@chemistry/crystalview 1.0.8 → 3.0.0

package/dist/molecule3d/Link.js

@@ -0,0 +1,9 @@
+export class Link {
+    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;IAUf,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 +1,8 @@
+export class Marker {
+    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;IAKjB,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 +1,7 @@
+export class MarkerContact {
+    constructor(position1, position2) {
+        this.position1 = position1;
+        this.position2 = position2;
+    }
+}
+//# sourceMappingURL=MarkerContact.js.map

package/dist/molecule3d/MarkerContact.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"MarkerContact.js","sourceRoot":"","sources":["../../src/molecule3d/MarkerContact.ts"],"names":[],"mappings":"AAEA,MAAM,OAAO,aAAa;IAIxB,YAAY,SAAe,EAAE,SAAe;QAC1C,IAAI,CAAC,SAAS,GAAG,SAAS,CAAC;QAC3B,IAAI,CAAC,SAAS,GAAG,SAAS,CAAC;IAC7B,CAAC;CACF"}

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 @@
+{"version":3,"file":"Molecule3D.d.ts","sourceRoot":"","sources":["../../src/molecule3d/Molecule3D.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,iBAAiB,CAAC;AACvC,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAGzC,OAAO,EAAE,MAAM,EAAE,MAAM,aAAa,CAAC;AACrC,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AAGnD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAEzC,qBAAa,UAAU;IACd,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAG,QAAQ,CAAC;IAEpB,SAAS,EAAE,QAAQ,EAAE,CAAC;IACtB,KAAK,EAAE,IAAI,EAAE,CAAC;IACd,KAAK,EAAE,IAAI,EAAE,CAAC;IACd,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,eAAe,EAAE,aAAa,EAAE,CAAC;IAExC,OAAO,CAAC,MAAM,CAAkB;IAChC,OAAO,CAAC,OAAO,CAAkB;IACjC,OAAO,CAAC,SAAS,CAAoB;IAErC,OAAO,CAAC,gBAAgB,CAAU;IAClC,OAAO,CAAC,MAAM,CAAc;IAC5B,OAAO,CAAC,MAAM,CAAS;;IAmBhB,IAAI,CAAC,KAAK,EAAE,MAAM;IAUlB,iBAAiB;IAOjB,KAAK;IAYL,WAAW,CAAC,IAAI,EAAE;QACvB,IAAI,EAAE,MAAM,CAAC;QACb,KAAK,EAAE,MAAM,CAAC;QACd,CAAC,EAAE,MAAM,CAAC;QACV,CAAC,EAAE,MAAM,CAAC;QACV,CAAC,EAAE,MAAM,CAAC;QACV,SAAS,EAAE,MAAM,CAAC;QAClB,IAAI,EAAE,MAAM,CAAC;QACb,QAAQ,EAAE,MAAM,CAAC;QACjB,KAAK,EAAE,MAAM,CAAC;KACf;IAuBM,OAAO,CAAC,IAAI,EAAE,IAAI;IAOzB;;OAEG;IACI,SAAS,IAAI,IAAI;IA2CjB,SAAS,IAAI,MAAM;IA4BnB,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI;CAG5C"}

package/dist/molecule3d/Molecule3D.js

@@ -0,0 +1,126 @@
+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 {
+    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

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package/dist/molecule3d/MoleculeBuilder.js

