+**Ketcher molecules mode** consists of the following elements:
-**Note** : Depending on the screen size, some tools on the _Tool
-palette_ can be displayed in expanded or collapsed forms.
+
-Using the _Tool palette_, you can
+**Note**: Depending on the screen size, some tools on the _Tool palette_ can be displayed in expanded or collapsed forms.
-- draw and edit a molecule or reaction by clicking on and dragging
- atoms, bonds, and other elements provided with the buttons on the
- _Atoms_ toolbar and _Tool palette_;
+Using the _Tool palette_, you can:
+- Draw and edit a molecule or a reaction by clicking on and dragging atoms, bonds, and other elements provided with the buttons on the _Atoms toolbar_ and _Tool palette_;
+- Delete any element of the drawing (atom or bond) by clicking on it with the _Erase tool_;
+- Delete the entire molecule or its fragment using the _Lasso_, _Rectangle_, or _Fragment selection tool_ and the _Erase tool_;
+- Draw special structures (see the following sections);
+- Select the entire molecule or its fragment in one of the following ways (
click on the bottom right corner to see the list of available options ![image]
):
+ - To select **one atom or bond**, click _Lasso_ (1) or _Rectangle Selection tool_ (2), and then click the atom or bond;
+ - To select the **entire structure**:
+ - Select the _Fragment Selection tool_ (3) and then click the object;
+ - Select the _Lasso_ or _Rectangle Selection tool_, and then drag the mouse to select the object;
+ -`Ctrl-click`with the _Lasso_ or _Rectangle Selection tool_.
+ - To select **multiple atoms, bonds, structures, or other objects**, do one of the following:
+ - `Shift-click` with the _Lasso_ or _Rectangle Selection tool_ selects some (connected or not) atoms/bonds;
+ - With the _Lasso_ or _Rectangle Selection tool_ click and drag the mouse around the atoms, bonds, or structures that you want to select.
-- delete any element of the drawing (atom or bond) by clicking on it
- with the Erase tool;
+ **Note**: `Ctrl+Shift-click` each structure with the _Lasso_ or _Rectangle Selection tool_ selects several structures.
-- delete the entire molecule or its fragment using the lasso,
- rectangle, or fragment selection and the Erase tool;
+You can use the buttons of the _Main_ toolbar:
-- draw special structures (see the following sections);
+
-- select the entire molecule or its fragment in one of the following
- ways (click on the button align=center to see the list of available options):
+- **Clear Canvas** (1) button to start clear the drawing area;
+- **Open…** (2) and **Save As…** (3) buttons to import a molecule from a molecular file or save it to a supported molecular file format;
+- **Copy** with additional abilties to **Copy As** (4), **Paste** (5), **Cut** (6) buttons to perform the corresponding actions;
+- **Undo** (7) / **Redo** (8) to manage the last actions taken on the canvas;
+- **Aromatize** (9) (`Alt+a`) / **Dearomatize** (10) (`Ctrl+Alt+a`) buttons to mark aromatic structures (to convert a structure to the aromatic or Kekule representation);
+- **Layout** button (11) to change the position of the structure to work with it with the most convenience;
+- **Clean Up** button (12) to improve the appearance of the structure by assigning them uniform bond lengths and angles;
+- **Calculate CIP** button (13) to determine R/S, r/s, and E/Z stereoconfigurations;
+- **Check Structure** button (14) (`Alt+s`) to check the bellow shown properties of the structure. Check will be conducted immediately when the operation is selected. You can check only the Settings you are interested in and check structure again with new settings by clicking on Check button. Apply button will save the Settings checked and they will be applied for the file saving;
-
+
-To select **one atom or bond**, click Lasso (1) or Rectangle Selection tool (2),
-and then click the atom or bond.
+- **Calculated Values** button (15) to display some properties of the structure;
-To select the **entire structure**:
+
-- Select the Fragment Selection tool (3) and then click the object.
+- **Add/Remove explicit hydrogens** button (16) to choose the representation of of explicit hydrogens (drawn with explicit bonds or associated with the atom label of the atom they are connected to);
+- **3D Viewer** button (17) to view the structure's in three-dimensional representation;
+- **Molecules/Macromolecules switcher** (18) to change between Ketcher's modes. Current mode always has a tick mark next to it. Clicking on the mode without a tick mark leads to it;
-- Select the Lasso or Rectangle Selection tool, and then drag the
- mouse to select the object.
+
--`Ctrl-click`with the Lasso or Rectangle Selection tool.
+- **Settings** button (19) to make some settings for molecular files;
-To select **multiple atoms, bonds, structures, or other objects**, do one
-of the following:
+
--`Shift-click`with the Lasso or Rectangle Selection tool selects
-some (connected or not) atoms/bonds.
+- **Help** button (20) to view Help;
+- **About** button (21) to display version and copyright information of the program;
+- **Fullscreen mode** button (22) allows to initiate displaying Ketcher window in the fullscreen mode;
+- **Zoom panel** (21) displays the current zoom percentage. Click to expand the Zoom panel and use the following actions: **Zoom percentage** (1) to set the view manually, **Zoom out** (2) / **Zoom in** (3) to scale the view gradually, **Zoom 100%** (4) to enable the default zoom setting.
-- With the Lasso or Rectangle Selection tool click and drag the
- mouse around the atoms, bonds, or structures that you want to
- select.
+
-**Note** :`Ctrl+Shift-click each structure`with the Lasso or Rectangle Selection tool
-selects several structures.
+## 3D Viewer
+The structure appears in a modal window after clicking on the **3D Viewer** button 
) on the top panel:
-You can use the buttons of the _Main_ toolbar:
+
-
-
+You can perform the following actions:
+- Rotate the structure holding the left mouse button;
+- Zoom In/Out the structure;
-- **Clear Canvas** (1) button to start drawing a new molecule; this
- command clears the drawing area;
+Ketcher Settings allow changing the appearance of the structure and background coloring on the 3D Viewer tab.
-- **Open…** (2) and **Save As…** (3) buttons to import a molecule
- from a molecular file or save it to a supported molecular file
- format;
+"Lines" drawing method, "Bright" atom name coloring method and "Light" background coloring are default.
-- **Copy** with additional abilties to **Copy As** (4), **Paste** (5), **Cut** (6) buttons to perform
- the corresponding actions;
+## Drawing Atoms
-- **Undo** (7) / **Redo** (8) to manage the last actions taken on the canvas;
+To draw/edit atoms you can:
+- Select an atom in the Atoms toolbar and click inside the drawing area;
+- If the desired atom is absent from the toolbar, click on the 
button to invoke the _Periodic Table_ and click on the desired atom (available options: _Single_ – selection of a single atom, _List_ – choose an atom from the list of selected options (To allow one atom from a list of atoms of your choice at that position), _Not List_ - exclude any atom on your list at that position);
-- **Aromatize** (Alt+a) / **Dearomatize** (Ctrl+Alt+a) buttons to mark aromatic
- structures (to convert a structure to the Aromatic or Kekule
- presentation);
+
-- **Layout** button (11) to change the position of the structure to
- work with it with the most convenience;
+- Add an atom to the existing molecule by selecting an atom in the _Atoms_ toolbar, clicking on an atom in the molecule, and dragging the cursor; the atom will be added with a single bond; vacant valences will be filled with the corresponding number of hydrogen atoms;
+- Change an atom by selecting an atom in the _Atoms_ toolbar and clicking on the atom to be changed; in the case a wrong valence appears the atom will be underlined in red;
+- Change an atom by clicking on an existing atom with the _Selection tool_ and starting to enter text after that;
-- **Clean Up** button (12) to improve the appearance of the
- structure by assigning them uniform bond lengths and angles.
