Issue #877: updated import paths

src/TmImageRenderer/index.ts

@@ -23,7 +23,7 @@ import { HeadlessPluginContext } from '../mol-plugin/headless-plugin-context';
 import { DefaultPluginSpec } from '../mol-plugin/spec';
 import { ExternalModules, STYLIZED_POSTPROCESSING } from '../mol-plugin/util/headless-screenshot';
 import { setFSModule } from '../mol-util/data-source';
-import { TMDETMembraneOrientation } from '../TmFv3DApp/tmdet-extension/behavior';
+import { TMDETMembraneOrientation } from '../tmdet-extension/behavior';
 
 
 setFSModule(fs);
@@ -50,8 +50,6 @@ async function main() {
 
     // Create a headless plugin
     const externalModules: ExternalModules = { gl, pngjs, 'jpeg-js': jpegjs };
-    const ps = DefaultPluginSpec();
-    ps.behaviors.push(TMDETMembraneOrientation);
     const plugin = new HeadlessPluginContext(externalModules, DefaultPluginSpec(), { width: 800, height: 800 });
     await plugin.init();
 

src/tmdet-extension/UniTmpHelper.ts

@@ -6,10 +6,10 @@
  * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
-import { PDBTMDescriptor } from "./tmdet-extension/types";
-import { setMembraneOrientation, TmDetDescriptorCache } from "./tmdet-extension/prop";
-import { createMembraneOrientation } from "./tmdet-extension/transformation";
-import { DebugUtil } from "./tmdet-extension/debug-utils";
+import { PDBTMDescriptor } from "./types";
+import { setMembraneOrientation, TmDetDescriptorCache } from "./prop";
+import { createMembraneOrientation } from "./transformation";
+import { DebugUtil } from "./debug-utils";
 
 export async function fetchDescriptor(url: string) {
     const response = await fetch(url);

src/tmdet-extension/algorithm.ts

@@ -13,9 +13,9 @@
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
-import { Vec3 } from 'molstar/lib/mol-math/linear-algebra';
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
-import 'molstar/lib/mol-util/polyfill';
+import { Vec3 } from '../mol-math/linear-algebra';
+import { ParamDefinition as PD } from '../mol-util/param-definition';
+import '../mol-util/polyfill';
 
 export const TMDETParams = {
     numberOfSpherePoints: PD.Numeric(140, { min: 35, max: 700, step: 1 }, { description: 'Number of spheres/directions to test for membrane placement. Original value is 350.' }),

src/tmdet-extension/behavior.ts

@@ -13,18 +13,18 @@
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
-import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from 'molstar/lib/mol-plugin-state/builder/structure/representation-preset';
-import { StateObject, StateObjectRef, StateObjectCell, StateTransformer, StateTransform } from 'molstar/lib/mol-state';
-import { Task } from 'molstar/lib/mol-task';
-import { PluginBehavior } from 'molstar/lib/mol-plugin/behavior';
-import { PluginStateObject, PluginStateTransform } from 'molstar/lib/mol-plugin-state/objects';
-import { PluginContext } from 'molstar/lib/mol-plugin/context';
-import { DefaultQueryRuntimeTable } from 'molstar/lib/mol-script/runtime/query/compiler';
-import { StructureSelectionQuery, StructureSelectionCategory } from 'molstar/lib/mol-plugin-state/helpers/structure-selection-query';
-import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
-import { GenericRepresentationRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
-import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context';
+import { ParamDefinition as PD } from '../mol-util/param-definition';
+import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../mol-plugin-state/builder/structure/representation-preset';
+import { StateObject, StateObjectRef, StateObjectCell, StateTransformer, StateTransform } from '../mol-state';
+import { Task } from '../mol-task';
+import { PluginBehavior } from '../mol-plugin/behavior';
+import { PluginStateObject, PluginStateTransform } from '../mol-plugin-state/objects';
+import { PluginContext } from '../mol-plugin/context';
+import { DefaultQueryRuntimeTable } from '../mol-script/runtime/query/compiler';
+import { StructureSelectionQuery, StructureSelectionCategory } from '../mol-plugin-state/helpers/structure-selection-query';
+import { MolScriptBuilder as MS } from '../mol-script/language/builder';
+import { GenericRepresentationRef } from '../mol-plugin-state/manager/structure/hierarchy-state';
+import { PluginUIContext } from '../mol-plugin-ui/context';
 
