Merge pull request #6 from privrja/dev

Dev
privrja · Jan 19, 2019 · e7cfd4e · e7cfd4e
2 parents 0e79cdf + e25a36c
commit e7cfd4e
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diff --git a/dist/smiles-drawer.js b/dist/smiles-drawer.js
@@ -5514,9 +5514,7 @@ var Drawer = function () {
     }, {
         key: 'buildBlockSmiles',
         value: function buildBlockSmiles() {
-            var tmpSmiles = this.graph.buildSmiles();
-            console.log(tmpSmiles);
-            return tmpSmiles;
+            return this.graph.buildSmiles();
         }
 
         /**
@@ -5583,7 +5581,6 @@ var Drawer = function () {
             this.drawEdges(this.opts.debug);
             this.drawVertices(this.opts.debug);
             this.canvasWrapper.reset();
-            console.log(this.graph);
         }
 
         /**
@@ -6918,8 +6915,9 @@ var Graph = function () {
             var stackSmiles = [];
             this.dfsSmiles(vertex, stackSmiles);
             stackSmiles = Graph.removeUnnecessaryParentheses(stackSmiles);
-            if (stackSmiles.length !== 0) {
-                smiles.push(stackSmiles.join(""));
+            var smile = Graph.removeUnnecessaryNumbers(stackSmiles.join(""));
+            if (smile.length !== 0) {
+                smiles.push(smile);
             }
         }
 
@@ -6948,6 +6946,13 @@ var Graph = function () {
             }
             vertex.vertexState = VertexState.VALUES.CLOSED;
         }
+
+        /**
+         * Remove numbers which is neighbours in SMILES notation -> need to perform in cyclic structures
+         * @param {String} smiles SMILES
+         * @return {String} repaired SMILES
+         */
+
     }], [{
         key: 'getConnectedComponents',
         value: function getConnectedComponents(adjacencyMatrix) {
@@ -7039,6 +7044,170 @@ var Graph = function () {
                 Graph._ccGetDfs(v, visited, adjacencyMatrix, component);
             }
         }
+    }, {
+        key: 'removeUnnecessaryNumbers',
+        value: function removeUnnecessaryNumbers(smiles) {
+            if (smiles === null) {
+                return '';
+            }
+            try {
+                var numbers = this.getNumbers(smiles);
+                var _iteratorNormalCompletion = true;
+                var _didIteratorError = false;
+                var _iteratorError = undefined;
+
+                try {
+                    for (var _iterator = numbers[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true) {
+                        var number = _step.value;
+
+                        var first = this.findFirst(smiles, number);
+                        var second = this.findSecond(smiles, first, number);
+                        var tmpRange = this.removeRangeLast(smiles, first, second);
+                        smiles = this.repairSmiles(smiles, tmpRange, first, second, number);
+                    }
+                } catch (err) {
+                    _didIteratorError = true;
+                    _iteratorError = err;
+                } finally {
+                    try {
+                        if (!_iteratorNormalCompletion && _iterator.return) {
+                            _iterator.return();
+                        }
+                    } finally {
+                        if (_didIteratorError) {
+                            throw _iteratorError;
+                        }
+                    }
+                }
+
+                return smiles;
+            } catch (ex) {
+                return smiles;
+            }
+        }
+
+        /**
+         * Remove unnecessary numbers from SMILES
+         * @param {String} smiles
+         * @param {Number} first
+         * @param {Number} second
+         * @return {*}
+         */
+
+    }, {
+        key: 'removeNumbers',
+        value: function removeNumbers(smiles, first, second) {
+            smiles = smiles.slice(0, first) + smiles.slice(first + 1);
+            return smiles.slice(0, second - 1) + smiles.slice(second);
+        }
+
+        /**
+         * Reapair SMILES
+         * @param {String} smiles
+         * @param {String} tmpRange
+         * @param {Number} first
+         * @param {Number} second
+         * @param {Number} number
+         * @return {String|*}
+         */
+
+    }, {
+        key: 'repairSmiles',
+        value: function repairSmiles(smiles, tmpRange, first, second, number) {
+            var pattern = new RegExp("^(Br|Cl|br|cl|[BCNOPSFIbcnopsfi])$");
+            if (pattern.test(tmpRange)) {
+                return this.removeNumbers(smiles, first, second);
+            }
+            var patternOrg = new RegExp("^(Br|Cl|br|cl|[BCNOPSFIbcnopsfi])");
+            if (patternOrg.test(tmpRange)) {
+                return smiles;
+            }
+
+            while (tmpRange.length !== 0) {
+                switch (tmpRange[0]) {
+                    case '(':
+                        tmpRange = tmpRange.substring(1);
+                        if (pattern.test(tmpRange)) {
+                            return this.removeNumbers(smiles, first, second);
+                        }
+                        break;
+                    case ')':
+                        tmpRange = tmpRange.substring(1);
+                        return this.repairSmiles(smiles, tmpRange, first, second, number);
+                    default:
+                        tmpRange = tmpRange.substring(1);
+                        break;
+                }
+            }
+            return smiles;
+        }
+        /**
+         * Substring in range and remove last Organic Subset
+         * @param smiles
+         * @param first
+         * @param second
+         * @return {string}
+         */
+
+    }, {
+        key: 'removeRangeLast',
+        value: function removeRangeLast(smiles, first, second) {
+            return smiles.substr(first + 1, second - first - 1);
+        }
+
+        /**
+         * Get numbers from SMILES
+         * @param smiles
+         * @return {Set<Number>}
+         */
+
+    }, {
+        key: 'getNumbers',
+        value: function getNumbers(smiles) {
+            var numbers = new Set();
+            for (var index = 0; index < smiles.length; ++index) {
+                if (!isNaN(smiles[index])) {
+                    numbers.add(smiles[index]);
+                }
+            }
+            return numbers;
+        }
+
+        /**
+         * return index of first occurrence number
+         * @param smiles
+         * @param number
+         * @return {number}
+         */
+
+    }, {
+        key: 'findFirst',
+        value: function findFirst(smiles, number) {
+            for (var index = 0; index < smiles.length; ++index) {
+                if (smiles[index] == number) {
+                    return index;
+                }
+            }
+        }
+
+        /**
+         * return index of first occurrence number from index + 1
+         * @param smiles
+         * @param from range no including this point (from, Infinity) = [from + 1, Infinity)
+         * @param number
+         * @return {*}
+         */
+
+    }, {
+        key: 'findSecond',
+        value: function findSecond(smiles, from, number) {
+            for (var index = from + 1; index < smiles.length; ++index) {
+                if (smiles[index] == number) {
+                    return index;
+                }
+            }
+            throw "Not Found";
+        }
     }, {
         key: 'smilesNumbersAdd',
         value: function smilesNumbersAdd(vertex) {

