diff --git a/src/apps/structure-info/volume.ts b/src/apps/structure-info/volume.ts
index ef38fcb190d1a90a8855321319ea18063188198c..cfedb46e9e4a7d520469ca3b1206d1992a0d5522 100644
--- a/src/apps/structure-info/volume.ts
+++ b/src/apps/structure-info/volume.ts
@@ -8,38 +8,36 @@ import * as fs from 'fs';
import * as argparse from 'argparse';
import * as util from 'util';
-import { VolumeData, VolumeIsoValue } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
import { downloadCif } from './helpers';
import { CIF } from '../../mol-io/reader/cif';
-import { DensityServer_Data_Database } from '../../mol-io/reader/cif/schema/density-server';
import { Table } from '../../mol-data/db';
import { StringBuilder } from '../../mol-util';
import { Task } from '../../mol-task';
import { createVolumeIsosurfaceMesh } from '../../mol-repr/volume/isosurface';
import { Theme } from '../../mol-theme/theme';
-import { volumeFromDensityServerData } from '../../mol-model-formats/volume/density-server';
+import { volumeFromDensityServerData, DscifFormat } from '../../mol-model-formats/volume/density-server';
require('util.promisify').shim();
const writeFileAsync = util.promisify(fs.writeFile);
-type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
-
async function getVolume(url: string): Promise<Volume> {
const cif = await downloadCif(url, true);
const data = CIF.schema.densityServer(cif.blocks[1]);
- return { source: data, volume: await volumeFromDensityServerData(data).run() };
+ return await volumeFromDensityServerData(data).run();
}
-function print(data: Volume) {
- const { volume_data_3d_info } = data.source;
+function print(volume: Volume) {
+ if (!DscifFormat.is(volume.sourceData)) return;
+ const { volume_data_3d_info } = volume.sourceData.data;
const row = Table.getRow(volume_data_3d_info, 0);
console.log(row);
- if (data.volume.transform) console.log(data.volume.transform);
- console.log(data.volume.dataStats);
+ console.log(volume.grid.transform);
+ console.log(volume.grid.stats);
}
-async function doMesh(data: Volume, filename: string) {
- const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, data.volume, Theme.createEmpty(), { isoValue: VolumeIsoValue.absolute(1.5) } )).run();
+async function doMesh(volume: Volume, filename: string) {
+ const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, volume, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) } )).run();
console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
// Export the mesh in OBJ format.
diff --git a/src/extensions/cellpack/property.ts b/src/extensions/cellpack/property.ts
index 700776fea1689c23bb2d4c3c0b76b28a0b03ee07..56e58cfb26c21b719ac79c5344c0effbfc909c33 100644
--- a/src/extensions/cellpack/property.ts
+++ b/src/extensions/cellpack/property.ts
@@ -5,9 +5,10 @@
*/
import { CustomStructureProperty } from '../../mol-model-props/common/custom-structure-property';
-import { Structure, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
import { CustomProperty } from '../../mol-model-props/common/custom-property';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
export type CellPackInfoValue = {
packingsCount: number
diff --git a/src/extensions/pdbe/preferred-assembly.ts b/src/extensions/pdbe/preferred-assembly.ts
index 52a2d3c3218cb7e82f803bce135ed94f1ceb5da7..f4a11f08bdd103c1d969d8f5403653cc85b5198c 100644
--- a/src/extensions/pdbe/preferred-assembly.ts
+++ b/src/extensions/pdbe/preferred-assembly.ts
@@ -7,9 +7,10 @@
import { Column, Table } from '../../mol-data/db';
import { toTable } from '../../mol-io/reader/cif/schema';
import { CifWriter } from '../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Model } from '../../mol-model/structure';
import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
export namespace PDBePreferredAssembly {
export type Property = string
diff --git a/src/extensions/pdbe/struct-ref-domain.ts b/src/extensions/pdbe/struct-ref-domain.ts
index 4b025f55230860d427b7c6be975b672e134d3881..c92a385b4984c10f73ed9e166ccf62a765238294 100644
--- a/src/extensions/pdbe/struct-ref-domain.ts
+++ b/src/extensions/pdbe/struct-ref-domain.ts
@@ -7,9 +7,10 @@
import { Column, Table } from '../../mol-data/db';
import { toTable } from '../../mol-io/reader/cif/schema';
import { CifWriter } from '../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Model } from '../../mol-model/structure';
import { PropertyWrapper } from '../../mol-model-props/common/wrapper';
import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
export namespace PDBeStructRefDomain {
export type Property = PropertyWrapper<Table<Schema['pdbe_struct_ref_domain']> | undefined>
diff --git a/src/extensions/pdbe/structure-quality-report/prop.ts b/src/extensions/pdbe/structure-quality-report/prop.ts
index e51f875867f89598a96b3e1dd063f0429c36b1ea..e1342d51b9abfe07a347bd4afcb9258b04ba0ac0 100644
--- a/src/extensions/pdbe/structure-quality-report/prop.ts
+++ b/src/extensions/pdbe/structure-quality-report/prop.ts
@@ -9,7 +9,7 @@ import { Column, Table } from '../../../mol-data/db';
import { toTable } from '../../../mol-io/reader/cif/schema';
import { mmCIF_residueId_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
import { CifWriter } from '../../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-model/structure';
+import { Model, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-model/structure';
import { residueIdFields } from '../../../mol-model/structure/export/categories/atom_site';
import { StructureElement, CifExportContext, Structure } from '../../../mol-model/structure/structure';
import { CustomPropSymbol } from '../../../mol-script/language/symbol';
@@ -22,6 +22,7 @@ import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
import { Asset } from '../../../mol-util/assets';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
export { StructureQualityReport };
diff --git a/src/extensions/rcsb/assembly-symmetry/prop.ts b/src/extensions/rcsb/assembly-symmetry/prop.ts
index 7bd1286448a08726257d2a3604adea9b8cc6f43f..c88daa19ab72297f9f86685d8263a7187beb2eed 100644
--- a/src/extensions/rcsb/assembly-symmetry/prop.ts
+++ b/src/extensions/rcsb/assembly-symmetry/prop.ts
@@ -8,7 +8,7 @@ import { AssemblySymmetryQuery, AssemblySymmetryQueryVariables } from '../graphq
import query from '../graphql/symmetry.gql';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { CustomPropertyDescriptor, Structure, Model, StructureSelection, QueryContext } from '../../../mol-model/structure';
+import { Structure, Model, StructureSelection, QueryContext } from '../../../mol-model/structure';
import { Database as _Database, Column } from '../../../mol-data/db';
import { GraphQLClient } from '../../../mol-util/graphql-client';
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
@@ -19,6 +19,7 @@ import { ReadonlyVec3 } from '../../../mol-math/linear-algebra/3d/vec3';
import { SetUtils } from '../../../mol-util/set';
import { MolScriptBuilder as MS } from '../../../mol-script/language/builder';
import { compile } from '../../../mol-script/runtime/query/compiler';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
const BiologicalAssemblyNames = new Set([
'author_and_software_defined_assembly',
diff --git a/src/extensions/rcsb/validation-report/prop.ts b/src/extensions/rcsb/validation-report/prop.ts
index a17bc6fd1feeab3b336e8057bbc93af2a1f8f825..aec4ea9a2956f4f6e1d3fa84129c788faeb1a840 100644
--- a/src/extensions/rcsb/validation-report/prop.ts
+++ b/src/extensions/rcsb/validation-report/prop.ts
@@ -5,7 +5,7 @@
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { CustomPropertyDescriptor, Structure, Unit } from '../../../mol-model/structure';
+import { Structure, Unit } from '../../../mol-model/structure';
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
import { Model, ElementIndex, ResidueIndex } from '../../../mol-model/structure/model';
@@ -21,6 +21,7 @@ import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
import { CustomPropSymbol } from '../../../mol-script/language/symbol';
import Type from '../../../mol-script/language/type';
import { Asset } from '../../../mol-util/assets';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
export { ValidationReport };
diff --git a/src/mol-model-formats/structure/basic/parser.ts b/src/mol-model-formats/structure/basic/parser.ts
index bf7129e2a08e21145a50020e227c1f8e6aac6ee2..8773e4e2a7d776c3f39e5630fb443942d8434424 100644
--- a/src/mol-model-formats/structure/basic/parser.ts
+++ b/src/mol-model-formats/structure/basic/parser.ts
@@ -10,7 +10,7 @@ import { RuntimeContext } from '../../../mol-task';
import UUID from '../../../mol-util/uuid';
import { Model } from '../../../mol-model/structure/model/model';
import { Entities } from '../../../mol-model/structure/model/properties/common';
-import { CustomProperties } from '../../../mol-model/structure';
+import { CustomProperties } from '../../../mol-model/custom-property';
import { getAtomicHierarchyAndConformation } from './atomic';
import { getCoarse, EmptyCoarse, CoarseData } from './coarse';
import { getSequence } from './sequence';
diff --git a/src/mol-model-formats/structure/common/property.ts b/src/mol-model-formats/structure/common/property.ts
index cbc1718f8a99beb821d9f81e0b947f05f982341a..63709daac1bbcfe8fb01c35602cc4fcc39fb09ae 100644
--- a/src/mol-model-formats/structure/common/property.ts
+++ b/src/mol-model-formats/structure/common/property.ts
@@ -4,8 +4,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { CustomPropertyDescriptor, Model } from '../../../mol-model/structure';
+import { Model } from '../../../mol-model/structure';
import { ModelFormat } from '../../format';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
class FormatRegistry<T> {
private map = new Map<ModelFormat['kind'], (model: Model) => T | undefined>()
diff --git a/src/mol-model-formats/structure/property/anisotropic.ts b/src/mol-model-formats/structure/property/anisotropic.ts
index 16cb3591e646ef9084ae255d4deeecc989bf3e5e..f6cc407d15d2c51ffd9319b82755f0fc50a2e0e6 100644
--- a/src/mol-model-formats/structure/property/anisotropic.ts
+++ b/src/mol-model-formats/structure/property/anisotropic.ts
@@ -5,7 +5,7 @@
*/
import { Table, Column } from '../../../mol-data/db';
-import { CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { CifWriter } from '../../../mol-io/writer/cif';
import { FormatPropertyProvider } from '../common/property';
diff --git a/src/mol-model-formats/structure/property/bonds/comp.ts b/src/mol-model-formats/structure/property/bonds/comp.ts
index ed510b10fa01f68e7efaf73a43e6720ef16dd331..b30e9dac92f4e5c62ec908ca22af7dc5a3485d3b 100644
--- a/src/mol-model-formats/structure/property/bonds/comp.ts
+++ b/src/mol-model-formats/structure/property/bonds/comp.ts
@@ -7,7 +7,7 @@
import { Model } from '../../../../mol-model/structure/model/model';
import { BondType } from '../../../../mol-model/structure/model/types';
-import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
import { CifWriter } from '../../../../mol-io/writer/cif';
import { Table } from '../../../../mol-data/db';
diff --git a/src/mol-model-formats/structure/property/bonds/index-pair.ts b/src/mol-model-formats/structure/property/bonds/index-pair.ts
index 7a09535eb37b4026a4055d0c7b7c7a91080528e1..485fe8d737818499cc809bdf4c5eb8a957da7dca 100644
--- a/src/mol-model-formats/structure/property/bonds/index-pair.ts
+++ b/src/mol-model-formats/structure/property/bonds/index-pair.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
import { IntAdjacencyGraph } from '../../../../mol-math/graph';
import { Column } from '../../../../mol-data/db';
import { FormatPropertyProvider } from '../../common/property';
diff --git a/src/mol-model-formats/structure/property/bonds/struct_conn.ts b/src/mol-model-formats/structure/property/bonds/struct_conn.ts
index 494ac4d2b6c0c62c28847de18753189b9730bbcf..ae48045cdadc8a6a6f9f4c1bf3708857e6d3697c 100644
--- a/src/mol-model-formats/structure/property/bonds/struct_conn.ts
+++ b/src/mol-model-formats/structure/property/bonds/struct_conn.ts
@@ -9,7 +9,7 @@ import { Model } from '../../../../mol-model/structure/model/model';
import { Structure } from '../../../../mol-model/structure';
import { BondType } from '../../../../mol-model/structure/model/types';
import { Column, Table } from '../../../../mol-data/db';
-import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
import { SortedArray } from '../../../../mol-data/int';
import { CifWriter } from '../../../../mol-io/writer/cif';
diff --git a/src/mol-model-formats/structure/property/secondary-structure.ts b/src/mol-model-formats/structure/property/secondary-structure.ts
index e79e9a321900da33f4def2872497d8a7b0d2b9f0..616cd18bf2a6fbbf5eabe1a7475b6f1914537467 100644
--- a/src/mol-model-formats/structure/property/secondary-structure.ts
+++ b/src/mol-model-formats/structure/property/secondary-structure.ts
@@ -13,7 +13,7 @@ import { SecondaryStructure } from '../../../mol-model/structure/model/propertie
import { Column, Table } from '../../../mol-data/db';
import { ChainIndex, ResidueIndex } from '../../../mol-model/structure/model/indexing';
import { FormatPropertyProvider } from '../common/property';
-import { CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
export { ModelSecondaryStructure };
diff --git a/src/mol-model-formats/structure/property/symmetry.ts b/src/mol-model-formats/structure/property/symmetry.ts
index 75330f6f657469b770f2345054864d98642d2f65..22f610e86430653c9cca30c4fc34305ee1b62e7a 100644
--- a/src/mol-model-formats/structure/property/symmetry.ts
+++ b/src/mol-model-formats/structure/property/symmetry.ts
@@ -10,7 +10,7 @@ import { Spacegroup, SpacegroupCell, SymmetryOperator } from '../../../mol-math/
import { Tensor, Vec3, Mat3 } from '../../../mol-math/linear-algebra';
import { Symmetry } from '../../../mol-model/structure/model/properties/symmetry';
import { createAssemblies } from './assembly';
-import { CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
import { FormatPropertyProvider } from '../common/property';
import { Table } from '../../../mol-data/db';
diff --git a/src/mol-model-formats/volume/ccp4.ts b/src/mol-model-formats/volume/ccp4.ts
index 8ccf5ad7aa02d9261492d427211a96a534a8a489..2a05fce5e6762e56abaa1fa7c446ff80f70325c3 100644
--- a/src/mol-model-formats/volume/ccp4.ts
+++ b/src/mol-model-formats/volume/ccp4.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
import { Task } from '../../mol-task';
import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
@@ -14,6 +14,7 @@ import { getCcp4ValueType } from '../../mol-io/reader/ccp4/parser';