+
-- **Calculate CIP** button (13) to determine R/S and E/Z
- configurations;
+- Change the charge of an atom by selecting the _Charge Plus_ or _Charge Minus tool_ and clicking consecutively on an atom to increase/decrease its charge;
-- **Check Structure** button (Alt+s) to check the following properties of the structure.
- Check will be conducted immediately when the operation is selected.
- You can check only the Settings you are interested in and check structure again with new settings by clicking on Check button.
- Apply button will save the Settings checked and they will be applied for the file saving.
+
- 
+- Change an atom or its properties by double-clicking on the atom to invoke the _Atom Properties dialog_ (the dialog also provides atom query features);
-- **Calculated Values** button (15) to display some properties of
- the structure:
+
-
+- Click on the 
button to use the _Extended table_ and select a corresponding _Generic group_ or _Special Node_;
-- **3D Viewer** button (16) to open the structure in the three-dimensional
+
+## Drawing Bonds
-- **Settings** button (17) to make some settings for molecular
- files:
+To draw/edit bonds you can:
- 
+- Click an arrow on the _Bond tool_ 
in the _Tool palette_ to open the drop-down list with the following bond types;
-- **Help** button (18) to view Help;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-- **About** button (19) to display version and copyright information
- of the program.
+- Select a bond type from the drop down list and click inside the drawing area; a bond of the selected type will be drawn;
+- Click on an atom in the molecule; a bond of the selected type will be added to the atom at the angle of 120 degrees;
+- Add a bond to the existing molecule by clicking on an atom in the molecule and dragging the cursor; in this case you can set the angle manually;
+- Change the bond type by clicking on it;
+- Use the _Chain Tool_ 
to draw consecutive single bonds;
+- Change a bond or its properties by double-clicking on the bond to invoke the _Bond Properties_ dialog:
-- **Fullscreen mode** button (20) allows to initiate displaying Ketcher window in the fullscreen mode.
+
-- **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.
+- Clicking on the drawn stereo and dative bonds change their direction;
+- Clicking with the _Single Bond tool_ or _Chain tool_ switches the bond type cyclically: Single-Double-Triple-Single.
- 
+## Drawing R-Groups
-# 3D Viewer
+Use the _R-Group_ toolbox 
to draw R-groups in Markush structures:
-The structure appears in a modal window after clicking on the **3D
-Viewer** button on the top panel:
+
-
+Selecting the _R-Group_ _Label_ Tool (1) and clicking on an atom in the structure invokes the dialog to select the R-Group label for a current atom position in the structure:
-You can perform the following actions:
+
-- Rotate the structure holding the left mouse button;
+Selecting the R-Group label and clicking **Apply** converts the structure into a Markush structure with the selected R-Group label:
-- Zoom In/Out the structure;
+
-Ketcher Settings allow to change the appearance of the structure and background coloring on the 3D Viewer tab.
+**Note**: You can choose several R-Group labels simultaneously:
-"Lines" drawing method, "Bright" atom name coloring
-method and "Light" background coloring are default.
+
-# Drawing Atoms
+Particular chemical fragments that may be substituted for a given R-Group form a set of R-Group members. R-Group members can be any structural fragment, including functional groups and single atoms or atom lists.
-To draw/edit atoms you can:
+To create a set of R-Group members:
+1. Draw a structure to become an R-Group member;
+2. Select the structure using the _R-Group Fragment Tool_ (2) to invoke the _R-Group dialog_; in this dialog select the label of the R-Group to assign the fragment to;
+3. Click on **Apply** to convert the structure into an R-Group member.
-- select an atom in the Atoms toolbar and click inside the drawing
- area;
+Schematically, the entire process of the R-Group member creation can be presented as:
-- if the desired atom is absent in the toolbar, click on
- the  button to invoke the Periodic Table and
- click on the desired atom (available options: _Single_ – selection
- of a single atom, _List_ – choose an atom from the list of selected
- options (To allow one atom from a list of atoms of your choice at
- that position), _Not List_ - exclude any atom on your list at that
- position).
+
-
+### R-Group attachment point
-- add an atom to the existing molecule by selecting an atom in the
- _Atoms_ toolbar, clicking on an atom in the molecule, and dragging
- the cursor; the atom will be added with a single bond; vacant
- valences will be filled with the corresponding number of hydrogen
- atoms;
+An R-Group attachment point is the atom in an R-Group member fragment that attaches the fragment to the initial Markush structure.
-- change an atom by selecting an atom in the _Atoms_ toolbar and
- clicking on the atom to be changed; in the case a wrong valence
- appears the atom will be underlined in red;
+Selecting the _Attachment Point Tool_ (3) and clicking on an atom in the R-Group fragment converts this atom into an attachment point. If the R-Group contains more than one attachment point, you can specify one of them as primary and the other as secondary. You can select between either the primary or secondary attachment point using the dialog that appears after clicking on the atom:
-- change an atom by clicking on an existing atom with the
- _Selection_ tool and starting to enter text after that; type another atom symbol in the text box:
+
- 
+Result view of R-Group attachment points (IUPAC style):
-- change the charge of an atom by selecting the Charge Plus or
- Charge Minus tool and clicking consecutively on an atom to
- increase/decrease its charge:
+
-
+If there are two attachment points on an R-Group member, there must be two corresponding attachments (bonds) to the R-Group atom that has the same R-Group label. Clicking on **Apply** in the above dialog creates the attachment points. Result view of R-Group attachment points both primary and secondary (IUPAC style):
-- change an atom or its properties by double-clicking on the atom to
- invoke the Atom Properties dialog (the dialog also provides atom
- query features):
+
-
+### R-Group Logic
-- click on the button to use the Extended table and
- select a corresponding Generic group or Special Node:
+**Ketcher** enables one to add logic when using R-Groups. To access the R-Group logic:
+1. Create an R-Group member fragment as described above;
+2. Move the cursor over the entire fragment for the green frame to appear, then click inside the fragment. The following dialog appears:
-
+
-# Drawing Bonds
+3. Specify **Occurrence** to define how many instances of an R-Group occur. If an R-Group atom appears several times in the initial structure, you will specify **Occurrence** > n, n being the number of occurrences; if it appears once, you see "R1 > 0".
+4. Specify H at **unoccupied** R-Group sites (**RestH**): check or clear the checkbox.
+5. Specify the logical **Condition**. Use the R-Group condition **If R(i) Then** to specify whether the presence of an R-Group is dependent on the presence of another R-Group.
-To draw/edit bonds you can:
+## Marking S-Groups
-- Click an arrow on the Bond tool in the Tool palette
- to open the drop-down list with the following bond types:
+To mark S-Groups, use the _S-Group tool_ 
and the following dialog that appears after selecting a fragment with this tool:
- 
-- select a bond type from the drop down list and click inside the
- drawing area; a bond of the selected type will be drawn;
+Available S-Group types:
+- _Data_ - an atom, a fragment, a multifragment, a single bond, or a group without the square brackets representation;
+- _Multiple group_ - indicates a number of replications of a fragment or a part of a structure in contracted form;
+- _SRU Polymer_ - the Structural Repeating Unit (SRU) brackets enclose the structural repeating of a polymer. You have three available patterns: head-to-tail (the default), head-to-head, and either/unknown;
+- _Superatom_ - part of the structure or the whole structure that will be abbreviated to a text label or expanded to see the group chemistry surrounded with square brackets;
+- _Queary component_ - a pair of square brackets enclosing the selected part(s) of the structure or whole structure(s), can be used to support SMARTS query properties.
