From 5007f5fb723e72dec3b1768b0d8470e01981f898 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 26 Apr 2020 13:05:39 -0700
Subject: [PATCH] added VolumeData.sourceData: ModelFormat
---
.../{structure => }/format.ts | 0
src/mol-model-formats/structure/3dg.ts | 2 +-
.../structure/basic/atomic.ts | 2 +-
.../structure/basic/parser.ts | 2 +-
src/mol-model-formats/structure/cif-core.ts | 2 +-
.../structure/common/property.ts | 2 +-
src/mol-model-formats/structure/cube.ts | 2 +-
src/mol-model-formats/structure/gro.ts | 2 +-
src/mol-model-formats/structure/mmcif.ts | 2 +-
src/mol-model-formats/structure/mol.ts | 2 +-
src/mol-model-formats/structure/psf.ts | 2 +-
src/mol-model-formats/volume/ccp4.ts | 20 ++++++++++++++++-
src/mol-model-formats/volume/cube.ts | 20 ++++++++++++++++-
.../volume/density-server.ts | 22 ++++++++++++++++---
src/mol-model-formats/volume/dsn6.ts | 22 ++++++++++++++++---
src/mol-model-formats/volume/dx.ts | 20 ++++++++++++++++-
src/mol-model/structure/model/model.ts | 2 +-
src/mol-model/structure/topology/topology.ts | 2 +-
src/mol-model/volume/data.ts | 5 ++++-
19 files changed, 111 insertions(+), 22 deletions(-)
rename src/mol-model-formats/{structure => }/format.ts (100%)
diff --git a/src/mol-model-formats/structure/format.ts b/src/mol-model-formats/format.ts
similarity index 100%
rename from src/mol-model-formats/structure/format.ts
rename to src/mol-model-formats/format.ts
diff --git a/src/mol-model-formats/structure/3dg.ts b/src/mol-model-formats/structure/3dg.ts
index ca82890bf..0e829bdaf 100644
--- a/src/mol-model-formats/structure/3dg.ts
+++ b/src/mol-model-formats/structure/3dg.ts
@@ -6,7 +6,7 @@
import { Model } from '../../mol-model/structure/model';
import { Task } from '../../mol-task';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
import { Column, Table } from '../../mol-data/db';
import { EntityBuilder } from './common/entity';
import { File3DG } from '../../mol-io/reader/3dg/parser';
diff --git a/src/mol-model-formats/structure/basic/atomic.ts b/src/mol-model-formats/structure/basic/atomic.ts
index d6dcc438d..de9c772db 100644
--- a/src/mol-model-formats/structure/basic/atomic.ts
+++ b/src/mol-model-formats/structure/basic/atomic.ts
@@ -16,7 +16,7 @@ import { ElementSymbol } from '../../../mol-model/structure/model/types';
import { Entities } from '../../../mol-model/structure/model/properties/common';
import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
import { AtomSite } from './schema';
-import { ModelFormat } from '../format';
+import { ModelFormat } from '../../format';
import { SymmetryOperator } from '../../../mol-math/geometry';
import { MmcifFormat } from '../mmcif';
import { AtomSiteOperatorMappingSchema } from '../../../mol-model/structure/export/categories/atom_site_operator_mapping';
diff --git a/src/mol-model-formats/structure/basic/parser.ts b/src/mol-model-formats/structure/basic/parser.ts
index 10273c258..bf7129e2a 100644
--- a/src/mol-model-formats/structure/basic/parser.ts
+++ b/src/mol-model-formats/structure/basic/parser.ts
@@ -15,7 +15,7 @@ import { getAtomicHierarchyAndConformation } from './atomic';
import { getCoarse, EmptyCoarse, CoarseData } from './coarse';
import { getSequence } from './sequence';
import { sortAtomSite } from './sort';
-import { ModelFormat } from '../format';
+import { ModelFormat } from '../../format';
import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
import { AtomSite, BasicData } from './schema';
import { getProperties } from './properties';
diff --git a/src/mol-model-formats/structure/cif-core.ts b/src/mol-model-formats/structure/cif-core.ts
index 00d95f6f9..542489d1e 100644
--- a/src/mol-model-formats/structure/cif-core.ts
+++ b/src/mol-model-formats/structure/cif-core.ts
@@ -12,7 +12,7 @@ import { createModels } from './basic/parser';
import { BasicSchema, createBasic } from './basic/schema';
import { ComponentBuilder } from './common/component';