import { TypedArrayValueType } from '../../mol-io/common/typed-array';
import { arrayMin, arrayRms, arrayMean, arrayMax } from '../../mol-util/array';
import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
/** When available (e.g. in MRC files) use ORIGIN records instead of N[CRS]START */
export function getCcp4Origin(header: Ccp4Header): Vec3 {
@@ -39,8 +40,8 @@ function getTypedArrayCtor(header: Ccp4Header) {
throw Error(`${valueType} is not a supported value format.`);
}
-export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, offset?: Vec3, label?: string }): Task<VolumeData> {
- return Task.create<VolumeData>('Create Volume Data', async ctx => {
+export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, offset?: Vec3, label?: string }): Task<Volume> {
+ return Task.create<Volume>('Create Volume', async ctx => {
const { header, values } = source;
const size = Vec3.create(header.xLength, header.yLength, header.zLength);
if (params && params.voxelSize) Vec3.mul(size, size, params.voxelSize);
@@ -69,15 +70,19 @@ export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, of
return {
label: params?.label,
- transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
- data,
- dataStats: {
- min: isNaN(header.AMIN) ? arrayMin(values) : header.AMIN,
- max: isNaN(header.AMAX) ? arrayMax(values) : header.AMAX,
- mean: isNaN(header.AMEAN) ? arrayMean(values) : header.AMEAN,
- sigma: (isNaN(header.ARMS) || header.ARMS === 0) ? arrayRms(values) : header.ARMS
+ grid: {
+ transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
+ cells: data,
+ stats: {
+ min: isNaN(header.AMIN) ? arrayMin(values) : header.AMIN,
+ max: isNaN(header.AMAX) ? arrayMax(values) : header.AMAX,
+ mean: isNaN(header.AMEAN) ? arrayMean(values) : header.AMEAN,
+ sigma: (isNaN(header.ARMS) || header.ARMS === 0) ? arrayRms(values) : header.ARMS
+ },
},
- sourceData: Ccp4Format.create(source)
+ sourceData: Ccp4Format.create(source),
+ customProperties: new CustomProperties(),
+ _propertyData: Object.create(null),
};
});
}
diff --git a/src/mol-model-formats/volume/cube.ts b/src/mol-model-formats/volume/cube.ts
index 416944d77a6e44ff6ef4d399b5f5fd23ef672f58..4db35bee33106fb05e7f2eabc1bc7e83b3b65056 100644
--- a/src/mol-model-formats/volume/cube.ts
+++ b/src/mol-model-formats/volume/cube.ts
@@ -6,13 +6,14 @@
import { CubeFile } from '../../mol-io/reader/cube/parser';
import { Mat4, Tensor } from '../../mol-math/linear-algebra';
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
import { Task } from '../../mol-task';
import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
-export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string }): Task<VolumeData> {
- return Task.create<VolumeData>('Create Volume Data', async () => {
+export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string }): Task<Volume> {
+ return Task.create<Volume>('Create Volume', async () => {
const { header, values: sourceValues } = source;
const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
@@ -45,15 +46,19 @@ export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number,
return {
label: params?.label,
- transform: { kind: 'matrix', matrix },
- data,
- dataStats: {
- min: arrayMin(values),
- max: arrayMax(values),
- mean: arrayMean(values),
- sigma: arrayRms(values)
+ grid: {
+ transform: { kind: 'matrix', matrix },
+ cells: data,
+ stats: {
+ min: arrayMin(values),
+ max: arrayMax(values),
+ mean: arrayMean(values),
+ sigma: arrayRms(values)
+ },
},
- sourceData: CubeFormat.create(source)
+ sourceData: CubeFormat.create(source),
+ customProperties: new CustomProperties(),
+ _propertyData: Object.create(null),
};
});
}
diff --git a/src/mol-model-formats/volume/density-server.ts b/src/mol-model-formats/volume/density-server.ts
index bb35f01408b9032a3c4bf3c8cf96fe8bdd809809..ad2a5ccd649f480d375cb88538cc937e72bfce30 100644
--- a/src/mol-model-formats/volume/density-server.ts
+++ b/src/mol-model-formats/volume/density-server.ts
@@ -5,14 +5,15 @@
*/
import { DensityServer_Data_Database } from '../../mol-io/reader/cif/schema/density-server';
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
import { Task } from '../../mol-task';
import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
-export function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
- return Task.create<VolumeData>('Create Volume Data', async ctx => {
+export function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<Volume> {
+ return Task.create<Volume>('Create Volume', async ctx => {
const { volume_data_3d_info: info, volume_data_3d: values } = source;
const cell = SpacegroupCell.create(
info.spacegroup_number.value(0),
@@ -35,15 +36,19 @@ export function volumeFromDensityServerData(source: DensityServer_Data_Database)
const dimensions = Vec3.ofArray(normalizeOrder(info.dimensions.value(0)));
return {
- transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin, Vec3.add(Vec3.zero(), origin, dimensions)) },
- data,
- dataStats: {
- min: info.min_sampled.value(0),
- max: info.max_sampled.value(0),
- mean: info.mean_sampled.value(0),
- sigma: info.sigma_sampled.value(0)
+ grid: {
+ transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin, Vec3.add(Vec3.zero(), origin, dimensions)) },
+ cells: data,
+ stats: {
+ min: info.min_sampled.value(0),
+ max: info.max_sampled.value(0),
+ mean: info.mean_sampled.value(0),
+ sigma: info.sigma_sampled.value(0)
+ },
},
- sourceData: DscifFormat.create(source)
+ sourceData: DscifFormat.create(source),
+ customProperties: new CustomProperties(),
+ _propertyData: Object.create(null),
};
});
}
diff --git a/src/mol-model-formats/volume/dsn6.ts b/src/mol-model-formats/volume/dsn6.ts
index f6ef76cd6da544664d58060905409f22b83a47f4..b49ed46f10e2a1c0011225373d3b2d4ff464a19d 100644
--- a/src/mol-model-formats/volume/dsn6.ts
+++ b/src/mol-model-formats/volume/dsn6.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
import { Task } from '../../mol-task';
import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
@@ -12,9 +12,10 @@ import { degToRad } from '../../mol-math/misc';
import { Dsn6File } from '../../mol-io/reader/dsn6/schema';
import { arrayMin, arrayMax, arrayMean, arrayRms } from '../../mol-util/array';
import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
-export function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: string }): Task<VolumeData> {
- return Task.create<VolumeData>('Create Volume Data', async ctx => {
+export function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: string }): Task<Volume> {
+ return Task.create<Volume>('Create Volume', async ctx => {
const { header, values } = source;
const size = Vec3.create(header.xlen, header.ylen, header.zlen);
if (params && params.voxelSize) Vec3.mul(size, size, params.voxelSize);
@@ -34,15 +35,19 @@ export function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, la
return {
label: params?.label,
- transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
- data,
- dataStats: {
- min: arrayMin(values),
- max: arrayMax(values),
- mean: arrayMean(values),
- sigma: header.sigma !== undefined ? header.sigma : arrayRms(values)
+ grid: {
+ transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
+ cells: data,
+ stats: {
+ min: arrayMin(values),
+ max: arrayMax(values),
+ mean: arrayMean(values),
+ sigma: header.sigma !== undefined ? header.sigma : arrayRms(values)
+ },
},
- sourceData: Dsn6Format.create(source)
+ sourceData: Dsn6Format.create(source),
+ customProperties: new CustomProperties(),
+ _propertyData: Object.create(null),
};
});
}
diff --git a/src/mol-model-formats/volume/dx.ts b/src/mol-model-formats/volume/dx.ts
index 2ec9007ca7b601639f74db0d8486f65816c524ef..08424a9232d83211778827a6942c0064560ce916 100644
--- a/src/mol-model-formats/volume/dx.ts
+++ b/src/mol-model-formats/volume/dx.ts
@@ -6,13 +6,14 @@
import { DxFile } from '../../mol-io/reader/dx/parser';
import { Mat4, Tensor } from '../../mol-math/linear-algebra';
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
import { Task } from '../../mol-task';
import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
-export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<VolumeData> {
- return Task.create<VolumeData>('Create Volume Data', async () => {
+export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<Volume> {
+ return Task.create<Volume>('Create Volume', async () => {
const { header, values } = source;
const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
const data = Tensor.create(space, Tensor.Data1(values));
@@ -22,15 +23,19 @@ export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<
return {
label: params?.label,
- transform: { kind: 'matrix', matrix },
- data,
- dataStats: {
- min: arrayMin(values),
- max: arrayMax(values),
- mean: arrayMean(values),
- sigma: arrayRms(values)
+ grid: {
+ transform: { kind: 'matrix', matrix },
+ cells: data,
+ stats: {
+ min: arrayMin(values),
+ max: arrayMax(values),
+ mean: arrayMean(values),
+ sigma: arrayRms(values)
+ },
},
- sourceData: DxFormat.create(source)
+ sourceData: DxFormat.create(source),
+ customProperties: new CustomProperties(),
+ _propertyData: Object.create(null),
};
});
}
diff --git a/src/mol-model-props/common/custom-element-property.ts b/src/mol-model-props/common/custom-element-property.ts
index a54b47798f5b1773653c19d9da4e8ba588d20eb8..afd22d801489a3736e89fb447052c17947750ded 100644
--- a/src/mol-model-props/common/custom-element-property.ts
+++ b/src/mol-model-props/common/custom-element-property.ts
@@ -5,7 +5,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ElementIndex, Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { ElementIndex, Model } from '../../mol-model/structure';
import { StructureElement } from '../../mol-model/structure/structure';
import { Location } from '../../mol-model/location';
import { ThemeDataContext } from '../../mol-theme/theme';
@@ -16,6 +16,7 @@ import { OrderedSet } from '../../mol-data/int';
import { CustomModelProperty } from './custom-model-property';
import { CustomProperty } from './custom-property';
import { LociLabelProvider } from '../../mol-plugin-state/manager/loci-label';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
export { CustomElementProperty };
diff --git a/src/mol-model-props/common/custom-model-property.ts b/src/mol-model-props/common/custom-model-property.ts
index 2e8f14f4c99e5369659b4a5cc9318259c3366e8c..75ce00d8f16a4179e830507728aa5935577b5017 100644
--- a/src/mol-model-props/common/custom-model-property.ts
+++ b/src/mol-model-props/common/custom-model-property.ts
@@ -4,10 +4,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { CustomPropertyDescriptor, Model } from '../../mol-model/structure';
+import { Model } from '../../mol-model/structure';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { ValueBox } from '../../mol-util';
import { CustomProperty } from './custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
export { CustomModelProperty };
diff --git a/src/mol-model-props/common/custom-property.ts b/src/mol-model-props/common/custom-property.ts
index 5aafd392f155b620a318513e7777eb3ba869f042..22fdaf35310f3811aca8830a3114fc12f66a446a 100644
--- a/src/mol-model-props/common/custom-property.ts
+++ b/src/mol-model-props/common/custom-property.ts
@@ -5,7 +5,7 @@
*/
import { RuntimeContext } from '../../mol-task';
-import { CustomPropertyDescriptor } from '../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { ValueBox } from '../../mol-util';
import { OrderedMap } from 'immutable';
diff --git a/src/mol-model-props/common/custom-structure-property.ts b/src/mol-model-props/common/custom-structure-property.ts
index fefa5f174fe1fe826aa2323ed62668323af76788..8f7a758b5a55ecb129a334b60f7aebb77ed4d569 100644
--- a/src/mol-model-props/common/custom-structure-property.ts
+++ b/src/mol-model-props/common/custom-structure-property.ts
@@ -4,10 +4,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { ValueBox } from '../../mol-util';
import { CustomProperty } from './custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
export { CustomStructureProperty };
diff --git a/src/mol-model-props/computed/accessible-surface-area.ts b/src/mol-model-props/computed/accessible-surface-area.ts
index a12020eb6128a0bcd40cd260b1018c5593a60753..009754df87eaf2c956712d7d49757c02a5b93d16 100644
--- a/src/mol-model-props/computed/accessible-surface-area.ts
+++ b/src/mol-model-props/computed/accessible-surface-area.ts
@@ -7,12 +7,13 @@
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { ShrakeRupleyComputationParams, AccessibleSurfaceArea } from './accessible-surface-area/shrake-rupley';
-import { Structure, CustomPropertyDescriptor, Unit } from '../../mol-model/structure';
+import { Structure, Unit } from '../../mol-model/structure';
import { CustomStructureProperty } from '../common/custom-structure-property';
import { CustomProperty } from '../common/custom-property';
import { QuerySymbolRuntime } from '../../mol-script/runtime/query/compiler';
import { CustomPropSymbol } from '../../mol-script/language/symbol';
import Type from '../../mol-script/language/type';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
export const AccessibleSurfaceAreaParams = {
...ShrakeRupleyComputationParams
diff --git a/src/mol-model-props/computed/interactions.ts b/src/mol-model-props/computed/interactions.ts
index bba29c192a3b0b46046c3b0102024df6afddc26a..e299e9f9692be384874a0ae63e85ef999b5cd9ba 100644
--- a/src/mol-model-props/computed/interactions.ts
+++ b/src/mol-model-props/computed/interactions.ts
@@ -4,11 +4,12 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { computeInteractions, Interactions, InteractionsParams as _InteractionsParams } from './interactions/interactions';
import { CustomStructureProperty } from '../common/custom-structure-property';
import { CustomProperty } from '../common/custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
export const InteractionsParams = {
..._InteractionsParams
diff --git a/src/mol-model-props/computed/secondary-structure.ts b/src/mol-model-props/computed/secondary-structure.ts
index 383703dfb011bab15855f8824a2cd9728d8997c6..68b790452b9eebdb9311d9a74598af90266ec6ed 100644
--- a/src/mol-model-props/computed/secondary-structure.ts
+++ b/src/mol-model-props/computed/secondary-structure.ts
@@ -12,7 +12,7 @@ import { Unit } from '../../mol-model/structure/structure';
import { CustomStructureProperty } from '../common/custom-structure-property';
import { CustomProperty } from '../common/custom-property';
