openchemlib-utils - npm Package Compare versions

Comparing version 5.18.0 to 5.19.0

lib-esm/hose/getHoseCodesForAtomsInternal.js

@@ -30,4 +30,4 @@ import { isCsp3 } from '../util/isCsp3.js';
     let max = 0;
-    const atomMask = new Array(molecule.getAllAtoms());
-    const atomList = new Array(molecule.getAllAtoms());
+    const atomMask = new Uint8Array(molecule.getAllAtoms());
+    const atomList = new Uint8Array(molecule.getAllAtoms());
     for (let sphere = 0; sphere <= maxSphereSize; sphere++) {
@@ -34,0 +34,0 @@ if (max === 0) {

lib-esm/topic/TopicMolecule.d.ts

 import type { Molecule } from 'openchemlib';
+import { AtomPath } from '../path/getAllAtomsPaths.js';
 import { HoseCodesOptions } from './HoseCodesOptions.js';
@@ -6,2 +7,26 @@ interface ToMolfileOptions {
 }
+interface TopicMoleculeOptions extends HoseCodesOptions {
+    /**
+     * The maximum path length to consider when calculating the paths between atoms
+     * @default 5
+     */
+    maxPathLength?: number;
+}
+type TopicMoleculeInternalOptions = Omit<TopicMoleculeOptions, 'maxPathLength'> & Required<Pick<TopicMoleculeOptions, 'maxPathLength'>>;
+interface GetAtomPathOptions {
+    distance?: number;
+}
+interface GetHoseFragmentOptions {
+    sphereSize?: number;
+    /**
+     * The atoms to tag in the fragment
+     * @default rootAtoms
+     */
+    tagAtoms?: number[];
+    /**
+     * The function to tag the atoms in place !
+     * @default tagAtom
+     */
+    tagAtomFct?: (molecule: Molecule, iAtom: number) => undefined;
+}
 /**
@@ -15,6 +40,9 @@ * This class deals with topicity information and hose codes
     idCode: string;
-    options: HoseCodesOptions;
+    options: TopicMoleculeInternalOptions;
     private cache;
-    constructor(molecule: Molecule, options?: HoseCodesOptions);
+    constructor(molecule: Molecule, options?: TopicMoleculeOptions);
     ensureMapNo(): void;
+    getHoseFragment(rootAtoms: number[], options?: GetHoseFragmentOptions): Molecule;
+    getAtomPaths(atom1: number, atom2: number, options?: GetAtomPathOptions): number[][];
+    get atomsPaths(): AtomPath[][][];
     toMolfile(options?: ToMolfileOptions): string;
@@ -33,3 +61,3 @@ getMolecule(): Molecule;
      */
-    get moleculeWithH(): any;
+    get moleculeWithH(): Molecule;
     private get xMolecule();
@@ -72,3 +100,3 @@ /**
     get finalRanks(): any;
-    toMolfileWithH(options?: ToMolfileOptions): any;
+    toMolfileWithH(options?: ToMolfileOptions): string;
     /**
@@ -75,0 +103,0 @@ * Returns an array of objects containing the oclID and the corresponding hydrogens and atoms

