openchemlib-utils - npm Package Compare versions

Comparing version 1.1.0 to 1.2.0

CHANGELOG.md

 # Changelog
 
+## [1.2.0](https://www.github.com/cheminfo/openchemlib-utils/compare/v1.1.0...v1.2.0) (2021-05-11)
+
+
+### Features
+
+* add toVisualizerMolfile ([3d8ee95](https://www.github.com/cheminfo/openchemlib-utils/commit/3d8ee950fa281c64b01d14c4adbd21fed7726e39))
+
 ## [1.1.0](https://www.github.com/cheminfo/openchemlib-utils/compare/v1.0.0...v1.1.0) (2021-05-10)
@@ -4,0 +11,0 @@

lib/index.js

@@ -1477,2 +1477,86 @@ 'use strict';
 
+/**
+ * Get diastereotopicAtomIDs of the molecule as well as information about connected hydrogens
+ * @param {OCL.Molecule}} molecule
+ * @returns
+ */
+
+function getExtendedDiastereotopicAtomIDs(molecule) {
+  const OCL = molecule.getOCL();
+  molecule = molecule.getCompactCopy();
+  molecule.addImplicitHydrogens();
+  // TODO Temporary code ???
+
+  molecule.ensureHelperArrays(OCL.Molecule.cHelperNeighbours);
+
+  const diaIDs = molecule.getDiastereotopicAtomIDs();
+  const newDiaIDs = [];
+
+  for (let i = 0; i < diaIDs.length; i++) {
+    const diaID = diaIDs[i];
+    const newDiaID = {
+      oclID: diaID,
+      hydrogenOCLIDs: [],
+      nbHydrogens: 0,
+    };
+    for (let j = 0; j < molecule.getAllConnAtoms(i); j++) {
+      const atom = molecule.getConnAtom(i, j);
+      if (molecule.getAtomicNo(atom) === 1) {
+        newDiaID.nbHydrogens++;
+        if (newDiaID.hydrogenOCLIDs.indexOf(diaIDs[atom]) === -1) {
+          newDiaID.hydrogenOCLIDs.push(diaIDs[atom]);
+        }
+      }
+    }
+
+    newDiaIDs.push(newDiaID);
+  }
+
+  return newDiaIDs;
+}
+
+function toVisualizerMolfile(molecule, options = {}) {
+  const { diastereotopic, heavyAtomHydrogen } = options;
+
+  let highlight = [];
+  let atoms = {};
+  if (diastereotopic) {
+    let hydrogenInfo = {};
+    let extendedIDs = getExtendedDiastereotopicAtomIDs(molecule);
+    for (let line of extendedIDs) {
+      hydrogenInfo[line.oclID] = line;
+    }
+
+    let diaIDs = getGroupedDiastereotopicAtomIDs(molecule);
+    for (const diaID of diaIDs) {
+      atoms[diaID.oclID] = diaID.atoms;
+      highlight.push(diaID.oclID);
+      if (heavyAtomHydrogen) {
+        if (
+          hydrogenInfo[diaID.oclID] &&
+          hydrogenInfo[diaID.oclID].nbHydrogens > 0
+        ) {
+          for (let id of hydrogenInfo[diaID.oclID].hydrogenOCLIDs) {
+            highlight.push(id);
+            atoms[id] = diaID.atoms;
+          }
+        }
+      }
+    }
+  } else {
+    let size = this.getAllAtoms();
+    highlight = new Array(size).fill(0).map((a, index) => index);
+    atoms = highlight.map((a) => [a]);
+  }
+
+  let molfile = {
+    type: 'mol2d',
+    value: molecule.toMolfile(),
+    _highlight: highlight,
+    _atoms: atoms,
+  };
+
+  return molfile;
+}
+
 exports.FULL_HOSE_CODE = FULL_HOSE_CODE;
@@ -1498,1 +1582,2 @@ exports.HOSE_CODE_CUT_C_SP3_SP3 = HOSE_CODE_CUT_C_SP3_SP3;
 exports.toDiastereotopicSVG = toDiastereotopicSVG;
+exports.toVisualizerMolfile = toVisualizerMolfile;

package.json

 {
   "name": "openchemlib-utils",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "description": "",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/index.js

@@ -23,1 +23,3 @@ export * from './diastereotopic/addDiastereotopicMissingChirality';
 export * from './db/MoleculesDB';
+
+export * from './misc/toVisualizerMolfile';

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Improved metrics

Total package byte prevSize

109744

increased by5.28%

Number of package files

40

increased by8.11%

Lines of code

2957

increased by5.72%

No dependency changes