update: fix bonds

Author: VsevolodX

dist/components/ThreeDEditor.d.ts

@@ -233,7 +233,7 @@ export namespace ThreeDEditor {
     namespace propTypes {
         let material: PropTypes.Validator<NonNullable<{
             _json: import("@mat3ra/made/dist/js/material").MaterialSchemaJSON;
-            toJSON(): import("@mat3ra/made/dist/js/types/material").MaterialJSON;
+            toJSON(): import("@mat3ra/made/dist/js/types").MaterialJSON;
             src: import("@mat3ra/esse/dist/js/types").FileSourceSchema | undefined;
             updateFormula(): void;
             isNonPeriodic: boolean;

dist/mixins/bonds.js

@@ -36,6 +36,7 @@ export const BondsMixin = (superclass) => class extends superclass {
      * @param bondsData {Array} an array of bond data entries for unique element pairs inside structure.
      * @returns {Boolean}
      */
+    // TODO: move to made basis bonded
     areElementsBonded(element1, coordinate1, element2, coordinate2, bondsData) {
         const distance = Made.math.vDist(coordinate1, coordinate2);
         const connectivityFactor = this.settings.chemicalConnectivityFactor;
@@ -50,6 +51,7 @@ export const BondsMixin = (superclass) => class extends superclass {
      * combinations as it is required to repeat the cell in all directions to determine the bonds.
      * @returns {Array} an array of bond data entries for unique element pairs inside structure.
      */
+    // TODO: move to made basis bonded
     getBondsDataForUniqueElementPairs() {
         const bonds = [];
         const { uniqueElements } = this.basis;
@@ -67,6 +69,7 @@ export const BondsMixin = (superclass) => class extends superclass {
      * @param bondsData {Array} an array of bond data entries for unique element pairs inside structure.
      * @returns {Number}
      */
+    // TODO: move to made basis bonded
     getMaxBondLength(bondsData) {
         const connectivityFactor = this.settings.chemicalConnectivityFactor;
         return (connectivityFactor *
@@ -80,14 +83,15 @@ export const BondsMixin = (superclass) => class extends superclass {
      * @param maxBondLength {Number}
      * @return {Array}
      */
+    // TODO: move to made basis bonded
     getElementsAndCoordinatesArrayWithEdgeNeighbors(maxBondLength) {
         const newBasis = this.basis.clone();
         const basisCloneInCrystalCoordinates = this.basis.clone();
         newBasis.toCrystal();
         basisCloneInCrystalCoordinates.toCrystal();
         const planes = this.getCellPlanes(this.cell);
         basisCloneInCrystalCoordinates.elements.forEach((element, index) => {
-            const coord = basisCloneInCrystalCoordinates.getCoordinateByIndex(index).value;
+            const coord = basisCloneInCrystalCoordinates.getCoordinateValueByIndex(index);
             if (planes.find((plane) => plane.distanceToPoint(new THREE.Vector3(...coord)) <= maxBondLength)) {
                 [-1, 0, 1].forEach((shiftI) => {
                     [-1, 0, 1].forEach((shiftJ) => {
@@ -115,6 +119,7 @@ export const BondsMixin = (superclass) => class extends superclass {
      * k-d tree algorithm is used to optimize the time to find the element's neighbors.
      * See https://en.wikipedia.org/wiki/K-d_tree for more information.
      */
+    // TODO: move to made basis bonded - refactor to return bonds array and use the array in createBondsGroup
     createBondsGroup() {
         const bondsGroup = new THREE.Group();
         const bondsData = this.getBondsDataForUniqueElementPairs();

dist/mixins/boundary.js

@@ -82,7 +82,7 @@ export const BoundaryMixin = (superclass) => class extends superclass {
         newBasis.toCrystal();
         basisCloneInCrystalCoordinates.toCrystal();
         basisCloneInCrystalCoordinates.elements.forEach((element, index) => {
-            const coord = basisCloneInCrystalCoordinates.getCoordinateByIndex(index);
+            const coord = basisCloneInCrystalCoordinates.getCoordinateValueByIndex(index);
             newBasis.addAtom({
                 element,
                 coordinate: [

dist/mixins/cell.js

@@ -25,6 +25,7 @@ export const CellMixin = (superclass) => class extends superclass {
      * @param cell {Object} unitCell class instance.
      * @param zMultiplier {Number} specifies a multiplier to adjust the z coordinates of the cell vertices with.
      */
+    // TODO: move to made.unit_cell
     // eslint-disable-next-line class-methods-use-this
     getCellVertices(cell, zMultiplier = 1) {
         return [

