diff --git a/src/mol-model/structure/query/queries/internal.ts b/src/mol-model/structure/query/queries/internal.ts
index eba048265c342b9b1363859ce40395669471076a..23b495f72a26920add9f871533c740b841b7242d 100644
--- a/src/mol-model/structure/query/queries/internal.ts
+++ b/src/mol-model/structure/query/queries/internal.ts
@@ -105,4 +105,4 @@ export function spheres(): StructureQuery {
}
return StructureSelection.Singletons(inputStructure, new Structure(units, { parent: inputStructure }));
};
-}
+}
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
index 951ec3946342d207d28d3f0dd001d69adcac0485..8a5da762cb8ce85f352247902ac3f62f2c0940d4 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
@@ -212,7 +212,7 @@ export namespace VolumeStreaming {
});
this.subscribeObservable(this.plugin.behaviors.interaction.click, ({ current, buttons, modifiers }) => {
- if (!Binding.match(this.params.bindings.clickVolumeAroundOnly, buttons, modifiers)) return;
+ if (!Binding.match(this.params.bindings.clickVolumeAroundOnly || DefaultBindings.clickVolumeAroundOnly, buttons, modifiers)) return;
if (this.params.view.name !== 'selection-box') {
this.lastLoci = current;
} else {
diff --git a/src/mol-plugin/state/actions/structure.ts b/src/mol-plugin/state/actions/structure.ts
index 7cfa14dd6e73f839576efd7e4165edb99dfbd9ff..8ad9d2cbd9a85dbc065737a2007ed2a044b23bc0 100644
--- a/src/mol-plugin/state/actions/structure.ts
+++ b/src/mol-plugin/state/actions/structure.ts
@@ -17,6 +17,7 @@ import { DataFormatProvider, guessCifVariant, DataFormatBuilderOptions } from '.
import { FileInfo } from '../../../mol-util/file-info';
import { Task } from '../../../mol-task';
import { StructureElement } from '../../../mol-model/structure';
+import { createDefaultStructureComplex } from '../../util/structure-comlex-helper';
export const MmcifProvider: DataFormatProvider<any> = {
label: 'mmCIF',
@@ -251,7 +252,7 @@ function createStructureTree(ctx: PluginContext, b: StateBuilder.To<PluginStateO
root = root.apply(StateTransforms.Model.CustomModelProperties);
}
const structure = root.apply(StateTransforms.Model.StructureAssemblyFromModel);
- complexRepresentation(ctx, structure);
+ createDefaultStructureComplex(ctx, structure);
return root;
}
@@ -287,7 +288,7 @@ export const CreateComplexRepresentation = StateAction.build({
from: PluginStateObject.Molecule.Structure
})(({ ref, state }, ctx: PluginContext) => {
const root = state.build().to(ref);
- complexRepresentation(ctx, root);
+ createDefaultStructureComplex(ctx, root);
return state.updateTree(root);
});
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 5bc63f833d33c86bf468ac312c43e1c4e72d8275..6f749464e6e05b893cc0b243c58fe879f68915fc 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -28,6 +28,7 @@ import { ensureSecondaryStructure } from './helpers';
import { Script } from '../../../mol-script/script';
import { parse3DG } from '../../../mol-io/reader/3dg/parser';
import { trajectoryFrom3DG } from '../../../mol-model-formats/structure/3dg';
+import { CompiledStructureSelectionQueries } from '../../util/structure-selection-helper';
export { TrajectoryFromBlob };
export { TrajectoryFromMmCif };
@@ -425,7 +426,7 @@ const StructureSelectionFromScript = PluginStateTransform.BuiltIn({
return new SO.Molecule.Structure(s, props);
},
update: ({ a, b, oldParams, newParams, cache }) => {
- if (Script.areEqual(oldParams.script, newParams.script)) {
+ if (!Script.areEqual(oldParams.script, newParams.script)) {
return StateTransformer.UpdateResult.Recreate;
}
@@ -502,27 +503,58 @@ const StructureSelectionFromBundle = PluginStateTransform.BuiltIn({
}
});
-namespace StructureComplexElement {
- export type Types = 'atomic-sequence' | 'water' | 'atomic-het' | 'spheres'
-}
-const StructureComplexElementTypes: [StructureComplexElement.Types, StructureComplexElement.Types][] = ['atomic-sequence', 'water', 'atomic-het', 'spheres'].map(t => [t, t] as any);
+export const StructureComplexElementTypes = {
+ 'protein-and-nucleic': 'protein-and-nucleic',
+
+ 'protein': 'protein',
+ 'nucleic': 'nucleic',
+ 'water': 'water',
+
+ 'branched': 'branched', // = carbs
+ 'ligand': 'ligand',
+ 'modified': 'modified',
+
+ 'coarse': 'coarse',
+
+ // Legacy
+ 'atomic-sequence': 'atomic-sequence',
+ 'atomic-het': 'atomic-het',
+ 'spheres': 'spheres'
+} as const
+export type StructureComplexElementTypes = keyof typeof StructureComplexElementTypes
+
+const StructureComplexElementTypeTuples = Object.keys(StructureComplexElementTypes).map(t => [t, t] as any);
+
type StructureComplexElement = typeof StructureComplexElement
const StructureComplexElement = PluginStateTransform.BuiltIn({
name: 'structure-complex-element',
display: { name: 'Complex Element', description: 'Create a molecular structure from the specified model.' },
from: SO.Molecule.Structure,
to: SO.Molecule.Structure,
- params: { type: PD.Select<StructureComplexElement.Types>('atomic-sequence', StructureComplexElementTypes, { isHidden: true }) }
+ params: { type: PD.Select<StructureComplexElementTypes>('atomic-sequence', StructureComplexElementTypeTuples, { isHidden: true }) }
})({
apply({ a, params }) {
// TODO: update function.
