molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-math/geometry/spacegroup/construction.js

@@ -1,169 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.SpacegroupCell = exports.Spacegroup = void 0;
-var linear_algebra_1 = require("../../linear-algebra");
-var tables_1 = require("./tables");
-var geometry_1 = require("../../geometry");
-var SpacegroupCell;
-(function (SpacegroupCell) {
-    /** Create a 'P 1' with cellsize [1, 1, 1] */
-    SpacegroupCell.Zero = create('P 1', linear_algebra_1.Vec3.create(1, 1, 1), linear_algebra_1.Vec3.create(Math.PI / 2, Math.PI / 2, Math.PI / 2));
-    /** True if 'P 1' with cellsize [1, 1, 1] */
-    function isZero(cell) {
-        if (!cell)
-            return true;
-        return cell.index === 0 && cell.size[0] === 1 && cell.size[1] === 1 && cell.size[1] === 1;
-    }
-    SpacegroupCell.isZero = isZero;
-    /** Returns Zero cell if the spacegroup does not exist */
-    function create(nameOrNumber, size, anglesInRadians) {
-        var index = (0, tables_1.getSpacegroupIndex)(nameOrNumber);
-        if (index < 0) {
-            console.warn("Unknown spacegroup '".concat(nameOrNumber, "', returning a 'P 1' with cellsize [1, 1, 1]"));
-            return SpacegroupCell.Zero;
-        }
-        var volume = size[0] * size[1] * size[2];
-        var alpha = anglesInRadians[0];
-        var beta = anglesInRadians[1];
-        var gamma = anglesInRadians[2];
-        var xScale = size[0], yScale = size[1], zScale = size[2];
-        var z1 = Math.cos(beta);
-        var z2 = (Math.cos(alpha) - Math.cos(beta) * Math.cos(gamma)) / Math.sin(gamma);
-        var z3 = Math.sqrt(1.0 - z1 * z1 - z2 * z2);
-        var x = [xScale, 0.0, 0.0];
-        var y = [Math.cos(gamma) * yScale, Math.sin(gamma) * yScale, 0.0];
-        var z = [z1 * zScale, z2 * zScale, z3 * zScale];
-        var fromFractional = linear_algebra_1.Mat4.ofRows([
-            [x[0], y[0], z[0], 0],
-            [0, y[1], z[1], 0],
-            [0, 0, z[2], 0],
-            [0, 0, 0, 1.0]
-        ]);
-        var toFractional = linear_algebra_1.Mat4.invert(linear_algebra_1.Mat4.zero(), fromFractional);
-        return { index: index, size: size, volume: volume, anglesInRadians: anglesInRadians, toFractional: toFractional, fromFractional: fromFractional };
-    }
-    SpacegroupCell.create = create;
-})(SpacegroupCell || (SpacegroupCell = {}));
-exports.SpacegroupCell = SpacegroupCell;
-var Spacegroup;
-(function (Spacegroup) {
-    /** P1 with [1, 1, 1] cell */
-    Spacegroup.ZeroP1 = create(SpacegroupCell.Zero);
-    function create(cell) {
-        var operators = tables_1.GroupData[cell.index].map(function (i) { return getOperatorMatrix(tables_1.OperatorData[i]); });
-        var name = tables_1.SpacegroupName[cell.index];
-        var num = tables_1.SpacegroupNumber[cell.index];
-        return { name: name, num: num, cell: cell, operators: operators };
-    }
-    Spacegroup.create = create;
-    var _ijkVec = (0, linear_algebra_1.Vec3)();
-    var _tempMat = (0, linear_algebra_1.Mat4)();
-    function setOperatorMatrix(spacegroup, index, i, j, k, target) {
-        linear_algebra_1.Vec3.set(_ijkVec, i, j, k);
-        linear_algebra_1.Mat4.fromTranslation(_tempMat, _ijkVec);
-        return linear_algebra_1.Mat4.mul(target, linear_algebra_1.Mat4.mul(target, linear_algebra_1.Mat4.mul(target, spacegroup.cell.fromFractional, _tempMat), spacegroup.operators[index]), spacegroup.cell.toFractional);
-    }
-    Spacegroup.setOperatorMatrix = setOperatorMatrix;
-    function getSymmetryOperator(spacegroup, spgrOp, i, j, k) {