 
 // TMDET imports

src/tmdet-extension/camera.ts

@@ -7,10 +7,10 @@
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
-import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context';
-import { Quat, Vec3 } from 'molstar/lib/mol-math/linear-algebra';
-import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
-import { Camera } from 'molstar/lib/mol-canvas3d/camera';
+import { PluginUIContext } from '../mol-plugin-ui/context';
+import { Quat, Vec3 } from '../mol-math/linear-algebra';
+import { PluginCommands } from '../mol-plugin/commands';
+import { Camera } from '../mol-canvas3d/camera';
 import { DebugUtil } from './debug-utils';
 
 let initialSnapshot: Camera.Snapshot;

src/tmdet-extension/debug-utils.ts

@@ -7,16 +7,16 @@
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
-import { mmCIF_Database } from "molstar/lib/mol-io/reader/cif/schema/mmcif";
-import { Mat4, Vec3 } from "molstar/lib/mol-math/linear-algebra";
-import { MmcifFormat } from "molstar/lib/mol-model-formats/structure/mmcif";
-import { Model } from "molstar/lib/mol-model/structure";
-import { AtomicConformation } from "molstar/lib/mol-model/structure/model/properties/atomic";
-import { createStructureRepresentationParams } from "molstar/lib/mol-plugin-state/helpers/structure-representation-params";
-import { StateTransforms } from "molstar/lib/mol-plugin-state/transforms";
-import { PluginUIContext } from "molstar/lib/mol-plugin-ui/context";
-import { Expression } from "molstar/lib/mol-script/language/expression";
-import { Color } from "molstar/lib/mol-util/color";
+import { mmCIF_Database } from "../mol-io/reader/cif/schema/mmcif";
+import { Mat4, Vec3 } from "../mol-math/linear-algebra";
+import { MmcifFormat } from "../mol-model-formats/structure/mmcif";
+import { Model } from "../mol-model/structure";
+import { AtomicConformation } from "../mol-model/structure/model/properties/atomic";
+import { createStructureRepresentationParams } from "../mol-plugin-state/helpers/structure-representation-params";
+import { StateTransforms } from "../mol-plugin-state/transforms";
+import { PluginUIContext } from "../mol-plugin-ui/context";
+import { Expression } from "../mol-script/language/expression";
+import { Color } from "../mol-util/color";
 import { rotateCamera as RC } from "./camera";
 import { TmDetDescriptorCache } from "./prop";
 import { getChainExpression as GCE, getCurrentHierarchy as GCH, transformationForStateTransform, transformWholeModel } from "./transformation";

src/tmdet-extension/labeling.ts

@@ -7,9 +7,9 @@
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
-import { Loci } from 'molstar/lib/mol-model/loci';
-import { StructureElement } from 'molstar/lib/mol-model/structure';
-import { LociLabel, LociLabelProvider } from 'molstar/lib/mol-plugin-state/manager/loci-label';
+import { Loci } from '../mol-model/loci';
+import { StructureElement } from '../mol-model/structure';
+import { LociLabel, LociLabelProvider } from '../mol-plugin-state/manager/loci-label';
 import { TmDetChainListCache, TmDetDescriptorCache } from './prop';
 import { createResidueListsPerChain, getChainAndResidueIds } from './tmdet-color-theme';
 import { ChainList, getResidue, ResidueItem } from './types';

