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Macro: #3869 - Left-to-right ("Snake-like") layout for RNA #3932

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merged 21 commits into from
Feb 2, 2024
Merged

Macro: #3869 - Left-to-right ("Snake-like") layout for RNA #3932

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20d7fa7
#3869 Left-to-right ("Snake-like") layout for RNA
StarlaStarla Jan 18, 2024
4bff65c
#3869 snake mode for rna chain
StarlaStarla Jan 19, 2024
916d69e
#3869 revert changes
StarlaStarla Jan 19, 2024
a8dbc32
#3869 fix snake line issue
StarlaStarla Jan 21, 2024
c835c2e
Merge branch 'master' of github.com:epam/ketcher into 3869-macro-left…
StarlaStarla Jan 23, 2024
f705c8a
#3869 fix screenshot
StarlaStarla Jan 23, 2024
219fc53
#3869 small fix and tests
StarlaStarla Jan 24, 2024
debbbe9
#3869 add rearrange logic for nucleoside
StarlaStarla Jan 24, 2024
fc7d6c7
#3869 small fix for code and test
StarlaStarla Jan 25, 2024
8b455e1
#3869 refactor side chain logic
StarlaStarla Jan 29, 2024
53f4793
Merge branch 'master' of github.com:epam/ketcher into 3869-macro-left…
StarlaStarla Jan 29, 2024
6a1a825
#3869 update screenshot
StarlaStarla Jan 29, 2024
187aedb
#3869 enhancement
StarlaStarla Jan 30, 2024
639f783
# 3869 fix issue
StarlaStarla Jan 30, 2024
f77a9c1
Merge branch 'master' of github.com:epam/ketcher into 3869-macro-left…
StarlaStarla Jan 31, 2024
f53ce80
#3869 fix snake mode issue for same attachment points and autotests
StarlaStarla Jan 31, 2024
8019421
#3869 remove only of test
StarlaStarla Jan 31, 2024
4cc6baa
- fixed cases with side connections
rrodionov91 Feb 1, 2024
00910a8
#3869 fix single monomer and nucleoside case
StarlaStarla Feb 2, 2024
1946733
#3869 fix some comments issues
StarlaStarla Feb 2, 2024
0e25fd6
#3869 fix autotests
StarlaStarla Feb 2, 2024
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376 changes: 375 additions & 1 deletion ketcher-autotests/tests/Macromolecule-editor/Polymer-Bond-Tool/snake-bond-tool.spec.ts
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import { Page, test, expect } from '@playwright/test';
import {
addMonomerToCanvas,
addRnaPresetOnCanvas,
clickRedo,
clickUndo,
selectSingleBondTool,
Expand Down Expand Up @@ -119,7 +120,7 @@ test.describe('Snake Bond Tool', () => {
await takeEditorScreenshot(page);
});

test('Check snake mode arrange', async ({ page }) => {
test('Check snake mode arrange for peptides chain', async ({ page }) => {
/*
Test case: #3280 - Check snake mode
Description: Snake bond tool
Expand Down Expand Up @@ -269,4 +270,377 @@ test.describe('Snake Bond Tool', () => {
await clickRedo(page);
await expect(snakeModeButton).toHaveClass(/active/);
});

test('Create snake bond between RNA nucleotides', async ({ page }) => {
await page.getByText('RNA').click();
await selectSnakeBondTool(page);

await addRnaPresetOnCanvas(page, 'A_A_R_P', 300, 300);
await addRnaPresetOnCanvas(page, 'C_C_R_P', 400, 600);
await addRnaPresetOnCanvas(page, 'G_G_R_P', 600, 400);

await selectSingleBondTool(page);

const phosphate1 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(0);

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I would propose to add it to addRnaPresetOnCanvas method so that it will return object with 3 locators, one for each part of rna preset

const phosphate2 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(1);

const sugar1 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(1);
const sugar2 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(2);

await bondTwoMonomers(page, phosphate1, sugar1);
await bondTwoMonomers(page, phosphate2, sugar2);

await takeEditorScreenshot(page);
});

test('Check snake mode arrange for RNA chain', async ({ page }) => {
await page.getByText('RNA').click();