-        var operator = setOperatorMatrix(spacegroup, spgrOp, i, j, k, linear_algebra_1.Mat4.zero());
-        return geometry_1.SymmetryOperator.create("".concat(spgrOp + 1, "_").concat(5 + i).concat(5 + j).concat(5 + k), operator, { hkl: linear_algebra_1.Vec3.create(i, j, k), spgrOp: spgrOp });
-    }
-    Spacegroup.getSymmetryOperator = getSymmetryOperator;
-    var _translationRef = (0, linear_algebra_1.Vec3)();
-    var _translationRefSymop = (0, linear_algebra_1.Vec3)();
-    var _translationRefOffset = (0, linear_algebra_1.Vec3)();
-    var _translationSymop = (0, linear_algebra_1.Vec3)();
-    /**
-     * Get Symmetry operator for transformation around the given
-     * reference point `ref` in fractional coordinates
-     */
-    function getSymmetryOperatorRef(spacegroup, spgrOp, i, j, k, ref) {
-        var operator = linear_algebra_1.Mat4.zero();
-        linear_algebra_1.Vec3.set(_ijkVec, i, j, k);
-        linear_algebra_1.Vec3.floor(_translationRef, ref);
-        linear_algebra_1.Mat4.copy(operator, spacegroup.operators[spgrOp]);
-        linear_algebra_1.Vec3.floor(_translationRefSymop, linear_algebra_1.Vec3.transformMat4(_translationRefSymop, ref, operator));
-        linear_algebra_1.Mat4.getTranslation(_translationSymop, operator);
-        linear_algebra_1.Vec3.sub(_translationSymop, _translationSymop, _translationRefSymop);
-        linear_algebra_1.Vec3.add(_translationSymop, _translationSymop, _translationRef);
-        linear_algebra_1.Vec3.add(_translationSymop, _translationSymop, _ijkVec);
-        linear_algebra_1.Mat4.setTranslation(operator, _translationSymop);
-        linear_algebra_1.Mat4.mul(operator, spacegroup.cell.fromFractional, operator);
-        linear_algebra_1.Mat4.mul(operator, operator, spacegroup.cell.toFractional);
-        linear_algebra_1.Vec3.sub(_translationRefOffset, _translationRefSymop, _translationRef);
-        var _i = i - _translationRefOffset[0];
-        var _j = j - _translationRefOffset[1];
-        var _k = k - _translationRefOffset[2];
-        // const operator = setOperatorMatrixRef(spacegroup, spgrOp, i, j, k, ref, Mat4.zero());
-        return geometry_1.SymmetryOperator.create("".concat(spgrOp + 1, "_").concat(5 + _i).concat(5 + _j).concat(5 + _k), operator, { hkl: linear_algebra_1.Vec3.create(_i, _j, _k), spgrOp: spgrOp });
-    }
-    Spacegroup.getSymmetryOperatorRef = getSymmetryOperatorRef;
-    function getOperatorMatrix(ids) {
-        var r1 = tables_1.TransformData[ids[0]];
-        var r2 = tables_1.TransformData[ids[1]];
-        var r3 = tables_1.TransformData[ids[2]];
-        return linear_algebra_1.Mat4.ofRows([r1, r2, r3, [0, 0, 0, 1]]);
-    }
-    function getOperatorXyz(op) {
-        return [
-            formatElement(getRotation(op[0], op[4], op[8]), getShift(op[12])),
-            formatElement(getRotation(op[1], op[5], op[9]), getShift(op[13])),
-            formatElement(getRotation(op[2], op[6], op[10]), getShift(op[14]))
-        ].join(',');
-    }
-    Spacegroup.getOperatorXyz = getOperatorXyz;
-    function getRotation(x, y, z) {
-        var r = [];
-        if (x > 0)
-            r.push('+X');
-        else if (x < 0)
-            r.push('-X');
-        if (y > 0)
-            r.push('+Y');
-        else if (y < 0)
-            r.push('-Y');
-        if (z > 0)
-            r.push('+Z');
-        else if (z < 0)
-            r.push('-Z');
-        if (r.length === 1) {
-            return r[0].charAt(0) === '+' ? r[0].substr(1) : r[0];
-        }
-        if (r.length === 2) {
-            var s0 = r[0].charAt(0);
-            var s1 = r[1].charAt(0);
-            if (s0 === '+')