diff --git a/dist/smiles-drawer.min.js b/dist/smiles-drawer.min.js
diff --git a/dist/smiles-drawer.min.js.map b/dist/smiles-drawer.min.js.map
diff --git a/doc/ArrayHelper.html b/doc/ArrayHelper.html
diff --git a/doc/ArrayHelper.js.html b/doc/ArrayHelper.js.html
diff --git a/doc/Atom.html b/doc/Atom.html
diff --git a/doc/Atom.js.html b/doc/Atom.js.html
diff --git a/doc/CanvasWrapper.html b/doc/CanvasWrapper.html
diff --git a/doc/CanvasWrapper.js.html b/doc/CanvasWrapper.js.html
diff --git a/doc/DecayPoint.js.html b/doc/DecayPoint.js.html
diff --git a/doc/Drawer.html b/doc/Drawer.html
diff --git a/doc/Drawer.js.html b/doc/Drawer.js.html
diff --git a/doc/Edge.html b/doc/Edge.html
diff --git a/doc/Edge.js.html b/doc/Edge.js.html
diff --git a/doc/Graph.html b/doc/Graph.html
diff --git a/doc/Graph.js.html b/doc/Graph.js.html
diff --git a/doc/Line.html b/doc/Line.html
diff --git a/doc/Line.js.html b/doc/Line.js.html
diff --git a/doc/MathHelper.html b/doc/MathHelper.html
diff --git a/doc/MathHelper.js.html b/doc/MathHelper.js.html
diff --git a/doc/Ring.html b/doc/Ring.html
diff --git a/doc/Ring.js.html b/doc/Ring.js.html
diff --git a/doc/RingConnection.html b/doc/RingConnection.html
diff --git a/doc/RingConnection.js.html b/doc/RingConnection.js.html
diff --git a/doc/SSSR.html b/doc/SSSR.html
diff --git a/doc/SSSR.js.html b/doc/SSSR.js.html
diff --git a/doc/Vector2.html b/doc/Vector2.html
diff --git a/doc/Vector2.js.html b/doc/Vector2.js.html
diff --git a/doc/Vertex.html b/doc/Vertex.html
diff --git a/doc/Vertex.js.html b/doc/Vertex.js.html
diff --git a/doc/VertexState.js.html b/doc/VertexState.js.html
diff --git a/doc/all.md b/doc/all.md
@@ -1734,6 +1734,12 @@ A class representing the molecular graph.
         * [.getConnectedComponentCount(adjacencyMatrix)](#Graph.getConnectedComponentCount) ⇒ <code>Number</code>
         * [._ccCountDfs()](#Graph._ccCountDfs)
         * [._ccGetDfs()](#Graph._ccGetDfs)
+        * [.removeUnnecessaryNumbers(smiles)](#Graph.removeUnnecessaryNumbers) ⇒ <code>String</code>
+        * [.repairSmiles(smiles, tmpRange, first, second, number)](#Graph.repairSmiles) ⇒ <code>String</code> &#124; <code>\*</code>
+        * [.removeRangeLast(smiles, first, second)](#Graph.removeRangeLast) ⇒ <code>string</code>
+        * [.getNumbers(smiles)](#Graph.getNumbers) ⇒ <code>Set.&lt;Number&gt;</code>
+        * [.findFirst(smiles, number)](#Graph.findFirst) ⇒ <code>number</code>
+        * [.findSecond(smiles, from, number)](#Graph.findSecond) ⇒ <code>\*</code>
         * [.getProperVertex(vertexId, sourceId, targetId)](#Graph.getProperVertex) ⇒ <code>Number</code>
         * [.removeUnnecessaryParentheses(stackRight)](#Graph.removeUnnecessaryParentheses) ⇒ <code>Array</code>
         * [.removeParentheses(stack, end, literal,)](#Graph.removeParentheses)
@@ -2064,7 +2070,7 @@ Revert decay point value and update list of decay points
when edge isn't decay p
 <a name="Graph+buildSmiles"></a>
 