import { ModelSecondaryStructure } from '../../mol-model-formats/structure/property/secondary-structure';
-import { CustomPropertyDescriptor } from '../../mol-model/structure/common/custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
import { Model } from '../../mol-model/structure/model';
function getSecondaryStructureParams(data?: Structure) {
diff --git a/src/mol-model-props/computed/valence-model.ts b/src/mol-model-props/computed/valence-model.ts
index 8fa1d24ba17bb44fa3ca30e39d4b6aa70fc638ec..b1fb1959fd25949d4458e01297d58e285ef2e293 100644
--- a/src/mol-model-props/computed/valence-model.ts
+++ b/src/mol-model-props/computed/valence-model.ts
@@ -4,11 +4,12 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { calcValenceModel, ValenceModel, ValenceModelParams as _ValenceModelParams } from './chemistry/valence-model';
import { CustomStructureProperty } from '../common/custom-structure-property';
import { CustomProperty } from '../common/custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
export const ValenceModelParams = {
..._ValenceModelParams
diff --git a/src/mol-model-props/integrative/cross-link-restraint/format.ts b/src/mol-model-props/integrative/cross-link-restraint/format.ts
index b4e2704e3323abd4f22744d14fb5e3ae1f9eba08..3d65c86b6f1cff33ee6606b9f5995a574b148847 100644
--- a/src/mol-model-props/integrative/cross-link-restraint/format.ts
+++ b/src/mol-model-props/integrative/cross-link-restraint/format.ts
@@ -7,9 +7,10 @@
import { Model } from '../../../mol-model/structure/model/model';
import { Table } from '../../../mol-data/db';
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
-import { Unit, CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { Unit } from '../../../mol-model/structure';
import { ElementIndex } from '../../../mol-model/structure/model/indexing';
import { FormatPropertyProvider } from '../../../mol-model-formats/structure/common/property';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
export { ModelCrossLinkRestraint };
diff --git a/src/mol-model-props/integrative/cross-link-restraint/property.ts b/src/mol-model-props/integrative/cross-link-restraint/property.ts
index 8b7f07ee495dda32725b3f724c4b51295cded89a..1b2059173832cdb448fbf30be45d67558a62a09b 100644
--- a/src/mol-model-props/integrative/cross-link-restraint/property.ts
+++ b/src/mol-model-props/integrative/cross-link-restraint/property.ts
@@ -5,7 +5,7 @@
*/
import { ModelCrossLinkRestraint } from './format';
-import { Unit, StructureElement, Structure, CustomPropertyDescriptor, Bond} from '../../../mol-model/structure';
+import { Unit, StructureElement, Structure, Bond} from '../../../mol-model/structure';
import { PairRestraints, PairRestraint } from '../pair-restraints';
import { CustomStructureProperty } from '../../common/custom-structure-property';
import { CustomProperty } from '../../common/custom-property';
@@ -15,6 +15,7 @@ import { Sphere3D } from '../../../mol-math/geometry';
import { CentroidHelper } from '../../../mol-math/geometry/centroid-helper';
import { bondLabel } from '../../../mol-theme/label';
import { Vec3 } from '../../../mol-math/linear-algebra';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
export type CrossLinkRestraintValue = PairRestraints<CrossLinkRestraint>
diff --git a/src/mol-model/structure/common/custom-property.ts b/src/mol-model/custom-property.ts
similarity index 90%
rename from src/mol-model/structure/common/custom-property.ts
rename to src/mol-model/custom-property.ts
index 3c6723d768a82570d86941c5135ab6519c134c90..0bf52fa2cfc7a015742774d7cd857562ae19dee2 100644
--- a/src/mol-model/structure/common/custom-property.ts
+++ b/src/mol-model/custom-property.ts
@@ -5,11 +5,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { CifWriter } from '../../../mol-io/writer/cif';
-import { CifExportContext } from '../export/mmcif';
-import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
-import { UUID } from '../../../mol-util';
-import { Asset } from '../../../mol-util/assets';
+import { CifWriter } from '../mol-io/writer/cif';
+import { CifExportContext } from './structure/export/mmcif';
+import { QuerySymbolRuntime } from '../mol-script/runtime/query/compiler';
+import { UUID } from '../mol-util';
+import { Asset } from '../mol-util/assets';
export { CustomPropertyDescriptor, CustomProperties };
diff --git a/src/mol-model/structure.ts b/src/mol-model/structure.ts
index 1069f684fafcdee5f86a16dc8877d2f8d3350083..d8ab4a1a8c79065037c93708cc2864720beda46d 100644
--- a/src/mol-model/structure.ts
+++ b/src/mol-model/structure.ts
@@ -9,5 +9,4 @@ export * from './structure/coordinates';
export * from './structure/topology';
export * from './structure/model';
export * from './structure/structure';
-export * from './structure/query';
-export * from './structure/common/custom-property';
\ No newline at end of file
+export * from './structure/query';
\ No newline at end of file
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index cbbbb2582947178d4cc2b1ae6fe44523b35ae98c..fffe06a4c05e0e8df131e053669fc36779f0424b 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -15,7 +15,7 @@ import { _chem_comp, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './
import { Model } from '../model';
import { getUniqueEntityIndicesFromStructures, copy_mmCif_category, copy_source_mmCifCategory } from './categories/utils';
import { _struct_asym, _entity_poly, _entity_poly_seq } from './categories/sequence';
-import { CustomPropertyDescriptor } from '../common/custom-property';
+import { CustomPropertyDescriptor } from '../../custom-property';
import { atom_site_operator_mapping } from './categories/atom_site_operator_mapping';
import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 00e90d1c9c18ee29abea6000147e029a2054d306..8fe22966d28ef7ad0659a584dd3b254979051109 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -10,7 +10,7 @@ import StructureSequence from './properties/sequence';
import { AtomicHierarchy, AtomicConformation, AtomicRanges } from './properties/atomic';
import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
import { Entities, ChemicalComponentMap, MissingResidues, StructAsymMap } from './properties/common';
-import { CustomProperties } from '../common/custom-property';
+import { CustomProperties } from '../../custom-property';
import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
import { ModelFormat } from '../../../mol-model-formats/format';
import { calcModelCenter } from './util';
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 05bee252c46352762c0364f5b24ed6098ae57e86..4e40ad996444d318bb3bc051ab59b6207d13053e 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -25,7 +25,7 @@ import { Vec3, Mat4 } from '../../../mol-math/linear-algebra';
import { idFactory } from '../../../mol-util/id-factory';
import { GridLookup3D } from '../../../mol-math/geometry';
import { UUID } from '../../../mol-util';
-import { CustomProperties } from '../common/custom-property';
+import { CustomProperties } from '../../custom-property';
import { AtomicHierarchy } from '../model/properties/atomic';
import { StructureSelection } from '../query/selection';
import { getBoundary } from '../../../mol-math/geometry/boundary';
diff --git a/src/mol-model/volume.ts b/src/mol-model/volume.ts
index 70aad4db3d39bd24f02fb1cede4b3ec389d69824..f566b4be1baa69113884780c3b18758ab4289b74 100644
--- a/src/mol-model/volume.ts
+++ b/src/mol-model/volume.ts
@@ -1,7 +1,9 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-export * from './volume/data';
\ No newline at end of file
+export * from './volume/volume';
+export * from './volume/grid';
\ No newline at end of file
diff --git a/src/mol-model/volume/data.ts b/src/mol-model/volume/data.ts
deleted file mode 100644
index 2ab5681126a681ba73062b93fed4b485c2695fb1..0000000000000000000000000000000000000000
--- a/src/mol-model/volume/data.ts
+++ /dev/null
@@ -1,96 +0,0 @@
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
-import { Tensor, Mat4, Vec3 } from '../../mol-math/linear-algebra';
-import { equalEps } from '../../mol-math/linear-algebra/3d/common';
-import { ModelFormat } from '../../mol-model-formats/format';
-
-/** The basic unit cell that contains the data. */
-interface VolumeDataBase {
- readonly label?: string,
- readonly transform: { kind: 'spacegroup', cell: SpacegroupCell, fractionalBox: Box3D } | { kind: 'matrix', matrix: Mat4 },
- readonly data: Tensor,
- readonly dataStats: Readonly<{
- min: number,
- max: number,
- mean: number,
- sigma: number
- }>
- readonly sourceData: ModelFormat,
-}
-
-interface VolumeData extends VolumeDataBase {
- readonly colorVolume?: VolumeDataBase
-}
-
-namespace VolumeData {
- export const One: VolumeData = {
- transform: { kind: 'matrix', matrix: Mat4.identity() },
- data: Tensor.create(Tensor.Space([1, 1, 1], [0, 1, 2]), Tensor.Data1([0])),
- dataStats: { min: 0, max: 0, mean: 0, sigma: 0 },
- sourceData: { kind: '', data: '', name: '' }
- };
-
- const _scale = Mat4.zero(), _translate = Mat4.zero();
- export function getGridToCartesianTransform(volume: VolumeData) {
- if (volume.transform.kind === 'matrix') {
- return Mat4.copy(Mat4(), volume.transform.matrix);
- }
-
- if (volume.transform.kind === 'spacegroup') {
- const { data: { space } } = volume;
- const scale = Mat4.fromScaling(_scale, Vec3.div(Vec3.zero(), Box3D.size(Vec3.zero(), volume.transform.fractionalBox), Vec3.ofArray(space.dimensions)));
- const translate = Mat4.fromTranslation(_translate, volume.transform.fractionalBox.min);
- return Mat4.mul3(Mat4.zero(), volume.transform.cell.fromFractional, translate, scale);
- }
-
- return Mat4.identity();
- }
-
- export function areEquivalent(volA: VolumeData, volB: VolumeData) {
- return volA === volB;
- }
-}
-
-type VolumeIsoValue = VolumeIsoValue.Absolute | VolumeIsoValue.Relative
-
-namespace VolumeIsoValue {
- export type Relative = Readonly<{ kind: 'relative', relativeValue: number }>
- export type Absolute = Readonly<{ kind: 'absolute', absoluteValue: number }>
-
- export function areSame(a: VolumeIsoValue, b: VolumeIsoValue, stats: VolumeData['dataStats']) {
- return equalEps(toAbsolute(a, stats).absoluteValue, toAbsolute(b, stats).absoluteValue, stats.sigma / 100);
- }
-
- export function absolute(value: number): Absolute { return { kind: 'absolute', absoluteValue: value }; }
- export function relative(value: number): Relative { return { kind: 'relative', relativeValue: value }; }
-
- export function calcAbsolute(stats: VolumeData['dataStats'], relativeValue: number): number {
- return relativeValue * stats.sigma + stats.mean;
- }
-
- export function calcRelative(stats: VolumeData['dataStats'], absoluteValue: number): number {
- return stats.sigma === 0 ? 0 : ((absoluteValue - stats.mean) / stats.sigma);
- }
-
- export function toAbsolute(value: VolumeIsoValue, stats: VolumeData['dataStats']): Absolute {
- return value.kind === 'absolute' ? value : { kind: 'absolute', absoluteValue: VolumeIsoValue.calcAbsolute(stats, value.relativeValue) };
- }
-
- export function toRelative(value: VolumeIsoValue, stats: VolumeData['dataStats']): Relative {
- return value.kind === 'relative' ? value : { kind: 'relative', relativeValue: VolumeIsoValue.calcRelative(stats, value.absoluteValue) };
- }
-
- export function toString(value: VolumeIsoValue) {
- return value.kind === 'relative'
- ? `${value.relativeValue.toFixed(2)} σ`
- : `${value.absoluteValue.toPrecision(4)}`;
- }
-}
-
-export { VolumeData, VolumeIsoValue };
\ No newline at end of file
diff --git a/src/mol-model/volume/grid.ts b/src/mol-model/volume/grid.ts
new file mode 100644
index 0000000000000000000000000000000000000000..53ec19a96f216f04087c77b9a3b76d3995f72deb
--- /dev/null
+++ b/src/mol-model/volume/grid.ts
@@ -0,0 +1,57 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
+import { Tensor, Mat4, Vec3 } from '../../mol-math/linear-algebra';
+
+/** The basic unit cell that contains the grid data. */
+interface Grid {
+ readonly transform: Grid.Transform,
+ readonly cells: Tensor,
+ readonly stats: Readonly<{
+ min: number,
+ max: number,
+ mean: number,
+ sigma: number
+ }>
+}
+
+namespace Grid {
+ export const One: Grid = {
+ transform: { kind: 'matrix', matrix: Mat4.identity() },
+ cells: Tensor.create(Tensor.Space([1, 1, 1], [0, 1, 2]), Tensor.Data1([0])),
+ stats: { min: 0, max: 0, mean: 0, sigma: 0 },
+ };
+
+ export type Transform = { kind: 'spacegroup', cell: SpacegroupCell, fractionalBox: Box3D } | { kind: 'matrix', matrix: Mat4 }
+
+ const _scale = Mat4.zero(), _translate = Mat4.zero();
+ export function getGridToCartesianTransform(grid: Grid) {
+ if (grid.transform.kind === 'matrix') {
+ return Mat4.copy(Mat4(), grid.transform.matrix);
+ }
+
+ if (grid.transform.kind === 'spacegroup') {
+ const { cells: { space } } = grid;
+ const scale = Mat4.fromScaling(_scale, Vec3.div(Vec3.zero(), Box3D.size(Vec3.zero(), grid.transform.fractionalBox), Vec3.ofArray(space.dimensions)));
+ const translate = Mat4.fromTranslation(_translate, grid.transform.fractionalBox.min);
+ return Mat4.mul3(Mat4.zero(), grid.transform.cell.fromFractional, translate, scale);
+ }
+
+ return Mat4.identity();
+ }
+
+ export function areEquivalent(gridA: Grid, gridB: Grid) {
+ return gridA === gridB;
+ }
+
+ export function isEmpty(grid: Grid) {
+ return grid.cells.data.length === 0;
+ }
+}
+
+export { Grid };
\ No newline at end of file
diff --git a/src/mol-model/volume/volume.ts b/src/mol-model/volume/volume.ts
index f61fed8e84ee6c8feacd8fdc86c5b38b5b9c3678..69afd4a966816b2fda54c68c82832eca8fd01981 100644
--- a/src/mol-model/volume/volume.ts
+++ b/src/mol-model/volume/volume.ts
@@ -4,32 +4,105 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { VolumeData, VolumeIsoValue } from './data';
+import { Grid } from './grid';
import { OrderedSet } from '../../mol-data/int';
import { Sphere3D } from '../../mol-math/geometry';
import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
import { CubeFormat } from '../../mol-model-formats/volume/cube';
+import { equalEps } from '../../mol-math/linear-algebra/3d/common';
+import { ModelFormat } from '../../mol-model-formats/format';
+import { CustomProperties } from '../custom-property';
+
+export interface Volume {
+ readonly label?: string
+ readonly grid: Grid
+ readonly sourceData: ModelFormat
+
+ // TODO use...
+ customProperties: CustomProperties
+
+ /**
+ * Not to be accessed directly, each custom property descriptor
+ * defines property accessors that use this field to store the data.
+ */
+ _propertyData: { [name: string]: any }
+
+ // TODO add as customProperty?