src/tmdet-extension/prop.ts

@@ -13,16 +13,16 @@
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
-import { Structure, StructureProperties, Unit } from 'molstar/lib/mol-model/structure';
-import { CustomPropertyDescriptor } from 'molstar/lib/mol-model/custom-property';
+import { ParamDefinition as PD } from '../mol-util/param-definition';
+import { Structure, StructureProperties, Unit } from '../mol-model/structure';
+import { CustomPropertyDescriptor } from '../mol-model/custom-property';
 import { isInMembranePlane, TMDETParams } from './algorithm';
-import { CustomStructureProperty } from 'molstar/lib/mol-model-props/common/custom-structure-property';
-import { CustomProperty } from 'molstar/lib/mol-model-props/common/custom-property';
-import { Vec3 } from 'molstar/lib/mol-math/linear-algebra';
-import { QuerySymbolRuntime } from 'molstar/lib/mol-script/runtime/query/base';
-import { CustomPropSymbol } from 'molstar/lib/mol-script/language/symbol';
-import { Type } from 'molstar/lib/mol-script/language/type';
+import { CustomStructureProperty } from '../mol-model-props/common/custom-structure-property';
+import { CustomProperty } from '../mol-model-props/common/custom-property';
+import { Vec3 } from '../mol-math/linear-algebra';
+import { QuerySymbolRuntime } from '../mol-script/runtime/query/base';
+import { CustomPropSymbol } from '../mol-script/language/symbol';
+import { Type } from '../mol-script/language/type';
 import { ChainList, PDBTMDescriptor } from './types';
 
 export const MembraneOrientationParams = {

src/tmdet-extension/representation.ts

@@ -5,26 +5,26 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
-import { Vec3, Mat4 } from 'molstar/lib/mol-math/linear-algebra';
-import { Representation, RepresentationContext, RepresentationParamsGetter } from 'molstar/lib/mol-repr/representation';
-import { Structure } from 'molstar/lib/mol-model/structure';
-import { StructureRepresentationProvider, StructureRepresentation, StructureRepresentationStateBuilder } from 'molstar/lib/mol-repr/structure/representation';
+import { ParamDefinition as PD } from '../mol-util/param-definition';
+import { Vec3, Mat4 } from '../mol-math/linear-algebra';
+import { Representation, RepresentationContext, RepresentationParamsGetter } from '../mol-repr/representation';
+import { Structure } from '../mol-model/structure';
+import { StructureRepresentationProvider, StructureRepresentation, StructureRepresentationStateBuilder } from '../mol-repr/structure/representation';
 import { MembraneOrientation, MembraneOrientationProvider } from './prop';
-import { ThemeRegistryContext } from 'molstar/lib/mol-theme/theme';
-import { ShapeRepresentation } from 'molstar/lib/mol-repr/shape/representation';
-import { Shape } from 'molstar/lib/mol-model/shape';
-import { RuntimeContext } from 'molstar/lib/mol-task';
-import { Lines } from 'molstar/lib/mol-geo/geometry/lines/lines';
-import { Mesh } from 'molstar/lib/mol-geo/geometry/mesh/mesh';
-import { LinesBuilder } from 'molstar/lib/mol-geo/geometry/lines/lines-builder';
-import { Circle } from 'molstar/lib/mol-geo/primitive/circle';
-import { transformPrimitive } from 'molstar/lib/mol-geo/primitive/primitive';
-import { MeshBuilder } from 'molstar/lib/mol-geo/geometry/mesh/mesh-builder';
-import { MarkerActions } from 'molstar/lib/mol-util/marker-action';
-import { lociLabel } from 'molstar/lib/mol-theme/label';
-import { ColorNames } from 'molstar/lib/mol-util/color/names';
-import { CustomProperty } from 'molstar/lib/mol-model-props/common/custom-property';
+import { ThemeRegistryContext } from '../mol-theme/theme';
+import { ShapeRepresentation } from '../mol-repr/shape/representation';
+import { Shape } from '../mol-model/shape';
+import { RuntimeContext } from '../mol-task';
+import { Lines } from '../mol-geo/geometry/lines/lines';
+import { Mesh } from '../mol-geo/geometry/mesh/mesh';
+import { LinesBuilder } from '../mol-geo/geometry/lines/lines-builder';
+import { Circle } from '../mol-geo/primitive/circle';
+import { transformPrimitive } from '../mol-geo/primitive/primitive';
+import { MeshBuilder } from '../mol-geo/geometry/mesh/mesh-builder';
+import { MarkerActions } from '../mol-util/marker-action';
+import { lociLabel } from '../mol-theme/label';
+import { ColorNames } from '../mol-util/color/names';
+import { CustomProperty } from '../mol-model-props/common/custom-property';
 
