@chemistry/crystalview 1.0.8 → 3.0.0

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

@@ -1,35 +1,36 @@
-import { Matrix3x4, Vec3 } from "@chemistry/math";
-import { SpaceGroup } from "@crystallography/space-groups";
-export declare class UnitCell {
-    /**
-     * Will construct Transformation Matrix from Crystallographic notation
-     * e.g. x,y,z -x+1/2, -y, z+1/2
-     */
-    static getMatrixFromSymetry(symetryCode: string): Matrix3x4;
-    a: number;
-    b: number;
-    c: number;
-    alpha: number;
-    beta: number;
-    gamma: number;
-    spaceGroup: SpaceGroup;
-    volume: number;
-    symetryList: Matrix3x4[];
-    private mOrthMatrix;
-    private mOrthMatrixInvert;
-    constructor(a: number, b: number, c: number, alpha: number, beta: number, gamma: number, spaceGroup: SpaceGroup);
-    /**
-     * Convert fractional coordinates to Orth
-     */
-    fractToOrth(coord: Vec3): Vec3;
-    /**
-     * Convert Orth coordinates to fractional
-     */
-    orthToFract(coord: Vec3): Vec3;
-    /**
-     * Based on Orth box conner coordinates Return
-     * posible tranactions to get evry posible dot from this box
-     */
-    transactionsFromOrthBox(point1: Vec3, point2: Vec3): Vec3[];
-    private init();
-}
+import { Matrix3x4, Vec3 } from '@chemistry/math';
+import type { SpaceGroupInfo } from '@chemistry/space-groups';
+export declare class UnitCell {
+    /**
+     * Will construct Transformation Matrix from Crystallographic notation
+     * e.g. x,y,z -x+1/2, -y, z+1/2
+     */
+    static getMatrixFromSymetry(symetryCode: string): Matrix3x4;
+    a: number;
+    b: number;
+    c: number;
+    alpha: number;
+    beta: number;
+    gamma: number;
+    spaceGroup: SpaceGroupInfo;
+    volume: number;
+    symetryList: Matrix3x4[];
+    private mOrthMatrix;
+    private mOrthMatrixInvert;
+    constructor(a: number, b: number, c: number, alpha: number, beta: number, gamma: number, spaceGroup: SpaceGroupInfo);
+    /**
+     * Convert fractional coordinates to Orth
+     */
+    fractToOrth(coord: Vec3): Vec3;
+    /**
+     * Convert Orth coordinates to fractional
+     */
+    orthToFract(coord: Vec3): Vec3;
+    /**
+     * Based on Orth box conner coordinates Return
+     * posible tranactions to get evry posible dot from this box
+     */
+    transactionsFromOrthBox(point1: Vec3, point2: Vec3): Vec3[];
+    private init;
+}
+//# sourceMappingURL=UnitCell.d.ts.map