lib-esm/topic/TopicMolecule.js

@@ -0,2 +1,4 @@
+import { getAllAtomsPaths } from '../path/getAllAtomsPaths.js';
 import { getConnectivityMatrix } from '../util/getConnectivityMatrix.js';
+import { tagAtom } from '../util/tagAtom.js';
 import { getCanonizedDiaIDs } from './getCanonizedDiaIDs';
@@ -15,3 +17,3 @@ import { getCanonizedHoseCodes } from './getCanonizedHoseCodes';
         this.originalMolecule = molecule;
-        this.options = options;
+        this.options = { maxPathLength: 5, ...options };
         this.idCode = molecule.getIDCode();
@@ -46,2 +48,77 @@ this.molecule = this.originalMolecule.getCompactCopy();
     }
+    getHoseFragment(rootAtoms, options = {}) {
+        const { sphereSize = 2, tagAtoms = rootAtoms, tagAtomFct = tagAtom, } = options;
+        this.moleculeWithH.ensureHelperArrays(this.moleculeWithH.getOCL().Molecule.cHelperNeighbours);
+        const copy = this.moleculeWithH.getCompactCopy();
+        copy.ensureHelperArrays(copy.getOCL().Molecule.cHelperNeighbours);
+        for (let i = 0; i < copy.getAllAtoms(); i++) {
+            copy.setAtomMass(i, copy.getAtomMass(i) + 2);
+        }
+        const atomMask = new Array(copy.getAllAtoms()).fill(false);
+        const atomList = new Uint8Array(copy.getAllAtoms());
+        const atomMapping = new Array(copy.getAllAtoms()).fill(-1);
+        const Molecule = copy.getOCL().Molecule;
+        const fragment = new Molecule(0, 0);
+        fragment.setFragment(true);
+        let min = 0;
+        let max = 0;
+        for (let sphere = 0; sphere <= sphereSize; sphere++) {
+            if (max === 0) {
+                for (const rootAtom of rootAtoms) {
+                    atomList[max] = rootAtom;
+                    atomMask[rootAtom] = 1;
+                    max++;
+                }
+            }
+            else {
+                let newMax = max;
+                for (let i = min; i < max; i++) {
+                    const atom = atomList[i];
+                    for (let j = 0; j < this.moleculeWithH.getAllConnAtoms(atom); j++) {
+                        const connAtom = this.moleculeWithH.getConnAtom(atom, j);
+                        if (!atomMask[connAtom]) {
+                            atomMask[connAtom] = 1;
+                            atomList[newMax++] = connAtom;
+                        }
+                    }
+                }
+                min = max;
+                max = newMax;
+            }
+        }
+        copy.copyMoleculeByAtoms(fragment, atomMask, true, atomMapping);
+        for (let i = 0; i < fragment.getAllAtoms(); i++) {
+            fragment.setAtomMass(i, fragment.getAtomMass(i) - 2);
+        }
+        for (const atom of tagAtoms) {
+            tagAtomFct(fragment, atomMapping[atom]);
+        }
+        return fragment;
+    }
+    getAtomPaths(atom1, atom2, options = {}) {
+        const { distance } = options;
+        if (distance !== undefined && distance > this.options.maxPathLength) {
+            throw new Error('The distance is too long, you should increase the maxPathLength when instanciating the TopicMolecule');
+        }
+        const atomPaths = this.atomsPaths[atom1];
+        const minDistance = distance || 0;
+        const maxDistance = distance || this.options.maxPathLength;
+        const paths = [];
+        for (let i = minDistance; i <= maxDistance; i++) {
+            for (const atomPath of atomPaths[i]) {
+                if (atomPath.path.at(-1) === atom2) {
+                    paths.push(atomPath.path);
+                }
+            }
+        }
+        return paths;
+    }
+    get atomsPaths() {
+        if (this.cache.atomsPaths)
+            return this.cache.atomsPaths;
+        this.cache.atomsPaths = getAllAtomsPaths(this.moleculeWithH, {
+            maxPathLength: this.options.maxPathLength,
+        });
+        return this.cache.atomsPaths;
+    }
     toMolfile(options = {}) {
@@ -48,0 +125,0 @@ const { version = 2 } = options;

lib/hose/getHoseCodesForAtomsInternal.js

@@ -33,4 +33,4 @@ "use strict";
     let max = 0;
-    const atomMask = new Array(molecule.getAllAtoms());
-    const atomList = new Array(molecule.getAllAtoms());
+    const atomMask = new Uint8Array(molecule.getAllAtoms());
+    const atomList = new Uint8Array(molecule.getAllAtoms());
     for (let sphere = 0; sphere <= maxSphereSize; sphere++) {
@@ -37,0 +37,0 @@ if (max === 0) {

