diff --git a/src/mol-math/geometry/spacegroup/construction.ts b/src/mol-math/geometry/spacegroup/construction.ts
index dee2c694c6f9ab60647d6db90ac8097c0f2505de..2a49c7843fdefb24128d51425d5f5615980fada8 100644
--- a/src/mol-math/geometry/spacegroup/construction.ts
+++ b/src/mol-math/geometry/spacegroup/construction.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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>
*/
import { Vec3, Mat4 } from '../../linear-algebra'
@@ -73,7 +74,7 @@ namespace SpacegroupCell {
namespace Spacegroup {
- // P1 with [1, 1, 1] cell.
+ /** P1 with [1, 1, 1] cell */
export const ZeroP1 = create(SpacegroupCell.Zero);
export function create(cell: SpacegroupCell): Spacegroup {
@@ -81,18 +82,56 @@ namespace Spacegroup {
return { name: SpacegroupNames[cell.index], cell, operators };
}
- const _tempVec = Vec3.zero(), _tempMat = Mat4.zero();
- export function updateOperatorMatrix(spacegroup: Spacegroup, index: number, i: number, j: number, k: number, target: Mat4) {
- _tempVec[0] = i;
- _tempVec[1] = j;
- _tempVec[2] = k;
-
- Mat4.fromTranslation(_tempMat, _tempVec);
- return Mat4.mul(target, Mat4.mul(target, Mat4.mul(target, spacegroup.cell.fromFractional, _tempMat), spacegroup.operators[index]), spacegroup.cell.toFractional);
+ const _ijkVec = Vec3();
+ const _tempMat = Mat4();
+ export function setOperatorMatrix(spacegroup: Spacegroup, index: number, i: number, j: number, k: number, target: Mat4) {
+ Vec3.set(_ijkVec, i, j, k);
+
+ Mat4.fromTranslation(_tempMat, _ijkVec);
+ return Mat4.mul(
+ target,
+ Mat4.mul(
+ target,
+ Mat4.mul(target, spacegroup.cell.fromFractional, _tempMat),
+ spacegroup.operators[index]
+ ),
+ spacegroup.cell.toFractional
+ );
}
export function getSymmetryOperator(spacegroup: Spacegroup, index: number, i: number, j: number, k: number): SymmetryOperator {
- const operator = updateOperatorMatrix(spacegroup, index, i, j, k, Mat4.zero());
+ const operator = setOperatorMatrix(spacegroup, index, i, j, k, Mat4.zero());
+ return SymmetryOperator.create(`${index + 1}_${5 + i}${5 + j}${5 + k}`, operator, { id: '', operList: [] }, '', Vec3.create(i, j, k), index);
+ }
+
+ const _translationRef = Vec3()
+ const _translationRefSymop = Vec3()
+ const _translationSymop = Vec3()
+ export function setOperatorMatrixRef(spacegroup: Spacegroup, index: number, i: number, j: number, k: number, ref: Vec3, target: Mat4) {
+ Vec3.set(_ijkVec, i, j, k);
+ Vec3.floor(_translationRef, ref)
+
+ Mat4.copy(target, spacegroup.operators[index])
+
+ Vec3.floor(_translationRefSymop, Vec3.transformMat4(_translationRefSymop, ref, target))
+
+ Mat4.getTranslation(_translationSymop, target)
+ Vec3.sub(_translationSymop, _translationSymop, _translationRefSymop)
+ Vec3.add(_translationSymop, _translationSymop, _translationRef)
+ Vec3.add(_translationSymop, _translationSymop, _ijkVec)
+
+ Mat4.setTranslation(target, _translationSymop)
+ Mat4.mul(target, spacegroup.cell.fromFractional, target)
+ Mat4.mul(target, target, spacegroup.cell.toFractional)
+ return target
+ }
+
+ /**
+ * Get Symmetry operator for transformation around the given
+ * reference point `ref` in fractional coordinates
+ */
+ export function getSymmetryOperatorRef(spacegroup: Spacegroup, index: number, i: number, j: number, k: number, ref: Vec3) {
+ const operator = setOperatorMatrixRef(spacegroup, index, i, j, k, ref, Mat4.zero());
return SymmetryOperator.create(`${index + 1}_${5 + i}${5 + j}${5 + k}`, operator, { id: '', operList: [] }, '', Vec3.create(i, j, k), index);
}
diff --git a/src/mol-model/structure/model/properties/symmetry.ts b/src/mol-model/structure/model/properties/symmetry.ts
index ee3a9c5e28103a0df624f6ad7513291c6389b937..38b9e5e12642ac80ad7c8e5ae1daa661bd6334a9 100644
--- a/src/mol-model/structure/model/properties/symmetry.ts
+++ b/src/mol-model/structure/model/properties/symmetry.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
@@ -9,6 +9,7 @@ import { arrayFind } from '../../../../mol-data/util'
import { StructureQuery } from '../../query'
import { Model } from '../../model'
import { Spacegroup } from '../../../../mol-math/geometry';
+import { Vec3 } from '../../../../mol-math/linear-algebra';
/** Determine an atom set and a list of operators that should be applied to that set */
