mf-parser - npm Package Compare versions

Comparing version 3.0.1 to 3.1.0

lib/index.js

@@ -590,2 +590,152 @@ 'use strict';
 
+function flatten(parsed, options = {}) {
+  const { groupIdentical = false, limit = 100000 } = options;
+  if (parsed.length === 0) return [''];
+
+  let parts = [];
+  let parenthesisLevel = 0;
+  let currentPart;
+  let comments = [];
+
+  for (const entry of parsed) {
+    if (
+      (entry.kind === 'atom' ||
+        entry.kind === 'isotope' ||
+        entry.kind === 'openingParenthesis' ||
+        !currentPart) &&
+      parenthesisLevel === 0
+    ) {
+      currentPart = {
+        mf: '',
+        min: 1,
+        max: 1,
+      };
+      parts.push(currentPart);
+    }
+    switch (entry.kind) {
+      case 'atom':
+        currentPart.mf += entry.value;
+        break;
+      case 'isotope':
+        currentPart.mf += `[${entry.value.isotope}${entry.value.atom}]`;
+        break;
+      case 'multiplier':
+        currentPart.mf += entry.value;
+        break;
+      case 'multiplierRange':
+        if (parenthesisLevel !== 0) {
+          throw new Error(
+            'Range definition inside parenthesis is not allowed.',
+          );
+        }
+        currentPart.min = entry.value.from;
+        currentPart.max = entry.value.to;
+        break;
+      case 'openingParenthesis':
+        parenthesisLevel++;
+        currentPart.mf += entry.value;
+        break;
+      case 'charge':
+        if (entry.value === 1) {
+          currentPart.mf += '+';
+        } else if (entry.value > 1) {
+          currentPart.mf += `(+${entry.value})`;
+        } else if (entry.value < 0) {
+          currentPart.mf += `(${entry.value})`;
+        }
+        break;
+      case 'closingParenthesis':
+        parenthesisLevel--;
+        currentPart.mf += entry.value;
+        break;
+      case 'comment':
+        comments.push(entry.value);
+        break;
+      case 'text':
+        break;
+      default:
+        throw new Error(
+          `Could not flatten the parsed MF. Unknown kind: ${entry.kind}`,
+        );
+    }
+  }
+  if (groupIdentical) {
+    parts = optimizeRanges(parts);
+  }
+  const mfs = createMFs(parts, comments.join(' '), limit);
+  return mfs;
+}
+
+/**
+ * If we have many times the same mf we can combine them
+ * This should only be applied if there are acutally some ranges
+ */
+function optimizeRanges(parts) {
+  let newParts = [];
+  let mfsObject = {};
+  let hasRange = false;
+  for (const mf of parts) {
+    if (mf.min !== mf.max) {
+      hasRange = true;
+      break;
+    }
+  }
+  if (!hasRange) return parts;
+  for (const mf of parts) {
+    if (!mfsObject[mf.mf]) {
+      mfsObject[mf.mf] = {
+        mf: mf.mf,
+        min: mf.min,
+        max: mf.max,
+      };
+      newParts.push(mfsObject[mf.mf]);
+    } else {
+      mfsObject[mf.mf].min = mfsObject[mf.mf].min + mf.min;
+      mfsObject[mf.mf].max = mfsObject[mf.mf].max + mf.max;
+    }
+  }
+  return newParts;
+}
+
+function createMFs(parts, comment, limit) {
+  const currents = new Array(parts.length);
+  for (let i = 0; i < currents.length; i++) {
+    currents[i] = parts[i].min;
+  }
+  const mfs = [];
+  let position = 0;
+  while (position < currents.length) {
+    if (currents[position] < parts[position].max) {
+      mfs.push(getMF(parts, currents, comment));
+      currents[position]++;
+      for (let i = 0; i < position; i++) {
+        currents[i] = parts[i].min;
+      }
+      position = 0;
+    } else {
+      position++;
+    }
+    if (mfs.length > limit) {
+      throw Error(`MF.flatten generates too many fragments (over ${limit})`);
+    }
+  }
+  mfs.push(getMF(parts, currents, comment));
+  return mfs;
+}
+
+function getMF(parts, currents, comment) {
+  let mf = '';
+  for (let i = 0; i < parts.length; i++) {
+    if (currents[i] === 0) {
+      continue;
+    }
+    mf += parts[i].mf;
+    if (currents[i] !== 1) {
+      mf += currents[i];
+    }
+  }
+  if (comment) mf += `$${comment}`;
+  return mf;
+}
+
 function getIsotopeRatioInfo(value) {
@@ -1483,2 +1633,6 @@ let result = { mass: 0, monoisotopicMass: 0 };
   }
+
+  flatten(options) {
+    return flatten(this.parsed, options);
+  }
 }
@@ -1485,0 +1639,0 @@

package.json

 {
   "name": "mf-parser",
-  "version": "3.0.1",
+  "version": "3.1.0",
   "description": "Parse a molecular formula",
@@ -26,3 +26,3 @@ "main": "lib/index.js",
     "chemical-groups": "^2.1.0",
-    "mf-utilities": "^3.0.1"
+    "mf-utilities": "^3.1.0"
   },
@@ -32,3 +32,3 @@ "devDependencies": {
   },
-  "gitHead": "a731fb03357ed5adbae7f72c791547691333a88c"
+  "gitHead": "deb282f3f2d6ae966112bc520b28fb75af3c327b"
 }

src/MF.js

 import { ensureCase } from './ensureCase';
 import { parse } from './parse';
+import { flatten } from './util/flatten';
 import { getEA } from './util/getEA';
@@ -138,2 +139,6 @@ import { getElements } from './util/getElements';
   }
+
+  flatten(options) {
+    return flatten(this.parsed, options);
+  }
 }

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Improved metrics

Total package byte prevSize

124522

increased by8.44%

Number of package files

45

increased by4.65%

Lines of code

4239

increased by9.37%

Dependency changes

• Updatedmf-utilities@^3.1.0