@chemistry/crystalview 1.0.9 → 3.1.1

package/dist/molecule3d/io/MoleculeReaderJCIF.d.ts.map

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

@@ -0,0 +1,115 @@
+import { SpaceGroup } from '@chemistry/space-groups';
+import { UnitCell } from '../UnitCell.js';
+export class MoleculeReaderJCIF {
+    name;
+    extension;
+    description;
+    constructor() {
+        this.name = 'jcif';
+        this.extension = ['jcif'];
+        this.description = 'jcif molecule format';
+    }
+    loadMolecule(molecule, data) {
+        molecule.clear();
+        const jcif = data;
+        const a = parseFloat(jcif.a);
+        const b = parseFloat(jcif.b);
+        const c = parseFloat(jcif.c);
+        const alpha = parseFloat(jcif.alpha);
+        const beta = parseFloat(jcif.beta);
+        const gamma = parseFloat(jcif.gamma);
+        if (!isFinite(a) ||
+            !isFinite(b) ||
+            !isFinite(c) ||
+            !isFinite(alpha) ||
+            !isFinite(beta) ||
+            !isFinite(gamma)) {
+            throw new Error('Wrong Unit Cell Params');
+        }
+        if (!jcif.sgHall && !jcif.sg) {
+            throw new Error('Space Group is not provided');
+        }
+        let spaceGroup = null;
+        if (jcif.sgHall) {
+            spaceGroup = SpaceGroup.getByHallName(jcif.sgHall);
+        }
+        if (!spaceGroup && jcif.sg) {
+            spaceGroup = SpaceGroup.getByHMName(jcif.sg);
+        }
+        if (!spaceGroup) {
+            throw new Error('Space Group not founnd');
+        }
+        // Create Unit Cell object
+        const unitCell = new UnitCell(a, b, c, alpha, beta, gamma, spaceGroup);
+        molecule.unitCell = unitCell;
+        const coordLoop = this.extractCoordLoop(jcif);
+        let atomRows = [];
+        if (coordLoop.length > 0) {
+            atomRows = this.remapCoordLoop(coordLoop[0]);
+        }
+        atomRows.forEach((atomData) => {
+            molecule.addCellAtom(atomData);
+        });
+    }
+    remapCoordLoop(data) {
+        const colsMap = {
+            _atom_site_U_iso_or_equiv: -1,
+            _atom_site_disorder_assembly: -1,
+            _atom_site_disorder_group: -1,
+            _atom_site_fract_x: -1,
+            _atom_site_fract_y: -1,
+            _atom_site_fract_z: -1,
+            _atom_site_label: -1,
+            _atom_site_occupancy: -1,
+            _atom_site_type_symbol: -1,
+        };
+        // Set position
+        Object.keys(colsMap).forEach((key) => {
+            colsMap[key] = data.columns.indexOf(key);
+        });
+        function getData(code, row) {
+            if (typeof colsMap[code] === 'number' && colsMap[code] !== -1) {
+                return row[colsMap[code]];
+            }
+            return undefined;
+        }
+        function getDataNum(code, row, defaultValue) {
+            const valueStr = getData(code, row);
+            if (valueStr === undefined) {
+                return defaultValue;
+            }
+            const value = parseFloat(valueStr);
+            if (!isFinite(value)) {
+                return defaultValue;
+            }
+            return value;
+        }
+        let atomRows = [];
+        if (Array.isArray(data.data)) {
+            atomRows = data.data.map((row) => {
+                const type = getData('_atom_site_type_symbol', row) ?? 'Q';
+                return {
+                    assembly: getData('_atom_site_disorder_assembly', row) ?? '',
+                    group: getData('_atom_site_disorder_group', row) ?? '',
+                    label: getData('_atom_site_label', row) ?? type,
+                    occupancy: getDataNum('_atom_site_occupancy', row, 1),
+                    type,
+                    uiso: getDataNum('_atom_site_U_iso_or_equiv', row, 0),
+                    x: getDataNum('_atom_site_fract_x', row, 0),
+                    y: getDataNum('_atom_site_fract_y', row, 0),
+                    z: getDataNum('_atom_site_fract_z', row, 0),
+                };
+            });
+        }
+        return atomRows;
+    }
+    extractCoordLoop(data) {
+        if (Array.isArray(data.loops)) {
+            return data.loops.filter((loopItem) => {
+                return loopItem.columns.includes('_atom_site_fract_x');
+            });
+        }
+        return [];
+    }
+}
+//# sourceMappingURL=MoleculeReaderJCIF.js.map