+ readonly colorVolume?: Volume
+}
export namespace Volume {
export type CellIndex = { readonly '@type': 'cell-index' } & number
- export function isOrbitals(volume: VolumeData) {
+ export type IsoValue = IsoValue.Absolute | IsoValue.Relative
+
+ export namespace IsoValue {
+ export type Relative = Readonly<{ kind: 'relative', relativeValue: number }>
+ export type Absolute = Readonly<{ kind: 'absolute', absoluteValue: number }>
+
+ export function areSame(a: IsoValue, b: IsoValue, stats: Grid['stats']) {
+ return equalEps(toAbsolute(a, stats).absoluteValue, toAbsolute(b, stats).absoluteValue, stats.sigma / 100);
+ }
+
+ export function absolute(value: number): Absolute { return { kind: 'absolute', absoluteValue: value }; }
+ export function relative(value: number): Relative { return { kind: 'relative', relativeValue: value }; }
+
+ export function calcAbsolute(stats: Grid['stats'], relativeValue: number): number {
+ return relativeValue * stats.sigma + stats.mean;
+ }
+
+ export function calcRelative(stats: Grid['stats'], absoluteValue: number): number {
+ return stats.sigma === 0 ? 0 : ((absoluteValue - stats.mean) / stats.sigma);
+ }
+
+ export function toAbsolute(value: IsoValue, stats: Grid['stats']): Absolute {
+ return value.kind === 'absolute' ? value : { kind: 'absolute', absoluteValue: IsoValue.calcAbsolute(stats, value.relativeValue) };
+ }
+
+ export function toRelative(value: IsoValue, stats: Grid['stats']): Relative {
+ return value.kind === 'relative' ? value : { kind: 'relative', relativeValue: IsoValue.calcRelative(stats, value.absoluteValue) };
+ }
+
+ export function toString(value: IsoValue) {
+ return value.kind === 'relative'
+ ? `${value.relativeValue.toFixed(2)} σ`
+ : `${value.absoluteValue.toPrecision(4)}`;
+ }
+ }
+
+ export const One: Volume = {
+ label: '',
+ grid: Grid.One,
+ sourceData: { kind: '', name: '', data: {} },
+ customProperties: new CustomProperties(),
+ _propertyData: Object.create(null),
+ };
+
+ export function areEquivalent(volA: Volume, volB: Volume) {
+ return Grid.areEquivalent(volA.grid, volB.grid);
+ }
+
+ export function isEmpty(vol: Volume) {
+ return Grid.isEmpty(vol.grid);
+ }
+
+ export function isOrbitals(volume: Volume) {
if (!CubeFormat.is(volume.sourceData)) return false;
return volume.sourceData.data.header.orbitals;
}
- export interface Loci { readonly kind: 'volume-loci', readonly volume: VolumeData }
- export function Loci(volume: VolumeData): Loci { return { kind: 'volume-loci', volume }; }
+ export interface Loci { readonly kind: 'volume-loci', readonly volume: Volume }
+ export function Loci(volume: Volume): Loci { return { kind: 'volume-loci', volume }; }
export function isLoci(x: any): x is Loci { return !!x && x.kind === 'volume-loci'; }
export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume; }
- export function isLociEmpty(loci: Loci) { return loci.volume.data.data.length === 0; }
+ export function isLociEmpty(loci: Loci) { return Grid.isEmpty(loci.volume.grid); }
- export function getBoundingSphere(volume: VolumeData, boundingSphere?: Sphere3D) {
+ export function getBoundingSphere(volume: Volume, boundingSphere?: Sphere3D) {
if (!boundingSphere) boundingSphere = Sphere3D();
- const transform = VolumeData.getGridToCartesianTransform(volume);
- const [x, y, z] = volume.data.space.dimensions;
+ const transform = Grid.getGridToCartesianTransform(volume.grid);
+ const [x, y, z] = volume.grid.cells.space.dimensions;
const cpA = Vec3.create(0, 0, 0); Vec3.transformMat4(cpA, cpA, transform);
const cpB = Vec3.create(x, y, z); Vec3.transformMat4(cpB, cpB, transform);
@@ -52,31 +125,31 @@ export namespace Volume {
}
export namespace Isosurface {
- export interface Loci { readonly kind: 'isosurface-loci', readonly volume: VolumeData, readonly isoValue: VolumeIsoValue }
- export function Loci(volume: VolumeData, isoValue: VolumeIsoValue): Loci { return { kind: 'isosurface-loci', volume, isoValue }; }
+ export interface Loci { readonly kind: 'isosurface-loci', readonly volume: Volume, readonly isoValue: Volume.IsoValue }
+ export function Loci(volume: Volume, isoValue: Volume.IsoValue): Loci { return { kind: 'isosurface-loci', volume, isoValue }; }
export function isLoci(x: any): x is Loci { return !!x && x.kind === 'isosurface-loci'; }
- export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && VolumeIsoValue.areSame(a.isoValue, b.isoValue, a.volume.dataStats); }
- export function isLociEmpty(loci: Loci) { return loci.volume.data.data.length === 0; }
+ export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && Volume.IsoValue.areSame(a.isoValue, b.isoValue, a.volume.grid.stats); }
+ export function isLociEmpty(loci: Loci) { return loci.volume.grid.cells.data.length === 0; }
- export function getBoundingSphere(volume: VolumeData, isoValue: VolumeIsoValue, boundingSphere?: Sphere3D) {
+ export function getBoundingSphere(volume: Volume, isoValue: Volume.IsoValue, boundingSphere?: Sphere3D) {
// TODO get bounding sphere for subgrid with values >= isoValue
return Volume.getBoundingSphere(volume, boundingSphere);
}
}
export namespace Cell {
- export interface Loci { readonly kind: 'cell-loci', readonly volume: VolumeData, readonly indices: OrderedSet<CellIndex> }
- export function Loci(volume: VolumeData, indices: OrderedSet<CellIndex>): Loci { return { kind: 'cell-loci', volume, indices }; }
+ export interface Loci { readonly kind: 'cell-loci', readonly volume: Volume, readonly indices: OrderedSet<CellIndex> }
+ export function Loci(volume: Volume, indices: OrderedSet<CellIndex>): Loci { return { kind: 'cell-loci', volume, indices }; }
export function isLoci(x: any): x is Loci { return !!x && x.kind === 'cell-loci'; }
export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && OrderedSet.areEqual(a.indices, b.indices); }
export function isLociEmpty(loci: Loci) { return OrderedSet.size(loci.indices) === 0; }
const boundaryHelper = new BoundaryHelper('98');
const tmpBoundaryPos = Vec3();
- export function getBoundingSphere(volume: VolumeData, indices: OrderedSet<CellIndex>, boundingSphere?: Sphere3D) {
+ export function getBoundingSphere(volume: Volume, indices: OrderedSet<CellIndex>, boundingSphere?: Sphere3D) {
boundaryHelper.reset();
- const transform = VolumeData.getGridToCartesianTransform(volume);
- const { getCoords } = volume.data.space;
+ const transform = Grid.getGridToCartesianTransform(volume.grid);
+ const { getCoords } = volume.grid.cells.space;
for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
const o = OrderedSet.getAt(indices, i);
diff --git a/src/mol-plugin-state/formats/volume.ts b/src/mol-plugin-state/formats/volume.ts
index b39e288e1e3ab02b87f22b5c307b160c8f3fb55a..853c32bd70a1359eaf85e0687b9564301a44c410 100644
--- a/src/mol-plugin-state/formats/volume.ts
+++ b/src/mol-plugin-state/formats/volume.ts
@@ -12,10 +12,9 @@ import { StateObjectSelector } from '../../mol-state';
import { PluginStateObject } from '../objects';
import { VolumeRepresentation3DHelpers } from '../transforms/representation';
import { ColorNames } from '../../mol-util/color/names';
-import { VolumeIsoValue } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
import { createVolumeRepresentationParams } from '../helpers/volume-representation-params';
import { objectForEach } from '../../mol-util/object';
-import { Volume } from '../../mol-model/volume/volume';
const Category = 'Volume';
@@ -110,13 +109,13 @@ export const CubeProvider = DataFormatProvider({
if (volumeData && Volume.isOrbitals(volumeData)) {
const volumePos = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
type: 'isosurface',
- typeParams: { isoValue: VolumeIsoValue.relative(1), alpha: 0.4 },
+ typeParams: { isoValue: Volume.IsoValue.relative(1), alpha: 0.4 },
color: 'uniform',
colorParams: { value: ColorNames.blue }
}));
const volumeNeg = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
type: 'isosurface',
- typeParams: { isoValue: VolumeIsoValue.relative(-1), alpha: 0.4 },
+ typeParams: { isoValue: Volume.IsoValue.relative(-1), alpha: 0.4 },
color: 'uniform',
colorParams: { value: ColorNames.red }
}));
@@ -124,7 +123,7 @@ export const CubeProvider = DataFormatProvider({
} else {
const volume = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
type: 'isosurface',
- typeParams: { isoValue: VolumeIsoValue.relative(2), alpha: 0.4 },
+ typeParams: { isoValue: Volume.IsoValue.relative(2), alpha: 0.4 },
color: 'uniform',
colorParams: { value: ColorNames.grey }
}));
@@ -176,13 +175,13 @@ export const DscifProvider = DataFormatProvider({
if (volumes.length > 0) {
visuals[0] = tree
.to(volumes[0])
- .apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 1 }, 'uniform', { value: ColorNames.teal }))
+ .apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: Volume.IsoValue.relative(1.5), alpha: 1 }, 'uniform', { value: ColorNames.teal }))
.selector;
}
if (volumes.length > 1) {
- const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green });
- const negParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(-3), alpha: 0.3 }, 'uniform', { value: ColorNames.red });
+ const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: Volume.IsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green });
+ const negParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: Volume.IsoValue.relative(-3), alpha: 0.3 }, 'uniform', { value: ColorNames.red });
visuals[visuals.length] = tree.to(volumes[1]).apply(StateTransforms.Representation.VolumeRepresentation3D, posParams).selector;
visuals[visuals.length] = tree.to(volumes[1]).apply(StateTransforms.Representation.VolumeRepresentation3D, negParams).selector;
}
diff --git a/src/mol-plugin-state/helpers/volume-representation-params.ts b/src/mol-plugin-state/helpers/volume-representation-params.ts
index 3dae058f303eb03f87c8241432b44833533d3e83..55d9ab3bd2ffe0f71b03a101e8809825337c8f1b 100644
--- a/src/mol-plugin-state/helpers/volume-representation-params.ts
+++ b/src/mol-plugin-state/helpers/volume-representation-params.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { VolumeData } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
import { PluginContext } from '../../mol-plugin/context';
import { RepresentationProvider } from '../../mol-repr/representation';
import { VolumeRepresentationRegistry } from '../../mol-repr/volume/registry';
@@ -30,7 +30,7 @@ export interface VolumeRepresentationBuiltInProps<
}
export interface VolumeRepresentationProps<
- R extends RepresentationProvider<VolumeData> = RepresentationProvider<VolumeData>,
+ R extends RepresentationProvider<Volume> = RepresentationProvider<Volume>,
C extends ColorTheme.Provider = ColorTheme.Provider,
S extends SizeTheme.Provider = SizeTheme.Provider> {
type?: R,
@@ -41,43 +41,43 @@ export interface VolumeRepresentationProps<
sizeParams?: Partial<SizeTheme.ParamValues<S>>
}
-export function createVolumeRepresentationParams<R extends VolumeRepresentationRegistry.BuiltIn, C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(ctx: PluginContext, volume?: VolumeData, props?: VolumeRepresentationBuiltInProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
-export function createVolumeRepresentationParams<R extends RepresentationProvider<VolumeData>, C extends ColorTheme.Provider, S extends SizeTheme.Provider>(ctx: PluginContext, volume?: VolumeData, props?: VolumeRepresentationProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
-export function createVolumeRepresentationParams(ctx: PluginContext, volume?: VolumeData, props: any = {}): StateTransformer.Params<VolumeRepresentation3D> {
+export function createVolumeRepresentationParams<R extends VolumeRepresentationRegistry.BuiltIn, C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(ctx: PluginContext, volume?: Volume, props?: VolumeRepresentationBuiltInProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
+export function createVolumeRepresentationParams<R extends RepresentationProvider<Volume>, C extends ColorTheme.Provider, S extends SizeTheme.Provider>(ctx: PluginContext, volume?: Volume, props?: VolumeRepresentationProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
+export function createVolumeRepresentationParams(ctx: PluginContext, volume?: Volume, props: any = {}): StateTransformer.Params<VolumeRepresentation3D> {
const p = props as VolumeRepresentationBuiltInProps;
- if (typeof p.type === 'string' || typeof p.color === 'string' || typeof p.size === 'string') return createParamsByName(ctx, volume || VolumeData.One, props);
- return createParamsProvider(ctx, volume || VolumeData.One, props);
+ if (typeof p.type === 'string' || typeof p.color === 'string' || typeof p.size === 'string') return createParamsByName(ctx, volume || Volume.One, props);
+ return createParamsProvider(ctx, volume || Volume.One, props);
}
-export function getVolumeThemeTypes(ctx: PluginContext, volume?: VolumeData) {
+export function getVolumeThemeTypes(ctx: PluginContext, volume?: Volume) {
const { themes: themeCtx } = ctx.representation.volume;
if (!volume) return themeCtx.colorThemeRegistry.types;
return themeCtx.colorThemeRegistry.getApplicableTypes({ volume });
}
-export function createVolumeColorThemeParams<T extends ColorTheme.BuiltIn>(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName: T, params?: ColorTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
-export function createVolumeColorThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
-export function createVolumeColorThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme'] {
+export function createVolumeColorThemeParams<T extends ColorTheme.BuiltIn>(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName: T, params?: ColorTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
+export function createVolumeColorThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
+export function createVolumeColorThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme'] {
const { registry, themes } = ctx.representation.volume;
const repr = registry.get(typeName || registry.default.name);
const color = themes.colorThemeRegistry.get(themeName || repr.defaultColorTheme.name);
- const colorDefaultParams = PD.getDefaultValues(color.getParams({ volume: volume || VolumeData.One }));
+ const colorDefaultParams = PD.getDefaultValues(color.getParams({ volume: volume || Volume.One }));
if (color.name === repr.defaultColorTheme.name) Object.assign(colorDefaultParams, repr.defaultColorTheme.props);
return { name: color.name, params: Object.assign(colorDefaultParams, params) };
}
-export function createVolumeSizeThemeParams<T extends SizeTheme.BuiltIn>(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName: T, params?: SizeTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
-export function createVolumeSizeThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
-export function createVolumeSizeThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme'] {
+export function createVolumeSizeThemeParams<T extends SizeTheme.BuiltIn>(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName: T, params?: SizeTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
+export function createVolumeSizeThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
+export function createVolumeSizeThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme'] {
const { registry, themes } = ctx.representation.volume;
const repr = registry.get(typeName || registry.default.name);
const size = themes.sizeThemeRegistry.get(themeName || repr.defaultSizeTheme.name);
