@chemistry/crystalview 1.0.9 → 3.0.0

package/dist/crystal-view.js

@@ -0,0 +1,169 @@
+import { Camera } from './camera/Camera.js';
+import { Molecule3D } from './molecule3d/Molecule3D.js';
+import { Painter } from './painter/Painter.js';
+import { ContextMenu } from './ui/ContextMenu.js';
+import { ContextMenuItem } from './ui/ContextMenuItem.js';
+export class Mol3DView {
+    constructor(options) {
+        this.options = {
+            bgcolor: options.bgcolor ?? '#2b303b',
+            showLabels: false,
+            showMarkers: true,
+            showUnitCell: false,
+        };
+        this.initDone = false;
+        this.subscriptions = [];
+        this.molecule = new Molecule3D();
+    }
+    append(element) {
+        if (this.viewElement || this.initDone) {
+            throw new Error('append or init were alredy done');
+        }
+        const viewEl = document.createElement('div');
+        viewEl.className = 'jcmolview';
+        const canvas = document.createElement('canvas');
+        viewEl.appendChild(canvas);
+        viewEl.style.backgroundColor = this.options.bgcolor;
+        viewEl.style.display = 'block';
+        viewEl.style.height = '100%';
+        viewEl.style.position = 'absolute';
+        viewEl.style.width = '100%';
+        canvas.style.display = 'block';
+        element.appendChild(viewEl);
+        this.viewElement = viewEl;
+        this.canvasElement = canvas;
+        this.context = this.canvasElement.getContext('2d');
+        this.painer = new Painter(this.context, this.options);
+        this.camera = new Camera({
+            element: this.canvasElement,
+            onClick: (x, y) => {
+                if (!this.options.showMarkers) {
+                    return;
+                }
+                const marker = this.painer.uprojectToMarker({
+                    camera: this.camera,
+                    molecule: this.molecule,
+                    x,
+                    y,
+                });
+                if (marker) {
+                    this.molecule.extendByMarker(marker);
+                    this.redraw();
+                }
+            },
+            onRedraw: () => {
+                this.redraw();
+            },
+        });
+        this.contextMenu = new ContextMenu([
+            new ContextMenuItem({
+                command: () => {
+                    this.center();
+                },
+                title: 'Center Molecule',
+                type: 'item',
+            }),
+            new ContextMenuItem({
+                title: '----',
+                type: 'delimer',
+            }),
+            new ContextMenuItem({
+                command: () => {
+                    this.options.showMarkers = !this.options.showMarkers;
+                    this.redraw();
+                },
+                isChecked: () => {
+                    return this.options.showMarkers;
+                },
+                title: 'Show Markers',
+                type: 'checkbox',
+            }),
+            new ContextMenuItem({
+                command: () => {
+                    this.options.showUnitCell = !this.options.showUnitCell;
+                    this.redraw();
+                },
+                isChecked: () => {
+                    return this.options.showUnitCell;
+                },
+                title: 'Show Unit Cell',
+                type: 'checkbox',
+            }),
+            new ContextMenuItem({
+                command: () => {
+                    this.options.showLabels = !this.options.showLabels;
+                    this.redraw();
+                },
+                isChecked: () => {
+                    return this.options.showLabels;
+                },
+                title: 'Show Labels',
+                type: 'checkbox',
+            }),
+        ]);
+    }
+    load(jcif) {
+        this.molecule.clear();
+        this.molecule.load(jcif);
+        this.center();
+    }
+    center() {
+        // Center the molecule
+        if (this.molecule?.atoms?.length > 2) {
+            const center = this.molecule.getCenter();
+            const scale = Math.min(this.viewElement.clientWidth - 10, this.viewElement.clientHeight - 10) /
+                this.molecule.getRadius();
+            this.camera.setCameraView(scale / 2, center);
+            this.redraw();
+        }
+        this.redraw();
+    }
+    onInit() {
+        if (!this.viewElement) {
+            throw new Error('append has to be called first');
+        }
+        if (this.initDone) {
+            throw new Error('Init has to be called once');
+        }
+        this.camera.onInit();
+        const event = () => {
+            this.resizeCanvas();
+        };
+        window.addEventListener('resize', event);
+        // save subscription
+        this.subscriptions.push(() => {
+            window.removeEventListener('resize', event);
+        });
+        setTimeout(() => {
+            this.resizeCanvas();
+        }, 0);
+        this.contextMenu.onInit(this.viewElement);
+        this.initDone = true;
+    }
+    onDestroy() {
+        this.camera.onDestroy();
+        this.subscriptions.forEach((fn) => {
+            fn();
+        });
+    }
+    redraw() {
+        if (!this.height || !this.width) {
+            return;
+        }
+        this.painer.draw(this.molecule, this.camera);
+    }
+    resizeCanvas() {
+        const width = this.viewElement.clientWidth;
+        const height = this.viewElement.clientHeight;
+        // Same width alredy seted
+        if (width === this.width && height === this.height) {
+            return;
+        }
+        this.width = width;
+        this.height = height;
+        this.canvasElement.width = this.width;
+        this.canvasElement.height = this.height;
+        this.redraw();
+    }
+}
+//# sourceMappingURL=crystal-view.js.map

