mf-finder - npm Package Compare versions

Comparing version 0.9.1 to 0.12.0

package.json

 {
   "name": "mf-finder",
-  "version": "0.9.1",
+  "version": "0.12.0",
   "description": "Find a molecular formula from a monoisotopic mass",
@@ -21,8 +21,9 @@ "main": "src/index.js",
   "dependencies": {
-    "atom-sorter": "^0.9.1",
-    "chemical-elements": "^0.9.1",
-    "mf-parser": "^0.9.1",
-    "mf-utilities": "^0.9.1",
+    "atom-sorter": "^0.12.0",
+    "chemical-elements": "^0.12.0",
+    "mf-parser": "^0.12.0",
+    "mf-utilities": "^0.12.0",
     "molecular-formula": "^1.1.0"
-  }
+  },
+  "gitHead": "aa2e6571c5f7121dda616b7d6920b7a653a8f9c7"
 }

src/__tests__/mfFinder.test.js

@@ -10,3 +10,3 @@ 'use strict';
       precision: 1e5,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -20,3 +20,3 @@ expect(result.mfs).toHaveLength(1);
       precision: 1e5,
-      ionizations: 'H+'
+      ionizations: 'H+',
     });
@@ -31,7 +31,7 @@ expect(result.mfs).toHaveLength(1);
       ms: {
-        delta: 1.00727645232093,
+        delta: -1.00727645232093,
         em: 25.00727645232093,
-        ppm: 41969.85218003875,
-        charge: 1
-      }
+        ppm: -40279.33446656661,
+        charge: 1,
+      },
     });
@@ -44,3 +44,3 @@ });
       precision: 1e6,
-      ionizations: 'H+'
+      ionizations: 'H+',
     });
@@ -54,3 +54,3 @@ expect(result.mfs).toHaveLength(2);
       precision: 1e6,
-      ionizations: 'H++'
+      ionizations: 'H++',
     });
@@ -65,6 +65,6 @@ expect(result.mfs[1]).toMatchObject({
         em: 6.50336393620593,
-        delta: -17.49663606379407,
+        delta: 17.49663606379407,
         charge: 2,
-        ppm: 729026.5026580864
-      }
+        ppm: 2690397.8057241603,
+      },
     });
@@ -79,3 +79,3 @@
       precision: 1e5,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -94,4 +94,4 @@ expect(result.mfs).toHaveLength(2);
         min: 0,
-        max: 1
-      }
+        max: 1,
+      },
     });
@@ -110,4 +110,4 @@ expect(result.mfs).toHaveLength(2);
         max: 1,
-        onlyInteger: true
-      }
+        onlyInteger: true,
+      },
     });
@@ -123,6 +123,6 @@ expect(result.mfs).toHaveLength(1);
         { mf: 'H', min: 0, max: 1 },
-        { mf: 'S', min: 0, max: 100 }
+        { mf: 'S', min: 0, max: 100 },
       ],
       precision: 1e5,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -138,3 +138,3 @@ expect(result.mfs).toHaveLength(2);
       precision: 1e5,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -146,2 +146,12 @@ expect(result.mfs).toHaveLength(2);
 
