Merge pull request #8 from privrja/dev

Dev
privrja · Jan 27, 2019 · 28100ea · 28100ea
2 parents 08249ce + fe2206a
commit 28100ea
Show file tree

Hide file tree

Showing 35 changed files with 415 additions and 122 deletions.
diff --git a/dist/smiles-drawer.js b/dist/smiles-drawer.js
@@ -6907,9 +6907,11 @@ var Graph = function () {
         key: 'startDfs',
         value: function startDfs(vertex, smiles) {
             var stackSmiles = [];
+            this.first = vertex.id;
             this.dfsSmiles(vertex, stackSmiles);
             stackSmiles = Graph.removeUnnecessaryParentheses(stackSmiles);
             var smile = Graph.removeUnnecessaryNumbers(stackSmiles.join(""));
+            smile = Graph.repairNumbers(smile);
             if (smile.length !== 0) {
                 smiles.push(smile);
             }
@@ -6932,16 +6934,36 @@ var Graph = function () {
                 return;
             }
 
-            if (vertex.value.isPartOfAromaticRing) {
-                stackSmiles.push(vertex.value.element.toLowerCase() + Graph.smilesNumbersAdd(vertex));
+            if (this.first === vertex.id && vertex.value.element === "C") {
+                stackSmiles.push("O");
+            }
+
+            if (vertex.value.bracket) {
+                stackSmiles.push("[");
+                Graph.printVertexValue(stackSmiles, vertex);
+                if (vertex.value.bracket.hcount > 0) {
+                    stackSmiles.push('H');
+                    if (vertex.value.bracket.hcount > 1) {
+                        stackSmiles.push(vertex.value.bracket.hcount);
+                    }
+                }
+                if (vertex.value.bracket.charge > 0) {
+                    stackSmiles.push('+');
+                    stackSmiles.push(vertex.value.bracket.charge);
+                } else if (vertex.value.bracket.charge < 0) {
+                    stackSmiles.push(vertex.value.bracket.charge);
+                }
+                stackSmiles.push("]");
             } else {
-                stackSmiles.push(vertex.value.element + Graph.smilesNumbersAdd(vertex));
+                Graph.printVertexValue(stackSmiles, vertex);
             }
+            stackSmiles.push(Graph.smilesNumbersAdd(vertex));
+
             vertex.vertexState = VertexState.VALUES.OPEN;
             for (var i = 0; i < vertex.edges.length; ++i) {
                 var edge = this.edges[vertex.edges[i]];
                 if (edge.isDecay) {
-                    if (vertex.value.element === "C") {
+                    if (vertex.value.element === "C" && vertex.id !== this.first) {
                         stackSmiles.push("(");
                         stackSmiles.push("O");
                         stackSmiles.push(")");
@@ -6956,13 +6978,6 @@ 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) {
@@ -7054,6 +7069,22 @@ var Graph = function () {
                 Graph._ccGetDfs(v, visited, adjacencyMatrix, component);
             }
         }
+    }, {
+        key: 'printVertexValue',
+        value: function printVertexValue(stackSmiles, vertex) {
+            if (vertex.value.isPartOfAromaticRing) {
+                stackSmiles.push(vertex.value.element.toLowerCase());
+            } else {
+                stackSmiles.push(vertex.value.element);
+            }
+        }
+
+        /**
+         * Remove numbers which is neighbours in SMILES notation -> need to perform in cyclic structures
+         * @param {String} smiles SMILES
+         * @return {String} repaired SMILES
+         */
+
     }, {
         key: 'removeUnnecessaryNumbers',
         value: function removeUnnecessaryNumbers(smiles) {
@@ -7071,8 +7102,8 @@ var Graph = function () {
                         var number = _step.value;
 
