Removing initial plugin-based Kinemage reader stubs, leaving the extension that handles both File/Open and drag-and-drop

src/apps/mesoscale-explorer/data/generic/preset.ts

@@ -14,8 +14,8 @@ import { Mat3, Quat, Vec3 } from '../../../../mol-math/linear-algebra';
 import { GraphicsMode, MesoscaleGroup, MesoscaleState, getGraphicsModeProps, getMesoscaleGroupParams } from '../state';
 import { ColorNames } from '../../../../mol-util/color/names';
 import { ShapeRepresentation3D, StructureRepresentation3D } from '../../../../mol-plugin-state/transforms/representation';
-import { ParseCif, ParsePly, ParseKin, ReadFile } from '../../../../mol-plugin-state/transforms/data';
-import { ModelFromTrajectory, ShapeFromPly, ShapeLinesFromKin, TrajectoryFromGRO, TrajectoryFromMOL, TrajectoryFromMOL2, TrajectoryFromMmCif, TrajectoryFromPDB, TrajectoryFromSDF, TrajectoryFromXYZ } from '../../../../mol-plugin-state/transforms/model';
+import { ParseCif, ParsePly, ReadFile } from '../../../../mol-plugin-state/transforms/data';
+import { ModelFromTrajectory, ShapeFromPly, TrajectoryFromGRO, TrajectoryFromMOL, TrajectoryFromMOL2, TrajectoryFromMmCif, TrajectoryFromPDB, TrajectoryFromSDF, TrajectoryFromXYZ } from '../../../../mol-plugin-state/transforms/model';
 import { Euler } from '../../../../mol-math/linear-algebra/3d/euler';
 import { Asset } from '../../../../mol-util/assets';
 import { Clip } from '../../../../mol-util/clip';
@@ -104,34 +104,6 @@ function getPlyShapeParams(color: Color, clipVariant: Clip.Variant) {
     };
 }
 
-function getKinShapeParams(color: Color, clipVariant: Clip.Variant) {
-  return {
-    ...PD.getDefaultValues(BaseGeometry.Params),
-    instanceGranularity: true,
-    ignoreLight: true,
-    clip: {
-      variant: clipVariant,
-      objects: [],
-    },
-    quality: 'custom',
-    doubleSided: true,
-    coloring: {
-      name: 'uniform',
-      params: { color }
-    },
-    grouping: {
-      name: 'none',
-      params: {}
-    },
-    material: {
-      metalness: 0.0,
-      roughness: 1.0,
-      bumpiness: 1.0,
-    },
-    bumpAmplitude: 0.1,
-    bumpFrequency: 0.1 / 10,
-  };
-}
 export async function createGenericHierarchy(plugin: PluginContext, file: Asset.File) {
     const asset = await plugin.runTask(plugin.managers.asset.resolve(file, 'zip'));
     let manifest: GenericManifest;
@@ -280,15 +252,6 @@ export async function createGenericHierarchy(plugin: PluginContext, file: Asset.
                             .apply(ShapeFromPly, { label, transforms })
                             .apply(ShapeRepresentation3D, getPlyShapeParams(color, clipVariant), { tags });
                     }
-                } else if (['kin'].includes(info.ext)) {
-                  if (['kin'].includes(info.ext)) {
-                    const transforms = await getTransforms(plugin, instances);
-                    const clipVariant = transforms.length === 1 ? 'pixel' : 'instance';
-                    build = build
-                      .apply(ParseKin)
-                      .apply(ShapeLinesFromKin, { label, transforms })
-                      .apply(ShapeRepresentation3D, getKinShapeParams(color, clipVariant), { tags });
-                  }
                 } else {
                     console.warn(`unknown file format '${info.ext}'`);
                 }

src/mol-plugin-state/formats/shape.ts

@@ -37,34 +37,8 @@ export const PlyProvider = DataFormatProvider({
     }
 });
 