+  it('simple combinations for polymers', () => {
+    let result = findMFs(92.99814, {
+      ranges: '(CH2)0-10NOCl',
+      precision: 1e4,
+      allowNeutral: true,
+    });
+    expect(result.mfs).toHaveLength(1);
+    expect(result.mfs[0].mf).toBe('((CH2))2(NOCl)');
+  });
+
   it('simple combinations from string ranges with ionizations', () => {
@@ -152,6 +162,6 @@ let result = findMFs(12, {
         { mf: 'H', min: 0, max: 1 },
-        { mf: 'H+', min: 0, max: 2 }
+        { mf: 'H+', min: 0, max: 2 },
       ],
       precision: 1e5,
-      ionizations: 'H+, H++'
+      ionizations: 'H+, H++',
     });
@@ -167,6 +177,6 @@ expect(result.mfs).toHaveLength(4);
         { mf: 'N', min: 0, max: 100 },
-        { mf: 'S', min: 0, max: 100 }
+        { mf: 'S', min: 0, max: 100 },
       ],
       precision: 1e4,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -181,6 +191,6 @@ expect(result.mfs).toHaveLength(0);
         { mf: 'H', min: 0, max: 100 },
-        { mf: 'S', min: 0, max: 100 }
+        { mf: 'S', min: 0, max: 100 },
       ],
       precision: 1000,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -197,6 +207,6 @@ expect(result.info.numberResults).toBe(1);
         { mf: 'H', min: 0, max: 100 },
-        { mf: 'S', min: 0, max: 100 }
+        { mf: 'S', min: 0, max: 100 },
       ],
       precision: 10000,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -214,3 +224,3 @@ expect(result.info.numberResults).toBe(3);
       precision: 1,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -230,6 +240,6 @@ expect(result.info.numberMFEvaluated).toBeLessThan(50);
         { mf: 'N', min: 0, max: 100 },
-        { mf: 'O', min: 0, max: 100 }
+        { mf: 'O', min: 0, max: 100 },
       ],
       precision: 0.0001,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -249,6 +259,6 @@ expect(result.info.numberMFEvaluated).toBeLessThan(500000);
         { mf: 'N', min: 0, max: 10 },
-        { mf: 'O', min: 0, max: 10 }
+        { mf: 'O', min: 0, max: 10 },
       ],
       precision: 1,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -261,3 +271,3 @@ expect(result.mfs[0].mf).toBe('C88H5N3O4S');
       ranges: [{ mf: 'C', min: 0, max: 2 }, { mf: 'H+', min: 0, max: 2 }],
-      precision: 1e4
+      precision: 1e4,
     });
@@ -270,3 +280,3 @@ expect(result.mfs).toHaveLength(0);
       ranges: [{ mf: 'C', min: 0, max: 2 }, { mf: 'C+', min: 0, max: 2 }],
-      precision: 1e5
+      precision: 1e5,
     });
@@ -283,5 +293,5 @@ expect(result.mfs).toHaveLength(2);
         { mf: 'C+', min: 0, max: 2 },
-        { mf: 'S+', min: 0, max: 2 }
+        { mf: 'S+', min: 0, max: 2 },
       ],
-      precision: 1e5
+      precision: 1e5,
     });
@@ -297,7 +307,7 @@
         { mf: 'C+', min: 0, max: 2 },
-        { mf: 'S+', min: 0, max: 2 }
+        { mf: 'S+', min: 0, max: 2 },
       ],
       precision: 1e5,
       maxCharge: 1,
-      minCharge: 1
+      minCharge: 1,
     });
@@ -311,3 +321,3 @@ expect(result.mfs).toHaveLength(1);
       ranges: [{ mf: 'C', min: 1, max: 1 }],
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -321,3 +331,3 @@ expect(result.mfs).toHaveLength(1);
       ranges: [{ mf: 'C', min: 0, max: 100 }, { mf: 'H', min: 0, max: 100 }],
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -332,3 +342,3 @@ expect(result.mfs).toHaveLength(1);
       precision: 10000,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -341,3 +351,3 @@ expect(result.mfs).toHaveLength(3);
       ranges: [{ mf: 'C+', min: 1, max: 2 }],
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -344,0 +354,0 @@ expect(result.mfs).toHaveLength(2);

src/__tests__/preprocessRanges.test.js

@@ -13,3 +13,3 @@ 'use strict';
       { mf: 'Me', min: 0, max: 1 },
-      { mf: 'Ca++', min: 0, max: 1 }
+      { mf: 'Ca++', min: 0, max: 1 },
     ]);
@@ -22,3 +22,3 @@ expect(Array.isArray(possibilities)).toBe(true);
       charge: 1,
-      unsaturation: -2
+      unsaturation: -2,
     });
@@ -32,5 +32,4 @@ });
       { mf: 'Cl(-)', min: 0, max: 2 },
-      { mf: '(C-1H)2', min: 0, max: 2 }
+      { mf: '(C-1H)2', min: 0, max: 2 },
     ]);
-
     expect(Array.isArray(possibilities)).toBe(true);
@@ -41,3 +40,3 @@ expect(possibilities[0]).toMatchObject({
       minInnerCharge: -2,
-      maxInnerCharge: 2
+      maxInnerCharge: 2,
     });
@@ -49,10 +48,23 @@ });
     expect(Array.isArray(possibilities)).toBe(true);
-    expect(possibilities).toHaveLength(4);
+    expect(possibilities).toHaveLength(3);
     expect(possibilities[0]).toMatchObject({
       minCharge: 0,
       maxCharge: 0,
-      originalMinCount: 2,
-      originalMaxCount: 2
+      originalMinCount: 1,
+      originalMaxCount: 1,
     });
   });
+
+  it('check a string polymer kind', () => {
+    let possibilities = preprocessRanges('ClBr2(CH2)0-2NO');
+    expect(Array.isArray(possibilities)).toBe(true);
+    expect(possibilities).toHaveLength(2);
+    expect(possibilities[0]).toMatchObject({
+      mf: 'ClBr2NO',
+      minCharge: 0,
+      maxCharge: 0,
+      originalMinCount: 1,
+      originalMaxCount: 1,
+    });
+  });
 });

