@chemistry/crystalview 1.0.9 → 3.1.1

package/dist/molecule3d/CellAtom.js

@@ -0,0 +1,132 @@
+import { ChemElements } from '@chemistry/elements';
+import { Vec3 } from '@chemistry/math';
+import { Atom } from './Atom.js';
+import { Link } from './Link.js';
+export class CellAtom {
+    /**
+     * Atom ID within molecule
+     */
+    id;
+    /**
+     * label
+     * @type {string}
+     */
+    label;
+    /**
+     * Element
+     */
+    element;
+    /**
+     * Cartezian position of Atom
+     */
+    position;
+    /**
+     * Unit Cell
+     */
+    unitCell;
+    /**
+     * Fractional position of Atom
+     */
+    fractional;
+    /**
+     * Occupancy
+     */
+    occupancy;
+    /**
+     * Isotropic U
+     */
+    uiso;
+    /**
+     * Disorder Assembly
+     */
+    assembly;
+    /**
+     * Disorder Group
+     */
+    group;
+    /**
+     * List of Atoms Created From this Cell Atom
+     */
+    children;
+    /**
+     * List of connected atoms
+     */
+    links;
+    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 @@
+{"version":3,"file":"Link.d.ts","sourceRoot":"","sources":["../../src/molecule3d/Link.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,iBAAiB,CAAC;AACvC,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAC;AAC5C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAEzC,qBAAa,IAAI;IACR,IAAI,EAAE,QAAQ,CAAC;IACf,OAAO,EAAE,SAAS,CAAC;IACnB,KAAK,EAAE,MAAM,CAAC;IACrB;;;OAGG;IACI,UAAU,EAAE,IAAI,CAAC;gBAEZ,IAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,MAAM;CAM/D"}

package/dist/molecule3d/Link.js

@@ -0,0 +1,17 @@
+export class Link {
+    atom;
+    symetry;
+    order;
+    /**
+     * Calc position of atom
+     * @type {Vec3}
+     */
+    fractional;
+    constructor(atom, symetry, order) {
+        this.atom = atom;
+        this.symetry = symetry;
+        this.order = order ?? 1;
+        this.fractional = symetry.project(atom.fractional);
+    }
+}
+//# sourceMappingURL=Link.js.map

package/dist/molecule3d/Link.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Link.js","sourceRoot":"","sources":["../../src/molecule3d/Link.ts"],"names":[],"mappings":"AAIA,MAAM,OAAO,IAAI;IACR,IAAI,CAAW;IACf,OAAO,CAAY;IACnB,KAAK,CAAS;IACrB;;;OAGG;IACI,UAAU,CAAO;IAExB,YAAY,IAAc,EAAE,OAAkB,EAAE,KAAc;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC;QACvB,IAAI,CAAC,KAAK,GAAG,KAAK,IAAI,CAAC,CAAC;QACxB,IAAI,CAAC,UAAU,GAAG,OAAO,CAAC,OAAO,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;IACrD,CAAC;CACF"}

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

@@ -1,8 +1,9 @@
-import { Matrix3x4, Vec3 } from "@chemistry/math";
-import { CellAtom } from "./CellAtom";
-export declare class Marker {
-    position: Vec3;
-    symetry: Matrix3x4;
-    cellAtom: CellAtom;
-    constructor(position: Vec3, symetry: Matrix3x4, cellAtom: CellAtom);
-}
+import { Matrix3x4, Vec3 } from '@chemistry/math';
+import { CellAtom } from './CellAtom.js';
+export declare class Marker {
+    position: Vec3;
+    symetry: Matrix3x4;
+    cellAtom: CellAtom;
+    constructor(position: Vec3, symetry: Matrix3x4, cellAtom: CellAtom);
+}
+//# sourceMappingURL=Marker.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"Marker.d.ts","sourceRoot":"","sources":["../../src/molecule3d/Marker.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,MAAM,iBAAiB,CAAC;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAEzC,qBAAa,MAAM;IACV,QAAQ,EAAE,IAAI,CAAC;IACf,OAAO,EAAE,SAAS,CAAC;IACnB,QAAQ,EAAE,QAAQ,CAAC;gBAEd,QAAQ,EAAE,IAAI,EAAE,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,QAAQ;CAKnE"}

package/dist/molecule3d/Marker.js

@@ -0,0 +1,11 @@
+export class Marker {
+    position;
+    symetry;
+    cellAtom;
+    constructor(position, symetry, cellAtom) {
+        this.position = position;
+        this.symetry = symetry;
+        this.cellAtom = cellAtom;
+    }
+}
+//# sourceMappingURL=Marker.js.map

package/dist/molecule3d/Marker.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Marker.js","sourceRoot":"","sources":["../../src/molecule3d/Marker.ts"],"names":[],"mappings":"AAGA,MAAM,OAAO,MAAM;IACV,QAAQ,CAAO;IACf,OAAO,CAAY;IACnB,QAAQ,CAAW;IAE1B,YAAY,QAAc,EAAE,OAAkB,EAAE,QAAkB;QAChE,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC;QACvB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;IAC3B,CAAC;CACF"}