package/dist/crystal-view.js.map

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package/dist/crystalview.css

@@ -0,0 +1,47 @@
+.jcmolview-dropdown-menu {
+  top: 100%;
+  left: 0;
+  z-index: 1000;
+  display: none;
+  float: left;
+  min-width: 10rem;
+  padding: 0.5rem 0;
+  margin: 0.125rem 0 0;
+  font-size: 1rem;
+  color: #292b2c;
+  text-align: left;
+  list-style: none;
+  background-color: #fff;
+  background-clip: padding-box;
+  border: 1px solid rgba(0, 0, 0, 0.15);
+  border-radius: 0.25rem;
+}
+
+.jcmolview-dropdown-item {
+  box-sizing: border-box;
+  display: block;
+  text-decoration: none;
+  width: 100%;
+  padding: 3px 1.5rem 3px 1rem;
+  clear: both;
+  font-weight: 400;
+  color: #292b2c;
+  text-align: inherit;
+  white-space: nowrap;
+  background: 0 0;
+  border: 0;
+}
+
+.jcmolview-dropdown-item:hover,
+.jcmolview-dropdown-item:focus {
+  color: #1d1e1f;
+  text-decoration: none;
+  background-color: #f7f7f9;
+}
+
+.jcmolview-dropdown-divider {
+  height: 1px;
+  margin: 0.5rem 0;
+  overflow: hidden;
+  background-color: #eceeef;
+}

package/dist/index.d.ts

@@ -0,0 +1,2 @@
+export { Mol3DView } from './crystal-view.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/index.js

@@ -0,0 +1,2 @@
+export { Mol3DView } from './crystal-view.js';
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/{src/molecule3d → molecule3d}/Atom.d.ts

@@ -1,13 +1,14 @@
-import { Matrix3x4, Vec3 } from "@chemistry/math";
-import { CellAtom } from "./CellAtom";
-export declare class Atom {
-    fractional: Vec3;
-    position: Vec3;
-    parent: CellAtom;
-    symetry: Matrix3x4;
-    constructor(parent: CellAtom, symetry: Matrix3x4);
-    /**
-     * Return color of the element
-     */
-    getColor(): string;
-}
+import { Matrix3x4, Vec3 } from '@chemistry/math';
+import { CellAtom } from './CellAtom.js';
+export declare class Atom {
+    fractional: Vec3;
+    position: Vec3;
+    parent: CellAtom;
+    symetry: Matrix3x4;
+    constructor(parent: CellAtom, symetry: Matrix3x4);
+    /**
+     * Return color of the element
+     */
+    getColor(): string;
+}
+//# sourceMappingURL=Atom.d.ts.map