-export const KinProvider = DataFormatProvider({
-  label: 'KIN',
-  description: 'KIN',
-  category: ShapeFormatCategory,
-  stringExtensions: ['kin'],
-  parse: async (plugin, data) => {
-    // This returns the last kinemage in the file if there are multiple
-    const format = plugin.state.data.build()
-      .to(data)
-      .apply(StateTransforms.Data.ParseKin, {}, { state: { isGhost: true } });
-
-    const shape = format.apply(StateTransforms.Model.ShapeLinesFromKin);
-
-    await format.commit();
-
-    return { format: format.selector, shape: shape.selector };
-  },
-  visuals(plugin: PluginContext, data: { shape: StateObjectRef<PluginStateObject.Shape.Provider> }) {
-    const repr = plugin.state.data.build()
-      .to(data.shape)
-      .apply(StateTransforms.Representation.ShapeRepresentation3D);
-    return repr.commit();
-  }
-});
-
 export const BuiltInShapeFormats = [
   ['ply', PlyProvider] as const,
-  /// @todo Replaced the plugin loader with an extension ['kin', KinProvider] as const,
 ] as const;
 
-export type BuiltInShapeFormat = (typeof BuiltInShapeFormats)[number][0]
+export type BuiltInShapeFormat = (typeof BuiltInShapeFormats)[number][0]

src/mol-plugin-state/objects.ts

@@ -10,7 +10,6 @@ import { CifFile } from '../mol-io/reader/cif';
 import { DcdFile } from '../mol-io/reader/dcd/parser';
 import { Dsn6File } from '../mol-io/reader/dsn6/schema';
 import { PlyFile } from '../mol-io/reader/ply/schema';
-import { Kinemage } from '../mol-io/reader/kin/schema';
 import { PsfFile } from '../mol-io/reader/psf/parser';
 import { ShapeProvider } from '../mol-model/shape/provider';
 import { Coordinates as _Coordinates, Model as _Model, Structure as _Structure, Trajectory as _Trajectory, StructureElement, Topology as _Topology } from '../mol-model/structure';
@@ -80,7 +79,6 @@ export namespace PluginStateObject {
         export class Prmtop extends Create<PrmtopFile>({ name: 'PRMTOP File', typeClass: 'Data' }) { }
         export class Top extends Create<TopFile>({ name: 'TOP File', typeClass: 'Data' }) { }
         export class Ply extends Create<PlyFile>({ name: 'PLY File', typeClass: 'Data' }) { }
-        export class Kin extends Create<Kinemage>({ name: 'KIN File', typeClass: 'Data' }) { }
         export class Ccp4 extends Create<Ccp4File>({ name: 'CCP4/MRC/MAP File', typeClass: 'Data' }) { }
         export class Dsn6 extends Create<Dsn6File>({ name: 'DSN6/BRIX File', typeClass: 'Data' }) { }
         export class Dx extends Create<DxFile>({ name: 'DX File', typeClass: 'Data' }) { }
@@ -97,7 +95,6 @@ export namespace PluginStateObject {
             { kind: 'dsn6', data: Dsn6File } |
             { kind: 'dx', data: DxFile } |
             { kind: 'ply', data: PlyFile } |
-            { kind: 'kin', data: Kinemage } |
             // For non-built-in extensions
             { kind: 'custom', data: unknown, tag: string }
         )
@@ -158,4 +155,4 @@ export namespace PluginStateObject {
 export namespace PluginStateTransform {
     export const CreateBuiltIn = StateTransformer.factory('ms-plugin');
     export const BuiltIn = StateTransformer.builderFactory('ms-plugin');
-}
+}