 ### graph.buildSmiles()
-Build block of SMILES based on decay pointsDFS pass through graphif there is a ring need second DFS pass for right SMILES notation
+Build block of SMILES based on decay pointsDFS pass through graphif there is a ring need second DFS pass for right SMILES notationbut the numbers are already setup in vertex.value.ringbonds array so no need to second pass of dfs
 
 **Kind**: instance method of <code>[Graph](#Graph)</code>  
 <a name="Graph+dfsSmilesInitialization"></a>
@@ -2144,6 +2150,81 @@ PRIVATE FUNCTION used by getConnectedComponentCount().
 PRIVATE FUNCTION used by getConnectedComponents().
 
 **Kind**: static method of <code>[Graph](#Graph)</code>  
+<a name="Graph.removeUnnecessaryNumbers"></a>
+
+### Graph.removeUnnecessaryNumbers(smiles) ⇒ <code>String</code>
+Remove numbers which is neighbours in SMILES notation -> need to perform in cyclic structures
+
+**Kind**: static method of <code>[Graph](#Graph)</code>  
+
+| Param | Type |
+| --- | --- |
+| smiles | <code>String</code> | 
+
+<a name="Graph.repairSmiles"></a>
+
+### Graph.repairSmiles(smiles, tmpRange, first, second, number) ⇒ <code>String</code> &#124; <code>\*</code>
+Reapair SMILES
+
+**Kind**: static method of <code>[Graph](#Graph)</code>  
+
+| Param | Type |
+| --- | --- |
+| smiles | <code>String</code> | 
+| tmpRange | <code>String</code> | 
+| first | <code>Number</code> | 
+| second | <code>Number</code> | 
+| number | <code>Number</code> | 
+
+<a name="Graph.removeRangeLast"></a>
+
+### Graph.removeRangeLast(smiles, first, second) ⇒ <code>string</code>
+Substring in range and remove last Organic Subset
+
+**Kind**: static method of <code>[Graph](#Graph)</code>  
+
+| Param |
+| --- |
+| smiles | 
+| first | 
+| second | 
+
+<a name="Graph.getNumbers"></a>
+
+### Graph.getNumbers(smiles) ⇒ <code>Set.&lt;Number&gt;</code>
+Get numbers from SMILES
+
+**Kind**: static method of <code>[Graph](#Graph)</code>  
+
+| Param |
+| --- |
+| smiles | 
+
+<a name="Graph.findFirst"></a>
+
+### Graph.findFirst(smiles, number) ⇒ <code>number</code>
+return index of first occurrence number
+
+**Kind**: static method of <code>[Graph](#Graph)</code>  
+
+| Param |
+| --- |
+| smiles | 
+| number | 
+
+<a name="Graph.findSecond"></a>
+
+### Graph.findSecond(smiles, from, number) ⇒ <code>\*</code>
+return index of first occurrence number from index + 1
+
+**Kind**: static method of <code>[Graph](#Graph)</code>  
+
+| Param | Description |
+| --- | --- |
+| smiles |  |
+| from | range no including this point (from, Infinity) = [from + 1, Infinity) |
+| number |  |
+
 <a name="Graph.getProperVertex"></a>
 
