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midlikmidlik
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Avoid import alias (Molstar -> molstar/lib)
1 parent 9790a15 commit 217488d

33 files changed

+302
-292
lines changed

‎src/app/alphafold-transparency.ts

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,15 +1,15 @@
1-
import { Structure, StructureElement } from 'Molstar/mol-model/structure';
2-
import { PluginStateObject } from 'Molstar/mol-plugin-state/objects';
3-
import { StateTransforms } from 'Molstar/mol-plugin-state/transforms';
4-
import { PluginContext } from 'Molstar/mol-plugin/context';
5-
import { StateBuilder, StateObjectCell, StateSelection, StateTransform } from 'Molstar/mol-state';
6-
import { StructureComponentRef, StructureRef } from 'Molstar/mol-plugin-state/manager/structure/hierarchy-state';
7-
import { isEmptyLoci, Loci } from 'Molstar/mol-model/loci';
8-
import { Transparency } from 'Molstar/mol-theme/transparency';
9-
import { MolScriptBuilder as MS } from 'Molstar/mol-script/language/builder';
10-
import { QualityAssessment } from 'Molstar/extensions/model-archive/quality-assessment/prop';
11-
import { compile } from 'Molstar/mol-script/runtime/query/compiler';
12-
import { StructureSelection, QueryContext } from 'Molstar/mol-model/structure';
1+
import { QualityAssessment } from 'molstar/lib/extensions/model-archive/quality-assessment/prop';
2+
import { Loci, isEmptyLoci } from 'molstar/lib/mol-model/loci';
3+
import { QueryContext, Structure, StructureElement, StructureSelection } from 'molstar/lib/mol-model/structure';
4+
import { StructureComponentRef, StructureRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
5+
import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
6+
import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
7+
import { PluginContext } from 'molstar/lib/mol-plugin/context';
8+
import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
9+
import { compile } from 'molstar/lib/mol-script/runtime/query/compiler';
10+
import { StateBuilder, StateObjectCell, StateSelection, StateTransform } from 'molstar/lib/mol-state';
11+
import { Transparency } from 'molstar/lib/mol-theme/transparency';
12+
1313

1414
type TransparencyEachReprCallback = (update: StateBuilder.Root, repr: StateObjectCell<PluginStateObject.Molecule.Structure.Representation3D, StateTransform<typeof StateTransforms.Representation.StructureRepresentation3D>>, transparency?: StateObjectCell<any, StateTransform<typeof StateTransforms.Representation.TransparencyStructureRepresentation3DFromBundle>>) => Promise<void>
1515
const TransparencyManagerTag = 'transparency-controls';

‎src/app/custom-events.ts

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,8 @@
1-
import { PluginContext } from 'Molstar/mol-plugin/context';
2-
import { lociDetails, EventDetail } from './loci-details';
3-
import { InteractivityManager } from 'Molstar/mol-plugin-state/manager/interactivity';
1+
import { InteractivityManager } from 'molstar/lib/mol-plugin-state/manager/interactivity';
2+
import { PluginContext } from 'molstar/lib/mol-plugin/context';
43
import { debounceTime } from 'rxjs/operators';
4+
import { EventDetail, lociDetails } from './loci-details';
5+
56

67
export namespace CustomEvents {
78

‎src/app/domain-annotations/behavior.ts

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,9 @@
1-
import { DomainAnnotationsProvider } from './prop';
1+
import { Loci } from 'molstar/lib/mol-model/loci';
2+
import { PluginBehavior } from 'molstar/lib/mol-plugin/behavior';
3+
import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
24
import { DomainAnnotationsColorThemeProvider } from './color';
3-
import { Loci } from 'Molstar/mol-model/loci';
4-
import { ParamDefinition as PD } from 'Molstar/mol-util/param-definition';
5-
import { PluginBehavior } from 'Molstar/mol-plugin/behavior';
5+
import { DomainAnnotationsProvider } from './prop';
6+
67

78
export const PDBeDomainAnnotations = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
89
name: 'pdbe-domain-annotations-prop',

