diff --git a/src/apps/structure-info/density.ts b/src/apps/structure-info/density.ts
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/src/apps/structure-info/helpers.ts b/src/apps/structure-info/helpers.ts
index 45fb1c0322837fbf02d7ced63000c1e9f2fc3f2d..94095a99055759cdbab8d9b2c677345632520848 100644
--- a/src/apps/structure-info/helpers.ts
+++ b/src/apps/structure-info/helpers.ts
@@ -29,7 +29,7 @@ async function parseCif(data: string|Uint8Array) {
const comp = CIF.parse(data);
const parsed = await Run(comp, p => console.log(Progress.format(p)), 250);
if (parsed.isError) throw parsed;
- return parsed
+ return parsed.result;
}
export async function openCif(path: string) {
diff --git a/src/apps/structure-info/index.ts b/src/apps/structure-info/model.ts
similarity index 98%
rename from src/apps/structure-info/index.ts
rename to src/apps/structure-info/model.ts
index 93b84cb096bb82196e6658cfd56d2bd9d12f3c59..8ab4ad1dbf361bdda44c7d36492d95e616ca126a 100644
--- a/src/apps/structure-info/index.ts
+++ b/src/apps/structure-info/model.ts
@@ -22,12 +22,12 @@ import { openCif, downloadCif } from './helpers';
async function downloadFromPdb(pdb: string) {
// `https://files.rcsb.org/download/${pdb}.cif`
const parsed = await downloadCif(`http://www.ebi.ac.uk/pdbe/static/entry/${pdb}_updated.cif`, false);
- return CIF.schema.mmCIF(parsed.result.blocks[0]);
+ return CIF.schema.mmCIF(parsed.blocks[0]);
}
async function readPdbFile(path: string) {
const parsed = await openCif(path);
- return CIF.schema.mmCIF(parsed.result.blocks[0]);
+ return CIF.schema.mmCIF(parsed.blocks[0]);
}
export function atomLabel(model: Model, aI: number) {
diff --git a/src/apps/structure-info/volume.ts b/src/apps/structure-info/volume.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e3b4b2e1efdba2514a0f052feea69932ac21f2cd
--- /dev/null
+++ b/src/apps/structure-info/volume.ts
@@ -0,0 +1,47 @@
+
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as argparse from 'argparse'
+import { VolumeData, parseDensityServerData } 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 { Run } from 'mol-task';
+import { Table } from 'mol-data/db';
+
+type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
+
+async function getVolume(url: string): Promise<Volume> {
+ const cif = await downloadCif(url, false);
+ const data = CIF.schema.densityServer(cif.blocks[1]);
+ return { source: data, volume: await Run(parseDensityServerData(data)) };
+}
+
+function print(volume: Volume) {
+ const { volume_data_3d_info } = volume.source;
+ const row = Table.getRow(volume_data_3d_info, 0);
+ console.log(row);
+}
+
+async function run(url: string) {
+ const volume = await getVolume(url);
+ print(volume);
+}
+
+const parser = new argparse.ArgumentParser({
+addHelp: true,
+description: 'Info about VolumeData from mol-model module'
+});
+parser.addArgument([ '--emdb', '-e' ], {
+ help: 'EMDB id, for example 8116',
+});
+interface Args {
+ emdb?: string
+}
+const args: Args = parser.parseArgs();
+
+run(`https://webchem.ncbr.muni.cz/DensityServer/em/emd-${args.emdb}/cell?detail=1&encoding=cif`);
\ No newline at end of file
diff --git a/src/mol-data/db/column.ts b/src/mol-data/db/column.ts
index 1b0f46ce483df2f61039f0ae9d8612e927cdc130..355c1c365a7ba7f51c1cf41f7ede0d691f25d48c 100644
--- a/src/mol-data/db/column.ts
+++ b/src/mol-data/db/column.ts
@@ -47,8 +47,8 @@ namespace Column {
export function Int(defaultValue = 0): Int { return { '@type': 'int', T: defaultValue, valueType: 'int' } };
export function Float(defaultValue = 0): Float { return { '@type': 'float', T: defaultValue, valueType: 'float' } };
