openchemlib-utils - npm Package Compare versions

Comparing version 0.6.0 to 0.6.1

CHANGELOG.md

 # Changelog
 
+### [0.6.1](https://www.github.com/cheminfo/openchemlib-utils/compare/v0.6.0...v0.6.1) (2021-01-17)
+
+
+### Bug Fixes
+
+* correctly export combineSmiles ([a8354c3](https://www.github.com/cheminfo/openchemlib-utils/commit/a8354c37df48ef3648ca36d1c500c954d067dd60))
+
 ## [0.6.0](https://www.github.com/cheminfo/openchemlib-utils/compare/v0.5.3...v0.6.0) (2021-01-17)
@@ -4,0 +11,0 @@

lib/index.js

@@ -431,3 +431,171 @@ 'use strict';
 
+const MAX_R = 10;
+
 /**
+ * Generate molecules and calcule predicted properties form a list of smiles and fragments
+ * @param {string} [coreSmiles]
+ * @param {array} [fragments] Array of {smiles,R1,R2,...}
+ * @param {object} [options={}]
+ * @param {function} [options.onStep] method to execute each new molecules
+ * @param {boolean} [options.complexity] returns only the number of molecules to evaluate
+ * @return {Promise} promise that resolves to molecules or complexity as a number
+ */
+async function combineSmiles(coreSmiles, fragments, options = {}) {
+  const { complexity = false } = options;
+  const core = getCore(coreSmiles);
+  const rGroups = getRGroups(core, fragments);
+  if (complexity) {
+    return getComplexity(rGroups);
+  }
+  return generate(core, rGroups, options);
+}
+
+function getComplexity(rGroups) {
+  let complexity = 1;
+  for (let rGroup of rGroups) {
+    complexity *= rGroup.smiles.length;
+  }
+  return complexity;
+}
+
+async function generate(core, rGroups, options = {}) {
+  const { onStep } = options;
+  const molecules = {};
+  const sizes = new Array(rGroups.length);
+  const currents = new Array(rGroups.length);
+  for (let i = 0; i < rGroups.length; i++) {
+    sizes[i] = rGroups[i].smiles.length - 1;
+    currents[i] = 0;
+  }
+  let position = 0;
+  let counter = 0;
+
+  while (true) {
+    counter++;
+    while (position < currents.length) {
+      if (currents[position] < sizes[position]) {
+        if (onStep) {
+          await onStep(counter);
+        }
+        appendMolecule(molecules, core, rGroups, currents);
+        currents[position]++;
+        for (let i = 0; i < position; i++) {
+          currents[i] = 0;
+        }
+        position = 0;
+      } else {
+        position++;
+      }
+    }
+    if ((position = currents.length)) {
+      if (onStep) {
+        await onStep(counter);
+      }
+      appendMolecule(molecules, core, rGroups, currents);
+      break;
+    }
+  }
+  return Object.keys(molecules)
+    .map((key) => molecules[key])
+    .sort((m1, m2) => m1.mw - m2.mw);
+}
+
+function appendMolecule(molecules, core, rGroups, currents) {
+  let newSmiles = core.smiles;
+  for (let i = 0; i < currents.length; i++) {
+    newSmiles += `.${rGroups[i].smiles[currents[i]]}`;
+  }
+
+  const OCL = getOCL();
+
+  const currentMol = OCL.Molecule.fromSmiles(newSmiles);
+  const idCode = currentMol.getIDCode();
+
+  if (!molecules[idCode]) {
+    let molecule = {};
+    molecules[idCode] = molecule;
+    molecule.smiles = currentMol.toSmiles();
+    molecule.combinedSmiles = newSmiles;
+    molecule.idCode = idCode;
+    molecule.molfile = currentMol.toMolfile();
+
+    const props = new OCL.MoleculeProperties(currentMol);
+    molecule.nbHAcceptor = props.acceptorCount;
