From 52a02fa922fea252a77ca2d167cd9c1c54ff296f Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 6 Nov 2018 17:57:55 +0100
Subject: [PATCH] mol-plugin: structure transform3d
---
src/mol-model/structure/structure/structure.ts | 16 +++++++++++++++-
src/mol-plugin/state/transforms/model.ts | 7 +++++--
2 files changed, 20 insertions(+), 3 deletions(-)
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 224ec2f08..d4e76255b 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -21,7 +21,7 @@ import StructureProperties from './properties';
import { ResidueIndex, ChainIndex, EntityIndex } from '../model/indexing';
import { Carbohydrates } from './carbohydrates/data';
import { computeCarbohydrates } from './carbohydrates/compute';
-import { Vec3 } from 'mol-math/linear-algebra';
+import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { idFactory } from 'mol-util/id-factory';
import { GridLookup3D } from 'mol-math/geometry';
import { UUID } from 'mol-util';
@@ -344,6 +344,20 @@ namespace Structure {
}
}
+ export function transform(s: Structure, transform: Mat4) {
+ if (Mat4.isIdentity(transform)) return s;
+ if (!Mat4.isRotationAndTranslation(transform)) throw new Error('Only rotation/translation combination can be applied.');
+
+ const units: Unit[] = [];
+ for (const u of s.units) {
+ const old = u.conformation.operator;
+ const op = SymmetryOperator.create(old.name, transform, old.hkl);
+ units.push(u.applyOperator(u.id, op));
+ }
+
+ return new Structure(units);
+ }
+
export class StructureBuilder {
private units: Unit[] = [];
private invariantId = idFactory()
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 535003639..1ebe478e2 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -11,6 +11,7 @@ import { Model, Format, Structure, ModelSymmetry, StructureSymmetry, QueryContex
import { ParamDefinition as PD } from 'mol-util/param-definition';
import Expression from 'mol-script/language/expression';
import { compile } from 'mol-script/runtime/query/compiler';
+import { Mat4 } from 'mol-math/linear-algebra';
export { ParseModelsFromMmCif }
namespace ParseModelsFromMmCif { export interface Params { blockHeader?: string } }
@@ -46,7 +47,7 @@ const ParseModelsFromMmCif = PluginStateTransform.Create<SO.Data.Cif, SO.Models,
});
export { CreateStructureFromModel }
-namespace CreateStructureFromModel { export interface Params { modelIndex: number } }
+namespace CreateStructureFromModel { export interface Params { modelIndex: number, transform3d?: Mat4 } }
const CreateStructureFromModel = PluginStateTransform.Create<SO.Models, SO.Structure, CreateStructureFromModel.Params>({
name: 'create-structure-from-model',
display: {
@@ -59,9 +60,11 @@ const CreateStructureFromModel = PluginStateTransform.Create<SO.Models, SO.Struc
default: () => ({ modelIndex: 0 }),
controls: a => ({ modelIndex: PD.Range('Model Index', 'Model Index', 0, 0, Math.max(0, a.data.length - 1), 1) })
},
+ isApplicable: a => a.data.length > 0,
apply({ a, params }) {
if (params.modelIndex < 0 || params.modelIndex >= a.data.length) throw new Error(`Invalid modelIndex ${params.modelIndex}`);
- const s = Structure.ofModel(a.data[params.modelIndex]);
+ let s = Structure.ofModel(a.data[params.modelIndex]);
+ if (params.transform3d) s = Structure.transform(s, params.transform3d);
return new SO.Structure({ label: `Model ${s.models[0].modelNum}`, description: s.elementCount === 1 ? '1 element' : `${s.elementCount} elements` }, s);
}
});
--
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