‎src/app/domain-annotations/color.ts

Lines changed: 8 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,12 @@
1+
import { CustomProperty } from 'molstar/lib/mol-model-props/common/custom-property';
2+
import { Location } from 'molstar/lib/mol-model/location';
3+
import { StructureElement } from 'molstar/lib/mol-model/structure';
4+
import { ColorTheme, LocationColor } from 'molstar/lib/mol-theme/color';
5+
import { ThemeDataContext } from 'molstar/lib/mol-theme/theme';
6+
import { Color } from 'molstar/lib/mol-util/color';
7+
import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
18
import { DomainAnnotations, DomainAnnotationsProvider } from './prop';
2-
import { Location } from 'Molstar/mol-model/location';
3-
import { StructureElement } from 'Molstar/mol-model/structure';
4-
import { ColorTheme, LocationColor } from 'Molstar/mol-theme/color';
5-
import { ThemeDataContext } from 'Molstar/mol-theme/theme';
6-
import { Color } from 'Molstar/mol-util/color';
7-
import { ParamDefinition as PD } from 'Molstar/mol-util/param-definition';
8-
import { CustomProperty } from 'Molstar/mol-model-props/common/custom-property';
9+
910

1011
const DomainColors = [
1112
Color.fromRgb(170, 170, 170), // not applicable

‎src/app/domain-annotations/prop.ts

Lines changed: 11 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,14 @@
1-
import { Model, ResidueIndex, Unit, IndexedCustomProperty } from 'Molstar/mol-model/structure';
2-
import { StructureElement, Structure } from 'Molstar/mol-model/structure/structure';
3-
import { PropertyWrapper } from 'Molstar/mol-model-props/common/wrapper';
4-
import { CustomModelProperty } from 'Molstar/mol-model-props/common/custom-model-property';
5-
import { ParamDefinition as PD } from 'Molstar/mol-util/param-definition';
6-
import { CustomProperty } from 'Molstar/mol-model-props/common/custom-property';
7-
import { arraySetAdd } from 'Molstar/mol-util/array';
8-
import { Asset } from 'Molstar/mol-util/assets';
9-
import { CustomPropertyDescriptor } from 'Molstar/mol-model/custom-property';
10-
import { ChainIndex } from 'Molstar/mol-model/structure/model/indexing';
1+
import { CustomModelProperty } from 'molstar/lib/mol-model-props/common/custom-model-property';
2+
import { CustomProperty } from 'molstar/lib/mol-model-props/common/custom-property';
3+
import { PropertyWrapper } from 'molstar/lib/mol-model-props/common/wrapper';
4+
import { CustomPropertyDescriptor } from 'molstar/lib/mol-model/custom-property';
5+
import { IndexedCustomProperty, Model, ResidueIndex, Unit } from 'molstar/lib/mol-model/structure';
6+
import { ChainIndex } from 'molstar/lib/mol-model/structure/model/indexing';
7+
import { Structure, StructureElement } from 'molstar/lib/mol-model/structure/structure';
8+
import { arraySetAdd } from 'molstar/lib/mol-util/array';
9+
import { Asset } from 'molstar/lib/mol-util/assets';
10+
import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
11+
1112

1213
export { DomainAnnotations };
1314
type DomainAnnotations = PropertyWrapper<{

‎src/app/extensions/foldseek.ts

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
11
/** Helper functions to allow visualizing Foldseek results and superposing them on the query structure */
22

3-
import { exportHierarchy } from 'Molstar/extensions/model-export/export';
4-
import { Mat4 } from 'Molstar/mol-math/linear-algebra';
5-
import { MinimizeRmsd } from 'Molstar/mol-math/linear-algebra/3d/minimize-rmsd';
6-
import { ElementIndex, ResidueIndex, Structure } from 'Molstar/mol-model/structure';
3+
import { exportHierarchy } from 'molstar/lib/extensions/model-export/export';
4+
import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
5+
import { MinimizeRmsd } from 'molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd';
6+
import { ElementIndex, ResidueIndex, Structure } from 'molstar/lib/mol-model/structure';
77
import { PDBeMolstarPlugin } from '..';
88
import { transform } from '../superposition';
99