await addRnaPresetOnCanvas(page, 'A_A_R_P', 300, 300);
await addRnaPresetOnCanvas(page, 'C_C_R_P', 400, 600);
await addRnaPresetOnCanvas(page, 'G_G_R_P', 600, 400);
await addRnaPresetOnCanvas(page, 'T_T_R_P', 800, 200);
await addRnaPresetOnCanvas(page, 'T_T_R_P', 100, 100);

await selectSingleBondTool(page);

const phosphate1 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(0);
const phosphate2 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(1);
const phosphate3 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(2);
const phosphate4 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(3);
const sugar1 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(1);
const sugar2 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(2);
const sugar3 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(3);
const sugar4 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(4);

await bondTwoMonomers(page, phosphate1, sugar1);
await bondTwoMonomers(page, phosphate2, sugar2);
await bondTwoMonomers(page, phosphate3, sugar3);
await bondTwoMonomers(page, phosphate4, sugar4);

await selectSnakeBondTool(page);
await takeEditorScreenshot(page);
});

test('Create snake bond for mix chains with nucleotides and peptides', async ({
page,
}) => {
const peptide1 = await addMonomerToCanvas(
page,
MONOMER_NAME_TZA,
MONOMER_ALIAS_TZA,
500,
500,
0,
);
const peptide2 = await addMonomerToCanvas(
page,
MONOMER_NAME_TZA,
MONOMER_ALIAS_TZA,
600,
600,
1,
);

const peptide3 = await addMonomerToCanvas(
page,
MONOMER_NAME_TZA,
MONOMER_ALIAS_TZA,
650,
650,
2,
);

const peptide4 = await addMonomerToCanvas(
page,
MONOMER_NAME_TZA,
MONOMER_ALIAS_TZA,
700,
500,
3,
);
const peptide5 = await addMonomerToCanvas(
page,
MONOMER_NAME_TZA,
MONOMER_ALIAS_TZA,
750,
550,
4,
);
const peptide6 = await addMonomerToCanvas(
page,
MONOMER_NAME_TZA,
MONOMER_ALIAS_TZA,
800,
600,
5,
);
const peptide7 = await addMonomerToCanvas(
page,
MONOMER_NAME_TZA,
MONOMER_ALIAS_TZA,
850,
650,
6,
);
await page.getByText('RNA').click();
await selectSnakeBondTool(page);

await addRnaPresetOnCanvas(page, 'A_A_R_P', 200, 200);
await addRnaPresetOnCanvas(page, 'C_C_R_P', 300, 500);
await addRnaPresetOnCanvas(page, 'G_G_R_P', 400, 300);

await selectSingleBondTool(page);

const phosphate1 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(0);
const phosphate2 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(1);
const phosphate3 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(2);

const sugar1 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(1);
const sugar2 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(2);

await bondTwoMonomers(page, phosphate1, sugar1);
await bondTwoMonomers(page, phosphate2, sugar2);
await bondTwoMonomers(page, phosphate3, peptide1);

await page.locator('button[title=R1]').nth(1).click();
await page.locator('button[title=Connect]').click();
await bondTwoMonomers(page, peptide1, peptide2);
await bondTwoMonomers(page, peptide2, peptide3);

await bondTwoMonomers(page, peptide4, peptide5);
await bondTwoMonomers(page, peptide5, peptide6);
await bondTwoMonomers(page, peptide6, peptide7);

await takeEditorScreenshot(page);

await selectSnakeBondTool(page);
await takeEditorScreenshot(page);

await selectSnakeBondTool(page);
await takeEditorScreenshot(page);
});

test('Create snake bond for chain with nucleoside', async ({ page }) => {
await page.getByText('RNA').click();
await selectSnakeBondTool(page);

await addRnaPresetOnCanvas(page, 'A_A_R_P', 200, 200);
await addRnaPresetOnCanvas(page, 'G_G_R_P', 700, 300);

await page.getByTestId('summary-Sugars').click();
const sugarOfNucleoside = await addMonomerToCanvas(
page,
'R___Ribose',
'R',
500,
500,
2,
);
await page.getByTestId('summary-Bases').click();
const baseOfNucleoside = await addMonomerToCanvas(
page,
'A___Adenine',
'A',
600,
600,
1,
);

await selectSingleBondTool(page);
await bondTwoMonomers(page, sugarOfNucleoside, baseOfNucleoside);

const phosphate = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(0);

const sugar = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(1);

await bondTwoMonomers(page, phosphate, sugarOfNucleoside);
await bondTwoMonomers(page, sugarOfNucleoside, sugar);

