From d597f1e88c0a0516ff0488c2a8c26560415b855b Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 9 Nov 2017 21:34:46 +0100
Subject: [PATCH] Higher tolerance for "symmetry operators"
---
src/mol-math/geometry/symmetry-operator.ts | 4 +++-
src/perf-tests/structure.ts | 10 ++++++----
2 files changed, 9 insertions(+), 5 deletions(-)
diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index 2e7bfabc8..053113865 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -21,10 +21,12 @@ namespace SymmetryOperator {
export const DefaultName = '1_555'
export const Default: SymmetryOperator = create(DefaultName, Mat4.identity());
+ const RotationEpsilon = 0.0001;
+
export function create(name: string, matrix: Mat4, hkl?: number[]): SymmetryOperator {
const _hkl = hkl ? Vec3.create(hkl[0], hkl[1], hkl[2]) : Vec3.zero();
if (Mat4.isIdentity(matrix)) return { name, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl };
- if (!Mat4.isRotationAndTranslation(matrix)) throw new Error(`Symmetry operator (${name}) must be a composition of rotation and translation.`);
+ if (!Mat4.isRotationAndTranslation(matrix, RotationEpsilon)) throw new Error(`Symmetry operator (${name}) must be a composition of rotation and translation.`);
return { name, matrix, inverse: Mat4.invert(Mat4.zero(), matrix), isIdentity: false, hkl: _hkl };
}
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 5a7e48b41..9898edf50 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -241,9 +241,11 @@ export namespace PropertyAccess {
console.log(to_mmCIF('test', s));
}
- export function testAssembly(s: Structure) {
+ export function testAssembly(id: string, s: Structure) {
+ console.time('assembly')
const a = Symmetry.buildAssembly(s, '1');
- fs.writeFileSync('e:/test/molstar/1hrv_assembly.cif', to_mmCIF('test', a, false));
+ console.timeEnd('assembly')
+ fs.writeFileSync(`e:/test/molstar/${id}_assembly.bcif`, to_mmCIF(id, a, true));
console.log('exported');
//write(a);
}
@@ -252,12 +254,12 @@ export namespace PropertyAccess {
//const { structures, models, mmcif } = await readCIF('./examples/1cbs_full.bcif');
//const { structures, models, mmcif } = await readCIF('e:/test/quick/3j3q_full.bcif');
//const { structures, models, mmcif } = await readCIF('e:/test/quick/1cbs_updated.cif');
- const { structures, models/*, mmcif*/ } = await readCIF('e:/test/quick/1hrv_updated.cif');
+ const { structures, models/*, mmcif*/ } = await readCIF('e:/test/quick/5j7v_updated.cif');
//console.log(mmcif.pdbx_struct_oper_list.matrix.toArray());
// console.log(mmcif.pdbx_struct_oper_list.vector.toArray());
- testAssembly(structures[0]);
+ testAssembly('5j7v', structures[0]);
throw '';
console.log(models[0].symmetry.assemblies);
--
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