lib/topic/TopicMolecule.d.ts

 import type { Molecule } from 'openchemlib';
+import { AtomPath } from '../path/getAllAtomsPaths.js';
 import { HoseCodesOptions } from './HoseCodesOptions.js';
@@ -6,2 +7,26 @@ interface ToMolfileOptions {
 }
+interface TopicMoleculeOptions extends HoseCodesOptions {
+    /**
+     * The maximum path length to consider when calculating the paths between atoms
+     * @default 5
+     */
+    maxPathLength?: number;
+}
+type TopicMoleculeInternalOptions = Omit<TopicMoleculeOptions, 'maxPathLength'> & Required<Pick<TopicMoleculeOptions, 'maxPathLength'>>;
+interface GetAtomPathOptions {
+    distance?: number;
+}
+interface GetHoseFragmentOptions {
+    sphereSize?: number;
+    /**
+     * The atoms to tag in the fragment
+     * @default rootAtoms
+     */
+    tagAtoms?: number[];
+    /**
+     * The function to tag the atoms in place !
+     * @default tagAtom
+     */
+    tagAtomFct?: (molecule: Molecule, iAtom: number) => undefined;
+}
 /**
@@ -15,6 +40,9 @@ * This class deals with topicity information and hose codes
     idCode: string;
-    options: HoseCodesOptions;
+    options: TopicMoleculeInternalOptions;
     private cache;
-    constructor(molecule: Molecule, options?: HoseCodesOptions);
+    constructor(molecule: Molecule, options?: TopicMoleculeOptions);
     ensureMapNo(): void;
+    getHoseFragment(rootAtoms: number[], options?: GetHoseFragmentOptions): Molecule;
+    getAtomPaths(atom1: number, atom2: number, options?: GetAtomPathOptions): number[][];
+    get atomsPaths(): AtomPath[][][];
     toMolfile(options?: ToMolfileOptions): string;
@@ -33,3 +61,3 @@ getMolecule(): Molecule;
      */
-    get moleculeWithH(): any;
+    get moleculeWithH(): Molecule;
     private get xMolecule();
@@ -72,3 +100,3 @@ /**
     get finalRanks(): any;
-    toMolfileWithH(options?: ToMolfileOptions): any;
+    toMolfileWithH(options?: ToMolfileOptions): string;
     /**
@@ -75,0 +103,0 @@ * Returns an array of objects containing the oclID and the corresponding hydrogens and atoms