-                return "".concat(r[0].substr(1)).concat(r[1]);
-            if (s1 === '+')
-                return "".concat(r[1].substr(1)).concat(r[0]);
-        }
-        throw new Error("unknown rotation '".concat(r, "', ").concat(x, " ").concat(y, " ").concat(z));
-    }
-    function getShift(s) {
-        switch (s) {
-            case 1 / 2: return '1/2';
-            case 1 / 4: return '1/4';
-            case 3 / 4: return '3/4';
-            case 1 / 3: return '1/3';
-            case 2 / 3: return '2/3';
-            case 1 / 6: return '1/6';
-            case 5 / 6: return '5/6';
-        }
-        return '';
-    }
-    function formatElement(rotation, shift) {
-        if (shift === '')
-            return rotation;
-        if (rotation.length > 2)
-            return "".concat(rotation, "+").concat(shift);
-        return rotation.charAt(0) === '-' ? "".concat(shift).concat(rotation) : "".concat(shift, "+").concat(rotation);
-    }
-})(Spacegroup || (Spacegroup = {}));
-exports.Spacegroup = Spacegroup;
-//# sourceMappingURL=construction.js.map

package/lib/commonjs/mol-math/geometry/spacegroup/tables.d.ts

@@ -1,371 +0,0 @@
-/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-export declare const TransformData: number[][];
-export declare const OperatorData: number[][];
-export declare const GroupData: number[][];
-export declare const SpacegroupNameToIndexMap: {
-    'P 1': number;
-    'P -1': number;
-    'P 1 2 1': number;
-    'P 1 21 1': number;
-    'C 1 2 1': number;
-    'P 1 m 1': number;
-    'P 1 c 1': number;
-    'C 1 m 1': number;
-    'C 1 c 1': number;
-    'P 1 2/m 1': number;
-    'P 1 21/m 1': number;
-    'C 1 2/m 1': number;
-    'P 1 2/c 1': number;
-    'P 1 21/c 1': number;
-    'C 1 2/c 1': number;
-    'P 2 2 2': number;
-    'P 2 2 21': number;
-    'P 21 21 2': number;
-    'P 21 21 21': number;
-    'C 2 2 21': number;
-    'C 2 2 2': number;
-    'F 2 2 2': number;
-    'I 2 2 2': number;
-    'I 21 21 21': number;
-    'P m m 2': number;
-    'P m c 21': number;
-    'P c c 2': number;
-    'P m a 2': number;
-    'P c a 21': number;
-    'P n c 2': number;
-    'P m n 21': number;
-    'P b a 2': number;
-    'P n a 21': number;
-    'P n n 2': number;
-    'C m m 2': number;
-    'C m c 21': number;
-    'C c c 2': number;
-    'A m m 2': number;
-    'A b m 2': number;
-    'A m a 2': number;
-    'A b a 2': number;
-    'F m m 2': number;
-    'F d d 2': number;
-    'I m m 2': number;
-    'I b a 2': number;
-    'I m a 2': number;
-    'P 2/m 2/m 2/m': number;
-    'P m m m': number;
-    'P 2/n 2/n 2/n': number;
-    'P n n n': number;
-    'P 2/c 2/c 2/m': number;
-    'P c c m': number;
-    'P 2/b 2/a 2/n': number;
-    'P b a n': number;
-    'P 21/m 2/m 2/a': number;
-    'P m m a': number;
-    'P 2/n 21/n 2/a': number;
-    'P n n a': number;
-    'P 2/m 2/n 21/a': number;
-    'P m n a': number;
-    'P 21/c 2/c 2/a': number;
-    'P c c a': number;
-    'P 21/b 21/a 2/m': number;
-    'P b a m': number;
-    'P 21/c 21/c 2/n': number;
-    'P c c n': number;
-    'P 2/b 21/c 21/m': number;
-    'P b c m': number;
-    'P 21/n 21/n 2/m': number;
-    'P n n m': number;
-    'P 21/m 21/m 2/n': number;
-    'P m m n': number;
-    'P 21/b 2/c 21/n': number;
-    'P b c n': number;
-    'P 21/b 21/c 21/a': number;
-    'P b c a': number;
-    'P 21/n 21/m 21/a': number;
-    'P n m a': number;
-    'C 2/m 2/c 21/m': number;
-    'C m c m': number;
-    'C 2/m 2/c 21/a': number;
-    'C m c a': number;
-    'C 2/m 2/m 2/m': number;
-    'C m m m': number;
-    'C 2/c 2/c 2/m': number;
-    'C c c m': number;
-    'C 2/m 2/m 2/a': number;