dist/utils.d.ts

@@ -5,7 +5,7 @@
  */
 export function ThreeDSceneDataToMaterial(scene: any): {
     _json: import("@mat3ra/made/dist/js/material").MaterialSchemaJSON;
-    toJSON(): import("@mat3ra/made/dist/js/types/material").MaterialJSON;
+    toJSON(): import("@mat3ra/made/dist/js/types").MaterialJSON;
     src: import("@mat3ra/esse/dist/js/types").FileSourceSchema | undefined;
     updateFormula(): void;
     isNonPeriodic: boolean;

package-lock.json

@@ -64,7 +64,7 @@
         "@exabyte-io/eslint-config": "^2025.1.15-0",
         "@mat3ra/code": "2025.4.27-0",
         "@mat3ra/esse": "2025.4.22-0",
-        "@mat3ra/made": "2025.4.25-0",
+        "@mat3ra/made": "git+https://github.com/Exabyte-io/made.git#cf284620644e9c1840ee381ae73c4a19e5a3fc15",
         "@mat3ra/tsconfig": "^2024.6.3-0",
         "@types/react": "^18.2.8",
         "@types/react-dom": "^18.2.4",

package.json

@@ -49,6 +49,7 @@ export const BondsMixin = (superclass: any) =>
          * @param bondsData {Array} an array of bond data entries for unique element pairs inside structure.
          * @returns {Boolean}
          */
+        // TODO: move to made basis bonded
         areElementsBonded(
             element1: string,
             coordinate1: number[],
@@ -76,6 +77,7 @@ export const BondsMixin = (superclass: any) =>
          * combinations as it is required to repeat the cell in all directions to determine the bonds.
          * @returns {Array} an array of bond data entries for unique element pairs inside structure.
          */
+        // TODO: move to made basis bonded
         getBondsDataForUniqueElementPairs(): BondDataInterface[] {
             const bonds: BondDataInterface[] = [];
             const { uniqueElements } = this.basis;
@@ -94,6 +96,7 @@ export const BondsMixin = (superclass: any) =>
          * @param bondsData {Array} an array of bond data entries for unique element pairs inside structure.
          * @returns {Number}
          */
+        // TODO: move to made basis bonded
         getMaxBondLength(bondsData: BondDataInterface[]): number {
             const connectivityFactor = this.settings.chemicalConnectivityFactor;
             return (
@@ -110,6 +113,7 @@ export const BondsMixin = (superclass: any) =>
          * @param maxBondLength {Number}
          * @return {Array}
          */
+        // TODO: move to made basis bonded
         getElementsAndCoordinatesArrayWithEdgeNeighbors(
             maxBondLength: number,
         ): ElementAndCoordinateAsArray[] {
@@ -123,7 +127,7 @@ export const BondsMixin = (superclass: any) =>
 
             basisCloneInCrystalCoordinates.elements.forEach(
                 (element: AtomicElementSchema, index: number) => {
-                    const coord = basisCloneInCrystalCoordinates.getCoordinateByIndex(index).value;
+                    const coord = basisCloneInCrystalCoordinates.getCoordinateValueByIndex(index);
                     if (
                         planes.find(
                             (plane: THREE.Plane) =>
@@ -158,6 +162,7 @@ export const BondsMixin = (superclass: any) =>
          * k-d tree algorithm is used to optimize the time to find the element's neighbors.
          * See https://en.wikipedia.org/wiki/K-d_tree for more information.
          */
+        // TODO: move to made basis bonded - refactor to return bonds array and use the array in createBondsGroup
         createBondsGroup(): THREE.Group {
             const bondsGroup = new THREE.Group();
             const bondsData = this.getBondsDataForUniqueElementPairs();

src/mixins/bonds.ts

@@ -113,7 +113,7 @@ export const BoundaryMixin = (superclass) =>
             basisCloneInCrystalCoordinates.toCrystal();
 
             basisCloneInCrystalCoordinates.elements.forEach((element, index) => {
-                const coord = basisCloneInCrystalCoordinates.getCoordinateByIndex(index);
+                const coord = basisCloneInCrystalCoordinates.getCoordinateValueByIndex(index);
                 newBasis.addAtom({
                     element,
                     coordinate: [

src/mixins/boundary.js

@@ -56,6 +56,7 @@ export const CellMixin = (superclass: any) =>
          * @param cell {Object} unitCell class instance.
          * @param zMultiplier {Number} specifies a multiplier to adjust the z coordinates of the cell vertices with.
          */
+        // TODO: move to made.unit_cell
         // eslint-disable-next-line class-methods-use-this
         getCellVertices(cell: UnitCell, zMultiplier = 1) {
             return [