src/mol-plugin-state/transforms/data.ts

@@ -10,8 +10,6 @@ import * as CCP4 from '../../mol-io/reader/ccp4/parser';
 import { CIF } from '../../mol-io/reader/cif';
 import * as DSN6 from '../../mol-io/reader/dsn6/parser';
 import * as PLY from '../../mol-io/reader/ply/parser';
-import * as KIN from '../../mol-io/reader/kin/parser';
-import { Kinemage } from '../../mol-io/reader/kin/schema';
 import { parsePsf } from '../../mol-io/reader/psf/parser';
 import { PluginContext } from '../../mol-plugin/context';
 import { StateObject, StateTransformer } from '../../mol-state';
@@ -43,7 +41,6 @@ export { ParsePsf };
 export { ParsePrmtop };
 export { ParseTop };
 export { ParsePly };
-export { ParseKin }
 export { ParseCcp4 };
 export { ParseDsn6 };
 export { ParseDx };
@@ -406,26 +403,6 @@ const ParsePly = PluginStateTransform.BuiltIn({
     }
 });
 
-type ParseKin = typeof ParseKin
-const ParseKin = PluginStateTransform.BuiltIn({
-  name: 'parse-kin',
-  display: { name: 'Parse KIN', description: 'Parse KIN from String data' },
-  from: [SO.Data.String],
-  to: SO.Format.Kin
-})({
-  apply({ a }) {
-    return Task.create('Parse KIN', async ctx => {
-      const parsedList = await KIN.parseKin(a.data).runInContext(ctx);
-      if (parsedList.isError) throw new Error(parsedList.message);
-      // Read the last entry, handling the case where it is an error
-      const kinemages: Kinemage[] = parsedList.result;
-      const parsed = kinemages.length ? parsedList.result[kinemages.length - 1] : undefined;
-      if (!parsed) return StateObject.Null;
-      return new SO.Format.Kin(parsed, { label: parsed.comments[0] || 'KIN Data' });
-    });
-  }
-});
-
 type ParseCcp4 = typeof ParseCcp4
 const ParseCcp4 = PluginStateTransform.BuiltIn({
     name: 'parse-ccp4',

src/mol-plugin-state/transforms/model.ts

@@ -12,7 +12,6 @@ import { parseGRO } from '../../mol-io/reader/gro/parser';
 import { parsePDB } from '../../mol-io/reader/pdb/parser';
 import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
 import { shapeFromPly } from '../../mol-model-formats/shape/ply';
-import { shapeLinesFromKin } from '../../mol-model-formats/shape/kin';
 import { coordinatesFromDcd } from '../../mol-model-formats/structure/dcd';
 import { trajectoryFromGRO } from '../../mol-model-formats/structure/gro';
 import { trajectoryFromCCD, trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
@@ -95,7 +94,6 @@ export { StructureComponent };
 export { CustomModelProperties };
 export { CustomStructureProperties };
 export { ShapeFromPly };
-export { ShapeLinesFromKin };
 
 type CoordinatesFromDcd = typeof CoordinatesFromDcd
 const CoordinatesFromDcd = PluginStateTransform.BuiltIn({
@@ -1320,24 +1318,3 @@ const ShapeFromPly = PluginStateTransform.BuiltIn({
     }
 });
 
-type ShapeLinesFromKin = typeof ShapeLinesFromKin
-const ShapeLinesFromKin = PluginStateTransform.BuiltIn({
-  name: 'shape-lines-from-kin',
-  display: { name: 'Shape Lines from KIN', description: 'Create Shape from KIN data' },
-  from: SO.Format.Kin,
-  to: SO.Shape.Provider,
-  params(a) {
-    return {
-      transforms: PD.Optional(PD.Value<Mat4[]>([], { isHidden: true })),
-      label: PD.Optional(PD.Text('', { isHidden: true }))
-    };
-  }
-})({
-  apply({ a, params }) {
-    return Task.create('Create shape from KIN', async ctx => {
-      const shape = await shapeLinesFromKin(a.data, params).runInContext(ctx);
-      const props = { label: params.label || 'Shape' };
-      return new SO.Shape.Provider(shape, props);
-    });
-  }
-});