 const SharedParams = {
     color: PD.Color(ColorNames.lightgrey),

src/tmdet-extension/symmetry.ts

@@ -7,13 +7,13 @@
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
-import { MmcifFormat } from 'molstar/lib/mol-model-formats/structure/mmcif';
-import { Column, Table } from 'molstar/lib/mol-data/db';
-import { mmCIF_Schema } from 'molstar/lib/mol-io/reader/cif/schema/mmcif';
-import { Model } from 'molstar/lib/mol-model/structure';
-import { ModelSymmetry } from 'molstar/lib/mol-model-formats/structure/property/symmetry';
+import { MmcifFormat } from '../mol-model-formats/structure/mmcif';
+import { Column, Table } from '../mol-data/db';
+import { mmCIF_Schema } from '../mol-io/reader/cif/schema/mmcif';
+import { Model } from '../mol-model/structure';
+import { ModelSymmetry } from '../mol-model-formats/structure/property/symmetry';
 import { PDBTMDescriptor } from './types';
-import { Mat3, Mat4, Vec3 } from 'molstar/lib/mol-math/linear-algebra';
+import { Mat3, Mat4, Vec3 } from '../mol-math/linear-algebra';
 import { transformationForStateTransform } from './transformation';
 
 export function registerTmDetSymmetry(pdbtmDescriptor: PDBTMDescriptor) {

src/tmdet-extension/tmdet-color-theme.ts

@@ -7,13 +7,13 @@
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
-import { StructureElement, Unit } from 'molstar/lib/mol-model/structure';
-import { ColorTheme } from 'molstar/lib/mol-theme/color';
-import { ThemeDataContext } from 'molstar/lib/mol-theme/theme';
-import { Color } from 'molstar/lib/mol-util/color';
-import { ColorNames } from 'molstar/lib/mol-util/color/names';
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
-import { Location } from 'molstar/lib/mol-model/location';
+import { StructureElement, Unit } from '../mol-model/structure';
+import { ColorTheme } from '../mol-theme/color';
+import { ThemeDataContext } from '../mol-theme/theme';
+import { Color } from '../mol-util/color';
+import { ColorNames } from '../mol-util/color/names';
+import { ParamDefinition as PD } from '../mol-util/param-definition';
+import { Location } from '../mol-model/location';
 import { ChainList, getResidue, PDBTMChain } from './types';
 import { TmDetChainListCache, TmDetDescriptorCache } from './prop';
 

src/tmdet-extension/transformation.ts

@@ -7,17 +7,17 @@
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
-import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
-import { Mat4, Vec3 } from 'molstar/lib/mol-math/linear-algebra';
+import { MolScriptBuilder as MS } from '../mol-script/language/builder';
+import { Mat4, Vec3 } from '../mol-math/linear-algebra';
 import { PDBTMDescriptor, PDBTMTransformationMatrix, PMS } from './types';
-import { createStructureRepresentationParams } from 'molstar/lib/mol-plugin-state/helpers/structure-representation-params';
-import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
-import { StateObjectRef, StateBuilder } from 'molstar/lib/mol-state';
-import { Expression } from 'molstar/lib/mol-script/language/expression';
+import { createStructureRepresentationParams } from '../mol-plugin-state/helpers/structure-representation-params';
+import { StateTransforms } from '../mol-plugin-state/transforms';
+import { StateObjectRef, StateBuilder } from '../mol-state';
+import { Expression } from '../mol-script/language/expression';
 import { MembraneOrientation } from './prop';
 import { TmDetColorThemeProvider } from './tmdet-color-theme';
 import { DebugUtil } from './debug-utils';
-import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { PluginContext } from '../mol-plugin/context';
 
 export function applyTransformations(plugin: PluginContext, pdbtmDescriptor: PDBTMDescriptor) {
     const annotations = pdbtmDescriptor.additional_entry_annotations;

src/tmdet-extension/types.ts

@@ -7,9 +7,9 @@
  * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
  */
 
-import { PluginStateObject } from "molstar/lib/mol-plugin-state/objects";
-import { StateObject, StateTransformer } from 'molstar/lib/mol-state';
-import { StateObjectSelector } from "molstar/lib/mol-state/object";
+import { PluginStateObject } from "../mol-plugin-state/objects";
+import { StateObject, StateTransformer } from '../mol-state';
+import { StateObjectSelector } from "../mol-state/object";
 
 export type PMS = PluginStateObject.Molecule.Structure;