@@ -0,0 +1,130 @@
+import { Bond } from './Bond.js';
+import { Marker } from './Marker.js';
+import { MarkerContact } from './MarkerContact.js';
+import { UnitCell } from './UnitCell.js';
+export class MoleculeBuilder {
+    constructor(molecule) {
+        this.molecule = molecule;
+    }
+    /**
+     * Add Unique Atoms to Molecule
+     */
+    addUniqueAtoms() {
+        this.addAtomsBySymetry(['x,y,z']);
+    }
+    addAtomsBySymetry(symetryList) {
+        for (const catom of this.molecule.cellAtoms) {
+            for (const symetryCode of symetryList) {
+                const symetry = UnitCell.getMatrixFromSymetry(symetryCode);
+                // Add atom with bonds
+                this.addAtomWithBonds(catom, symetry);
+            }
+        }
+        this.addMarkers();
+    }
+    addAtomWithBonds(catom, symetry) {
+        const markers = [];
+        // build atoms connectivity
+        this.molecule.buildConnectivity();
+        // Predict inserted atom position
+        const predictedPostion = symetry.project(catom.fractional);
+        const zatom = catom.getChild(predictedPostion);
+        let atom;
+        // Atom with predicted position not found
+        if (!zatom) {
+            // Create Atom and Add it as Chield
+            atom = catom.createAtom(symetry, true);
+            this.molecule.addAtom(atom);
+        }
+        else {
+            atom = zatom;
+        }
+        // let makers = [];
+        // loop throught links
+        const links = catom.getLinks();
+        for (const link of links) {
+            // connected atom
+            const conAtom = link.atom;
+            // connected atom predicted position
+            const predicted = symetry.project(link.fractional);
+            const xatom = conAtom.getChild(predicted);
+            // Atom alredy exists ..
+            if (xatom) {
+                const bond = new Bond(atom, xatom, 1);
+                this.molecule.bonds.push(bond);
+            }
+            else {
+                markers.push({
+                    atom: conAtom,
+                    symetry,
+                });
+            }
+        }
+        return markers;
+    }
+    extendByMarker(marker) {
+        const markersList = [];
+        markersList.push({
+            atom: marker.cellAtom,
+            symetry: marker.symetry,
+        });
+        const sym = marker.symetry;
+        let j = 1000;
+        while (markersList.length > 0 && j > 0) {
+            j--;
+            const currentMarker = markersList.shift();
+            if (!currentMarker) {
+                continue;
+            }
+            if (!currentMarker.symetry.equals(sym)) {
+                continue;
+            }
+            {
+                const markers = this.addAtomWithBonds(currentMarker.atom, currentMarker.symetry);
+                markersList.push(...markers);
+            }
+        }
+        this.addMarkers();
+    }
+    addMarkers() {
+        const cellAtoms = this.molecule.cellAtoms;
+        const unitCell = this.molecule.unitCell;
+        const markersPositions = [];
+        this.molecule.markers = [];
+        this.molecule.markersContacts = [];
+        const markers = this.molecule.markers;
+        const markersContacts = this.molecule.markersContacts;
+        const inList = (position) => {
+            for (const mposition of markersPositions) {
+                if (mposition.equals(position)) {
+                    return true;
+                }
+            }
+            return false;
+        };
+        // Loop througt all cell atoms
+        for (const catom of cellAtoms) {
+            for (const atom of catom.children) {
+                const atomSymetry = atom.symetry;
+                for (const link of catom.links) {
+                    const conAtom = link.atom;
+                    const symetry = link.symetry;
+                    const totalSymetry = atomSymetry.multiply(symetry);
+                    // var predicted1 = totalSymetry.multiple(conAtom.fractional);
+                    let predicted = symetry.project(conAtom.fractional);
+                    predicted = atomSymetry.project(predicted);
+                    const xatom = conAtom.getChild(predicted);
+                    if (!xatom) {
+                        const mPosition = unitCell.fractToOrth(predicted);
+                        if (!inList(mPosition)) {
+                            markersPositions.push(mPosition);
+                            markers.push(new Marker(mPosition, totalSymetry, conAtom));
+                            markersContacts.push(new MarkerContact(atom.position, mPosition));
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
+//# sourceMappingURL=MoleculeBuilder.js.map

package/dist/molecule3d/MoleculeBuilder.js.map

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

@@ -0,0 +1,10 @@
+import { Molecule3D } from './Molecule3D.js';
+export declare class MoleculeConnector {
+    private molecule;
+    constructor(molecule: Molecule3D);
+    buildConnectivity(): void;
+    private calculateCellLinks;
+    private isSutableByAssembly;
+    private isConnected;
+}
+//# sourceMappingURL=MoleculeConnector.d.ts.map

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

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package/dist/molecule3d/MoleculeConnector.js