import { EntityBuilder } from './common/entity';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
import { CifCore_Database } from '../../mol-io/reader/cif/schema/cif-core';
import { CifFrame, CIF } from '../../mol-io/reader/cif';
import { Spacegroup, SpacegroupCell } from '../../mol-math/geometry';
diff --git a/src/mol-model-formats/structure/common/property.ts b/src/mol-model-formats/structure/common/property.ts
index c5f6b277e..cbc1718f8 100644
--- a/src/mol-model-formats/structure/common/property.ts
+++ b/src/mol-model-formats/structure/common/property.ts
@@ -5,7 +5,7 @@
*/
import { CustomPropertyDescriptor, Model } from '../../../mol-model/structure';
-import { ModelFormat } from '../format';
+import { ModelFormat } from '../../format';
class FormatRegistry<T> {
private map = new Map<ModelFormat['kind'], (model: Model) => T | undefined>()
diff --git a/src/mol-model-formats/structure/cube.ts b/src/mol-model-formats/structure/cube.ts
index 1ab1a2829..3b72a034b 100644
--- a/src/mol-model-formats/structure/cube.ts
+++ b/src/mol-model-formats/structure/cube.ts
@@ -12,7 +12,7 @@ import { createModels } from './basic/parser';
import { BasicSchema, createBasic } from './basic/schema';
import { ComponentBuilder } from './common/component';
import { EntityBuilder } from './common/entity';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
import { CubeFile } from '../../mol-io/reader/cube/parser';
async function getModels(cube: CubeFile, ctx: RuntimeContext): Promise<Model[]> {
diff --git a/src/mol-model-formats/structure/gro.ts b/src/mol-model-formats/structure/gro.ts
index 88d699041..06093e2e1 100644
--- a/src/mol-model-formats/structure/gro.ts
+++ b/src/mol-model-formats/structure/gro.ts
@@ -6,7 +6,7 @@
import { Model } from '../../mol-model/structure/model';
import { Task } from '../../mol-task';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
import { GroFile, GroAtoms } from '../../mol-io/reader/gro/schema';
import { Column, Table } from '../../mol-data/db';
import { guessElementSymbolString } from './util';
diff --git a/src/mol-model-formats/structure/mmcif.ts b/src/mol-model-formats/structure/mmcif.ts
index d71656526..7f3a337c7 100644
--- a/src/mol-model-formats/structure/mmcif.ts
+++ b/src/mol-model-formats/structure/mmcif.ts
@@ -7,7 +7,7 @@
import { Model } from '../../mol-model/structure/model/model';
import { Task } from '../../mol-task';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
import { CifFrame, CIF } from '../../mol-io/reader/cif';
import { mmCIF_Database } from '../../mol-io/reader/cif/schema/mmcif';
import { createModels } from './basic/parser';
diff --git a/src/mol-model-formats/structure/mol.ts b/src/mol-model-formats/structure/mol.ts
index c23612ee9..dbfc11390 100644
--- a/src/mol-model-formats/structure/mol.ts
+++ b/src/mol-model-formats/structure/mol.ts
@@ -14,7 +14,7 @@ import { createModels } from './basic/parser';
import { BasicSchema, createBasic } from './basic/schema';
import { ComponentBuilder } from './common/component';
import { EntityBuilder } from './common/entity';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
import { IndexPairBonds } from './property/bonds/index-pair';
async function getModels(mol: MolFile, ctx: RuntimeContext): Promise<Model[]> {
diff --git a/src/mol-model-formats/structure/psf.ts b/src/mol-model-formats/structure/psf.ts
index 73383d745..08446d212 100644
--- a/src/mol-model-formats/structure/psf.ts
+++ b/src/mol-model-formats/structure/psf.ts
@@ -12,7 +12,7 @@ import { guessElementSymbolString } from './util';
import { MoleculeType, getMoleculeType } from '../../mol-model/structure/model/types';
import { getChainId } from './common/util';
import { Task } from '../../mol-task';
-import { ModelFormat } from './format';
+import { ModelFormat } from '../format';
import { Topology } from '../../mol-model/structure/topology/topology';
import { createBasic, BasicSchema } from './basic/schema';
diff --git a/src/mol-model-formats/volume/ccp4.ts b/src/mol-model-formats/volume/ccp4.ts
