openchemlib-utils - npm Package Compare versions

Comparing version 3.0.0 to 3.1.0

package.json

 {
   "name": "openchemlib-utils",
-  "version": "3.0.0",
+  "version": "3.1.0",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/diastereotopic/getDiastereotopicAtomIDs.js

@@ -1,2 +0,2 @@
-import { getXAtomicNumber } from '../util/getXAtomicNumber.js';
+import { getSymmetryRanks } from '../util/getSymmetryRanks';
 import { makeRacemic } from '../util/makeRacemic';
@@ -15,16 +15,4 @@ import { tagAtom } from '../util/tagAtom';
 
-  const xAtomNumber = getXAtomicNumber(molecule);
+  const symmetryRanks = getSymmetryRanks(molecule);
 
-  // most of the molecules have some symetry
-  const internalMolecule = molecule.getCompactCopy();
-  for (let i = 0; i < internalMolecule.getAllAtoms(); i++) {
-    // hydrogens are not taken into account during canonization, we need to change them with an atom with a valence of 1
-    if (internalMolecule.getAtomicNo(i) === 1) {
-      internalMolecule.setAtomicNo(i, xAtomNumber);
-    }
-  }
-  internalMolecule.ensureHelperArrays(
-    Molecule.cHelperSymmetryStereoHeterotopicity,
-  );
-
   let numberAtoms = molecule.getAllAtoms();
@@ -34,3 +22,3 @@ let ids = [];
   for (let iAtom = 0; iAtom < numberAtoms; iAtom++) {
-    const rank = internalMolecule.getSymmetryRank(iAtom);
+    const rank = symmetryRanks[iAtom];
     if (rank && cache[rank]) {
@@ -37,0 +25,0 @@ ids[iAtom] = cache[rank];

src/diastereotopic/getDiastereotopicAtomIDsFromMolfile.js

@@ -6,3 +6,3 @@ import { getDiastereotopicAtomIDsAndH } from './getDiastereotopicAtomIDsAndH.js';
  * The map allows to reload properties assigned to the atom molfile
- * Pelase take care than numbering of atoms starts at 0 !
+ * Please take care than numbering of atoms starts at 0 !
  * @param {import('openchemlib')} OCL - openchemlib library
@@ -9,0 +9,0 @@ * @param {string} molfile

src/hose/getHoseCodes.js

 import { ensureHeterotopicChiralBonds } from '../diastereotopic/ensureHeterotopicChiralBonds.js';
-import { makeRacemic } from '../util/makeRacemic.js';
 import { tagAtom } from '../util/tagAtom.js';
 
+import { getHoseCodesForAtomsInternal } from './getHoseCodesForAtomsInternal.js';
+
 /**
@@ -15,3 +16,3 @@ * Returns the hose codes for all atoms in the molecule
 export function getHoseCodes(molecule, options = {}) {
-  const { atomLabels } = options;
+  const { atomLabels, minSphereSize, maxSphereSize } = options;
   const { Molecule } = molecule.getOCL();
@@ -26,5 +27,2 @@
   ensureHeterotopicChiralBonds(internalMolecule);
-  internalMolecule.ensureHelperArrays(
-    Molecule.cHelperSymmetryStereoHeterotopicity,
-  );
 