lib/topic/TopicMolecule.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.groupDiastereotopicAtomIDs = exports.TopicMolecule = void 0;
+const getAllAtomsPaths_js_1 = require("../path/getAllAtomsPaths.js");
 const getConnectivityMatrix_js_1 = require("../util/getConnectivityMatrix.js");
+const tagAtom_js_1 = require("../util/tagAtom.js");
 const getCanonizedDiaIDs_1 = require("./getCanonizedDiaIDs");
@@ -18,3 +20,3 @@ const getCanonizedHoseCodes_1 = require("./getCanonizedHoseCodes");
         this.originalMolecule = molecule;
-        this.options = options;
+        this.options = { maxPathLength: 5, ...options };
         this.idCode = molecule.getIDCode();
@@ -49,2 +51,77 @@ this.molecule = this.originalMolecule.getCompactCopy();
     }
+    getHoseFragment(rootAtoms, options = {}) {
+        const { sphereSize = 2, tagAtoms = rootAtoms, tagAtomFct = tagAtom_js_1.tagAtom, } = options;
+        this.moleculeWithH.ensureHelperArrays(this.moleculeWithH.getOCL().Molecule.cHelperNeighbours);
+        const copy = this.moleculeWithH.getCompactCopy();
+        copy.ensureHelperArrays(copy.getOCL().Molecule.cHelperNeighbours);
+        for (let i = 0; i < copy.getAllAtoms(); i++) {
+            copy.setAtomMass(i, copy.getAtomMass(i) + 2);
+        }
+        const atomMask = new Array(copy.getAllAtoms()).fill(false);
+        const atomList = new Uint8Array(copy.getAllAtoms());
+        const atomMapping = new Array(copy.getAllAtoms()).fill(-1);
+        const Molecule = copy.getOCL().Molecule;
+        const fragment = new Molecule(0, 0);
+        fragment.setFragment(true);
+        let min = 0;
+        let max = 0;
+        for (let sphere = 0; sphere <= sphereSize; sphere++) {
+            if (max === 0) {
+                for (const rootAtom of rootAtoms) {
+                    atomList[max] = rootAtom;
+                    atomMask[rootAtom] = 1;
+                    max++;
+                }
+            }
+            else {
+                let newMax = max;
+                for (let i = min; i < max; i++) {
+                    const atom = atomList[i];
+                    for (let j = 0; j < this.moleculeWithH.getAllConnAtoms(atom); j++) {
+                        const connAtom = this.moleculeWithH.getConnAtom(atom, j);
+                        if (!atomMask[connAtom]) {
+                            atomMask[connAtom] = 1;
+                            atomList[newMax++] = connAtom;
+                        }
+                    }
+                }
+                min = max;
+                max = newMax;
+            }
+        }
+        copy.copyMoleculeByAtoms(fragment, atomMask, true, atomMapping);
+        for (let i = 0; i < fragment.getAllAtoms(); i++) {
+            fragment.setAtomMass(i, fragment.getAtomMass(i) - 2);
+        }
+        for (const atom of tagAtoms) {
+            tagAtomFct(fragment, atomMapping[atom]);
+        }
+        return fragment;
+    }
+    getAtomPaths(atom1, atom2, options = {}) {
+        const { distance } = options;
+        if (distance !== undefined && distance > this.options.maxPathLength) {
+            throw new Error('The distance is too long, you should increase the maxPathLength when instanciating the TopicMolecule');
+        }
+        const atomPaths = this.atomsPaths[atom1];
+        const minDistance = distance || 0;
+        const maxDistance = distance || this.options.maxPathLength;
+        const paths = [];
+        for (let i = minDistance; i <= maxDistance; i++) {
+            for (const atomPath of atomPaths[i]) {
+                if (atomPath.path.at(-1) === atom2) {
+                    paths.push(atomPath.path);
+                }
+            }
+        }
+        return paths;
+    }
+    get atomsPaths() {
+        if (this.cache.atomsPaths)
+            return this.cache.atomsPaths;
+        this.cache.atomsPaths = (0, getAllAtomsPaths_js_1.getAllAtomsPaths)(this.moleculeWithH, {
+            maxPathLength: this.options.maxPathLength,
+        });
+        return this.cache.atomsPaths;
+    }
     toMolfile(options = {}) {
@@ -51,0 +128,0 @@ const { version = 2 } = options;

package.json

 {
   "name": "openchemlib-utils",
-  "version": "5.18.0",
+  "version": "5.19.0",
   "description": "Various utilities that extends openchemlib-js like HOSE codes or diastereotopic IDs",
@@ -43,19 +43,19 @@ "main": "./lib/index.js",
   "devDependencies": {
-    "@types/node": "^20.12.6",
-    "@vitest/coverage-v8": "^1.4.0",
+    "@types/node": "^20.12.11",
+    "@vitest/coverage-v8": "^1.6.0",
     "cheminfo-build": "^1.2.0",
     "cheminfo-types": "^1.7.3",
     "eslint": "^8.57.0",
-    "eslint-config-cheminfo-typescript": "^12.2.0",
+    "eslint-config-cheminfo-typescript": "^12.4.0",
     "fifo-logger": "^1.0.0",
-    "mf-parser": "^3.1.0",
+    "mf-parser": "^3.1.1",
     "openchemlib": "^8.9.0",
     "prettier": "^3.2.5",
-    "rimraf": "^5.0.5",
+    "rimraf": "^5.0.7",
     "ts-node": "^10.9.2",
-    "typescript": "^5.4.4",
-    "vitest": "^1.4.0"
+    "typescript": "^5.4.5",
+    "vitest": "^1.6.0"
   },
   "dependencies": {
-    "atom-sorter": "^2.0.0",
+    "atom-sorter": "^2.0.1",
     "ensure-string": "^1.2.0",
@@ -62,0 +62,0 @@ "get-value": "^3.0.1",

