-Thr-ol___D-threoninol" }, { "$ref": "monomerTemplate-Gly-al___2-aminoacetaldehyde" @@ -1117,49 +1105,49 @@ "$ref": "monomerTemplate-LhArgE___(2S)-2-amino-6-{[bis(ethylamino)methylidene]amino}hexanoic acid" }, { - "$ref": "monomerTemplate-Met_O___(2S)-2-amino-4-methanesulfinylbutanoic acid" + "$ref": "monomerTemplate-Met_O___L-methionine sulfoxide" }, { - "$ref": "monomerTemplate-nTyr___(2S)-2-amino-2-(4-hydroxyphenyl)acetic acid" + "$ref": "monomerTemplate-nTyr___L-4-Hydroxyphenylglycine" }, { - "$ref": "monomerTemplate-Oic3aR___(2S,3aR,7aS)-octahydro-1H-indole-2-carboxylic acid" + "$ref": "monomerTemplate-Oic3aR___(2S,3aR,7aS)-perhydroindolic acid" }, { - "$ref": "monomerTemplate-Phe_2F___(2S)-2-amino-3-(2-fluorophenyl)propanoic acid" + "$ref": "monomerTemplate-Phe_2F___2-fluoro-L-phenylalanine" }, { - "$ref": "monomerTemplate-Phe_3F___(2S)-2-amino-3-(3-fluorophenyl)propanoic acid" + "$ref": "monomerTemplate-Phe_3F___3-fluoro-L-phenylalanine" }, { - "$ref": "monomerTemplate-Phe_4F___(2S)-2-amino-3-(4-fluorophenyl)propanoic acid" + "$ref": "monomerTemplate-Phe_4F___4-fluoro-L-phenylalanine" }, { - "$ref": "monomerTemplate-Phe4NO___(2S)-2-amino-3-(4-nitrophenyl)propanoic acid" + "$ref": "monomerTemplate-Phe4NO___4-nitro-L-phenylalanine" }, { "$ref": "monomerTemplate-Phebbd___(2S)-2-amino-3-methyl-3-phenylbutanoic acid" }, { - "$ref": "monomerTemplate-Trp5OH___(2S)-2-amino-3-(5-hydroxy-1H-indol-3-yl)propanoic acid" + "$ref": "monomerTemplate-Trp5OH___5-hydroxy-L-tryptophan" }, { "$ref": "monomerTemplate-TrpOme___(2S)-2-amino-3-(1-methoxy-1H-indol-3-yl)propanoic acid" }, { - "$ref": "monomerTemplate-Tyr35d___(2S)-2-amino-3-(4-hydroxy-3,5-diiodophenyl)propanoic acid" + "$ref": "monomerTemplate-Tyr35d___3,5-diiodo-L-tyrosine" }, { - "$ref": "monomerTemplate-Tyr3OH___(2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid" + "$ref": "monomerTemplate-Tyr3OH___3-hydroxy-L-tyrosine" }, { - "$ref": "monomerTemplate-Tyr_Me___(2S)-2-amino-3-(4-methoxyphenyl)propanoic acid" + "$ref": "monomerTemplate-Tyr_Me___O-methyl-L-tyrosine" }, { - "$ref": "monomerTemplate-TyrPO3___(2S)-2-amino-3-[4-(phosphonooxy)phenyl]propanoic acid" + "$ref": "monomerTemplate-TyrPO3___O-phospho-L-tyrosine" }, { - "$ref": "monomerTemplate-xiHyp___(2S)-4-hydroxypyrrolidine-2-carboxylic acid" + "$ref": "monomerTemplate-xiHyp___4-hydroxy-L-proline" }, { "$ref": "monomerTemplate-xiThr___(2S)-2-amino-3-hydroxybutanoic acid" @@ -1168,19 +1156,19 @@ "$ref": "monomerTemplate-NMe4Ab___4-(methylamino)benzoic acid" }, { - "$ref": "monomerTemplate-aMeTyr___(2S)-2-amino-3-(4-hydroxyphenyl)-2-methylpropanoic acid" + "$ref": "monomerTemplate-aMeTyr___L-metyrosine" }, { "$ref": "monomerTemplate-Aoda___(2S)-2-amino-8-oxodecanoic acid" }, { - "$ref": "monomerTemplate-Bpa___(2S)-2-amino-3-(4-benzoylphenyl)propanoic acid" + "$ref": "monomerTemplate-Bpa___4-benzoylphenylalanine" }, { - "$ref": "monomerTemplate-Cys_Me___(2R)-2-amino-3-(methylsulfanyl)propanoic acid" + "$ref": "monomerTemplate-Cys_Me___S-methylcysteine" }, { - "$ref": "monomerTemplate-Dip___(2S)-2-amino-3,3-diphenylpropanoic acid" + "$ref": "monomerTemplate-Dip___3,3-diphenylalanine" }, { "$ref": "monomerTemplate-hArg___(2S)-2-amino-6-[(diaminomethyl)amino]hexanoic acid" @@ -1189,34 +1177,31 @@ "$ref": "monomerTemplate-His1Bn___(2S)-2-amino-3-(1-benzyl-1H-imidazol-4-yl)propanoic acid" }, { - "$ref": "monomerTemplate-His3Me___(2S)-2-amino-3-(1-methyl-1H-imidazol-5-yl)propanoic acid" - }, - { - "$ref": "monomerTemplate-Hyl5xi___(2S)-2,6-diamino-5-hydroxyhexanoic acid" + "$ref": "monomerTemplate-His3Me___3-methyl-L-histidine" }, { - "$ref": "monomerTemplate-Bip___(2S)-2-amino-3-{[1,1'-biphenyl]-4-yl}propanoic acid" + "$ref": "monomerTemplate-Bip___Biphenylalanine" }, { - "$ref": "monomerTemplate-Abu23D___2-aminobut-2-enoic acid" + "$ref": "monomerTemplate-Abu23D___(2Z)-2-aminobut-2-enoic acid" }, { - "$ref": "monomerTemplate-D-Dip___(2R)-2-amino-3,3-diphenylpropanoic acid" + "$ref": "monomerTemplate-D-Dip___3,3-diphenyl-D-alanine" }, { - "$ref": "monomerTemplate-Dha___2-aminoprop-2-enoic acid" + "$ref": "monomerTemplate-Dha___Dehydroalanine" }, { "$ref": "monomerTemplate-DhArgE___(2R)-2-amino-6-{[bis(ethylamino)methylidene]amino}hexanoic acid" }, { - "$ref": "monomerTemplate-DMetSO___(2R)-2-amino-4-[(S)-methanesulfinyl]butanoic acid" + "$ref": "monomerTemplate-DMetSO___L-methionine (S)-S-oxide" }, { "$ref": "monomerTemplate-DHis1B___(2R)-2-amino-3-(1-benzyl-1H-imidazol-4-yl)propanoic acid" }, { - "$ref": "monomerTemplate-D-nTyr___(2R)-2-amino-2-(4-hydroxyphenyl)acetic acid" + "$ref": "monomerTemplate-D-nTyr___D-4-Hydroxyphenylglycine" }, { "$ref": "monomerTemplate-DPhe4u___(2R)-2-amino-3-[4-(carbamoylamino)phenyl]propanoic acid" @@ -17728,7 +17713,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Aad___2-aminoadipic acid": { + "monomerTemplate-Aad___L-2-aminoadipic acid": { "type": "monomerTemplate", "atoms": [ { @@ -17911,8 +17896,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Aad___2-aminoadipic acid", - "fullName": "2-aminoadipic acid", + "id": "Aad___L-2-aminoadipic acid", + "fullName": "L-2-aminoadipic acid", "alias": "Aad", "attachmentPoints": [ { @@ -17943,9 +17928,9 @@ "type": "side" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "K" }, - "monomerTemplate-Abu___2-aminobutanoic acid": { + "monomerTemplate-Abu___L-2-aminobutyric acid": { "type": "monomerTemplate", "atoms": [ { @@ -18068,8 +18053,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Abu___2-aminobutanoic acid", - "fullName": "2-aminobutanoic acid", + "id": "Abu___L-2-aminobutyric acid", + "fullName": "L-2-aminobutyric acid", "alias": "Abu", "attachmentPoints": [ { @@ -18091,9 +18076,9 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "A" }, - "monomerTemplate-Aca___2-aminocapric acid": { + "monomerTemplate-Aca___L-decyline": { "type": "monomerTemplate", "atoms": [ { @@ -18306,8 +18291,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Aca___2-aminocapric acid", - "fullName": "2-aminocapric acid", + "id": "Aca___L-decyline", + "fullName": "L-decyline", "alias": "Aca", "attachmentPoints": [ { @@ -18331,7 +18316,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Aib___alpha-aminoisobutyric acid (2-aminoalanine)": { + "monomerTemplate-Aib___2-aminoisobutyric acid": { "type": "monomerTemplate", "atoms": [ { @@ -18452,8 +18437,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Aib___alpha-aminoisobutyric acid (2-aminoalanine)", - "fullName": "alpha-aminoisobutyric acid (2-aminoalanine)", + "id": "Aib___2-aminoisobutyric acid", + "fullName": "2-aminoisobutyric acid", "alias": "Aib", "attachmentPoints": [ { @@ -18477,7 +18462,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Apm___2-aminopimelic acid": { + "monomerTemplate-Apm___L-2-aminopimelic acid": { "type": "monomerTemplate", "atoms": [ { @@ -18675,8 +18660,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Apm___2-aminopimelic acid", - "fullName": "2-aminopimelic acid", + "id": "Apm___L-2-aminopimelic acid", + "fullName": "L-2-aminopimelic acid", "alias": "Apm", "attachmentPoints": [ { @@ -18709,7 +18694,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-App___gamma-amino-beta-hydroxybenzenepentanoic acid": { + "monomerTemplate-App___(3R,4S)-4-amino-3-hydroxy-5-phenylpentanoic acid": { "type": "monomerTemplate", "atoms": [ { @@ -18961,8 +18946,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "App___gamma-amino-beta-hydroxybenzenepentanoic acid", - "fullName": "gamma-amino-beta-hydroxybenzenepentanoic acid", + "id": "App___(3R,4S)-4-amino-3-hydroxy-5-phenylpentanoic acid", + "fullName": "(3R,4S)-4-amino-3-hydroxy-5-phenylpentanoic acid", "alias": "App", "attachmentPoints": [ { @@ -18986,7 +18971,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Asu___2-aminosuberic acid": { + "monomerTemplate-Asu___(R)-2-aminooctanedioic acid": { "type": "monomerTemplate", "atoms": [ { @@ -19199,8 +19184,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Asu___2-aminosuberic acid", - "fullName": "2-aminosuberic acid", + "id": "Asu___(R)-2-aminooctanedioic acid", + "fullName": "(R)-2-aminooctanedioic acid", "alias": "Asu", "attachmentPoints": [ { @@ -19233,7 +19218,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Aze___2-carboxyazetidine": { + "monomerTemplate-Aze___L-azetidine-2-carboxylic acid": { "type": "monomerTemplate", "atoms": [ { @@ -19363,8 +19348,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Aze___2-carboxyazetidine", - "fullName": "2-carboxyazetidine", + "id": "Aze___L-azetidine-2-carboxylic acid", + "fullName": "L-azetidine-2-carboxylic acid", "alias": "Aze", "attachmentPoints": [ { @@ -19386,9 +19371,9 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "P" }, - "monomerTemplate-Bal___beta-Alanine": { + "monomerTemplate-bAla___beta-Alanine": { "type": "monomerTemplate", "atoms": [ { @@ -19494,9 +19479,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Bal___beta-Alanine", + "id": "bAla___beta-Alanine", "fullName": "beta-Alanine", - "alias": "Bal", + "alias": "bAla", "attachmentPoints": [ { "attachmentAtom": 5, @@ -19519,7 +19504,7 @@ ], "naturalAnalogShort": "A" }, - "monomerTemplate-Bua___butanoic acid": { + "monomerTemplate-Bua-___N-Terminal butanoyl": { "type": "monomerTemplate", "atoms": [ { @@ -19610,9 +19595,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Bua___butanoic acid", - "fullName": "butanoic acid", - "alias": "Bua", + "id": "Bua-___N-Terminal butanoyl", + "fullName": "N-Terminal butanoyl", + "alias": "Bua-", "attachmentPoints": [ { "attachmentAtom": 3, @@ -19626,7 +19611,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Bux___4-amino-3-hydroxybutanoic acid": { + "monomerTemplate-Bux___(3S)-4-amino-3-hydroxybutanoic acid": { "type": "monomerTemplate", "atoms": [ { @@ -19764,8 +19749,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Bux___4-amino-3-hydroxybutanoic acid", - "fullName": "4-amino-3-hydroxybutanoic acid", + "id": "Bux___(3S)-4-amino-3-hydroxybutanoic acid", + "fullName": "(3S)-4-amino-3-hydroxybutanoic acid", "alias": "Bux", "attachmentPoints": [ { @@ -19961,7 +19946,7 @@ ], "naturalAnalogShort": "C" }, - "monomerTemplate-Cap___gamma-amino-beta-hydroxycyclohexanepentanoic acid": { + "monomerTemplate-Cap___(2R,3S)-3-amino-2-hydroxy-5-cyclohexylpentanoic acid": { "type": "monomerTemplate", "atoms": [ { @@ -20213,8 +20198,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Cap___gamma-amino-beta-hydroxycyclohexanepentanoic acid", - "fullName": "gamma-amino-beta-hydroxycyclohexanepentanoic acid", + "id": "Cap___(2R,3S)-3-amino-2-hydroxy-5-cyclohexylpentanoic acid", + "fullName": "(2R,3S)-3-amino-2-hydroxy-5-cyclohexylpentanoic acid", "alias": "Cap", "attachmentPoints": [ { @@ -20468,7 +20453,7 @@ ], "naturalAnalogShort": "A" }, - "monomerTemplate-Cit___citrullin": { + "monomerTemplate-Cit___Citrulline": { "type": "monomerTemplate", "atoms": [ { @@ -20666,8 +20651,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Cit___citrullin", - "fullName": "citrullin", + "id": "Cit___Citrulline", + "fullName": "Citrulline", "alias": "Cit", "attachmentPoints": [ { @@ -20689,9 +20674,9 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "R" }, - "monomerTemplate-Cya___3-sulfoalanine": { + "monomerTemplate-Cya___Cysteic acid": { "type": "monomerTemplate", "atoms": [ { @@ -20859,8 +20844,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Cya___3-sulfoalanine", - "fullName": "3-sulfoalanine", + "id": "Cya___Cysteic acid", + "fullName": "Cysteic acid", "alias": "Cya", "attachmentPoints": [ { @@ -21086,7 +21071,7 @@ ], "naturalAnalogShort": "D" }, - "monomerTemplate-AspOH___Aspartic acid (OH)": { + "monomerTemplate-D*___Aspartic acid*": { "type": "monomerTemplate", "atoms": [ { @@ -21239,9 +21224,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "AspOH___Aspartic acid (OH)", - "fullName": "Aspartic acid (OH)", - "alias": "AspOH", + "id": "D*___Aspartic acid*", + "fullName": "Aspartic acid*", + "alias": "D*", "attachmentPoints": [ { "attachmentAtom": 3, @@ -21387,7 +21372,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Dab___2,4-diaminobutanoic acid": { + "monomerTemplate-Dab___L-2,4-diaminobutanoic acid": { "type": "monomerTemplate", "atoms": [ { @@ -21540,8 +21525,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Dab___2,4-diaminobutanoic acid", - "fullName": "2,4-diaminobutanoic acid", + "id": "Dab___L-2,4-diaminobutanoic acid", + "fullName": "L-2,4-diaminobutanoic acid", "alias": "Dab", "attachmentPoints": [ { @@ -21578,126 +21563,121 @@ "type": "monomerTemplate", "atoms": [ { - "label": "C", + "label": "N", "location": [ - 0.8356, - -0.3752, + 19.116983281500758, + -12.425035594508643, 0 ] }, { "label": "C", "location": [ - 0.8363, - -1.876, + 19.982972134194153, + -11.925040971203767, 0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", "location": [ - 2.136, - -2.6267, + 20.84901200849872, + -12.425033687158692, 0 ] }, { "label": "O", "location": [ - 2.1366, - -3.8266, + 21.715065234252933, + -11.925003777879738, 0 ] }, { "label": "O", "location": [ - 3.1751, - -2.0264, + 20.84903489669812, + -13.425000045569043, 0 ] }, { - "label": "N", + "label": "H", "location": [ - -0.4632, - -2.6267, + 18.25096057334575, + -11.925003777879738, 0 ] }, { "label": "C", "location": [ - -0.4641, - 0.3753, + 19.98297880991898, + -10.925015484944957, 0 ] }, { "label": "C", "location": [ - -0.4649, - 1.8761, + 19.116952763901555, + -10.42501323224028, 0 ] }, { "label": "C", "location": [ - -1.7646, - 2.6267, + 19.116953240739043, + -9.425014925718264, 0 ] }, { "label": "C", "location": [ - -1.7653, - 4.1275, + 18.250923856859206, + -8.925031746513088, 0 - ] + ], + "stereoLabel": "abs" }, { - "label": "H", + "label": "C", "location": [ - -0.4637, - -3.8268, + 18.250925764209157, + -7.9250227111476015, 0 ] }, { "label": "O", "location": [ - -0.7262, - 4.7276, + 17.38493476574707, + -7.424999954430959, 0 ] }, { "label": "O", "location": [ - -2.8045, - 4.7277, + 19.11698661936317, + -7.424999954430959, 0 ] }, { "label": "N", "location": [ - -0.2031, - -1.2765, + 17.38493500416581, + -9.425001574268611, 0 ] } ], "bonds": [ - { - "type": 1, - "atoms": [ - 1, - 0 - ] - }, { "type": 1, "atoms": [ @@ -21706,14 +21686,14 @@ ] }, { - "type": 2, + "type": 1, "atoms": [ 2, 3 ] }, { - "type": 1, + "type": 2, "atoms": [ 2, 4 @@ -21722,14 +21702,14 @@ { "type": 1, "atoms": [ - 1, + 0, 5 ] }, { "type": 