@@ -40,53 +38,14 @@ const results = [];
     } else {
-      results.push(getHoseCodesForAtom(internalMolecule, i, options));
-    }
-  }
-
-  return results;
-}
-
-function getHoseCodesForAtom(molecule, rootAtom, options = {}) {
-  const { minSphereSize = 0, maxSphereSize = 4 } = options;
-  const { Molecule } = molecule.getOCL();
-
-  let results = [];
-  let min = 0;
-  let max = 0;
-  let atomMask = new Array(molecule.getAllAtoms());
-  let atomList = new Array(molecule.getAllAtoms());
-
-  for (let sphere = 0; sphere <= maxSphereSize; sphere++) {
-    let fragment = new Molecule(0, 0);
-    if (max === 0) {
-      atomList[max] = rootAtom;
-      atomMask[rootAtom] = true;
-      max++;
-    } else {
-      let newMax = max;
-      for (let i = min; i < max; i++) {
-        let atom = atomList[i];
-        for (let j = 0; j < molecule.getAllConnAtoms(atom); j++) {
-          let connAtom = molecule.getConnAtom(atom, j);
-          if (!atomMask[connAtom]) {
-            atomMask[connAtom] = true;
-            atomList[newMax++] = connAtom;
-          }
-        }
-      }
-      min = max;
-      max = newMax;
-    }
-    const atomMap = [];
-    molecule.copyMoleculeByAtoms(fragment, atomMask, false, atomMap);
-    tagAtom(fragment, atomMap[rootAtom]);
-    if (sphere >= minSphereSize) {
-      makeRacemic(fragment);
+      const tempMolecule = internalMolecule.getCompactCopy();
+      tagAtom(tempMolecule, i);
       results.push(
-        fragment.getCanonizedIDCode(
-          Molecule.CANONIZER_ENCODE_ATOM_CUSTOM_LABELS,
-        ),
+        getHoseCodesForAtomsInternal(tempMolecule, {
+          minSphereSize,
+          maxSphereSize,
+        }),
       );
     }
   }
+
   return results;
 }

src/hose/getHoseCodesForAtoms.js

 import { ensureHeterotopicChiralBonds } from '../diastereotopic/ensureHeterotopicChiralBonds.js';
-import { isCsp3 } from '../util/isCsp3';
-import { makeRacemic } from '../util/makeRacemic';
 import { tagAtom } from '../util/tagAtom';
 
+import { getHoseCodesForAtomsInternal } from './getHoseCodesForAtomsInternal.js';
+
 export const FULL_HOSE_CODE = 1;
@@ -14,3 +14,2 @@ export const HOSE_CODE_CUT_C_SP3_SP3 = 2;
  * @param {object} [options={}]
- * @param {boolean} [options.isTagged] Specify is the atoms are already tagged
  * @param {number} [options.minSphereSize=0] Smallest hose code sphere
@@ -25,3 +24,2 @@ * @param {number} [options.maxSphereSize=4] Largest hose code sphere
 ) {
-  const OCL = originalMolecule.getOCL();
   const {
@@ -31,77 +29,21 @@ minSphereSize = 0,
     kind = FULL_HOSE_CODE,
-    isTagged = false,
   } = options;
 
   const molecule = originalMolecule.getCompactCopy();
+  // those 2 lines should be done only once
+  molecule.addImplicitHydrogens();
+  ensureHeterotopicChiralBonds(molecule);
 
-  if (!isTagged) {
-    const tags = [];
-    for (let i = 0; i < rootAtoms.length; i++) {
-      let rootAtom = rootAtoms[i];
-      tags.push(tagAtom(molecule, rootAtom));
-      molecule.addImplicitHydrogens();
-      ensureHeterotopicChiralBonds(molecule);
-      molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);
-      // because ensuring helper reorder atoms we need to look again for it
-    }
-    rootAtoms.length = 0;
-    for (let j = 0; j < molecule.getAllAtoms(); j++) {
-      if (tags.includes(molecule.getAtomCustomLabel(j))) {
-        rootAtoms.push(j);
-      }
-    }
+  const allowedCustomLabels = [];
+  for (let i = 0; i < rootAtoms.length; i++) {
+    let rootAtom = rootAtoms[i];
+    allowedCustomLabels.push(tagAtom(molecule, rootAtom));
   }
 