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

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

@@ -0,0 +1,227 @@
+import { Matrix3x3, Matrix3x4, Vec3 } from '@chemistry/math';
+export class UnitCell {
+    /**
+     * Will construct Transformation Matrix from Crystallographic notation
+     * e.g. x,y,z -x+1/2, -y, z+1/2
+     */
+    static getMatrixFromSymetry(symetryCode) {
+        function replaceAll(str, find, replace) {
+            return str.replace(new RegExp(find.replace(/[-/\\^$*+?.()|[\]{}]/g, '\\$&'), 'g'), replace);
+        }
+        function prseSym1(str) {
+            const res = [0, 0, 0, 0];
+            const spl = str.split('+');
+            // loop throught all splits
+            for (const sp2 of spl) {
+                const res2 = prseSym2(sp2);
+                res[0] = res[0] + res2[0];
+                res[1] = res[1] + res2[1];
+                res[2] = res[2] + res2[2];
+                res[3] = res[3] + res2[3];
+            }
+            return res;
+        }
+        function prseSym2(str) {
+            const res = [0, 0, 0, 0];
+            const spl = str.split('-');
+            let res2;
+            //  -x-y, _x-z
+            for (let i = 0; i < spl.length; i++) {
+                if (i === 0 && spl[i] === '') {
+                    continue;
+                }
+                let znak = -1;
+                if (i === 0) {
+                    znak = 1;
+                }
+                res2 = prseSym3(spl[i]);
+                res[0] = res[0] + res2[0] * znak;
+                res[1] = res[1] + res2[1] * znak;
+                res[2] = res[2] + res2[2] * znak;
+                res[3] = res[3] + res2[3] * znak;
+            }
+            return res;
+        }
+        // Parse Symetry 3
+        function prseSym3(str) {
+            const res = [0, 0, 0, 0];
+            if (str.includes('x')) {
+                // 1/2x,0.25*x
+                res[0] = prseSym5(str, 'x');
+            }
+            else if (str.includes('y')) {
+                res[1] = prseSym5(str, 'y');
+            }
+            else if (str.includes('z')) {
+                res[2] = prseSym5(str, 'z');
+            }
+            else {
+                // : 1/2 0.33  + 1
+                res[3] = prseSym4(str);
+            }
+            return res;
+        }
+        function prseSym4(str) {
+            let res;
+            if (str.includes('/')) {
+                // 1/2
+                const xpl = str.split('/');
+                res = parseFloat(xpl[0]) / parseFloat(xpl[1]);
+            }
+            else {
+                const stp = str.replace('.', ',');
+                res = parseFloat(stp);
+            }
+            return res;
+        }
+        function prseSym5(str, ch) {
+            let res = 0;
+            if (str.includes(ch)) {
+                if (str.includes('*')) {
+                    // 1/2x,0.25*x
+                    const xpl = str.split('*');
+                    res = prseSym4(xpl[0]);
+                    if (xpl[1] !== ch) {
+                        throw new Error('Incorect formula');
+                    }
+                }
+                else {
+                    if (ch === str) {
+                        return 1;
+                    }
+                    res = prseSym4(str.replace(ch, '')); // Replace(ch.ToString(), "")
+                }
+            }
+            return res;
+        }
+        const s = replaceAll(symetryCode.toLowerCase(), ' ', '');
+        const pils = s.split(',');
+        if (pils.length !== 3) {
+            throw new Error('can not parse symetry code : ' + symetryCode);
+        }
+        const xv = prseSym1(pils[0]);
+        const yv = prseSym1(pils[1]);
+        const zv = prseSym1(pils[2]);
+        // Double check if the matrix were parsed correctly
+        for (let i = 0; i < 4; i++) {
+            let r = typeof xv[i] !== 'number' || !isFinite(xv[i]);
+            r = r || typeof yv[i] !== 'number' || !isFinite(yv[i]);
+            r = r || typeof zv[i] !== 'number' || !isFinite(zv[i]);
+            if (r) {
+                throw new Error('can not parse symetry code : ' + symetryCode);
+            }
+        }
+        return new Matrix3x4([
+            xv[0],
+            xv[1],
+            xv[2],
+            xv[3],
+            yv[0],
+            yv[1],
+            yv[2],
+            yv[3],
+            zv[0],
+            zv[1],
+            zv[2],
+            zv[3],
+        ]);
+    }
+    constructor(a, b, c, alpha, beta, gamma, spaceGroup) {
+        this.a = a;
+        this.b = b;
+        this.c = c;
+        this.alpha = alpha;
+        this.beta = beta;
+        this.gamma = gamma;
+        this.spaceGroup = spaceGroup;
+        this.init();
+    }
+    /**
+     * Convert fractional coordinates to Orth
+     */
+    fractToOrth(coord) {
+        return this.mOrthMatrix.project(coord);
+    }
+    /**
+     * Convert Orth coordinates to fractional
+     */
+    orthToFract(coord) {
+        return this.mOrthMatrixInvert.project(coord);
+    }
+    /**
+     * Based on Orth box conner coordinates Return
+     * posible tranactions to get evry posible dot from this box
+     */
+    transactionsFromOrthBox(point1, point2) {
+        // Normalize points
+        const p1 = new Vec3(Math.min(point1.x, point2.x), Math.min(point1.y, point2.y), Math.min(point1.z, point2.z));
+        const p2 = new Vec3(Math.max(point1.x, point2.x), Math.max(point1.y, point2.y), Math.max(point1.z, point2.z));
+        // Create vectors of the box
+        const v1 = new Vec3(p1.x, p1.y, p1.z);
+        const v2 = new Vec3(p2.x, p1.y, p1.z);
+        const v3 = new Vec3(p1.x, p2.y, p1.z);
+        const v4 = new Vec3(p1.x, p1.y, p2.z);
+        const v5 = new Vec3(p2.x, p2.y, p1.z);
+        const v6 = new Vec3(p2.x, p1.y, p2.z);
+        const v7 = new Vec3(p1.x, p2.y, p2.z);
+        const v8 = new Vec3(p2.x, p2.y, p2.z);
+        // VP 1 - VP2
+        const vp1 = this.orthToFract(v1);
+        const vp2 = this.orthToFract(v2);
+        const vp3 = this.orthToFract(v3);
+        const vp4 = this.orthToFract(v4);
+        const vp5 = this.orthToFract(v5);
+        const vp6 = this.orthToFract(v6);
+        const vp7 = this.orthToFract(v7);
+        const vp8 = this.orthToFract(v8);
+        const MinX = Math.floor(Math.min(vp1.x, vp2.x, vp3.x, vp4.x, vp5.x, vp6.x, vp7.x, vp8.x));
+        const MinY = Math.floor(Math.min(vp1.y, vp2.y, vp3.y, vp4.y, vp5.y, vp6.y, vp7.y, vp8.y));
+        const MinZ = Math.floor(Math.min(vp1.z, vp2.z, vp3.z, vp4.z, vp5.z, vp6.z, vp7.z, vp8.z));
+        const MaxX = Math.ceil(Math.max(vp1.x, vp2.x, vp3.x, vp4.x, vp5.x, vp6.x, vp7.x, vp8.x));
+        const MaxY = Math.ceil(Math.max(vp1.y, vp2.y, vp3.y, vp4.y, vp5.y, vp6.y, vp7.y, vp8.y));
+        const MaxZ = Math.ceil(Math.max(vp1.z, vp2.z, vp3.z, vp4.z, vp5.z, vp6.z, vp7.z, vp8.z));
+        const res = [];
+        // Create range of posible translations;
+        for (let i = MinX; i < MaxX; i++) {
+            for (let j = MinY; j < MaxY; j++) {
+                for (let k = MinZ; k < MaxZ; k++) {
+                    res.push(new Vec3(i, j, k));
+                }
+            }
+        }
+        return res;
+    }
+    init() {
+        // PREPARE PROJECTION MATRIXES
+        const pAlpha = this.alpha * 0.017453292519943295; // pi/180 ;
+        const pBeta = this.beta * 0.017453292519943295;
+        const pGamma = this.gamma * 0.017453292519943295;
+        const v = Math.sqrt(1 -
+            Math.cos(pAlpha) * Math.cos(pAlpha) -
+            Math.cos(pBeta) * Math.cos(pBeta) -
+            Math.cos(pGamma) * Math.cos(pGamma) +
+            2 * Math.cos(pAlpha) * Math.cos(pBeta) * Math.cos(pGamma));
+        const cc = Math.sin(pGamma) / this.c / v;
+        const alphaa = Math.acos((Math.cos(pBeta) * Math.cos(pGamma) - Math.cos(pAlpha)) / Math.sin(pBeta) / Math.sin(pGamma));
+        this.mOrthMatrix = new Matrix3x3();
+        this.mOrthMatrix.set(0, 0, this.a);
+        this.mOrthMatrix.set(0, 1, this.b * Math.cos(pGamma));
+        this.mOrthMatrix.set(0, 2, this.c * Math.cos(pBeta));
+        this.mOrthMatrix.set(1, 0, 0);
+        this.mOrthMatrix.set(1, 1, this.b * Math.sin(pGamma));
+        this.mOrthMatrix.set(1, 2, -this.c * Math.sin(pBeta) * Math.cos(alphaa));
+        this.mOrthMatrix.set(2, 0, 0);
+        this.mOrthMatrix.set(2, 1, 0);
+        this.mOrthMatrix.set(2, 2, 1 / cc);
+        this.mOrthMatrixInvert = Matrix3x3.inverse(this.mOrthMatrix);
+        this.volume = v;
+        this.symetryList = [];
+        // PREPARE Symetry LIST
+        //
+        for (const symStr of this.spaceGroup.s) {
+            const sym = UnitCell.getMatrixFromSymetry(symStr);
+            this.symetryList.push(sym);
+        }
+    }
+}
+//# sourceMappingURL=UnitCell.js.map