package/dist/molecule3d/io/MoleculeReaderJCIF.js.map

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

@@ -1,14 +1,15 @@
-export declare class CanvasContext {
-    private context;
-    constructor(context: CanvasRenderingContext2D);
-    save(): void;
-    restore(): void;
-    center(): void;
-    getCenterX(): number;
-    getCenterY(): number;
-    clear(bgcolor: string): void;
-    circle(x: number, y: number, r: number, color: string): void;
-    line(x1: number, y1: number, x2: number, y2: number, color: string): void;
-    linedashed(x1: number, y1: number, x2: number, y2: number, color: string, dash: number[]): void;
-    text(text: string, x: number, y: number, color: string, font: string): void;
-}
+export declare class CanvasContext {
+    private context;
+    constructor(context: CanvasRenderingContext2D);
+    save(): void;
+    restore(): void;
+    center(): void;
+    getCenterX(): number;
+    getCenterY(): number;
+    clear(bgcolor: string): void;
+    circle(x: number, y: number, r: number, color: string): void;
+    line(x1: number, y1: number, x2: number, y2: number, color: string): void;
+    linedashed(x1: number, y1: number, x2: number, y2: number, color: string, dash: number[]): void;
+    text(text: string, x: number, y: number, color: string, font: string): void;
+}
+//# sourceMappingURL=CanvasContext.d.ts.map

package/dist/painter/CanvasContext.d.ts.map

@@ -0,0 +1 @@
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package/dist/painter/CanvasContext.js

@@ -0,0 +1,68 @@
+export class CanvasContext {
+    context;
+    constructor(context) {
+        this.context = context;
+    }
+    save() {
+        this.context.save();
+    }
+    restore() {
+        this.context.restore();
+    }
+    center() {
+        const ctx = this.context;
+        // Change coordinates; so (0,0) :: now corespond to coordinate center
+        ctx.translate(this.getCenterX(), this.getCenterY());
+    }
+    getCenterX() {
+        return this.context.canvas.width / 2;
+    }
+    getCenterY() {
+        return this.context.canvas.height / 2;
+    }
+    clear(bgcolor) {
+        const ctx = this.context;
+        const width = this.context.canvas.width;
+        const height = this.context.canvas.height;
+        ctx.fillStyle = bgcolor;
+        ctx.fillRect(0, 0, width, height);
+    }
+    circle(x, y, r, color) {
+        const ctx = this.context;
+        ctx.beginPath();
+        ctx.arc(x, y, r, 0, 2 * Math.PI, true);
+        ctx.closePath();
+        ctx.fillStyle = color;
+        ctx.fill();
+    }
+    line(x1, y1, x2, y2, color) {
+        const ctx = this.context;
+        ctx.beginPath();
+        ctx.moveTo(x1, y1);
+        ctx.lineTo(x2, y2);
+        ctx.strokeStyle = color;
+        ctx.lineWidth = 1;
+        ctx.stroke();
+    }
+    linedashed(x1, y1, x2, y2, color, dash) {
+        const ctx = this.context;
+        ctx.save();
+        if (ctx.setLineDash) {
+            ctx.setLineDash(dash);
+        }
+        ctx.beginPath();
+        ctx.moveTo(x1, y1);
+        ctx.lineTo(x2, y2);
+        ctx.strokeStyle = color;
+        ctx.lineWidth = 1;
+        ctx.stroke();
+        this.restore();
+    }
+    text(text, x, y, color, font) {
+        const ctx = this.context;
+        ctx.font = font;
+        ctx.fillStyle = color;
+        ctx.fillText(text, x, y);
+    }
+}
+//# sourceMappingURL=CanvasContext.js.map

package/dist/painter/CanvasContext.js.map

@@ -0,0 +1 @@
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package/dist/painter/Painter.d.ts