export interface OperatorGroup {
@@ -47,8 +48,14 @@ interface ModelSymmetry {
readonly isNonStandardCrytalFrame: boolean,
readonly ncsOperators?: ReadonlyArray<SymmetryOperator>,
- // optionally cached operators from [-3, -3, -3] to [3, 3, 3]
- _operators_333?: SymmetryOperator[]
+ /**
+ * optionally cached operators from [-3, -3, -3] to [3, 3, 3]
+ * around reference point `ref` in fractional coordinates
+ */
+ _operators_333?: {
+ ref: Vec3,
+ operators: SymmetryOperator[]
+ }
}
namespace ModelSymmetry {
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index b472051b1e9cd5473d486353441768dfa06cc34e..6dbd5de05659c58bfaf2d7a46346d2baf49f8249 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -10,7 +10,7 @@ import { EquivalenceClasses } from '../../../mol-data/util';
import { Spacegroup, SpacegroupCell, SymmetryOperator } from '../../../mol-math/geometry';
import { Vec3, Mat4 } from '../../../mol-math/linear-algebra';
import { RuntimeContext, Task } from '../../../mol-task';
-import { ModelSymmetry } from '../model';
+import { ModelSymmetry, Model } from '../model';
import { QueryContext, StructureSelection } from '../query';
import Structure from './structure';
import Unit from './unit';
@@ -95,7 +95,7 @@ namespace StructureSymmetry {
}
}
-function getOperators(symmetry: ModelSymmetry, ijkMin: Vec3, ijkMax: Vec3) {
+function getOperators(symmetry: ModelSymmetry, ijkMin: Vec3, ijkMax: Vec3, modelCenter: Vec3) {
const { spacegroup, ncsOperators } = symmetry;
const ncsCount = (ncsOperators && ncsOperators.length) || 0
const operators: SymmetryOperator[] = [];
@@ -107,13 +107,17 @@ function getOperators(symmetry: ModelSymmetry, ijkMin: Vec3, ijkMax: Vec3) {
operators[0] = Spacegroup.getSymmetryOperator(spacegroup, 0, 0, 0, 0)
}
+ const { toFractional } = spacegroup.cell
+ const ref = Vec3.transformMat4(Vec3(), modelCenter, toFractional)
+
for (let op = 0; op < spacegroup.operators.length; op++) {
for (let i = ijkMin[0]; i <= ijkMax[0]; i++) {
for (let j = ijkMin[1]; j <= ijkMax[1]; j++) {
for (let k = ijkMin[2]; k <= ijkMax[2]; k++) {
// check if we have added identity as the 1st operator.
if (!ncsCount && op === 0 && i === 0 && j === 0 && k === 0) continue;
- const symOp = Spacegroup.getSymmetryOperator(spacegroup, op, i, j, k);
+
+ const symOp = Spacegroup.getSymmetryOperatorRef(spacegroup, op, i, j, k, ref)
if (ncsCount) {
for (let u = 0; u < ncsCount; ++u) {
const ncsOp = ncsOperators![u]
@@ -131,10 +135,15 @@ function getOperators(symmetry: ModelSymmetry, ijkMin: Vec3, ijkMax: Vec3) {
return operators;
}
-function getOperatorsCached333(symmetry: ModelSymmetry) {
- if (typeof symmetry._operators_333 !== 'undefined') return symmetry._operators_333;
- symmetry._operators_333 = getOperators(symmetry, Vec3.create(-3, -3, -3), Vec3.create(3, 3, 3));
- return symmetry._operators_333;
+function getOperatorsCached333(symmetry: ModelSymmetry, ref: Vec3) {
+ if (symmetry._operators_333 && Vec3.equals(ref, symmetry._operators_333.ref)) {
+ return symmetry._operators_333.operators;
+ }
+ symmetry._operators_333 = {
+ ref: Vec3.clone(ref),
+ operators: getOperators(symmetry, Vec3.create(-3, -3, -3), Vec3.create(3, 3, 3), ref)
+ };
+ return symmetry._operators_333.operators;
}
function assembleOperators(structure: Structure, operators: ReadonlyArray<SymmetryOperator>) {
@@ -164,7 +173,8 @@ async function findSymmetryRange(ctx: RuntimeContext, structure: Structure, ijkM
const { spacegroup } = models[0].symmetry;
if (SpacegroupCell.isZero(spacegroup.cell)) return structure;
- const operators = getOperators(models[0].symmetry, ijkMin, ijkMax);
+ const modelCenter = Model.getCenter(models[0])
+ const operators = getOperators(models[0].symmetry, ijkMin, ijkMax, modelCenter);
return assembleOperators(structure, operators);
}
@@ -177,7 +187,8 @@ async function findMatesRadius(ctx: RuntimeContext, structure: Structure, radius
if (SpacegroupCell.isZero(spacegroup.cell)) return structure;
if (ctx.shouldUpdate) await ctx.update('Initialing...');
- const operators = getOperatorsCached333(symmetry);
+ const modelCenter = Model.getCenter(models[0])
+ const operators = getOperatorsCached333(symmetry, modelCenter);
const lookup = structure.lookup3d;
const assembler = Structure.Builder();