Merge branch 'master' into #1640-add-cdx-support

epam · Jun 14, 2022 · 1176988 · 1176988
2 parents 07a454a + 6ebb073
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -11,7 +11,7 @@ assignees: AndreiMazol
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
-4. See error
+
 
 **Expected behavior**
 A clear and concise description of what you expected to happen.

diff --git a/README.md b/README.md
@@ -17,7 +17,6 @@ Ketcher is an open-source web-based chemical structure editor incorporating high
 - 🛠️ Settings support (Rendering, Displaying, Debugging)
 - :camera: Use of SVG to achieve best quality in-browser chemical structure rendering
 
-
 ### Editor builtin tools:
 
 - Atom Tool, Bond Tool, and Template Tool to draw and edit structures
@@ -27,34 +26,17 @@ Ketcher is an open-source web-based chemical structure editor incorporating high
 - MW and Structure Parameters Calculate Tool
 - Select, modify, and erase connected and unconnected atoms and bonds using Selection Tool, or using Shift key
 - Advanced Structure Clean up Tool (+ stereochemistry checking and structure layout)
-- Simple Structure Clean up Tool (checks bonds length, angles and spatial arrangement of atoms) 
+- Simple Structure Clean up Tool (checks bonds length, angles and spatial arrangement of atoms)
 - Easy to use R-Group and S-Group tools (Generic, Multiple group, SRU polymer, peratom, Data S-Group)
 - Reaction Tool (reaction generating, manual and automatic atom-to-atom mapping)
 - Flip/Rotate Tool
 
-
 ## Installation and usage
 
-At this moment Ketcher library is delivered as a [react component library](https://www.npmjs.com/package/ketcher-react) and [zip archive](https://lifescience.opensource.epam.com/download/ketcher.html)
-
-```
-npm install ketcher-standalone
-```
-
-```tsx
-import { StandaloneStructServiceProvider } from 'ketcher-standalone'
-
-const structServiceProvider = new StandaloneStructServiceProvider()
-
-const MyComponent = () => {
-  return (
-    <Editor
-      staticResourcesUrl={process.env.PUBLIC_URL}
-      structServiceProvider={structServiceProvider}
-    />
-  )
-```
+At this moment Ketcher can be embedded into your application in two ways:
 
+- as a [react component library](https://www.npmjs.com/package/ketcher-react)
+- as ready-to-run application (to find desired version please look at Assets block of [releases](https://github.com/epam/ketcher/releases)). The application can be injected as IFrame or a separate page.
 
 ## FAQ
 
@@ -67,16 +49,13 @@ Look at the following [link](packages/ketcher-react/README.md) for details.
 You can find the instruction for service installation
 [here](http://lifescience.opensource.epam.com/indigo/service/index.html).
 
-
 ## Packages
 
-| Project | Status | Description |
-|---------|--------|-------------|
-| [ketcher-core](https://github.com/epam/ketcher/tree/master/packages/ketcher-core)          | [![npm version](https://badge.fury.io/js/ketcher-core.svg)](https://www.npmjs.com/package/ketcher-core) | Core functionality: domain, shared services, functions and interface declarations |
-| [ketcher-standalone](https://github.com/epam/ketcher/tree/master/packages/ketcher-standalone) | [![npm version](https://badge.fury.io/js/ketcher-standalone.svg)](https://www.npmjs.com/package/ketcher-standalone) | Contains only the functionality necessary to start Ketcher in standalone mode |
-| [ketcher-react](https://github.com/epam/ketcher/tree/master/packages/ketcher-react)          | [![npm version](https://badge.fury.io/js/ketcher-react.svg)](https://www.npmjs.com/package/ketcher-react) | Package contains only the functionality necessary to define components.  |
-
-
+| Project                                                                                       | Status                                                                                                              | Description                                                                       |
+| --------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- |
+| [ketcher-core](https://github.com/epam/ketcher/tree/master/packages/ketcher-core)             | [![npm version](https://badge.fury.io/js/ketcher-core.svg)](https://www.npmjs.com/package/ketcher-core)             | Core functionality: domain, shared services, functions and interface declarations |
+| [ketcher-standalone](https://github.com/epam/ketcher/tree/master/packages/ketcher-standalone) | [![npm version](https://badge.fury.io/js/ketcher-standalone.svg)](https://www.npmjs.com/package/ketcher-standalone) | Contains only the functionality necessary to start Ketcher in standalone mode     |
+| [ketcher-react](https://github.com/epam/ketcher/tree/master/packages/ketcher-react)           | [![npm version](https://badge.fury.io/js/ketcher-react.svg)](https://www.npmjs.com/package/ketcher-react)           | Package contains only the functionality necessary to define components.           |
 
 ## 3D Viewer
 
@@ -85,17 +64,14 @@ Ketcher uses Miew-React for viewing and editing data in 3D.
 You can find the latest version of Miew-React [here](https://github.com/epam/miew/tree/master/packages/miew-react).
 The last checked version - [1.0.0](https://www.npmjs.com/package/miew-react).
 