index a9e5e703f..8ccf5ad7a 100644
--- a/src/mol-model-formats/volume/ccp4.ts
+++ b/src/mol-model-formats/volume/ccp4.ts
@@ -13,6 +13,7 @@ import { degToRad } from '../../mol-math/misc';
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';
/** When available (e.g. in MRC files) use ORIGIN records instead of N[CRS]START */
export function getCcp4Origin(header: Ccp4Header): Vec3 {
@@ -75,7 +76,24 @@ export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, of
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)
};
});
+}
+
+//
+
+export { Ccp4Format };
+
+type Ccp4Format = ModelFormat<Ccp4File>
+
+namespace Ccp4Format {
+ export function is(x: ModelFormat): x is Ccp4Format {
+ return x.kind === 'ccp4';
+ }
+
+ export function create(ccp4: Ccp4File): Ccp4Format {
+ return { kind: 'ccp4', name: ccp4.name, data: ccp4 };
+ }
}
\ No newline at end of file
diff --git a/src/mol-model-formats/volume/cube.ts b/src/mol-model-formats/volume/cube.ts
index 8ed1613f9..416944d77 100644
--- a/src/mol-model-formats/volume/cube.ts
+++ b/src/mol-model-formats/volume/cube.ts
@@ -9,6 +9,7 @@ import { Mat4, Tensor } from '../../mol-math/linear-algebra';
import { VolumeData } from '../../mol-model/volume/data';
import { Task } from '../../mol-task';
import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
+import { ModelFormat } from '../format';
export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string }): Task<VolumeData> {
return Task.create<VolumeData>('Create Volume Data', async () => {
@@ -51,7 +52,24 @@ export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number,
max: arrayMax(values),
mean: arrayMean(values),
sigma: arrayRms(values)
- }
+ },
+ sourceData: CubeFormat.create(source)
};
});
+}
+
+//
+
+export { CubeFormat };
+
+type CubeFormat = ModelFormat<CubeFile>
+
+namespace CubeFormat {
+ export function is(x: ModelFormat): x is CubeFormat {
+ return x.kind === 'cube';
+ }
+
+ export function create(cube: CubeFile): CubeFormat {
+ return { kind: 'cube', name: cube.name, data: cube };
+ }
}
\ No newline at end of file
diff --git a/src/mol-model-formats/volume/density-server.ts b/src/mol-model-formats/volume/density-server.ts
index 57c43fa92..bb35f0140 100644
--- a/src/mol-model-formats/volume/density-server.ts
+++ b/src/mol-model-formats/volume/density-server.ts
@@ -9,8 +9,9 @@ import { VolumeData } from '../../mol-model/volume/data';
import { Task } from '../../mol-task';
import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
+import { ModelFormat } from '../format';
-function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
+export function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
return Task.create<VolumeData>('Create Volume Data', async ctx => {
const { volume_data_3d_info: info, volume_data_3d: values } = source;
const cell = SpacegroupCell.create(
@@ -41,9 +42,24 @@ function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<
max: info.max_sampled.value(0),
mean: info.mean_sampled.value(0),
sigma: info.sigma_sampled.value(0)
- }
+ },
+ sourceData: DscifFormat.create(source)
};
});
}
-export { volumeFromDensityServerData };
\ No newline at end of file
+//
+
+export { DscifFormat };
+
+type DscifFormat = ModelFormat<DensityServer_Data_Database>
+
+namespace DscifFormat {
+ export function is(x: ModelFormat): x is DscifFormat {
+ return x.kind === 'dscif';
+ }
+
+ export function create(dscif: DensityServer_Data_Database): DscifFormat {
+ return { kind: 'dscif', name: dscif._name, data: dscif };
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/volume/dsn6.ts b/src/mol-model-formats/volume/dsn6.ts
index 42b3fe632..f6ef76cd6 100644
--- a/src/mol-model-formats/volume/dsn6.ts
+++ b/src/mol-model-formats/volume/dsn6.ts
@@ -11,8 +11,9 @@ import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
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';
-function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: string }): Task<VolumeData> {