let query: StructureQuery, label: string;
switch (params.type) {
- case 'atomic-sequence': query = Queries.internal.atomicSequence(); label = 'Sequence'; break;
+ case 'protein-and-nucleic': query = CompiledStructureSelectionQueries.proteinAndNucleic; label = 'Sequence'; break;
+
+ case 'protein': query = CompiledStructureSelectionQueries.protein; label = 'Protein'; break;
+ case 'nucleic': query = CompiledStructureSelectionQueries.nucleic; label = 'Nucleic'; break;
case 'water': query = Queries.internal.water(); label = 'Water'; break;
+
+ case 'branched': query = CompiledStructureSelectionQueries.branchedPlusConnected; label = 'Branched'; break;
+ case 'ligand': query = CompiledStructureSelectionQueries.ligandPlusConnected; label = 'Ligand'; break;
+
+ case 'modified': query = CompiledStructureSelectionQueries.modified; label = 'Modified'; break;
+
+ case 'coarse': query = CompiledStructureSelectionQueries.coarse; label = 'Coarse'; break;
+
+ case 'atomic-sequence': query = Queries.internal.atomicSequence(); label = 'Sequence'; break;
case 'atomic-het': query = Queries.internal.atomicHet(); label = 'HET Groups/Ligands'; break;
case 'spheres': query = Queries.internal.spheres(); label = 'Coarse Spheres'; break;
+
default: throw new Error(`${params.type} is a not valid complex element.`);
}
diff --git a/src/mol-plugin/util/structure-comlex-helper.ts b/src/mol-plugin/util/structure-comlex-helper.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d22d839774cba29b3b71b2154dd99f745a1b10c7
--- /dev/null
+++ b/src/mol-plugin/util/structure-comlex-helper.ts
@@ -0,0 +1,43 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginContext } from '../context';
+import { StateBuilder } from '../../mol-state';
+import { PluginStateObject } from '../state/objects';
+import { StateTransforms } from '../state/transforms';
+import { StructureRepresentation3DHelpers } from '../state/transforms/representation';
+import { StructureComplexElementTypes } from '../state/transforms/model';
+
+export function createDefaultStructureComplex(
+ ctx: PluginContext, root: StateBuilder.To<PluginStateObject.Molecule.Structure>
+) {
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'protein-and-nucleic' }, { tags: StructureComplexElementTypes['protein-and-nucleic'] })
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'cartoon'));
+
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'ligand' }, { tags: StructureComplexElementTypes.ligand })
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick'));
+
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'modified' }, { tags: StructureComplexElementTypes.modified })
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick', void 0, 'polymer-id'));
+
+ const branched = root.apply(StateTransforms.Model.StructureComplexElement, { type: 'branched' }, { tags: StructureComplexElementTypes.branched })
+
+ branched.apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick', { alpha: 0.15 }));
+ branched.apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'carbohydrate'));
+
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'water' }, { tags: StructureComplexElementTypes.water })
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'ball-and-stick', { alpha: 0.51 }));
+
+ root.apply(StateTransforms.Model.StructureComplexElement, { type: 'coarse' }, { tags: StructureComplexElementTypes.coarse })
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'spacefill', {}, 'polymer-id'));
+}
\ No newline at end of file
diff --git a/src/mol-plugin/util/structure-selection-helper.ts b/src/mol-plugin/util/structure-selection-helper.ts
index e06e9c50ae4770227ce3fc87b693e9d299bbd595..db342c603b2ab8c5f4ec92e68c4ebb05518bced1 100644
--- a/src/mol-plugin/util/structure-selection-helper.ts
+++ b/src/mol-plugin/util/structure-selection-helper.ts
@@ -7,7 +7,7 @@
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { StateSelection } from '../../mol-state';
import { PluginStateObject } from '../state/objects';
-import { QueryContext, StructureSelection } from '../../mol-model/structure';
+import { QueryContext, StructureSelection, StructureQuery } from '../../mol-model/structure';
import { compile } from '../../mol-script/runtime/query/compiler';
import { Loci } from '../../mol-model/loci';
import { PluginContext } from '../context';
@@ -65,6 +65,18 @@ const nucleic = MS.struct.modifier.union([
})
])
+const proteinAndNucleic = MS.struct.modifier.union([
+ MS.struct.generator.atomGroups({
+ 'entity-test': MS.core.logic.and([
+ MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
+ MS.core.str.match([
+ MS.re('(polypeptide|cyclic-pseudo-peptide|nucleotide|peptide nucleic acid)', 'i'),
+ MS.ammp('entitySubtype')
+ ])
+ ])
+ })
+])
+
const water = MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'water'])
@@ -118,6 +130,12 @@ const ligandPlusConnected = MS.struct.modifier.union([
})
])
+const modified = MS.struct.modifier.union([
+ MS.struct.generator.atomGroups({
+ 'residue-test': MS.ammp('isModified')
+ })
+])
+
const coarse = MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'chain-test': MS.core.set.has([
@@ -132,15 +150,25 @@ export const StructureSelectionQueries = {
trace,
protein,
nucleic,
+ proteinAndNucleic,
water,
branched,
branchedPlusConnected,
branchedConnectedOnly,
ligand,
ligandPlusConnected,
+ modified,
coarse,
}
+export const CompiledStructureSelectionQueries = (function () {
+ const ret: { [K in keyof typeof StructureSelectionQueries]: StructureQuery } = Object.create(null);
+ for (const k of Object.keys(StructureSelectionQueries)) {
+ (ret as any)[k] = compile<StructureSelection>((StructureSelectionQueries as any)[k]);
+ }
+ return ret;
+})();
+
//
export type SelectionModifier = 'add' | 'remove' | 'only'