-- click on an atom in the molecule; a bond of the selected type will
- be added to the atom at the angle of 120 degrees;
+### Superatom S-Group
-- add a bond to the existing molecule by clicking on an atom in the
- molecule and dragging the cursor; in this case you can set the angle
- manually;
+An abbreviated structure (abbreviation) is all or part of a structure (molecule or reaction component) that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but their underlying structure is hidden.
-- change the bond type by clicking on it;
+
-- use the Chain Tool to draw consecutive single
- bonds;
+After applying Superatom S-Group - there is ability to contract the S-Group, and ability to remove the abbreviation, from the right-click menu on the S-Group:
-- change a bond or its properties by double-clicking on the bond to
- invoke the Bond Properties dialog:
+
-
+### Data S-Groups
-- clicking on the drawn stereo and dative bonds change their direction.
+You can attach data to an atom, a fragment, a multifragment, a single bond, or a group. The defined set of _Names_ and _Values_ is introduced for each type of selected elements:
-- clicking with the Single Bond tool or Chain tool switches the bond type
- cyclically: Single-Double-Triple-Single.
+
-# Drawing R-Groups
+- Select the appropriate S-Group Field Name;
+- Select the appropriate Field Value;
+- Labels can be specified as Absolute, Relative or Attached.
-Use the _R-Group_ toolbox to draw R-groups in Markush
-structures:
+## Changing Structure Display
-
+
-Selecting the _R-Group_ _Label_ Tool (1) and clicking on an atom in the
-structure invokes the dialog to select the R-Group label for a current
-atom position in the structure:
+Use the _Rotate_ tool (1) to change the structure display:
-
+
-Selecting the R-Group label and clicking **OK** converts the structure
-into a Markush structure with the selected R-Group label:
+_Rotate tool_ allows rotating objects:
+- If some objects are selected, the tool rotates all the selected objects;
+- If no objects are selected, or all objects are selected, the tool rotates the whole canvas;
+- The default rotation step is 15 degrees (this can be changed in _Settings_);
+- Press and hold the Ctrl key for more gradual continuous rotation with 1 degree rotation step.
-
+Select any bond on the structure and click `Alt+H` to rotate the structure so that the selected bond is placed horizontally.
+Select any bond on the structure and click `Alt+V` to rotate the structure so that the selected bond is placed vertically.
-**Note** : You can choose several R-Group labels simultaneously:
+_Flip tool_ (2, 3) flips the objects horizontally or vertically:
+- If some objects are selected, the Horizontal Flip tool (`Alt+H`) flips all the selected objects horizontally;
+- If no objects are selected, or all objects are selected, the Horizontal Flip tool (`Alt+H`) flips each structure horizontally;
+- If some objects are selected, the Vertical Flip tool (`Alt+V`) flips the selected objects vertically;
+- If no objects are selected, or all objects are selected, the Vertical Flip tool (`Alt+V`) flips each structure vertically.
-
+_Erase_ (`Del` or `Backspace`) tool (4) deletes all of the selected elements.
-Particular chemical fragments that may be substituted for a given
-R-Group form a set of R-Group members. R-Group members can be any
-structural fragment, including functional groups and single atoms or
-atom lists.
+### Highlighting atoms and bonds
-To create a set of R-Group members:
+Right-clicking on an atom, a bond, or multiple selected atoms and bonds allows highlighting of those elements with one of eight available colours:
-1. Draw a structure to become an R-Group member.
+
-2. Select the structure using the _R-Group Fragment Tool_ (2) to invoke
- the R-Group dialog; in this dialog select the label of the
- R-Group to assign the fragment to.
+### ACS (American Chemical Society) Style
-3. Click on **Apply** to convert the structure into an R-Group member.
+
-Schematically, the entire process of the R-Group member creation can
-be presented as:
+From the _Settings_, the user is able to _Set ACS Settings_ (1). Structures on canvas will change their appearance to comply with the ACS style. The action can be undone by resetting the settings to the default values (2).
-
+Ketcher default style:
-
+
-## R-Group attachment point
-An R-Group attachment point is the atom in an R-Group member fragment
-that attaches the fragment to the initial Markush structure.
+ACS Style:
-Selecting the _Attachment Point Tool_ (3) and clicking on an atom in the
-R-Group fragment converts this atom into an attachment point. If the
-R-Group contains more than one attachment point, you can specify one
-of them as primary and the other as secondary. You can select between
-either the primary or secondary attachment point using the dialog that
-appears after clicking on the atom:
-
+
-Result view of RGroup attachment points (IUPAC style):\
-
+## Drawing Reactions
-If there are two attachment points on an R-Group member, there must be
-two corresponding attachments (bonds) to the R-Group atom that has the
-same R-Group label. Clicking on **Apply** in the above dialog creates the
-attachment points.
-Result view of RGroup attachment points both primary and secondary (IUPAC style):
+To draw/edit reactions you can:
+- Draw reagents and products as described above;
+- Use options of the _Reaction Arrow Tool_ 
to draw an arrow. Select the arrow needed from the list 
;
+- Draw pluses in the reaction equation using the _Reaction Plus Tool_ 
;
+- Map same atoms in reagents and products with the _Reaction Mapping Tools_ 
Explore the available reaction mapping tools 
+ - _Reaction Auto-Mapping Tool_ (1);
+ - _Reaction Mapping Tool_ (2);
+ - _Reaction Unmapping Tool_ (3)
-
+### Drawing pathway reactions
-# R-Group Logic
+To draw pathway reactions you can:
+- Draw reagents and products as described above;
+- Use 
_Multi-Tailed Arrow Tool_ option from _Reaction Arrow Tool_;
+- Click anywhere on the canvas to add new multi-tailed arrow;
+- Adjust the length of the head or tail by grabbing its end and moving the cursor left and right;
+- Reposition the head or tail vertically by grabbing its end and moving the cursor up and down.
-**Ketcher** enables one to add logic when using R-Groups. To access
-the R-Group logic:
+## Drawing graphical objects
-1. Create an R-Group member fragment as described above.
+To draw graphical objects click the arrow on the _Shape Ellipse_ tool 
in the Tools palette to open the drop-down list with the following tools 
:
+- _Shape Ellipse_ (1);
+- _Shape Rectangle_ (2);
+- _Shape Line_ (3).
-2. Move the cursor over the entire fragment for the green frame to
- appear, then click inside the fragment. The following dialog
- appears:
+### Adding images on the canvas
-
+Select _Add Image_ tool 
in the Tools palette and click anywhere on the canvas.
+System dialog to choose image file will be opened and upon selection of supported format image will be added to the canvas.
+Center of the image will be at the place of the click.
+Supported image types are `.png` and `.svg`
-3. Specify **Occurrence** to define how many of an R-Group
- occurs. If an R-Group atom appears several times in the initial
- structure, you will specify **Occurrence**">n", n
- being the number of occurrences; if it appears once, you see
- "R1 > 0".
+### Adding text objects on the canvas
-4. Specify H at **unoccupied** R-Group sites ( **RestH** ): check or
- clear the checkbox.
