From f6462a3e7e8e2993d974f5b84dd7f48c7a21be13 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 29 May 2019 15:00:42 +0200
Subject: [PATCH] superposition examples
---
src/apps/basic-wrapper/helpers.ts | 29 +++++++++-
src/apps/basic-wrapper/index.html | 3 +-
src/apps/basic-wrapper/index.ts | 9 ++-
src/apps/basic-wrapper/superposition.ts | 55 ++++++++++++++++++-
src/mol-math/linear-algebra/3d.ts | 3 +-
.../linear-algebra/3d/minimize-rmsd.ts | 3 +-
.../structure/structure/util/superposition.ts | 2 +-
src/mol-state/state/selection.ts | 2 +-
8 files changed, 95 insertions(+), 11 deletions(-)
diff --git a/src/apps/basic-wrapper/helpers.ts b/src/apps/basic-wrapper/helpers.ts
index bbe9e92ab..342325ee8 100644
--- a/src/apps/basic-wrapper/helpers.ts
+++ b/src/apps/basic-wrapper/helpers.ts
@@ -11,6 +11,8 @@ import { StateTransforms } from 'mol-plugin/state/transforms';
import { StructureRepresentation3DHelpers } from 'mol-plugin/state/transforms/representation';
import { MolScriptBuilder as MS } from 'mol-script/language/builder';
import { StateBuilder } from 'mol-state';
+import Expression from 'mol-script/language/expression';
+import { BuiltInColorThemeName } from 'mol-theme/color';
type SupportedFormats = 'cif' | 'pdb'
export namespace StateHelper {
@@ -27,7 +29,7 @@ export namespace StateHelper {
}
export function structure(b: StateBuilder.To<PSO.Molecule.Model>) {
- return b.apply(StateTransforms.Model.StructureFromModel, { tags: 'struct' })
+ return b.apply(StateTransforms.Model.StructureFromModel, { tags: 'structure' })
};
export function selectChain(b: StateBuilder.To<PSO.Molecule.Structure>, auth_asym_id: string) {
@@ -37,6 +39,23 @@ export namespace StateHelper {
return b.apply(StateTransforms.Model.StructureSelection, { query, label: `Chain ${auth_asym_id}` });
}
+ export function select(b: StateBuilder.To<PSO.Molecule.Structure>, query: Expression) {
+ return b.apply(StateTransforms.Model.StructureSelection, { query });
+ }
+
+ export function selectSurroundingsOfFirstResidue(b: StateBuilder.To<PSO.Molecule.Structure>, comp_id: string, radius: number) {
+ const query = MS.struct.modifier.includeSurroundings({
+ 0: MS.struct.filter.first([
+ MS.struct.generator.atomGroups({
+ 'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), comp_id]),
+ 'group-by': MS.struct.atomProperty.macromolecular.residueKey()
+ })
+ ]),
+ radius
+ })
+ return b.apply(StateTransforms.Model.StructureSelection, { query, label: `Surr. ${comp_id} (${radius} ang)` });
+ }
+
export function identityTransform(b: StateBuilder.To<PSO.Molecule.Structure>, m: Mat4) {
return b.apply(StateTransforms.Model.TransformStructureConformation,
{ axis: Vec3.create(1, 0, 0), angle: 0, translation: Vec3.zero() },
@@ -64,4 +83,12 @@ export namespace StateHelper {
return visualRoot;
}
+ export function ballsAndSticks(ctx: PluginContext, visualRoot: StateBuilder.To<PSO.Molecule.Structure>, query: Expression, coloring?: BuiltInColorThemeName) {
+ visualRoot
+ .apply(StateTransforms.Model.StructureSelection, { query })
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick', void 0, coloring), { tags: 'het-visual' });
+ return visualRoot;
+ }
+
}
\ No newline at end of file
diff --git a/src/apps/basic-wrapper/index.html b/src/apps/basic-wrapper/index.html
index 1d68db266..6c9f2d9d5 100644
--- a/src/apps/basic-wrapper/index.html
+++ b/src/apps/basic-wrapper/index.html
@@ -107,7 +107,8 @@
addHeader('Tests');
- addControl('Static Super', () => BasicMolStarWrapper.tests.staticSuperposition());
+ addControl('Static Superposition', () => BasicMolStarWrapper.tests.staticSuperposition());
