diff --git a/src/mol-io/reader/ccp4/parser.ts b/src/mol-io/reader/ccp4/parser.ts
index 3a9266e9c03c0b945d5296179ab554dcc4eb5722..43cc24a8302bba97fc893f7eaee26ebcdabfb277 100644
--- a/src/mol-io/reader/ccp4/parser.ts
+++ b/src/mol-io/reader/ccp4/parser.ts
@@ -10,7 +10,7 @@ import Result from '../result'
import { FileHandle } from '../../common/file-handle';
async function parseInternal(file: FileHandle, ctx: RuntimeContext): Promise<Result<Ccp4File>> {
- await ctx.update({ message: 'Parsing CCP4 file...' });
+ await ctx.update({ message: 'Parsing CCP4/MRC file...' });
const { buffer } = await file.readBuffer(0, file.length)
const bin = buffer.buffer
diff --git a/src/mol-io/reader/dsn6/parser.ts b/src/mol-io/reader/dsn6/parser.ts
index 3e21bb7ba4e8e93918de065934d0f7c49b535dc4..a77c968662036b64dab1f21d0df9a90edd3d117d 100644
--- a/src/mol-io/reader/dsn6/parser.ts
+++ b/src/mol-io/reader/dsn6/parser.ts
@@ -26,9 +26,9 @@ function parseBrixHeader(str: string): Dsn6Header {
alpha: parseFloat(str.substr(103, 10)),
beta: parseFloat(str.substr(113, 10)),
gamma: parseFloat(str.substr(123, 10)),
- divisor: parseFloat(str.substr(138, 12)) / 100,
+ divisor: parseFloat(str.substr(138, 12)),
summand: parseInt(str.substr(155, 8)),
- sigma: parseFloat(str.substr(170, 12)) * 100
+ sigma: parseFloat(str.substr(170, 12))
}
}
@@ -57,7 +57,7 @@ function parseDsn6Header(int: Int16Array): Dsn6Header {
}
async function parseInternal(file: FileHandle, ctx: RuntimeContext): Promise<Result<Dsn6File>> {
- await ctx.update({ message: 'Parsing CCP4 file...' });
+ await ctx.update({ message: 'Parsing DSN6/BRIX file...' });
const { buffer } = await file.readBuffer(0, file.length)
const bin = buffer.buffer
@@ -67,18 +67,19 @@ async function parseInternal(file: FileHandle, ctx: RuntimeContext): Promise<Res
const brixStr = String.fromCharCode.apply(null, byteView.subarray(0, 512))
const isBrix = brixStr.startsWith(':-)')
- const header = isBrix ? parseBrixHeader(brixStr) : parseDsn6Header(intView)
- const { divisor, summand } = header
-
if (!isBrix) {
// for DSN6, swap byte order when big endian
- if (intView[ 18 ] !== 100) {
+ if (intView[18] !== 100) {
for (let i = 0, n = intView.length; i < n; ++i) {
- const val = intView[ i ]
- intView[ i ] = ((val & 0xff) << 8) | ((val >> 8) & 0xff)
+ const val = intView[i]
+ intView[i] = ((val & 0xff) << 8) | ((val >> 8) & 0xff)
}
}
}
+
+ const header = isBrix ? parseBrixHeader(brixStr) : parseDsn6Header(intView)
+ const { divisor, summand } = header
+
const values = new Float32Array(header.xExtent * header.yExtent * header.zExtent)
let offset = 512
diff --git a/src/mol-model/volume/formats/dsn6.ts b/src/mol-model/volume/formats/dsn6.ts
index 1a578ce14f3dd8cb0378468dfead083f93d31cb6..d945c19cfb03a6458fa57acd78138369c772c236 100644
--- a/src/mol-model/volume/formats/dsn6.ts
+++ b/src/mol-model/volume/formats/dsn6.ts
@@ -28,7 +28,7 @@ function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3 }): Task<V
const origin_frac = Vec3.create(gridOrigin[0] / grid[0], gridOrigin[1] / grid[1], gridOrigin[2] / grid[2]);
const dimensions_frac = Vec3.create(extent[0] / grid[0], extent[1] / grid[1], extent[2] / grid[2]);
- const space = Tensor.Space(extent, [2, 1, 0], Float32Array);
+ const space = Tensor.Space(extent, [0, 1, 2], Float32Array);
const data = Tensor.create(space, Tensor.Data1(values));
return {