+To add text to the canvas click the _Add text_ tool 
in the Tools palette and click the canvas to open the Text editor window:
-5. Specify the logical **Condition**. Use the R-Group condition **If
- R(i) Then** to specify whether the presence of an R-Group is
- dependent on the presence of another R-Group.
+
-# Marking S-Groups
+- To enter text, type in the Text editor field;
+- To edit text, double click the text object on the canvas;
+- Change the text style to bold and italic, make it subscript and superscript while typing or by selecting text and applying styles;
+- Add special symbols by clicking on omega:
-To mark S-Groups, use the _S-Group tool_ and the
-following dialog that appears after selecting a fragment with this
-tool:
+
- 
+## Templates toolbar
-Available S-Group types:
+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:
+
+
+
+To add a ring to the molecule, select a ring from the toolbar and click inside the drawing area, or click on an atom or a bond in the molecule.
-_Generic_
+Rules of using templates:
+- Selecting a template and clicking on an atom in the existing structure adds the template to the structure connected through the selected atom resulting in a fused structure:
-Generic is a pair of brackets without any labels.
+
-_Multiple group_
+- Selecting a template and dragging the cursor from an atom in the existing structure adds the template to this atom connected through a single bond:
-A Multiple group indicates a number of replications of a fragment or a part of a
-structure in contracted form.
+
-_SRU Polymer_
+- Dragging the cursor from an atom in the existing structure results in the single bond attachment if the cursor is dragged to more than the bond length; otherwise the fused structure is drawn.
+- Selecting a template and clicking on a bond in the existing structure created a bond-to-bond fused structure:
-The Structural Repeating Unit (SRU) brackets enclose the structural
-repeating of a polymer. You have three available patterns:
-head-to-tail (the default), head-to-head, and either/unknown.
+
-## Superatom S-Group
+ - The bond in the initial structure is replaced with the bond in the template;
+ - This procedure doesn't change the length of the bond in the initial structure;
+ - Dragging the cursor relative to the initial bond applies the template at the corresponding side of the bond;
+ - The added template will be fused by the default attachment atom or bond preset in the program;
+ - User is able to define the attachment atom and bond by clickingthe Edit button for template structure in the Template Library.
-An abbreviated structure (abbreviation) is all or part of a structure
-(molecule or reaction component) that has been abbreviated to a text
-label. Structures that you abbreviate keep their chemical
-significance, but their underlying structure is hidden.
+The _Custom Templates_ button 
allows to view the list of templates available; both built-in and createdby user:
-
+
-After applying Superatom S-Group - there is ability to contract the S-Group,
-and ability to remove the abbreviation, from the right-click menu on the S-Group:
+To create a user template:
+- Draw a structure;
+- Click the _Save as..._ button;
+- Click the _Save to Templates_ button. _Template edit_ form will be displayed:
-
+
-## Data S-Groups
+- Enter a name and define the attachment atom and bond by clicking on the structure preview. Click on _Save_ button to save the template;
+- Saved template will be available in _User Templates_ subsection at the bottom of the _Template Library_ tab.
-You can attach data to an atom, a fragment, a multifragment, a single bond, or a
-group. The defined set of _Names_ and _Values_ is introduced for each
-type of selected elements:
+### Functional Groups
- 
+Ketcher allows you to select and use Functional Groups to properly represent your structure on the canvas. Set of functional groups available is predefined and can't be changed right now.
-- Select the appropriate S-Group Field Name.
+Explore the list of the Functional Groups available in the Templates library. Open it using the icon in the bottom toolbar , Functional Groups tab.
-- Select the appropriate Field Value.
+To add a functional group to the canvas and join it to the structure do the following:
-- Labels can be specified as Absolute, Relative or Attached.
+1. Select the proper functional group in the _Functional Groups_ menu (you can filter them by name) and click on it to add it to the canvas:
-# Changing Structure Display
+ 
-Use the _Rotate_ tool 
to change the structure
-display:
+2. Click on the atom that the functional group should replace on the structure:
-
-
+ 
-_Rotate Tool_ (1)
-_Erase (Del)_ (4)
+3. You can just click on the canvas while having the functionaly group selected. To connect it with another structure on the canvas do the following:
+ - Select _Single Bond_ tool in the left Ketcher toolbar;
+ - Drag bond **from** the connection atom and drop it **to** the Functional Group on the canvas.
-This tool allows rotating objects.
+
-- If some objects are selected, the tool rotates the selected objects.
-- If no objects are selected, or all objects are selected, the tool rotates the whole canvas
-- The default rotation step is 15 degrees.
-- Press and hold the Ctrl key for more gradual continuous rotation with 1 degree rotation step
+#### Contracted s-group tooltip
-Select any bond on the structure and click Alt+H to rotate the structure so that the selected bond is placed horizontally.
-Select any bond on the structure and click Alt+V to rotate the structure so that the selected bond is placed vertically.
+Hover mouse cursor over the contracted S-group, and you will see the preview of the S-group.
-_Flip Tool_ (2, 3)
+
-This tool flips the objects horizontally or vertically.
+#### Expanding/Contracting S-group
-- If some objects are selected, the Horizontal Flip tool (or Alt+H) flips the selected objects horizontally
-- If no objects are selected, or all objects are selected, the Horizontal Flip tool (or Alt+H) flips each structure horizontally
-- If some objects are selected, the Vertical Flip tool (or Alt+V) flips the selected objects vertically
-- If no objects are selected, or all objects are selected, the Vertical Flip tool (or Alt+V) flips each structure vertically
+Functional Group on the canvas can be **Expanded** to view it's internal structure. Expanded group can be **Contracted** back to the compact presentation.
-# Drawing Reactions
+You can also **Remove the Abbreviation** on the group - it will allow you to work with the functional group atoms and bonds as with regular atoms and bonds on the canvas. To Expand, Contract and Remove Abbreviation:
-To draw/edit reactions you can:
+1. Click on the functional group with right mouse button:
-- draw reagents and products as described above
-- use options of the _Reaction Arrow Tool_ to draw an
- arrow. Select the arrow needed from the list
-- draw pluses in the reaction equation using the _Reaction Plus Tool_
-- map same atoms in reagents and products with the _Reaction Mapping Tools_ . Explore the available reaction mapping tools below:
+
-.
+2. Select the command from the context menu
-1 – Reaction Auto-Mapping Tool
+
-2 – Reaction Mapping Tool
+#### Inability to change S-group
-3 – Reaction Unmapping Tool
+Please, note that a lot of Ketcher's tools will not be able to be used on individual atoms and bonds of the functional group. Functional Groups can only be selected as a whole - they can only be deleted, moved, or rotated as an entire entity.
-# Drawing pathway reactions
+Ketcher will let you know if the tool is not applicable for the functional group and will suggest to Remove the Abbreviation immediately:
-To draw pathway reactions you can:
-* draw reagents and products as described above
-* use _Multi-Tailed Arrow Tool_ option from _Reaction Arrow Tool_
-* click anywhere on the canvas to add new multi-tailed arrow
-* adjust the length of the head or tail by grabbing its end and moving the cursor left and right
-* reposition the head or tail vertically by grabbing its end and moving the cursos up and down
+
+**Notes**:
+- _Aromatize_ & _Dearomatize_ operations will not be applied to the rings that are part of the functional group;
+- Functional groups will be considered as **super atoms** when opening and saving .mol files.