@@ -0,0 +1,36 @@
+import type { ICamera } from '../camera/ICamera.js';
+import { Marker } from '../molecule3d/Marker.js';
+import { Molecule3D } from '../molecule3d/Molecule3D.js';
+export declare class Painter {
+    private context;
+    private options;
+    private zBuffer;
+    constructor(context: CanvasRenderingContext2D, options: {
+        bgcolor: string;
+        showUnitCell: boolean;
+        showMarkers: boolean;
+        showLabels: boolean;
+    });
+    draw(molecule: Molecule3D, camera: ICamera): void;
+    uprojectToMarker(data: {
+        molecule: Molecule3D;
+        camera: ICamera;
+        x: number;
+        y: number;
+    }): Marker | null;
+    private drawZBuffer;
+    private unitCellLine;
+    private drawBondLine;
+    private drawAtom;
+    private drawMarker;
+    private drawMarkerContact;
+    private drawLabel;
+    private prepareMarkers;
+    private prepareLabels;
+    private prepareMarkersContacts;
+    private prepareAxis;
+    private prepareUnitCell;
+    private prepareBonds;
+    private prepareAtoms;
+}
+//# sourceMappingURL=Painter.d.ts.map

package/dist/painter/Painter.d.ts.map

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package/dist/painter/Painter.js

