SOF-7010: implement class method to strip label and return atomic symbol

.husky/post-checkout

@@ -1,3 +1,3 @@
 #!/bin/sh
-command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting the 'post-checkout' file in the hooks directory (set by 'core.hookspath'; usually '.git/hooks').\n"; exit 2; }
+command -v git-lfs >/dev/null 2>&1 || { printf >&2 "\n%s\n\n" "This repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting the 'post-checkout' file in the hooks directory (set by 'core.hookspath'; usually '.git/hooks')."; exit 2; }
 git lfs post-checkout "$@"

.husky/post-commit

@@ -1,3 +1,3 @@
 #!/bin/sh
-command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting the 'post-commit' file in the hooks directory (set by 'core.hookspath'; usually '.git/hooks').\n"; exit 2; }
+command -v git-lfs >/dev/null 2>&1 || { printf >&2 "\n%s\n\n" "This repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting the 'post-commit' file in the hooks directory (set by 'core.hookspath'; usually '.git/hooks')."; exit 2; }
 git lfs post-commit "$@"

.husky/post-merge

@@ -1,3 +1,3 @@
 #!/bin/sh
-command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting the 'post-merge' file in the hooks directory (set by 'core.hookspath'; usually '.git/hooks').\n"; exit 2; }
+command -v git-lfs >/dev/null 2>&1 || { printf >&2 "\n%s\n\n" "This repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting the 'post-merge' file in the hooks directory (set by 'core.hookspath'; usually '.git/hooks')."; exit 2; }
 git lfs post-merge "$@"

.husky/pre-push

@@ -1,3 +1,3 @@
 #!/bin/sh
-command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting the 'pre-push' file in the hooks directory (set by 'core.hookspath'; usually '.git/hooks').\n"; exit 2; }
+command -v git-lfs >/dev/null 2>&1 || { printf >&2 "\n%s\n\n" "This repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting the 'pre-push' file in the hooks directory (set by 'core.hookspath'; usually '.git/hooks')."; exit 2; }
 git lfs pre-push "$@"

dist/js/basis/basis.d.ts

@@ -127,6 +127,15 @@ export declare class Basis extends InMemoryEntity implements BasisSchema {
     get hashString(): string;
     get atomicLabelsArray(): string[];
     get elementsWithLabelsArray(): string[];
+    /**
+     * Strips any label associated with atomic symbol
+     * Possible labels:
+     *   (1) Fe1, Fe11
+     *   (2) Fe-a, Fe-b, Fe-1, Fe-1a
+     *   (3) Fe_a, Fe_b, Fe_1, Fe_1a
+     * As of Mar 2025, only single digit numerical labels are allowed
+     */
+    static stripLabelToGetElementSymbol: (elementWithLabel: string) => string;
     /**
      * Returns an array of strings with chemical elements and their atomic positions.
      * E.g., ``` ['Si 0 0 0', 'Li 0.5 0.5 0.5']```