‎src/app/helpers.ts

Lines changed: 23 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -1,21 +1,21 @@
1-
import { QualityAssessment } from 'Molstar/extensions/model-archive/quality-assessment/prop';
2-
import { Model, Queries, QueryContext, ResidueIndex, Structure, StructureProperties, StructureSelection } from 'Molstar/mol-model/structure';
3-
import { AtomsQueryParams } from 'Molstar/mol-model/structure/query/queries/generators';
4-
import { StructureQuery } from 'Molstar/mol-model/structure/query/query';
5-
import { BuiltInTrajectoryFormat } from 'Molstar/mol-plugin-state/formats/trajectory';
6-
import { StructureRef } from 'Molstar/mol-plugin-state/manager/structure/hierarchy-state';
7-
import { StateTransforms } from 'Molstar/mol-plugin-state/transforms';
8-
import { CreateVolumeStreamingInfo } from 'Molstar/mol-plugin/behavior/dynamic/volume-streaming/transformers';
9-
import { PluginCommands } from 'Molstar/mol-plugin/commands';
10-
import { PluginContext } from 'Molstar/mol-plugin/context';
11-
import { MolScriptBuilder as MS } from 'Molstar/mol-script/language/builder';
12-
import Expression from 'Molstar/mol-script/language/expression';
13-
import { compile } from 'Molstar/mol-script/runtime/query/compiler';
14-
import { StateSelection } from 'Molstar/mol-state';
15-
import { Task } from 'Molstar/mol-task';
16-
import { Overpaint } from 'Molstar/mol-theme/overpaint';
17-
import { Color } from 'Molstar/mol-util/color';
18-
import { ColorName, ColorNames } from 'Molstar/mol-util/color/names';
1+
import { QualityAssessment } from 'molstar/lib/extensions/model-archive/quality-assessment/prop';
2+
import { Model, Queries, QueryContext, ResidueIndex, Structure, StructureProperties, StructureSelection } from 'molstar/lib/mol-model/structure';
3+
import { AtomsQueryParams } from 'molstar/lib/mol-model/structure/query/queries/generators';
4+
import { StructureQuery } from 'molstar/lib/mol-model/structure/query/query';
5+
import { BuiltInTrajectoryFormat } from 'molstar/lib/mol-plugin-state/formats/trajectory';
6+
import { StructureRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
7+
import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
8+
import { CreateVolumeStreamingInfo } from 'molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers';
9+
import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
10+
import { PluginContext } from 'molstar/lib/mol-plugin/context';
11+
import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
12+
import { Expression } from 'molstar/lib/mol-script/language/expression';
13+
import { compile } from 'molstar/lib/mol-script/runtime/query/compiler';
14+
import { StateSelection } from 'molstar/lib/mol-state';
15+
import { Task } from 'molstar/lib/mol-task';
16+
import { Overpaint } from 'molstar/lib/mol-theme/overpaint';
17+
import { Color } from 'molstar/lib/mol-util/color';
18+
import { ColorName, ColorNames } from 'molstar/lib/mol-util/color/names';
1919
import { SIFTSMapping, SIFTSMappingMapping } from './sifts-mapping';
2020
import { AnyColor, InitParams } from './spec';
2121

@@ -113,7 +113,7 @@ export type LigandQueryParam = {
113113

114114

115115
export namespace LigandView {
116-
export function query(ligandViewParams: LigandQueryParam): { core: Expression.Expression, surroundings: Expression.Expression } {
116+
export function query(ligandViewParams: LigandQueryParam): { core: Expression, surroundings: Expression } {
117117
const atomGroupsParams: any = {
118118
'group-by': MS.core.str.concat([MS.struct.atomProperty.core.operatorName(), MS.struct.atomProperty.macromolecular.residueKey()])
119119
};
@@ -151,7 +151,7 @@ export namespace LigandView {
151151

152152
}
153153

154-
export function branchedQuery(params: any): { core: Expression.Expression, surroundings: Expression.Expression } {
154+
export function branchedQuery(params: any): { core: Expression, surroundings: Expression } {
155155
const entityObjArray: any[] = [];
156156

157157
params.atom_site.forEach((param: any) => {
@@ -162,7 +162,7 @@ export namespace LigandView {
162162
entityObjArray.push(qEntities);
163163
});
164164

165-
const atmGroupsQueries: Expression.Expression[] = [];
165+
const atmGroupsQueries: Expression[] = [];
166166

167167
entityObjArray.forEach((entityObj: any) => {
168168
atmGroupsQueries.push(MS.struct.generator.atomGroups(entityObj));
@@ -221,7 +221,7 @@ export type QueryParam = {
221221

222222
export namespace QueryHelper {
223223

224-
export function getQueryObject(params: QueryParam[], contextData: Structure): Expression.Expression {
224+
export function getQueryObject(params: QueryParam[], contextData: Structure): Expression {
225225
const selections: Partial<AtomsQueryParams>[] = [];
226226
let siftMappings: SIFTSMappingMapping | undefined;
227227
let currentAccession: string;
@@ -310,7 +310,7 @@ export namespace QueryHelper {
310310
return StructureSelection.toLociWithSourceUnits(sel);
311311
}
312312

313-
export function getHetLoci(queryExp: Expression.Expression, contextData: Structure) {
313+
export function getHetLoci(queryExp: Expression, contextData: Structure) {
314314
const query = compile<StructureSelection>(queryExp);
315315
const sel = query(new QueryContext(contextData));
316316
return StructureSelection.toLociWithSourceUnits(sel);