await takeEditorScreenshot(page);

await selectSnakeBondTool(page);
await takeEditorScreenshot(page);

await selectSnakeBondTool(page);
await takeEditorScreenshot(page);
});

test('Create snake bond for chain with side chains', async ({ page }) => {
await page.getByText('RNA').click();

await addRnaPresetOnCanvas(page, 'A_A_R_P', 200, 200);
await addRnaPresetOnCanvas(page, 'G_G_R_P', 500, 300);
await addRnaPresetOnCanvas(page, 'T_T_R_P', 700, 300);
await addRnaPresetOnCanvas(page, 'U_U_R_P', 900, 300);

await page.getByTestId('summary-Sugars').click();
const sugarOfNucleoside = await addMonomerToCanvas(
page,
'R___Ribose',
'R',
350,
350,
4,
);
await page.getByTestId('summary-Bases').click();
const baseOfNucleoside = await addMonomerToCanvas(
page,
'nC6n8A___6-Aminohexyl-8-aminoadenine',
'nC6n8A',
350,
500,
0,
);

await page.getByTestId('PEPTIDES-TAB').click();

const monomer1 = await addMonomerToCanvas(
page,
'A___Alanine',
'A',
500,
500,
1,
);
const monomer2 = await addMonomerToCanvas(
page,
'Hcy___homocysteine',
'Hcy',
550,
550,
0,
);
const monomer3 = await addMonomerToCanvas(
page,
'A___Alanine',
'A',
600,
600,
2,
);
const monomer4 = await addMonomerToCanvas(
page,
'A___Alanine',
'A',
650,
650,
3,
);
const monomer5 = await addMonomerToCanvas(
page,
'A___Alanine',
'A',
700,
700,
4,
);
const monomer6 = await addMonomerToCanvas(
page,
'Bal___beta-Alanine',
'Bal',
600,
500,
0,
);
const monomer7 = await addMonomerToCanvas(
page,
'Bal___beta-Alanine',
'Bal',
650,
500,
1,
);
const monomer8 = await addMonomerToCanvas(
page,
'Bal___beta-Alanine',
'Bal',
750,
500,
2,
);
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It would be great to have some helper to create monomers like that:

await addMonomersToCanvas([
  { name: 'Bal', fullName: 'Bal___beta-Alanine', amount 5, x: 50, y: 100, deltaX: 100, deltaY: 100 }
])

Where deltaX and deltaY will be an increment of position of each monomer from initial x and y.

Also we probably can create addBondedMonomersToCanvas over it. If it is time consuming we can create a separate ticket for that. Please let me know if so.


await selectSingleBondTool(page);
await bondTwoMonomers(page, sugarOfNucleoside, baseOfNucleoside);
await bondTwoMonomers(page, baseOfNucleoside, monomer1);
await page.locator('button[title=R2]').nth(0).click();
await page.locator('button[title=R1]').nth(1).click();
await page.locator('button[title=Connect]').click();
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I would propose to move it to bondTwoMonomers. Check if modal window appeared after connecting monomers so choose attachment points (by default R2 - R1, but could be configured by function parameters) and click connect


await bondTwoMonomers(page, monomer1, monomer2);
await bondTwoMonomers(page, monomer2, monomer3);
await bondTwoMonomers(page, monomer3, monomer4);
await bondTwoMonomers(page, monomer2, monomer5);
await page.locator('button[title=R1]').nth(1).click();
await page.locator('button[title=Connect]').click();

const phosphate = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(0);

const sugar = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(1);
const sugar1 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='R']]`)
.nth(2);
const phosphate1 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(1);
const phosphate2 = await page
.locator(`//\*[name() = 'g' and ./\*[name()='text' and .='P']]`)
.nth(2);
await bondTwoMonomers(page, phosphate, sugarOfNucleoside);
await bondTwoMonomers(page, sugarOfNucleoside, sugar);
await bondTwoMonomers(page, phosphate1, sugar1);
await bondTwoMonomers(page, phosphate2, monomer6);
await page.locator('button[title=R1]').nth(1).click();
await page.locator('button[title=Connect]').click();
await bondTwoMonomers(page, monomer6, monomer7);
await bondTwoMonomers(page, monomer7, monomer8);

await takeEditorScreenshot(page);

await selectSnakeBondTool(page);
await takeEditorScreenshot(page);
});
});
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