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Merge branch 'release/2.12' of https://github.com/epam/ketcher into fix/
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#2837-programmatically-scroll-buttons-do-not-appear
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Iogsotot committed Jul 3, 2023
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207 changes: 104 additions & 103 deletions documentation/help.md
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ reactions. The application operates in two modes - Standalone and Remote:
- Remote version requires Indigo Service as a backend server to perform complex calculations (When the server is not responding you can continue to work in the application although some of the functions will be unavailable).

**Ketcher** consists of the following elements:
<img src = images/1_overviewn.png width = "100%"/>
<img src = images/1_overview.png width = "100%"/>

**Note** : Depending on the screen size, some tools on the _Tool
palette_ can be displayed in expanded or collapsed forms.
Expand Down Expand Up @@ -63,6 +63,7 @@ selects several structures.
You can use the buttons of the _Main_ toolbar:

![](images/4_main_toolbarn.png 'Main Toolbar')
<img src = images/4_main_toolbar.png width = "100%"/>

- **Clear Canvas** (1) button to start drawing a new molecule; this
command clears the drawing area;
Expand Down Expand Up @@ -101,31 +102,29 @@ You can use the buttons of the _Main_ toolbar:

<img src = images/6_calc_values.png width = "280" />

- **Stereochemistry** button (16) to assign and display enhanced stereochemistry properties of the structure
- **3D Viewer** button (16) to open the structure in the three-dimensional

- **3D Viewer** button (17) to open the structure in the
three-dimensional Viewer;

- **Settings** button (18) to make some settings for molecular
- **Settings** button (17) to make some settings for molecular
files:

<img src = images/7_settingsn.png width = "360" />

- **Help** button (19) to view Help;
- **Help** button (18) to view Help;

- **About** button (20) to display version and copyright information
- **About** button (19) to display version and copyright information
of the program.

- **Fullscreen mode** button (21) allows to initiate displaying Ketcher window in the fullscreen mode.
- **Fullscreen mode** button (20) allows to initiate displaying Ketcher window in the fullscreen mode.

- **Zoom panel** (22) displays the current zoom percentage. Click to expand the Zoom panel and use the following actions: **Zoom percentage** (23) to set the view manually, **Zoom in** (24) / **Zoom out** (25) to scale the view gradually, **Zoom 100%** (26) to enable the default zoom setting.
- **Zoom panel** (21) displays the current zoom percentage. Click to expand the Zoom panel and use the following actions: **Zoom percentage** (22) to set the view manually, **Zoom in** (23) / **Zoom out** (24) to scale the view gradually, **Zoom 100%** (25) to enable the default zoom setting.

<img src = images/4.png width = "180" />
<img src = images/8_zoom.png width = "180" />

# 3D Viewer

The structure appears in a modal window after clicking on the **3D
Viewer** button <img src = images/8_1_miew_icon.png width = "42" /> on the top panel:
Viewer** button <img src = images/9_3D_viewer.png width = "42" /> on the top panel:

<img src = images/8_miew1.png width = "800" />

Expand Down Expand Up @@ -377,12 +376,14 @@ type of selected elements:

# Changing Structure Display

Use the _Rotate_ tool <img src = images/32_rotate_icon.png width = "42" /> to change the structure
Use the _Rotate_ tool <img src = images/32_rotate_tool_icon.png width = "42" /> to change the structure
display:

<img src = images/33_rotate_menu.png width = "130" />
<img src = images/32_rotate_tool.png width = "130" />
<img src = images/32_rotate_tool_2.png width = "230" />

_Rotate Tool_ (1)
_Erase (Del)_ (4)

This tool allows rotating objects.

Expand Down Expand Up @@ -447,7 +448,7 @@ You can add templates (rings or other predefined structures) to the
structure using the _Templates_ toolbar together with the _Custom
Templates_ button located at the bottom:

<img src = images/43_templates_toolbarn.png align = left width = "360" /> <br/>
<img src = images/43_templates_toolbar.png align = left width = "360" /> <br/>
<br/>

To add a ring to the molecule, select a ring from the toolbar and
Expand Down Expand Up @@ -491,7 +492,7 @@ atom or bond preset in the program.
**Note** : User is able to define the attachment atom and bond by clicking
the Edit button for template structure in the Template Library.