export function Tensor(space: Tensors.Space, baseType: Int | Float = float): Tensor { return { '@type': 'tensor', T: space.create(), space, valueType: 'tensor', baseType }; }
- export function Vector(dim: number, baseType: Int | Float = float): Tensor { return Tensor(Tensors.Vector(dim), baseType); }
- export function Matrix(rows: number, cols: number, baseType: Int | Float = float): Tensor { return Tensor(Tensors.ColumnMajorMatrix(rows, cols), baseType); }
+ export function Vector(dim: number, baseType: Int | Float = float): Tensor { return Tensor(Tensors.Vector(dim, baseType['@type'] === 'int' ? Int32Array : Float64Array), baseType); }
+ export function Matrix(rows: number, cols: number, baseType: Int | Float = float): Tensor { return Tensor(Tensors.ColumnMajorMatrix(rows, cols, baseType['@type'] === 'int' ? Int32Array : Float64Array), baseType); }
export function Aliased<T>(t: Str | Int, defaultValue?: T): Aliased<T> {
if (typeof defaultValue !== 'undefined') return { ...t, T: defaultValue } as any as Aliased<T>;
diff --git a/src/mol-io/reader/cif.ts b/src/mol-io/reader/cif.ts
index 93c30be9a53b8069dfe6dccc0744b900b764944c..440be38553cb525327fd6e376bbd0f29490f4203 100644
--- a/src/mol-io/reader/cif.ts
+++ b/src/mol-io/reader/cif.ts
@@ -12,7 +12,8 @@ import { toDatabaseCollection, toDatabase } from './cif/schema'
import { mmCIF_Schema, mmCIF_Database } from './cif/schema/mmcif'
import { CCD_Schema, CCD_Database } from './cif/schema/ccd'
import { BIRD_Schema, BIRD_Database } from './cif/schema/bird'
-import { dic_Schema, dic_Database } from './cif/schema/dic';
+import { dic_Schema, dic_Database } from './cif/schema/dic'
+import { DensityServer_Data_Schema, DensityServer_Data_Database } from './cif/schema/density-server'
export default {
parse: (data: string|Uint8Array) => typeof data === 'string' ? parseText(data) : parseBinary(data),
@@ -24,7 +25,8 @@ export default {
mmCIF: (frame: Frame) => toDatabase<mmCIF_Schema, mmCIF_Database>(mmCIF_Schema, frame),
CCD: (frame: Frame) => toDatabase<CCD_Schema, CCD_Database>(CCD_Schema, frame),
BIRD: (frame: Frame) => toDatabase<BIRD_Schema, BIRD_Database>(BIRD_Schema, frame),
- dic: (frame: Frame) => toDatabase<dic_Schema, dic_Database>(dic_Schema, frame)
+ dic: (frame: Frame) => toDatabase<dic_Schema, dic_Database>(dic_Schema, frame),
+ densityServer: (frame: Frame) => toDatabase<DensityServer_Data_Schema, DensityServer_Data_Database>(DensityServer_Data_Schema, frame)
}
}
diff --git a/src/mol-io/reader/cif/data-model.ts b/src/mol-io/reader/cif/data-model.ts
index 8182d0fca61359721a06f525aa672b7faa404717..4a090d35163ec693de14ff65e0c4e559a6dbaf89 100644
--- a/src/mol-io/reader/cif/data-model.ts
+++ b/src/mol-io/reader/cif/data-model.ts
@@ -78,19 +78,21 @@ export interface Field {
toFloatArray(params?: Column.ToArrayParams<number>): ReadonlyArray<number>
}
-export function getTensor(category: Category, field: string, space: Tensor.Space, row: number): Tensor.Data {
+export function getTensor(category: Category, field: string, space: Tensor.Space, row: number, zeroIndexed: boolean): Tensor.Data {
const ret = space.create();
+ const offset = zeroIndexed ? 0 : 1;
+
if (space.rank === 1) {
const rows = space.dimensions[0];
for (let i = 0; i < rows; i++) {
- const f = category.getField(`${field}[${i + 1}]`);
+ const f = category.getField(`${field}[${i + offset}]`);
space.set(ret, i, !!f ? f.float(row) : 0.0);
}
} else if (space.rank === 2) {
const rows = space.dimensions[0], cols = space.dimensions[1];
for (let i = 0; i < rows; i++) {