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index 01f22b2b4b83d0655e24815ade299d18d997544f..4ddb9e25d026d7ee193c5e141d345c6dface33ee 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -15,6 +15,7 @@ import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data';
import { StructureRepresentation3DHelpers, VolumeRepresentation3DHelpers } from '../transforms/representation';
+import { getFileInfo } from 'mol-util/file-info';
// TODO: "structure parser provider"
@@ -161,25 +162,52 @@ export const UpdateTrajectory = StateAction.build({
//
-function createVolumeTree(ctx: PluginContext, b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>): StateTree {
- let root = b
- .apply(StateTransforms.Data.ParseCcp4)
- .apply(StateTransforms.Model.VolumeFromCcp4)
+const VolumeFormats = { 'ccp4': '', 'mrc': '', 'dsn6': '', 'brix': '' }
+type VolumeFormat = keyof typeof VolumeFormats
+
+function getVolumeData(format: VolumeFormat, b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>) {
+ switch (format) {
+ case 'ccp4': case 'mrc':
+ return b.apply(StateTransforms.Data.ParseCcp4).apply(StateTransforms.Model.VolumeFromCcp4);
+ case 'dsn6': case 'brix':
+ return b.apply(StateTransforms.Data.ParseDsn6).apply(StateTransforms.Model.VolumeFromDsn6);
+ }
+}
+
+function createVolumeTree(format: VolumeFormat, ctx: PluginContext, b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>): StateTree {
+
+ const root = getVolumeData(format, b)
.apply(StateTransforms.Representation.VolumeRepresentation3D,
VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface'));
return root.getTree();
}
+function getFileFormat(format: VolumeFormat | 'auto', file: File): VolumeFormat {
+ if (format === 'auto') {
+ const fileFormat = getFileInfo(file).ext
+ if (fileFormat in VolumeFormats) {
+ return fileFormat as VolumeFormat
+ } else {
+ throw new Error('unsupported format')
+ }
+ } else {
+ return format
+ }
+}
+
export const OpenVolume = StateAction.build({
display: { name: 'Open Volume', description: 'Load a volume from file and create its default visual' },
from: PluginStateObject.Root,
params: {
- file: PD.File({ accept: '.ccp4,.mrc'}),
- // format: PD.Select('auto', [['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC']]),
+ file: PD.File({ accept: '.ccp4,.mrc,.dsn6,.brix'}),
+ format: PD.Select('auto', [
+ ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['dsn6', 'DSN6'], ['brix', 'BRIX']
+ ]),
}
})(({ params, state }, ctx: PluginContext) => {
const b = state.build();
const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: true });
- return state.update(createVolumeTree(ctx, data));
+ const format = getFileFormat(params.format, params.file)
+ return state.update(createVolumeTree(format, ctx, data));
});
\ No newline at end of file
diff --git a/src/mol-plugin/state/objects.ts b/src/mol-plugin/state/objects.ts
index 38495fe64612eea479ca7e82d87cf9f0643909b4..a47bb8ed1794b5823ce010e966e729b6e9b519c7 100644
--- a/src/mol-plugin/state/objects.ts
+++ b/src/mol-plugin/state/objects.ts
@@ -14,6 +14,7 @@ import { StructureRepresentation } from 'mol-repr/structure/representation';
import { VolumeRepresentation } from 'mol-repr/volume/representation';
import { StateObject, Transformer } from 'mol-state';
import { Ccp4File } from 'mol-io/reader/ccp4/schema';
+import { Dsn6File } from 'mol-io/reader/dsn6/schema';
export type TypeClass = 'root' | 'data' | 'prop'
@@ -58,7 +59,8 @@ export namespace PluginStateObject {
export namespace Format {
export class Json extends Create<any>({ name: 'JSON Data', typeClass: 'Data' }) { }
export class Cif extends Create<CifFile>({ name: 'CIF File', typeClass: 'Data' }) { }