- const sizeDefaultParams = PD.getDefaultValues(size.getParams({ volume: volume || VolumeData.One }));
+ const sizeDefaultParams = PD.getDefaultValues(size.getParams({ volume: volume || Volume.One }));
if (size.name === repr.defaultSizeTheme.name) Object.assign(sizeDefaultParams, repr.defaultSizeTheme.props);
return { name: size.name, params: Object.assign(sizeDefaultParams, params) };
}
-function createParamsByName(ctx: PluginContext, volume: VolumeData, props: VolumeRepresentationBuiltInProps): StateTransformer.Params<VolumeRepresentation3D> {
+function createParamsByName(ctx: PluginContext, volume: Volume, props: VolumeRepresentationBuiltInProps): StateTransformer.Params<VolumeRepresentation3D> {
const typeProvider = (props.type && ctx.representation.volume.registry.get(props.type))
|| ctx.representation.volume.registry.default.provider;
const colorProvider = (props.color && ctx.representation.volume.themes.colorThemeRegistry.get(props.color))
@@ -95,7 +95,7 @@ function createParamsByName(ctx: PluginContext, volume: VolumeData, props: Volum
});
}
-function createParamsProvider(ctx: PluginContext, volume: VolumeData, props: VolumeRepresentationProps = {}): StateTransformer.Params<VolumeRepresentation3D> {
+function createParamsProvider(ctx: PluginContext, volume: Volume, props: VolumeRepresentationProps = {}): StateTransformer.Params<VolumeRepresentation3D> {
const { themes: themeCtx } = ctx.representation.volume;
const themeDataCtx = { volume };
diff --git a/src/mol-plugin-state/objects.ts b/src/mol-plugin-state/objects.ts
index 96d3488f4cf6034bfc6399e8f2533babc2bc680a..a9b18d77da426094dc91deb5d34415de6973afe6 100644
--- a/src/mol-plugin-state/objects.ts
+++ b/src/mol-plugin-state/objects.ts
@@ -14,7 +14,7 @@ import { PlyFile } from '../mol-io/reader/ply/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, StructureElement, Topology as _Topology } from '../mol-model/structure';
-import { VolumeData } from '../mol-model/volume';
+import { Volume as _Volume } from '../mol-model/volume';
import { PluginBehavior } from '../mol-plugin/behavior/behavior';
import { Representation } from '../mol-repr/representation';
import { ShapeRepresentation } from '../mol-repr/shape/representation';
@@ -121,7 +121,7 @@ export namespace PluginStateObject {
}
export namespace Volume {
- export class Data extends Create<VolumeData>({ name: 'Volume Data', typeClass: 'Object' }) { }
+ export class Data extends Create<_Volume>({ name: 'Volume', typeClass: 'Object' }) { }
export class Representation3D extends CreateRepresentation3D<VolumeRepresentation<any>>({ name: 'Volume 3D' }) { }
}
diff --git a/src/mol-plugin-state/transforms/representation.ts b/src/mol-plugin-state/transforms/representation.ts
index 0aee3349c202b7517cfec32d605203178b652b44..bcb1f8560550c73feba8220fa5b5cd7ac932c95b 100644
--- a/src/mol-plugin-state/transforms/representation.ts
+++ b/src/mol-plugin-state/transforms/representation.ts
@@ -6,7 +6,7 @@
*/
import { Structure, StructureElement } from '../../mol-model/structure';
-import { VolumeData, VolumeIsoValue } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
import { PluginContext } from '../../mol-plugin/context';
import { VolumeRepresentationRegistry } from '../../mol-repr/volume/registry';
import { VolumeParams } from '../../mol-repr/volume/representation';
@@ -441,7 +441,7 @@ const TransparencyStructureRepresentation3DFromBundle = PluginStateTransform.Bui
//
export namespace VolumeRepresentation3DHelpers {
- export function getDefaultParams(ctx: PluginContext, name: VolumeRepresentationRegistry.BuiltIn, volume: VolumeData, volumeParams?: Partial<PD.Values<VolumeParams>>): StateTransformer.Params<VolumeRepresentation3D> {
+ export function getDefaultParams(ctx: PluginContext, name: VolumeRepresentationRegistry.BuiltIn, volume: Volume, volumeParams?: Partial<PD.Values<VolumeParams>>): StateTransformer.Params<VolumeRepresentation3D> {
const type = ctx.representation.volume.registry.get(name);
const themeDataCtx = { volume };
@@ -467,7 +467,7 @@ export namespace VolumeRepresentation3DHelpers {
}
export function getDescription(props: any) {
- return props.isoValue && VolumeIsoValue.toString(props.isoValue);
+ return props.isoValue && Volume.IsoValue.toString(props.isoValue);
}
}
type VolumeRepresentation3D = typeof VolumeRepresentation3D
@@ -485,16 +485,16 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
type: PD.Mapped<any>(
registry.default.name,
registry.types,
- name => PD.Group<any>(registry.get(name).getParams(themeCtx, VolumeData.One))),
+ name => PD.Group<any>(registry.get(name).getParams(themeCtx, Volume.One))),
colorTheme: PD.Mapped<any>(
type.defaultColorTheme.name,
themeCtx.colorThemeRegistry.types,
- name => PD.Group<any>(themeCtx.colorThemeRegistry.get(name).getParams({ volume: VolumeData.One }))
+ name => PD.Group<any>(themeCtx.colorThemeRegistry.get(name).getParams({ volume: Volume.One }))
),
sizeTheme: PD.Mapped<any>(
type.defaultSizeTheme.name,
themeCtx.sizeThemeRegistry.types,
- name => PD.Group<any>(themeCtx.sizeThemeRegistry.get(name).getParams({ volume: VolumeData.One }))
+ name => PD.Group<any>(themeCtx.sizeThemeRegistry.get(name).getParams({ volume: Volume.One }))
)
};
}
diff --git a/src/mol-plugin-state/transforms/volume.ts b/src/mol-plugin-state/transforms/volume.ts
index 1e85fb0bdcf91d5ddfcab18b9ba9340e8fb2df47..e9cee9706606348e5ba87c144b9af2485ae478c4 100644
--- a/src/mol-plugin-state/transforms/volume.ts
+++ b/src/mol-plugin-state/transforms/volume.ts
@@ -15,7 +15,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { PluginStateObject as SO, PluginStateTransform } from '../objects';
import { volumeFromCube } from '../../mol-model-formats/volume/cube';
import { volumeFromDx } from '../../mol-model-formats/volume/dx';
-import { VolumeData } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
import { PluginContext } from '../../mol-plugin/context';
import { StateSelection } from '../../mol-state';
@@ -160,8 +160,8 @@ const AssignColorVolume = PluginStateTransform.BuiltIn({
if (!dependencies || !dependencies[params.ref]) {
throw new Error('Dependency not available.');
}
- const colorVolume = dependencies[params.ref].data as VolumeData;
- const volume: VolumeData = {
+ const colorVolume = dependencies[params.ref].data as Volume;
+ const volume: Volume = {
...a.data,
colorVolume
};
diff --git a/src/mol-plugin-ui/custom/volume.tsx b/src/mol-plugin-ui/custom/volume.tsx
index 261ede7e7b7709ebb99daf70db2b906da2dfba0e..b0beddb56e50e12f5523f5cab83d913d595b5622 100644
--- a/src/mol-plugin-ui/custom/volume.tsx
+++ b/src/mol-plugin-ui/custom/volume.tsx
@@ -12,7 +12,7 @@ import { ExpandableControlRow, IconButton } from '../controls/common';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { ParameterControls, ParamOnChange } from '../controls/parameters';
import { Slider } from '../controls/slider';
-import { VolumeIsoValue, VolumeData } from '../../mol-model/volume';
+import { Volume, Grid } from '../../mol-model/volume';
import { Vec3 } from '../../mol-math/linear-algebra';
import { ColorNames } from '../../mol-util/color/names';
import { toPrecision } from '../../mol-util/number';
@@ -34,7 +34,7 @@ class Channel extends PluginUIComponent<{
channels: { [k: string]: VolumeStreaming.ChannelParams },
isRelative: boolean,
params: StateTransformParameters.Props,
- stats: VolumeData['dataStats'],
+ stats: Grid['stats'],
changeIso: (name: string, value: number, isRelative: boolean) => void,
changeParams: (name: string, param: string, value: any) => void,
bCell: StateObjectCell,
@@ -111,7 +111,7 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
...old.entry.params.channels,
[name]: {
...(old.entry.params.channels as any)[name],
- isoValue: isRelative ? VolumeIsoValue.relative(value) : VolumeIsoValue.absolute(value)
+ isoValue: isRelative ? Volume.IsoValue.relative(value) : Volume.IsoValue.absolute(value)
}
}
}
@@ -139,11 +139,11 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
});
};
- convert(channel: any, stats: VolumeData['dataStats'], isRelative: boolean) {
+ convert(channel: any, stats: Grid['stats'], isRelative: boolean) {
return {
...channel, isoValue: isRelative
- ? VolumeIsoValue.toRelative(channel.isoValue, stats)
- : VolumeIsoValue.toAbsolute(channel.isoValue, stats)
+ ? Volume.IsoValue.toRelative(channel.isoValue, stats)
+ : Volume.IsoValue.toAbsolute(channel.isoValue, stats)
};
}
@@ -215,7 +215,7 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
const params = this.props.params as VolumeStreaming.Params;
const detailLevel = ((this.props.info.params as VolumeStreaming.ParamDefinition)
.entry.map(params.entry.name) as PD.Group<VolumeStreaming.EntryParamDefinition>).params.detailLevel;
- const isRelative = ((params.entry.params.channels as any)[pivot].isoValue as VolumeIsoValue).kind === 'relative';
+ const isRelative = ((params.entry.params.channels as any)[pivot].isoValue as Volume.IsoValue).kind === 'relative';
const sampling = b.info.header.sampling[0];
diff --git a/src/mol-plugin-ui/structure/volume.tsx b/src/mol-plugin-ui/structure/volume.tsx
index 4c1eb90d848eae0574e854656fae41f7d9832924..3291975cbdb9101f1c0c008dd73fab3725b62d32 100644
--- a/src/mol-plugin-ui/structure/volume.tsx
+++ b/src/mol-plugin-ui/structure/volume.tsx
@@ -137,7 +137,7 @@ export class VolumeSourceControls extends CollapsableControls<{}, VolumeSourceCo
private item = (ref: VolumeRef) => {
const selected = this.plugin.managers.volume.hierarchy.selection;
- const label = ref.cell.obj?.data.label || 'Volume';
+ const label = ref.cell.obj?.label || 'Volume';
const item: ActionMenu.Item = { kind: 'item', label: label || ref.kind, selected: selected === ref, value: ref };
return item;
}
@@ -172,7 +172,7 @@ export class VolumeSourceControls extends CollapsableControls<{}, VolumeSourceCo
get label() {
const selected = this.plugin.managers.volume.hierarchy.selection;
if (!selected) return 'Nothing Selected';
- return selected?.cell.obj?.data.label || 'Volume';
+ return selected?.cell.obj?.label || 'Volume';
}
selectCurrent: ActionMenu.OnSelect = (item) => {
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
index 20648b515f4e77e492d700226377a722e288a3ba..b0d271f709c1fed8e6e610d01ee2842a53f71b6c 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
@@ -7,7 +7,7 @@
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
import { PluginStateObject } from '../../../../mol-plugin-state/objects';
-import { VolumeIsoValue, VolumeData } from '../../../../mol-model/volume';
+import { Volume, Grid } from '../../../../mol-model/volume';
import { createIsoValueParam } from '../../../../mol-repr/volume/isosurface';
import { VolumeServerHeader, VolumeServerInfo } from './model';
import { Box3D } from '../../../../mol-math/geometry';
@@ -31,13 +31,13 @@ export namespace VolumeStreaming {
export const RootTag = 'volume-streaming-info';
export interface ChannelParams {
- isoValue: VolumeIsoValue,
+ isoValue: Volume.IsoValue,
color: Color,
wireframe: boolean,
opacity: number
}
- function channelParam(label: string, color: Color, defaultValue: VolumeIsoValue, stats: VolumeData['dataStats'], defaults: Partial<ChannelParams> = {}) {
+ function channelParam(label: string, color: Color, defaultValue: Volume.IsoValue, stats: Grid['stats'], defaults: Partial<ChannelParams> = {}) {
return PD.Group<ChannelParams>({
isoValue: createIsoValueParam(typeof defaults.isoValue !== 'undefined' ? defaults.isoValue : defaultValue, stats),
color: PD.Color(typeof defaults.color !== 'undefined' ? defaults.color : color),
@@ -71,7 +71,7 @@ export namespace VolumeStreaming {
const { entryData, defaultView, structure, channelParams = { } } = options;
// fake the info
- const info = entryData || { kind: 'em', header: { sampling: [fakeSampling], availablePrecisions: [{ precision: 0, maxVoxels: 0 }] }, emDefaultContourLevel: VolumeIsoValue.relative(0) };
+ const info = entryData || { kind: 'em', header: { sampling: [fakeSampling], availablePrecisions: [{ precision: 0, maxVoxels: 0 }] }, emDefaultContourLevel: Volume.IsoValue.relative(0) };
const box = (structure && structure.boundary.box) || Box3D.empty();
return {
@@ -93,12 +93,12 @@ export namespace VolumeStreaming {
info.header.availablePrecisions.map((p, i) => [i, `${i + 1} [ ${Math.pow(p.maxVoxels, 1 / 3) | 0}^3 cells ]`] as [number, string]), { description: 'Determines the maximum number of voxels. Depending on the size of the volume options are in the range from 0 (0.52M voxels) to 6 (25.17M voxels).' }),
channels: info.kind === 'em'
? PD.Group({
- 'em': channelParam('EM', Color(0x638F8F), info.emDefaultContourLevel || VolumeIsoValue.relative(1), info.header.sampling[0].valuesInfo[0], channelParams['em'])
+ 'em': channelParam('EM', Color(0x638F8F), info.emDefaultContourLevel || Volume.IsoValue.relative(1), info.header.sampling[0].valuesInfo[0], channelParams['em'])
}, { isFlat: true })
: PD.Group({
- '2fo-fc': channelParam('2Fo-Fc', Color(0x3362B2), VolumeIsoValue.relative(1.5), info.header.sampling[0].valuesInfo[0], channelParams['2fo-fc']),
- 'fo-fc(+ve)': channelParam('Fo-Fc(+ve)', Color(0x33BB33), VolumeIsoValue.relative(3), info.header.sampling[0].valuesInfo[1], channelParams['fo-fc(+ve)']),
- 'fo-fc(-ve)': channelParam('Fo-Fc(-ve)', Color(0xBB3333), VolumeIsoValue.relative(-3), info.header.sampling[0].valuesInfo[1], channelParams['fo-fc(-ve)']),
+ '2fo-fc': channelParam('2Fo-Fc', Color(0x3362B2), Volume.IsoValue.relative(1.5), info.header.sampling[0].valuesInfo[0], channelParams['2fo-fc']),
+ 'fo-fc(+ve)': channelParam('Fo-Fc(+ve)', Color(0x33BB33), Volume.IsoValue.relative(3), info.header.sampling[0].valuesInfo[1], channelParams['fo-fc(+ve)']),
+ 'fo-fc(-ve)': channelParam('Fo-Fc(-ve)', Color(0xBB3333), Volume.IsoValue.relative(-3), info.header.sampling[0].valuesInfo[1], channelParams['fo-fc(-ve)']),
}, { isFlat: true }),
};
}
@@ -110,16 +110,16 @@ export namespace VolumeStreaming {
export type ParamDefinition = typeof createParams extends (...args: any[]) => (infer T) ? T : never
export type Params = ParamDefinition extends PD.Params ? PD.Values<ParamDefinition> : {}
- type ChannelsInfo = { [name in ChannelType]?: { isoValue: VolumeIsoValue, color: Color, wireframe: boolean, opacity: number } }
- type ChannelsData = { [name in 'EM' | '2FO-FC' | 'FO-FC']?: VolumeData }
+ type ChannelsInfo = { [name in ChannelType]?: { isoValue: Volume.IsoValue, color: Color, wireframe: boolean, opacity: number } }
+ type ChannelsData = { [name in 'EM' | '2FO-FC' | 'FO-FC']?: Volume }
export type ChannelType = 'em' | '2fo-fc' | 'fo-fc(+ve)' | 'fo-fc(-ve)'
export const ChannelTypeOptions: [ChannelType, string][] = [['em', 'em'], ['2fo-fc', '2fo-fc'], ['fo-fc(+ve)', 'fo-fc(+ve)'], ['fo-fc(-ve)', 'fo-fc(-ve)']];
export interface ChannelInfo {
- data: VolumeData,
+ data: Volume,
color: Color,
wireframe: boolean,
- isoValue: VolumeIsoValue.Relative,
+ isoValue: Volume.IsoValue.Relative,
opacity: number
}
export type Channels = { [name in ChannelType]?: ChannelInfo }
@@ -329,24 +329,24 @@ export namespace VolumeStreaming {
const info = params.entry.params.channels as ChannelsInfo;
if (this.info.kind === 'x-ray') {
- this.channels['2fo-fc'] = this.createChannel(data['2FO-FC'] || VolumeData.One, info['2fo-fc'], this.info.header.sampling[0].valuesInfo[0]);
- this.channels['fo-fc(+ve)'] = this.createChannel(data['FO-FC'] || VolumeData.One, info['fo-fc(+ve)'], this.info.header.sampling[0].valuesInfo[1]);
- this.channels['fo-fc(-ve)'] = this.createChannel(data['FO-FC'] || VolumeData.One, info['fo-fc(-ve)'], this.info.header.sampling[0].valuesInfo[1]);
