diff --git a/src/mol-math/geometry/spacegroup/construction.ts b/src/mol-math/geometry/spacegroup/construction.ts
index a347c60e7307fade102bacacb931788d21f6b4b0..48d9cd359cd97bf77cc52d2ab2b1a8754aca4d25 100644
--- a/src/mol-math/geometry/spacegroup/construction.ts
+++ b/src/mol-math/geometry/spacegroup/construction.ts
@@ -90,7 +90,7 @@ namespace Spacegroup {
export function getSymmetryOperator(spacegroup: Spacegroup, index: number, i: number, j: number, k: number): SymmetryOperator {
const operator = updateOperatorMatrix(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));
+ return SymmetryOperator.create(`${index + 1}_${5 + i}${5 + j}${5 + k}`, operator, { id: '', operList: [] }, '', Vec3.create(i, j, k), index);
}
function getOperatorMatrix(ids: number[]) {
diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index e513259dca683f6bac349ddbe8dc76f831e7831d..4ee54d3537f7fc69025bfd05888612e65ad442b4 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -6,6 +6,7 @@
import { Vec3, Mat4, Mat3, Quat } from '../linear-algebra/3d'
import { lerp as scalar_lerp } from '../../mol-math/interpolate';
+import { defaults } from '../../mol-util';
interface SymmetryOperator {
readonly name: string,
@@ -21,6 +22,8 @@ interface SymmetryOperator {
readonly ncsId: string,
readonly hkl: Vec3,
+ /** spacegroup symmetry operator index, -1 if not applicable */
+ readonly spgrOp: number,
readonly matrix: Mat4,
// cache the inverse of the transform
@@ -35,12 +38,13 @@ namespace SymmetryOperator {
export const RotationTranslationEpsilon = 0.005;
- export function create(name: string, matrix: Mat4, assembly: SymmetryOperator['assembly'], ncsId?: string, hkl?: Vec3): SymmetryOperator {
+ export function create(name: string, matrix: Mat4, assembly: SymmetryOperator['assembly'], ncsId?: string, hkl?: Vec3, spgrOp?: number): SymmetryOperator {
const _hkl = hkl ? Vec3.clone(hkl) : Vec3.zero();
+ spgrOp = defaults(spgrOp, -1)
ncsId = ncsId || ''
- if (Mat4.isIdentity(matrix)) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, ncsId };
+ if (Mat4.isIdentity(matrix)) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId };
if (!Mat4.isRotationAndTranslation(matrix, RotationTranslationEpsilon)) throw new Error(`Symmetry operator (${name}) must be a composition of rotation and translation.`);
- return { name, assembly, matrix, inverse: Mat4.invert(Mat4.zero(), matrix), isIdentity: false, hkl: _hkl, ncsId };
+ return { name, assembly, matrix, inverse: Mat4.invert(Mat4.zero(), matrix), isIdentity: false, hkl: _hkl, spgrOp, ncsId };
}
export function checkIfRotationAndTranslation(rot: Mat3, offset: Vec3) {
@@ -106,11 +110,11 @@ namespace SymmetryOperator {
/**
* Apply the 1st and then 2nd operator. ( = second.matrix * first.matrix).
- * Keep `name`, `assembly`, `ncsId` and `hkl` properties from second.
+ * Keep `name`, `assembly`, `ncsId`, `hkl` and `spgrOpId` properties from second.
*/
export function compose(first: SymmetryOperator, second: SymmetryOperator) {
const matrix = Mat4.mul(Mat4.zero(), second.matrix, first.matrix);
- return create(second.name, matrix, second.assembly, second.ncsId, second.hkl);
+ return create(second.name, matrix, second.assembly, second.ncsId, second.hkl, second.spgrOp);
}
export interface CoordinateMapper<T extends number> { (index: T, slot: Vec3): Vec3 }
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 70a449b21cd13c5007377488bae78ec4929b7053..17aa1c75a40ec49304eb821a16f9159c912e2bcc 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -113,6 +113,8 @@ const entity = {
const unit = {
id: StructureElement.property(l => l.unit.id),
operator_name: StructureElement.property(l => l.unit.conformation.operator.name),
+ hkl: StructureElement.property(l => l.unit.conformation.operator.hkl),
+ spgrOp: StructureElement.property(l => l.unit.conformation.operator.spgrOp),
model_num: StructureElement.property(l => l.unit.model.modelNum),
pdbx_struct_assembly_id: StructureElement.property(l => l.unit.conformation.operator.assembly.id),
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index cb9d8ebf34dfdecd269468db5bccdfa30185064a..5379e19368273a32d207bbd2ff17e9fc6dcc28f8 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -117,7 +117,7 @@ function getOperators(symmetry: ModelSymmetry, ijkMin: Vec3, ijkMax: Vec3) {
for (let u = 0; u < ncsCount; ++u) {
const ncsOp = ncsOperators![u]
const matrix = Mat4.mul(Mat4.zero(), symOp.matrix, ncsOp.matrix)
- const operator = SymmetryOperator.create(`${symOp.name} ${ncsOp.name}`, matrix, symOp.assembly, ncsOp.ncsId, symOp.hkl);
+ const operator = SymmetryOperator.create(`${symOp.name} ${ncsOp.name}`, matrix, symOp.assembly, ncsOp.ncsId, symOp.hkl, symOp.spgrOp);
operators[operators.length] = operator;
}
} else {
diff --git a/src/mol-plugin/ui/sequence.tsx b/src/mol-plugin/ui/sequence.tsx
index b6855b9f569fd2fe06140cb333ac7b80ecff497d..b8f9569f5516dceb2cebca18f877f385237f12ad 100644
--- a/src/mol-plugin/ui/sequence.tsx
+++ b/src/mol-plugin/ui/sequence.tsx
@@ -18,8 +18,12 @@ import { MarkerAction } from '../../mol-util/marker-action';
import { ParameterControls } from './controls/parameters';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
-function opKey(ids: string[]) {
- return ids.sort().join(',')
+function opKey(l: StructureElement) {
+ const ids = SP.unit.pdbx_struct_oper_list_ids(l)
+ const ncs = SP.unit.struct_ncs_oper_id(l)
+ const hkl = SP.unit.hkl(l)
+ const spgrOp = SP.unit.spgrOp(l)
+ return `${ids.sort().join(',')}|${ncs}|${hkl}|${spgrOp}`
}
function getSequenceWrapper(state: SequenceViewState, structureSelection: StructureElementSelectionManager): SequenceWrapper.Any | undefined {
@@ -32,7 +36,7 @@ function getSequenceWrapper(state: SequenceViewState, structureSelection: Struct
StructureElement.set(l, unit, unit.elements[0])
if (SP.entity.id(l) !== entity) continue
if (SP.chain.label_asym_id(l) !== chain) continue
- if (opKey(SP.unit.pdbx_struct_oper_list_ids(l)) !== operator) continue
+ if (opKey(l) !== operator) continue
// console.log('new PolymerSequenceWrapper', structureSelection.get(structure))
const sw = new PolymerSequenceWrapper({ structure, unit })
@@ -96,10 +100,10 @@ function getOperatorOptions(structure: Structure, entityId: string, label_asym_i
if (SP.entity.id(l) !== entityId) return
if (SP.chain.label_asym_id(l) !== label_asym_id) return
- const id = opKey(SP.unit.pdbx_struct_oper_list_ids(l))
+ const id = opKey(l)
if (seen.has(id)) return
- const label = `${SP.unit.pdbx_struct_oper_list_ids(l).join(', ')}`
+ const label = unit.conformation.operator.name
options.push([ id, label ])
seen.add(id)
})