wip density-server cif loading

src/mol-model/volume/formats/density-server.ts

@@ -10,8 +10,8 @@ import { Task } from 'mol-task';
 import { SpacegroupCell, Box3D } from 'mol-math/geometry';
 import { Tensor, Vec3 } from 'mol-math/linear-algebra';
 
-function parseDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
-    return Task.create<VolumeData>('Parse Volume Data', async ctx => {
+function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
+    return Task.create<VolumeData>('Create Volume Data', async ctx => {
         const { volume_data_3d_info: info, volume_data_3d: values } = source;
         const cell = SpacegroupCell.create(
             info.spacegroup_number.value(0),
@@ -47,4 +47,4 @@ function parseDensityServerData(source: DensityServer_Data_Database): Task<Volum
     });
 }
 
-export { parseDensityServerData }
+export { volumeFromDensityServerData }
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src/mol-plugin/state/actions/basic.ts

@@ -162,7 +162,7 @@ export const UpdateTrajectory = StateAction.build({
 
 //
 
-const VolumeFormats = { 'ccp4': '', 'mrc': '', 'map': '', 'dsn6': '', 'brix': '' }
+const VolumeFormats = { 'ccp4': '', 'mrc': '', 'map': '', 'dsn6': '', 'brix': '', 'dscif': '' }
 type VolumeFormat = keyof typeof VolumeFormats
 
 function getVolumeData(format: VolumeFormat, b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>) {
@@ -171,6 +171,8 @@ function getVolumeData(format: VolumeFormat, b: StateTreeBuilder.To<PluginStateO
             return b.apply(StateTransforms.Data.ParseCcp4).apply(StateTransforms.Model.VolumeFromCcp4);
         case 'dsn6': case 'brix':
             return b.apply(StateTransforms.Data.ParseDsn6).apply(StateTransforms.Model.VolumeFromDsn6);
+        case 'dscif':
+            return b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.VolumeFromDensityServerCif);
     }
 }
 
@@ -200,14 +202,15 @@ export const OpenVolume = StateAction.build({
     display: { name: 'Open Volume', description: 'Load a volume from file and create its default visual' },
     from: PluginStateObject.Root,
     params: {
-        file: PD.File({ accept: '.ccp4,.mrc,.map,.dsn6,.brix'}),
+        file: PD.File({ accept: '.ccp4,.mrc,.map,.dsn6,.brix,.cif'}),
+        isBinary: PD.Boolean(true),
         format: PD.Select('auto', [
-            ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX']
+            ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX'], ['dscif', 'densityServerCIF']
         ]),
     }
 })(({ params, state }, ctx: PluginContext) => {
     const b = state.build();
-    const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: true });
+    const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: params.isBinary });
     const format = getFileFormat(params.format, params.file)
     return state.update(createVolumeTree(format, ctx, data));
 });
@@ -229,8 +232,9 @@ const DownloadDensity = StateAction.build({
             }, { isFlat: true }),
             'url': PD.Group({
                 url: PD.Text(''),
+                isBinary: PD.Boolean(true),
                 format: PD.Select('auto', [
-                    ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX']
+                    ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX'], ['dscif', 'densityServerCIF']
                 ]),
             }, { isFlat: true })
         }, {

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

@@ -19,6 +19,8 @@ import { stringToWords } from 'mol-util/string';
 import { volumeFromCcp4 } from 'mol-model/volume/formats/ccp4';
 import { Vec3 } from 'mol-math/linear-algebra';
 import { volumeFromDsn6 } from 'mol-model/volume/formats/dsn6';
+import { volumeFromDensityServerData } from 'mol-model/volume';
+import CIF from 'mol-io/reader/cif';
 
 export { TrajectoryFromMmCif }
 type TrajectoryFromMmCif = typeof TrajectoryFromMmCif
@@ -259,4 +261,37 @@ const VolumeFromDsn6 = PluginStateTransform.BuiltIn({
             return new SO.Volume.Data(volume, props);
         });
     }
+});
+
+export { VolumeFromDensityServerCif }
+type VolumeFromDensityServerCif = typeof VolumeFromDensityServerCif
+const VolumeFromDensityServerCif = PluginStateTransform.BuiltIn({
+    name: 'volume-from-density-server-cif',
+    display: { name: 'Volume from density-server CIF', description: 'Identify and create all separate models in the specified CIF data block' },
+    from: SO.Format.Cif,
+    to: SO.Volume.Data,
+    params(a) {
+        if (!a) {
+            return {
+                blockHeader: PD.makeOptional(PD.Text(void 0, { description: 'Header of the block to parse. If none is specifed, the 1st data block in the file is used.' }))
+            };
+        }
+        const blocks = a.data.blocks.slice(1); // zero block contains query meta-data
+        return {
+            blockHeader: PD.makeOptional(PD.Select(blocks[0] && blocks[0].header, blocks.map(b => [b.header, b.header] as [string, string]), { description: 'Header of the block to parse' }))
+        };
+    }
+})({
+    isApplicable: a => a.data.blocks.length > 0,
+    apply({ a, params }) {
+        return Task.create('Parse density-server CIF', async ctx => {
+            const header = params.blockHeader || a.data.blocks[1].header; // zero block contains query meta-data
+            const block = a.data.blocks.find(b => b.header === header);
+            if (!block) throw new Error(`Data block '${[header]}' not found.`);
+            const densityServerCif = CIF.schema.densityServer(block)
+            const volume = await volumeFromDensityServerData(densityServerCif).runInContext(ctx)
+            const props = { label: densityServerCif.volume_data_3d_info.name.value(0), description: `${densityServerCif.volume_data_3d_info.name.value(0)}` };
+            return new SO.Volume.Data(volume, props);
+        });
+    }
 });
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