package/dist/molecule3d/Atom.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"Atom.d.ts","sourceRoot":"","sources":["../../src/molecule3d/Atom.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,MAAM,iBAAiB,CAAC;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAEzC,qBAAa,IAAI;IACR,UAAU,EAAE,IAAI,CAAC;IACjB,QAAQ,EAAE,IAAI,CAAC;IACf,MAAM,EAAE,QAAQ,CAAC;IACjB,OAAO,EAAE,SAAS,CAAC;gBAEd,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,SAAS;IAOhD;;OAEG;IACI,QAAQ;CAGhB"}

package/dist/molecule3d/Atom.js

@@ -0,0 +1,15 @@
+export class Atom {
+    constructor(parent, symetry) {
+        this.parent = parent;
+        this.fractional = symetry.project(parent.fractional);
+        this.symetry = symetry;
+        this.position = parent.unitCell.fractToOrth(this.fractional);
+    }
+    /**
+     * Return color of the element
+     */
+    getColor() {
+        return this.parent.element.color;
+    }
+}
+//# sourceMappingURL=Atom.js.map

package/dist/molecule3d/Atom.js.map

@@ -0,0 +1 @@
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package/dist/{src/molecule3d → molecule3d}/Bond.d.ts

@@ -1,7 +1,8 @@
-import { Atom } from "./Atom";
-export declare class Bond {
-    atom1: Atom;
-    atom2: Atom;
-    order: number;
-    constructor(atom1: Atom, atom2: Atom, order?: number);
-}
+import { Atom } from './Atom.js';
+export declare class Bond {
+    atom1: Atom;
+    atom2: Atom;
+    order: number;
+    constructor(atom1: Atom, atom2: Atom, order?: number);
+}
+//# sourceMappingURL=Bond.d.ts.map

package/dist/molecule3d/Bond.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"Bond.d.ts","sourceRoot":"","sources":["../../src/molecule3d/Bond.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAEjC,qBAAa,IAAI;IACR,KAAK,EAAE,IAAI,CAAC;IACZ,KAAK,EAAE,IAAI,CAAC;IACZ,KAAK,EAAE,MAAM,CAAC;gBAET,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,CAAC,EAAE,MAAM;CAKrD"}

package/dist/molecule3d/Bond.js

@@ -0,0 +1,8 @@
+export class Bond {
+    constructor(atom1, atom2, order) {
+        this.atom1 = atom1;
+        this.atom2 = atom2;
+        this.order = order ?? 1;
+    }
+}
+//# sourceMappingURL=Bond.js.map

package/dist/molecule3d/Bond.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Bond.js","sourceRoot":"","sources":["../../src/molecule3d/Bond.ts"],"names":[],"mappings":"AAEA,MAAM,OAAO,IAAI;IAKf,YAAY,KAAW,EAAE,KAAW,EAAE,KAAc;QAClD,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC;QACnB,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC;QACnB,IAAI,CAAC,KAAK,GAAG,KAAK,IAAI,CAAC,CAAC;IAC1B,CAAC;CACF"}

