Introduce Graph format to Ketcher (#55)

* Remove unused style | .eslint

* struct schema + validation test

* tmp - don't see now

* rgroup, sgroup to schema

* atoms + bonds to graph

* sgroups (w/o DATA) + rgroups | fragments

* rgroups TMP

* Correct schemes: Add `rg-label` with ref to Rgroup. Add RGroup schema. Add rootSchema. Add validation example.

* Correct writing RGroups to Graph

* atom-list, data-sgroups

* graph parser v1.0.0-alpha

* Root field to Graph

* Refactor SGroupForest

* remove molecule ref
* remove validate method (checkOverlapping do his work before him)

* graph parser v1.0.1-alpha
code simplification +  rgroups merging

* tmp

* rxn

* Add new class `Fragment` for storage enhanced stereo flags

Now, struct.frags - Map of `Fragment`;
Fragment has methods for updating:
- enhancedStereoFlag
- marks in stereo atoms

* update struct.mergeInto() with frag.clone();

* rxn

* Add op.UpdateStereoAtom

* add op.UpdateStereoAtom call to `fromBondAddition`

* update `stereo` field in Struct.Bond
* add `stereoParity` field for Struct.Atom

* Add stereoChemistry info to GraphFormat

* [tmp] fromBondStereoUpdate...

* Actions for Deletions refactor. Add UpdateStereo to FragmentSplit

* [tmp] Upgrage operation (now undo not working)

* func instead 2 switchers

* works TMP

* Update StereoFrag operations | Split op to several files [WIP]

* Atom, Bond, Fragment Deletion actions with stereo works correctly

* eslint quiet option

* [eslint] Correct SwitchCase indent

* test + watcher + fixes

* [WIP] Add Enhanced Stereo dialog

* [WIP] First prototype of change atom marks

* [WIP] small corrections

* [WIP] Add Graph format to Save dialog

* tests

* Add enhanced Fragment and Atom dialogs | Refactor enhanced tool

* Chiral button was hidden

* [tmp] add stereo label to reatom.show()

* [tmp] 1 enhanced dialog, default stereo label change to AND-1

* Enhanced flag move

* tests for validator + true file structure

* Absolute label always w/o group number

* Reatom and ReEnhancedFlag corrections

* tests for validator

* StereoLabel info to atom property

* correct fragment operations
* it has bug with undo after delete atom

* Correct struct of Internal format

* Erace actions correct

* Remove Chiral flag. Update V2000, V3000 reading

* Small clean

* graph --> struct parser done
EPMLSOPKET-1316

* Fix after merge

* add header to graph --> struct parser

* Graph opening
EPMLSOPKET-1317

* Copy/paste internal format support

* sgroup display
EPMLSOPKET-1319

* Fix bugs with Rgroup and merging operations

* New molecule flags correct

* plus hotfix + sgroup display (2 fields: display and attached)
EPMLSOPKET-1321 (plus hotfix)

* sgroup display fix fields (2 fields: display and *placement)

* Sgroup parser done

* Help information already has table with supported formats

* add missing test for rxnToStruct.test.js

* fix issue related to io.js

* change some settings

* fix IO test

* fix and add new tests to moleculeToStruct.test.js

* fix bug with rgroups.mol

* add new test blocks to moleculeToStruct.test.js

* rename scripts in package.json

* delete unnecessary gitlab file

* remove gulp lint task

* remove TODO and empty lines

* Update src/script/chem/molfile/molfile.js

Co-authored-by: Nikita Ryzhov <vesdet@gmail.com>

* fix molfile.js

* delete unnecessary todos

* set Copyright to 2020 for new files

* add enhanced-stereo icon

* add new test structures

* fix moleculeToStruct test

* change enhanced-stereo icon

* set Copyright to 2020 for op.js

* fix

* fix

* delete unnecessary TODO

* delete loadStruct from index.js

Co-authored-by: Nikita_Ryzhov <Nikita_Ryzhov@epam.com>
Co-authored-by: Damir_Giliazetdinov <Damir_Giliazetdinov@epam.com>
Co-authored-by: Anna Kuznetsova1 <Anna_Kuznetsova1@epam.com>
Co-authored-by: Nikita Ryzhov <vesdet@gmail.com>