-    'C m m a': number;
-    'C 2/c 2/c 2/a': number;
-    'C c c a': number;
-    'F 2/m 2/m 2/m': number;
-    'F m m m': number;
-    'F 2/d 2/d 2/d': number;
-    'F d d d': number;
-    'I 2/m 2/m 2/m': number;
-    'I m m m': number;
-    'I 2/b 2/a 2/m': number;
-    'I b a m': number;
-    'I 21/b 21/c 21/a': number;
-    'I b c a': number;
-    'I 21/m 21/m 21/a': number;
-    'I m m a': number;
-    'P 4': number;
-    'P 41': number;
-    'P 42': number;
-    'P 43': number;
-    'I 4': number;
-    'I 41': number;
-    'P -4': number;
-    'I -4': number;
-    'P 4/m': number;
-    'P 42/m': number;
-    'P 4/n': number;
-    'P 42/n': number;
-    'I 4/m': number;
-    'I 41/a': number;
-    'P 4 2 2': number;
-    'P 4 21 2': number;
-    'P 41 2 2': number;
-    'P 41 21 2': number;
-    'P 42 2 2': number;
-    'P 42 21 2': number;
-    'P 43 2 2': number;
-    'P 43 21 2': number;
-    'I 4 2 2': number;
-    'I 41 2 2': number;
-    'P 4 m m': number;
-    'P 4 b m': number;
-    'P 42 c m': number;
-    'P 42 n m': number;
-    'P 4 c c': number;
-    'P 4 n c': number;
-    'P 42 m c': number;
-    'P 42 b c': number;
-    'I 4 m m': number;
-    'I 4 c m': number;
-    'I 41 m d': number;
-    'I 41 c d': number;
-    'P -4 2 m': number;
-    'P -4 2 c': number;
-    'P -4 21 m': number;
-    'P -4 21 c': number;
-    'P -4 m 2': number;
-    'P -4 c 2': number;
-    'P -4 b 2': number;
-    'P -4 n 2': number;
-    'I -4 m 2': number;
-    'I -4 c 2': number;
-    'I -4 2 m': number;
-    'I -4 2 d': number;
-    'P 4/m 2/m 2/m': number;
-    'P4/m m m': number;
-    'P 4/m 2/c 2/c': number;
-    'P4/m c c': number;
-    'P 4/n 2/b 2/m': number;
-    'P4/n b m': number;
-    'P 4/n 2/n 2/c': number;
-    'P4/n n c': number;
-    'P 4/m 21/b 2/m': number;
-    'P4/m b m': number;
-    'P 4/m 21/n 2/c': number;
-    'P4/m n c': number;
-    'P 4/n 21/m 2/m': number;
-    'P4/n m m': number;
-    'P 4/n 2/c 2/c': number;
-    'P4/n c c': number;
-    'P 42/m 2/m 2/c': number;
-    'P42/m m c': number;
-    'P 42/m 2/c 2/m': number;
-    'P42/m c m': number;
-    'P 42/n 2/b 2/c': number;
-    'P42/n b c': number;
-    'P 42/n 2/n 2/m': number;
-    'P42/n n m': number;
-    'P 42/m 21/b 2/c': number;
-    'P42/m b c': number;
-    'P 42/m 21/n 2/m': number;
-    'P42/m n m': number;
-    'P 42/n 21/m 2/c': number;
-    'P42/n m c': number;
-    'P 42/n 21/c 2/m': number;
-    'P42/n c m': number;
-    'I 4/m 2/m 2/m': number;
-    'I4/m m m': number;
-    'I 4/m 2/c 2/m': number;
-    'I4/m c m': number;
-    'I 41/a 2/m 2/d': number;
-    'I41/a m d': number;
-    'I 41/a 2/c 2/d': number;
-    'I41/a c d': number;
-    'P 3': number;
-    'P 31': number;
-    'P 32': number;
-    'H 3': number;
-    'R 3': number;
-    'P -3': number;
-    'H -3': number;
-    'R -3': number;
-    'P 3 1 2': number;
-    'P 3 2 1': number;
-    'P 31 1 2': number;
-    'P 31 2 1': number;
-    'P 32 1 2': number;
-    'P 32 2 1': number;
-    'H 3 2': number;
-    'R 3 2': number;
-    'P 3 m 1': number;
-    'P 3 1 m': number;
-    'P 3 c 1': number;
-    'P 3 1 c': number;
-    'H 3 m': number;
-    'R 3 m': number;
-    'H 3 c': number;
-    'R 3 c': number;
-    'P -3 1 2/m': number;
-    'P -3 1 m': number;
-    'P -3 1 2/c': number;
-    'P -3 1 c': number;
-    'P -3 2/m 1': number;
-    'P -3 m 1': number;
-    'P -3 2/c 1': number;
-    'P -3 c 1': number;
-    'H -3 2/m': number;
-    'H -3 m': number;
-    'R -3 2/m': number;
-    'R -3 m': number;
-    'H -3 2/c': number;
-    'H -3 c': number;
-    'R -3 2/c': number;
-    'R -3 c': number;