- export class Ccp4 extends Create<Ccp4File>({ name: 'CCP4 File', typeClass: 'Data' }) { }
+ export class Ccp4 extends Create<Ccp4File>({ name: 'CCP4/MRC File', typeClass: 'Data' }) { }
+ export class Dsn6 extends Create<Dsn6File>({ name: 'DSN6/BRIX File', typeClass: 'Data' }) { }
}
export namespace Molecule {
diff --git a/src/mol-plugin/state/transforms/data.ts b/src/mol-plugin/state/transforms/data.ts
index a32194ef65b7755933c08951798b56a5d9639dae..8cb114dcb34da78c494762a8c664f932370b3453 100644
--- a/src/mol-plugin/state/transforms/data.ts
+++ b/src/mol-plugin/state/transforms/data.ts
@@ -14,6 +14,7 @@ import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Transformer } from 'mol-state';
import { readFromFile } from 'mol-util/data-source';
import * as CCP4 from 'mol-io/reader/ccp4/parser'
+import * as DSN6 from 'mol-io/reader/dsn6/parser'
export { Download }
type Download = typeof Download
@@ -98,15 +99,32 @@ export { ParseCcp4 }
type ParseCcp4 = typeof ParseCcp4
const ParseCcp4 = PluginStateTransform.BuiltIn({
name: 'parse-ccp4',
- display: { name: 'Parse CCP4', description: 'Parse CCP4 from Binary data' },
+ display: { name: 'Parse CCP4/MRC', description: 'Parse CCP4/MRC from Binary data' },
from: [SO.Data.Binary],
to: SO.Format.Ccp4
})({
apply({ a }) {
- return Task.create('Parse CCP4', async ctx => {
+ return Task.create('Parse CCP4/MRC', async ctx => {
const parsed = await CCP4.parse(a.data).runInContext(ctx);
if (parsed.isError) throw new Error(parsed.message);
return new SO.Format.Ccp4(parsed.result);
});
}
+});
+
+export { ParseDsn6 }
+type ParseDsn6 = typeof ParseDsn6
+const ParseDsn6 = PluginStateTransform.BuiltIn({
+ name: 'parse-dsn6',
+ display: { name: 'Parse DSN6/BRIX', description: 'Parse CCP4/BRIX from Binary data' },
+ from: [SO.Data.Binary],
+ to: SO.Format.Dsn6
+})({
+ apply({ a }) {
+ return Task.create('Parse DSN6/BRIX', async ctx => {
+ const parsed = await DSN6.parse(a.data).runInContext(ctx);
+ if (parsed.isError) throw new Error(parsed.message);
+ return new SO.Format.Dsn6(parsed.result);
+ });
+ }
});
\ No newline at end of file
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index e0ac192283859f0b5ee745b275407970b16249dd..12cf4ec4d536cc6c86528e2fb7264d098d760f46 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -18,6 +18,7 @@ import { PluginContext } from 'mol-plugin/context';
import { stringToWords } from 'mol-util/string';
import { volumeFromCcp4 } from 'mol-model/volume/formats/ccp4';
import { Vec3 } from 'mol-math/linear-algebra';
+import { volumeFromDsn6 } from 'mol-model/volume/formats/dsn6';
export { TrajectoryFromMmCif }
type TrajectoryFromMmCif = typeof TrajectoryFromMmCif
@@ -233,4 +234,26 @@ const VolumeFromCcp4 = PluginStateTransform.BuiltIn({
return new SO.Volume.Data(volume, props);
});
}
+});
+
+export { VolumeFromDsn6 }
+type VolumeFromDsn6 = typeof VolumeFromDsn6
+const VolumeFromDsn6 = PluginStateTransform.BuiltIn({
+ name: 'volume-from-dsn6',
+ display: { name: 'Volume from DSN6/BRIX', description: 'Create Volume from DSN6/BRIX data' },
+ from: SO.Format.Dsn6,
+ to: SO.Volume.Data,
+ params(a) {
+ return {
+ voxelSize: PD.Vec3(Vec3.create(1, 1, 1))
+ };
+ }
+})({
+ apply({ a, params }) {
+ return Task.create('Create volume from DSN6/BRIX', async ctx => {
+ const volume = await volumeFromDsn6(a.data, params).runInContext(ctx)
+ const props = { label: 'Volume' };
+ return new SO.Volume.Data(volume, props);
+ });
+ }
});
\ No newline at end of file