+export function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: string }): Task<VolumeData> {
return Task.create<VolumeData>('Create Volume Data', async ctx => {
const { header, values } = source;
const size = Vec3.create(header.xlen, header.ylen, header.zlen);
@@ -40,9 +41,24 @@ function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: s
max: arrayMax(values),
mean: arrayMean(values),
sigma: header.sigma !== undefined ? header.sigma : arrayRms(values)
- }
+ },
+ sourceData: Dsn6Format.create(source)
};
});
}
-export { volumeFromDsn6 };
\ No newline at end of file
+//
+
+export { Dsn6Format };
+
+type Dsn6Format = ModelFormat<Dsn6File>
+
+namespace Dsn6Format {
+ export function is(x: ModelFormat): x is Dsn6Format {
+ return x.kind === 'dsn6';
+ }
+
+ export function create(dsn6: Dsn6File): Dsn6Format {
+ return { kind: 'dsn6', name: dsn6.name, data: dsn6 };
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/volume/dx.ts b/src/mol-model-formats/volume/dx.ts
index 79afcf071..2ec9007ca 100644
--- a/src/mol-model-formats/volume/dx.ts
+++ b/src/mol-model-formats/volume/dx.ts
@@ -9,6 +9,7 @@ import { Mat4, Tensor } from '../../mol-math/linear-algebra';
import { VolumeData } from '../../mol-model/volume/data';
import { Task } from '../../mol-task';
import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
+import { ModelFormat } from '../format';
export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<VolumeData> {
return Task.create<VolumeData>('Create Volume Data', async () => {
@@ -28,7 +29,24 @@ export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<
max: arrayMax(values),
mean: arrayMean(values),
sigma: arrayRms(values)
- }
+ },
+ sourceData: DxFormat.create(source)
};
});
+}
+
+//
+
+export { DxFormat };
+
+type DxFormat = ModelFormat<DxFile>
+
+namespace DxFormat {
+ export function is(x: ModelFormat): x is DxFormat {
+ return x.kind === 'dx';
+ }
+
+ export function create(dx: DxFile): DxFormat {
+ return { kind: 'dx', name: dx.name, data: dx };
+ }
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 2d4a95177..00e90d1c9 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -12,7 +12,7 @@ import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
import { Entities, ChemicalComponentMap, MissingResidues, StructAsymMap } from './properties/common';
import { CustomProperties } from '../common/custom-property';
import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
-import { ModelFormat } from '../../../mol-model-formats/structure/format';
+import { ModelFormat } from '../../../mol-model-formats/format';
import { calcModelCenter } from './util';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { Mutable } from '../../../mol-util/type-helpers';
diff --git a/src/mol-model/structure/topology/topology.ts b/src/mol-model/structure/topology/topology.ts
index f88632543..f65e90ce2 100644
--- a/src/mol-model/structure/topology/topology.ts
+++ b/src/mol-model/structure/topology/topology.ts
@@ -7,7 +7,7 @@
import { UUID } from '../../../mol-util';
import { Column } from '../../../mol-data/db';
import { BasicData } from '../../../mol-model-formats/structure/basic/schema';
-import { ModelFormat } from '../../../mol-model-formats/structure/format';
+import { ModelFormat } from '../../../mol-model-formats/format';
export { Topology };
diff --git a/src/mol-model/volume/data.ts b/src/mol-model/volume/data.ts
index b80149c85..2ab568112 100644
--- a/src/mol-model/volume/data.ts
+++ b/src/mol-model/volume/data.ts
@@ -8,6 +8,7 @@
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 {
@@ -20,6 +21,7 @@ interface VolumeDataBase {
mean: number,
sigma: number
}>
+ readonly sourceData: ModelFormat,
}
interface VolumeData extends VolumeDataBase {
@@ -30,7 +32,8 @@ 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 }
+ dataStats: { min: 0, max: 0, mean: 0, sigma: 0 },
+ sourceData: { kind: '', data: '', name: '' }
};
const _scale = Mat4.zero(), _translate = Mat4.zero();
--
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