 ### Graph.getProperVertex(vertexId, sourceId, targetId) ⇒ <code>Number</code>
@@ -3629,7 +3710,6 @@ A class representing a vertex.
 | neighbouringElements | <code>Array.&lt;String&gt;</code> | The element symbols associated with neighbouring vertices. |
 | forcePositioned | <code>Boolean</code> | A boolean indicating whether or not this vertex was positioned using a force-based approach. |
 | vertexState | <code>Number</code> | enum of VertexState for DFS. |
-| smilesNumbers | <code>Array.&lt;Number&gt;</code> | Numbers in notation for SMILES, need for second pass of DFS. |
 
 
 * [Vertex](#Vertex)

diff --git a/doc/index.html b/doc/index.html
diff --git a/spec/smilesNumbersSpec.js b/spec/smilesNumbersSpec.js
@@ -0,0 +1,71 @@
+const Graph = require('../src/Graph');
+
+describe("smiles numbers", function () {
+    it("righData", function () {
+        let result = Graph.removeUnnecessaryNumbers('C(C1(CC)N1)=O');
+        expect(result).toEqual('C(C(CC)N)=O');
+    });
+
+    it("righData 2", function () {
+        let result = Graph.removeUnnecessaryNumbers('C(C1(CC)(C1C)C)=O');
+        expect(result).toEqual('C(C(CC)(CC)C)=O');
+    });
+
+    it("righData 3", function () {
+        let result = Graph.removeUnnecessaryNumbers('C(C1(CC)C1(CC)C)=O');
+        expect(result).toEqual('C(C(CC)C(CC)C)=O');
+    });
+
+    it("righData 4", function () {
+        let result = Graph.removeUnnecessaryNumbers('C(C1(CC)C(CC)C1)=O');
+        expect(result).toEqual('C(C1(CC)C(CC)C1)=O');
+    });
+
+    it("righData 5", function () {
+        let result = Graph.removeUnnecessaryNumbers('C(C1(CC)C(CC)C)=O');
+        expect(result).toEqual('C(C1(CC)C(CC)C)=O');
+    });
+
+    it("righData 6", function () {
+        let result = Graph.removeUnnecessaryNumbers('C21C(CC(=O)CC1CC3C3C2)CC');
+        expect(result).toEqual('C21C(CC(=O)CC1CCCC2)CC');
+    });
+
+    it("righData 7", function () {
+        let result = Graph.removeUnnecessaryNumbers('C21C(CC(=O)CC1CC3(C3C)C2)CC');
+        expect(result).toEqual('C21C(CC(=O)CC1CC(CC)C2)CC');
+    });
+
+    it("no changes", function () {
+        let result = Graph.removeUnnecessaryNumbers('N(C(C=O)CC7=CC=C(C=C7)N(C)C)C');
+        expect(result).toEqual('N(C(C=O)CC7=CC=C(C=C7)N(C)C)C');
+    });
+
+    it("no changes 2", function () {
+        let result = Graph.removeUnnecessaryNumbers('N3CC(=CCC3C=O)CN6CCOCC6');
+        expect(result).toEqual('N3CC(=CCC3C=O)CN6CCOCC6');
+    });
+
+    it("no changes 3", function () {
+        let result = Graph.removeUnnecessaryNumbers('NC(C=O)C5=CC=CC=C5');
+        expect(result).toEqual('NC(C=O)C5=CC=CC=C5');
+    });
+
+    it("no changes 4", function () {
+        let result = Graph.removeUnnecessaryNumbers('OC(C(C=O)N)C');
+        expect(result).toEqual('OC(C(C=O)N)C');
+    });
+
+    it("test with null", function () {
+        let result = Graph.removeUnnecessaryNumbers(null);
+        expect(result).toEqual('');
+    });
+
+    it("test with empty string", function () {
+        let result = Graph.removeUnnecessaryNumbers('');
+        expect(result).toEqual('');
+    });
+
+
+
+});