                         var first = this.findFirst(smiles, number);
-                        var second = this.findSecond(smiles, first, number);
-                        var tmpRange = this.removeRangeLast(smiles, first, second);
+                        var second = this.findSecond(smiles, first + 1, number);
+                        var tmpRange = this.removeRangeLast(smiles, first, second, number);
                         smiles = this.repairSmiles(smiles, tmpRange, first, second, number);
                     }
                 } catch (err) {
@@ -7106,9 +7137,15 @@ var Graph = function () {
 
     }, {
         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);
+        value: function removeNumbers(smiles, first, second, number) {
+            if (number > 9) {
+                var numLength = number.toString().length;
+                smiles = smiles.slice(0, first - 1) + smiles.slice(first + numLength);
+                return smiles.slice(0, second - 2 - numLength) + smiles.slice(second - 1);
+            } else {
+                smiles = smiles.slice(0, first) + smiles.slice(first + 1);
+                return smiles.slice(0, second - 1) + smiles.slice(second);
+            }
         }
 
         /**
@@ -7126,7 +7163,7 @@ var Graph = function () {
         value: function repairSmiles(smiles, tmpRange, first, second, number) {
             var pattern = new RegExp("^(Br|Cl|[BCNOPSFIbcnopsfi])$");
             if (pattern.test(tmpRange)) {
-                return this.removeNumbers(smiles, first, second);
+                return this.removeNumbers(smiles, first, second, number);
             }
             var patternOrg = new RegExp("^(Br|Cl|[BCNOPSFIbcnopsfi])");
             if (patternOrg.test(tmpRange)) {
@@ -7137,7 +7174,7 @@ var Graph = function () {
                 if (tmpRange[0] === '(') {
                     tmpRange = tmpRange.substring(1);
                     if (pattern.test(tmpRange)) {
-                        return this.removeNumbers(smiles, first, second);
+                        return this.removeNumbers(smiles, first, second, number);
                     }
                     var leftBrackets = 1;
                     var rightBrackets = 0;
@@ -7173,8 +7210,12 @@ var Graph = function () {
 
     }, {
         key: 'removeRangeLast',
-        value: function removeRangeLast(smiles, first, second) {
-            return smiles.substring(first + 1, second);
+        value: function removeRangeLast(smiles, first, second, number) {
+            if (number > 9) {
+                return smiles.substring(first + number.toString().length, second - 1);
+            } else {
+                return smiles.substring(first + 1, second);
+            }
         }
 
         /**
@@ -7190,6 +7231,18 @@ var Graph = function () {
             for (var index = 0; index < smiles.length; ++index) {
                 if (!isNaN(smiles[index])) {
                     numbers.add(smiles[index]);
+                } else if (smiles[index] === '%') {
+                    index++;
+                    var num = "";
+                    while (!isNaN(smiles[index])) {
+                        num += smiles[index];
+                        index++;
+                        if (index >= smiles.length) {
+                            break;
+                        }
+                    }
+                    index--;
+                    numbers.add(num);
                 }
             }
             return numbers;
@@ -7205,11 +7258,7 @@ var Graph = function () {
     }, {
         key: 'findFirst',
         value: function findFirst(smiles, number) {
-            for (var index = 0; index < smiles.length; ++index) {
-                if (smiles[index] == number) {
-                    return index;
-                }
-            }
+            return smiles.indexOf(number);
         }
 