for (let j = 0; j < cols; j++) {
- const f = category.getField(`${field}[${i + 1}][${j + 1}]`);
+ const f = category.getField(`${field}[${i + offset}][${j + offset}]`);
space.set(ret, i, j, !!f ? f.float(row) : 0.0);
}
}
@@ -99,7 +101,7 @@ export function getTensor(category: Category, field: string, space: Tensor.Space
for (let i = 0; i < d0; i++) {
for (let j = 0; j < d1; j++) {
for (let k = 0; k < d2; k++) {
- const f = category.getField(`${field}[${i + 1}][${j + 1}][${k + 1}]`);
+ const f = category.getField(`${field}[${i + offset}][${j + offset}][${k + offset}]`);
space.set(ret, i, j, k, !!f ? f.float(row) : 0.0);
}
}
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index c0f7e1d20c8ef614911b68cff79680662bab1d63..c7710132f758dc4ec0509b0f2089c9f336289544 100644
--- a/src/mol-io/reader/cif/schema.ts
+++ b/src/mol-io/reader/cif/schema.ts
@@ -73,15 +73,18 @@ function createListColumn<T extends number|string>(schema: Column.Schema.List<T>
function createTensorColumn(schema: Column.Schema.Tensor, category: Data.Category, key: string): Column<Tensor.Data> {
const space = schema.space;
+ const zeroOffset = category.fieldNames.indexOf(`${key}[0]`) >= 0;
+ const fst = zeroOffset ? 0 : 1;
+
let firstFieldName: string;
switch (space.rank) {
- case 1: firstFieldName = `${key}[1]`; break;
- case 2: firstFieldName = `${key}[1][1]`; break;
- case 3: firstFieldName = `${key}[1][1][1]`; break;
+ case 1: firstFieldName = `${key}[${fst}]`; break;
+ case 2: firstFieldName = `${key}[${fst}][${fst}]`; break;
+ case 3: firstFieldName = `${key}[${fst}][${fst}][${fst}]`; break;
default: throw new Error('Tensors with rank > 3 or rank 0 are currently not supported.');
}
const first = category.getField(firstFieldName) || Column.Undefined(category.rowCount, schema);
- const value = (row: number) => Data.getTensor(category, key, space, row);
+ const value = (row: number) => Data.getTensor(category, key, space, row, zeroOffset);
const toArray: Column<Tensor.Data>['toArray'] = params => ColumnHelpers.createAndFillArray(category.rowCount, value, params)
return {
diff --git a/src/mol-model/volume.ts b/src/mol-model/volume.ts
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..aa8cf1ce46056532d4723f8c3584de3842c4e484 100644
--- a/src/mol-model/volume.ts
+++ b/src/mol-model/volume.ts
@@ -0,0 +1,8 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export * from './volume/data'
+export * from './volume/formats/density-server'
\ No newline at end of file
diff --git a/src/mol-model/volume/data.ts b/src/mol-model/volume/data.ts
index 628f4fe6b57b48c3b33833e09790c8671089c58c..19826278bb33abda9b02a791c90066cb287cda9a 100644
--- a/src/mol-model/volume/data.ts
+++ b/src/mol-model/volume/data.ts
@@ -21,18 +21,12 @@ interface VolumeData {
}
namespace VolumeData {
- const _scale = Mat4.zero(), _translate = Mat4.zero(), _perm = Mat4.zero();
+ const _scale = Mat4.zero(), _translate = Mat4.zero();
export function getGridToCartesianTransform(volume: VolumeData) {
const { data: { space } } = volume;
const scale = Mat4.fromScaling(_scale, Vec3.div(Vec3.zero(), Box3D.size(volume.fractionalBox), Vec3.ofArray(space.dimensions)));
const translate = Mat4.fromTranslation(_translate, volume.fractionalBox.min);
- const ret = Mat4.mul3(Mat4.zero(), volume.cell.fromFractional, translate, scale);
-
- const [x, y, z] = space.axisOrderSlowToFast;
- if (x !== 0 || y !== 1 || z !== 2) {
- Mat4.mul(ret, Mat4.fromPermutation(_perm, [x, y, z, 3]), ret);
- }
- return ret;
+ return Mat4.mul3(Mat4.zero(), volume.cell.fromFractional, translate, scale);
}
}