+ addControl('Dynamic Superposition', () => BasicMolStarWrapper.tests.dynamicSuperposition());
////////////////////////////////////////////////////////
diff --git a/src/apps/basic-wrapper/index.ts b/src/apps/basic-wrapper/index.ts
index fb4392f3d..3520372ac 100644
--- a/src/apps/basic-wrapper/index.ts
+++ b/src/apps/basic-wrapper/index.ts
@@ -13,10 +13,10 @@ import { StructureRepresentation3DHelpers } from 'mol-plugin/state/transforms/re
import { Color } from 'mol-util/color';
import { PluginStateObject as PSO } from 'mol-plugin/state/objects';
import { AnimateModelIndex } from 'mol-plugin/state/animation/built-in';
-import { StateBuilder } from 'mol-state';
+import { StateBuilder, StateTransform } from 'mol-state';
import { StripedResidues } from './coloring';
// import { BasicWrapperControls } from './controls';
-import { StaticSuperpositionTestData, buildStaticSuperposition } from './superposition';
+import { StaticSuperpositionTestData, buildStaticSuperposition, dynamicSuperpositionTest } from './superposition';
require('mol-plugin/skin/light.scss')
type SupportedFormats = 'cif' | 'pdb'
@@ -146,7 +146,12 @@ class BasicWrapper {
staticSuperposition: async () => {
const state = this.plugin.state.dataState;
const tree = buildStaticSuperposition(this.plugin, StaticSuperpositionTestData);
+ await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: StateTransform.RootRef });
await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
+ },
+ dynamicSuperposition: async () => {
+ await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.plugin.state.dataState, ref: StateTransform.RootRef });
+ await dynamicSuperpositionTest(this.plugin, ['1tqn', '2hhb', '4hhb'], 'HEM');
}
}
}
diff --git a/src/apps/basic-wrapper/superposition.ts b/src/apps/basic-wrapper/superposition.ts
index 1961aab48..c2b190603 100644
--- a/src/apps/basic-wrapper/superposition.ts
+++ b/src/apps/basic-wrapper/superposition.ts
@@ -9,6 +9,14 @@
import { PluginContext } from 'mol-plugin/context';
import { Mat4 } from 'mol-math/linear-algebra';
import { StateHelper } from './helpers';
+import { PluginCommands } from 'mol-plugin/command';
+import { StateSelection, StateBuilder } from 'mol-state';
+import { PluginStateObject as PSO } from 'mol-plugin/state/objects';
+import { MolScriptBuilder as MS } from 'mol-script/language/builder';
+import { compile } from 'mol-script/runtime/query/compiler';
+import { StructureSelection, QueryContext } from 'mol-model/structure';
+import { superposeStructures } from 'mol-model/structure/structure/util/superposition';
+import Expression from 'mol-script/language/expression';
export type SuperpositionTestInput = {
pdbId: string,
@@ -52,4 +60,49 @@ export const StaticSuperpositionTestData: SuperpositionTestInput = [
[-0.312, 0.949, 0.057, -12.255],
[-0.949, -0.307, -0.074, 53.562],
[0, 0, 0, 1]] )}
-];
\ No newline at end of file
+];
+
+export async function dynamicSuperpositionTest(ctx: PluginContext, src: string[], comp_id: string) {
+ const state = ctx.state.dataState;
+
+ const structures = state.build().toRoot();
+ for (const s of src) {
+ StateHelper.structure(
+ StateHelper.getModel(StateHelper.download(structures, `https://www.ebi.ac.uk/pdbe/static/entry/${s}_updated.cif`), 'cif'));
+ }
+
+ await PluginCommands.State.Update.dispatch(ctx, { state, tree: structures });
+
+ const pivot = MS.struct.filter.first([
+ MS.struct.generator.atomGroups({
+ 'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), comp_id]),
+ 'group-by': MS.struct.atomProperty.macromolecular.residueKey()