src/hose/getHoseCodesForAtomsInternal.js

@@ -42,4 +42,4 @@ import { isCsp3 } from '../util/isCsp3.js';
   let max = 0;
-  const atomMask = new Array(molecule.getAllAtoms());
-  const atomList = new Array(molecule.getAllAtoms());
+  const atomMask = new Uint8Array(molecule.getAllAtoms());
+  const atomList = new Uint8Array(molecule.getAllAtoms());
 
@@ -46,0 +46,0 @@ for (let sphere = 0; sphere <= maxSphereSize; sphere++) {

src/topic/TopicMolecule.ts

 import type { Molecule } from 'openchemlib';
 
+import { AtomPath, getAllAtomsPaths } from '../path/getAllAtomsPaths.js';
 import { getConnectivityMatrix } from '../util/getConnectivityMatrix.js';
+import { tagAtom } from '../util/tagAtom.js';
 
@@ -20,2 +22,40 @@ import { HoseCodesOptions } from './HoseCodesOptions.js';
 
+interface TopicMoleculeOptions extends HoseCodesOptions {
+  /**
+   * The maximum path length to consider when calculating the paths between atoms
+   * @default 5
+   */
+  maxPathLength?: number;
+}
+
+type TopicMoleculeInternalOptions = Omit<
+  TopicMoleculeOptions,
+  'maxPathLength'
+> &
+  Required<Pick<TopicMoleculeOptions, 'maxPathLength'>>;
+
+interface GetAtomPathOptions {
+  /*
+   * The distance between the two atoms. If not specified, all the distances will be considered
+   */
+  distance?: number;
+}
+
+interface GetHoseFragmentOptions {
+  /*
+   * The sphere size around any selected atoms to consider. Default is 2
+   */
+  sphereSize?: number;
+  /**
+   * The atoms to tag in the fragment
+   * @default rootAtoms
+   */
+  tagAtoms?: number[];
+  /**
+   * The function to tag the atoms in place !
+   * @default tagAtom
+   */
+  tagAtomFct?: (molecule: Molecule, iAtom: number) => undefined;
+}
+
 /**
@@ -29,9 +69,9 @@ * This class deals with topicity information and hose codes
   idCode: string;
-  options: HoseCodesOptions;
+  options: TopicMoleculeInternalOptions;
 
   private cache: any;
 
-  constructor(molecule: Molecule, options: HoseCodesOptions = {}) {
+  constructor(molecule: Molecule, options: TopicMoleculeOptions = {}) {
     this.originalMolecule = molecule;
-    this.options = options;
+    this.options = { maxPathLength: 5, ...options };
     this.idCode = molecule.getIDCode();
@@ -74,3 +114,95 @@ this.molecule = this.originalMolecule.getCompactCopy();
 