.babelrc

@@ -0,0 +1,13 @@
+{
+  "env": {
+    "test": {
+      "presets": ["@babel/preset-env"],
+      "plugins": [
+        ["transform-builtin-extend", {
+          "globals": ["Set", "Map"]
+        }]
+      ]
+    }
+  }
+}
+

.eslintrc

@@ -7,17 +7,17 @@
   "settings": {
     "react": { "pragma": "h" }
   },
-  "globals": {
-    "fetch": true,
-    "document": true,
-    "window": true,
-    "localStorage": true
+  "env": {
+    "browser": true,
+    "node": true,
+    "es6": true,
+    "jest": true
   },
   "rules": {
     "comma-dangle": ["error", "never"],
     "curly": ["error", "multi-or-nest", "consistent"],
     "dot-notation": "off",
-    "indent": ["error", "tab"],
+    "indent": ["error", "tab", { "SwitchCase": 1 }],
     "import/prefer-default-export": "off",
     "func-names": "off",
     "function-paren-newline": ["error", "consistent"],
@@ -53,7 +53,6 @@
     "radix": "off",
     "spaced-comment": ["error", "always", { "exceptions": ["*"] }],
     "unicode-bom": ["error", "never"],
-
     /* jsx */
     "react/jsx-first-prop-new-line": ["error", "multiline"],
     "react/jsx-indent": ["error", "tab"],

LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2018 EPAM Systems
+   Copyright 2020 EPAM Systems
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

doc/help.md

@@ -486,15 +486,14 @@ To create a user template:
 Ketcher supports the following molecular formats that can be entered
 either manually or from files:
 
-  * MDL Molfile or RXN file;
-
-  * Daylight SMILES (Server mode only);
-
-  * Daylight SMARTS (Server mode only);
-
-  * InChi string (Server mode only);
-
-  * CML file (Server mode only).
+|                              |  Graph  |  MDL  |  Daylight SMILES   |   Daylight SMARTS   |   InChi   |   CML  |
+| ---------------------------- |:-------:|:-----:|:------------------:|:-------------------:|:---------:|:------:|
+| Offline mode                 |    +    |   +   |          -         |          -          |     -     |    -   |
+| Reactions                    |    +    |   +   |          +         |          -          |     -     |    +   |
+| R-Groups                     |    +    |   +   |          -         |          -          |     -     |    -   |
+| S-Groups                     |    +    |   +   |          -         |          -          |     -     |    +   |
+| Standalone (Open/Save as...) |    +    |   +   |          -         |          -          |     -     |    -   |
+| Valency                      |    +    |   +   |          +         |          +          |     +     |    -   |
 
 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

gulp/assets.js

@@ -1,5 +1,5 @@
 /****************************************************************************
- * Copyright 2018 EPAM Systems
+ * Copyright 2020 EPAM Systems
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

gulp/check.js

@@ -1,5 +1,5 @@
 /****************************************************************************
- * Copyright 2018 EPAM Systems
+ * Copyright 2020 EPAM Systems
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -31,4 +31,4 @@ module.exports.checkDepsExact = function (options, cb) {
 	} else {
 		cb();
 	}
-};
+};

gulp/clean.js

@@ -1,5 +1,5 @@
 /****************************************************************************
- * Copyright 2018 EPAM Systems
+ * Copyright 2020 EPAM Systems
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

gulp/dev-script.js

@@ -1,5 +1,5 @@
 /****************************************************************************
- * Copyright 2018 EPAM Systems
+ * Copyright 2020 EPAM Systems
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

gulp/prod-script.js

@@ -1,5 +1,5 @@
 /****************************************************************************
- * Copyright 2018 EPAM Systems
+ * Copyright 2020 EPAM Systems
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

gulp/style-html.js

@@ -1,5 +1,5 @@
 /****************************************************************************
- * Copyright 2018 EPAM Systems
+ * Copyright 2020 EPAM Systems
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

gulp/tests.js

@@ -1,5 +1,5 @@
 /****************************************************************************
- * Copyright 2018 EPAM Systems
+ * Copyright 2020 EPAM Systems
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

gulp/utils.js

@@ -1,5 +1,5 @@
 /****************************************************************************
- * Copyright 2018 EPAM Systems
+ * Copyright 2020 EPAM Systems
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

gulpfile.js

@@ -1,5 +1,5 @@
 /****************************************************************************
- * Copyright 2018 EPAM Systems
+ * Copyright 2020 EPAM Systems
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.