-
 ## Contribution
 
 See [Contributing Guide](./DEVNOTES.md).
 
-
 ## License
 
 [Apache 2.0](LICENSE)
 
 Please read [LICENSE](LICENSE) and [NOTICE](NOTICE) for details.
 
 Copyright (c) 2021 [EPAM Systems, Inc.](https://www.epam.com/)
-
diff --git a/documentation/wiki/pages/RNA_Hydrogen_bonds_creation.md b/documentation/wiki/pages/RNA_Hydrogen_bonds_creation.md
@@ -0,0 +1,38 @@
+# [Create RNA Structure] As Ketcher User I want to create hydrogen bonds linking RNA monomers on the canvas
+
+| As                            | I want                                     | so that                                                      |
+| ----------------------------- | ------------------------------------------ | ------------------------------------------------------------ |
+| A Ketcher peptide editor user | to add hydrogen bonds between RNA monomers | I can reflect hydrogen bonds existing in real life between RNA polymer chains |
+
+
+
+#### 1. Context
+
+Glossary: [Peptide Glossary](https://github.com/epam/ketcher/wiki/Polymer-Glossary) 
+
+HB is a specific chemical type of bond which can be created between polar functional groups between monomers. Hydrogen bonds do not use of monomer's R attachment points. Hydrogen bonds can be created between RNA nucleobase type monomers. Only between complimentary ones
+
+#### 3. Assumptions
+
+| ID   | Assumption                                                   |
+| ---- | ------------------------------------------------------------ |
+| 1    | Ketcher Polymer Editor users are interested only in creating hydrogen bonds between complimentary natural type RNA nucleobase type monomers |
+| 2    | Single monomer can have only 1 hydrogen bond created         |
+| 3    | The same bond creation tool is used for hydrogen bond creation |
+| 4    | Complimentary rule is applicable only for natural type RNA nucleobase type monomers |
+| 5    | We do not allow users to create hydrogen bonds with unnatural RNA monomers, however users can create a hydrogen bond between natural analogs and |
+
+
+
+#### 8. Acceptance criteria
+
+
+
+| #    | User Group                  | GIVEN                                                        | WHEN                                                         | THEN                                                         |
+| ---- | --------------------------- | ------------------------------------------------------------ | ------------------------------------------------------------ | ------------------------------------------------------------ |
+| 1    | Ketcher Polymer editor User | There are at least 2 complimentary RNA nucleobase type monomers on the canvas without Hydrogen bonds connected to them<br /> AND<br />They all their R attachment points are occupied | dragging from the one RNA nucleobase type monomer to another complimentary one | Ketcher visualize the line representing chemical bond from the first monomer to the cursor while dragging<br />AND<br />when dropping Ketcher visualize the Hydrogen bond type line between involved monomers<br />AND<br />Ketches aligns the monomers on the canvas in accordance with Business rules<br />AND<br />Ketcher creates a Hydrogen bond<br /><br />Count of polymers is not changed<br />Polymer ID's in not changed |
+| 2    |                             | There are at least 2 non-complimentary RNA nucleobase type monomers on the canvas without Hydrogen bonds connected to them<br />AND<br />They all their R attachment points are occupied | dragging from the one RNA nucleobase type monomer to another non-complimentary one | Ketcher visualize the line representing chemical bond from the first monomer to the cursor while dragging<br />AND<br />when dropping Ketcher stop the line visualization<br />AND<br />Ketches shows notification message that  hydrogen bond can be crated only between complimentary natural type monomers<br /> |
+| 3    |                             | There are at least 2 RNA nucleobase type monomers on the canvas <br />AND<br />They all their R attachment points are occupied<br />AND<br />at least one of them have a hydrogen bond connected | dragging from the one RNA nucleobase type monomer to another  one | Ketcher visualize the line representing chemical bond from the first monomer to the cursor while dragging<br />AND<br />when dropping Ketcher stop the line visualization<br />AND<br />Ketches shows notification message that  only one hydrogen bond can be connected to the monomer<br /> |
+
+
+
diff --git a/example/package.json b/example/package.json
@@ -3,21 +3,21 @@
   "version": "1.0.0",
   "private": true,
   "scripts": {
-    "start:standalone": "cross-env MODE=standalone react-app-rewired start",
-    "start:remote": "cross-env MODE=remote react-app-rewired start",
+    "start:standalone": "cross-env MODE=standalone ENABLE_POLYMER_EDITOR=true react-app-rewired start",
+    "start:remote": "cross-env MODE=remote ENABLE_POLYMER_EDITOR=true react-app-rewired start",
     "clean:build": "shx rm -rf build",
     "delete:dist": "shx rm -rf dist/$MODE",
     "init:dist": "shx mkdir -p dist/$MODE",
     "copy:build": "shx cp -r build/. dist/$MODE",
     "prebuild": "run-s delete:dist init:dist",
     "postbuild": "run-s copy:build clean:build",
-    "build:remote": "cross-env MODE=remote run-s prebuild build:react postbuild",
-    "build:standalone": "cross-env MODE=standalone run-s prebuild build:react postbuild",
+    "build:remote": "cross-env MODE=remote ENABLE_POLYMER_EDITOR=true run-s prebuild build:react postbuild",
+    "build:standalone": "cross-env MODE=standalone ENABLE_POLYMER_EDITOR=true run-s prebuild build:react postbuild",
     "build:react": "react-app-rewired build",
     "build:react:analyze": "react-app-rewired build --analyze",
     "build": "run-s build:standalone 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",
+    "build:standalone:analyze": "cross-env MODE=standalone ENABLE_POLYMER_EDITOR=true run-s prebuild build:react:analyze postbuild",
+    "build:remote:analyze": "cross-env MODE=remote ENABLE_POLYMER_EDITOR=true run-s prebuild build:react:analyze postbuild",
     "test": "run-s test:prettier test:stylelint test:eslint test:unit",
     "test:eslint": "eslint . --ext .ts,.js,.jsx,.tsx",
     "test:unit": "react-app-rewired test --passWithNoTests",