package/dist/{src/molecule3d → molecule3d}/CellAtom.d.ts

@@ -1,96 +1,96 @@
-import { Element } from "@chemistry/elements";
-import { Matrix3x4, Vec3 } from "@chemistry/math";
-import { Atom } from "./Atom";
-import { Link } from "./Link";
-import { UnitCell } from "./UnitCell";
-export declare class CellAtom {
-    /**
-     * Atom ID within molecule
-     */
-    id: number;
-    /**
-     * label
-     * @type {string}
-     */
-    label: string;
-    /**
-     * Element
-     * @type {Element}
-     */
-    element: Element;
-    /**
-     * Cartezian position of Atom
-     */
-    position: Vec3;
-    /**
-     * Unit Cell
-     */
-    unitCell: UnitCell;
-    /**
-     * Fractional position of Atom
-     */
-    fractional: Vec3;
-    /**
-     * Occupancy
-     */
-    occupancy: number;
-    /**
-     * Isotropic U
-     */
-    uiso: number;
-    /**
-     * Disorder Assembly
-     */
-    assembly: string;
-    /**
-     * Disorder Group
-     */
-    group: string;
-    /**
-     * List of Atoms Created From this Cell Atom
-     */
-    children: Atom[];
-    /**
-     * List of connected atoms
-     */
-    links: Link[];
-    constructor(data: {
-        id: number;
-        unitCell: UnitCell;
-        type: string;
-        label: string;
-        x: number;
-        y: number;
-        z: number;
-        occupancy: number;
-        uiso: number;
-        assembly: string;
-        group: string;
-    });
-    /**
-     * Add link to another element
-     */
-    addLink(otherAtom: CellAtom, symetry: Matrix3x4): void;
-    getLinks(): Link[];
-    /**
-     * Returns true if Cell Atom has Chield with Specific position
-     */
-    hasChild(position: Vec3): boolean;
-    /**
-     * Return Chield Atom with Specifified Position or null if not found
-     */
-    getChild(position: Vec3): Atom;
-    /**
-     * Return true if has Atom with Specified symetry position
-     */
-    hasChieldWithSymetry(symetry: Matrix3x4): boolean;
-    /**
-     * Return Chield Atom with Specifified symetry or similar atom liing on the same spot
-     */
-    getChieldWithSymetry(symetry: Matrix3x4): Atom;
-    /**
-     * Create Atom & return it based on this Cell Atom
-     * and set correct settings
-     */
-    createAtom(symetry: Matrix3x4, addToChields: boolean): Atom;
-}
+import { ChemElementInfo } from '@chemistry/elements';
+import { Matrix3x4, Vec3 } from '@chemistry/math';
+import { Atom } from './Atom.js';
+import { Link } from './Link.js';
+import { UnitCell } from './UnitCell.js';
+export declare class CellAtom {
+    /**
+     * Atom ID within molecule
+     */
+    id: number;
+    /**
+     * label
+     * @type {string}
+     */
+    label: string;
+    /**
+     * Element
+     */
+    element: ChemElementInfo;
+    /**
+     * Cartezian position of Atom
+     */
+    position: Vec3;
+    /**
+     * Unit Cell
+     */
+    unitCell: UnitCell;
+    /**
+     * Fractional position of Atom
+     */
+    fractional: Vec3;
+    /**
+     * Occupancy
+     */
+    occupancy: number;
+    /**
+     * Isotropic U
+     */
+    uiso: number;
+    /**
+     * Disorder Assembly
+     */
+    assembly: string;
+    /**
+     * Disorder Group
+     */
+    group: string;
+    /**
+     * List of Atoms Created From this Cell Atom
+     */
+    children: Atom[];
+    /**
+     * List of connected atoms
+     */
+    links: Link[];
+    constructor(data: {
+        id: number;
+        unitCell: UnitCell;
+        type: string;
+        label: string;
+        x: number;
+        y: number;
+        z: number;
+        occupancy: number;
+        uiso: number;
+        assembly: string;
+        group: string;
+    });
+    /**
+     * Add link to another element
+     */
+    addLink(otherAtom: CellAtom, symetry: Matrix3x4): void;
+    getLinks(): Link[];
+    /**
+     * Returns true if Cell Atom has Chield with Specific position
+     */
+    hasChild(position: Vec3): boolean;
+    /**
+     * Return Chield Atom with Specifified Position or null if not found
+     */
+    getChild(position: Vec3): Atom | null;
+    /**
+     * Return true if has Atom with Specified symetry position
+     */
+    hasChieldWithSymetry(symetry: Matrix3x4): boolean;
+    /**
+     * Return Chield Atom with Specifified symetry or similar atom liing on the same spot
+     */
+    getChieldWithSymetry(symetry: Matrix3x4): Atom | null;
+    /**
+     * Create Atom & return it based on this Cell Atom
+     * and set correct settings
+     */
+    createAtom(symetry: Matrix3x4, addToChields: boolean): Atom;
+}
+//# sourceMappingURL=CellAtom.d.ts.map

package/dist/molecule3d/CellAtom.d.ts.map

@@ -0,0 +1 @@
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package/dist/molecule3d/CellAtom.js