src/__tests__/TargetMassCache.test.js

@@ -20,3 +20,3 @@ 'use strict';
       { mf: 'H+', min: 0, max: 2 },
-      { mf: 'O', min: 0, max: 0 }
+      { mf: 'O', min: 0, max: 0 },
     ]);
@@ -26,3 +26,3 @@ let cache = new TargetMassCache(100, possibilities);
       minCharge: 0,
-      maxCharge: 2
+      maxCharge: 2,
     });
@@ -35,3 +35,3 @@ });
       minCharge: -1,
-      maxCharge: 2
+      maxCharge: 2,
     });
@@ -48,3 +48,3 @@ expect(cache.minCharge).toBe(-1);
       precision: 1000,
-      allowNeutral: true
+      allowNeutral: true,
     });
@@ -54,3 +54,3 @@ expect(cache).toMatchObject({
       maxCharge: 0,
-      data: [{ charge: 0, minMass: 99.9, maxMass: 100.1 }]
+      data: [{ charge: 0, minMass: 99.9, maxMass: 100.1 }],
     });
@@ -64,3 +64,3 @@ });
       maxCharge: 2,
-      precision: 1000
+      precision: 1000,
     });
@@ -74,7 +74,7 @@ expect(cache).toMatchObject({
           minMass: Number.MAX_SAFE_INTEGER,
-          maxMass: Number.MIN_SAFE_INTEGER
+          maxMass: Number.MIN_SAFE_INTEGER,
         },
         { charge: 1, minMass: 99.90054857990907, maxMass: 100.10054857990906 },
-        { charge: 2, minMass: 199.80109715981814, maxMass: 200.20109715981812 }
-      ]
+        { charge: 2, minMass: 199.80109715981814, maxMass: 200.20109715981812 },
+      ],
     });
@@ -89,3 +89,3 @@ });
       allowNeutral: false,
-      precision: 1e6
+      precision: 1e6,
     });
@@ -100,6 +100,6 @@ expect(cache).toMatchObject({
           minMass: Number.MAX_SAFE_INTEGER,
-          maxMass: Number.MIN_SAFE_INTEGER
+          maxMass: Number.MIN_SAFE_INTEGER,
         },
-        { charge: 1, minMass: 0.00054857990907, maxMass: 200.00054857990906 }
-      ]
+        { charge: 1, minMass: 0.00054857990907, maxMass: 200.00054857990906 },
+      ],
     });
@@ -115,3 +115,3 @@ });
       allowNeutral: false,
-      precision: 1e6
+      precision: 1e6,
     });
@@ -125,8 +125,8 @@ expect(cache).toMatchObject({
           minMass: Number.MAX_SAFE_INTEGER,
-          maxMass: Number.MIN_SAFE_INTEGER
+          maxMass: Number.MIN_SAFE_INTEGER,
         },
-        { charge: 1, minMass: 0.00054857990907, maxMass: 200.00054857990906 }
-      ]
+        { charge: 1, minMass: 0.00054857990907, maxMass: 200.00054857990906 },
+      ],
     });
   });
 });

src/index.js

@@ -20,3 +20,3 @@ 'use strict';
 
-module.exports = function findMF(targetMass, options = {}) {
+module.exports = function (targetMass, options = {}) {
   const {
@@ -32,4 +32,4 @@ minCharge = Number.MIN_SAFE_INTEGER,
       { mf: 'O', min: 0, max: 100 },
-      { mf: 'N', min: 0, max: 100 }
-    ]
+      { mf: 'N', min: 0, max: 100 },
+    ],
   } = options;
@@ -56,4 +56,4 @@
       numberMFEvaluated: 0,
-      numberResults: 0
-    }
+      numberResults: 0,
+    },
   };
@@ -66,5 +66,5 @@ let orderMapping = []; // used to sort the atoms
     let currentIonization = {
-      currentMonoisotopicMass: ionization.em,
+      currentMonoisotopicMass: ionization.em || 0,
       currentCharge: ionization.charge,
-      currentUnsaturation: 0 // we don't take into account the unsaturation of the ionization agent
+      currentUnsaturation: 0, // we don't take into account the unsaturation of the ionization agent
     };
@@ -80,3 +80,3 @@ // if (DEBUG) console.log('new ionization', ionization.mf, ionization.em, ionization.charge);
       possibilities,
-      Object.assign({}, options, { charge: ionization.charge })
+      Object.assign({}, options, { charge: ionization.charge }),
     );
@@ -100,3 +100,3 @@
         throw Error(
-          `Iteration number is over the current maximum of: ${maxIterations}`
+          `Iteration number is over the current maximum of: ${maxIterations}`,
         );
@@ -141,4 +141,4 @@ }
             ionization,
-            orderMapping
-          )
+            orderMapping,
+          ),
         );
@@ -163,3 +163,3 @@ result.info.numberResults++;
               possibilities[currentPosition],
-              possibilities[currentPosition - 1]
+              possibilities[currentPosition - 1],
             );
@@ -180,3 +180,3 @@ } else {
 