‎src/app/index.ts

Lines changed: 44 additions & 44 deletions
Original file line numberDiff line numberDiff line change
@@ -1,46 +1,46 @@
1-
import { GeometryExport } from 'Molstar/extensions/geo-export';
2-
import { MAQualityAssessment } from 'Molstar/extensions/model-archive/quality-assessment/behavior';
3-
import { Mp4Export } from 'Molstar/extensions/mp4-export';
4-
import { MolViewSpec } from 'Molstar/extensions/mvs/behavior';
5-
import { CustomTooltipsProps, CustomTooltipsProvider } from 'Molstar/extensions/mvs/components/custom-tooltips-prop';
6-
import { PDBeStructureQualityReport } from 'Molstar/extensions/pdbe';
7-
import { RCSBAssemblySymmetry, RCSBAssemblySymmetryConfig } from 'Molstar/extensions/rcsb/assembly-symmetry/behavior';
8-
import { Canvas3DProps } from 'Molstar/mol-canvas3d/canvas3d';
9-
import { EmptyLoci, Loci } from 'Molstar/mol-model/loci';
10-
import { StructureElement } from 'Molstar/mol-model/structure';
11-
import { AnimateAssemblyUnwind } from 'Molstar/mol-plugin-state/animation/built-in/assembly-unwind';
12-
import { AnimateCameraRock } from 'Molstar/mol-plugin-state/animation/built-in/camera-rock';
13-
import { AnimateCameraSpin } from 'Molstar/mol-plugin-state/animation/built-in/camera-spin';
14-
import { AnimateModelIndex } from 'Molstar/mol-plugin-state/animation/built-in/model-index';
15-
import { AnimateStructureSpin } from 'Molstar/mol-plugin-state/animation/built-in/spin-structure';
16-
import { AnimateStateInterpolation } from 'Molstar/mol-plugin-state/animation/built-in/state-interpolation';
17-
import { AnimateStateSnapshots } from 'Molstar/mol-plugin-state/animation/built-in/state-snapshots';
18-
import { BuiltInTrajectoryFormat } from 'Molstar/mol-plugin-state/formats/trajectory';
19-
import { clearStructureOverpaint } from 'Molstar/mol-plugin-state/helpers/structure-overpaint';
20-
import { createStructureRepresentationParams } from 'Molstar/mol-plugin-state/helpers/structure-representation-params';
21-
import { StructureRef } from 'Molstar/mol-plugin-state/manager/structure/hierarchy-state';
22-
import { PluginStateObject } from 'Molstar/mol-plugin-state/objects';
23-
import { StateTransforms } from 'Molstar/mol-plugin-state/transforms';
24-
import { CustomStructureProperties, StructureComponent } from 'Molstar/mol-plugin-state/transforms/model';
25-
import { StructureRepresentation3D } from 'Molstar/mol-plugin-state/transforms/representation';
26-
import { createPluginUI } from 'Molstar/mol-plugin-ui/react18';
27-
import { PluginUISpec } from 'Molstar/mol-plugin-ui/spec';
28-
import { FocusLoci } from 'Molstar/mol-plugin/behavior/dynamic/camera';
29-
import { SelectLoci } from 'Molstar/mol-plugin/behavior/dynamic/representation';
30-
import { StructureFocusRepresentation } from 'Molstar/mol-plugin/behavior/dynamic/selection/structure-focus-representation';
31-
import { InitVolumeStreaming } from 'Molstar/mol-plugin/behavior/dynamic/volume-streaming/transformers';
32-
import { PluginCommands } from 'Molstar/mol-plugin/commands';
33-
import { PluginConfig } from 'Molstar/mol-plugin/config';
34-
import { PluginContext } from 'Molstar/mol-plugin/context';
35-
import { PluginLayoutStateParams } from 'Molstar/mol-plugin/layout';
36-
import { PluginSpec } from 'Molstar/mol-plugin/spec';
37-
import { Representation } from 'Molstar/mol-repr/representation';
38-
import { StateSelection, StateTransform } from 'Molstar/mol-state';
39-
import { ElementSymbolColorThemeParams } from 'Molstar/mol-theme/color/element-symbol';
40-
import { Overpaint } from 'Molstar/mol-theme/overpaint';
41-
import { Asset } from 'Molstar/mol-util/assets';
42-
import { Color } from 'Molstar/mol-util/color/color';
43-
import { RxEventHelper } from 'Molstar/mol-util/rx-event-helper';
1+
import { GeometryExport } from 'molstar/lib/extensions/geo-export';
2+
import { MAQualityAssessment } from 'molstar/lib/extensions/model-archive/quality-assessment/behavior';
3+
import { Mp4Export } from 'molstar/lib/extensions/mp4-export';
4+
import { MolViewSpec } from 'molstar/lib/extensions/mvs/behavior';
