From a65bba0969f466866f24225eac800c17efb5af59 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 18 Jun 2019 13:39:23 +0200
Subject: [PATCH] proteopedia-wrapper: better HET group focusing
---
src/examples/proteopedia-wrapper/changelog.md | 5 ++
src/examples/proteopedia-wrapper/helpers.ts | 3 +-
src/examples/proteopedia-wrapper/index.html | 2 +-
src/examples/proteopedia-wrapper/index.ts | 54 ++++++++++++-------
4 files changed, 42 insertions(+), 22 deletions(-)
diff --git a/src/examples/proteopedia-wrapper/changelog.md b/src/examples/proteopedia-wrapper/changelog.md
index 9680f701e..b9d8bd109 100644
--- a/src/examples/proteopedia-wrapper/changelog.md
+++ b/src/examples/proteopedia-wrapper/changelog.md
@@ -1,3 +1,8 @@
+== v3.2 ==
+
+* Fixed assembly loading.
+* Better HET group focus.
+
== v3.0 ==
* Fixed initial camera zoom.
diff --git a/src/examples/proteopedia-wrapper/helpers.ts b/src/examples/proteopedia-wrapper/helpers.ts
index 7d1360c3e..d8d4f2610 100644
--- a/src/examples/proteopedia-wrapper/helpers.ts
+++ b/src/examples/proteopedia-wrapper/helpers.ts
@@ -115,5 +115,6 @@ export enum StateElements {
Water = 'water',
WaterVisual = 'water-visual',
- HetGroupFocus = 'het-group-focus'
+ HetGroupFocus = 'het-group-focus',
+ HetGroupFocusGroup = 'het-group-focus-group'
}
\ No newline at end of file
diff --git a/src/examples/proteopedia-wrapper/index.html b/src/examples/proteopedia-wrapper/index.html
index 5fd7d7bbc..2a72e4b51 100644
--- a/src/examples/proteopedia-wrapper/index.html
+++ b/src/examples/proteopedia-wrapper/index.html
@@ -212,7 +212,7 @@
var l = document.createElement('button');
l.innerText = r.name;
l.onclick = function () {
- PluginWrapper.hetGroups.focusFirst(r.name);
+ PluginWrapper.hetGroups.focusFirst(r.name, r.indices[0]);
};
div.appendChild(l);
});
diff --git a/src/examples/proteopedia-wrapper/index.ts b/src/examples/proteopedia-wrapper/index.ts
index 0a5bf878b..248b96029 100644
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/src/examples/proteopedia-wrapper/index.ts
@@ -29,6 +29,7 @@ import { BuiltInSizeThemes } from '../../mol-theme/size';
import { ColorNames } from '../../mol-util/color/tables';
import { InitVolumeStreaming, CreateVolumeStreamingInfo } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
import { ParamDefinition } from '../../mol-util/param-definition';
+import { ResidueIndex } from '../../mol-model/structure';
// import { Vec3 } from 'mol-math/linear-algebra';
// import { ParamDefinition } from 'mol-util/param-definition';
// import { Text } from 'mol-geo/geometry/text/text';
@@ -36,7 +37,7 @@ require('../../mol-plugin/skin/light.scss')
class MolStarProteopediaWrapper {
static VERSION_MAJOR = 3;
- static VERSION_MINOR = 1;
+ static VERSION_MINOR = 2;
private _ev = RxEventHelper.create();
@@ -298,30 +299,34 @@ class MolStarProteopediaWrapper {
PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
PluginCommands.Camera.Reset.dispatch(this.plugin, { });
},
- focusFirst: async (resn: string) => {
+ focusFirst: async (resn: string, resIdx: ResidueIndex) => {
if (!this.state.transforms.has(StateElements.Assembly)) return;
+ await PluginCommands.Camera.Reset.dispatch(this.plugin, { });
// const asm = (this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure).data;
const update = this.state.build();
- update.delete(StateElements.HetGroupFocus);
-
- const surroundings = 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(), resn]),
- 'group-by': MS.struct.atomProperty.macromolecular.residueKey()
- })
- ]),
- radius: 5,
- 'as-whole-residues': true
- });
-
- const sel = update.to(StateElements.Assembly)
- .apply(StateTransforms.Model.StructureSelection, { label: resn, query: surroundings }, { ref: StateElements.HetGroupFocus });
-
- sel.apply(StateTransforms.Representation.StructureRepresentation3D, this.createSurVisualParams());
+ update.delete(StateElements.HetGroupFocusGroup);
+
+ const core = MS.struct.filter.first([
+ MS.struct.generator.atomGroups({
+ 'residue-test': MS.core.logic.and([
+ MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), resn]),
+ // the resIdx isn't very clear solution and is based on current implementation of residueKey()
+ MS.core.rel.eq([MS.struct.atomProperty.macromolecular.residueKey(), resIdx])
+ ]),
+ 'group-by': MS.core.str.concat([MS.struct.atomProperty.core.operatorName(), MS.struct.atomProperty.macromolecular.residueKey()])
+ })
+ ]);
+ const surroundings = MS.struct.modifier.includeSurroundings({ 0: core, radius: 5, 'as-whole-residues': true });
+
+ const group = update.to(StateElements.Assembly).group(StateTransforms.Misc.CreateGroup, { label: resn }, { ref: StateElements.HetGroupFocusGroup });
+
+ group.apply(StateTransforms.Model.StructureSelection, { label: 'Core', query: core }, { ref: StateElements.HetGroupFocus })
+ .apply(StateTransforms.Representation.StructureRepresentation3D, this.createCoreVisualParams());
+ group.apply(StateTransforms.Model.StructureSelection, { label: 'Surroundings', query: surroundings })
+ .apply(StateTransforms.Representation.StructureRepresentation3D, this.createSurVisualParams());
// sel.apply(StateTransforms.Representation.StructureLabels3D, {
// target: { name: 'residues', params: { } },
// options: {
@@ -341,7 +346,7 @@ class MolStarProteopediaWrapper {
// const position = Vec3.sub(Vec3.zero(), sphere.center, asmCenter);
// Vec3.normalize(position, position);
// Vec3.scaleAndAdd(position, sphere.center, position, sphere.radius);
- const snapshot = this.plugin.canvas3d.camera.getFocus(sphere.center, 0.75 * sphere.radius);
+ const snapshot = this.plugin.canvas3d.camera.getFocus(sphere.center, Math.max(sphere.radius, 5));
PluginCommands.Camera.SetSnapshot.dispatch(this.plugin, { snapshot, durationMs: 250 });
}
}
@@ -355,6 +360,15 @@ class MolStarProteopediaWrapper {
});
}
+ private createCoreVisualParams() {
+ const asm = this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure;
+ return StructureRepresentation3DHelpers.createParams(this.plugin, asm.data, {
+ repr: BuiltInStructureRepresentations['ball-and-stick'],
+ // color: [BuiltInColorThemes.uniform, () => ({ value: ColorNames.gray })],
+ // size: [BuiltInSizeThemes.uniform, () => ({ value: 0.33 } )]
+ });
+ }
+
snapshot = {
get: () => {
return this.plugin.state.getSnapshot();
--
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