+ this.channels['2fo-fc'] = this.createChannel(data['2FO-FC'] || Volume.One, info['2fo-fc'], this.info.header.sampling[0].valuesInfo[0]);
+ this.channels['fo-fc(+ve)'] = this.createChannel(data['FO-FC'] || Volume.One, info['fo-fc(+ve)'], this.info.header.sampling[0].valuesInfo[1]);
+ this.channels['fo-fc(-ve)'] = this.createChannel(data['FO-FC'] || Volume.One, info['fo-fc(-ve)'], this.info.header.sampling[0].valuesInfo[1]);
} else {
- this.channels['em'] = this.createChannel(data['EM'] || VolumeData.One, info['em'], this.info.header.sampling[0].valuesInfo[0]);
+ this.channels['em'] = this.createChannel(data['EM'] || Volume.One, info['em'], this.info.header.sampling[0].valuesInfo[0]);
}
return true;
}
- private createChannel(data: VolumeData, info: ChannelsInfo['em'], stats: VolumeData['dataStats']): ChannelInfo {
+ private createChannel(data: Volume, info: ChannelsInfo['em'], stats: Grid['stats']): ChannelInfo {
const i = info!;
return {
data,
color: i.color,
wireframe: i.wireframe,
opacity: i.opacity,
- isoValue: i.isoValue.kind === 'relative' ? i.isoValue : VolumeIsoValue.toRelative(i.isoValue, stats)
+ isoValue: i.isoValue.kind === 'relative' ? i.isoValue : Volume.IsoValue.toRelative(i.isoValue, stats)
};
}
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts
index 59f47b1534cc99394ea252a5a9f3f629992cf13f..13138d154e3fbac6335004781e055d723260f434 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts
@@ -1,12 +1,12 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { PluginStateObject } from '../../../../mol-plugin-state/objects';
-import { VolumeIsoValue } from '../../../../mol-model/volume';
+import { Volume } from '../../../../mol-model/volume';
import { Structure } from '../../../../mol-model/structure';
export class VolumeServerInfo extends PluginStateObject.Create<VolumeServerInfo.Data>({ name: 'Volume Streaming', typeClass: 'Object' }) { }
@@ -18,7 +18,7 @@ export namespace VolumeServerInfo {
// for em, the EMDB access code, for x-ray, the PDB id
dataId: string,
header: VolumeServerHeader,
- emDefaultContourLevel?: VolumeIsoValue,
+ emDefaultContourLevel?: Volume.IsoValue,
}
export interface Data {
serverUrl: string,
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
index d5d27521c32d13fdea57853ccc59b1e9efb30486..fdbf2f7ec8a2dd9de276586fe013268b80b007a5 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
@@ -12,7 +12,7 @@ import { Task } from '../../../../mol-task';
import { PluginContext } from '../../../../mol-plugin/context';
import { urlCombine } from '../../../../mol-util/url';
import { createIsoValueParam } from '../../../../mol-repr/volume/isosurface';
-import { VolumeIsoValue } from '../../../../mol-model/volume';
+import { Volume } from '../../../../mol-model/volume';
import { StateAction, StateObject, StateTransformer } from '../../../../mol-state';
import { getStreamingMethod, getIds, getContourLevel, getEmdbIds } from './util';
import { VolumeStreaming } from './behavior';
@@ -27,7 +27,7 @@ import { Model } from '../../../../mol-model/structure';
function addEntry(entries: InfoEntryProps[], method: VolumeServerInfo.Kind, dataId: string, emDefaultContourLevel: number) {
entries.push({
source: method === 'em'
- ? { name: 'em', params: { isoValue: VolumeIsoValue.absolute(emDefaultContourLevel || 0) } }
+ ? { name: 'em', params: { isoValue: Volume.IsoValue.absolute(emDefaultContourLevel || 0) } }
: { name: 'x-ray', params: { } },
dataId
});
@@ -157,7 +157,7 @@ const InfoEntryParams = {
dataId: PD.Text(''),
source: PD.MappedStatic('x-ray', {
'em': PD.Group({
- isoValue: createIsoValueParam(VolumeIsoValue.relative(1))
+ isoValue: createIsoValueParam(Volume.IsoValue.relative(1))
}),
'x-ray': PD.Group({ })
})
@@ -185,7 +185,7 @@ const CreateVolumeStreamingInfo = PluginStateTransform.BuiltIn({
for (let i = 0, il = params.entries.length; i < il; ++i) {
const e = params.entries[i];
const dataId = e.dataId;
- const emDefaultContourLevel = e.source.name === 'em' ? e.source.params.isoValue : VolumeIsoValue.relative(1);
+ const emDefaultContourLevel = e.source.name === 'em' ? e.source.params.isoValue : Volume.IsoValue.relative(1);
await taskCtx.update('Getting server header...');
const header = await plugin.fetch({ url: urlCombine(params.serverUrl, `${e.source.name}/${dataId.toLocaleLowerCase()}`), type: 'json' }).runInContext(taskCtx) as VolumeServerHeader;
entries.push({
diff --git a/src/mol-repr/volume/direct-volume.ts b/src/mol-repr/volume/direct-volume.ts
index f896bdbc1bb1b95b3b464495a89fc28bf4cb1dd2..da3cc458a499e22939392ddf591e305bad038113 100644
--- a/src/mol-repr/volume/direct-volume.ts
+++ b/src/mol-repr/volume/direct-volume.ts
@@ -7,7 +7,7 @@
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
import { Box3D } from '../../mol-math/geometry';
-import { VolumeData } from '../../mol-model/volume';
+import { Grid, Volume } from '../../mol-model/volume';
import { RuntimeContext } from '../../mol-task';
import { WebGLContext } from '../../mol-gl/webgl/context';
import { DirectVolume } from '../../mol-geo/geometry/direct-volume/direct-volume';
@@ -20,7 +20,6 @@ import { NullLocation } from '../../mol-model/location';
import { EmptyLoci } from '../../mol-model/loci';
import { VisualUpdateState } from '../util';
import { RepresentationContext, RepresentationParamsGetter } from '../representation';
-import { Volume } from '../../mol-model/volume/volume';
function getBoundingBox(gridDimension: Vec3, transform: Mat4) {
const bbox = Box3D.empty();
@@ -49,9 +48,8 @@ function getVolumeTexture2dLayout(dim: Vec3, maxTextureSize: number) {
return { width, height, columns, rows };
}
-function createVolumeTexture2d(volume: VolumeData, maxTextureSize: number) {
- const { data: tensor, dataStats: stats } = volume;
- const { space, data } = tensor;
+function createVolumeTexture2d(volume: Volume, maxTextureSize: number) {
+ const { cells: { space, data }, stats } = volume.grid;
const dim = space.dimensions as Vec3;
const { get } = space;
const { width, height, columns, rows } = getVolumeTexture2dLayout(dim, maxTextureSize);
@@ -85,11 +83,11 @@ function createVolumeTexture2d(volume: VolumeData, maxTextureSize: number) {
return textureImage;
}
-export function createDirectVolume2d(ctx: RuntimeContext, webgl: WebGLContext, volume: VolumeData, directVolume?: DirectVolume) {
- const gridDimension = volume.data.space.dimensions as Vec3;
+export function createDirectVolume2d(ctx: RuntimeContext, webgl: WebGLContext, volume: Volume, directVolume?: DirectVolume) {
+ const gridDimension = volume.grid.cells.space.dimensions as Vec3;
const textureImage = createVolumeTexture2d(volume, webgl.maxTextureSize);
// debugTexture(createImageData(textureImage.array, textureImage.width, textureImage.height), 1/3)
- const transform = VolumeData.getGridToCartesianTransform(volume);
+ const transform = Grid.getGridToCartesianTransform(volume.grid);
const bbox = getBoundingBox(gridDimension, transform);
const dim = Vec3.create(gridDimension[0], gridDimension[1], gridDimension[2]);
dim[0] += 1; // horizontal padding
@@ -103,9 +101,8 @@ export function createDirectVolume2d(ctx: RuntimeContext, webgl: WebGLContext, v
// 3d volume texture
-function createVolumeTexture3d(volume: VolumeData) {
- const { data: tensor, dataStats: stats } = volume;
- const { space, data } = tensor;
+function createVolumeTexture3d(volume: Volume) {
+ const { cells: { space, data }, stats } = volume.grid;
const [ width, height, depth ] = space.dimensions as Vec3;
const { get } = space;
@@ -128,10 +125,10 @@ function createVolumeTexture3d(volume: VolumeData) {
return textureVolume;
}
-export function createDirectVolume3d(ctx: RuntimeContext, webgl: WebGLContext, volume: VolumeData, directVolume?: DirectVolume) {
- const gridDimension = volume.data.space.dimensions as Vec3;
+export function createDirectVolume3d(ctx: RuntimeContext, webgl: WebGLContext, volume: Volume, directVolume?: DirectVolume) {
+ const gridDimension = volume.grid.cells.space.dimensions as Vec3;
const textureVolume = createVolumeTexture3d(volume);
- const transform = VolumeData.getGridToCartesianTransform(volume);
+ const transform = Grid.getGridToCartesianTransform(volume.grid);
// Mat4.invert(transform, transform)
const bbox = getBoundingBox(gridDimension, transform);
@@ -143,7 +140,7 @@ export function createDirectVolume3d(ctx: RuntimeContext, webgl: WebGLContext, v
//
-export async function createDirectVolume(ctx: VisualContext, volume: VolumeData, theme: Theme, props: PD.Values<DirectVolumeParams>, directVolume?: DirectVolume) {
+export async function createDirectVolume(ctx: VisualContext, volume: Volume, theme: Theme, props: PD.Values<DirectVolumeParams>, directVolume?: DirectVolume) {
const { runtime, webgl } = ctx;
if (webgl === undefined) throw new Error('DirectVolumeVisual requires `webgl` in props');
@@ -152,7 +149,7 @@ export async function createDirectVolume(ctx: VisualContext, volume: VolumeData,
createDirectVolume2d(runtime, webgl, volume, directVolume);
}
-function getLoci(volume: VolumeData, props: PD.Values<DirectVolumeParams>) {
+function getLoci(volume: Volume, props: PD.Values<DirectVolumeParams>) {
return Volume.Loci(volume);
}
@@ -163,7 +160,7 @@ export const DirectVolumeParams = {
...DirectVolume.Params
};
export type DirectVolumeParams = typeof DirectVolumeParams
-export function getDirectVolumeParams(ctx: ThemeRegistryContext, volume: VolumeData) {
+export function getDirectVolumeParams(ctx: ThemeRegistryContext, volume: Volume) {
return PD.clone(DirectVolumeParams);
}
@@ -171,16 +168,16 @@ export function DirectVolumeVisual(materialId: number): VolumeVisual<DirectVolum
return VolumeVisual<DirectVolume, DirectVolumeParams>({
defaultProps: PD.getDefaultValues(DirectVolumeParams),
createGeometry: createDirectVolume,
- createLocationIterator: (volume: VolumeData) => LocationIterator(1, 1, () => NullLocation),
+ createLocationIterator: (volume: Volume) => LocationIterator(1, 1, () => NullLocation),
getLoci: () => EmptyLoci,
eachLocation: () => false,
- setUpdateState: (state: VisualUpdateState, volume: VolumeData, newProps: PD.Values<DirectVolumeParams>, currentProps: PD.Values<DirectVolumeParams>) => {
+ setUpdateState: (state: VisualUpdateState, volume: Volume, newProps: PD.Values<DirectVolumeParams>, currentProps: PD.Values<DirectVolumeParams>) => {
},
geometryUtils: DirectVolume.Utils
}, materialId);
}
-export function DirectVolumeRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<VolumeData, DirectVolumeParams>): VolumeRepresentation<DirectVolumeParams> {
+export function DirectVolumeRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, DirectVolumeParams>): VolumeRepresentation<DirectVolumeParams> {
return VolumeRepresentation('Direct Volume', ctx, getParams, DirectVolumeVisual, getLoci);
}
@@ -193,5 +190,5 @@ export const DirectVolumeRepresentationProvider = VolumeRepresentationProvider({
defaultValues: PD.getDefaultValues(DirectVolumeParams),
defaultColorTheme: { name: 'uniform' },
defaultSizeTheme: { name: 'uniform' },
- isApplicable: (volume: VolumeData) => volume.data.data.length > 0
+ isApplicable: (volume: Volume) => !Volume.isEmpty(volume)
});
\ No newline at end of file
diff --git a/src/mol-repr/volume/isosurface.ts b/src/mol-repr/volume/isosurface.ts
index 6e6ddb7f9245cddb287032b96d41026e6abdc6b6..65d5bac070e5846e30c6c331a3455d7e988b88e5 100644
--- a/src/mol-repr/volume/isosurface.ts
+++ b/src/mol-repr/volume/isosurface.ts
@@ -6,7 +6,7 @@
*/
import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { VolumeData, VolumeIsoValue } from '../../mol-model/volume';
+import { Grid, Volume } from '../../mol-model/volume';
import { VisualContext } from '../visual';
import { Theme, ThemeRegistryContext } from '../../mol-theme/theme';
import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
@@ -18,15 +18,14 @@ import { VisualUpdateState } from '../util';
import { Lines } from '../../mol-geo/geometry/lines/lines';
import { RepresentationContext, RepresentationParamsGetter, Representation } from '../representation';
import { toPrecision } from '../../mol-util/number';
-import { Volume } from '../../mol-model/volume/volume';
import { PickingId } from '../../mol-geo/geometry/picking';
import { EmptyLoci, Loci } from '../../mol-model/loci';
import { Interval, OrderedSet } from '../../mol-data/int';
import { Tensor } from '../../mol-math/linear-algebra';
import { fillSerial } from '../../mol-util/array';
-const defaultStats: VolumeData['dataStats'] = { min: -1, max: 1, mean: 0, sigma: 0.1 };
-export function createIsoValueParam(defaultValue: VolumeIsoValue, stats?: VolumeData['dataStats']) {
+const defaultStats: Grid['stats'] = { min: -1, max: 1, mean: 0, sigma: 0.1 };
+export function createIsoValueParam(defaultValue: Volume.IsoValue, stats?: Grid['stats']) {
const sts = stats || defaultStats;
const { min, max, mean, sigma } = sts;
@@ -36,34 +35,34 @@ export function createIsoValueParam(defaultValue: VolumeIsoValue, stats?: Volume
let def = defaultValue;
if (defaultValue.kind === 'absolute') {
- if (defaultValue.absoluteValue < min) def = VolumeIsoValue.absolute(min);
- else if (defaultValue.absoluteValue > max) def = VolumeIsoValue.absolute(max);
+ if (defaultValue.absoluteValue < min) def = Volume.IsoValue.absolute(min);
+ else if (defaultValue.absoluteValue > max) def = Volume.IsoValue.absolute(max);
} else {
- if (defaultValue.relativeValue < relMin) def = VolumeIsoValue.relative(relMin);
- else if (defaultValue.relativeValue > relMax) def = VolumeIsoValue.relative(relMax);
+ if (defaultValue.relativeValue < relMin) def = Volume.IsoValue.relative(relMin);
+ else if (defaultValue.relativeValue > relMax) def = Volume.IsoValue.relative(relMax);
}
return PD.Conditioned(
def,
{
'absolute': PD.Converted(
- (v: VolumeIsoValue) => VolumeIsoValue.toAbsolute(v, VolumeData.One.dataStats).absoluteValue,
- (v: number) => VolumeIsoValue.absolute(v),
+ (v: Volume.IsoValue) => Volume.IsoValue.toAbsolute(v, Grid.One.stats).absoluteValue,
+ (v: number) => Volume.IsoValue.absolute(v),
PD.Numeric(mean, { min, max, step: toPrecision(sigma / 100, 2) })
),
'relative': PD.Converted(
- (v: VolumeIsoValue) => VolumeIsoValue.toRelative(v, VolumeData.One.dataStats).relativeValue,
- (v: number) => VolumeIsoValue.relative(v),
+ (v: Volume.IsoValue) => Volume.IsoValue.toRelative(v, Grid.One.stats).relativeValue,
+ (v: number) => Volume.IsoValue.relative(v),
PD.Numeric(Math.min(1, relMax), { min: relMin, max: relMax, step: toPrecision(Math.round(((max - min) / sigma)) / 100, 2) })
)
},
- (v: VolumeIsoValue) => v.kind === 'absolute' ? 'absolute' : 'relative',
- (v: VolumeIsoValue, c: 'absolute' | 'relative') => c === 'absolute' ? VolumeIsoValue.toAbsolute(v, sts) : VolumeIsoValue.toRelative(v, sts),
+ (v: Volume.IsoValue) => v.kind === 'absolute' ? 'absolute' : 'relative',
+ (v: Volume.IsoValue, c: 'absolute' | 'relative') => c === 'absolute' ? Volume.IsoValue.toAbsolute(v, sts) : Volume.IsoValue.toRelative(v, sts),
{ isEssential: true }
);
}
-export const IsoValueParam = createIsoValueParam(VolumeIsoValue.relative(2));
+export const IsoValueParam = createIsoValueParam(Volume.IsoValue.relative(2));
type IsoValueParam = typeof IsoValueParam
export const VolumeIsosurfaceParams = {
@@ -72,11 +71,11 @@ export const VolumeIsosurfaceParams = {
export type VolumeIsosurfaceParams = typeof VolumeIsosurfaceParams
export type VolumeIsosurfaceProps = PD.Values<VolumeIsosurfaceParams>
-function getLoci(volume: VolumeData, props: VolumeIsosurfaceProps) {