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

@@ -1,6 +1,7 @@
-import { Vec3 } from "@chemistry/math";
-export declare class MarkerContact {
-    position1: Vec3;
-    position2: Vec3;
-    constructor(position1: Vec3, position2: Vec3);
-}
+import { Vec3 } from '@chemistry/math';
+export declare class MarkerContact {
+    position1: Vec3;
+    position2: Vec3;
+    constructor(position1: Vec3, position2: Vec3);
+}
+//# sourceMappingURL=MarkerContact.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"MarkerContact.d.ts","sourceRoot":"","sources":["../../src/molecule3d/MarkerContact.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,iBAAiB,CAAC;AAEvC,qBAAa,aAAa;IACjB,SAAS,EAAE,IAAI,CAAC;IAChB,SAAS,EAAE,IAAI,CAAC;gBAEX,SAAS,EAAE,IAAI,EAAE,SAAS,EAAE,IAAI;CAI7C"}

package/dist/molecule3d/MarkerContact.js

@@ -0,0 +1,9 @@
+export class MarkerContact {
+    position1;
+    position2;
+    constructor(position1, position2) {
+        this.position1 = position1;
+        this.position2 = position2;
+    }
+}
+//# sourceMappingURL=MarkerContact.js.map

package/dist/molecule3d/MarkerContact.js.map

@@ -0,0 +1 @@
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package/dist/{src/molecule3d → molecule3d}/Molecule3D.d.ts

@@ -1,44 +1,45 @@
-import { Vec3 } from "@chemistry/math";
-import { Atom } from "./Atom";
-import { Bond } from "./Bond";
-import { CellAtom } from "./CellAtom";
-import { Marker } from "./Marker";
-import { MarkerContact } from "./MarkerContact";
-import { UnitCell } from "./UnitCell";
-export declare class Molecule3D {
-    title: string;
-    unitCell: UnitCell;
-    cellAtoms: CellAtom[];
-    atoms: Atom[];
-    bonds: Bond[];
-    markers: Marker[];
-    markersContacts: MarkerContact[];
-    private reader;
-    private builder;
-    private connector;
-    private initConnectivity;
-    private center;
-    private radius;
-    constructor();
-    load(input: object): void;
-    buildConnectivity(): void;
-    clear(): void;
-    addCellAtom(data: {
-        type: string;
-        label: string;
-        x: number;
-        y: number;
-        z: number;
-        occupancy: number;
-        uiso: number;
-        assembly: string;
-        group: string;
-    }): void;
-    addAtom(atom: Atom): void;
-    /**
-     * Rerutn molecule center
-     */
-    getCenter(): Vec3;
-    getRadius(): number;
-    extendByMarker(makers: Marker): void;
-}
+import { Vec3 } from '@chemistry/math';
+import { Atom } from './Atom.js';
+import { Bond } from './Bond.js';
+import { CellAtom } from './CellAtom.js';
+import { Marker } from './Marker.js';
+import { MarkerContact } from './MarkerContact.js';
+import { UnitCell } from './UnitCell.js';
+export declare class Molecule3D {
+    title: string;
+    unitCell: UnitCell;
+    cellAtoms: CellAtom[];
+    atoms: Atom[];
+    bonds: Bond[];
+    markers: Marker[];
+    markersContacts: MarkerContact[];
+    private reader;
+    private builder;
+    private connector;
+    private initConnectivity;
+    private center;
+    private radius;
+    constructor();
+    load(input: object): void;
+    buildConnectivity(): void;
+    clear(): void;
+    addCellAtom(data: {
+        type: string;
+        label: string;
+        x: number;
+        y: number;
+        z: number;
+        occupancy: number;
+        uiso: number;
+        assembly: string;
+        group: string;
+    }): void;
+    addAtom(atom: Atom): void;
+    /**
+     * Rerutn molecule center
+     */
+    getCenter(): Vec3;
+    getRadius(): number;
+    extendByMarker(makers: Marker): void;
+}
+//# sourceMappingURL=Molecule3D.d.ts.map

package/dist/molecule3d/Molecule3D.d.ts.map

@@ -0,0 +1 @@
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package/dist/molecule3d/Molecule3D.js