@@ -0,0 +1,83 @@
+import { ChemElements } from '@chemistry/elements';
+import { Vec3 } from '@chemistry/math';
+import { Atom } from './Atom.js';
+import { Link } from './Link.js';
+export class CellAtom {
+    constructor(data) {
+        const element = ChemElements.getBySymbol(data.type);
+        if (!element) {
+            throw new Error('Wrong Element Name or ID: ' + element);
+        }
+        this.element = element;
+        this.id = data.id;
+        this.unitCell = data.unitCell;
+        this.label = data.label || element.symbol || '';
+        this.fractional = new Vec3(data.x, data.y, data.z);
+        this.occupancy = data.occupancy;
+        this.uiso = data.uiso;
+        this.assembly = data.assembly || '';
+        this.group = data.group || '';
+        this.position = this.unitCell.fractToOrth(this.fractional);
+        this.children = [];
+        this.links = [];
+    }
+    /**
+     * Add link to another element
+     */
+    addLink(otherAtom, symetry) {
+        const link = new Link(otherAtom, symetry);
+        this.links.push(link);
+    }
+    getLinks() {
+        return this.links;
+    }
+    /**
+     * Returns true if Cell Atom has Chield with Specific position
+     */
+    hasChild(position) {
+        for (const ch of this.children) {
+            if (ch.fractional.equals(position)) {
+                return true;
+            }
+        }
+        return false;
+    }
+    /**
+     * Return Chield Atom with Specifified Position or null if not found
+     */
+    getChild(position) {
+        for (const ch of this.children) {
+            if (ch.fractional.equals(position)) {
+                return ch;
+            }
+        }
+        return null;
+    }
+    /**
+     * Return true if has Atom with Specified symetry position
+     */
+    hasChieldWithSymetry(symetry) {
+        // Predict inserted atom position
+        const predictedPostion = symetry.project(this.fractional);
+        return this.hasChild(predictedPostion);
+    }
+    /**
+     * Return Chield Atom with Specifified symetry or similar atom liing on the same spot
+     */
+    getChieldWithSymetry(symetry) {
+        const predictedPostion = symetry.project(this.fractional);
+        return this.getChild(predictedPostion);
+    }
+    /**
+     * Create Atom & return it based on this Cell Atom
+     * and set correct settings
+     */
+    createAtom(symetry, addToChields) {
+        const atom = new Atom(this, symetry);
+        if (addToChields) {
+            this.children.push(atom);
+        }
+        return atom;
+    }
+}
+//# sourceMappingURL=CellAtom.js.map

package/dist/molecule3d/CellAtom.js.map

@@ -0,0 +1 @@
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package/dist/{src/molecule3d → molecule3d}/Link.d.ts

@@ -1,14 +1,15 @@
-import { Vec3 } from "@chemistry/math";
-import { Matrix3x4 } from "@chemistry/math";
-import { CellAtom } from "./CellAtom";
-export declare class Link {
-    atom: CellAtom;
-    symetry: Matrix3x4;
-    order: number;
-    /**
-     * Calc position of atom
-     * @type {Vec3}
-     */
-    fractional: Vec3;
-    constructor(atom: CellAtom, symetry: Matrix3x4, order?: number);
-}
+import { Vec3 } from '@chemistry/math';
+import { Matrix3x4 } from '@chemistry/math';
+import { CellAtom } from './CellAtom.js';
+export declare class Link {
+    atom: CellAtom;
+    symetry: Matrix3x4;
+    order: number;
+    /**
+     * Calc position of atom
+     * @type {Vec3}
+     */
+    fractional: Vec3;
+    constructor(atom: CellAtom, symetry: Matrix3x4, order?: number);
+}
+//# sourceMappingURL=Link.d.ts.map

package/dist/molecule3d/Link.d.ts.map

@@ -0,0 +1 @@
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