-# Drawing graphical objects
+## Stereochemistry
-To draw graphical objects click the arrow on the _Shape Ellipse_ tool 
in the Tools palette
-to open the drop-down list with the following tools:
+If a stereogenic center is on canvas, clicking on _Calculate CIP_ button 
on the main toolbar will assign stereo-labels to the stereocenters. Supported labels/stereochemistry types are S/R, s/r, and E/Z.
-.
+When the structure with the correct tetrahedral stereochemistry is created on the canvas you can open the _Enhanced Stereochemistry_ window by clicking the _Stereochemistry_ button 
and assign stereo marks:
-_Shape Ellipse_ (1), _Shape Rectangle_ (2), and _Shape Line_ (3).
+ 
-# Adding images on the canvas
-You can add images to the canvas. Select _Add Image_ tool in the Tools palette and click anywhere on the canvas.
-System dialog to choose image file will be opened and upon selection of supported format image will be added to the canvas.
-Center of the image will be at the place of the click.
-Supported image types are: `.png`, `.svg`
+In the _Stereochemistry tab_ in _Settings_ you can:
+- Enable/disable display of the Stereo flags;
+- Set the text of the Absolute/AND/OR/Mixed flags;
+- Change the style of the Label display at stereogenic centers;
+- Select the color of Absolute/AND/OR stereogenic centers;
+- Choose one of the four color display modes;
+- Enable/disable option when Chiral flag is ignored.
+
+
+When option _Ignore the chiral flag_ is _true_ it will affect opening of MDL V2000 and MDL V3000 files, as well as the display of labels at stereogenic centers and stereo flags:
-# Creating text objects on the canvas
+- Stereo flags are not displayed:
-To add text to the canvas click the _Add text_ tool
-in the Tools palette and click the canvas to open the Text editor window:
+
-
+- Labels at stereogenic centers are displayed only for non-absolute groups:
-- To enter text, type in the Text editor field.
-- To edit text, double click the text object on the canvas.
-- Change the text style to bold and italic, make it subscript and superscript while typing or by selecting text and applying styles.
+
-# Templates toolbar
+# Ketcher Macromolecules Mode
-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:
+**Ketcher Macromolecules Mode** consists of the following elements:
-
+
-To add a ring to the molecule, select a ring from the toolbar and
-click inside the drawing area, or click on an atom or a bond in the
-molecule.
+You can use the buttons on the main toolbar:
-Rules of using templates:
+
-- Selecting a template and clicking on an atom in the existing
- structure adds the template to the structure connected with a single
- bond:
+- **Clear Canvas** (1) button to clear the drawing area;
+- **Open…** (2) and **Save As…** (3) buttons to import a drawing from a molecular file or save it to a supported molecular file format;
+- **Undo** (4) / **Redo** (5) to manage the last actions taken on the canvas;
+- **Macromolecules modes switcher** (6) to change the macromolecules view to **sequence layout mode** (1), **snake layout mode** (2), or **flex layout mode** (3);
- 
+
-- Selecting a template and dragging the cursor from an atom in the
- existing structure adds the template directly to this atom resulting
- in the fused structure:
+- **Sequence mode typing type switcher** (7) (available only in sequence layout mode) to change the way Ketcher interprets keyboard input (A can be a DNA nucleotide, and RNA nucleotide, or an amino acid);
+- **Molecules/Macromolecules switcher** (8) to change between Ketcher's modes. Current mode always has a tick mark next to it. Clicking on the mode without a tick mark leads to it;
+- **Fullscreen mode** (9) button allows to initiate displaying Ketcher window in the fullscreen mode;
+- **Zoom panel** (10) displays the current zoom percentage.
- 
+The left toolbar consists of the following elements:
-- Dragging the cursor from an atom in the existing structure results
- in the single bond attachment if the cursor is dragged to more than
- the bond length; otherwise the fused structure is drawn.
-- Selecting a template and clicking on a bond in the existing
- structure created a bond-to-bond fused structure:
+
- 
+- **Hand tool** (1) used to adjust the view and move around the canvas;
+- **Rectangle selection tool** (2) used to select elements on the canvas;
+- **Eraser** (3) used to delete elements on the canvas (disabled in sequence layout mode);
+- **Bond tool** (4) used to establish bonds (both single covalent (1) and hydrogen (2)) between elements on canvas in snake and flex layout modes:
-- The bond in the initial structure is replaced with the bond in the
- template.
+
-- This procedure doesn't change the length of the bond in the
- initial structure.
+## Macromolecules library
-- Dragging the cursor relative to the initial bond applies the
- template at the corresponding side of the bond.
+Macromolecules library has 4 tabs:
+- **Favorites tab** - by default the tab contains no elements, but the user can add them by clicking on the star in the monomer/preset library card;
+- **Peptides tab** - contains amino acid monomers organized alphabetically using the one letter symbol of the natural analogues (including the _X section_ for common N and C end modifications and amino acids with no natural analogue); the bottom of the section contains ambiguous amino acids;
+- **RNA tab** - contains RNA builder, a section containing presets, and monomers organized into sugars, bases, phosphates, and nucleotides sections;
+- **CHEM tab** - contains non-RNA and non-amino acid monomers, mostly linkers and tags.
-**Note** : The added template will be fused by the default attachment
-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.
+**Searching the library** is possible using monomer names, monomer symbols, or monomer IDT aliases:
-The _Custom Templates_ button allows to view the list of templates available; both built-in and created
-by user:
+
-
+Hovering over a library card will show the preview for that library element.
+In case of a non-ambiguous monomer the preview will contain the name, the chemical structure, the exact position and composition of attachment points, and the IDT alias(es) (if the monomer has IDT alias(es)):
-To create a user template:
+
-- draw a structure.
+In case of a preset, the symbol of the preset and the names and symbols of monomers making up that preset will be shown, as well as IDT alias(es) (if the preset has IDT alias(es)):
-- click the Save as button.
+
-- click the Save to Templates button. _Template edit_ form will be displayed
+In case of an ambiguous monomer, names of monomers making up that ambiguous monomer will be shown, as well as a type of ambiguous monomer (alternatives or mixed):
-
+
-- enter a name and define the attachment atom and bond by clicking on the structure preview. Click on Apply button to save the template.
+### RNA Builder
-Saved template will be available in User Templates tab in the list of templates.
+RNA builder can be found in the RNA section of the library. It can be used to create presets - a collection of 2 or 3 monomers together making up a nucleotide, nucleoside, or a sugar-phosphate pair. Once created and saved (in browser cache), presets can be added to the canvas as already assembled collections of monomers.
-# Functional Groups
+#### Creating presets
-Ketcher allows you to select and use Functional Groups to properly represent your structure on the canvas.
-Set of functional groups available is predefined and can't be changed right now.
+To create a preset either click on the downwards pointing arrow to open RNA Builder or on _New Preset_ in the Presets section of the library:
-Explore the list of the Functional Groups available in the Templates library.
-Open it using the icon in the bottom toolbar:\
-
+
-Navigate to the Functional Groups tab to explore the FGs available:
+Clicking on _Sugar_, _Base_, or _Phosphate_ will open appropriate sections of the library where monomers can be picked. Library search is also available while RNA builder is active.