+ })
+ ]);
+ const rest = MS.struct.modifier.exceptBy({
+ 0: MS.struct.generator.all(),
+ by: pivot
+ });
+
+ const query = compile<StructureSelection>(pivot);
+ const xs = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure));
+ const selections = xs.map(s => StructureSelection.toLoci(query(new QueryContext(s.obj!.data))));
+
+ const transforms = superposeStructures(selections);
+ const visuals = state.build();
+
+ siteVisual(ctx, StateHelper.selectSurroundingsOfFirstResidue(visuals.to(xs[0].transform.ref), 'HEM', 7), pivot, rest);
+ for (let i = 1; i < selections.length; i++) {
+ const root = visuals.to(xs[i].transform.ref);
+ siteVisual(ctx,
+ StateHelper.transform(StateHelper.selectSurroundingsOfFirstResidue(root, 'HEM', 7), transforms[i - 1].bTransform),
+ pivot, rest);
+ }
+
+ await PluginCommands.State.Update.dispatch(ctx, { state, tree: visuals });
+}
+
+function siteVisual(ctx: PluginContext, b: StateBuilder.To<PSO.Molecule.Structure>, pivot: Expression, rest: Expression) {
+ StateHelper.ballsAndSticks(ctx, b, pivot, 'residue-name');
+ StateHelper.ballsAndSticks(ctx, b, rest, 'uniform');
+}
\ No newline at end of file
diff --git a/src/mol-math/linear-algebra/3d.ts b/src/mol-math/linear-algebra/3d.ts
index 88ba25f81..3a98d5ba7 100644
--- a/src/mol-math/linear-algebra/3d.ts
+++ b/src/mol-math/linear-algebra/3d.ts
@@ -23,7 +23,6 @@ import Vec2 from './3d/vec2'
import Vec3 from './3d/vec3'
import Vec4 from './3d/vec4'
import Quat from './3d/quat'
-import MinimizeRmsd from './3d/minimize-rmsd'
import { EPSILON } from './3d/common'
-export { Mat4, Mat3, Vec2, Vec3, Vec4, Quat, EPSILON, MinimizeRmsd }
\ No newline at end of file
+export { Mat4, Mat3, Vec2, Vec3, Vec4, Quat, EPSILON }
\ No newline at end of file
diff --git a/src/mol-math/linear-algebra/3d/minimize-rmsd.ts b/src/mol-math/linear-algebra/3d/minimize-rmsd.ts
index 1296e10f3..b757b2e7a 100644
--- a/src/mol-math/linear-algebra/3d/minimize-rmsd.ts
+++ b/src/mol-math/linear-algebra/3d/minimize-rmsd.ts
@@ -10,8 +10,7 @@ import { EVD } from '../matrix/evd';
import { CentroidHelper } from 'mol-math/geometry/centroid-helper';
import Matrix from '../matrix/matrix';
-export default MinimizeRmsd;
-
+export { MinimizeRmsd };
namespace MinimizeRmsd {
export interface Result {
bTransform: Mat4,
diff --git a/src/mol-model/structure/structure/util/superposition.ts b/src/mol-model/structure/structure/util/superposition.ts
index 8c41ba996..bcd726258 100644
--- a/src/mol-model/structure/structure/util/superposition.ts
+++ b/src/mol-model/structure/structure/util/superposition.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { MinimizeRmsd } from 'mol-math/linear-algebra';
+import { MinimizeRmsd } from 'mol-math/linear-algebra/3d/minimize-rmsd';
import StructureElement from '../element';
import { OrderedSet } from 'mol-data/int';
diff --git a/src/mol-state/state/selection.ts b/src/mol-state/state/selection.ts
index 2a47745f5..097d73b70 100644
--- a/src/mol-state/state/selection.ts
+++ b/src/mol-state/state/selection.ts
@@ -49,7 +49,7 @@ namespace StateSelection {
parent(): Builder<C>;
first(): Builder<C>;
filter(p: (n: C) => boolean): Builder<C>;
- withTag(tag: string): Builder<C>;
+ withTag<D extends StateObjectCell = C>(tag: string): Builder<D>;
withTransformer<T extends StateTransformer<any, StateObjectCell.Obj<C>, any>>(t: T): Builder<StateObjectCell<StateObjectCell.Obj<C>, StateTransform<T>>>;
withStatus(s: StateObjectCell.Status): Builder<C>;
subtree(): Builder;
--
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