diff --git a/packages/ketcher-core/package.json b/packages/ketcher-core/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ketcher-core",
-  "version": "1.3.0",
+  "version": "1.4.0",
   "description": "Web-based molecule sketcher",
   "license": "Apache-2.0",
   "homepage": "http://lifescience.opensource.epam.com/ketcher",

diff --git a/packages/ketcher-core/src/application/ketcher.ts b/packages/ketcher-core/src/application/ketcher.ts
@@ -164,6 +164,10 @@ export class Ketcher {
     throw Error('not implemented yet')
   }
 
+  recognize(image: Blob, version?: string): Promise<Struct> {
+    return this.#indigo.recognize(image, { version: version })
+  }
+
   async generateImage(
     data: string,
     options: GenerateImageOptions = { outputFormat: 'png' }

diff --git a/packages/ketcher-polymer-editor-react/package.json b/packages/ketcher-polymer-editor-react/package.json
@@ -1,4 +1,5 @@
 {
+  "private": true,
   "name": "ketcher-polymer-editor-react",
   "version": "1.0.0",
   "description": "Web-based molecule sketcher",

diff --git a/packages/ketcher-react/package.json b/packages/ketcher-react/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ketcher-react",
-  "version": "2.4.2",
+  "version": "2.5.0",
   "description": "Web-based molecule sketcher",
   "license": "Apache-2.0",
   "homepage": "http://lifescience.opensource.epam.com/ketcher",

diff --git a/packages/ketcher-react/src/icons/files/compressed-hand.svg b/packages/ketcher-react/src/icons/files/compressed-hand.svg
diff --git a/packages/ketcher-react/src/icons/files/hand.svg b/packages/ketcher-react/src/icons/files/hand.svg
diff --git a/packages/ketcher-react/src/icons/index.tsx b/packages/ketcher-react/src/icons/index.tsx
@@ -55,6 +55,8 @@ import EraseIcon from './files/erase.svg'
 import ExtendedTableIcon from './files/extended-table.svg'
 import FileThumbnailIcon from './files/file-thumbnail.svg'
 import GenericGroupsIcon from './files/generic-groups.svg'
+import HandIcon from './files/hand.svg'
+import CompressedHandIcon from './files/compressed-hand.svg'
 import HelpIcon from './files/help.svg'
 import HistoryIcon from './files/history.svg'
 import ImageFrameIcon from './files/image-frame.svg'
@@ -292,6 +294,8 @@ const icons = {
   'fullscreen-enter': FullscreenEnterIcon,
   'fullscreen-exit': FullscreenExitIcon,
   'generic-groups': GenericGroupsIcon,
+  hand: HandIcon,
+  compressedhand: CompressedHandIcon,
   help: HelpIcon,
   history: HistoryIcon,
   'image-frame': ImageFrameIcon,

diff --git a/packages/ketcher-react/src/script/editor/Editor.ts b/packages/ketcher-react/src/script/editor/Editor.ts
@@ -124,6 +124,7 @@ class Editor implements KetcherEditor {
     dearomatizeStruct: PipelineSubscription
     enhancedStereoEdit: PipelineSubscription
     confirm: PipelineSubscription
+    cursor: Subscription
   }
 
   lastEvent: any
@@ -162,7 +163,8 @@ class Editor implements KetcherEditor {
       dearomatizeStruct: new PipelineSubscription(),
       // TODO: correct
       enhancedStereoEdit: new PipelineSubscription(),
-      confirm: new PipelineSubscription()
+      confirm: new PipelineSubscription(),
+      cursor: new PipelineSubscription()
     }
 
     domEventSetup(this, clientArea)
@@ -518,7 +520,8 @@ function domEventSetup(editor: Editor, clientArea) {
     'mousedown',
     'mousemove',
     'mouseup',
-    'mouseleave'
+    'mouseleave',
+    'mouseover'
   ].forEach((eventName) => {
     editor.event[eventName] = new DOMSubscription()
     const subs = editor.event[eventName]