-
+
-Filter Functional Groups by name: 
-2. Click on the atom FG should connect with on the canvas:
- bond will be created automatically and FG will be joined to the structure.\
- 
+
-You can just click on the canvas having the FG selected. To connect it with other structure on the canvas do the following:
+#### Modifying nucleotides in sequence mode
-1. Select Simple Bond tool in the left Ketcher toolbar
-2. Drag bond **from** the connection atom and drop it **to** the Functional Group on the canvas.
+Right clicking on selected presets in sequence mode gives the option to _Modify in RNA Builder..._
-
+
+
-### Contracted s-group tooltip
-Hover mouse cursor over the contracted s-group, and you will see the preview of the s-group.
+Clicking on _Sugar_, _Base_, or _Phosphate_ will again open appropriate sections of the library so that selected nucleotides can be conveniently modified.
-
+After choosing needed replacement(s), click on _Update_ and (in case of modifying multiple nucleotides) on _Yes_ in the warning message window.
-### Expanding/Contracting s-group
-Functional Group on the canvas can be **Expanded** to view it's internal structure. Expanded group can be **Contracted** back to the compact presentation.
+
+
-You can also **Remove the Abbreviation** on the group - it will allows you to work with the functional group atoms and bonds as with regular atoms and bonds on the canvas. To Expand, Contract and Remove Abbreviation:
+### RNA Builder
-1. Click on the FG with right mouse button:
-2. Select the command from the context menu
+## Sequence mode
-### Disability to change s-group
-Please, note that a lot of Ketcher tools will be not applicable for the separate atoms and bonds of FG.
-FG can only be selected as a whole.
-It can also be deleted, moved, or rotated only as an entire entity.
+Sequence layout mode is a text-editor-like view mode for macromolecules. All nucleotides and amino acids are represented with single letter codes based on their natural analogue with accompanying information about modifications.
-Ketcher will let you know if the tool is not applicable for the FG and will suggest to Remove the Abbreviation immediately:
-
-# Working with Files
+For peptides, the modified amino acids are underlined:
-Ketcher supports the following molecular formats that can be entered
-either manually or from files:
+
-
+All other elements on the canvas (not nucleotides, nucleosides, phosphates at the terminal positions, or amino acids) are represented with an @ symbol:
-You can use the _Open…_ and _Save As…_ buttons of the _Main_
-toolbar to import a molecule from a molecular file or save it to a
-supported molecular file format.
+
-The **_Open Structure_** dialog enables
-one to either browse for a file or manually input, e.g.
-the Molfile ctable for the molecule to be imported:
+Based on the typing type switcher appropriate entities are added to the canvas when the user types on the keyboard, or pastes text.
-
+
-The text editor form is initiated for the text from the Clipboard and when the file is selected for opening. It allows to immediately edit the text representation before opening the structure:
+Backbone connections (R1-R2) are established automatically within one sequence. For example, R1 of an amino acid is the hydrogen of the amino group, and R2 is the hydroxyl of a carboxyl group, thus making an R1-R2 connection a peptide bond.
-
+In addition to typing and pasting text formats who always result in natural monomers, other formats can also be pasted and monomers can be added by clicking on their library cards - this allows the user to add modified monomers to the canvas.
-Ketcher suggests 2 ways for structure to be opened:
+Already existing monomers can also be replaced by selecting them and clicking on a library card, or modified in RNA builder by choosing _Modify in RNA Builder..._ from the right-click drop-down menu (see above).
-_Open as New Project_ will clear the canvas and position new structure on it.
-_Add to Canvas_ will save the structure in the clipboard. Click on the canvas to place it.
+## Snake and flex modes
-The **_Save Structure_** dialog enables one to save the molecular file:
+As opposed to sequence mode where multiple monomers can be represented with one symbol, every single monomer is represented with a shape in snake and flex modes.
-
+In sequence mode:
-Select the format needed in the _File Format_ drop down.
-
-
+In snake/flex mode:
-# Stereochemistry
+
-When the structure with the correct tetrahedral stereochemistry is created on the canvas you can open the ‘Enhanced Stereochemistry’ window by clicking the _Stereochemistry_ button and assign stereo marks:
+Different shapes of monomers indicate different monomer types:
-
+
-In the _Stereochemistry tab_ in _Settings_ you can:
+- **Hexagons** (1) represent amino acids; different natural analogues are coloured differently - acidic ones with shades of red, basic ones with shades of blue, polar neutral ones with shades of purple, and non-polar ones with shades of yellow and green;
+- **White boxes with a black outline** (2) represent CHEMs;
+- **Blue rounded squares** (3) represent sugars;
+- **Rhombuses** (4) represent bases; purines are shades of gray and pyrimidines are yellow (C), light orange (T), or dark purple (U);
+- **Coral circles** (5) represent phosphates;
+- **Pentagons** (6) represent unsplit nucleotides; logic for the colouring is the same as for bases;
+- **Dark rounded squares** (7) represent unresolved IDT nucleotides (see section _Working with files_).
-- enable/disable display of the Stereo flags
-- set the text of the Absolute/AND/OR/Mixed flags
-- change the style of the Label display at stereogenic centers
-- select the color of Absolute/AND/OR stereogenic centers
-- choose one of the four color display modes
-- enable/disable option when Chiral flag is ignored (_false_ by default)
+Modifications are also noted for amino acids, sugars, bases and phosphates using a banner over the monomer symbol:
-
+
-When option _Ignore the chiral flag_ is _true_ it will affect opening of MDL V2000 and MDL V3000 files, as well as the display of labels at stereogenic centers and stereo flags:
+### Establishing bonds
+
+In snake and flex modes monomers are added to the canvas by clicking on their library cards and then clicking on the canvas. Hovering over the monomers with a bond tool shows attachment points of that monomer:
+
+
+
+#### Covalent bonds
-- stereo flags are not displayed
+Covalent bonds can be **created** by connecting monomers with the _Bond tool_ either at their center (not choosing attachment points) or at their attachment points.
-
+- Connect attachment point to attachment point:
-- labels at stereogenic centers are displayed only for non-absolute groups
+
-
+- Connect center to attachment point:
-- MDL V2000 and MDL V3000 file formats will save stereo information according to the following table
+
-
+- Connect center to center:
-This parameter can be changed via _ketcher.setSettings()_ api, e.g. _ketcher.setSettings({ ignoreChiralFlag: true })_
+
+
+If a default bond cannot be established a _Select Connection Points_ dialog will open. Default bonds are:
+- R1-R2 between amino acids;
+- R1-R2 between sugars and phosphates;
+- R3-R1 between sugars and bases;
+- R1-R2 between unsplit nucleotides and sugars;
+- R1-R2 between unsplit nucleotides and phosphates;
+- A bond at any attachment points if there is only one available attachment point for both monomers.
+
+_Select Connection Point_ dialog contains structures of both monomers and allows the user to select the exact attachment points and by clicking on _Connect_ to establish a bond:
+
+
+
+
+Covalent bonds can be **eddited** by choosing _Edit Connection Points..._ from the right-click menu. _Edit Connection Points..._ allows the user to change the attachment points and reestablish the bond.
+
+
+
+
+#### Hydrogen bonds
+
+Hydrogen bonds can only be **created** between monomer centers at they do not require attachment points.
+
+
+
+Bond preview and _Edit Connection Points..._ dialog are not available for hydrogen bonds.
