From 5c085bead69efdd9fd23446195b87e57a0042855 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 11 Feb 2019 17:21:55 -0800
Subject: [PATCH] wip density-server cif loading
---
.../volume/formats/density-server.ts | 6 ++--
src/mol-plugin/state/actions/basic.ts | 14 +++++---
src/mol-plugin/state/transforms/model.ts | 35 +++++++++++++++++++
3 files changed, 47 insertions(+), 8 deletions(-)
diff --git a/src/mol-model/volume/formats/density-server.ts b/src/mol-model/volume/formats/density-server.ts
index c01282e8e..2f539d379 100644
--- a/src/mol-model/volume/formats/density-server.ts
+++ b/src/mol-model/volume/formats/density-server.ts
@@ -10,8 +10,8 @@ import { Task } from 'mol-task';
import { SpacegroupCell, Box3D } from 'mol-math/geometry';
import { Tensor, Vec3 } from 'mol-math/linear-algebra';
-function parseDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
- return Task.create<VolumeData>('Parse Volume Data', async ctx => {
+function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
+ return Task.create<VolumeData>('Create Volume Data', async ctx => {
const { volume_data_3d_info: info, volume_data_3d: values } = source;
const cell = SpacegroupCell.create(
info.spacegroup_number.value(0),
@@ -47,4 +47,4 @@ function parseDensityServerData(source: DensityServer_Data_Database): Task<Volum
});
}
-export { parseDensityServerData }
\ No newline at end of file
+export { volumeFromDensityServerData }
\ No newline at end of file
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index e2be44425..b2c372fa2 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -162,7 +162,7 @@ export const UpdateTrajectory = StateAction.build({
//
-const VolumeFormats = { 'ccp4': '', 'mrc': '', 'map': '', 'dsn6': '', 'brix': '' }
+const VolumeFormats = { 'ccp4': '', 'mrc': '', 'map': '', 'dsn6': '', 'brix': '', 'dscif': '' }
type VolumeFormat = keyof typeof VolumeFormats
function getVolumeData(format: VolumeFormat, b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>) {
@@ -171,6 +171,8 @@ function getVolumeData(format: VolumeFormat, b: StateTreeBuilder.To<PluginStateO
return b.apply(StateTransforms.Data.ParseCcp4).apply(StateTransforms.Model.VolumeFromCcp4);
case 'dsn6': case 'brix':
return b.apply(StateTransforms.Data.ParseDsn6).apply(StateTransforms.Model.VolumeFromDsn6);
+ case 'dscif':
+ return b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.VolumeFromDensityServerCif);
}
}
@@ -200,14 +202,15 @@ export const OpenVolume = StateAction.build({
display: { name: 'Open Volume', description: 'Load a volume from file and create its default visual' },
from: PluginStateObject.Root,
params: {
- file: PD.File({ accept: '.ccp4,.mrc,.map,.dsn6,.brix'}),
+ file: PD.File({ accept: '.ccp4,.mrc,.map,.dsn6,.brix,.cif'}),
+ isBinary: PD.Boolean(true),
format: PD.Select('auto', [
- ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX']
+ ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX'], ['dscif', 'densityServerCIF']
]),
}
})(({ params, state }, ctx: PluginContext) => {
const b = state.build();
- const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: true });
+ const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: params.isBinary });
const format = getFileFormat(params.format, params.file)
return state.update(createVolumeTree(format, ctx, data));
});
@@ -229,8 +232,9 @@ const DownloadDensity = StateAction.build({
}, { isFlat: true }),
'url': PD.Group({
url: PD.Text(''),
+ isBinary: PD.Boolean(true),
format: PD.Select('auto', [
- ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX']
+ ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX'], ['dscif', 'densityServerCIF']
]),
}, { isFlat: true })
}, {
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 958e2ef90..9e697bfc2 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -19,6 +19,8 @@ import { stringToWords } from 'mol-util/string';
import { volumeFromCcp4 } from 'mol-model/volume/formats/ccp4';
import { Vec3 } from 'mol-math/linear-algebra';
import { volumeFromDsn6 } from 'mol-model/volume/formats/dsn6';
+import { volumeFromDensityServerData } from 'mol-model/volume';
+import CIF from 'mol-io/reader/cif';
export { TrajectoryFromMmCif }
type TrajectoryFromMmCif = typeof TrajectoryFromMmCif
@@ -259,4 +261,37 @@ const VolumeFromDsn6 = PluginStateTransform.BuiltIn({
return new SO.Volume.Data(volume, props);
});
}
+});
+
+export { VolumeFromDensityServerCif }
+type VolumeFromDensityServerCif = typeof VolumeFromDensityServerCif
+const VolumeFromDensityServerCif = PluginStateTransform.BuiltIn({
+ name: 'volume-from-density-server-cif',
+ display: { name: 'Volume from density-server CIF', description: 'Identify and create all separate models in the specified CIF data block' },
+ from: SO.Format.Cif,
+ to: SO.Volume.Data,
+ params(a) {
+ if (!a) {
+ return {
+ blockHeader: PD.makeOptional(PD.Text(void 0, { description: 'Header of the block to parse. If none is specifed, the 1st data block in the file is used.' }))
+ };
+ }
+ const blocks = a.data.blocks.slice(1); // zero block contains query meta-data
+ return {
+ blockHeader: PD.makeOptional(PD.Select(blocks[0] && blocks[0].header, blocks.map(b => [b.header, b.header] as [string, string]), { description: 'Header of the block to parse' }))
+ };
+ }
+})({
+ isApplicable: a => a.data.blocks.length > 0,
+ apply({ a, params }) {
+ return Task.create('Parse density-server CIF', async ctx => {
+ const header = params.blockHeader || a.data.blocks[1].header; // zero block contains query meta-data
+ const block = a.data.blocks.find(b => b.header === header);
+ if (!block) throw new Error(`Data block '${[header]}' not found.`);
+ const densityServerCif = CIF.schema.densityServer(block)
+ const volume = await volumeFromDensityServerData(densityServerCif).runInContext(ctx)
+ const props = { label: densityServerCif.volume_data_3d_info.name.value(0), description: `${densityServerCif.volume_data_3d_info.name.value(0)}` };
+ return new SO.Volume.Data(volume, props);
+ });
+ }
});
\ No newline at end of file
--
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