+function getLoci(volume: Volume, props: VolumeIsosurfaceProps) {
return Volume.Isosurface.Loci(volume, props.isoValue);
}
-function getIsosurfaceLoci(pickingId: PickingId, volume: VolumeData, props: VolumeIsosurfaceProps, id: number) {
+function getIsosurfaceLoci(pickingId: PickingId, volume: Volume, props: VolumeIsosurfaceProps, id: number) {
const { objectId, groupId } = pickingId;
if (id === objectId) {
return Volume.Cell.Loci(volume, Interval.ofSingleton(groupId as Volume.CellIndex));
@@ -84,17 +83,17 @@ function getIsosurfaceLoci(pickingId: PickingId, volume: VolumeData, props: Volu
return EmptyLoci;
}
-function eachIsosurface(loci: Loci, volume: VolumeData, props: VolumeIsosurfaceProps, apply: (interval: Interval) => boolean) {
+function eachIsosurface(loci: Loci, volume: Volume, props: VolumeIsosurfaceProps, apply: (interval: Interval) => boolean) {
let changed = false;
if (Volume.isLoci(loci)) {
- if (!VolumeData.areEquivalent(loci.volume, volume)) return false;
- if (apply(Interval.ofLength(volume.data.data.length))) changed = true;
+ if (!Volume.areEquivalent(loci.volume, volume)) return false;
+ if (apply(Interval.ofLength(volume.grid.cells.data.length))) changed = true;
} else if (Volume.Isosurface.isLoci(loci)) {
- if (!VolumeData.areEquivalent(loci.volume, volume)) return false;
- if (!VolumeIsoValue.areSame(loci.isoValue, props.isoValue, volume.dataStats)) return false;
- if (apply(Interval.ofLength(volume.data.data.length))) changed = true;
+ if (!Volume.areEquivalent(loci.volume, volume)) return false;
+ if (!Volume.IsoValue.areSame(loci.isoValue, props.isoValue, volume.grid.stats)) return false;
+ if (apply(Interval.ofLength(volume.grid.cells.data.length))) changed = true;
} else if (Volume.Cell.isLoci(loci)) {
- if (!VolumeData.areEquivalent(loci.volume, volume)) return false;
+ if (!Volume.areEquivalent(loci.volume, volume)) return false;
if (Interval.is(loci.indices)) {
if (apply(loci.indices)) changed = true;
} else {
@@ -108,18 +107,18 @@ function eachIsosurface(loci: Loci, volume: VolumeData, props: VolumeIsosurfaceP
//
-export async function createVolumeIsosurfaceMesh(ctx: VisualContext, volume: VolumeData, theme: Theme, props: VolumeIsosurfaceProps, mesh?: Mesh) {
+export async function createVolumeIsosurfaceMesh(ctx: VisualContext, volume: Volume, theme: Theme, props: VolumeIsosurfaceProps, mesh?: Mesh) {
ctx.runtime.update({ message: 'Marching cubes...' });
- const ids = fillSerial(new Int32Array(volume.data.data.length));
+ const ids = fillSerial(new Int32Array(volume.grid.cells.data.length));
const surface = await computeMarchingCubesMesh({
- isoLevel: VolumeIsoValue.toAbsolute(props.isoValue, volume.dataStats).absoluteValue,
- scalarField: volume.data,
- idField: Tensor.create(volume.data.space, Tensor.Data1(ids))
+ isoLevel: Volume.IsoValue.toAbsolute(props.isoValue, volume.grid.stats).absoluteValue,
+ scalarField: volume.grid.cells,
+ idField: Tensor.create(volume.grid.cells.space, Tensor.Data1(ids))
}, mesh).runAsChild(ctx.runtime);
- const transform = VolumeData.getGridToCartesianTransform(volume);
+ const transform = Grid.getGridToCartesianTransform(volume.grid);
ctx.runtime.update({ message: 'Transforming mesh...' });
Mesh.transform(surface, transform);
return surface;
@@ -136,11 +135,11 @@ export function IsosurfaceMeshVisual(materialId: number): VolumeVisual<Isosurfac
return VolumeVisual<Mesh, IsosurfaceMeshParams>({
defaultProps: PD.getDefaultValues(IsosurfaceMeshParams),
createGeometry: createVolumeIsosurfaceMesh,
- createLocationIterator: (volume: VolumeData) => LocationIterator(volume.data.data.length, 1, () => NullLocation),
+ createLocationIterator: (volume: Volume) => LocationIterator(volume.grid.cells.data.length, 1, () => NullLocation),
getLoci: getIsosurfaceLoci,
eachLocation: eachIsosurface,
- setUpdateState: (state: VisualUpdateState, volume: VolumeData, newProps: PD.Values<IsosurfaceMeshParams>, currentProps: PD.Values<IsosurfaceMeshParams>) => {
- if (!VolumeIsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.dataStats)) state.createGeometry = true;
+ setUpdateState: (state: VisualUpdateState, volume: Volume, newProps: PD.Values<IsosurfaceMeshParams>, currentProps: PD.Values<IsosurfaceMeshParams>) => {
+ if (!Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats)) state.createGeometry = true;
},
geometryUtils: Mesh.Utils
}, materialId);
@@ -148,18 +147,18 @@ export function IsosurfaceMeshVisual(materialId: number): VolumeVisual<Isosurfac
//
-export async function createVolumeIsosurfaceWireframe(ctx: VisualContext, volume: VolumeData, theme: Theme, props: VolumeIsosurfaceProps, lines?: Lines) {
+export async function createVolumeIsosurfaceWireframe(ctx: VisualContext, volume: Volume, theme: Theme, props: VolumeIsosurfaceProps, lines?: Lines) {
ctx.runtime.update({ message: 'Marching cubes...' });
- const ids = fillSerial(new Int32Array(volume.data.data.length));
+ const ids = fillSerial(new Int32Array(volume.grid.cells.data.length));
const wireframe = await computeMarchingCubesLines({
- isoLevel: VolumeIsoValue.toAbsolute(props.isoValue, volume.dataStats).absoluteValue,
- scalarField: volume.data,
- idField: Tensor.create(volume.data.space, Tensor.Data1(ids))
+ isoLevel: Volume.IsoValue.toAbsolute(props.isoValue, volume.grid.stats).absoluteValue,
+ scalarField: volume.grid.cells,
+ idField: Tensor.create(volume.grid.cells.space, Tensor.Data1(ids))
}, lines).runAsChild(ctx.runtime);
- const transform = VolumeData.getGridToCartesianTransform(volume);
+ const transform = Grid.getGridToCartesianTransform(volume.grid);
Lines.transform(wireframe, transform);
return wireframe;
@@ -177,11 +176,11 @@ export function IsosurfaceWireframeVisual(materialId: number): VolumeVisual<Isos
return VolumeVisual<Lines, IsosurfaceWireframeParams>({
defaultProps: PD.getDefaultValues(IsosurfaceWireframeParams),
createGeometry: createVolumeIsosurfaceWireframe,
- createLocationIterator: (volume: VolumeData) => LocationIterator(volume.data.data.length, 1, () => NullLocation),
+ createLocationIterator: (volume: Volume) => LocationIterator(volume.grid.cells.data.length, 1, () => NullLocation),
getLoci: getIsosurfaceLoci,
eachLocation: eachIsosurface,
- setUpdateState: (state: VisualUpdateState, volume: VolumeData, newProps: PD.Values<IsosurfaceWireframeParams>, currentProps: PD.Values<IsosurfaceWireframeParams>) => {
- if (!VolumeIsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.dataStats)) state.createGeometry = true;
+ setUpdateState: (state: VisualUpdateState, volume: Volume, newProps: PD.Values<IsosurfaceWireframeParams>, currentProps: PD.Values<IsosurfaceWireframeParams>) => {
+ if (!Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats)) state.createGeometry = true;
},
geometryUtils: Lines.Utils
}, materialId);
@@ -190,8 +189,8 @@ export function IsosurfaceWireframeVisual(materialId: number): VolumeVisual<Isos
//
const IsosurfaceVisuals = {
- 'solid': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<VolumeData, IsosurfaceMeshParams>) => VolumeRepresentation('Isosurface mesh', ctx, getParams, IsosurfaceMeshVisual, getLoci),
- 'wireframe': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<VolumeData, IsosurfaceWireframeParams>) => VolumeRepresentation('Isosurface wireframe', ctx, getParams, IsosurfaceWireframeVisual, getLoci),
+ 'solid': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, IsosurfaceMeshParams>) => VolumeRepresentation('Isosurface mesh', ctx, getParams, IsosurfaceMeshVisual, getLoci),
+ 'wireframe': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, IsosurfaceWireframeParams>) => VolumeRepresentation('Isosurface wireframe', ctx, getParams, IsosurfaceWireframeVisual, getLoci),
};
export const IsosurfaceParams = {
@@ -200,15 +199,15 @@ export const IsosurfaceParams = {
visuals: PD.MultiSelect(['solid'], PD.objectToOptions(IsosurfaceVisuals)),
};
export type IsosurfaceParams = typeof IsosurfaceParams
-export function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: VolumeData) {
+export function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: Volume) {
const p = PD.clone(IsosurfaceParams);
- p.isoValue = createIsoValueParam(VolumeIsoValue.relative(2), volume.dataStats);
+ p.isoValue = createIsoValueParam(Volume.IsoValue.relative(2), volume.grid.stats);
return p;
}
export type IsosurfaceRepresentation = VolumeRepresentation<IsosurfaceParams>
-export function IsosurfaceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<VolumeData, IsosurfaceParams>): IsosurfaceRepresentation {
- return Representation.createMulti('Isosurface', ctx, getParams, Representation.StateBuilder, IsosurfaceVisuals as unknown as Representation.Def<VolumeData, IsosurfaceParams>);
+export function IsosurfaceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, IsosurfaceParams>): IsosurfaceRepresentation {
+ return Representation.createMulti('Isosurface', ctx, getParams, Representation.StateBuilder, IsosurfaceVisuals as unknown as Representation.Def<Volume, IsosurfaceParams>);
}
export const IsosurfaceRepresentationProvider = VolumeRepresentationProvider({
@@ -220,5 +219,5 @@ export const IsosurfaceRepresentationProvider = VolumeRepresentationProvider({
defaultValues: PD.getDefaultValues(IsosurfaceParams),
defaultColorTheme: { name: 'uniform' },
defaultSizeTheme: { name: 'uniform' },
- isApplicable: (volume: VolumeData) => volume.data.data.length > 0
+ isApplicable: (volume: Volume) => !Volume.isEmpty(volume)
});
\ No newline at end of file
diff --git a/src/mol-repr/volume/registry.ts b/src/mol-repr/volume/registry.ts
index ee7b0050c6540ddd10f408711e5a8c6d3fa5dbf7..8f952a20cc4733a20eb405b810e7a46a481039bb 100644
--- a/src/mol-repr/volume/registry.ts
+++ b/src/mol-repr/volume/registry.ts
@@ -5,12 +5,12 @@
*/
import { RepresentationRegistry, Representation, RepresentationProvider } from '../representation';
-import { VolumeData } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
import { IsosurfaceRepresentationProvider } from './isosurface';
import { objectForEach } from '../../mol-util/object';
import { SliceRepresentationProvider } from './slice';
-export class VolumeRepresentationRegistry extends RepresentationRegistry<VolumeData, Representation.State> {
+export class VolumeRepresentationRegistry extends RepresentationRegistry<Volume, Representation.State> {
constructor() {
super();
objectForEach(VolumeRepresentationRegistry.BuiltIn, (p, k) => {
diff --git a/src/mol-repr/volume/representation.ts b/src/mol-repr/volume/representation.ts
index e5f2a7685e357a01ad85289243e99a6c65ba11d2..7e97b98365fcfd42ef3bc2c14e1f711b65b1dc4c 100644
--- a/src/mol-repr/volume/representation.ts
+++ b/src/mol-repr/volume/representation.ts
@@ -6,7 +6,7 @@
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Visual, VisualContext } from '../visual';
-import { VolumeData } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
import { Geometry, GeometryUtils } from '../../mol-geo/geometry/geometry';
import { LocationIterator } from '../../mol-geo/util/location-iterator';
import { Theme } from '../../mol-theme/theme';
@@ -30,9 +30,9 @@ import { Subject } from 'rxjs';
import { Task } from '../../mol-task';
import { SizeValues } from '../../mol-gl/renderable/schema';
-export interface VolumeVisual<P extends VolumeParams> extends Visual<VolumeData, P> { }
+export interface VolumeVisual<P extends VolumeParams> extends Visual<Volume, P> { }
-function createVolumeRenderObject<G extends Geometry>(volume: VolumeData, geometry: G, locationIt: LocationIterator, theme: Theme, props: PD.Values<Geometry.Params<G>>, materialId: number) {
+function createVolumeRenderObject<G extends Geometry>(volume: Volume, geometry: G, locationIt: LocationIterator, theme: Theme, props: PD.Values<Geometry.Params<G>>, materialId: number) {
const { createValues, createRenderableState } = Geometry.getUtils(geometry);
const transform = createIdentityTransform();
const values = createValues(geometry, transform, locationIt, theme, props);
@@ -42,11 +42,11 @@ function createVolumeRenderObject<G extends Geometry>(volume: VolumeData, geomet
interface VolumeVisualBuilder<P extends VolumeParams, G extends Geometry> {
defaultProps: PD.Values<P>
- createGeometry(ctx: VisualContext, volume: VolumeData, theme: Theme, props: PD.Values<P>, geometry?: G): Promise<G> | G
- createLocationIterator(volume: VolumeData): LocationIterator
- getLoci(pickingId: PickingId, volume: VolumeData, props: PD.Values<P>, id: number): Loci
- eachLocation(loci: Loci, volume: VolumeData, props: PD.Values<P>, apply: (interval: Interval) => boolean): boolean
- setUpdateState(state: VisualUpdateState, volume: VolumeData, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme): void
+ createGeometry(ctx: VisualContext, volume: Volume, theme: Theme, props: PD.Values<P>, geometry?: G): Promise<G> | G
+ createLocationIterator(volume: Volume): LocationIterator
+ getLoci(pickingId: PickingId, volume: Volume, props: PD.Values<P>, id: number): Loci
+ eachLocation(loci: Loci, volume: Volume, props: PD.Values<P>, apply: (interval: Interval) => boolean): boolean
+ setUpdateState(state: VisualUpdateState, volume: Volume, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme): void
}
interface VolumeVisualGeometryBuilder<P extends VolumeParams, G extends Geometry> extends VolumeVisualBuilder<P, G> {
@@ -62,16 +62,16 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
let newProps: PD.Values<P>;
let newTheme: Theme;
- let newVolume: VolumeData;
+ let newVolume: Volume;
let currentProps: PD.Values<P> = Object.assign({}, defaultProps);
let currentTheme: Theme = Theme.createEmpty();
- let currentVolume: VolumeData;
+ let currentVolume: Volume;
let geometry: G;
let locationIt: LocationIterator;
- function prepareUpdate(theme: Theme, props: Partial<PD.Values<P>>, volume: VolumeData) {
+ function prepareUpdate(theme: Theme, props: Partial<PD.Values<P>>, volume: Volume) {
if (!volume && !currentVolume) {
throw new Error('missing volume');
}
@@ -84,7 +84,7 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
if (!renderObject) {
updateState.createNew = true;
- } else if (!currentVolume || !VolumeData.areEquivalent(newVolume, currentVolume)) {
+ } else if (!currentVolume || !Volume.areEquivalent(newVolume, currentVolume)) {
updateState.createNew = true;
}
@@ -158,7 +158,7 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
return {
get groupCount() { return locationIt ? locationIt.count : 0; },
get renderObject () { return renderObject; },
- async createOrUpdate(ctx: VisualContext, theme: Theme, props: Partial<PD.Values<P>> = {}, volume?: VolumeData) {
+ async createOrUpdate(ctx: VisualContext, theme: Theme, props: Partial<PD.Values<P>> = {}, volume?: Volume) {
prepareUpdate(theme, props, volume || currentVolume);
if (updateState.createGeometry) {
const newGeometry = createGeometry(ctx, newVolume, newTheme, newProps, geometry);
@@ -198,9 +198,9 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
};
}
-export interface VolumeRepresentation<P extends VolumeParams> extends Representation<VolumeData, P> { }
+export interface VolumeRepresentation<P extends VolumeParams> extends Representation<Volume, P> { }
-export type VolumeRepresentationProvider<P extends VolumeParams, Id extends string = string> = RepresentationProvider<VolumeData, P, Representation.State, Id>
+export type VolumeRepresentationProvider<P extends VolumeParams, Id extends string = string> = RepresentationProvider<Volume, P, Representation.State, Id>