-  let fragment = new OCL.Molecule(0, 0);
-  let results = [];
-  let min = 0;
-  let max = 0;
-  let atomMask = new Array(molecule.getAllAtoms());
-  let atomList = new Array(molecule.getAllAtoms());
-
-  for (let sphere = 0; sphere <= maxSphereSize; sphere++) {
-    if (max === 0) {
-      for (let rootAtom of rootAtoms) {
-        atomList[max] = rootAtom;
-        atomMask[rootAtom] = true;
-        max++;
-      }
-    } else {
-      let newMax = max;
-      for (let i = min; i < max; i++) {
-        let atom = atomList[i];
-        for (let j = 0; j < molecule.getAllConnAtoms(atom); j++) {
-          let connAtom = molecule.getConnAtom(atom, j);
-          if (!atomMask[connAtom]) {
-            switch (kind) {
-              case FULL_HOSE_CODE:
-                atomMask[connAtom] = true;
-                atomList[newMax++] = connAtom;
-                break;
-              case HOSE_CODE_CUT_C_SP3_SP3:
-                if (!(isCsp3(molecule, atom) && isCsp3(molecule, connAtom))) {
-                  atomMask[connAtom] = true;
-                  atomList[newMax++] = connAtom;
-                }
-                break;
-              default:
-                throw new Error('getHoseCoesForAtom unknown kind');
-            }
-          }
-        }
-      }
-      min = max;
-      max = newMax;
-    }
-    molecule.copyMoleculeByAtoms(fragment, atomMask, true, null);
-    if (sphere >= minSphereSize) {
-      makeRacemic(fragment);
-      results.push(
-        fragment.getCanonizedIDCode(
-          OCL.Molecule.CANONIZER_ENCODE_ATOM_CUSTOM_LABELS,
-        ),
-      );
-    }
-  }
-  return results;
+  return getHoseCodesForAtomsInternal(molecule, {
+    minSphereSize,
+    maxSphereSize,
+    allowedCustomLabels,
+    kind,
+  });
 }

src/hose/getHoseCodesFromDiastereotopicID.js

 import { ensureHeterotopicChiralBonds } from '../diastereotopic/ensureHeterotopicChiralBonds.js';
 
-import { getHoseCodesForAtom } from './getHoseCodesForAtom';
+import { getHoseCodesForAtomsInternal } from './getHoseCodesForAtomsInternal.js';
 /**
  * Returns the hose code for a specific marked atom
- * @param {import('openchemlib').Molecule} diastereotopicID
+ * @param {import('openchemlib').Molecule} molecule
  * @param {object} options
@@ -13,18 +13,3 @@ */
   ensureHeterotopicChiralBonds(molecule);
-
-  // One of the atom has to be marked !
-  let atomID = -1;
-  for (let i = 0; i < molecule.getAllAtoms(); i++) {
-    // we need to find the marked atom
-    const atomCustomLabel = molecule.getAtomCustomLabel(i);
-    if (atomCustomLabel != null && atomCustomLabel.endsWith('*')) {
-      atomID = i;
-      break;
-    }
-  }
-  if (atomID >= 0) {
-    options.isTagged = true;
-    return getHoseCodesForAtom(molecule, atomID, options);
-  }
-  return undefined;
+  return getHoseCodesForAtomsInternal(molecule, options);
 }

src/index.js

@@ -15,2 +15,3 @@ export * from './diastereotopic/ensureHeterotopicChiralBonds';
 export * from './hose/getHoseCodesForPath';
+export * from './hose/getHosesAndInfoFromMolfile';
 
@@ -17,0 +18,0 @@ export * from './util/combineSmiles';

src/util/getXAtomicNumber.js

 let xAtomicNumber = 0;
 
+/**
+ * Returns the atomic number of the X atom
+ * @param {import('openchemlib').Molecule} molecule An instance of a molecule
+ * @returns
+ */
 export function getXAtomicNumber(molecule) {
@@ -4,0 +9,0 @@ if (!xAtomicNumber) {

src/util/makeRacemic.js

@@ -19,2 +19,5 @@ /**
   }
+
+  // after the change we need to recalculate the CIP
+  molecule.ensureHelperArrays(Molecule.cHelperCIP);
 }

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Improved metrics

Total package byte prevSize

320758

increased by1.56%

Number of package files

79

increased by3.95%

Lines of code

6364

increased by1.87%

No dependency changes