+    molecule.nbHDonor = props.donorCount;
+    molecule.logP = props.logP;
+    molecule.logS = props.logS;
+    molecule.PSA = props.polarSurfaceArea;
+    molecule.nbRottable = props.rotatableBondCount;
+    molecule.nbStereoCenter = props.stereoCenterCount;
+    let mf = currentMol.getMolecularFormula();
+    molecule.mf = mf.formula;
+    molecule.mw = mf.relativeWeight;
+  }
+}
+
+function getCore(coreSmiles) {
+  let core = {
+    originalSmiles: coreSmiles,
+    smiles: coreSmiles.replace(/\[R([1-4])\]/g, '%5$1'),
+  };
+
+  for (let i = 0; i < MAX_R; i++) {
+    if (core.originalSmiles.indexOf(`[R${i}]`) > -1) core[`R${i}`] = true;
+  }
+  return core;
+}
+
+function getRGroups(core, fragments) {
+  let rGroups = {};
+  for (const fragment of fragments) {
+    if (fragment.smiles) {
+      const smiles = updateRPosition(fragment.smiles);
+      for (let i = 0; i < MAX_R; i++) {
+        if (core[`R${i}`]) {
+          // we only consider the R that are in the core
+          if (fragment[`R${i}`]) {
+            if (!rGroups[`R${i}`]) {
+              rGroups[`R${i}`] = {
+                group: `R${i}`,
+                smiles: [],
+              };
+            }
+            rGroups[`R${i}`].smiles.push(smiles.replace(/\[R\]/, `(%5${i})`));
+          }
+        }
+      }
+    }
+  }
+  return Object.keys(rGroups).map((key) => rGroups[key]);
+}
+
+function updateRPosition(smiles) {
+  // R group should not be at the beginning
+  if (smiles.indexOf('[R]') !== 0) return smiles;
+  if (smiles.length === 3) return '[H][R]';
+  // we are in trouble ... we need to move the R
+  let newSmiles = smiles.replace('[R]', '');
+  // we need to check where we should put the R group
+  let level = 0;
+  for (let j = 0; j < newSmiles.length; j++) {
+    let currentChar = newSmiles.charAt(j);
+    let currentSubstring = newSmiles.substr(j);
+    if (currentChar === '(') {
+      level++;
+    } else if (currentChar === ')') {
+      level--;
+    } else if (level === 0) {
+      if (currentSubstring.match(/^[a-z]/)) {
+        return `${newSmiles.substr(0, j + 1)}([R])${newSmiles.substr(j + 1)}`;
+      } else if (currentSubstring.match(/^[A-Z][a-z]/)) {
+        return `${newSmiles.substr(0, j + 2)}([R])${newSmiles.substr(j + 2)}`;
+      } else if (currentSubstring.match(/^[A-Z]/)) {
+        return `${newSmiles.substr(0, j + 1)}([R])${newSmiles.substr(j + 1)}`;
+      }
+    }
+  }
+  return smiles;
+}
+
+/**
  * Returns various information about atoms in the molecule
@@ -917,2 +1085,3 @@ * @param {OCL.Molecule} [molecule]
 exports.addDiastereotopicMissingChirality = addDiastereotopicMissingChirality;
+exports.combineSmiles = combineSmiles;
 exports.getAtomsInfo = getAtomsInfo;
@@ -919,0 +1088,0 @@ exports.getConnectivityMatrix = getConnectivityMatrix;

package.json

 {
   "name": "openchemlib-utils",
-  "version": "0.6.0",
+  "version": "0.6.1",
   "description": "",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/index.js

@@ -11,2 +11,3 @@ export * from './diastereotopic/addDiastereotopicMissingChirality';
 
+export * from './util/combineSmiles';
 export * from './util/getAtomsInfo';
@@ -13,0 +14,0 @@ export * from './util/getConnectivityMatrix';

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

78499

increased by7.39%

Lines of code

2101

increased by8.02%

No dependency changes