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volume.ts 3.84 KiB
/**
* Copyright (c) 2018-2019 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 CIF from 'mol-io/reader/cif';
import { Vec3 } from 'mol-math/linear-algebra';
import { volumeFromCcp4 } from 'mol-model-formats/volume/ccp4';
import { volumeFromDensityServerData } from 'mol-model-formats/volume/density-server';
import { volumeFromDsn6 } from 'mol-model-formats/volume/dsn6';
import { Task } from 'mol-task';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { PluginStateObject as SO, PluginStateTransform } from '../objects';
export { VolumeFromCcp4 };
export { VolumeFromDsn6 };
export { VolumeFromDensityServerCif };
type VolumeFromCcp4 = typeof VolumeFromCcp4
const VolumeFromCcp4 = PluginStateTransform.BuiltIn({
name: 'volume-from-ccp4',
display: { name: 'Volume from CCP4/MRC/MAP', description: 'Create Volume from CCP4/MRC/MAP data' },
from: SO.Format.Ccp4,
to: SO.Volume.Data,
params(a) {
return {
voxelSize: PD.Vec3(Vec3.create(1, 1, 1))
};
}
})({
apply({ a, params }) {
return Task.create('Create volume from CCP4/MRC/MAP', async ctx => {
const volume = await volumeFromCcp4(a.data, params).runInContext(ctx)
const props = { label: 'Volume' };
return new SO.Volume.Data(volume, props);
});
}
});
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);
});
}
});
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);
});
}
});