The _Custom Templates_ button <img src = images/43.png width = "42" /> allows to view the list of templates available; both built-in and created
The _Custom Templates_ button <img src = images/43_custom_templates_icon.png width = "42" /> allows to view the list of templates available; both built-in and created
by user:

<img src = images/43-1.png width = "520" />
Expand All @@ -516,7 +517,7 @@ Ketcher allows you to select and use Functional Groups to properly represent you
Set of functional groups available is predefined and can't be changed right now.

Explore the list of the Functional Groups available in the Templates library. Open it using the icon in the bottom toolbar: <br>
<img src = images/43.png width = "42" /> <br>
<img src = images/43_custom_templates_icon.png width = "42" /> <br>
Navigate to the Functional Groups tab to explore the FGs available:

![](images/FG_tab.png)
Expand Down Expand Up @@ -636,114 +637,114 @@ it will appear in brackets after the description of the button.
_NOTE: `Mod` key is `Command` on OSX and `Ctrl` on PC systems_

**General**
| Shortcut| Action |
| --- | --- |
| `Mod+Delete` | Clear Canvas |
| `Mod+o` | Open… |
| `Mod+s` | Save As… |
| `Mod+z` | Undo |
| `Mod+Shift+z, Mod+y` | Redo |
| `Mod+x` | Cut |
| `Mod+c` | Copy |
| `Mod+Shift+f` | Copy Image |
| `Mod+m` | Copy as MOL |
| `Mod+Shift+k` | Copy as KET |
| `Mod+v` | Paste |
| `Mod+a` | Select All |
| `Mod+Shift+a` | Deselect All |
| `Mod+d` | Select descriptors |
| Shortcut | Action |
| -------------------- | ------------------ |
| `Mod+Delete` | Clear Canvas |
| `Mod+o` | Open… |
| `Mod+s` | Save As… |
| `Mod+z` | Undo |
| `Mod+Shift+z, Mod+y` | Redo |
| `Mod+x` | Cut |
| `Mod+c` | Copy |
| `Mod+Shift+f` | Copy Image |
| `Mod+m` | Copy as MOL |
| `Mod+Shift+k` | Copy as KET |
| `Mod+v` | Paste |
| `Mod+a` | Select All |
| `Mod+Shift+a` | Deselect All |
| `Mod+d` | Select descriptors |

**Server**
| Shortcut| Action |
| --- | --- |
| `Alt+a` | Aromatize |
| `Ctrl+Alt+a` | Dearomatize |
| `Mod+l` | Layout |
| `Mod+Shift+l` | Clean Up |
| `Mod+p` | Calculate CIP |
| `Alt+s` | Check structure |
| `Alt+c` | Calculate values |
| Shortcut | Action |
| ------------- | ---------------- |
| `Alt+a` | Aromatize |
| `Ctrl+Alt+a` | Dearomatize |
| `Mod+l` | Layout |
| `Mod+Shift+l` | Clean Up |
| `Mod+p` | Calculate CIP |
| `Alt+s` | Check structure |
| `Alt+c` | Calculate values |

**Debug**
| Shortcut| Action |
| --- | --- |
| Shortcut | Action |
| ------------- | ------------ |
| `Mod+Shift+r` | force-update |
| `Alt+Shift+r` | qs-serialize |