-  result.mfs.sort((a, b) => a.ms.ppm - b.ms.ppm);
+  result.mfs.sort((a, b) => Math.abs(a.ms.ppm) - Math.abs(b.ms.ppm));
   return result;
@@ -201,3 +201,3 @@ };
   ionization,
-  orderMapping
+  orderMapping,
 ) {
@@ -211,3 +211,3 @@ let lastPossibility = possibilities[possibilities.length - 1];
     charge: lastPossibility.currentCharge - ionization.charge,
-    ionization
+    ionization,
   };
@@ -256,5 +256,5 @@
           currentAtom.maxInnerMass) /
-          currentAtom.em
+          currentAtom.em,
       ),
-      currentAtom.originalMinCount
+      currentAtom.originalMinCount,
     );
@@ -266,5 +266,5 @@ currentAtom.currentMaxCount = Math.min(
           currentAtom.minInnerMass) /
-          currentAtom.em
+          currentAtom.em,
       ),
-      currentAtom.originalMaxCount
+      currentAtom.originalMaxCount,
     );
@@ -293,3 +293,3 @@ currentAtom.currentCount = currentAtom.currentMinCount - 1;
     `max:${a.currentMaxCount}`,
-    `charge:${a.currentCharge}`
+    `charge:${a.currentCharge}`,
   ]);
@@ -296,0 +296,0 @@ }

src/preprocessRanges.js

@@ -11,25 +11,51 @@ 'use strict';
     // need to convert to ranges
-    let parsed = parse(ranges.replace(/ /g, ''));
+    let parsed = parse(ranges.replace(/[\r\n\t ]/g, ''));
     let newRanges = [];
-    let current;
+    let current = {
+      mf: '',
+      min: 1,
+      max: 1,
+    };
+
+    // example ClBr2(CH2)0-2NO
+    // the idea is that has long as we don't have a range we don't really care
+    // there is a limitation is that the range has to be first level of parenthesis
+    let parenthesisLevel = 0;
+    let currentMF = ''; // start at an atom first level or a parenthesis
     for (let item of parsed) {
       switch (item.kind) {
         case Kind.ATOM:
-          current = {
-            mf: item.value,
-            min: 1,
-            max: 1
-          };
-          newRanges.push(current);
+          if (parenthesisLevel === 0 && currentMF) {
+            current.mf += currentMF;
+            currentMF = '';
+          }
+          currentMF += item.value;
           break;
         case Kind.MULTIPLIER:
-          if (current) {
-            current.min = item.value;
-            current.max = item.value;
+          if (parenthesisLevel === 0 && currentMF) {
+            current.mf += currentMF + item.value;
+            currentMF = '';
+          } else {
+            currentMF += item.value;
           }
           break;
         case Kind.MULTIPLIER_RANGE:
-          current.min = item.value.from;
-          current.max = item.value.to;
+          if (parenthesisLevel !== 0) {
+            throw new Error('Range multiplier can only be at the first level');
+          }
+          newRanges.push({
+            mf: currentMF,
+            min: item.value.from,
+            max: item.value.to,
+          });
+          currentMF = '';
           break;
+        case Kind.OPENING_PARENTHESIS:
+          parenthesisLevel++;
+          currentMF += '(';
+          break;
+        case Kind.CLOSING_PARENTHESIS:
+          parenthesisLevel--;
+          currentMF += ')';
+          break;
         default:
@@ -39,5 +65,12 @@ throw Error(`can not preprocess ${ranges}`);
     }
+    if (currentMF) {
+      current.mf += currentMF;
+    }
+    if (current.mf) {
+      newRanges.push(current);
+    }
     ranges = newRanges;
   }
-  var possibilities = [];
+
+  let possibilities = [];
   for (let i = 0; i < ranges.length; i++) {
@@ -66,3 +99,3 @@ let range = ranges[i];
       maxMass: 0,
-      innerCharge: false
+      innerCharge: false,
     };
@@ -80,3 +113,3 @@ possibilities.push(possibility);
   possibilities = possibilities.filter(
-    (r) => r.originalMinCount !== 0 || r.originalMaxCount !== 0
+    (r) => r.originalMinCount !== 0 || r.originalMaxCount !== 0,
   );
@@ -83,0 +116,0 @@ // we will sort the way we analyse the data