+
+#### Creating antisense chains
+
+When a chain is selected an option to _Create Antisense Strand_ exists in the right-click drop-down menu. An RNA antisense strand is added with the bases connected via hydrogen bonds:
+
+
+
+
+### Snake and flex modes differences
+
+There are two differences between snake and flex modes:
+1. **Different bond appearance** - all bonds in flex mode (left) are straight lines connecting monomer centers whereas in snake mode (right) some bonds are "snake-like" bonds with joints that do not overlap with other monomers:
+
+
+
+2. **Automatic layout upon entrance of the mode** - every time snake mode is entered, monomers on canvas get layouted; when flex mode is entered, no layout is applied.
+
+## Macromolecules and molecules mode integration
+
+Drawn macromolecules structures are visible (but not editable) when molecules mode is entered and drawn molecules are visible (but not editable) when macromolecules are entered.
+
+Macromolecules (snake) mode:
+
+
+
+Molecules mode:
+
+
+
+Currently the appearance of monomers in molecule mode is different than in macromolecules mode - the monomers are not represented with shapes (like in snake and flex) or with one letter codes (like in sequence), but with full abbreviations.
+
+### Establishing bonds between molecules and monomers
+
+To draw a structure contatining both monomers and monomers:
+1. Draw the needed structure in **molecules mode**;
+
+
+
+2. Draw the meeded structure in **macromolecules mode** (order of steps 1 and 2 is arbitrary);
+
+
+
+3. **In macromolecules mode** position the structures and establish a bond using the _Bond tool_ by dragging **from an attachment point of the monomer to the atom of the molecular structure**;
+
+
+
+Whole structure in macromolecules (snake) mode:
+
+
+
+Whole structure in molecules mode:
+
+
+
+### Expanding monomers in molecules mode
+
+After switching to molecules mode, right-clicking on a monomer gives the option to _Expand monomer_.
+
+
+
+
+Multiple monomers can be expanded at the same time.
+
+Expanded monomers behave like S-groups.
+
+# Working with Files
+
+In **molecules mode**, following file formats are supported:
+- Ket Format;
+- MDL Molfile V2000;
+- MDL Molfile V300O;
+- SDF V2000;
+- SDF V3000;
+- RDF V2000;
+- RDF V3000;
+- Daylight SMILES;
+- Extended SMILES;
+- CML;
+- InChI;
+- InChI AuxInfo;
+- InChIKey;
+- SVG Document;
+- PNG Image;
+- CDXML;
+- Base64 CDX;
+- CDX.
+
+In **macromolecules mode**, the supported file formats are:
+- Ket Format;
+- MDL Molfile V3000;
+- Sequence (1-letter code);
+- Sequence (3-letter code);
+- FASTA;
+- IDT*;
+- SVG Document;
+- HELM;
+
+* _IDT is a vendor of oligonucleotides where modifications are indicated in their own format._
+
+Structures can be opened using the _Open..._ button on the main toolbars of both modes:
+
+
+
+- _Paste From Clipboard_ allows pasting of the file contents (for both modes) and selecting of the format (only for macromolecules mode - in molecules mode the recondition of the format is possible unambiguously);
+
+
+
+- _Open from File_ allows browsing for a file. After the file is selected editable file contents are visible before the structure is added to the canvas;
+
+
+
+- _Open as New (Project)_ will clear the canvas and position the new structure on it.
+- _Add to Canvas_ will save the structure in the clipboard that can be added to the canvas via a click (for molecules mode) or add the structure to the canvas without the need to click on it (for macromolecules mode).
+
+The _Save as..._ dialog enables choosing of the file name and format, previewing the file contents and copying it to the clipboard:
+
+
+
+In Molecules mode an additional tab - _Warnings_ - may appear. It contains warning about the structure's inaccuracies:
+
+
# Hotkeys
-You can use keyboard hotkeys (including Numeric keypad) for some
-features/commands of the Editor. To display the hotkeys just place the
-cursor over a toolbar button. If a hotkey is available for the button,
-it will appear in brackets after the description of the button.
+You can use keyboard hotkeys (including Numeric keypad) for some features/commands of the Editor. To display the hotkeys just place the cursor over a toolbar button. If a hotkey is available for the button, it will appear in brackets after the description of the button.
_NOTE: `Mod` key is `Command` on OSX and `Ctrl` on PC systems_
@@ -772,15 +872,21 @@ _NOTE: `Mod` key is `Command` on OSX and `Ctrl` on PC systems_
| `Shift+t` | Structure Library |
| `t` | Rotate between: Benzene, Cyclopentadiene, Cyclohexane, Cyclopentane, Cyclopropane, Cyclobutane, Cycloheptane, Cyclooctane |
-**FunctionalGroups**
+**Functional Groups**
| Shortcut | Action |
| --------- | ----------------- |
| `Shift+f` | Functional Groups |
+**Macromolecules Specific Hotkeys**
+| Shortcut | Action |
+| --- | --- |
+| `Ctrl+Alt+R` | Change the sequence mode typing type to RNA |
+| `Ctrl+Alt+D` | Change the sequence mode typing type to DNA |
+| `Ctrl+Alt+P` | Change the sequence mode typing type to Peptide |
+
**Help**
| Shortcut | Action |
| --------------- | ------ |
| `?, &, Shift+/` | Help |
-**Note** : Please, use`Ctrl+V`to paste the selected object in
-Google Chrome and Mozilla Firefox browsers.
+**Note** : Please, use`Ctrl+V`to paste the selected object in Google Chrome and Mozilla Firefox browsers.
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diff --git a/example-separate-editors/.eslintignore b/example-separate-editors/.eslintignore
deleted file mode 100644
index a55244bff2..0000000000
--- a/example-separate-editors/.eslintignore
+++ /dev/null
@@ -1,4 +0,0 @@
-dist/
-public/
-build/
-config/
\ No newline at end of file
diff --git a/example-separate-editors/.eslintrc.json b/example-separate-editors/.eslintrc.json
deleted file mode 100644
index f78afb96b3..0000000000
--- a/example-separate-editors/.eslintrc.json
+++ /dev/null
@@ -1,34 +0,0 @@
-{
- "root": false,
- "env": {
- "browser": true
- },
- "extends": [
- "plugin:react/jsx-runtime",
- "plugin:jsx-a11y/recommended",
- "plugin:react-hooks/recommended",
- "plugin:jest/recommended"
- ],
- "rules": {
- "@typescript-eslint/ban-ts-comment": "warn",
- "jsx-a11y/label-has-associated-control": "warn",
- "jsx-a11y/no-static-element-interactions": "warn",
- "jsx-a11y/no-autofocus": "warn",
- "jsx-a11y/no-noninteractive-element-interactions": "warn",
- "jsx-a11y/alt-text": "warn",
- "jsx-a11y/click-events-have-key-events": "warn"
- },
- "overrides": [
- {
- "files": [
- "**/__tests__/**/*.[jt]s?(x)",
- "**/?(*.)+(spec|test).[jt]s?(x)"
- ],
- "extends": ["plugin:testing-library/react"],
- "rules": {
- "testing-library/no-container": "warn",
- "testing-library/no-node-access": "warn"
- }
- }
- ]
-}
diff --git a/example-separate-editors/.prettierignore b/example-separate-editors/.prettierignore
deleted file mode 100644
index edd9d60a7a..0000000000
--- a/example-separate-editors/.prettierignore
+++ /dev/null
@@ -1,2 +0,0 @@
-build/
-dist/
diff --git a/example-separate-editors/.stylelintignore b/example-separate-editors/.stylelintignore
deleted file mode 100644
index edd9d60a7a..0000000000
--- a/example-separate-editors/.stylelintignore
+++ /dev/null
@@ -1,2 +0,0 @@
-build/
-dist/
diff --git a/example-separate-editors/README.md b/example-separate-editors/README.md
deleted file mode 100644
index 3394f7cdee..0000000000
--- a/example-separate-editors/README.md
+++ /dev/null
@@ -1,6 +0,0 @@
-This example was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
-
-It is linked to the @ketcher/react package in the parent directory for development purposes.