         /**
@@ -7223,12 +7272,11 @@ var Graph = function () {
     }, {
         key: 'findSecond',
         value: function findSecond(smiles, from, number) {
-            for (var index = from + 1; index < smiles.length; ++index) {
-                if (smiles[index] == number) {
-                    return index;
-                }
+            var result = smiles.indexOf(number, from);
+            if (result === -1) {
+                throw "Not Found";
             }
-            throw "Not Found";
+            return result;
         }
     }, {
         key: 'smilesNumbersAdd',
@@ -7260,6 +7308,55 @@ var Graph = function () {
         value: function getProperVertex(vertexId, sourceId, targetId) {
             if (vertexId === sourceId) return targetId;else return sourceId;
         }
+    }, {
+        key: 'repairNumbers',
+        value: function repairNumbers(smiles) {
+            var numbers = Array.from(this.getNumbers(smiles));
+            numbers.sort(function (a, b) {
+                return b - a;
+            });
+
+            var index = 1;
+            var _iteratorNormalCompletion2 = true;
+            var _didIteratorError2 = false;
+            var _iteratorError2 = undefined;
+
+            try {
+                for (var _iterator2 = numbers[Symbol.iterator](), _step2; !(_iteratorNormalCompletion2 = (_step2 = _iterator2.next()).done); _iteratorNormalCompletion2 = true) {
+                    var number = _step2.value;
+
+                    if (index === number) {
+                        continue;
+                    }
+                    var first = this.findFirst(smiles, number);
+                    if (number > 9) {
+                        smiles = smiles.slice(0, first - 1) + index + smiles.slice(first + number.toString().length);
+                        var second = this.findSecond(smiles, first + 1, number);
+                        smiles = smiles.slice(0, second - 1) + index + smiles.slice(second + number.toString().length);
+                    } else {
+                        smiles = smiles.slice(0, first) + index + smiles.slice(first + 1);
+                        var _second = this.findSecond(smiles, first + 1, number);
+                        smiles = smiles.slice(0, _second) + index + smiles.slice(_second + 1);
+                    }
+                    index++;
+                }
+            } catch (err) {
+                _didIteratorError2 = true;
+                _iteratorError2 = err;
+            } finally {
+                try {
+                    if (!_iteratorNormalCompletion2 && _iterator2.return) {
+                        _iterator2.return();
+                    }
+                } finally {
+                    if (_didIteratorError2) {
+                        throw _iteratorError2;
+                    }
+                }
+            }
+
+            return smiles;
+        }
 
         /**
          * Remove unnecessary parentheses from SMILES

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
@@ -3333,7 +3333,7 @@ <h5>Returns:</h5>
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>

diff --git a/doc/ArrayHelper.js.html b/doc/ArrayHelper.js.html
@@ -431,7 +431,7 @@ <h1 class="page-title">ArrayHelper.js</h1>
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>

diff --git a/doc/Atom.html b/doc/Atom.html
@@ -2853,7 +2853,7 @@ <h4 class="name" id="restoreRings"><span class="type-signature"></span>restoreRi
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>

diff --git a/doc/Atom.js.html b/doc/Atom.js.html
@@ -589,7 +589,7 @@ <h1 class="page-title">Atom.js</h1>
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>

diff --git a/doc/CanvasWrapper.html b/doc/CanvasWrapper.html
@@ -3718,7 +3718,7 @@ <h5>Parameters:</h5>
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>

diff --git a/doc/CanvasWrapper.js.html b/doc/CanvasWrapper.js.html
@@ -947,7 +947,7 @@ <h1 class="page-title">CanvasWrapper.js</h1>
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>

diff --git a/doc/DecayPoint.js.html b/doc/DecayPoint.js.html
@@ -66,7 +66,7 @@ <h1 class="page-title">DecayPoint.js</h1>
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>

diff --git a/doc/Drawer.html b/doc/Drawer.html
@@ -10711,7 +10711,7 @@ <h5>Parameters:</h5>
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>

diff --git a/doc/Drawer.js.html b/doc/Drawer.js.html
@@ -3203,7 +3203,7 @@ <h1 class="page-title">Drawer.js</h1>
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>

diff --git a/doc/Edge.html b/doc/Edge.html
@@ -957,7 +957,7 @@ <h5>Parameters:</h5>
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>

diff --git a/doc/Edge.js.html b/doc/Edge.js.html
@@ -117,7 +117,7 @@ <h1 class="page-title">Edge.js</h1>
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Wed Jan 23 2019 16:51:02 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
+    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.5.5</a> on Sun Jan 27 2019 14:35:28 GMT+0100 (Střední Evropa (běžný čas)) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
 </footer>
 
 <script>prettyPrint();</script>