src/TargetMassCache.js

@@ -9,3 +9,7 @@ 'use strict';
 
-let TargetMassCache = function TargetMassCache(targetMass, possibilities, options = {}) {
+let TargetMassCache = function TargetMassCache(
+  targetMass,
+  possibilities,
+  options = {},
+) {
   const {
@@ -16,3 +20,3 @@ allowNeutral = false, // msem because em in this case !
     charge = 0,
-    precision = 100
+    precision = 100,
   } = options;
@@ -22,4 +26,10 @@ if (!possibilities || possibilities.length === 0) return {};
   let firstPossibility = possibilities[0];
-  let currentMinCharge = Math.max(minCharge, firstPossibility.minCharge + charge);
-  let currentMaxCharge = Math.min(maxCharge, firstPossibility.maxCharge + charge);
+  let currentMinCharge = Math.max(
+    minCharge,
+    firstPossibility.minCharge + charge,
+  );
+  let currentMaxCharge = Math.min(
+    maxCharge,
+    firstPossibility.maxCharge + charge,
+  );
 
@@ -33,3 +43,3 @@ this.minCharge = currentMinCharge;
   let maxMass = 0;
-  let range = targetMass * precision / 1e6;
+  let range = (targetMass * precision) / 1e6;
   for (let i = 0; i < size; i++) {
@@ -46,11 +56,14 @@ let currentCharge = i + this.minCharge;
     } else {
-      minMass = (targetMass - range) * Math.abs(currentCharge) + ELECTRON_MASS * currentCharge;
-      maxMass = (targetMass + range) * Math.abs(currentCharge) + ELECTRON_MASS * currentCharge;
+      minMass =
+        (targetMass - range) * Math.abs(currentCharge) +
+        ELECTRON_MASS * currentCharge;
+      maxMass =
+        (targetMass + range) * Math.abs(currentCharge) +
+        ELECTRON_MASS * currentCharge;
     }
 
-
     this.data.push({
       charge: currentCharge,
       minMass,
-      maxMass
+      maxMass,
     });
@@ -63,7 +76,11 @@ }
 TargetMassCache.prototype.getMinMass = function (charge) {
-  return (this.data[charge - this.minCharge]) ? this.data[charge - this.minCharge].minMass : Number.MAX_SAFE_INTEGER;
+  return this.data[charge - this.minCharge]
+    ? this.data[charge - this.minCharge].minMass
+    : Number.MAX_SAFE_INTEGER;
 };
 
 TargetMassCache.prototype.getMaxMass = function (charge) {
-  return (this.data[charge - this.minCharge]) ? this.data[charge - this.minCharge].maxMass : Number.MIN_SAFE_INTEGER;
+  return this.data[charge - this.minCharge]
+    ? this.data[charge - this.minCharge].maxMass
+    : Number.MIN_SAFE_INTEGER;
 };

No alert changes

Improved metrics

Total package byte prevSize

33775

increased by6.04%

Lines of code

974

increased by7.74%

Dependency changes

• + Addedatom-sorter@0.12.0(transitive)

• + Addedchemical-elements@0.12.1(transitive)

• + Addedchemical-groups@0.12.1(transitive)

• + Addedmf-parser@0.12.0(transitive)

• + Addedmf-utilities@0.12.1(transitive)

• + Addedpapaparse@5.5.2(transitive)

• - Removedatom-sorter@0.9.1(transitive)

• - Removedchemical-elements@0.9.1(transitive)

• - Removedchemical-groups@0.9.1(transitive)

• - Removedmf-parser@0.9.1(transitive)

• - Removedmf-utilities@0.9.1(transitive)

• - Removedpapaparse@4.6.3(transitive)

• Updatedatom-sorter@^0.12.0

• Updatedchemical-elements@^0.12.0

• Updatedmf-parser@^0.12.0

• Updatedmf-utilities@^0.12.0