**Tools**
| Shortcut| Action |
| --- | --- |
| `Mod+h` | Hand tool |
| `Escape` | Rotate between: Lasso Selection, Rectangle Selection, Fragment Selection |
| `Delete, Backspace` | Erase |
| `Alt+e` | Stereochemistry |
| `+` | Charge Plus |
| `-` | Charge Minus |
| `Alt+r` | Rotate Tool |
| `Alt+h` | Horizontal Flip |
| `Alt+v` | Vertical Flip |
| `Mod+g` | Rotate between: S-Group, Data S-Group |
| `Mod+r` | Rotate between: R-Group Label Tool, Attachment Point Tool |
| `Mod+Shift+r, Mod+r` | R-Group Fragment Tool |
| `1` | Rotate between: Single Bond, Single Up Bond, Single Down Bond, Single Up/Down Bond |
| `2` | Rotate between: Double Bond, Double Cis/Trans Bond |
| `3` | Triple Bond |
| `4` | Aromatic Bond |
| `0` | Any Bond |
| `Alt+t` | Add text |
| Shortcut | Action |
| -------------------- | ---------------------------------------------------------------------------------- |
| `Mod+h` | Hand tool |
| `Escape` | Rotate between: Lasso Selection, Rectangle Selection, Fragment Selection |
| `Delete, Backspace` | Erase |
| `Alt+e` | Stereochemistry |
| `+` | Charge Plus |
| `-` | Charge Minus |
| `Alt+r` | Rotate Tool |
| `Alt+h` | Horizontal Flip |
| `Alt+v` | Vertical Flip |
| `Mod+g` | Rotate between: S-Group, Data S-Group |
| `Mod+r` | Rotate between: R-Group Label Tool, Attachment Point Tool |
| `Mod+Shift+r, Mod+r` | R-Group Fragment Tool |
| `1` | Rotate between: Single Bond, Single Up Bond, Single Down Bond, Single Up/Down Bond |
| `2` | Rotate between: Double Bond, Double Cis/Trans Bond |
| `3` | Triple Bond |
| `4` | Aromatic Bond |
| `0` | Any Bond |
| `Alt+t` | Add text |

**Atoms**
| Shortcut| Action |
| --- | --- |
| `h` | Atom H |
| `c` | Atom C |
| `n` | Atom N |
| `o` | Atom O |
| `s` | Atom S |
| `p` | Atom P |
| `f` | Atom F |
| `b` | Atom Br |
| `i` | Atom I |
| `k` | Atom K |
| `Shift+c` | Atom Cl |
| `Shift+s` | Atom Si |
| `Shift+n` | Atom Na |
| `Shift+b` | Atom B |
| `r` | Pseudoatom |
| `d` | Deuterium |
| `a` | Any atom |
| `q` | Any heteroatom |
| `m` | Any metal |
| `x` | Any halogen |
| `/` | Display the Atom Properties dialog box |
| Shortcut | Action |
| --------- | -------------------------------------- |
| `h` | Atom H |
| `c` | Atom C |
| `n` | Atom N |
| `o` | Atom O |
| `s` | Atom S |
| `p` | Atom P |
| `f` | Atom F |
| `b` | Atom Br |
| `i` | Atom I |
| `k` | Atom K |
| `Shift+c` | Atom Cl |
| `Shift+s` | Atom Si |
| `Shift+n` | Atom Na |
| `Shift+b` | Atom B |
| `r` | Pseudoatom |
| `d` | Deuterium |
| `a` | Any atom |
| `q` | Any heteroatom |
| `m` | Any metal |
| `x` | Any halogen |
| `/` | Display the Atom Properties dialog box |

**Bonds**
| Shortcut| Action |
| --- | --- |
| `/` | Open bond properties |
| Shortcut | Action |
| -------- | -------------------- |
| `/` | Open bond properties |

**Zoom**
| Shortcut| Action |
| --- | --- |
| `Mod+_, Mod+-` | Zoom Out |
| `Mod+=, Mod++` | Zoom In |
| `Mod+Shift+0` | Zoom 100% |
| Shortcut | Action |
| -------------- | --------- |
| `Mod+_, Mod+-` | Zoom Out |
| `Mod+=, Mod++` | Zoom In |
| `Mod+Shift+0` | Zoom 100% |

**Templates**
| Shortcut| Action |
| --- | --- |
| `Shift+t` | Custom Templates |
| `t` | Rotate between: Benzene, Cyclopentadiene, Cyclohexane, Cyclopentane, Cyclopropane, Cyclobutane, Cycloheptane, Cyclooctane |
| Shortcut | Action |
| --------- | ------------------------------------------------------------------------------------------------------------------------- |
| `Shift+t` | Structure Library |
| `t` | Rotate between: Benzene, Cyclopentadiene, Cyclohexane, Cyclopentane, Cyclopropane, Cyclobutane, Cycloheptane, Cyclooctane |

**FunctionalGroups**
| Shortcut| Action |
| --- | --- |
| Shortcut | Action |
| --------- | ----------------- |
| `Shift+f` | Functional Groups |

**Help**
| Shortcut| Action |
| --- | --- |
| `?, &, Shift+/` | Help |
| Shortcut | Action |
| --------------- | ------ |
| `?, &, Shift+/` | Help |