export function VolumeRepresentationProvider<P extends VolumeParams, Id extends string>(p: VolumeRepresentationProvider<P, Id>): VolumeRepresentationProvider<P, Id> { return p; }
//
@@ -210,7 +210,7 @@ export const VolumeParams = {
};
export type VolumeParams = typeof VolumeParams
-export function VolumeRepresentation<P extends VolumeParams>(label: string, ctx: RepresentationContext, getParams: RepresentationParamsGetter<VolumeData, P>, visualCtor: (materialId: number) => VolumeVisual<P>, getLoci: (volume: VolumeData, props: PD.Values<P>) => Loci): VolumeRepresentation<P> {
+export function VolumeRepresentation<P extends VolumeParams>(label: string, ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, P>, visualCtor: (materialId: number) => VolumeVisual<P>, getLoci: (volume: Volume, props: PD.Values<P>) => Loci): VolumeRepresentation<P> {
let version = 0;
const updated = new Subject<number>();
const materialId = getNextMaterialId();
@@ -218,12 +218,12 @@ export function VolumeRepresentation<P extends VolumeParams>(label: string, ctx:
const _state = Representation.createState();
let visual: VolumeVisual<P> | undefined;
- let _volume: VolumeData;
+ let _volume: Volume;
let _params: P;
let _props: PD.Values<P>;
let _theme = Theme.createEmpty();
- function createOrUpdate(props: Partial<PD.Values<P>> = {}, volume?: VolumeData) {
+ function createOrUpdate(props: Partial<PD.Values<P>> = {}, volume?: Volume) {
if (volume && volume !== _volume) {
_params = getParams(ctx, volume);
_volume = volume;
diff --git a/src/mol-repr/volume/slice.ts b/src/mol-repr/volume/slice.ts
index 3b9314597846f81a9abcdf1979eda652059ae50f..485d17d8464e815ea5bf8425d5aacdd4043a6ebd 100644
--- a/src/mol-repr/volume/slice.ts
+++ b/src/mol-repr/volume/slice.ts
@@ -7,14 +7,13 @@
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Image } from '../../mol-geo/geometry/image/image';
import { ThemeRegistryContext, Theme } from '../../mol-theme/theme';
-import { VolumeData, VolumeIsoValue } from '../../mol-model/volume';
+import { Grid, Volume } from '../../mol-model/volume';
import { VolumeVisual, VolumeRepresentation, VolumeRepresentationProvider } from './representation';
import { LocationIterator } from '../../mol-geo/util/location-iterator';
import { VisualUpdateState } from '../util';
import { NullLocation } from '../../mol-model/location';
import { RepresentationContext, RepresentationParamsGetter } from '../representation';
import { VisualContext } from '../visual';
-import { Volume } from '../../mol-model/volume/volume';
import { PickingId } from '../../mol-geo/geometry/picking';
import { EmptyLoci, Loci } from '../../mol-model/loci';
import { Interval, OrderedSet, SortedArray } from '../../mol-data/int';
@@ -25,12 +24,12 @@ import { createIsoValueParam, IsoValueParam } from './isosurface';
import { Color } from '../../mol-util/color';
import { ColorTheme } from '../../mol-theme/color';
-export async function createImage(ctx: VisualContext, volume: VolumeData, theme: Theme, props: PD.Values<SliceParams>, image?: Image) {
+export async function createImage(ctx: VisualContext, volume: Volume, theme: Theme, props: PD.Values<SliceParams>, image?: Image) {
const { dimension: { name: dim }, isoValue } = props;
- const { space, data: data } = volume.data;
- const { min, max } = volume.dataStats;
- const isoVal = VolumeIsoValue.toAbsolute(isoValue, volume.dataStats).absoluteValue;
+ const { space, data } = volume.grid.cells;
+ const { min, max } = volume.grid.stats;
+ const isoVal = Volume.IsoValue.toAbsolute(isoValue, volume.grid.stats).absoluteValue;
// TODO more color themes
const color = theme.color.color(NullLocation, false);
@@ -41,7 +40,7 @@ export async function createImage(ctx: VisualContext, volume: VolumeData, theme:
x, y, z,
x0, y0, z0,
nx, ny, nz
- } = getSliceInfo(volume, props);
+ } = getSliceInfo(volume.grid, props);
const corners = new Float32Array(
dim === 'x' ? [x, 0, 0, x, y, 0, x, 0, z, x, y, z] :
@@ -50,7 +49,7 @@ export async function createImage(ctx: VisualContext, volume: VolumeData, theme:
);
const imageArray = new Float32Array(width * height * 4);
- const groupArray = getGroupArray(volume, props);
+ const groupArray = getGroupArray(volume.grid, props);
let i = 0;
for (let iy = y0; iy < ny; ++iy) {
@@ -72,15 +71,15 @@ export async function createImage(ctx: VisualContext, volume: VolumeData, theme:
const imageTexture = { width, height, array: imageArray, flipY: true };
const groupTexture = { width, height, array: groupArray, flipY: true };
- const transform = VolumeData.getGridToCartesianTransform(volume);
+ const transform = Grid.getGridToCartesianTransform(volume.grid);
transformPositionArray(transform, corners, 0, 4);
return Image.create(imageTexture, corners, groupTexture, image);
}
-function getSliceInfo(volume: VolumeData, props: PD.Values<SliceParams>) {
+function getSliceInfo(grid: Grid, props: PD.Values<SliceParams>) {
const { dimension: { name: dim, params: index } } = props;
- const { space } = volume.data;
+ const { space } = grid.cells;
let width, height;
let x, y, z;
@@ -108,9 +107,9 @@ function getSliceInfo(volume: VolumeData, props: PD.Values<SliceParams>) {
};
}
-function getGroupArray(volume: VolumeData, props: PD.Values<SliceParams>) {
- const { space } = volume.data;
- const { width, height, x0, y0, z0, nx, ny, nz } = getSliceInfo(volume, props);
+function getGroupArray(grid: Grid, props: PD.Values<SliceParams>) {
+ const { space } = grid.cells;
+ const { width, height, x0, y0, z0, nx, ny, nz } = getSliceInfo(grid, props);
const groupArray = new Float32Array(width * height);
let j = 0;
@@ -125,13 +124,13 @@ function getGroupArray(volume: VolumeData, props: PD.Values<SliceParams>) {
return groupArray;
}
-function getLoci(volume: VolumeData, props: PD.Values<SliceParams>) {
+function getLoci(volume: Volume, props: PD.Values<SliceParams>) {
// TODO cache somehow?
- const groupArray = getGroupArray(volume, props);
+ const groupArray = getGroupArray(volume.grid, props);
return Volume.Cell.Loci(volume, SortedArray.ofUnsortedArray(groupArray));
}
-function getSliceLoci(pickingId: PickingId, volume: VolumeData, props: PD.Values<SliceParams>, id: number) {
+function getSliceLoci(pickingId: PickingId, volume: Volume, props: PD.Values<SliceParams>, id: number) {
const { objectId, groupId } = pickingId;
if (id === objectId) {
return Volume.Cell.Loci(volume, Interval.ofSingleton(groupId as Volume.CellIndex));
@@ -139,24 +138,24 @@ function getSliceLoci(pickingId: PickingId, volume: VolumeData, props: PD.Values
return EmptyLoci;
}
-function eachSlice(loci: Loci, volume: VolumeData, props: PD.Values<SliceParams>, apply: (interval: Interval) => boolean) {
+function eachSlice(loci: Loci, volume: Volume, props: PD.Values<SliceParams>, apply: (interval: Interval) => boolean) {
let changed = false;
if (Volume.isLoci(loci)) {
- if (!VolumeData.areEquivalent(loci.volume, volume)) return false;
- if (apply(Interval.ofLength(volume.data.data.length))) changed = true;
+ if (!Volume.areEquivalent(loci.volume, volume)) return false;
+ if (apply(Interval.ofLength(volume.grid.cells.data.length))) changed = true;
} else if (Volume.Isosurface.isLoci(loci)) {
- if (!VolumeData.areEquivalent(loci.volume, volume)) return false;
+ if (!Volume.areEquivalent(loci.volume, volume)) return false;
// TODO find a cheaper way?
- const { dataStats, data: { data } } = volume;
- const eps = dataStats.sigma;
- const v = VolumeIsoValue.toAbsolute(loci.isoValue, dataStats).absoluteValue;
+ const { stats, cells: { data } } = volume.grid;
+ const eps = stats.sigma;
+ const v = Volume.IsoValue.toAbsolute(loci.isoValue, stats).absoluteValue;
for (let i = 0, il = data.length; i < il; ++i) {
if (equalEps(v, data[i], eps)) {
if (apply(Interval.ofSingleton(i))) changed = true;
}
}
} else if (Volume.Cell.isLoci(loci)) {
- if (!VolumeData.areEquivalent(loci.volume, volume)) return false;
+ if (!Volume.areEquivalent(loci.volume, volume)) return false;
if (Interval.is(loci.indices)) {
if (apply(loci.indices)) changed = true;
} else {
@@ -181,15 +180,15 @@ export const SliceParams = {
isoValue: IsoValueParam,
};
export type SliceParams = typeof SliceParams
-export function getSliceParams(ctx: ThemeRegistryContext, volume: VolumeData) {
+export function getSliceParams(ctx: ThemeRegistryContext, volume: Volume) {
const p = PD.clone(SliceParams);
- const dim = volume.data.space.dimensions;
+ const dim = volume.grid.cells.space.dimensions;
p.dimension = PD.MappedStatic('x', {
x: PD.Numeric(0, { min: 0, max: dim[0] - 1, step: 1 }),
y: PD.Numeric(0, { min: 0, max: dim[1] - 1, step: 1 }),
z: PD.Numeric(0, { min: 0, max: dim[2] - 1, step: 1 }),
}, { isEssential: true });
- p.isoValue = createIsoValueParam(VolumeIsoValue.absolute(volume.dataStats.min), volume.dataStats);
+ p.isoValue = createIsoValueParam(Volume.IsoValue.absolute(volume.grid.stats.min), volume.grid.stats);
return p;
}
@@ -197,14 +196,14 @@ export function SliceVisual(materialId: number): VolumeVisual<SliceParams> {
return VolumeVisual<Image, SliceParams>({
defaultProps: PD.getDefaultValues(SliceParams),
createGeometry: createImage,
- createLocationIterator: (volume: VolumeData) => LocationIterator(volume.data.data.length, 1, () => NullLocation),
+ createLocationIterator: (volume: Volume) => LocationIterator(volume.grid.cells.data.length, 1, () => NullLocation),
getLoci: getSliceLoci,
eachLocation: eachSlice,
- setUpdateState: (state: VisualUpdateState, volume: VolumeData, newProps: PD.Values<SliceParams>, currentProps: PD.Values<SliceParams>, newTheme: Theme, currentTheme: Theme) => {
+ setUpdateState: (state: VisualUpdateState, volume: Volume, newProps: PD.Values<SliceParams>, currentProps: PD.Values<SliceParams>, newTheme: Theme, currentTheme: Theme) => {
state.createGeometry = (
newProps.dimension.name !== currentProps.dimension.name ||
newProps.dimension.params !== currentProps.dimension.params ||
- !VolumeIsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.dataStats) ||
+ !Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats) ||
!ColorTheme.areEqual(newTheme.color, currentTheme.color)
);
},
@@ -226,7 +225,7 @@ function updateRenderableState(state: RenderableState, props: PD.Values<SlicePar
state.writeDepth = true;
}
-export function SliceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<VolumeData, SliceParams>): VolumeRepresentation<SliceParams> {
+export function SliceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, SliceParams>): VolumeRepresentation<SliceParams> {
return VolumeRepresentation('Slice', ctx, getParams, SliceVisual, getLoci);
}
@@ -239,5 +238,5 @@ export const SliceRepresentationProvider = VolumeRepresentationProvider({
defaultValues: PD.getDefaultValues(SliceParams),
defaultColorTheme: { name: 'uniform' },
defaultSizeTheme: { name: 'uniform' },
- isApplicable: (volume: VolumeData) => volume.data.data.length > 0
+ isApplicable: (volume: Volume) => !Volume.isEmpty(volume)
});
\ No newline at end of file
diff --git a/src/mol-script/runtime/query/base.ts b/src/mol-script/runtime/query/base.ts
index dabc80ad3deb1efa464997beb2d6dc91ab8e8a92..8f77598a0da57c2e87293fa3eb69121f2bf6a0db 100644
--- a/src/mol-script/runtime/query/base.ts
+++ b/src/mol-script/runtime/query/base.ts
@@ -5,8 +5,9 @@
*/
import Expression from '../../language/expression';
-import { QueryContext, QueryFn, Structure, CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { QueryContext, QueryFn, Structure } from '../../../mol-model/structure';
import { MSymbol } from '../../language/symbol';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
export class QueryRuntimeTable {
private map = new Map<string, QuerySymbolRuntime>();
diff --git a/src/mol-theme/label.ts b/src/mol-theme/label.ts
index b1d530d8ce4cc6c53abed9961950e646675585dc..2d8cc64cf64a792419d8cad06d67f7c88f655c4b 100644
--- a/src/mol-theme/label.ts
+++ b/src/mol-theme/label.ts
@@ -12,7 +12,7 @@ import { capitalize, stripTags } from '../mol-util/string';
import { Column } from '../mol-data/db';
import { Vec3 } from '../mol-math/linear-algebra';
import { radToDeg } from '../mol-math/misc';
-import { VolumeIsoValue } from '../mol-model/volume';
+import { Volume } from '../mol-model/volume';
export type LabelGranularity = 'element' | 'conformation' | 'residue' | 'chain' | 'structure'
@@ -51,19 +51,19 @@ export function lociLabel(loci: Loci, options: Partial<LabelOptions> = {}): stri
case 'isosurface-loci':
return [
`${loci.volume.label || 'Volume'}`,
- `Isosurface at ${VolumeIsoValue.toString(loci.isoValue)}`
+ `Isosurface at ${Volume.IsoValue.toString(loci.isoValue)}`
].join(' | ');
case 'cell-loci':
const size = OrderedSet.size(loci.indices);
const start = OrderedSet.start(loci.indices);
- const absVal = VolumeIsoValue.absolute(loci.volume.data.data[start]);
- const relVal = VolumeIsoValue.toRelative(absVal, loci.volume.dataStats);
+ const absVal = Volume.IsoValue.absolute(loci.volume.grid.cells.data[start]);
+ const relVal = Volume.IsoValue.toRelative(absVal, loci.volume.grid.stats);
const label = [
`${loci.volume.label || 'Volume'}`,
`${size === 1 ? `Cell #${start}` : `${size} Cells`}`
];
if (size === 1) {
- label.push(`${VolumeIsoValue.toString(absVal)} (${VolumeIsoValue.toString(relVal)})`);
+ label.push(`${Volume.IsoValue.toString(absVal)} (${Volume.IsoValue.toString(relVal)})`);
}
return label.join(' | ');
}
diff --git a/src/mol-theme/theme.ts b/src/mol-theme/theme.ts
index 83c4fe8bdf1826bab80d79a07853f6460171a738..2bd1543cdda981926c974bbacda80cc5340ee406 100644
--- a/src/mol-theme/theme.ts
+++ b/src/mol-theme/theme.ts
@@ -7,7 +7,7 @@
import { ColorTheme } from './color';
import { SizeTheme } from './size';
import { Structure } from '../mol-model/structure';
-import { VolumeData } from '../mol-model/volume';
+import { Volume } from '../mol-model/volume';
import { ParamDefinition as PD } from '../mol-util/param-definition';
import { Shape } from '../mol-model/shape';
import { CustomProperty } from '../mol-model-props/common/custom-property';
@@ -21,7 +21,7 @@ export interface ThemeRegistryContext {
export interface ThemeDataContext {
[k: string]: any
structure?: Structure
- volume?: VolumeData
+ volume?: Volume
shape?: Shape
}
diff --git a/src/perf-tests/mol-script.ts b/src/perf-tests/mol-script.ts
index eb40e8848ed8c442534e3e89802f263ebb888325..3b4fc50308bd02c3add42349b52764e91e292dff 100644
--- a/src/perf-tests/mol-script.ts
+++ b/src/perf-tests/mol-script.ts
@@ -1,6 +1,6 @@
import { MolScriptBuilder } from '../mol-script/language/builder';
import { compile, QuerySymbolRuntime, DefaultQueryRuntimeTable } from '../mol-script/runtime/query/compiler';
-import { QueryContext, Structure, StructureQuery, CustomPropertyDescriptor } from '../mol-model/structure';
+import { QueryContext, Structure, StructureQuery } from '../mol-model/structure';
import { readCifFile, getModelsAndStructure } from '../apps/structure-info/model';
import { CustomPropSymbol } from '../mol-script/language/symbol';
import Type from '../mol-script/language/type';
@@ -10,6 +10,7 @@ import { transpileMolScript } from '../mol-script/script/mol-script/symbols';
import { formatMolScript } from '../mol-script/language/expression-formatter';
import { StructureQualityReport, StructureQualityReportProvider } from '../extensions/pdbe/structure-quality-report/prop';
import fetch from 'node-fetch';
+import { CustomPropertyDescriptor } from '../mol-model/custom-property';
// import Examples from 'mol-script/script/mol-script/examples'
// import { parseMolScript } from 'mol-script/script/mol-script/parser'