@@ -0,0 +1,237 @@
+import { Vec3 } from '@chemistry/math';
+import { CanvasContext } from './CanvasContext.js';
+const ATOM_RADIUS_FACTOR = 0.25;
+export class Painter {
+    context;
+    options;
+    zBuffer = [];
+    constructor(context, options) {
+        this.context = new CanvasContext(context);
+        this.options = options;
+    }
+    draw(molecule, camera) {
+        const context = this.context;
+        this.zBuffer = [];
+        context.save();
+        context.clear(this.options.bgcolor);
+        context.center();
+        this.prepareAtoms(molecule, camera);
+        this.prepareBonds(molecule, camera);
+        if (this.options.showMarkers) {
+            this.prepareMarkers(molecule, camera);
+            this.prepareMarkersContacts(molecule, camera);
+        }
+        if (this.options.showUnitCell) {
+            this.prepareUnitCell(molecule, camera);
+        }
+        if (this.options.showLabels) {
+            this.prepareLabels(molecule, camera);
+        }
+        this.zBuffer.sort((i1, i2) => {
+            return i1.z - i2.z;
+        });
+        this.drawZBuffer();
+        context.restore();
+        this.zBuffer = [];
+    }
+    uprojectToMarker(data) {
+        const currentZ = -Infinity;
+        const camera = data.camera;
+        const molecule = data.molecule;
+        let currentMarker = null;
+        const tx = data.x - this.context.getCenterX();
+        const ty = data.y - this.context.getCenterY();
+        const clickR = 9;
+        const clickR2 = clickR * clickR;
+        for (const marker of molecule.markers) {
+            const projection = camera.project(marker.position);
+            if (Math.abs(projection.x - tx) < clickR && Math.abs(projection.y - ty) < clickR) {
+                const length = Math.sqrt((projection.x - tx) * (projection.x - tx) + (projection.y - ty) * (projection.y - ty));
+                if (length < clickR2 && currentZ < projection.z) {
+                    currentMarker = marker;
+                }
+            }
+        }
+        return currentMarker;
+    }
+    drawZBuffer() {
+        const context = this.context;
+        for (const item of this.zBuffer) {
+            switch (item.type) {
+                case 'atom':
+                    this.drawAtom(context, item);
+                    break;
+                case 'label':
+                    this.drawLabel(context, item);
+                    break;
+                case 'bond-line':
+                    this.drawBondLine(context, item);
+                    break;
+                case 'marker':
+                    this.drawMarker(context, item);
+                    break;
+                case 'marker-contact':
+                    this.drawMarkerContact(context, item);
+                    break;
+                case 'unit-cell-line':
+                    this.unitCellLine(context, item);
+                    break;
+                default:
+                    break;
+            }
+        }
+    }
+    unitCellLine(context, obj) {
+        context.line(obj.x1, obj.y1, obj.x2, obj.y2, obj.color);
+    }
+    drawBondLine(context, obj) {
+        context.line(obj.x1, obj.y1, obj.x2, obj.y2, obj.color);
+    }
+    drawAtom(context, obj) {
+        context.circle(obj.x, obj.y, obj.r, obj.color);
+    }
+    drawMarker(context, obj) {
+        context.circle(obj.x, obj.y, 3, '#ffda4d');
+    }
+    drawMarkerContact(context, obj) {
+        context.linedashed(obj.x1, obj.y1, obj.x2, obj.y2, '#ffda4d', [4, 7]);
+    }
+    drawLabel(context, obj) {
+        context.text(obj.label, obj.x, obj.y, '#ffffff', '12px Arial');
+    }
+    prepareMarkers(molecule, camera) {
+        for (const marker of molecule.markers) {
+            const projection = camera.project(marker.position);
+            this.zBuffer.push({
+                type: 'marker',
+                x: projection.x,
+                y: projection.y,
+                z: projection.z,
+            });
+        }
+    }
+    prepareLabels(molecule, camera) {
+        const scale = camera.extractScale() * ATOM_RADIUS_FACTOR;
+        for (const atom of molecule.atoms) {
+            const projection = camera.project(atom.position);
+            const r = atom.parent.element.RCow * scale;
+            const label = atom.parent.label;
+            if (label) {
+                this.zBuffer.push({
+                    label,
+                    r: atom.parent.element.RCow * scale,
+                    type: 'label',
+                    x: projection.x + r + 3,
+                    y: projection.y - r,
+                    z: projection.z,
+                });
+            }
+        }
+    }
+    prepareMarkersContacts(molecule, camera) {
+        for (const marker of molecule.markersContacts) {
+            const p1 = camera.project(marker.position1);
+            const p2 = camera.project(marker.position2);
+            this.zBuffer.push({
+                type: 'marker-contact',
+                x1: p1.x,