dist/js/basis/basis.js

@@ -290,11 +290,9 @@ class Basis extends entity_1.InMemoryEntity {
         const clsInstance = this.clone();
         clsInstance.toStandardRepresentation();
         const standardRep = clsInstance.elementsAndCoordinatesAndLabelsArray.map((entry) => {
-            const element = entry[0];
-            const coordinate = entry[1];
-            const atomicLabel = entry[2];
-            const toleratedCoordinate = coordinate.map((x) => math_1.default.round(x, constants_1.HASH_TOLERANCE));
-            return `${element}${atomicLabel} ${toleratedCoordinate.join()}`;
+            const [element, coordinate, atomicLabel] = entry;
+            const toleratedCoordinates = coordinate.map((x) => math_1.default.round(x, constants_1.HASH_TOLERANCE));
+            return `${element}${atomicLabel} ${toleratedCoordinates.join()}`;
         });
         return `${standardRep.sort().join(";")};`;
     }
@@ -336,10 +334,8 @@ class Basis extends entity_1.InMemoryEntity {
      * E.g., ``` ['Si 0 0 0', 'Li 0.5 0.5 0.5']```
      */
     get atomicPositions() {
-        return this.elementsAndCoordinatesAndLabelsArray.map((entry, idx) => {
-            const element = entry[0];
-            const coordinate = entry[1];
-            const atomicLabel = this.atomicLabelsArray[idx];
+        return this.elementsAndCoordinatesAndLabelsArray.map((entry) => {
+            const [element, coordinate, atomicLabel] = entry;
             return `${element}${atomicLabel} ${coordinate}`;
         });
     }
@@ -478,3 +474,22 @@ class Basis extends entity_1.InMemoryEntity {
 }
 exports.Basis = Basis;
 Basis.defaultConfig = DEFAULT_BASIS_CONFIG;
+/**
+ * Strips any label associated with atomic symbol
+ * Possible labels:
+ *   (1) Fe1, Fe11
+ *   (2) Fe-a, Fe-b, Fe-1, Fe-1a
+ *   (3) Fe_a, Fe_b, Fe_1, Fe_1a
+ * As of Mar 2025, only single digit numerical labels are allowed
+ */
+Basis.stripLabelToGetElementSymbol = (elementWithLabel) => {
+    // Strip anything after `-` or `_`
+    let elementSymbol = elementWithLabel.split(/[- _]/)[0];
+    // Exclude digit labels at the end of the symbol if present
+    elementSymbol = elementSymbol.replace(/\d+$/, "");
+    // Return symbol in title case
+    elementSymbol =
+        elementSymbol.charAt(0).toUpperCase() + elementSymbol.slice(1).toLowerCase();
+    // We can improve by validating element symbol matches one from the periodic table
+    return elementSymbol;
+};

dist/js/lattice/lattice_bravais.js

@@ -1,7 +1,9 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
+var __importDefault =
+    (this && this.__importDefault) ||
+    function (mod) {
+        return mod && mod.__esModule ? mod : { default: mod };
+    };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.LatticeBravais = void 0;
 const constants_1 = __importDefault(require("../constants"));
@@ -16,14 +18,24 @@ class LatticeBravais {
      * Create a Bravais lattice.
      */
     constructor(config) {
-        const { a = 1, // default lattice is cubic with unity in edge sizes
-        b = a, c = a, alpha = 90, beta = alpha, gamma = alpha, 
-        // if we do not know what lattice type this is => set to TRI
-        type = "TRI", units = {
-            length: "angstrom",
-            angle: "degree",
-        }, } = config;
-        const k = constants_1.default.units.bohr === units.length ? constants_1.default.coefficients.BOHR_TO_ANGSTROM : 1;
+        const {
+            a = 1, // default lattice is cubic with unity in edge sizes
+            b = a,
+            c = a,
+            alpha = 90,
+            beta = alpha,
+            gamma = alpha,
+            // if we do not know what lattice type this is => set to TRI
+            type = "TRI",
+            units = {
+                length: "angstrom",
+                angle: "degree",
+            },
+        } = config;
+        const k =
+            constants_1.default.units.bohr === units.length
+                ? constants_1.default.coefficients.BOHR_TO_ANGSTROM
+                : 1;
         this.a = a * k;
         this.b = b * k;
         this.c = c * k;
@@ -39,7 +51,15 @@ class LatticeBravais {
     /**
      * Create a Bravais lattice from vectors.
      */
-    static fromVectors({ a, b, c, alat = 1, units = "angstrom", type = "TRI", skipRounding = false, }) {
+    static fromVectors({
+        a,
+        b,
+        c,
+        alat = 1,
+        units = "angstrom",
+        type = "TRI",
+        skipRounding = false,
+    }) {
         const roundValue = skipRounding ? (x) => x : this._roundValue;
         const config = {
             a: roundValue(math_1.default.vlen(a) * alat),
@@ -77,7 +97,11 @@ class LatticeBravais {
     get editables() {
         var _a;
         const object = {};
-        const editablesList = (_a = types_1.LATTICE_TYPE_CONFIGS.find((entry) => entry.code === this.type)) === null || _a === void 0 ? void 0 : _a.editables;
+        const editablesList =
+            (_a = types_1.LATTICE_TYPE_CONFIGS.find((entry) => entry.code === this.type)) ===
+                null || _a === void 0
+                ? void 0
+                : _a.editables;
         // ["a", "gamma"] => {a: true, gamma: true}
         if (editablesList) {
             editablesList.forEach((element) => {