-  toMolfile(options: ToMolfileOptions = {}) {
+  getHoseFragment(
+    rootAtoms: number[],
+    options: GetHoseFragmentOptions = {},
+  ): Molecule {
+    const {
+      sphereSize = 2,
+      tagAtoms = rootAtoms,
+      tagAtomFct = tagAtom,
+    } = options;
+    this.moleculeWithH.ensureHelperArrays(
+      this.moleculeWithH.getOCL().Molecule.cHelperNeighbours,
+    );
+
+    const copy = this.moleculeWithH.getCompactCopy();
+    copy.ensureHelperArrays(copy.getOCL().Molecule.cHelperNeighbours);
+
+    for (let i = 0; i < copy.getAllAtoms(); i++) {
+      copy.setAtomMass(i, copy.getAtomMass(i) + 2);
+    }
+
+    const atomMask = new Array(copy.getAllAtoms()).fill(false);
+    const atomList = new Uint8Array(copy.getAllAtoms());
+    const atomMapping = new Array(copy.getAllAtoms()).fill(-1);
+    const Molecule = copy.getOCL().Molecule;
+    const fragment = new Molecule(0, 0);
+    fragment.setFragment(true);
+    let min = 0;
+    let max = 0;
+    for (let sphere = 0; sphere <= sphereSize; sphere++) {
+      if (max === 0) {
+        for (const rootAtom of rootAtoms) {
+          atomList[max] = rootAtom;
+          atomMask[rootAtom] = 1;
+          max++;
+        }
+      } else {
+        let newMax = max;
+        for (let i = min; i < max; i++) {
+          const atom = atomList[i];
+          for (let j = 0; j < this.moleculeWithH.getAllConnAtoms(atom); j++) {
+            const connAtom = this.moleculeWithH.getConnAtom(atom, j);
+            if (!atomMask[connAtom]) {
+              atomMask[connAtom] = 1;
+              atomList[newMax++] = connAtom;
+            }
+          }
+        }
+        min = max;
+        max = newMax;
+      }
+    }
+    copy.copyMoleculeByAtoms(fragment, atomMask, true, atomMapping);
+    for (let i = 0; i < fragment.getAllAtoms(); i++) {
+      fragment.setAtomMass(i, fragment.getAtomMass(i) - 2);
+    }
+
+    for (const atom of tagAtoms) {
+      tagAtomFct(fragment, atomMapping[atom]);
+    }
+
+    return fragment;
+  }
+
+  getAtomPaths(atom1: number, atom2: number, options: GetAtomPathOptions = {}) {
+    const { distance } = options;
+    if (distance !== undefined && distance > this.options.maxPathLength) {
+      throw new Error(
+        'The distance is too long, you should increase the maxPathLength when instanciating the TopicMolecule',
+      );
+    }
+    const atomPaths = this.atomsPaths[atom1];
+    const minDistance = distance || 0;
+    const maxDistance = distance || this.options.maxPathLength;
+    const paths = [];
+    for (let i = minDistance; i <= maxDistance; i++) {
+      for (const atomPath of atomPaths[i]) {
+        if (atomPath.path.at(-1) === atom2) {
+          paths.push(atomPath.path);
+        }
+      }
+    }
+    return paths;
+  }
+
+  get atomsPaths(): AtomPath[][][] {
+    if (this.cache.atomsPaths) return this.cache.atomsPaths;
+    this.cache.atomsPaths = getAllAtomsPaths(this.moleculeWithH, {
+      maxPathLength: this.options.maxPathLength,
+    });
+    return this.cache.atomsPaths;
+  }
+
+  toMolfile(options: ToMolfileOptions = {}): string {
     const { version = 2 } = options;
@@ -111,3 +243,3 @@ if (version === 2) {
    */
-  get moleculeWithH() {
+  get moleculeWithH(): Molecule {
     if (this.cache.moleculeWithH) return this.cache.moleculeWithH;
@@ -118,3 +250,3 @@ this.cache.moleculeWithH = getMoleculeWithH(this.molecule);
 
-  private get xMolecule() {
+  private get xMolecule(): Molecule {
     if (this.cache.xMolecule) return this.cache.xMolecule;
@@ -121,0 +253,0 @@ this.cache.xMolecule = getXMolecule(this.moleculeWithH);

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

1128843

increased by2.92%

Number of package files

828

increased by1.1%

Lines of code

16996

increased by3.21%

Dependency changes

• Updatedatom-sorter@^2.0.1