@@ -0,0 +1,139 @@
+import { Vec3 } from '@chemistry/math';
+import { CellAtom } from './CellAtom.js';
+import { MoleculeReaderJCIF } from './io/MoleculeReaderJCIF.js';
+import { MoleculeBuilder } from './MoleculeBuilder.js';
+import { MoleculeConnector } from './MoleculeConnector.js';
+export class Molecule3D {
+    title;
+    unitCell;
+    cellAtoms;
+    atoms;
+    bonds;
+    markers;
+    markersContacts;
+    reader;
+    builder;
+    connector;
+    initConnectivity;
+    center;
+    radius;
+    constructor() {
+        this.reader = new MoleculeReaderJCIF();
+        this.title = '';
+        this.cellAtoms = [];
+        this.atoms = [];
+        this.bonds = [];
+        this.markers = [];
+        this.markersContacts = [];
+        this.initConnectivity = false;
+        this.builder = new MoleculeBuilder(this);
+        this.connector = new MoleculeConnector(this);
+        this.center = null;
+        this.radius = 0;
+    }
+    load(input) {
+        this.reader.loadMolecule(this, input);
+        // Connect atoms
+        this.buildConnectivity();
+        // Add unique Atoms
+        this.builder.addUniqueAtoms();
+    }
+    buildConnectivity() {
+        if (!this.initConnectivity) {
+            this.connector.buildConnectivity();
+            this.initConnectivity = true;
+        }
+    }
+    clear() {
+        this.title = '';
+        this.cellAtoms = [];
+        this.atoms = [];
+        this.bonds = [];
+        this.markers = [];
+        this.markersContacts = [];
+        this.center = null;
+        this.radius = 0;
+    }
+    addCellAtom(data) {
+        const o = data;
+        o.id = this.cellAtoms.length + 1;
+        o.unitCell = this.unitCell;
+        const atom = new CellAtom(o);
+        this.cellAtoms.push(atom);
+    }
+    addAtom(atom) {
+        this.atoms.push(atom);
+        this.center = null;
+        this.radius = 0;
+    }
+    /**
+     * Rerutn molecule center
+     */
+    getCenter() {
+        if (this.center) {
+            return this.center;
+        }
+        if (this.atoms.length === 0) {
+            return new Vec3(0, 0, 0);
+        }
+        if (this.atoms.length === 1) {
+            return new Vec3(this.atoms[0].position.x, this.atoms[0].position.y, this.atoms[0].position.z);
+        }
+        let minX = Infinity;
+        let minY = Infinity;
+        let maxX = -Infinity;
+        let minZ = Infinity;
+        let maxY = -Infinity;
+        let maxZ = -Infinity;
+        for (let i = this.atoms.length - 1; i >= 0; i--) {
+            const p = this.atoms[i].position;
+            if (minX > p.x) {
+                minX = p.x;
+            }
+            if (minY > p.y) {
+                minY = p.y;
+            }
+            if (minZ > p.z) {
+                minZ = p.z;
+            }
+            if (maxX < p.x) {
+                maxX = p.x;
+            }
+            if (maxY < p.y) {
+                maxY = p.y;
+            }
+            if (maxZ < p.z) {
+                maxZ = p.z;
+            }
+        }
+        this.center = new Vec3((minX + maxX) / 2, (minY + maxY) / 2, (minZ + maxZ) / 2);
+        return this.center;
+    }
+    getRadius() {
+        if (this.radius !== 0 && this.radius !== undefined) {
+            return this.radius;
+        }
+        this.radius = 0;
+        const center = this.getCenter();
+        let r2 = 0; // Radius squared
+        if (this.atoms.length === 0 || this.atoms.length === 1) {
+            return 0;
+        }
+        for (let i = this.atoms.length - 1; i >= 0; i--) {
+            const p = this.atoms[i].position;
+            const dx = p.x - center.x;
+            const dy = p.y - center.y;
+            const dz = p.z - center.z;
+            const r1 = dx * dx + dy * dy + dz * dz;
+            if (r1 > r2) {
+                r2 = r1;
+            }
+        }
+        this.radius = Math.sqrt(r2);
+        return this.radius;
+    }
+    extendByMarker(makers) {
+        this.builder.extendByMarker(makers);
+    }
+}
+//# sourceMappingURL=Molecule3D.js.map

package/dist/molecule3d/Molecule3D.js.map

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

@@ -1,19 +1,20 @@
-import { Matrix3x4 } from "@chemistry/math";
-import { CellAtom } from "./CellAtom";
-import { Marker } from "./Marker";
-import { Molecule3D } from "./Molecule3D";
-export declare class MoleculeBuilder {
-    private molecule;
-    constructor(molecule: Molecule3D);
-    /**
-     * Add Unique Atoms to Molecule
-     */
-    addUniqueAtoms(): void;
-    addAtomsBySymetry(symetryList: string[]): void;
-    addAtomWithBonds(catom: CellAtom, symetry: Matrix3x4): Array<{
-        atom: CellAtom;
-        symetry: Matrix3x4;
-    }>;
-    extendByMarker(marker: Marker): void;
-    addMarkers(): void;
-}
+import { Matrix3x4 } from '@chemistry/math';
+import { CellAtom } from './CellAtom.js';
+import { Marker } from './Marker.js';
+import { Molecule3D } from './Molecule3D.js';
+export declare class MoleculeBuilder {
+    private molecule;
+    constructor(molecule: Molecule3D);
+    /**
+     * Add Unique Atoms to Molecule
+     */
+    addUniqueAtoms(): void;
+    addAtomsBySymetry(symetryList: string[]): void;
+    addAtomWithBonds(catom: CellAtom, symetry: Matrix3x4): {
+        atom: CellAtom;
+        symetry: Matrix3x4;
+    }[];
+    extendByMarker(marker: Marker): void;
+    addMarkers(): void;
+}
+//# sourceMappingURL=MoleculeBuilder.d.ts.map

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

@@ -0,0 +1 @@
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