package/dist/molecule3d/UnitCell.js.map

@@ -0,0 +1 @@
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package/dist/molecule3d/io/IMoleculeReader.d.ts

@@ -0,0 +1,8 @@
+import { Molecule3D } from '../Molecule3D.js';
+export interface IMoleculeReader {
+    name: string;
+    extension: string[];
+    description: string;
+    loadMolecule(molecule: Molecule3D, data: string | object): void;
+}
+//# sourceMappingURL=IMoleculeReader.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"IMoleculeReader.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/io/IMoleculeReader.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAC;AAE9C,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,QAAQ,EAAE,UAAU,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAAC;CACjE"}

package/dist/molecule3d/io/IMoleculeReader.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=IMoleculeReader.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"IMoleculeReader.js","sourceRoot":"","sources":["../../../src/molecule3d/io/IMoleculeReader.ts"],"names":[],"mappings":""}

package/dist/{src/molecule3d → molecule3d}/io/MoleculeReaderJCIF.d.ts

@@ -1,11 +1,12 @@
-import { Molecule3D } from "../Molecule3D";
-import { IMoleculeReader } from "./IMoleculeReader";
-export declare class MoleculeReaderJCIF implements IMoleculeReader {
-    name: string;
-    extension: string[];
-    description: string;
-    constructor();
-    loadMolecule(molecule: Molecule3D, data: object): void;
-    private remapCoordLoop(data);
-    private extractCoordLoop(data);
-}
+import { Molecule3D } from '../Molecule3D.js';
+import { IMoleculeReader } from './IMoleculeReader.js';
+export declare class MoleculeReaderJCIF implements IMoleculeReader {
+    name: string;
+    extension: string[];
+    description: string;
+    constructor();
+    loadMolecule(molecule: Molecule3D, data: object): void;
+    private remapCoordLoop;
+    private extractCoordLoop;
+}
+//# sourceMappingURL=MoleculeReaderJCIF.d.ts.map

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

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

@@ -0,0 +1,112 @@
+import { SpaceGroup } from '@chemistry/space-groups';
+import { UnitCell } from '../UnitCell.js';
+export class MoleculeReaderJCIF {
+    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 +1,67 @@
+export class CanvasContext {
+    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

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