1, "atoms": [ - 0, + 1, 6 ] }, @@ -21757,30 +21737,39 @@ { "type": 1, "atoms": [ - 5, + 9, 10 ] }, { - "type": 1, + "type": 2, "atoms": [ - 9, + 10, 11 ] }, { - "type": 2, + "type": 1, "atoms": [ - 9, + 10, 12 ] }, { "type": 1, "atoms": [ - 1, + 9, 13 - ] + ], + "stereo": 6 + }, + { + "type": 1, + "atoms": [ + 1, + 0 + ], + "stereo": 6 } ], "class": "AminoAcid", @@ -21790,10 +21779,10 @@ "alias": "Dpm", "attachmentPoints": [ { - "attachmentAtom": 5, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 10 + 5 ] }, "type": "left" @@ -21802,15 +21791,15 @@ "attachmentAtom": 2, "leavingGroup": { "atoms": [ - 4 + 3 ] }, "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "K" }, - "monomerTemplate-Dpr___2,3-diaminopropanoic acid": { + "monomerTemplate-Dap___3-aminoalanine": { "type": "monomerTemplate", "atoms": [ { @@ -21948,9 +21937,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Dpr___2,3-diaminopropanoic acid", - "fullName": "2,3-diaminopropanoic acid", - "alias": "Dpr", + "id": "Dap___3-aminoalanine", + "fullName": "3-aminoalanine", + "alias": "Dap", "attachmentPoints": [ { "attachmentAtom": 5, @@ -21980,9 +21969,9 @@ "type": "side" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "S" }, - "monomerTemplate-Dsu___2,7-diaminosuberic acid (2,7-diaminooctanedioic acid)": { + "monomerTemplate-Dsu___2,7-diaminosuberic acid": { "type": "monomerTemplate", "atoms": [ { @@ -22210,8 +22199,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Dsu___2,7-diaminosuberic acid (2,7-diaminooctanedioic acid)", - "fullName": "2,7-diaminosuberic acid (2,7-diaminooctanedioic acid)", + "id": "Dsu___2,7-diaminosuberic acid", + "fullName": "2,7-diaminosuberic acid", "alias": "Dsu", "attachmentPoints": [ { @@ -22991,7 +22980,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-Ggu___gamma-glutamic acid": { + "monomerTemplate-gGlu___gamma-glutamic acid": { "type": "monomerTemplate", "atoms": [ { @@ -23159,9 +23148,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Ggu___gamma-glutamic acid", + "id": "gGlu___gamma-glutamic acid", "fullName": "gamma-glutamic acid", - "alias": "Ggu", + "alias": "gGlu", "attachmentPoints": [ { "attachmentAtom": 6, @@ -23532,167 +23521,6 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Glp___pyroglutamic acid": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 9.1574, - -4.5963, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 7.6654, - -4.4422, - 0 - ] - }, - { - "label": "C", - "location": [ - 7.351, - -2.9755, - 0 - ] - }, - { - "label": "C", - "location": [ - 8.6486, - -2.2231, - 0 - ] - }, - { - "label": "C", - "location": [ - 9.9062, - -5.894, - 0 - ] - }, - { - "label": "O", - "location": [ - 8.7719, - -1.0295, - 0 - ] - }, - { - "label": "O", - "location": [ - 9.3065, - -6.9335, - 0 - ] - }, - { - "label": "N", - "location": [ - 9.7651, - -3.2249, - 0 - ] - }, - { - "label": "O", - "location": [ - 11.1062, - -5.894, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 4, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 1 - ], - "stereo": 6 - }, - { - "type": 1, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 2, - "atoms": [ - 3, - 5 - ] - }, - { - "type": 2, - "atoms": [ - 4, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 7 - ] - } - ], - "class": "AminoAcid", - "classHELM": "PEPTIDE", - "id": "Glp___pyroglutamic acid", - "fullName": "pyroglutamic acid", - "alias": "Glp", - "attachmentPoints": [ - { - "attachmentAtom": 4, - "leavingGroup": { - "atoms": [ - 8 - ] - }, - "type": "right" - } - ], - "naturalAnalogShort": "E" - }, "monomerTemplate-H___Histidine": { "type": "monomerTemplate", "atoms": [ @@ -24363,200 +24191,215 @@ { "label": "C", "location": [ - 1.8022, - -2.6822, + 18.65178064200201, + -11.099793087375417, + 0 + ] + }, + { + "label": "O", + "location": [ + 19.51780604578645, + -10.599793087375417, 0 ] }, { "label": "C", "location": [ - 0.5019, - -1.9329, + 17.785755238217572, + -10.599793087375417, 0 ], "stereoLabel": "abs" }, { - "label": "C", + "label": "N", "location": [ - 0.4996, - -0.4321, + 16.919729834433134, + -11.099793087375417, 0 ] }, { - "label": "C", + "label": "H", "location": [ - -0.8031, - 1.8154, + 16.053704430648693, + -10.599793087375417, 0 ] }, { "label": "C", "location": [ - -0.0518, - 4.1233, + 17.785755238217572, + -9.599793087375417, 0 ] }, { - "label": "C", + "label": "O", "location": [ - -2.016, - 2.6978, + 18.65178064200201, + -12.099793087375417, 0 ] }, { - "label": "N", + "label": "C", "location": [ - 0.4109, - 2.6965, + 16.919729834433134, + -9.099793087375417, 0 ] }, { - "label": "N", + "label": "C", "location": [ - -1.5517, - 4.1242, + 16.919729834433134, + -8.099793087375417, 0 ] }, { "label": "N", "location": [ - -0.7985, - -2.6822, + 16.419306289067077, + -6.559712382811686, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 1.8041, - -3.8822, + 16.110089044192286, + -7.505952267954141, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 2.8409, - -2.081, + 17.420081152981293, + -6.559688915783971, 0 ] }, { - "label": "H", + "label": "N", "location": [ - -1.8377, - -2.082, + 17.729442851491882, + -7.505914295956596, 0 ] }, { - "label": "C", + "label": "H", "location": [ - -0.8008, - 0.3172, + 15.832193954213551, + -5.750206912624583, 0 ] } ], "bonds": [ { - "type": 2, + "type": 1, "atoms": [ - 9, - 0 + 0, + 1 ] }, { "type": 1, "atoms": [ 0, - 1 + 2 ] }, { "type": 1, "atoms": [ - 0, - 10 + 2, + 3 ] }, { "type": 1, "atoms": [ - 1, - 8 + 3, + 4 ] }, { "type": 1, "atoms": [ - 1, - 2 + 2, + 5 ], "stereo": 1 }, { "type": 2, "atoms": [ - 5, - 3 + 0, + 6 ] }, { "type": 1, "atoms": [ - 6, - 3 + 5, + 7 ] }, { - "type": 2, + "type": 1, "atoms": [ - 6, - 4 + 7, + 8 ] }, { "type": 1, "atoms": [ - 4, - 7 + 8, + 12 ] }, { - "type": 1, + "type": 2, "atoms": [ - 7, - 5 + 12, + 11 ] }, { "type": 1, "atoms": [ - 8, - 11 + 11, + 9 ] }, { "type": 1, "atoms": [ - 2, - 12 + 9, + 10 + ] + }, + { + "type": 2, + "atoms": [ + 10, + 8 ] }, { "type": 1, "atoms": [ - 3, - 12 + 9, + 13 ] } ], @@ -24567,10 +24410,10 @@ "alias": "Hhs", "attachmentPoints": [ { - "attachmentAtom": 8, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 11 + 4 ] }, "type": "left" @@ -24579,152 +24422,22 @@ "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 10 + 1 ] }, "type": "right" - } - ], - "naturalAnalogShort": "H" - }, - "monomerTemplate-Hiv___2-hydroxyisovaleric acid": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 9.4238, - -6.6063, - 0 - ] - }, - { - "label": "O", - "location": [ - 8.8334, - -7.6296, - 0 - ] - }, - { - "label": "C", - "location": [ - 8.6853, - -5.3265, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "N", - "location": [ - 7.2077, - -5.3296, - 0 - ] - }, - { - "label": "C", - "location": [ - 9.4237, - -4.0465, - 0 - ] - }, - { - "label": "C", - "location": [ - 8.8333, - -3.0233, - 0 - ] - }, - { - "label": "C", - "location": [ - 10.6051, - -4.0465, - 0 - ] - }, - { - "label": "O", - "location": [ - 10.6052, - -6.6063, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 1, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 4 - ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 6 - ] }, { - "type": 1, - "atoms": [ - 0, - 7 - ] - } - ], - "class": "AminoAcid", - "classHELM": "PEPTIDE", - "id": "Hiv___2-hydroxyisovaleric acid", - "fullName": "2-hydroxyisovaleric acid", - "alias": "Hiv", - "attachmentPoints": [ - { - "attachmentAtom": 0, + "attachmentAtom": 9, "leavingGroup": { "atoms": [ - 7 + 13 ] }, - "type": "right" + "type": "side" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "H" }, "monomerTemplate-Hse___homoserine": { "type": "monomerTemplate", @@ -24889,7 +24602,7 @@ ], "naturalAnalogShort": "S" }, - "monomerTemplate-Hva___2-hydroxypentanoic acid": { + "monomerTemplate-Hva___(2S)-2-hydroxypentanoic acid": { "type": "monomerTemplate", "atoms": [ { @@ -25012,8 +24725,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Hva___2-hydroxypentanoic acid", - "fullName": "2-hydroxypentanoic acid", + "id": "Hva___(2S)-2-hydroxypentanoic acid", + "fullName": "(2S)-2-hydroxypentanoic acid", "alias": "Hva", "attachmentPoints": [ { @@ -25028,7 +24741,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Hyl___5-hydroxylysine": { + "monomerTemplate-Hyl5xi___5-hydroxylysine": { "type": "monomerTemplate", "atoms": [ { @@ -25226,9 +24939,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Hyl___5-hydroxylysine", + "id": "Hyl5xi___5-hydroxylysine", "fullName": "5-hydroxylysine", - "alias": "Hyl", + "alias": "Hyl5xi", "attachmentPoints": [ { "attachmentAtom": 7, @@ -25260,7 +24973,7 @@ ], "naturalAnalogShort": "K" }, - "monomerTemplate-Hyp___4-hydroxyproline": { + "monomerTemplate-Hyp___trans-4-hydroxy-L-proline": { "type": "monomerTemplate", "atoms": [ { @@ -25422,8 +25135,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Hyp___4-hydroxyproline", - "fullName": "4-hydroxyproline", + "id": "Hyp___trans-4-hydroxy-L-proline", + "fullName": "trans-4-hydroxy-L-proline", "alias": "Hyp", "attachmentPoints": [ { @@ -26185,7 +25898,7 @@ ], "naturalAnalogShort": "L" }, - "monomerTemplate-Lac___lactic acid": { + "monomerTemplate-L-OAla___lactic acid": { "type": "monomerTemplate", "atoms": [ { @@ -26278,9 +25991,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Lac___lactic acid", + "id": "L-OAla___lactic acid", "fullName": "lactic acid", - "alias": "Lac", + "alias": "L-OAla", "attachmentPoints": [ { "attachmentAtom": 1, @@ -26292,7 +26005,7 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "A" }, "monomerTemplate-M___Methionine": { "type": "monomerTemplate", @@ -26472,123 +26185,7 @@ ], "naturalAnalogShort": "M" }, - "monomerTemplate-Maa___mercaptoacetic acid": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 0.55, - 1.3, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.3, - 0, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.7003, - -1.0394, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.5, - 0, - 0 - ] - }, - { - "label": "S", - "location": [ - 1.3, - 2.6, - 0 - ] - }, - { - "label": "H", - "location": [ - 0.7003, - 3.6394, - 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 - ] - } - ], - "class": "AminoAcid", - "classHELM": "PEPTIDE", - "id": "Maa___mercaptoacetic acid", - "fullName": "mercaptoacetic acid", - "alias": "Maa", - "attachmentPoints": [ - { - "attachmentAtom": 1, - "leavingGroup": { - "atoms": [ - 3 - ] - }, - "type": "right" - }, - { - "attachmentAtom": 4, - "leavingGroup": { - "atoms": [ - 5 - ] - }, - "type": "side" - } - ], - "naturalAnalogShort": "X" - }, - "monomerTemplate-Mba___mercaptobutanoic acid (GMBA)": { + "monomerTemplate-Mba___(2S)-2-mercaptobutyric acid": { "type": "monomerTemplate", "atoms": [ { @@ -26711,8 +26308,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Mba___mercaptobutanoic acid (GMBA)", - "fullName": "mercaptobutanoic acid (GMBA)", + "id": "Mba___(2S)-2-mercaptobutyric acid", + "fullName": "(2S)-2-mercaptobutyric acid", "alias": "Mba", "attachmentPoints": [ { @@ -26736,7 +26333,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Mhp___4-methyl-3-hydroxyproline": { + "monomerTemplate-Mhp___3-hydroxy-4-methylproline": { "type": "monomerTemplate", "atoms": [ { @@ -26911,8 +26508,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Mhp___4-methyl-3-hydroxyproline", - "fullName": "4-methyl-3-hydroxyproline", + "id": "Mhp___3-hydroxy-4-methylproline", + "fullName": "3-hydroxy-4-methylproline", "alias": "Mhp", "attachmentPoints": [ { @@ -26936,7 +26533,7 @@ ], "naturalAnalogShort": "P" }, - "monomerTemplate-Mpa___mercaptopropanoic acid": { + "monomerTemplate-Mpa___Thiolactic acid": { "type": "monomerTemplate", "atoms": [ { @@ -27044,8 +26641,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Mpa___mercaptopropanoic acid", - "fullName": "mercaptopropanoic acid", + "id": "Mpa___Thiolactic acid", + "fullName": "Thiolactic acid", "alias": "Mpa", "attachmentPoints": [ { @@ -27271,7 +26868,7 @@ ], "naturalAnalogShort": "N" }, - "monomerTemplate-Nal___3-naphthylalanine": { + "monomerTemplate-2Nal___3-(2-naphthyl)-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -27543,9 +27140,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Nal___3-naphthylalanine", - "fullName": "3-naphthylalanine", - "alias": "Nal", + "id": "2Nal___3-(2-naphthyl)-alanine", + "fullName": "3-(2-naphthyl)-alanine", + "alias": "2Nal", "attachmentPoints": [ { "attachmentAtom": 3, @@ -27746,296 +27343,6 @@ ], "naturalAnalogShort": "L" }, - "monomerTemplate-Nty___nitrotyrosine": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 0.3609, - -1.4586, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.3835, - -0.8682, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.6616, - -0.8683, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - -0.6616, - 0.3125, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.3609, - 0.9029, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.3608, - 2.0837, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.3834, - 2.6741, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.4059, - 2.0838, - 0 - ] - }, - { - "label": "O", - "location": [ - 3.4285, - 2.6742, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.406, - 0.903, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.3835, - 0.3126, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.6842, - -1.4586, - 0 - ] - }, - { - "label": "N", - "location": [ - -2.7068, - -0.8684, - 0 - ] - }, - { - "label": "O", - "location": [ - -2.7068, - 0.3124, - 0 - ] - }, - { - "label": "O", - "location": [ - -3.7293, - -1.4588, - 0 - ] - }, - { - "label": "H", - "location": [ - -1.6841, - -2.6394, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.361, - -2.6393, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 2, - "atoms": [ - 5, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 2, - "atoms": [ - 6, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 7, - 9 - ] - }, - { - "type": 2, - "atoms": [ - 9, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 10, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 11 - ] - }, - { - "type": 1, - "atoms": [ - 11, - 12 - ] - }, - { - "type": 2, - "atoms": [ - 12, - 13 - ] - }, - { - "type": 2, - "atoms": [ - 12, - 14 - ] - }, - { - "type": 1, - "atoms": [ - 11, - 15 - ] - }, - { - "type": 2, - "atoms": [ - 16, - 0 - ] - } - ], - "class": "AminoAcid", - "classHELM": "PEPTIDE", - "id": "Nty___nitrotyrosine", - "fullName": "nitrotyrosine", - "alias": "Nty", - "attachmentPoints": [ - { - "attachmentAtom": 11, - "leavingGroup": { - "atoms": [ - 15 - ] - }, - "type": "left" - }, - { - "attachmentAtom": 0, - "leavingGroup": { - "atoms": [ - 1 - ] - }, - "type": "right" - } - ], - "naturalAnalogShort": "Y" - }, "monomerTemplate-Nva___norvaline": { "type": "monomerTemplate", "atoms": [ @@ -28199,7 +27506,7 @@ ], "naturalAnalogShort": "V" }, - "monomerTemplate-Oic___2-carboxyocthydroindole": { + "monomerTemplate-Oic___(2S)-perhydroindolic acid": { "type": "monomerTemplate", "atoms": [ { @@ -28411,8 +27718,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Oic___2-carboxyocthydroindole", - "fullName": "2-carboxyocthydroindole", + "id": "Oic___(2S)-perhydroindolic acid", + "fullName": "(2S)-perhydroindolic acid", "alias": "Oic", "attachmentPoints": [ { @@ -28808,7 +28115,7 @@ ], "naturalAnalogShort": "P" }, - "monomerTemplate-Pen___penicillamine (3-mercaptovaline)": { + "monomerTemplate-Pen___Penicillamine": { "type": "monomerTemplate", "atoms": [ { @@ -28976,8 +28283,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Pen___penicillamine (3-mercaptovaline)", - "fullName": "penicillamine (3-mercaptovaline)", + "id": "Pen___Penicillamine", + "fullName": "Penicillamine", "alias": "Pen", "attachmentPoints": [ { @@ -29010,7 +28317,7 @@ ], "naturalAnalogShort": "V" }, - "monomerTemplate-Phg___2-phenylglycine": { + "monomerTemplate-Phg___L-phenylglycine": { "type": "monomerTemplate", "atoms": [ { @@ -29200,8 +28507,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Phg___2-phenylglycine", - "fullName": "2-phenylglycine", + "id": "Phg___L-phenylglycine", + "fullName": "L-phenylglycine", "alias": "Phg", "attachmentPoints": [ { @@ -29225,7 +28532,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-Pqa___Piperazine quinazolinone acetic acid, 2-(4-oxo-6-piperazin-1-yl-quinazolin-3-yl)acetic acid": { + "monomerTemplate-Pqa___2-(4-xxo-6-(piperazin-1-yl)quinazolin-3(4H)-yl)acetic acid": { "type": "monomerTemplate", "atoms": [ { @@ -29577,8 +28884,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Pqa___Piperazine quinazolinone acetic acid, 2-(4-oxo-6-piperazin-1-yl-quinazolin-3-yl)acetic acid", - "fullName": "Piperazine quinazolinone acetic acid, 2-(4-oxo-6-piperazin-1-yl-quinazolin-3-yl)acetic acid", + "id": "Pqa___2-(4-xxo-6-(piperazin-1-yl)quinazolin-3(4H)-yl)acetic acid", + "fullName": "2-(4-xxo-6-(piperazin-1-yl)quinazolin-3(4H)-yl)acetic acid", "alias": "Pqa", "attachmentPoints": [ { @@ -30238,7 +29545,7 @@ ], "naturalAnalogShort": "S" }, - "monomerTemplate-Sar___sarcosine (N-methylglycine)": { + "monomerTemplate-meG___Sarcosine": { "type": "monomerTemplate", "atoms": [ { @@ -30344,9 +29651,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Sar___sarcosine (N-methylglycine)", - "fullName": "sarcosine (N-methylglycine)", - "alias": "Sar", + "id": "meG___Sarcosine", + "fullName": "Sarcosine", + "alias": "meG", "attachmentPoints": [ { "attachmentAtom": 4, @@ -30369,87 +29676,86 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-Spg___1-amino-1-carboxycyclopentane": { + "monomerTemplate-Ar5c___Cycloleucine": { "type": "monomerTemplate", "atoms": [ { "label": "C", "location": [ - 1.0834, - 0.6054, + 8.925, + -7.793135603832753, 0 ] }, { "label": "C", "location": [ - -0.1301, - -0.2763, + 8.116010039350328, + -7.205342898183956, 0 - ], - "stereoLabel": "abs" + ] }, { "label": "C", "location": [ - -1.3437, - 0.6051, + 8.425006204790067, + -6.254254700935622, 0 ] }, { "label": "C", "location": [ - -0.8803, - 2.0318, + 9.424993795209932, + -6.254254700935622, 0 ] }, { "label": "C", "location": [ - 0.6197, - 2.032, + 9.733989960649673, + -7.205342898183956, 0 ] }, { - "label": "N", + "label": "C", "location": [ - -1.43, - -0.9996, + 9.816011499938906, + -8.247116337979724, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 1.1702, - -0.9996, + 8.033988500061096, + -8.247116337979724, 0 ] }, { "label": "O", "location": [ - 1.1712, - -2.1996, + 9.868358401308372, + -9.245745299064378, 0 ] }, { "label": "O", "location": [ - 2.209, - -0.3991, + 10.654676098508345, + -7.702468111042041, 0 ] }, { "label": "H", "location": [ - -2.4695, - -0.4001, + 7.195323901491657, + -7.702468111042042, 0 ] } @@ -30459,82 +29765,81 @@ "type": 1, "atoms": [ 0, - 1 + 4 ] }, { "type": 1, "atoms": [ - 1, - 2 - ], - "stereo": 1 + 4, + 3 + ] }, { "type": 1, "atoms": [ - 2, - 3 + 3, + 2 ] }, { "type": 1, "atoms": [ - 3, - 4 + 2, + 1 ] }, { "type": 1, "atoms": [ - 0, - 4 + 1, + 0 ] }, { "type": 1, "atoms": [ - 1, + 0, 5 ] }, { "type": 1, "atoms": [ - 1, + 0, 6 ] }, { "type": 2, "atoms": [ - 6, + 5, 7 ] }, { "type": 1, "atoms": [ - 6, + 5, 8 ] }, { "type": 1, "atoms": [ - 5, + 6, 9 ] } ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Spg___1-amino-1-carboxycyclopentane", - "fullName": "1-amino-1-carboxycyclopentane", - "alias": "Spg", + "id": "Ar5c___Cycloleucine", + "fullName": "Cycloleucine", + "alias": "Ar5c", "attachmentPoints": [ { - "attachmentAtom": 5, + "attachmentAtom": 6, "leavingGroup": { "atoms": [ 9 @@ -30543,7 +29848,7 @@ "type": "left" }, { - "attachmentAtom": 6, + "attachmentAtom": 5, "leavingGroup": { "atoms": [ 8 @@ -30552,9 +29857,9 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "L" }, - "monomerTemplate-Sta___statin (4-amino-3-hydroxy-6-methylheptanoic acid)": { + "monomerTemplate-Sta___Statine": { "type": "monomerTemplate", "atoms": [ { @@ -30754,8 +30059,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Sta___statin (4-amino-3-hydroxy-6-methylheptanoic acid)", - "fullName": "statin (4-amino-3-hydroxy-6-methylheptanoic acid)", + "id": "Sta___Statine", + "fullName": "Statine", "alias": "Sta", "attachmentPoints": [ { @@ -30968,7 +30273,7 @@ ], "naturalAnalogShort": "T" }, - "monomerTemplate-Thi___3-thienylalanine": { + "monomerTemplate-Thi___3-(2-thienyl)-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -31158,8 +30463,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Thi___3-thienylalanine", - "fullName": "3-thienylalanine", + "id": "Thi___3-(2-thienyl)-alanine", + "fullName": "3-(2-thienyl)-alanine", "alias": "Thi", "attachmentPoints": [ { @@ -31435,7 +30740,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Tle___3-methylvaline": { + "monomerTemplate-tLeu___L-tert-leucine": { "type": "monomerTemplate", "atoms": [ { @@ -31588,9 +30893,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Tle___3-methylvaline", - "fullName": "3-methylvaline", - "alias": "Tle", + "id": "tLeu___L-tert-leucine", + "fullName": "L-tert-leucine", + "alias": "tLeu", "attachmentPoints": [ { "attachmentAtom": 6, @@ -31611,9 +30916,9 @@ "type": "right" } ], - "naturalAnalogShort": "V" + "naturalAnalogShort": "L" }, - "monomerTemplate-Tml___epsilon-N-trimethyllysine": { + "monomerTemplate-LysMe3___epsilon-N-trimethyllysine": { "type": "monomerTemplate", "atoms": [ { @@ -31827,9 +31132,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Tml___epsilon-N-trimethyllysine", + "id": "LysMe3___epsilon-N-trimethyllysine", "fullName": "epsilon-N-trimethyllysine", - "alias": "Tml", + "alias": "LysMe3", "attachmentPoints": [ { "attachmentAtom": 7, @@ -31852,7 +31157,7 @@ ], "naturalAnalogShort": "K" }, - "monomerTemplate-Tza___3-thiazolylalanine": { + "monomerTemplate-Tza___3-(4-Thiazolyl)-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -32042,8 +31347,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Tza___3-thiazolylalanine", - "fullName": "3-thiazolylalanine", + "id": "Tza___3-(4-Thiazolyl)-alanine", + "fullName": "3-(4-Thiazolyl)-alanine", "alias": "Tza", "attachmentPoints": [ { @@ -32536,7 +31841,7 @@ ], "naturalAnalogShort": "W" }, - "monomerTemplate-Wil___alpha-amino-2,4-dioxopyrimidinepropanoic acid": { + "monomerTemplate-Wil___Willardiine": { "type": "monomerTemplate", "atoms": [ { @@ -32771,8 +32076,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Wil___alpha-amino-2,4-dioxopyrimidinepropanoic acid", - "fullName": "alpha-amino-2,4-dioxopyrimidinepropanoic acid", + "id": "Wil___Willardiine", + "fullName": "Willardiine", "alias": "Wil", "attachmentPoints": [ { @@ -33065,7 +32370,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-ac___N-Terminal Acetic Acid": { + "monomerTemplate-Ac-___N-Terminal acetyl": { "type": "monomerTemplate", "atoms": [ { @@ -33126,9 +32431,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "ac___N-Terminal Acetic Acid", - "fullName": "N-Terminal Acetic Acid", - "alias": "ac", + "id": "Ac-___N-Terminal acetyl", + "fullName": "N-Terminal acetyl", + "alias": "Ac-", "attachmentPoints": [ { "attachmentAtom": 1, @@ -33142,7 +32447,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-am___C-Terminal amine": { + "monomerTemplate-Am-___C-Terminal amino": { "type": "monomerTemplate", "atoms": [ { @@ -33173,9 +32478,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "am___C-Terminal amine", - "fullName": "C-Terminal amine", - "alias": "am", + "id": "Am-___C-Terminal amino", + "fullName": "C-Terminal amino", + "alias": "Am-", "attachmentPoints": [ { "attachmentAtom": 0, @@ -37070,7 +36375,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-fmoc___fmoc N-Terminal Protection Group": { + "monomerTemplate-fmoc-___N-Terminal fluorenylmethoxycarbonyl": { "type": "monomerTemplate", "atoms": [ { @@ -37362,9 +36667,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "fmoc___fmoc N-Terminal Protection Group", - "fullName": "fmoc N-Terminal Protection Group", - "alias": "fmoc", + "id": "fmoc-___N-Terminal fluorenylmethoxycarbonyl", + "fullName": "N-Terminal fluorenylmethoxycarbonyl", + "alias": "fmoc-", "attachmentPoints": [ { "attachmentAtom": 15, @@ -42420,30 +41725,284 @@ ] }, { - "type": 1, + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 5 + ] + }, + { + "type": 2, + "atoms": [ + 5, + 6 + ] + }, + { + "type": 1, + "atoms": [ + 5, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 2, + "atoms": [ + 9, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 11, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 12, + 11 + ] + }, + { + "type": 2, + "atoms": [ + 12, + 13 + ] + }, + { + "type": 1, + "atoms": [ + 14, + 12 + ] + }, + { + "type": 1, + "atoms": [ + 14, + 15 + ] + }, + { + "type": 2, + "atoms": [ + 16, + 14 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 16 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 17 + ] + }, + { + "type": 1, + "atoms": [ + 17, + 18 + ] + }, + { + "type": 2, + "atoms": [ + 18, + 19 + ] + }, + { + "type": 1, + "atoms": [ + 18, + 20 + ] + } + ], + "class": "AminoAcid", + "classHELM": "PEPTIDE", + "id": "pnT___PNA Thymine", + "fullName": "PNA Thymine", + "alias": "pnT", + "attachmentPoints": [ + { + "attachmentAtom": 1, + "leavingGroup": { + "atoms": [ + 0 + ] + }, + "type": "left" + }, + { + "attachmentAtom": 18, + "leavingGroup": { + "atoms": [ + 20 + ] + }, + "type": "right" + } + ], + "naturalAnalogShort": "X" + }, + "monomerTemplate-U___Selenocysteine": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "N", + "location": [ + 14.558974596215561, + -10.200000000000001, + 0 + ] + }, + { + "label": "C", + "location": [ + 15.425, + -9.700000000000001, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 16.291025403784438, + -10.200000000000003, + 0 + ] + }, + { + "label": "O", + "location": [ + 17.15705080756888, + -9.700000000000003, + 0 + ] + }, + { + "label": "O", + "location": [ + 16.291025403784438, + -11.200000000000003, + 0 + ] + }, + { + "label": "H", + "location": [ + 13.692949192431122, + -9.700000000000001, + 0 + ] + }, + { + "label": "C", + "location": [ + 15.425, + -8.700000000000001, + 0 + ] + }, + { + "label": "Se", + "location": [ + 14.558974596215563, + -8.2, + 0 + ] + }, + { + "label": "H", + "location": [ + 14.558974596215563, + -7.2, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 3 + ] + }, + { + "type": 2, "atoms": [ - 3, + 2, 4 ] }, { "type": 1, "atoms": [ - 4, + 0, 5 ] }, { - "type": 2, + "type": 1, "atoms": [ - 5, + 1, 6 - ] + ], + "stereo": 1 }, { "type": 1, "atoms": [ - 5, + 6, 7 ] }, @@ -42453,273 +42012,43 @@ 7, 8 ] - }, - { - "type": 1, - "atoms": [ - 8, - 9 - ] - }, - { - "type": 2, - "atoms": [ - 9, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 11, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 12, - 11 - ] - }, - { - "type": 2, - "atoms": [ - 12, - 13 - ] - }, - { - "type": 1, - "atoms": [ - 14, - 12 - ] - }, - { - "type": 1, - "atoms": [ - 14, - 15 - ] - }, - { - "type": 2, - "atoms": [ - 16, - 14 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 16 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 17 - ] - }, - { - "type": 1, - "atoms": [ - 17, - 18 - ] - }, - { - "type": 2, - "atoms": [ - 18, - 19 - ] - }, - { - "type": 1, - "atoms": [ - 18, - 20 - ] } ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "pnT___PNA Thymine", - "fullName": "PNA Thymine", - "alias": "pnT", + "id": "U___Selenocysteine", + "fullName": "Selenocysteine", + "alias": "U", "attachmentPoints": [ { - "attachmentAtom": 1, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 0 + 5 ] }, "type": "left" }, { - "attachmentAtom": 18, + "attachmentAtom": 2, "leavingGroup": { "atoms": [ - 20 + 3 ] }, "type": "right" - } - ], - "naturalAnalogShort": "X" - }, - "monomerTemplate-seC___SelenoCysteine": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.2682, - -0.7312, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.0321, - 0.018, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - -0.0344, - 1.5189, - 0 - ] - }, - { - "label": "Se", - "location": [ - -1.0742, - 2.1179, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.3325, - -0.7312, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.27, - -1.9313, - 0 - ] }, { - "label": "O", - "location": [ - 2.3068, - -0.13, - 0 - ] - }, - { - "label": "H", - "location": [ - -2.3717, - -0.1311, - 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 - ], - "stereo": 1 - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 7 - ] - } - ], - "class": "AminoAcid", - "classHELM": "PEPTIDE", - "id": "seC___SelenoCysteine", - "fullName": "SelenoCysteine", - "alias": "seC", - "attachmentPoints": [ - { - "attachmentAtom": 4, - "leavingGroup": { - "atoms": [ - 7 - ] - }, - "type": "left" - }, - { - "attachmentAtom": 0, + "attachmentAtom": 7, "leavingGroup": { "atoms": [ - 6 + 8 ] }, - "type": "right" + "type": "side" } ], - "naturalAnalogShort": "C" + "naturalAnalogShort": "U" }, "monomerTemplate-Test-6-Ch___Test-6-AP-Chem": { "type": "monomerTemplate", @@ -43287,7 +42616,7 @@ } ] }, - "monomerTemplate-Az___Azide": { + "monomerTemplate-Az___4-azidobutyric acid": { "type": "monomerTemplate", "atoms": [ { @@ -43425,8 +42754,8 @@ ], "class": "CHEM", "classHELM": "CHEM", - "id": "Az___Azide", - "fullName": "Azide", + "id": "Az___4-azidobutyric acid", + "fullName": "4-azidobutyric acid", "alias": "Az", "attachmentPoints": [ { @@ -43985,7 +43314,7 @@ } ] }, - "monomerTemplate-SMCC___SMCC linker from Pierce": { + "monomerTemplate-SMCC___SMCC": { "type": "monomerTemplate", "atoms": [ { @@ -44270,8 +43599,8 @@ ], "class": "CHEM", "classHELM": "CHEM", - "id": "SMCC___SMCC linker from Pierce", - "fullName": "SMCC linker from Pierce", + "id": "SMCC___SMCC", + "fullName": "SMCC", "alias": "SMCC", "attachmentPoints": [ { @@ -44294,7 +43623,7 @@ } ] }, - "monomerTemplate-SMPEG2___SM(PEG)2 linker from Pierce": { + "monomerTemplate-SMPEG2___SM(PEG)2": { "type": "monomerTemplate", "atoms": [ { @@ -44662,8 +43991,8 @@ ], "class": "CHEM", "classHELM": "CHEM", - "id": "SMPEG2___SM(PEG)2 linker from Pierce", - "fullName": "SM(PEG)2 linker from Pierce", + "id": "SMPEG2___SM(PEG)2", + "fullName": "SM(PEG)2", "alias": "SMPEG2", "attachmentPoints": [ { @@ -44891,7 +44220,7 @@ } ] }, - "monomerTemplate-hxy___Hexynyl alcohol": { + "monomerTemplate-hxy___5-hexyn-1-ol": { "type": "monomerTemplate", "atoms": [ { @@ -45012,8 +44341,8 @@ ], "class": "CHEM", "classHELM": "CHEM", - "id": "hxy___Hexynyl alcohol", - "fullName": "Hexynyl alcohol", + "id": "hxy___5-hexyn-1-ol", + "fullName": "5-hexyn-1-ol", "alias": "hxy", "attachmentPoints": [ { @@ -45406,7 +44735,7 @@ } ] }, - "monomerTemplate-dPyl___D-Pyl": { + "monomerTemplate-dO___D-pyrrolysine": { "type": "monomerTemplate", "atoms": [ { @@ -45703,9 +45032,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "dPyl___D-Pyl", - "fullName": "D-Pyl", - "alias": "dPyl", + "id": "dO___D-pyrrolysine", + "fullName": "D-pyrrolysine", + "alias": "dO", "attachmentPoints": [ { "attachmentAtom": 1, @@ -45726,9 +45055,9 @@ "type": "right" } ], - "naturalAnalogShort": "K" + "naturalAnalogShort": "O" }, - "monomerTemplate-dSec___D-SelenoCysteine": { + "monomerTemplate-dU___D-selenocysteine": { "type": "monomerTemplate", "atoms": [ { @@ -45866,9 +45195,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "dSec___D-SelenoCysteine", - "fullName": "D-SelenoCysteine", - "alias": "dSec", + "id": "dU___D-selenocysteine", + "fullName": "D-selenocysteine", + "alias": "dU", "attachmentPoints": [ { "attachmentAtom": 1, @@ -45898,9 +45227,9 @@ "type": "side" } ], - "naturalAnalogShort": "C" + "naturalAnalogShort": "U" }, - "monomerTemplate-Pyl___Pyl": { + "monomerTemplate-O___Pyrrolysine": { "type": "monomerTemplate", "atoms": [ { @@ -46197,9 +45526,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Pyl___Pyl", - "fullName": "Pyl", - "alias": "Pyl", + "id": "O___Pyrrolysine", + "fullName": "Pyrrolysine", + "alias": "O", "attachmentPoints": [ { "attachmentAtom": 1, @@ -46220,9 +45549,9 @@ "type": "right" } ], - "naturalAnalogShort": "K" + "naturalAnalogShort": "O" }, - "monomerTemplate-NMe___C-Terminal NMe": { + "monomerTemplate--NMe___C-Terminal methylamino": { "type": "monomerTemplate", "atoms": [ { @@ -46268,9 +45597,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "NMe___C-Terminal NMe", - "fullName": "C-Terminal NMe", - "alias": "NMe", + "id": "-NMe___C-Terminal methylamino", + "fullName": "C-Terminal methylamino", + "alias": "-NMe", "attachmentPoints": [ { "attachmentAtom": 0, @@ -46284,7 +45613,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-OMe___C-Terminal OMe": { + "monomerTemplate--OMe___C-Terminal methoxy": { "type": "monomerTemplate", "atoms": [ { @@ -46330,9 +45659,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "OMe___C-Terminal OMe", - "fullName": "C-Terminal OMe", - "alias": "OMe", + "id": "-OMe___C-Terminal methoxy", + "fullName": "C-Terminal methoxy", + "alias": "-OMe", "attachmentPoints": [ { "attachmentAtom": 0, @@ -46346,7 +45675,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-OtBu___C-Terminal OtBu": { + "monomerTemplate--OtBu___C-Terminal tert-butoxy": { "type": "monomerTemplate", "atoms": [ { @@ -46437,9 +45766,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "OtBu___C-Terminal OtBu", - "fullName": "C-Terminal OtBu", - "alias": "OtBu", + "id": "-OtBu___C-Terminal tert-butoxy", + "fullName": "C-Terminal tert-butoxy", + "alias": "-OtBu", "attachmentPoints": [ { "attachmentAtom": 0, @@ -46453,7 +45782,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Oxa___C-Terminal Oxa": { + "monomerTemplate-Oxa___2‑oxazoline": { "type": "monomerTemplate", "atoms": [ { @@ -46551,8 +45880,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Oxa___C-Terminal Oxa", - "fullName": "C-Terminal Oxa", + "id": "Oxa___2‑oxazoline", + "fullName": "2‑oxazoline", "alias": "Oxa", "attachmentPoints": [ { @@ -46567,7 +45896,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-OBz___C-Terminal OBz": { + "monomerTemplate--OBn___C-Terminal benzyloxy": { "type": "monomerTemplate", "atoms": [ { @@ -46710,9 +46039,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "OBz___C-Terminal OBz", - "fullName": "C-Terminal OBz", - "alias": "OBz", + "id": "-OBn___C-Terminal benzyloxy", + "fullName": "C-Terminal benzyloxy", + "alias": "-OBn", "attachmentPoints": [ { "attachmentAtom": 2, @@ -47578,7 +46907,7 @@ ], "naturalAnalogShort": "F" }, - "monomerTemplate-D-Hyp___D-4-Hydroxyproline": { + "monomerTemplate-D-Hyp___trans-4-hydroxy-D-proline": { "type": "monomerTemplate", "atoms": [ { @@ -47740,8 +47069,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-Hyp___D-4-Hydroxyproline", - "fullName": "D-4-Hydroxyproline", + "id": "D-Hyp___trans-4-hydroxy-D-proline", + "fullName": "trans-4-hydroxy-D-proline", "alias": "D-Hyp", "attachmentPoints": [ { @@ -50536,7 +49865,7 @@ ], "naturalAnalogShort": "T" }, - "monomerTemplate-D-2Nal___D-3-naphthylalanine": { + "monomerTemplate-D-2Nal___D-3-(2-naphtyl)-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -50808,8 +50137,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-2Nal___D-3-naphthylalanine", - "fullName": "D-3-naphthylalanine", + "id": "D-2Nal___D-3-(2-naphtyl)-alanine", + "fullName": "D-3-(2-naphtyl)-alanine", "alias": "D-2Nal", "attachmentPoints": [ { @@ -50833,7 +50162,7 @@ ], "naturalAnalogShort": "A" }, - "monomerTemplate-D-2Thi___D-3-thienylalanine": { + "monomerTemplate-D-2Thi___3-(2-thienyl)-D-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -51023,8 +50352,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-2Thi___D-3-thienylalanine", - "fullName": "D-3-thienylalanine", + "id": "D-2Thi___3-(2-thienyl)-D-alanine", + "fullName": "3-(2-thienyl)-D-alanine", "alias": "D-2Thi", "attachmentPoints": [ { @@ -51048,7 +50377,7 @@ ], "naturalAnalogShort": "A" }, - "monomerTemplate-D-aHyp___D-allo-4-hydroxyproline": { + "monomerTemplate-D-aHyp___cis-4-hydroxy-D-proline": { "type": "monomerTemplate", "atoms": [ { @@ -51210,8 +50539,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-aHyp___D-allo-4-hydroxyproline", - "fullName": "D-allo-4-hydroxyproline", + "id": "D-aHyp___cis-4-hydroxy-D-proline", + "fullName": "cis-4-hydroxy-D-proline", "alias": "D-aHyp", "attachmentPoints": [ { @@ -51415,7 +50744,7 @@ ], "naturalAnalogShort": "I" }, - "monomerTemplate-D-Phg___D-2-phenylglycine": { + "monomerTemplate-D-Phg___D-phenylglycine": { "type": "monomerTemplate", "atoms": [ { @@ -51605,8 +50934,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-Phg___D-2-phenylglycine", - "fullName": "D-2-phenylglycine", + "id": "D-Phg___D-phenylglycine", + "fullName": "D-phenylglycine", "alias": "D-Phg", "attachmentPoints": [ { @@ -52648,7 +51977,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-aHyp___L-allo-4-hydroxyproline": { + "monomerTemplate-aHyp___cis-4-hydroxy-L-proline": { "type": "monomerTemplate", "atoms": [ { @@ -52810,8 +52139,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "aHyp___L-allo-4-hydroxyproline", - "fullName": "L-allo-4-hydroxyproline", + "id": "aHyp___cis-4-hydroxy-L-proline", + "fullName": "cis-4-hydroxy-L-proline", "alias": "aHyp", "attachmentPoints": [ { @@ -53542,7 +52871,7 @@ ], "naturalAnalogShort": "T" }, - "monomerTemplate-D-Cha___D-2-Amino-3-cyclohexyl-propionic acid": { + "monomerTemplate-D-Cha___3-cyclohexyl-D-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -53747,8 +53076,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-Cha___D-2-Amino-3-cyclohexyl-propionic acid", - "fullName": "D-2-Amino-3-cyclohexyl-propionic acid", + "id": "D-Cha___3-cyclohexyl-D-alanine", + "fullName": "3-cyclohexyl-D-alanine", "alias": "D-Cha", "attachmentPoints": [ { @@ -53772,7 +53101,7 @@ ], "naturalAnalogShort": "A" }, - "monomerTemplate-D-Pen___D-penicillamine (3-mercaptovaline)": { + "monomerTemplate-D-Pen___D-penicillamine": { "type": "monomerTemplate", "atoms": [ { @@ -53940,8 +53269,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-Pen___D-penicillamine (3-mercaptovaline)", - "fullName": "D-penicillamine (3-mercaptovaline)", + "id": "D-Pen___D-penicillamine", + "fullName": "D-penicillamine", "alias": "D-Pen", "attachmentPoints": [ { @@ -54479,7 +53808,7 @@ ], "naturalAnalogShort": "S" }, - "monomerTemplate-MsO___Mesylate": { + "monomerTemplate-MsO-___N-Terminal methanesulfonyl": { "type": "monomerTemplate", "atoms": [ { @@ -54555,9 +53884,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "MsO___Mesylate", - "fullName": "Mesylate", - "alias": "MsO", + "id": "MsO-___N-Terminal methanesulfonyl", + "fullName": "N-Terminal methanesulfonyl", + "alias": "MsO-", "attachmentPoints": [ { "attachmentAtom": 1, @@ -54571,7 +53900,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Oic3aS___Perhydroindolic acid": { + "monomerTemplate-Oic3aS___(2S,3aS,7aS)-perhydroindolic acid": { "type": "monomerTemplate", "atoms": [ { @@ -54787,8 +54116,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Oic3aS___Perhydroindolic acid", - "fullName": "Perhydroindolic acid", + "id": "Oic3aS___(2S,3aS,7aS)-perhydroindolic acid", + "fullName": "(2S,3aS,7aS)-perhydroindolic acid", "alias": "Oic3aS", "attachmentPoints": [ { @@ -55225,7 +54554,7 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "A" }, "monomerTemplate-4Pal___3-(4-Pyridyl)-alanine": { "type": "monomerTemplate", @@ -55455,7 +54784,7 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "A" }, "monomerTemplate-Chg___Alpha-cyclohexylglycine": { "type": "monomerTemplate", @@ -55670,9 +54999,9 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "G" }, - "monomerTemplate-D-3Pal___D-3-(2-pyridyl)-alanine": { + "monomerTemplate-D-3Pal___D-3-(3-pyridyl)-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -55877,8 +55206,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-3Pal___D-3-(2-pyridyl)-alanine", - "fullName": "D-3-(2-pyridyl)-alanine", + "id": "D-3Pal___D-3-(3-pyridyl)-alanine", + "fullName": "D-3-(3-pyridyl)-alanine", "alias": "D-3Pal", "attachmentPoints": [ { @@ -55900,81 +55229,81 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "A" }, "monomerTemplate-DaMeAb___D-Isovaline": { "type": "monomerTemplate", "atoms": [ { - "label": "C", + "label": "N", "location": [ - -2.077, - 1.3017, + 13.908974596215561, + -9.375, 0 ] }, { "label": "C", "location": [ - -0.577, - 1.3004, + 14.775, + -8.875, 0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", "location": [ - 0.1731, - 0.0004, + 15.64102540378444, + -9.375, 0 - ], - "stereoLabel": "abs" + ] }, { - "label": "C", + "label": "O", "location": [ - -0.5777, - -1.2982, + 16.507050807568877, + -8.875, 0 ] }, { - "label": "N", + "label": "H", "location": [ - -1.3569, - -0.0009, + 13.042949192431124, + -8.875, 0 ] }, { - "label": "H", + "label": "O", "location": [ - -2.1066, - -1.3001, + 15.64102540378444, + -10.375, 0 ] }, { "label": "C", "location": [ - 1.6739, - -0.0009, + 14.775, + -7.875, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 2.4247, - 1.2977, + 15.64102540378444, + -8.375, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 2.4235, - -1.3001, + 13.908974596215561, + -7.375, 0 ] } @@ -55990,8 +55319,8 @@ { "type": 1, "atoms": [ - 2, - 1 + 1, + 2 ] }, { @@ -55999,39 +55328,40 @@ "atoms": [ 2, 3 - ], - "stereo": 1 + ] }, { "type": 1, "atoms": [ - 2, + 0, 4 ] }, { - "type": 1, + "type": 2, "atoms": [ - 4, + 2, 5 ] }, { "type": 1, "atoms": [ - 2, + 1, 6 - ] + ], + "stereo": 6 }, { "type": 1, "atoms": [ - 6, + 1, 7 - ] + ], + "stereo": 1 }, { - "type": 2, + "type": 1, "atoms": [ 6, 8 @@ -56045,25 +55375,25 @@ "alias": "DaMeAb", "attachmentPoints": [ { - "attachmentAtom": 4, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 5 + 4 ] }, "type": "left" }, { - "attachmentAtom": 6, + "attachmentAtom": 2, "leavingGroup": { "atoms": [ - 7 + 3 ] }, "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "V" }, "monomerTemplate-D-Chg___D-Alpha-cyclohexylglycine": { "type": "monomerTemplate", @@ -56278,9 +55608,9 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "G" }, - "monomerTemplate-D-Cit___D-Citrullin": { + "monomerTemplate-D-Cit___D-citrulline": { "type": "monomerTemplate", "atoms": [ { @@ -56478,8 +55808,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-Cit___D-Citrullin", - "fullName": "D-Citrullin", + "id": "D-Cit___D-citrulline", + "fullName": "D-citrulline", "alias": "D-Cit", "attachmentPoints": [ { @@ -56501,7 +55831,7 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "R" }, "monomerTemplate-D-Dab___D-2,4-diaminobutanoic acid": { "type": "monomerTemplate", @@ -57355,7 +56685,7 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "A" }, "monomerTemplate-D-Abu___D-2-aminobutanoic acid": { "type": "monomerTemplate", @@ -57503,9 +56833,9 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "A" }, - "monomerTemplate-D-Dap___D-2,3-diaminopropanoic acid": { + "monomerTemplate-D-Dap___3-amino-D-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -57643,8 +56973,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-Dap___D-2,3-diaminopropanoic acid", - "fullName": "D-2,3-diaminopropanoic acid", + "id": "D-Dap___3-amino-D-alanine", + "fullName": "3-amino-D-alanine", "alias": "D-Dap", "attachmentPoints": [ { @@ -57675,9 +57005,9 @@ "type": "side" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "S" }, - "monomerTemplate-Cbz___Carboxybenzyl": { + "monomerTemplate-Cbz-___N-Terminal carboxybenzyl": { "type": "monomerTemplate", "atoms": [ { @@ -57850,9 +57180,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Cbz___Carboxybenzyl", - "fullName": "Carboxybenzyl", - "alias": "Cbz", + "id": "Cbz-___N-Terminal carboxybenzyl", + "fullName": "N-Terminal carboxybenzyl", + "alias": "Cbz-", "attachmentPoints": [ { "attachmentAtom": 1, @@ -57928,7 +57258,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-NHEt___Ethanamine": { + "monomerTemplate--NHEt___C-Terminal ethylamino": { "type": "monomerTemplate", "atoms": [ { @@ -57989,9 +57319,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "NHEt___Ethanamine", - "fullName": "Ethanamine", - "alias": "NHEt", + "id": "-NHEt___C-Terminal ethylamino", + "fullName": "C-Terminal ethylamino", + "alias": "-NHEt", "attachmentPoints": [ { "attachmentAtom": 2, @@ -58005,7 +57335,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-OEt___Ethanol": { + "monomerTemplate--OEt___C-terminal ethoxy": { "type": "monomerTemplate", "atoms": [ { @@ -58066,9 +57396,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "OEt___Ethanol", - "fullName": "Ethanol", - "alias": "OEt", + "id": "-OEt___C-terminal ethoxy", + "fullName": "C-terminal ethoxy", + "alias": "-OEt", "attachmentPoints": [ { "attachmentAtom": 2, @@ -58082,7 +57412,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Tos___Tosyl": { + "monomerTemplate-Tos-___N-Terminal tosyl": { "type": "monomerTemplate", "atoms": [ { @@ -58255,9 +57585,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Tos___Tosyl", - "fullName": "Tosyl", - "alias": "Tos", + "id": "Tos-___N-Terminal tosyl", + "fullName": "N-Terminal tosyl", + "alias": "Tos-", "attachmentPoints": [ { "attachmentAtom": 7, @@ -58271,7 +57601,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-D-Thz___(4S)-1,3-thiazolidine-4-carboxylic acid": { + "monomerTemplate-D-Thz___D-thioproline": { "type": "monomerTemplate", "atoms": [ { @@ -58416,8 +57746,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-Thz___(4S)-1,3-thiazolidine-4-carboxylic acid", - "fullName": "(4S)-1,3-thiazolidine-4-carboxylic acid", + "id": "D-Thz___D-thioproline", + "fullName": "D-thioproline", "alias": "D-Thz", "attachmentPoints": [ { @@ -58439,7 +57769,7 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "P" }, "monomerTemplate-DACys___Deamino-Cysteine": { "type": "monomerTemplate", @@ -59058,7 +58388,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-DAGlyT___2-(thiophen-2-yl)acetic acid": { + "monomerTemplate-DAGlyT___2-thiopheneacetic acid": { "type": "monomerTemplate", "atoms": [ { @@ -59201,8 +58531,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DAGlyT___2-(thiophen-2-yl)acetic acid", - "fullName": "2-(thiophen-2-yl)acetic acid", + "id": "DAGlyT___2-thiopheneacetic acid", + "fullName": "2-thiopheneacetic acid", "alias": "DAGlyT", "attachmentPoints": [ { @@ -59217,7 +58547,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-DTrpFo___(2R)-2-amino-3-(1-formyl-1H-indol-3-yl)propanoic acid": { + "monomerTemplate-DTrpFo___1-formyl-D-tryptophan": { "type": "monomerTemplate", "atoms": [ { @@ -59504,8 +58834,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DTrpFo___(2R)-2-amino-3-(1-formyl-1H-indol-3-yl)propanoic acid", - "fullName": "(2R)-2-amino-3-(1-formyl-1H-indol-3-yl)propanoic acid", + "id": "DTrpFo___1-formyl-D-tryptophan", + "fullName": "1-formyl-D-tryptophan", "alias": "DTrpFo", "attachmentPoints": [ { @@ -59529,7 +58859,7 @@ ], "naturalAnalogShort": "W" }, - "monomerTemplate-DANcy___2-sulfanylacetic acid": { + "monomerTemplate-DANcy___Thioglycolic acid": { "type": "monomerTemplate", "atoms": [ { @@ -59605,8 +58935,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DANcy___2-sulfanylacetic acid", - "fullName": "2-sulfanylacetic acid", + "id": "DANcy___Thioglycolic acid", + "fullName": "Thioglycolic acid", "alias": "DANcy", "attachmentPoints": [ { @@ -59621,7 +58951,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-DAPhe___Deamino-Phenylalanine": { + "monomerTemplate-PhLA___3-phenyllactic acid": { "type": "monomerTemplate", "atoms": [ { @@ -59809,9 +59139,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DAPhe___Deamino-Phenylalanine", - "fullName": "Deamino-Phenylalanine", - "alias": "DAPhe", + "id": "PhLA___3-phenyllactic acid", + "fullName": "3-phenyllactic acid", + "alias": "PhLA", "attachmentPoints": [ { "attachmentAtom": 3, @@ -60029,7 +59359,7 @@ ], "naturalAnalogShort": "F" }, - "monomerTemplate-DALeu___Deamino-Leucine": { + "monomerTemplate-DALeu___4-methylpentanoic acid": { "type": "monomerTemplate", "atoms": [ { @@ -60150,8 +59480,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DALeu___Deamino-Leucine", - "fullName": "Deamino-Leucine", + "id": "DALeu___4-methylpentanoic acid", + "fullName": "4-methylpentanoic acid", "alias": "DALeu", "attachmentPoints": [ { @@ -60166,7 +59496,7 @@ ], "naturalAnalogShort": "L" }, - "monomerTemplate-D-OAla___(2R)-2-hydroxypropanoic acid": { + "monomerTemplate-D-OAla___D-lactic acid": { "type": "monomerTemplate", "atoms": [ { @@ -60259,8 +59589,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-OAla___(2R)-2-hydroxypropanoic acid", - "fullName": "(2R)-2-hydroxypropanoic acid", + "id": "D-OAla___D-lactic acid", + "fullName": "D-lactic acid", "alias": "D-OAla", "attachmentPoints": [ { @@ -60275,7 +59605,7 @@ ], "naturalAnalogShort": "A" }, - "monomerTemplate-L-OVal___(2S)-2-hydroxy-3-methylbutanoic acid": { + "monomerTemplate-L-OVal___2-hydroxyisovaleric acid": { "type": "monomerTemplate", "atoms": [ { @@ -60398,8 +59728,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "L-OVal___(2S)-2-hydroxy-3-methylbutanoic acid", - "fullName": "(2S)-2-hydroxy-3-methylbutanoic acid", + "id": "L-OVal___2-hydroxyisovaleric acid", + "fullName": "2-hydroxyisovaleric acid", "alias": "L-OVal", "attachmentPoints": [ { @@ -60414,7 +59744,7 @@ ], "naturalAnalogShort": "V" }, - "monomerTemplate-NHBn-___N-Terminal 1-phenylmethanamine": { + "monomerTemplate-NHBn-___N-Terminal benzylamino": { "type": "monomerTemplate", "atoms": [ { @@ -60557,8 +59887,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "NHBn-___N-Terminal 1-phenylmethanamine", - "fullName": "N-Terminal 1-phenylmethanamine", + "id": "NHBn-___N-Terminal benzylamino", + "fullName": "N-Terminal benzylamino", "alias": "NHBn-", "attachmentPoints": [ { @@ -60573,7 +59903,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Bz___Benzaldehyde": { + "monomerTemplate-Bz-___N-Terminal benzoyl": { "type": "monomerTemplate", "atoms": [ { @@ -60716,9 +60046,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Bz___Benzaldehyde", - "fullName": "Benzaldehyde", - "alias": "Bz", + "id": "Bz-___N-Terminal benzoyl", + "fullName": "N-Terminal benzoyl", + "alias": "Bz-", "attachmentPoints": [ { "attachmentAtom": 1, @@ -60841,7 +60171,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-DTyrEt___(2R)-2-amino-3-(4-ethoxyphenyl)propanoic acid": { + "monomerTemplate-DTyrEt___O-ethyl-D-tyrosine": { "type": "monomerTemplate", "atoms": [ { @@ -61091,8 +60421,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DTyrEt___(2R)-2-amino-3-(4-ethoxyphenyl)propanoic acid", - "fullName": "(2R)-2-amino-3-(4-ethoxyphenyl)propanoic acid", + "id": "DTyrEt___O-ethyl-D-tyrosine", + "fullName": "O-ethyl-D-tyrosine", "alias": "DTyrEt", "attachmentPoints": [ { @@ -61116,7 +60446,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-Lys_Ac___(2S)-2-amino-6-acetamidohexanoic acid": { + "monomerTemplate-Lys_Ac___N-epsilon-acetyl-L-lysine": { "type": "monomerTemplate", "atoms": [ { @@ -61329,8 +60659,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Lys_Ac___(2S)-2-amino-6-acetamidohexanoic acid", - "fullName": "(2S)-2-amino-6-acetamidohexanoic acid", + "id": "Lys_Ac___N-epsilon-acetyl-L-lysine", + "fullName": "N-epsilon-acetyl-L-lysine", "alias": "Lys_Ac", "attachmentPoints": [ { @@ -61354,30 +60684,30 @@ ], "naturalAnalogShort": "K" }, - "monomerTemplate-OMe-___N-Terminal methanol": { + "monomerTemplate-OMe-___N-Terminal methoxy": { "type": "monomerTemplate", "atoms": [ { "label": "C", "location": [ - 0.0007, - 0.0004, + 6.916987298107781, + -6.65, 0 ] }, { "label": "O", "location": [ - 1.3, - 0.75, + 7.78301270189222, + -6.15, 0 ] }, { - "label": "O", + "label": "H", "location": [ - 2.5993, - 0.0004, + 8.649038105676658, + -6.650000000000001, 0 ] } @@ -61400,8 +60730,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "OMe-___N-Terminal methanol", - "fullName": "N-Terminal methanol", + "id": "OMe-___N-Terminal methoxy", + "fullName": "N-Terminal methoxy", "alias": "OMe-", "attachmentPoints": [ { @@ -61813,110 +61143,111 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-PheaDH___2-amino-3-phenylprop-2-enoic acid": { + "monomerTemplate-PheaDH___Dehydrophenylalanine": { "type": "monomerTemplate", "atoms": [ { - "label": "H", + "label": "C", "location": [ - -0.0041, - -2.9953, + 17.59849876455248, + -10.599687850560374, 0 ] }, { - "label": "N", + "label": "O", "location": [ - 1.2925, - -3.7494, + 18.46452416833692, + -10.099687850560374, 0 ] }, { "label": "C", "location": [ - 2.5951, - -3.0039, + 16.732473360768044, + -10.099687850560374, 0 - ] + ], + "stereoLabel": "abs" }, { - "label": "C", + "label": "N", "location": [ - 2.5973, - -1.5031, + 15.866447956983603, + -10.599687850560374, 0 ] }, { - "label": "C", + "label": "O", "location": [ - 1.299, - -0.75, + 17.59849876455248, + -11.599687850560372, 0 ] }, { - "label": "C", + "label": "H", "location": [ - 1.299, - 0.75, + 15.000422553199165, + -10.099687850560374, 0 ] }, { "label": "C", "location": [ - 0, - 1.5, + 16.732473360768044, + -9.099687850560374, 0 ] }, { "label": "C", "location": [ - -1.299, - 0.75, + 15.866447956983603, + -8.599687850560372, 0 ] }, { "label": "C", "location": [ - -1.299, - -0.75, + 14.136146975524628, + -8.601333225940827, 0 ] }, { "label": "C", "location": [ - 0, - -1.5, + 14.999995122406478, + -9.100376458179426, 0 ] }, { "label": "C", "location": [ - 3.8933, - -3.757, + 14.135475831663083, + -7.600390612300804, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 5.1937, - -3.0093, + 15.86577412919726, + -7.594742436841567, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 3.8912, - -5.257, + 14.996470709151687, + -7.100312149439627, 0 ] } @@ -61925,14 +61256,14 @@ { "type": 1, "atoms": [ - 1, - 0 + 0, + 1 ] }, { - "type": 2, + "type": 1, "atoms": [ - 1, + 0, 2 ] }, @@ -61944,96 +61275,97 @@ ] }, { - "type": 1, + "type": 2, "atoms": [ - 3, + 0, 4 ] }, { - "type": 2, + "type": 1, "atoms": [ - 4, + 3, 5 ] }, { - "type": 1, + "type": 2, "atoms": [ - 5, + 2, 6 - ] + ], + "stereo": 3 }, { - "type": 2, + "type": 1, "atoms": [ 6, 7 ] }, { - "type": 1, + "type": 2, "atoms": [ - 7, - 8 + 9, + 7 ] }, { - "type": 2, + "type": 1, "atoms": [ - 8, - 9 + 7, + 11 ] }, { - "type": 1, + "type": 2, "atoms": [ - 4, - 9 + 11, + 12 ] }, { "type": 1, "atoms": [ - 2, + 12, 10 ] }, { - "type": 1, + "type": 2, "atoms": [ 10, - 11 + 8 ] }, { - "type": 2, + "type": 1, "atoms": [ - 10, - 12 + 8, + 9 ] } ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "PheaDH___2-amino-3-phenylprop-2-enoic acid", - "fullName": "2-amino-3-phenylprop-2-enoic acid", + "id": "PheaDH___Dehydrophenylalanine", + "fullName": "Dehydrophenylalanine", "alias": "PheaDH", "attachmentPoints": [ { - "attachmentAtom": 1, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 0 + 5 ] }, "type": "left" }, { - "attachmentAtom": 10, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 11 + 1 ] }, "type": "right" @@ -62262,7 +61594,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-TyrabD___2-amino-3-(4-methoxyphenyl)prop-2-enoic acid": { + "monomerTemplate-TyrabD___(2E)-2-amino-3-(4-methoxyphenyl)prop-2-enoic acid": { "type": "monomerTemplate", "atoms": [ { @@ -62495,8 +61827,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "TyrabD___2-amino-3-(4-methoxyphenyl)prop-2-enoic acid", - "fullName": "2-amino-3-(4-methoxyphenyl)prop-2-enoic acid", + "id": "TyrabD___(2E)-2-amino-3-(4-methoxyphenyl)prop-2-enoic acid", + "fullName": "(2E)-2-amino-3-(4-methoxyphenyl)prop-2-enoic acid", "alias": "TyrabD", "attachmentPoints": [ { @@ -62520,22 +61852,22 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-DAlaol___(2R)-2-aminopropan-1-ol": { + "monomerTemplate-DAlaol___D-alaninol": { "type": "monomerTemplate", "atoms": [ { "label": "N", "location": [ - 2.6, - -1.5, + 12.9509618654083, + -7.700000021463854, 0 ] }, { "label": "C", "location": [ - 2.6, - 0, + 13.816987288469432, + -8.200000007154618, 0 ], "stereoLabel": "abs" @@ -62543,45 +61875,29 @@ { "label": "C", "location": [ - 1.3, - 0.75, + 14.683012711530566, + -7.700000021463854, 0 ] }, { "label": "O", "location": [ - 0.0007, - 0.0004, + 15.5490381345917, + -8.200000007154618, 0 ] }, { "label": "C", "location": [ - 3.9, - 0.75, - 0 - ] - }, - { - "label": "O", - "location": [ - 5.1992, - 0.0004, + 13.816987288469432, + -9.199999978536148, 0 ] } ], "bonds": [ - { - "type": 1, - "atoms": [ - 1, - 0 - ], - "stereo": 1 - }, { "type": 1, "atoms": [ @@ -62606,22 +61922,23 @@ { "type": 1, "atoms": [ - 4, - 5 - ] + 1, + 0 + ], + "stereo": 1 } ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DAlaol___(2R)-2-aminopropan-1-ol", - "fullName": "(2R)-2-aminopropan-1-ol", + "id": "DAlaol___D-alaninol", + "fullName": "D-alaninol", "alias": "DAlaol", "attachmentPoints": [ { - "attachmentAtom": 4, + "attachmentAtom": 2, "leavingGroup": { "atoms": [ - 5 + 3 ] }, "type": "right" @@ -62629,188 +61946,190 @@ ], "naturalAnalogShort": "A" }, - "monomerTemplate-DPhgol___2-amino-2-methylpropan-1-ol": { + "monomerTemplate-DPhgol___D-phenylglycinol": { "type": "monomerTemplate", "atoms": [ { - "label": "H", + "label": "C", "location": [ - 5.1965, - -1.5117, + 17.1770495180024, + -5.829784629779761, 0 ] }, { - "label": "N", + "label": "C", "location": [ - 6.6965, - -1.5117, + 18.675751912417496, + -6.69302699358475, 0 ] }, { "label": "C", "location": [ - 7.4478, - -0.2124, + 18.17833776387144, + -5.829663517660678, 0 ] }, { "label": "C", "location": [ - 6.6951, - 1.086, + 18.177324999537063, + -7.5610976302946105, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 5.1951, - 1.0844, + 16.67536306793278, + -6.6979744713312375, 0 ] }, { "label": "C", "location": [ - 8.9486, - -0.2108, + 17.17917136418319, + -7.564358121122529, 0 ] }, { "label": "C", "location": [ - 9.7027, - -1.5074, + 15.676067927015579, + -6.701157717421788, 0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", "location": [ - 11.2027, - -1.5027, + 15.17391896216048, + -5.836075784500959, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 11.9486, - -0.2013, + 15.178935101895739, + -7.568045842102804, 0 ] }, { - "label": "C", + "label": "H", "location": [ - 11.1945, - 1.0954, + 14.17926327367903, + -7.570336482339323, 0 ] }, { - "label": "C", + "label": "O", "location": [ - 9.6945, - 1.0906, + 14.174248087582502, + -5.838354027433951, 0 ] } ], "bonds": [ { - "type": 1, + "type": 2, "atoms": [ - 1, - 2 + 2, + 0 ] }, { "type": 1, "atoms": [ - 2, - 3 + 0, + 4 ] }, { - "type": 1, + "type": 2, "atoms": [ - 3, - 4 + 4, + 5 ] }, { "type": 1, "atoms": [ - 2, - 5 + 5, + 3 ] }, { "type": 2, "atoms": [ - 5, - 6 + 3, + 1 ] }, { "type": 1, "atoms": [ - 6, - 7 + 1, + 2 ] }, { - "type": 2, + "type": 1, "atoms": [ - 7, - 8 + 4, + 6 ] }, { "type": 1, "atoms": [ - 8, - 9 - ] + 6, + 7 + ], + "stereo": 1 }, { - "type": 2, + "type": 1, "atoms": [ - 9, - 10 + 6, + 8 ] }, { "type": 1, "atoms": [ - 10, - 5 + 8, + 9 ] }, { "type": 1, "atoms": [ - 0, - 1 + 7, + 10 ] } ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DPhgol___2-amino-2-methylpropan-1-ol", - "fullName": "2-amino-2-methylpropan-1-ol", + "id": "DPhgol___D-phenylglycinol", + "fullName": "D-phenylglycinol", "alias": "DPhgol", "attachmentPoints": [ { - "attachmentAtom": 1, + "attachmentAtom": 8, "leavingGroup": { "atoms": [ - 0 + 9 ] }, "type": "left" @@ -62818,7 +62137,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-DThrol___(2R,3R)-2-aminobutane-1,3-diol": { + "monomerTemplate-DThrol___L-threoninol": { "type": "monomerTemplate", "atoms": [ { @@ -62943,8 +62262,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DThrol___(2R,3R)-2-aminobutane-1,3-diol", - "fullName": "(2R,3R)-2-aminobutane-1,3-diol", + "id": "DThrol___L-threoninol", + "fullName": "L-threoninol", "alias": "DThrol", "attachmentPoints": [ { @@ -63036,7 +62355,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-Ala-ol___(2S)-2-aminopropan-1-ol": { + "monomerTemplate-Ala-ol___L-Alaninol": { "type": "monomerTemplate", "atoms": [ { @@ -63129,8 +62448,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Ala-ol___(2S)-2-aminopropan-1-ol", - "fullName": "(2S)-2-aminopropan-1-ol", + "id": "Ala-ol___L-Alaninol", + "fullName": "L-Alaninol", "alias": "Ala-ol", "attachmentPoints": [ { @@ -63314,7 +62633,7 @@ ], "naturalAnalogShort": "K" }, - "monomerTemplate-Phg-ol___(2S)-2-amino-2-phenylethan-1-ol": { + "monomerTemplate-Phg-ol___L-phenylglycinol": { "type": "monomerTemplate", "atoms": [ { @@ -63489,8 +62808,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Phg-ol___(2S)-2-amino-2-phenylethan-1-ol", - "fullName": "(2S)-2-amino-2-phenylethan-1-ol", + "id": "Phg-ol___L-phenylglycinol", + "fullName": "L-phenylglycinol", "alias": "Phg-ol", "attachmentPoints": [ { @@ -63505,7 +62824,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-Pro-ol___[(2S)-pyrrolidin-2-yl]methanol": { + "monomerTemplate-Pro-ol___L-prolinol": { "type": "monomerTemplate", "atoms": [ { @@ -63635,8 +62954,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Pro-ol___[(2S)-pyrrolidin-2-yl]methanol", - "fullName": "[(2S)-pyrrolidin-2-yl]methanol", + "id": "Pro-ol___L-prolinol", + "fullName": "L-prolinol", "alias": "Pro-ol", "attachmentPoints": [ { @@ -63651,7 +62970,7 @@ ], "naturalAnalogShort": "P" }, - "monomerTemplate-Val-ol___(2S)-2-amino-3-methylbutan-1-ol": { + "monomerTemplate-Val-ol___L-valinol": { "type": "monomerTemplate", "atoms": [ { @@ -63774,8 +63093,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Val-ol___(2S)-2-amino-3-methylbutan-1-ol", - "fullName": "(2S)-2-amino-3-methylbutan-1-ol", + "id": "Val-ol___L-valinol", + "fullName": "L-valinol", "alias": "Val-ol", "attachmentPoints": [ { @@ -63899,7 +63218,7 @@ 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] }, { "type": 1, @@ -69798,343 +69335,112 @@ ] }, { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, + "type": 2, "atoms": [ - 1, + 3, 5 ] }, { "type": 1, "atoms": [ - 5, + 2, 6 - ] + ], + "stereo": 6 }, { "type": 1, "atoms": [ - 1, + 6, 7 ] }, { "type": 1, "atoms": [ - 7, + 2, 8 - ] - }, - { - "type": 2, - "atoms": [ - 7, - 9 - ] - } - ], - "class": "AminoAcid", - "classHELM": "PEPTIDE", - "id": "aMePro___(2S)-2-methylpyrrolidine-2-carboxylic acid", - "fullName": "(2S)-2-methylpyrrolidine-2-carboxylic acid", - "alias": "aMePro", - "attachmentPoints": [ - { - "attachmentAtom": 5, - "leavingGroup": { - "atoms": [ - 6 - ] - }, - "type": "left" - }, - { - "attachmentAtom": 7, - "leavingGroup": { - "atoms": [ - 8 - ] - }, - "type": "right" - } - ], - "naturalAnalogShort": "P" - }, - "monomerTemplate-aMeTy3___(2S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - -1.4451, - 3.4938, - 0 - ] 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acid", - "fullName": "(2S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid", + "id": "aMeTy3___L-methyldopa", + "fullName": "L-methyldopa", "alias": "aMeTy3", "attachmentPoints": [ { - "attachmentAtom": 11, + "attachmentAtom": 1, "leavingGroup": { "atoms": [ - 12 + 0 ] }, "type": "left" }, { - "attachmentAtom": 13, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 14 + 4 ] }, "type": "right" @@ -70142,7 +69448,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-Bmt___(2S,3R,4R)-2-amino-3-hydroxy-4-methyloct-6-enoic acid": { + "monomerTemplate-Bmt___(2S,3R,4R,6E)-2-amino-3-hydroxy-4-methyloct-6-enoic acid": { "type": "monomerTemplate", "atoms": [ { @@ -70359,8 +69665,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Bmt___(2S,3R,4R)-2-amino-3-hydroxy-4-methyloct-6-enoic acid", - "fullName": "(2S,3R,4R)-2-amino-3-hydroxy-4-methyloct-6-enoic acid", + "id": "Bmt___(2S,3R,4R,6E)-2-amino-3-hydroxy-4-methyloct-6-enoic acid", + "fullName": "(2S,3R,4R,6E)-2-amino-3-hydroxy-4-methyloct-6-enoic acid", "alias": "Bmt", "attachmentPoints": [ { @@ -70384,7 +69690,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Cys_Bn___(2R)-2-amino-3-(benzylsulfanyl)propanoic acid": { + "monomerTemplate-Cys_Bn___S-benzylcysteine": { "type": "monomerTemplate", "atoms": [ { @@ -70619,8 +69925,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Cys_Bn___(2R)-2-amino-3-(benzylsulfanyl)propanoic acid", - "fullName": "(2R)-2-amino-3-(benzylsulfanyl)propanoic acid", + "id": "Cys_Bn___S-benzylcysteine", + "fullName": "S-benzylcysteine", "alias": "Cys_Bn", "attachmentPoints": [ { @@ -70644,7 +69950,7 @@ ], "naturalAnalogShort": "C" }, - "monomerTemplate-His1Me___(2S)-2-amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acid": { + "monomerTemplate-His1Me___1-methyl-L-histidine": { "type": "monomerTemplate", "atoms": [ { @@ -70849,8 +70155,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "His1Me___(2S)-2-amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acid", - "fullName": "(2S)-2-amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acid", + "id": "His1Me___1-methyl-L-histidine", + "fullName": "1-methyl-L-histidine", "alias": "His1Me", "attachmentPoints": [ { @@ -71207,7 +70513,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-Hsl___(3S)-3-aminooxolan-2-one": { + "monomerTemplate-Hsl___L-homoserine lactone": { "type": "monomerTemplate", "atoms": [ { @@ -71337,8 +70643,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Hsl___(3S)-3-aminooxolan-2-one", - "fullName": "(3S)-3-aminooxolan-2-one", + "id": "Hsl___L-homoserine lactone", + "fullName": "L-homoserine lactone", "alias": "Hsl", "attachmentPoints": [ { @@ -71353,7 +70659,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-AspPh2___(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid": { + "monomerTemplate-Kyn___Kynurenine": { "type": "monomerTemplate", "atoms": [ { @@ -71603,9 +70909,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "AspPh2___(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid", - "fullName": "(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid", - "alias": "AspPh2", + "id": "Kyn___Kynurenine", + "fullName": "Kynurenine", + "alias": "Kyn", "attachmentPoints": [ { "attachmentAtom": 11, @@ -71626,7 +70932,7 @@ "type": "right" } ], - "naturalAnalogShort": "D" + "naturalAnalogShort": "W" }, "monomerTemplate-Azi___(2S)-aziridine-2-carboxylic acid": { "type": "monomerTemplate", @@ -71768,7 +71074,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-2Abz___2-Aminobenzoic acid": { + "monomerTemplate-2Abz___Anthranilic acid": { "type": "monomerTemplate", "atoms": [ { @@ -71941,8 +71247,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "2Abz___2-Aminobenzoic acid", - "fullName": "2-Aminobenzoic acid", + "id": "2Abz___Anthranilic acid", + "fullName": "Anthranilic acid", "alias": "2Abz", "attachmentPoints": [ { @@ -72515,7 +71821,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Ac6c___1-aminocyclohexane-1-carboxylic acid": { + "monomerTemplate-Ac6c___Homocycloleucine": { "type": "monomerTemplate", "atoms": [ { @@ -72688,8 +71994,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Ac6c___1-aminocyclohexane-1-carboxylic acid", - "fullName": "1-aminocyclohexane-1-carboxylic acid", + "id": "Ac6c___Homocycloleucine", + "fullName": "Homocycloleucine", "alias": "Ac6c", "attachmentPoints": [ { @@ -72713,7 +72019,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-D-Bmt___(2R,3S,4S)-2-amino-3-hydroxy-4-methyloct-6-enoic acid": { + "monomerTemplate-D-Bmt___(2R,3S,4S,6E)-2-amino-3-hydroxy-4-methyloct-6-enoic acid": { "type": "monomerTemplate", "atoms": [ { @@ -72930,8 +72236,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-Bmt___(2R,3S,4S)-2-amino-3-hydroxy-4-methyloct-6-enoic acid", - "fullName": "(2R,3S,4S)-2-amino-3-hydroxy-4-methyloct-6-enoic acid", + "id": "D-Bmt___(2R,3S,4S,6E)-2-amino-3-hydroxy-4-methyloct-6-enoic acid", + "fullName": "(2R,3S,4S,6E)-2-amino-3-hydroxy-4-methyloct-6-enoic acid", "alias": "D-Bmt", "attachmentPoints": [ { @@ -72955,7 +72261,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-D-hArg___(2R)-2-amino-6-[(diaminomethylidene)amino]hexanoic acid": { + "monomerTemplate-D-hArg___D-homoarginine": { "type": "monomerTemplate", "atoms": [ { @@ -73168,8 +72474,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-hArg___(2R)-2-amino-6-[(diaminomethylidene)amino]hexanoic acid", - "fullName": "(2R)-2-amino-6-[(diaminomethylidene)amino]hexanoic acid", + "id": "D-hArg___D-homoarginine", + "fullName": "D-homoarginine", "alias": "D-hArg", "attachmentPoints": [ { @@ -73193,7 +72499,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-DPhe4F___(2R)-2-amino-3-(4-fluorophenyl)propanoic acid": { + "monomerTemplate-DPhe4F___4-fluoro-D-phenylalanine": { "type": "monomerTemplate", "atoms": [ { @@ -73413,8 +72719,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DPhe4F___(2R)-2-amino-3-(4-fluorophenyl)propanoic acid", - "fullName": "(2R)-2-amino-3-(4-fluorophenyl)propanoic acid", + "id": "DPhe4F___4-fluoro-D-phenylalanine", + "fullName": "4-fluoro-D-phenylalanine", "alias": "DPhe4F", "attachmentPoints": [ { @@ -73438,143 +72744,143 @@ ], "naturalAnalogShort": "F" }, - "monomerTemplate-DTrp2M___(2R)-2-amino-3-(2-methyl-1H-indol-3-yl)propanoic acid": { + "monomerTemplate-DTrp2M___2-methyl-D-tryptophan": { "type": "monomerTemplate", "atoms": [ { - "label": "C", + "label": "H", "location": [ - -1.7477, - 1.9238, + 18.209488456000955, + -8.306892911126628, 0 ] }, { - "label": "C", + "label": "N", "location": [ - -1.4399, - 0.4557, + 19.07680774604924, + -7.806145885543897, 0 ] }, { - "label": "N", + "label": "C", "location": [ - -2.4466, - -0.6562, + 19.944127036097523, + -8.306892911126628, 0 - ] + ], + "stereoLabel": "abs" }, { "label": "C", "location": [ - -1.7004, - -1.9565, + 20.81144632614581, + -7.806145885543897, 0 ] }, { - "label": "C", + "label": "O", "location": [ - -2.1678, - -3.3818, + 21.67876561619409, + -8.306892911126628, 0 ] }, { - "label": "C", + "label": "O", "location": [ - -1.1672, - -4.4993, + 20.81144632614581, + -6.804651834378432, 0 ] }, { "label": "C", "location": [ - 0.3009, - -4.1914, + 19.944127036097523, + -9.308386962292094, 0 ] }, { "label": "C", "location": [ - 0.7683, - -2.7661, + 19.44338001051479, + -10.17570625234038, 0 ] }, { "label": "C", "location": [ - -0.2323, - -1.6487, + 19.10621617263748, + -11.762033557513277, 0 ] }, { "label": "C", "location": [ - -0.0712, - -0.1581, + 19.848233061905802, + -11.09618106774609, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 1.2269, - 0.5899, + 18.238213077124904, + -11.260918874536086, 0 ] }, { "label": "C", "location": [ - 1.2292, - 2.0907, + 18.443717253056903, + -10.285327399220696, 0 - ], - "stereoLabel": "abs" + ] }, { - "label": "N", + "label": "C", "location": [ - -0.0712, - 2.84, + 17.77123438380591, + -9.543197272434451, 0 ] }, { - "label": "H", + "label": "C", "location": [ - -1.3701, - 2.0897, + 20.792772740657206, + -11.405515071067617, 0 ] }, { "label": "C", "location": [ - 2.5296, - 2.84, + 20.99873753352748, + -12.381210034858032, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 3.8277, - 2.0884, + 19.313004625004204, + -12.741630355259712, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 2.5318, - 4.34, + 20.26191653003306, + -13.04534816562157, 0 ] } @@ -73602,25 +72908,26 @@ ] }, { - "type": 2, + "type": 1, "atoms": [ 3, 4 ] }, { - "type": 1, + "type": 2, "atoms": [ - 4, + 3, 5 ] }, { - "type": 2, + "type": 1, "atoms": [ - 5, + 2, 6 - ] + ], + "stereo": 1 }, { "type": 1, @@ -73633,27 +72940,27 @@ "type": 2, "atoms": [ 7, - 8 + 11 ] }, { "type": 1, "atoms": [ - 3, - 8 + 11, + 10 ] }, { "type": 1, "atoms": [ - 8, - 9 + 10, + 8 ] }, { "type": 2, "atoms": [ - 1, + 8, 9 ] }, @@ -73661,73 +72968,72 @@ "type": 1, "atoms": [ 9, - 10 + 7 ] }, { "type": 1, "atoms": [ 11, - 10 - ], - "stereo": 1 + 12 + ] }, { "type": 1, "atoms": [ - 11, - 12 + 8, + 15 ] }, { - "type": 1, + "type": 2, "atoms": [ - 12, - 13 + 15, + 16 ] }, { "type": 1, "atoms": [ - 11, + 16, 14 ] }, { - "type": 1, + "type": 2, "atoms": [ 14, - 15 + 13 ] }, { - "type": 2, + "type": 1, "atoms": [ - 14, - 16 + 13, + 9 ] } ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DTrp2M___(2R)-2-amino-3-(2-methyl-1H-indol-3-yl)propanoic acid", - "fullName": "(2R)-2-amino-3-(2-methyl-1H-indol-3-yl)propanoic acid", + "id": "DTrp2M___2-methyl-D-tryptophan", + "fullName": "2-methyl-D-tryptophan", "alias": "DTrp2M", "attachmentPoints": [ { - "attachmentAtom": 12, + "attachmentAtom": 1, "leavingGroup": { "atoms": [ - 13 + 0 ] }, "type": "left" }, { - "attachmentAtom": 14, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 15 + 4 ] }, "type": "right" @@ -73735,7 +73041,7 @@ ], "naturalAnalogShort": "W" }, - "monomerTemplate-DTyr3O___(2R)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid": { + "monomerTemplate-DTyr3O___D-methyldopa": { "type": "monomerTemplate", "atoms": [ { @@ -73970,8 +73276,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DTyr3O___(2R)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid", - "fullName": "(2R)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid", + "id": "DTyr3O___D-methyldopa", + "fullName": "D-methyldopa", "alias": "DTyr3O", "attachmentPoints": [ { @@ -73986,7 +73292,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-DTyrMe___(2R)-2-amino-3-(4-methoxyphenyl)propanoic acid": { + "monomerTemplate-DTyrMe___O-methyl-D-tyrosine": { "type": "monomerTemplate", "atoms": [ { @@ -74221,8 +73527,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DTyrMe___(2R)-2-amino-3-(4-methoxyphenyl)propanoic acid", - "fullName": "(2R)-2-amino-3-(4-methoxyphenyl)propanoic acid", + "id": "DTyrMe___O-methyl-D-tyrosine", + "fullName": "O-methyl-D-tyrosine", "alias": "DTyrMe", "attachmentPoints": [ { @@ -74662,7 +73968,7 @@ ], "naturalAnalogShort": "K" }, - "monomerTemplate--Bn___C-Terminal toluene": { + "monomerTemplate--Bn___C-Terminal benzyl": { "type": "monomerTemplate", "atoms": [ { @@ -74790,8 +74096,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "-Bn___C-Terminal toluene", - "fullName": "C-Terminal toluene", + "id": "-Bn___C-Terminal benzyl", + "fullName": "C-Terminal benzyl", "alias": "-Bn", "attachmentPoints": [ { @@ -74806,7 +74112,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Ph___Phenyl": { + "monomerTemplate--Ph___C-terminal phenyl": { "type": "monomerTemplate", "atoms": [ { @@ -74919,9 +74225,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Ph___Phenyl", - "fullName": "Phenyl", - "alias": "Ph", + "id": "-Ph___C-terminal phenyl", + "fullName": "C-terminal phenyl", + "alias": "-Ph", "attachmentPoints": [ { "attachmentAtom": 1, @@ -74935,7 +74241,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Boc___Tert-butyloxycarbonyl": { + "monomerTemplate-Boc-___N-Terminal tert-butyloxycarbonyl": { "type": "monomerTemplate", "atoms": [ { @@ -75056,9 +74362,9 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Boc___Tert-butyloxycarbonyl", - "fullName": "Tert-butyloxycarbonyl", - "alias": "Boc", + "id": "Boc-___N-Terminal tert-butyloxycarbonyl", + "fullName": "N-Terminal tert-butyloxycarbonyl", + "alias": "Boc-", "attachmentPoints": [ { "attachmentAtom": 5, @@ -75873,7 +75179,7 @@ ], "naturalAnalogShort": "F" }, - "monomerTemplate-DAnTyr___2-(4-methoxyphenyl)acetic acid": { + "monomerTemplate-DAnTyr___4-methoxyphenylacetic acid": { "type": "monomerTemplate", "atoms": [ { @@ -76061,8 +75367,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DAnTyr___2-(4-methoxyphenyl)acetic acid", - "fullName": "2-(4-methoxyphenyl)acetic acid", + "id": "DAnTyr___4-methoxyphenylacetic acid", + "fullName": "4-methoxyphenylacetic acid", "alias": "DAnTyr", "attachmentPoints": [ { @@ -76077,7 +75383,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-DAPhg4___2-(4-chlorophenyl)acetic acid": { + "monomerTemplate-DAPhg4___4-chlorophenylacetic acid": { "type": "monomerTemplate", "atoms": [ { @@ -76250,8 +75556,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DAPhg4___2-(4-chlorophenyl)acetic acid", - "fullName": "2-(4-chlorophenyl)acetic acid", + "id": "DAPhg4___4-chlorophenylacetic acid", + "fullName": "4-chlorophenylacetic acid", "alias": "DAPhg4", "attachmentPoints": [ { @@ -76266,7 +75572,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-D-OVal___(2R)-2-hydroxy-3-methylbutanoic acid": { + "monomerTemplate-D-OVal___D-2-hydroxyisovaleric acid": { "type": "monomerTemplate", "atoms": [ { @@ -76389,8 +75695,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-OVal___(2R)-2-hydroxy-3-methylbutanoic acid", - "fullName": "(2R)-2-hydroxy-3-methylbutanoic acid", + "id": "D-OVal___D-2-hydroxyisovaleric acid", + "fullName": "D-2-hydroxyisovaleric acid", "alias": "D-OVal", "attachmentPoints": [ { @@ -76405,7 +75711,7 @@ ], "naturalAnalogShort": "V" }, - "monomerTemplate-OLeu___(2S)-2-hydroxy-4-methylpentanoic acid": { + "monomerTemplate-OLeu___L-leucic acid": { "type": "monomerTemplate", "atoms": [ { @@ -76543,8 +75849,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "OLeu___(2S)-2-hydroxy-4-methylpentanoic acid", - "fullName": "(2S)-2-hydroxy-4-methylpentanoic acid", + "id": "OLeu___L-leucic acid", + "fullName": "L-leucic acid", "alias": "OLeu", "attachmentPoints": [ { @@ -76559,143 +75865,143 @@ ], "naturalAnalogShort": "L" }, - "monomerTemplate-Bn-___N-Terminal toluene": { + "monomerTemplate-Bn-___N-Terminal benzyl": { "type": "monomerTemplate", "atoms": [ { - "label": "O", + "label": "C", "location": [ - 2.5951, - -3.0031, + 8.884849152128567, + -5.825074417174607, 0 ] }, { "label": "C", "location": [ - 2.5973, - -1.5031, + 10.615150847871433, + -5.824589229177203, 0 ] }, { "label": "C", "location": [ - 1.299, - -0.75, + 9.751637509491239, + -5.324966888850188, 0 ] }, { "label": "C", "location": [ - 1.299, - 0.75, + 10.615150847871433, + -6.825532067822148, 0 ] }, { "label": "C", "location": [ - 0, - 1.5, + 8.884849152128567, + -6.830020056798137, 0 ] }, { "label": "C", "location": [ - -1.299, - 0.75, + 9.753820855479558, + -7.325033111149812, 0 ] }, { "label": "C", "location": [ - -1.299, - -0.75, + 11.481656825240831, + -7.3246987646110115, 0 ] }, { - "label": "C", + "label": "H", "location": [ - 0, - -1.5, + 11.48261877378321, + -8.324698301938405, 0 ] } ], "bonds": [ { - "type": 1, + "type": 2, "atoms": [ - 0, - 1 + 2, + 0 ] }, { "type": 1, "atoms": [ - 1, - 2 + 0, + 4 ] }, { "type": 2, "atoms": [ - 2, - 3 + 4, + 5 ] }, { "type": 1, "atoms": [ - 3, - 4 + 5, + 3 ] }, { "type": 2, "atoms": [ - 4, - 5 + 3, + 1 ] }, { "type": 1, "atoms": [ - 5, - 6 + 1, + 2 ] }, { - "type": 2, + "type": 1, "atoms": [ - 6, - 7 + 3, + 6 ] }, { "type": 1, "atoms": [ - 2, + 6, 7 ] } ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Bn-___N-Terminal toluene", - "fullName": "N-Terminal toluene", + "id": "Bn-___N-Terminal benzyl", + "fullName": "N-Terminal benzyl", "alias": "Bn-", "attachmentPoints": [ { - "attachmentAtom": 1, + "attachmentAtom": 6, "leavingGroup": { "atoms": [ - 0 + 7 ] }, "type": "right" @@ -76703,101 +76009,108 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-OBn-___N-Terminal phenylmethanol": { + "monomerTemplate-OBn-___N-Terminal benzyloxy": { "type": "monomerTemplate", "atoms": [ { - "label": "O", + "label": "C", "location": [ - 3.8926, - -3.7566, + 6.834849152128566, + -3.8000744171746073, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 2.5951, - -3.0039, + 8.565150847871434, + -3.799589229177203, 0 ] }, { "label": "C", "location": [ - 2.5973, - -1.5031, + 7.701637509491239, + -3.299966888850187, 0 ] }, { "label": "C", "location": [ - 1.299, - -0.75, + 8.565150847871434, + -4.800532067822148, 0 ] }, { "label": "C", "location": [ - 1.299, - 0.75, + 6.834849152128566, + -4.805020056798138, 0 ] }, { "label": "C", "location": [ - 0, - 1.5, + 7.703820855479559, + -5.300033111149813, 0 ] }, { "label": "C", "location": [ - -1.299, - 0.75, + 9.431656825240832, + -5.299698764611012, 0 ] }, { - "label": "C", + "label": "O", "location": [ - -1.299, - -0.75, + 9.432618773783211, + -6.299698301938406, 0 ] }, { - "label": "C", + "label": "H", "location": [ - 0, - -1.5, + 10.29912475115261, + -6.798864998727269, 0 ] } ], "bonds": [ + { + "type": 2, + "atoms": [ + 2, + 0 + ] + }, { "type": 1, "atoms": [ 0, - 1 + 4 ] }, { - "type": 1, + "type": 2, "atoms": [ - 1, - 2 + 4, + 5 ] }, { "type": 1, "atoms": [ - 2, + 5, 3 ] }, @@ -76805,20 +76118,20 @@ "type": 2, "atoms": [ 3, - 4 + 1 ] }, { "type": 1, "atoms": [ - 4, - 5 + 1, + 2 ] }, { - "type": 2, + "type": 1, "atoms": [ - 5, + 3, 6 ] }, @@ -76829,32 +76142,25 @@ 7 ] }, - { - "type": 2, - "atoms": [ - 7, - 8 - ] - }, { "type": 1, "atoms": [ - 3, + 7, 8 ] } ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "OBn-___N-Terminal phenylmethanol", - "fullName": "N-Terminal phenylmethanol", + "id": "OBn-___N-Terminal benzyloxy", + "fullName": "N-Terminal benzyloxy", "alias": "OBn-", "attachmentPoints": [ { - "attachmentAtom": 1, + "attachmentAtom": 7, "leavingGroup": { "atoms": [ - 0 + 8 ] }, "type": "right" @@ -76862,7 +76168,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-DALys___Deamino-Lysine": { + "monomerTemplate-DALys___6-amino-2-hydroxyhexanoic acid": { "type": "monomerTemplate", "atoms": [ { @@ -77013,8 +76319,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DALys___Deamino-Lysine", - "fullName": "Deamino-Lysine", + "id": "DALys___6-amino-2-hydroxyhexanoic acid", + "fullName": "6-amino-2-hydroxyhexanoic acid", "alias": "DALys", "attachmentPoints": [ { @@ -77630,7 +76936,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-DProol___[(2R)-pyrrolidin-2-yl]methanol": { + "monomerTemplate-DProol___D-prolinol": { "type": "monomerTemplate", "atoms": [ { @@ -77760,8 +77066,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DProol___[(2R)-pyrrolidin-2-yl]methanol", - "fullName": "[(2R)-pyrrolidin-2-yl]methanol", + "id": "DProol___D-prolinol", + "fullName": "D-prolinol", "alias": "DProol", "attachmentPoints": [ { @@ -77776,7 +77082,7 @@ ], "naturalAnalogShort": "P" }, - "monomerTemplate-Leu-ol___(2S)-2-amino-4-methylpentan-1-ol": { + "monomerTemplate-Leu-ol___L-leucinol": { "type": "monomerTemplate", "atoms": [ { @@ -77914,8 +77220,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Leu-ol___(2S)-2-amino-4-methylpentan-1-ol", - "fullName": "(2S)-2-amino-4-methylpentan-1-ol", + "id": "Leu-ol___L-leucinol", + "fullName": "L-leucinol", "alias": "Leu-ol", "attachmentPoints": [ { @@ -77930,7 +77236,7 @@ ], "naturalAnalogShort": "L" }, - "monomerTemplate-Phe-ol___(2S)-2-amino-3-phenylpropan-1-ol": { + "monomerTemplate-Phe-ol___L-phenylalaninol": { "type": "monomerTemplate", "atoms": [ { @@ -78120,8 +77426,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Phe-ol___(2S)-2-amino-3-phenylpropan-1-ol", - "fullName": "(2S)-2-amino-3-phenylpropan-1-ol", + "id": "Phe-ol___L-phenylalaninol", + "fullName": "L-phenylalaninol", "alias": "Phe-ol", "attachmentPoints": [ { @@ -78136,7 +77442,7 @@ ], "naturalAnalogShort": "F" }, - "monomerTemplate-Thr-ol___(2S,3S)-2-aminobutane-1,3-diol": { + "monomerTemplate-Thr-ol___D-threoninol": { "type": "monomerTemplate", "atoms": [ { @@ -78261,8 +77567,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Thr-ol___(2S,3S)-2-aminobutane-1,3-diol", - "fullName": "(2S,3S)-2-aminobutane-1,3-diol", + "id": "Thr-ol___D-threoninol", + "fullName": "D-threoninol", "alias": "Thr-ol", "attachmentPoints": [ { @@ -79027,7 +78333,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-Met_O___(2S)-2-amino-4-methanesulfinylbutanoic acid": { + "monomerTemplate-Met_O___L-methionine sulfoxide": { "type": "monomerTemplate", "atoms": [ { @@ -79195,8 +78501,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Met_O___(2S)-2-amino-4-methanesulfinylbutanoic acid", - "fullName": "(2S)-2-amino-4-methanesulfinylbutanoic acid", + "id": "Met_O___L-methionine sulfoxide", + "fullName": "L-methionine sulfoxide", "alias": "Met_O", "attachmentPoints": [ { @@ -79220,7 +78526,7 @@ ], "naturalAnalogShort": "M" }, - "monomerTemplate-nTyr___(2S)-2-amino-2-(4-hydroxyphenyl)acetic acid": { + "monomerTemplate-nTyr___L-4-Hydroxyphenylglycine": { "type": "monomerTemplate", "atoms": [ { @@ -79425,8 +78731,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "nTyr___(2S)-2-amino-2-(4-hydroxyphenyl)acetic acid", - "fullName": "(2S)-2-amino-2-(4-hydroxyphenyl)acetic acid", + "id": "nTyr___L-4-Hydroxyphenylglycine", + "fullName": "L-4-Hydroxyphenylglycine", "alias": "nTyr", "attachmentPoints": [ { @@ -79450,7 +78756,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-Oic3aR___(2S,3aR,7aS)-octahydro-1H-indole-2-carboxylic acid": { + "monomerTemplate-Oic3aR___(2S,3aR,7aS)-perhydroindolic acid": { "type": "monomerTemplate", "atoms": [ { @@ -79666,8 +78972,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Oic3aR___(2S,3aR,7aS)-octahydro-1H-indole-2-carboxylic acid", - "fullName": "(2S,3aR,7aS)-octahydro-1H-indole-2-carboxylic acid", + "id": "Oic3aR___(2S,3aR,7aS)-perhydroindolic acid", + "fullName": "(2S,3aR,7aS)-perhydroindolic acid", "alias": "Oic3aR", "attachmentPoints": [ { @@ -79691,7 +78997,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Phe_2F___(2S)-2-amino-3-(2-fluorophenyl)propanoic acid": { + "monomerTemplate-Phe_2F___2-fluoro-L-phenylalanine": { "type": "monomerTemplate", "atoms": [ { @@ -79911,8 +79217,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Phe_2F___(2S)-2-amino-3-(2-fluorophenyl)propanoic acid", - "fullName": "(2S)-2-amino-3-(2-fluorophenyl)propanoic acid", + "id": "Phe_2F___2-fluoro-L-phenylalanine", + "fullName": "2-fluoro-L-phenylalanine", "alias": "Phe_2F", "attachmentPoints": [ { @@ -79936,7 +79242,7 @@ ], "naturalAnalogShort": "F" }, - "monomerTemplate-Phe_3F___(2S)-2-amino-3-(3-fluorophenyl)propanoic acid": { + "monomerTemplate-Phe_3F___3-fluoro-L-phenylalanine": { "type": "monomerTemplate", "atoms": [ { @@ -80156,8 +79462,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Phe_3F___(2S)-2-amino-3-(3-fluorophenyl)propanoic acid", - "fullName": "(2S)-2-amino-3-(3-fluorophenyl)propanoic acid", + "id": "Phe_3F___3-fluoro-L-phenylalanine", + "fullName": "3-fluoro-L-phenylalanine", "alias": "Phe_3F", "attachmentPoints": [ { @@ -80181,7 +79487,7 @@ ], "naturalAnalogShort": "F" }, - "monomerTemplate-Phe_4F___(2S)-2-amino-3-(4-fluorophenyl)propanoic acid": { + "monomerTemplate-Phe_4F___4-fluoro-L-phenylalanine": { "type": "monomerTemplate", "atoms": [ { @@ -80401,8 +79707,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Phe_4F___(2S)-2-amino-3-(4-fluorophenyl)propanoic acid", - "fullName": "(2S)-2-amino-3-(4-fluorophenyl)propanoic acid", + "id": "Phe_4F___4-fluoro-L-phenylalanine", + "fullName": "4-fluoro-L-phenylalanine", "alias": "Phe_4F", "attachmentPoints": [ { @@ -80426,7 +79732,7 @@ ], "naturalAnalogShort": "F" }, - "monomerTemplate-Phe4NO___(2S)-2-amino-3-(4-nitrophenyl)propanoic acid": { + "monomerTemplate-Phe4NO___4-nitro-L-phenylalanine": { "type": "monomerTemplate", "atoms": [ { @@ -80678,8 +79984,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Phe4NO___(2S)-2-amino-3-(4-nitrophenyl)propanoic acid", - "fullName": "(2S)-2-amino-3-(4-nitrophenyl)propanoic acid", + "id": "Phe4NO___4-nitro-L-phenylalanine", + "fullName": "4-nitro-L-phenylalanine", "alias": "Phe4NO", "attachmentPoints": [ { @@ -80963,7 +80269,7 @@ ], "naturalAnalogShort": "F" }, - "monomerTemplate-Trp5OH___(2S)-2-amino-3-(5-hydroxy-1H-indol-3-yl)propanoic acid": { + "monomerTemplate-Trp5OH___5-hydroxy-L-tryptophan": { "type": "monomerTemplate", "atoms": [ { @@ -81235,8 +80541,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Trp5OH___(2S)-2-amino-3-(5-hydroxy-1H-indol-3-yl)propanoic acid", - "fullName": "(2S)-2-amino-3-(5-hydroxy-1H-indol-3-yl)propanoic acid", + "id": "Trp5OH___5-hydroxy-L-tryptophan", + "fullName": "5-hydroxy-L-tryptophan", "alias": "Trp5OH", "attachmentPoints": [ { @@ -81572,7 +80878,7 @@ ], "naturalAnalogShort": "W" }, - "monomerTemplate-Tyr35d___(2S)-2-amino-3-(4-hydroxy-3,5-diiodophenyl)propanoic acid": { + "monomerTemplate-Tyr35d___3,5-diiodo-L-tyrosine": { "type": "monomerTemplate", "atoms": [ { @@ -81822,8 +81128,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Tyr35d___(2S)-2-amino-3-(4-hydroxy-3,5-diiodophenyl)propanoic acid", - "fullName": "(2S)-2-amino-3-(4-hydroxy-3,5-diiodophenyl)propanoic acid", + "id": "Tyr35d___3,5-diiodo-L-tyrosine", + "fullName": "3,5-diiodo-L-tyrosine", "alias": "Tyr35d", "attachmentPoints": [ { @@ -81847,7 +81153,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-Tyr3OH___(2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid": { + "monomerTemplate-Tyr3OH___3-hydroxy-L-tyrosine": { "type": "monomerTemplate", "atoms": [ { @@ -82082,8 +81388,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Tyr3OH___(2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid", - "fullName": "(2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid", + "id": "Tyr3OH___3-hydroxy-L-tyrosine", + "fullName": "3-hydroxy-L-tyrosine", "alias": "Tyr3OH", "attachmentPoints": [ { @@ -82107,7 +81413,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-Tyr_Me___(2S)-2-amino-3-(4-methoxyphenyl)propanoic acid": { + "monomerTemplate-Tyr_Me___O-methyl-L-tyrosine": { "type": "monomerTemplate", "atoms": [ { @@ -82342,8 +81648,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Tyr_Me___(2S)-2-amino-3-(4-methoxyphenyl)propanoic acid", - "fullName": "(2S)-2-amino-3-(4-methoxyphenyl)propanoic acid", + "id": "Tyr_Me___O-methyl-L-tyrosine", + "fullName": "O-methyl-L-tyrosine", "alias": "Tyr_Me", "attachmentPoints": [ { @@ -82367,7 +81673,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-TyrPO3___(2S)-2-amino-3-[4-(phosphonooxy)phenyl]propanoic acid": { + "monomerTemplate-TyrPO3___O-phospho-L-tyrosine": { "type": "monomerTemplate", "atoms": [ { @@ -82647,8 +81953,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "TyrPO3___(2S)-2-amino-3-[4-(phosphonooxy)phenyl]propanoic acid", - "fullName": "(2S)-2-amino-3-[4-(phosphonooxy)phenyl]propanoic acid", + "id": "TyrPO3___O-phospho-L-tyrosine", + "fullName": "O-phospho-L-tyrosine", "alias": "TyrPO3", "attachmentPoints": [ { @@ -82672,7 +81978,7 @@ ], "naturalAnalogShort": "Y" }, - "monomerTemplate-xiHyp___(2S)-4-hydroxypyrrolidine-2-carboxylic acid": { + "monomerTemplate-xiHyp___4-hydroxy-L-proline": { "type": "monomerTemplate", "atoms": [ { @@ -82832,8 +82138,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "xiHyp___(2S)-4-hydroxypyrrolidine-2-carboxylic acid", - "fullName": "(2S)-4-hydroxypyrrolidine-2-carboxylic acid", + "id": "xiHyp___4-hydroxy-L-proline", + "fullName": "4-hydroxy-L-proline", "alias": "xiHyp", "attachmentPoints": [ { @@ -83138,30 +82444,269 @@ { "type": 1, "atoms": [ - 1, + 1, + 3 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 5 + ] + }, + { + "type": 2, + "atoms": [ + 5, + 6 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 2, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 10 + ] + }, + { + "type": 2, + "atoms": [ + 9, + 11 + ] + } + ], + "class": "AminoAcid", + "classHELM": "PEPTIDE", + "id": "NMe4Ab___4-(methylamino)benzoic acid", + "fullName": "4-(methylamino)benzoic acid", + "alias": "NMe4Ab", + "attachmentPoints": [ + { + 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"type": 2, + "type": 1, "atoms": [ - 5, + 2, 6 - ] + ], + "stereo": 6 }, { "type": 1, @@ -83170,322 +82715,84 @@ 7 ] }, - { - "type": 2, - "atoms": [ - 7, - 8 - ] - }, { "type": 1, "atoms": [ - 3, + 2, 8 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 9, - 10 - ] - }, - { - "type": 2, - "atoms": [ - 9, - 11 - ] - } - ], - "class": "AminoAcid", - "classHELM": "PEPTIDE", - "id": "NMe4Ab___4-(methylamino)benzoic acid", - "fullName": "4-(methylamino)benzoic acid", - "alias": "NMe4Ab", - "attachmentPoints": [ - { - "attachmentAtom": 1, - "leavingGroup": { - "atoms": [ - 2 - ] - }, - "type": "left" - }, - { - "attachmentAtom": 9, - "leavingGroup": { - "atoms": [ - 10 - ] - }, - "type": "right" - } - ], - "naturalAnalogShort": "X" - }, - "monomerTemplate-aMeTyr___(2S)-2-amino-3-(4-hydroxyphenyl)-2-methylpropanoic acid": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - -1.2419, - 3.3801, - 0 - ] - }, - { - "label": "C", 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"attachmentPoints": [ { - "attachmentAtom": 10, + "attachmentAtom": 1, "leavingGroup": { "atoms": [ - 11 + 0 ] }, "type": "left" }, { - "attachmentAtom": 12, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 13 + 4 ] }, "type": "right" @@ -83746,7 +83053,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Bpa___(2S)-2-amino-3-(4-benzoylphenyl)propanoic acid": { + "monomerTemplate-Bpa___4-benzoylphenylalanine": { "type": "monomerTemplate", "atoms": [ { @@ -84078,8 +83385,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Bpa___(2S)-2-amino-3-(4-benzoylphenyl)propanoic acid", - "fullName": "(2S)-2-amino-3-(4-benzoylphenyl)propanoic acid", + "id": "Bpa___4-benzoylphenylalanine", + "fullName": "4-benzoylphenylalanine", "alias": "Bpa", "attachmentPoints": [ { @@ -84101,9 +83408,9 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "F" }, - "monomerTemplate-Cys_Me___(2R)-2-amino-3-(methylsulfanyl)propanoic acid": { + "monomerTemplate-Cys_Me___S-methylcysteine": { "type": "monomerTemplate", "atoms": [ { @@ -84241,8 +83548,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Cys_Me___(2R)-2-amino-3-(methylsulfanyl)propanoic acid", - "fullName": "(2R)-2-amino-3-(methylsulfanyl)propanoic acid", + "id": "Cys_Me___S-methylcysteine", + "fullName": "S-methylcysteine", "alias": "Cys_Me", "attachmentPoints": [ { @@ -84266,7 +83573,7 @@ ], "naturalAnalogShort": "C" }, - "monomerTemplate-Dip___(2S)-2-amino-3,3-diphenylpropanoic acid": { + "monomerTemplate-Dip___3,3-diphenylalanine": { "type": "monomerTemplate", "atoms": [ { @@ -84568,8 +83875,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Dip___(2S)-2-amino-3,3-diphenylpropanoic acid", - "fullName": "(2S)-2-amino-3,3-diphenylpropanoic acid", + "id": "Dip___3,3-diphenylalanine", + "fullName": "3,3-diphenylalanine", "alias": "Dip", "attachmentPoints": [ { @@ -85158,7 +84465,7 @@ ], "naturalAnalogShort": "H" }, - "monomerTemplate-His3Me___(2S)-2-amino-3-(1-methyl-1H-imidazol-5-yl)propanoic acid": { + "monomerTemplate-His3Me___3-methyl-L-histidine": { "type": "monomerTemplate", "atoms": [ { @@ -85363,8 +84670,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "His3Me___(2S)-2-amino-3-(1-methyl-1H-imidazol-5-yl)propanoic acid", - "fullName": "(2S)-2-amino-3-(1-methyl-1H-imidazol-5-yl)propanoic acid", + "id": "His3Me___3-methyl-L-histidine", + "fullName": "3-methyl-L-histidine", "alias": "His3Me", "attachmentPoints": [ { @@ -85388,215 +84695,7 @@ ], "naturalAnalogShort": "H" }, - "monomerTemplate-Hyl5xi___(2S)-2,6-diamino-5-hydroxyhexanoic acid": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "N", - "location": [ - -2.0635, - -4.4369, - 0 - ] - }, - { - "label": "C", - "location": [ - -2.0613, - -2.9369, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.7609, - -2.1876, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.5373, - -2.9391, - 0 - ] - }, - { - "label": "C", 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"atoms": [ - 6, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 9, - 10 - ] - }, - { - "type": 2, - "atoms": [ - 9, - 11 - ] - } - ], - "class": "AminoAcid", - "classHELM": "PEPTIDE", - "id": "Hyl5xi___(2S)-2,6-diamino-5-hydroxyhexanoic acid", - "fullName": "(2S)-2,6-diamino-5-hydroxyhexanoic acid", - "alias": "Hyl5xi", - "attachmentPoints": [ - { - "attachmentAtom": 7, - "leavingGroup": { - "atoms": [ - 8 - ] - }, - "type": "left" - }, - { - "attachmentAtom": 9, - "leavingGroup": { - "atoms": [ - 10 - ] - }, - "type": "right" - } - ], - "naturalAnalogShort": "K" - }, - "monomerTemplate-Bip___(2S)-2-amino-3-{[1,1'-biphenyl]-4-yl}propanoic acid": { + "monomerTemplate-Bip___Biphenylalanine": { "type": "monomerTemplate", "atoms": [ { @@ -85898,8 +84997,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Bip___(2S)-2-amino-3-{[1,1'-biphenyl]-4-yl}propanoic acid", - "fullName": "(2S)-2-amino-3-{[1,1'-biphenyl]-4-yl}propanoic acid", + "id": "Bip___Biphenylalanine", + "fullName": "Biphenylalanine", "alias": "Bip", "attachmentPoints": [ { @@ -85921,72 +85020,72 @@ "type": "right" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "F" }, - "monomerTemplate-Abu23D___2-aminobut-2-enoic acid": { + "monomerTemplate-Abu23D___(2Z)-2-aminobut-2-enoic acid": { "type": "monomerTemplate", "atoms": [ { - "label": "C", + "label": "H", "location": [ - -1.3017, - 2.2489, + 13.417949192431124, + -9.925, 0 ] }, { - "label": "C", + "label": "N", "location": [ - -0.002, - 1.5001, + 14.283974596215561, + -9.425, 0 ] }, { "label": "C", "location": [ - 0.0003, - -0.0008, + 15.15, + -9.925, 0 ] }, { - "label": "N", + "label": "C", "location": [ - -1.3001, - -0.75, + 16.01602540378444, + -9.425, 0 ] }, { - "label": "H", + "label": "O", "location": [ - -2.599, - 0.0002, + 16.882050807568877, + -9.925, 0 ] }, { - "label": "C", + "label": "O", "location": [ - 1.3007, - -0.75, + 16.01602540378444, + -8.425, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 2.5988, - 0.0015, + 15.15, + -10.925, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 1.3029, - -2.25, + 14.283974596215561, + -11.425, 0 ] } @@ -86007,7 +85106,7 @@ ] }, { - "type": 2, + "type": 1, "atoms": [ 2, 3 @@ -86021,47 +85120,47 @@ ] }, { - "type": 1, + "type": 2, "atoms": [ - 2, + 3, 5 ] }, { - "type": 1, + "type": 2, "atoms": [ - 5, + 2, 6 ] }, { - "type": 2, + "type": 1, "atoms": [ - 5, + 6, 7 ] } ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Abu23D___2-aminobut-2-enoic acid", - "fullName": "2-aminobut-2-enoic acid", + "id": "Abu23D___(2Z)-2-aminobut-2-enoic acid", + "fullName": "(2Z)-2-aminobut-2-enoic acid", "alias": "Abu23D", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 1, "leavingGroup": { "atoms": [ - 4 + 0 ] }, "type": "left" }, { - "attachmentAtom": 5, + "attachmentAtom": 3, "leavingGroup": { "atoms": [ - 6 + 4 ] }, "type": "right" @@ -86069,7 +85168,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-D-Dip___(2R)-2-amino-3,3-diphenylpropanoic acid": { + "monomerTemplate-D-Dip___3,3-diphenyl-D-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -86371,8 +85470,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-Dip___(2R)-2-amino-3,3-diphenylpropanoic acid", - "fullName": "(2R)-2-amino-3,3-diphenylpropanoic acid", + "id": "D-Dip___3,3-diphenyl-D-alanine", + "fullName": "3,3-diphenyl-D-alanine", "alias": "D-Dip", "attachmentPoints": [ { @@ -86396,62 +85495,62 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-Dha___2-aminoprop-2-enoic acid": { + "monomerTemplate-Dha___Dehydroalanine": { "type": "monomerTemplate", "atoms": [ { "label": "C", "location": [ - 2.6, - -1.5, + 12.625, + -9.100000000000001, 0 ] }, { "label": "C", "location": [ - 2.6, - 0, + 13.491025403784437, + -8.600000000000001, 0 ] }, { - "label": "N", + "label": "O", "location": [ - 1.3, - 0.75, + 14.357050807568877, + -9.100000000000001, 0 ] }, { - "label": "H", + "label": "O", "location": [ - 0.0007, - 0.0004, + 13.49102540378444, + -7.6000000000000005, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 3.9, - 0.75, + 11.75897459621556, + -8.600000000000001, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 3.9, - 2.25, + 12.625, + -10.1, 0 ] }, { - "label": "O", + "label": "H", "location": [ - 5.1992, - 0.0004, + 10.892949192431121, + -9.100000000000001, 0 ] } @@ -86474,26 +85573,26 @@ { "type": 1, "atoms": [ - 2, + 1, 3 ] }, { "type": 1, "atoms": [ - 1, + 0, 4 ] }, { - "type": 1, + "type": 2, "atoms": [ - 4, + 0, 5 ] }, { - "type": 2, + "type": 1, "atoms": [ 4, 6 @@ -86502,24 +85601,24 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "Dha___2-aminoprop-2-enoic acid", - "fullName": "2-aminoprop-2-enoic acid", + "id": "Dha___Dehydroalanine", + "fullName": "Dehydroalanine", "alias": "Dha", "attachmentPoints": [ { - "attachmentAtom": 2, + "attachmentAtom": 4, "leavingGroup": { "atoms": [ - 3 + 6 ] }, "type": "left" }, { - "attachmentAtom": 4, + "attachmentAtom": 1, "leavingGroup": { "atoms": [ - 5 + 3 ] }, "type": "right" @@ -86825,7 +85924,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-DMetSO___(2R)-2-amino-4-[(S)-methanesulfinyl]butanoic acid": { + "monomerTemplate-DMetSO___L-methionine (S)-S-oxide": { "type": "monomerTemplate", "atoms": [ { @@ -86995,8 +86094,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "DMetSO___(2R)-2-amino-4-[(S)-methanesulfinyl]butanoic acid", - "fullName": "(2R)-2-amino-4-[(S)-methanesulfinyl]butanoic acid", + "id": "DMetSO___L-methionine (S)-S-oxide", + "fullName": "L-methionine (S)-S-oxide", "alias": "DMetSO", "attachmentPoints": [ { @@ -87347,7 +86446,7 @@ ], "naturalAnalogShort": "H" }, - "monomerTemplate-D-nTyr___(2R)-2-amino-2-(4-hydroxyphenyl)acetic acid": { + "monomerTemplate-D-nTyr___D-4-Hydroxyphenylglycine": { "type": "monomerTemplate", "atoms": [ { @@ -87552,8 +86651,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-nTyr___(2R)-2-amino-2-(4-hydroxyphenyl)acetic acid", - "fullName": "(2R)-2-amino-2-(4-hydroxyphenyl)acetic acid", + "id": "D-nTyr___D-4-Hydroxyphenylglycine", + "fullName": "D-4-Hydroxyphenylglycine", "alias": "D-nTyr", "attachmentPoints": [ { @@ -171651,7 +170750,7 @@ "classHELM": "RNA", "idtAliases": { "base": "5Br-dU", - "modifications": { + "modifications": { "endpoint5": "55Br-dU", "internal": "i5Br-dU" }