5+
import { CustomTooltipsProps, CustomTooltipsProvider } from 'molstar/lib/extensions/mvs/components/custom-tooltips-prop';
6+
import { PDBeStructureQualityReport } from 'molstar/lib/extensions/pdbe';
7+
import { RCSBAssemblySymmetry, RCSBAssemblySymmetryConfig } from 'molstar/lib/extensions/rcsb/assembly-symmetry/behavior';
8+
import { Canvas3DProps } from 'molstar/lib/mol-canvas3d/canvas3d';
9+
import { EmptyLoci, Loci } from 'molstar/lib/mol-model/loci';
10+
import { StructureElement } from 'molstar/lib/mol-model/structure';
11+
import { AnimateAssemblyUnwind } from 'molstar/lib/mol-plugin-state/animation/built-in/assembly-unwind';
12+
import { AnimateCameraRock } from 'molstar/lib/mol-plugin-state/animation/built-in/camera-rock';
13+
import { AnimateCameraSpin } from 'molstar/lib/mol-plugin-state/animation/built-in/camera-spin';
14+
import { AnimateModelIndex } from 'molstar/lib/mol-plugin-state/animation/built-in/model-index';
15+
import { AnimateStructureSpin } from 'molstar/lib/mol-plugin-state/animation/built-in/spin-structure';
16+
import { AnimateStateInterpolation } from 'molstar/lib/mol-plugin-state/animation/built-in/state-interpolation';
17+
import { AnimateStateSnapshots } from 'molstar/lib/mol-plugin-state/animation/built-in/state-snapshots';
18+
import { BuiltInTrajectoryFormat } from 'molstar/lib/mol-plugin-state/formats/trajectory';
19+
import { clearStructureOverpaint } from 'molstar/lib/mol-plugin-state/helpers/structure-overpaint';
20+
import { createStructureRepresentationParams } from 'molstar/lib/mol-plugin-state/helpers/structure-representation-params';
21+
import { StructureRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
22+
import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
23+
import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
24+
import { CustomStructureProperties, StructureComponent } from 'molstar/lib/mol-plugin-state/transforms/model';
25+
import { StructureRepresentation3D } from 'molstar/lib/mol-plugin-state/transforms/representation';
26+
import { createPluginUI } from 'molstar/lib/mol-plugin-ui/react18';
27+
import { PluginUISpec } from 'molstar/lib/mol-plugin-ui/spec';
28+
import { FocusLoci } from 'molstar/lib/mol-plugin/behavior/dynamic/camera';
29+
import { SelectLoci } from 'molstar/lib/mol-plugin/behavior/dynamic/representation';
30+
import { StructureFocusRepresentation } from 'molstar/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation';
31+
import { InitVolumeStreaming } from 'molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers';
32+
import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
33+
import { PluginConfig } from 'molstar/lib/mol-plugin/config';
34+
import { PluginContext } from 'molstar/lib/mol-plugin/context';
35+
import { PluginLayoutStateParams } from 'molstar/lib/mol-plugin/layout';
36+
import { PluginSpec } from 'molstar/lib/mol-plugin/spec';
37+
import { Representation } from 'molstar/lib/mol-repr/representation';
38+
import { StateSelection, StateTransform } from 'molstar/lib/mol-state';
39+
import { ElementSymbolColorThemeParams } from 'molstar/lib/mol-theme/color/element-symbol';
40+
import { Overpaint } from 'molstar/lib/mol-theme/overpaint';
41+
import { Asset } from 'molstar/lib/mol-util/assets';
42+
import { Color } from 'molstar/lib/mol-util/color/color';
43+
import { RxEventHelper } from 'molstar/lib/mol-util/rx-event-helper';
4444
import { CustomEvents } from './custom-events';
4545
import { PDBeDomainAnnotations } from './domain-annotations/behavior';
4646
import * as Foldseek from './extensions/foldseek';
@@ -57,7 +57,7 @@ import { PDBeLigandViewStructureTools, PDBeStructureTools, PDBeSuperpositionStru
5757
import { PDBeViewportControls } from './ui/pdbe-viewport-controls';
5858
import { SuperpostionViewport } from './ui/superposition-viewport';
5959

60-
import 'Molstar/mol-plugin-ui/skin/dark.scss';
60+
import 'molstar/lib/mol-plugin-ui/skin/dark.scss';
6161
import './overlay.scss';
6262

6363

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