**Note** : Please, use`Ctrl+V`to paste the selected object in
Google Chrome and Mozilla Firefox browsers.
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,13 @@ import {
moveMouseToTheMiddleOfTheScreen,
selectAtomInToolbar,
takeEditorScreenshot,
pressButton,
AtomButton,
selectFunctionalGroups,
selectSaltsAndSolvents,
FunctionalGroups,
resetCurrentTool,
SaltsAndSolvents,
selectTemplate,
} from '@utils';

test.describe('Click Functional Group on canvas', () => {
Expand All @@ -33,7 +33,7 @@ test.describe('Click Functional Group on canvas', () => {
*/
await selectAtomInToolbar(AtomButton.Nitrogen, page);
await clickInTheMiddleOfTheScreen(page);
await pressButton(page, 'Custom Templates');
await selectTemplate(page);
await page.getByRole('tab', { name: 'Functional Groups' }).click();
await selectFunctionalGroups(FunctionalGroups.Boc, page);
await clickInTheMiddleOfTheScreen(page);
Expand All @@ -44,11 +44,11 @@ test.describe('Click Functional Group on canvas', () => {
Test case: EPMLSOPKET-10106
Description: when clicking with an FG template on an FG it should replace it
*/
await pressButton(page, 'Custom Templates');
await selectTemplate(page);
await page.getByRole('tab', { name: 'Functional Groups' }).click();
await selectFunctionalGroups(FunctionalGroups.Boc, page);
await clickInTheMiddleOfTheScreen(page);
await pressButton(page, 'Custom Templates');
await selectTemplate(page);
await selectFunctionalGroups(FunctionalGroups.Cbz, page);
await clickInTheMiddleOfTheScreen(page);
});
Expand All @@ -58,12 +58,12 @@ test.describe('Click Functional Group on canvas', () => {
Test case: EPMLSOPKET-10107
Description: when clicking with an FG template on a Salts and Solvents it should replace it
*/
await pressButton(page, 'Custom Templates');
await selectTemplate(page);
await page.getByRole('tab', { name: 'Salts and Solvents' }).click();
await selectSaltsAndSolvents(SaltsAndSolvents.MethaneSulphonicAcid, page);
await clickInTheMiddleOfTheScreen(page);

await pressButton(page, 'Custom Templates');
await selectTemplate(page);
await page.getByRole('tab', { name: 'Functional Groups' }).click();
await selectFunctionalGroups(FunctionalGroups.CCl3, page);
await clickInTheMiddleOfTheScreen(page);
Expand All @@ -84,7 +84,7 @@ test.describe('Click Functional Group on canvas', () => {
await dragMouseTo(coordinatesWithShift, y, page);
await resetCurrentTool(page);

await pressButton(page, 'Custom Templates');
await selectTemplate(page);
await page.getByRole('tab', { name: 'Functional Groups' }).click();
await selectFunctionalGroups(FunctionalGroups.CO2tBu, page);
await clickInTheMiddleOfTheScreen(page);
Expand All @@ -98,15 +98,15 @@ test.describe('Click Functional Group on canvas', () => {
await selectAtomInToolbar(AtomButton.Oxygen, page);
await clickInTheMiddleOfTheScreen(page);

await pressButton(page, 'Custom Templates');
await selectTemplate(page);
await page.getByRole('tab', { name: 'Functional Groups' }).click();
await selectFunctionalGroups(FunctionalGroups.Cbz, page);
await moveMouseToTheMiddleOfTheScreen(page);
const { x, y } = await getCoordinatesOfTheMiddleOfTheScreen(page);
const coordinatesWithShift = x + MAX_BOND_LENGTH;
await dragMouseTo(coordinatesWithShift, y, page);

await pressButton(page, 'Custom Templates');
await selectTemplate(page);
await page.getByRole('tab', { name: 'Functional Groups' }).click();
await selectFunctionalGroups(FunctionalGroups.Ms, page);
await page.mouse.click(coordinatesWithShift, y);
Expand Down
2 changes: 1 addition & 1 deletion ketcher-autotests/tests/utils/selectors/buttons.ts
Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ export enum RingButton {
Cyclooctane = 'Cyclooctane',
}

export const CustomTemplatesButton = 'Custom Templates';
export const CustomTemplatesButton = 'Structure Library';

export type ToolbarButton =
| AtomButton
Expand Down
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