@@ -0,0 +1,106 @@
+import { Vec3 } from '@chemistry/math';
+const CW_BOND_FROM = 0.4;
+const CW_BOND_TO = 1.2;
+export class MoleculeConnector {
+    constructor(molecule) {
+        this.molecule = molecule;
+    }
+    buildConnectivity() {
+        // no atoms ?
+        if (this.molecule.cellAtoms.length === 0) {
+            return;
+        }
+        // ORDER IS IMPORTANT
+        // Calculate Cell Links
+        this.calculateCellLinks();
+    }
+    calculateCellLinks() {
+        const cellAtoms = this.molecule.cellAtoms;
+        const unitCell = this.molecule.unitCell;
+        let maxRCow = -Infinity;
+        // get atom with bigest RcoW
+        for (const atom of cellAtoms) {
+            maxRCow = Math.max(atom.element.RCow, maxRCow);
+        }
+        // Maximal posible length
+        const maxRCow2 = maxRCow * 2 * CW_BOND_TO;
+        // Detect min and Max vectors of the cell atoms
+        let p1 = new Vec3(Infinity, Infinity, Infinity);
+        let p2 = new Vec3(-Infinity, -Infinity, -Infinity);
+        for (const atom of cellAtoms) {
+            p1.x = Math.min(p1.x, atom.position.x);
+            p1.y = Math.min(p1.y, atom.position.y);
+            p1.z = Math.min(p1.z, atom.position.z);
+            p2.x = Math.max(p2.x, atom.position.x);
+            p2.y = Math.max(p2.y, atom.position.y);
+            p2.z = Math.max(p2.z, atom.position.z);
+        }
+        // Double RVdW and fill by atoms
+        const vRcow = new Vec3(2 * maxRCow, 2 * maxRCow, 2 * maxRCow);
+        p1 = p1.sub(vRcow);
+        p2 = p2.add(vRcow);
+        const symetryList = unitCell.symetryList;
+        const translations = unitCell.transactionsFromOrthBox(p1, p2);
+        // Loop througt all cell atoms
+        for (let i = 0; i < cellAtoms.length; i++) {
+            const catom = cellAtoms[i];
+            // Loop throught all Symetries
+            for (const symetry of symetryList) {
+                // fill unit cell
+                const pre1 = symetry.project(catom.fractional);
+                // The atom inside unit cell
+                const pre2 = Vec3.getDecimal(pre1);
+                // Translation from orign to get atom
+                const transFromOrign = Vec3.sub(pre1, pre2);
+                for (const tr of translations) {
+                    const pre3 = Vec3.add(pre2, tr); // new fractional coordinates
+                    // Orth position prediction
+                    const pred = unitCell.fractToOrth(pre3);
+                    const px = p1.x <= pred.x && p2.x >= pred.x;
+                    const py = p1.y <= pred.y && p2.y >= pred.y;
+                    const pz = p1.z <= pred.z && p2.z >= pred.z;
+                    if (px && py && pz) {
+                        const trans = Vec3.sub(tr, transFromOrign);
+                        for (let m = i + 1; m < cellAtoms.length; m++) {
+                            const catom2 = cellAtoms[m];
+                            if (!this.isSutableByAssembly(catom, catom2)) {
+                                continue;
+                            }
+                            const disV = new Vec3(Math.abs(catom2.position.x - pred.x), Math.abs(catom2.position.y - pred.y), Math.abs(catom2.position.z - pred.z));
+                            const covBond = disV.x <= maxRCow2 && disV.y <= maxRCow2 && disV.z <= maxRCow2;
+                            if (!covBond) {
+                                continue;
+                            }
+                            if (this.isConnected(catom2, catom, pred)) {
+                                const sym = symetry.translate(trans);
+                                const symInverse = sym.inverse();
+                                catom2.addLink(catom, sym);
+                                catom.addLink(catom2, symInverse);
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+    isSutableByAssembly(atom1, atom2) {
+        if (atom1.assembly || atom2.assembly || atom1.group || atom2.group) {
+            if (atom1.group && atom1.group !== '-1' && atom1.group !== '1') {
+                return false;
+            }
+            if (atom2.group && atom2.group !== '-1' && atom2.group !== '1') {
+                return false;
+            }
+            return true;
+        }
+        return true;
+    }
+    isConnected(atom1, atom2, pred) {
+        const disV = new Vec3(atom1.position.x - pred.x, atom1.position.y - pred.y, atom1.position.z - pred.z);
+        const l = disV.length;
+        const r = atom1.element.RCow + atom2.element.RCow;
+        const hasBond = l <= r * CW_BOND_TO && l >= r * CW_BOND_FROM;
+        return hasBond;
+    }
+}
+//# sourceMappingURL=MoleculeConnector.js.map

package/dist/molecule3d/MoleculeConnector.js.map

@@ -0,0 +1 @@
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