-
-To run application for development purposes, please check instructions:
-[DEVNOTES.md](https://github.com/epam/ketcher/blob/master/DEVNOTES.md)
diff --git a/example-separate-editors/config/webpack.config.js b/example-separate-editors/config/webpack.config.js
deleted file mode 100644
index 48fcf2e56b..0000000000
--- a/example-separate-editors/config/webpack.config.js
+++ /dev/null
@@ -1,51 +0,0 @@
-const {
- override,
- addBundleVisualizer,
- addWebpackModuleRule,
- addWebpackPlugin,
-} = require('customize-cra');
-const webpack = require('webpack');
-const HtmlReplaceWebpackPlugin = require('html-replace-webpack-plugin');
-const GitRevisionPlugin = require('git-revision-webpack-plugin');
-const CopyPlugin = require('copy-webpack-plugin');
-
-const gitRevisionPlugin = new GitRevisionPlugin();
-const applicationVersion = gitRevisionPlugin.version().split('-')[0];
-
-const envVariables = {
- MODE: process.env.MODE || 'standalone',
- API_PATH: process.env.REACT_APP_API_PATH,
- ENABLE_POLYMER_EDITOR: !!process.env.ENABLE_POLYMER_EDITOR,
- KETCHER_ENABLE_REDUX_LOGGER: JSON.stringify(false),
-};
-
-module.exports = override(
- addBundleVisualizer({}, true),
- addWebpackModuleRule({
- test: /\.js$/,
- enforce: 'pre',
- loader: 'source-map-loader',
- exclude: /node_modules/,
- }),
- addWebpackPlugin(new webpack.EnvironmentPlugin(envVariables)),
- addWebpackPlugin(
- new HtmlReplaceWebpackPlugin([
- {
- pattern: '@@version',
- replacement: applicationVersion,
- },
- ]),
- ),
- addWebpackPlugin(
- new CopyPlugin({
- patterns: [
- {
- from: '../node_modules/ketcher-standalone/**/*.wasm',
- to: '[name][ext]',
- },
- ],
- }),
- ),
-);
-
-module.exports.envVariables = envVariables;
diff --git a/example-separate-editors/package.json b/example-separate-editors/package.json
deleted file mode 100644
index e7929d8611..0000000000
--- a/example-separate-editors/package.json
+++ /dev/null
@@ -1,94 +0,0 @@
-{
- "name": "example-separate-editors",
- "version": "1.0.0",
- "private": true,
- "scripts": {
- "dev:standalone": "cross-env MODE=standalone vite",
- "dev:standalone:macro": "cross-env ENABLE_POLYMER_EDITOR=true MODE=standalone vite",
- "dev:remote": "cross-env MODE=remote vite",
- "start:standalone": "cross-env MODE=standalone react-app-rewired start",
- "start:remote": "cross-env MODE=remote react-app-rewired start",
- "init:build": "shx mkdir -p build",
- "init:dist": "cross-env-shell shx mkdir -p dist/$MODE",
- "delete:dist": "cross-env-shell shx rm -rf dist/$MODE",
- "copy:build": "cross-env-shell shx cp -r build/. dist/$MODE",
- "prebuild": "cross-env-shell run-s init:build delete:dist init:dist",
- "postbuild": "cross-env-shell npm run copy:build",
- "build:remote": "cross-env-shell MODE=remote run-s prebuild build:react postbuild",
- "build:standalone": "cross-env-shell MODE=standalone run-s prebuild build:react postbuild",
- "build:react": "cross-env-shell MODE=$MODE react-app-rewired build && echo $MODE",
- "build:react:analyze": "react-app-rewired build --analyze",
- "build": "npm run build:standalone && npm run build:remote",
- "build:standalone:analyze": "cross-env MODE=standalone run-s prebuild build:react:analyze postbuild",
- "build:remote:analyze": "cross-env MODE=remote run-s prebuild build:react:analyze postbuild",
- "test": "run-s test:prettier test:stylelint test:eslint:quiet test:types test:unit",
- "test:eslint": "eslint . --ext .ts,.js,.jsx,.tsx",
- "test:eslint:quiet": "npm run test:eslint -- --quiet",
- "test:eslint:fix": "npm run test:eslint -- --fix",
- "test:types": "tsc --noEmit",
- "test:unit": "react-app-rewired test --passWithNoTests --watchAll=false",
- "test:stylelint": "stylelint \"./**/*.{css,less}\" --formatter",
- "test:prettier": "prettier --check \"./**/*.{js,ts,jsx,tsx,json}\"",
- "prettier:write": "prettier --write \"./**/*.{js,jsx,json,ts,tsx}\"",
- "stylelint:fix": "stylelint \"./**/*.{css,less}\" --formatter verbose --fix",
- "serve:remote": "serve -s dist/remote -l 4001",
- "serve:standalone": "serve -s dist/standalone -l 4002",
- "eject": "react-scripts eject"
- },
- "dependencies": {
- "ketcher-core": "*",
- "ketcher-macromolecules": "*",
- "ketcher-react": "*",
- "ketcher-standalone": "*",
- "normalize.css": "^8.0.1",
- "react": "^18.2.0",
- "react-app-polyfill": "^2.0.0",
- "react-dom": "^18.2.0"
- },
- "devDependencies": {
- "@rollup/plugin-replace": "^5.0.2",
- "@testing-library/jest-dom": "^4.2.4",
- "@testing-library/react": "^9.5.0",
- "@testing-library/user-event": "^7.2.1",
- "@types/jest": "^27.0.3",
- "@types/node": "^16.11.12",
- "@types/react": "^18.0.25",
- "@types/react-dom": "^18.0.8",
- "@vitejs/plugin-react": "^4.0.0",
- "@welldone-software/why-did-you-render": "^4.3.1",
- "copy-webpack-plugin": "^12.0.2",
- "cross-env": "^7.0.3",
- "customize-cra": "^1.0.0",
- "eslint": "^8.44.0",
- "git-revision-webpack-plugin": "^3.0.6",
- "html-replace-webpack-plugin": "^2.5.6",
- "npm-run-all": "^4.1.5",
- "prettier": "^2.5.1",
- "react-app-rewired": "^2.2.1",
- "react-scripts": "^5.0.1",
- "serve": "^13.0.2",
- "shx": "^0.3.3",
- "source-map-loader": "^3.0.1",
- "stylelint": "13.13.1",
- "typescript": "^4.5.2",
- "vite": "^4.5.5",
- "vite-plugin-html": "^3.2.0",
- "vite-plugin-raw": "^1.0.3",
- "vite-plugin-svgr": "^2.4.0",
- "webpack-bundle-analyzer": "^4.8.0"
- },
- "browserslist": {
- "production": [
- ">0.2%",
- "not dead",
- "not op_mini all"
- ],
- "development": [
- "ie 11",
- "last 1 chrome version",
- "last 1 firefox version",
- "last 1 safari version"
- ]
- },
- "config-overrides-path": "config/webpack.config.js"
-}
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