+                x2: p2.x,
+                y1: p1.y,
+                y2: p2.y,
+                z: (p1.z + p2.z) / 2,
+            });
+        }
+    }
+    prepareAxis(p1, p2, color, num) {
+        const det = Vec3.sub(p2, p1).scale(1 / num);
+        for (let i = 0; i < num; i++) {
+            this.zBuffer.push({
+                color,
+                type: 'unit-cell-line',
+                x1: p1.x + det.x * i,
+                x2: p1.x + det.x * (i + 1),
+                y1: p1.y + det.y * i,
+                y2: p1.y + det.y * (i + 1),
+                z: (p1.z + det.z * i + p1.z + det.z * (i + 1)) / 2,
+            });
+        }
+    }
+    prepareUnitCell(molecule, camera) {
+        const uc = molecule.unitCell;
+        if (!uc) {
+            return;
+        }
+        const v000 = uc.fractToOrth(new Vec3(0, 0, 0));
+        const v100 = uc.fractToOrth(new Vec3(1, 0, 0));
+        const v010 = uc.fractToOrth(new Vec3(0, 1, 0));
+        const v001 = uc.fractToOrth(new Vec3(0, 0, 1));
+        const v101 = uc.fractToOrth(new Vec3(1, 0, 1));
+        const v011 = uc.fractToOrth(new Vec3(0, 1, 1));
+        const v110 = uc.fractToOrth(new Vec3(1, 1, 0));
+        const v111 = uc.fractToOrth(new Vec3(1, 1, 1));
+        const p000 = camera.project(v000);
+        const p100 = camera.project(v100);
+        const p010 = camera.project(v010);
+        const p001 = camera.project(v001);
+        const p101 = camera.project(v101);
+        const p011 = camera.project(v011);
+        const p110 = camera.project(v110);
+        const p111 = camera.project(v111);
+        this.prepareAxis(p000, p100, '#b00000', Math.ceil(v100.length / 4));
+        this.prepareAxis(p100, p101, '#707070', Math.ceil(v001.length / 4));
+        this.prepareAxis(p100, p110, '#707070', Math.ceil(v010.length / 4));
+        this.prepareAxis(p010, p011, '#707070', Math.ceil(v001.length / 4));
+        this.prepareAxis(p000, p010, '#00b000', Math.ceil(v010.length / 4));
+        this.prepareAxis(p010, p110, '#707070', Math.ceil(v100.length / 4));
+        this.prepareAxis(p000, p001, '#0000b0', Math.ceil(v100.length / 4));
+        this.prepareAxis(p001, p011, '#707070', Math.ceil(v010.length / 4));
+        this.prepareAxis(p001, p101, '#707070', Math.ceil(v100.length / 4));
+        this.prepareAxis(p111, p101, '#707070', Math.ceil(v010.length / 4));
+        this.prepareAxis(p111, p011, '#707070', Math.ceil(v100.length / 4));
+        this.prepareAxis(p111, p110, '#707070', Math.ceil(v001.length / 4));
+    }
+    prepareBonds(molecule, camera) {
+        for (const bond of molecule.bonds) {
+            const a1 = bond.atom1;
+            const a2 = bond.atom2;
+            const p1 = camera.project(a1.position);
+            const p2 = camera.project(a2.position);
+            const pmidx = (p1.x + p2.x) / 2;
+            const pmidy = (p1.y + p2.y) / 2;
+            const pmidz = (p1.z + p2.z) / 2;
+            this.zBuffer.push({
+                color: a1.getColor(),
+                type: 'bond-line',
+                x1: p1.x,
+                x2: pmidx,
+                y1: p1.y,
+                y2: pmidy,
+                z: (p1.z + pmidz) / 2,
+            });
+            this.zBuffer.push({
+                color: a2.getColor(),
+                type: 'bond-line',
+                x1: p2.x,
+                x2: pmidx,
+                y1: p2.y,
+                y2: pmidy,
+                z: (p2.z + pmidz) / 2,
+            });
+        }
+    }
+    prepareAtoms(molecule, camera) {
+        const scale = camera.extractScale() * ATOM_RADIUS_FACTOR;
+        for (const atom of molecule.atoms) {
+            const projection = camera.project(atom.position);
+            this.zBuffer.push({
+                color: atom.getColor(),
+                r: atom.parent.element.RCow * scale,
+                type: 'atom',
+                x: projection.x,
+                y: projection.y,
+                z: projection.z,
+            });
+        }
+    }
+}
+//# sourceMappingURL=Painter.js.map

package/dist/painter/Painter.js.map

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package/dist/ui/ContextMenu.d.ts

@@ -0,0 +1,24 @@
+import { ContextMenuItem } from './ContextMenuItem.js';
+export declare class ContextMenu {
+    private static initDone;
+    private static instances;
+    private static subscription;
+    private static getInstances;
+    private static init;
+    private static off;
+    private static hideAll;
+    private static addInstance;
+    private static removeInstance;
+    private widget;
+    private view;
+    private intervalID;
+    private menuItems;
+    constructor(menuItems: ContextMenuItem[]);
+    onInit(element: HTMLElement): void;
+    onDestroy(): void;
+    hide(): void;
+    show(posX: number, posY: number): void;
+    private attach;
+    private getView;
+}
+//# sourceMappingURL=ContextMenu.d.ts.map

package/dist/ui/ContextMenu.d.ts.map

@@ -0,0 +1 @@
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