-    'P 6': number;
-    'P 61': number;
-    'P 65': number;
-    'P 62': number;
-    'P 64': number;
-    'P 63': number;
-    'P -6': number;
-    'P 6/m': number;
-    'P 63/m': number;
-    'P 6 2 2': number;
-    'P 61 2 2': number;
-    'P 65 2 2': number;
-    'P 62 2 2': number;
-    'P 64 2 2': number;
-    'P 63 2 2': number;
-    'P 6 m m': number;
-    'P 6 c c': number;
-    'P 63 c m': number;
-    'P 63 m c': number;
-    'P -6 m 2': number;
-    'P -6 c 2': number;
-    'P -6 2 m': number;
-    'P -6 2 c': number;
-    'P 6/m 2/m 2/m': number;
-    'P 6/m m m': number;
-    'P 6/m 2/c 2/c': number;
-    'P 6/m c c': number;
-    'P 63/m 2/c 2/m': number;
-    'P 63/m c m': number;
-    'P 63/m 2/m 2/c': number;
-    'P 63/m m c': number;
-    'P 2 3': number;
-    'F 2 3': number;
-    'I 2 3': number;
-    'P 21 3': number;
-    'I 21 3': number;
-    'P 2/m -3': number;
-    'P m -3': number;
-    'P 2/n -3': number;
-    'P n -3': number;
-    'F 2/m -3': number;
-    'F m -3': number;
-    'F 2/d -3': number;
-    'F d -3': number;
-    'I 2/m -3': number;
-    'I m -3': number;
-    'P 21/a -3': number;
-    'P a -3': number;
-    'I 21/a -3': number;
-    'I a -3': number;
-    'P 4 3 2': number;
-    'P 42 3 2': number;
-    'F 4 3 2': number;
-    'F 41 3 2': number;
-    'I 4 3 2': number;
-    'P 43 3 2': number;
-    'P 41 3 2': number;
-    'I 41 3 2': number;
-    'P -4 3 m': number;
-    'F -4 3 m': number;
-    'I -4 3 m': number;
-    'P -4 3 n': number;
-    'F -4 3 c': number;
-    'I -4 3 d': number;
-    'P 4/m -3 2/m': number;
-    'P m -3 m': number;
-    'P 4/n -3 2/n': number;
-    'P n -3 n': number;
-    'P 42/m -3 2/n': number;
-    'P m -3 n': number;
-    'P 42/n -3 2/m': number;
-    'P n -3 m': number;
-    'F 4/m -3 2/m': number;
-    'F m -3 m': number;
-    'F 4/m -3 2/c': number;
-    'F m -3 c': number;
-    'F 41/d -3 2/m': number;
-    'F d -3 m': number;
-    'F 41/d -3 2/c': number;
-    'F d -3 c': number;
-    'I 4/m -3 2/m': number;
-    'I m -3 m': number;
-    'I 41/a -3 2/d': number;
-    'I a -3 d': number;
-    'P 1 1 2': number;
-    'P 1 1 21': number;
-    'B 1 1 2': number;
-    'B 2': number;
-    'A 1 2 1': number;
-    'C 1 21 1': number;
-    'I 1 2 1': number;
-    'I 2': number;
-    'I 1 21 1': number;
-    'P 1 1 m': number;
-    'P 1 1 b': number;
-    'B 1 1 m': number;
-    'B 1 1 b': number;
-    'P 1 1 2/m': number;
-    'P 1 1 21/m': number;
-    'B 1 1 2/m': number;
-    'P 1 1 2/b': number;
-    'P 1 1 21/b': number;
-    'P 1 21/n 1': number;
-    'P 1 21/a 1': number;
-    'B 1 1 2/b': number;
-    'P 21 2 2': number;
-    'P 2 21 2': number;
-    'P 21 21 2 (a)': number;
-    'P 21 2 21': number;
-    'P 2 21 21': number;
-    'C 2 2 21a)': number;
-    'C 2 2 2a': number;
-    'F 2 2 2a': number;
-    'I 2 2 2a': number;
-    'P 21/m 21/m 2/n a': number;
-    'P 42 21 2a': number;
-    'I 2 3a': number;
-};
-export declare function getSpacegroupIndexFromNumber(num: number): number;
-export declare function getSpacegroupNumberFromIndex(idx: number): number;
-export declare type SpacegroupName = keyof typeof SpacegroupNameToIndexMap;
-/** Maps spacegroup index to Hermann-Mauguin spacegroup name */
-export declare const SpacegroupName: {
-    [idx: number]: SpacegroupName;
-};
-/** Maps spacegroup index to spacegroup number from International Tables for Crystallography */
-export declare const SpacegroupNumber: {
-    [idx: number]: number;
-};
-/** return -1 if the spacegroup does not exist */
-export declare function getSpacegroupIndex(nameOrNumber: number | string | SpacegroupName): number;