diff --git a/src/mol-base/collections/database/column.ts b/src/mol-base/collections/database/column.ts
index 23bf57ec4ec7dd73f4b7b9c76f5afa61c2916807..4a373652bd9dd5ac70b9180fbef80b22f529febf 100644
--- a/src/mol-base/collections/database/column.ts
+++ b/src/mol-base/collections/database/column.ts
@@ -5,6 +5,7 @@
*/
import * as ColumnHelpers from './column-helpers'
+import Tensors from '../../math/tensor'
interface Column<T> {
readonly '@type': Column.Type,
@@ -19,27 +20,25 @@ interface Column<T> {
}
namespace Column {
- export type Type<T = any> = Type.Str | Type.Int | Type.Float | Type.Vector | Type.Matrix | Type.Aliased<T>
+ export type Type<T = any> = Type.Str | Type.Int | Type.Float | Type.Tensor | Type.Aliased<T>
export type ArrayCtor<T> = { new(size: number): ArrayLike<T> }
export namespace Type {
export type Str = { T: string, kind: 'str' }
export type Int = { T: number, kind: 'int' }
export type Float = { T: number, kind: 'float' }
- export type Vector = { T: number[], dim: number, kind: 'vector' };
- export type Matrix = { T: number[][], rows: number, cols: number, kind: 'matrix' };
+ export type Tensor = { T: Tensors, space: Tensors.Space, kind: 'tensor' };
export type Aliased<T> = { T: T } & { kind: 'str' | 'int' | 'float' }
export const str: Str = { T: '', kind: 'str' };
export const int: Int = { T: 0, kind: 'int' };
export const float: Float = { T: 0, kind: 'float' };
- export function vector(dim: number): Vector { return { T: [] as number[], dim, kind: 'vector' }; }
- export function matrix(rows: number, cols: number): Matrix { return { T: [] as number[][], rows, cols, kind: 'matrix' }; }
+ export function tensor(space: Tensors.Space): Tensor { return { T: space.create(), space, kind: 'tensor' }; }
export function aliased<T>(t: Type): Aliased<T> { return t as any as Aliased<T>; }
}
- export type Schema<T = any> = Schema.Scalar<T> | Schema.Vector | Schema.Matrix
+ export type Schema<T = any> = Schema.Str | Schema.Int | Schema.Float | Schema.Coordinate | Schema.Aliased<T> | Schema.Tensor
export namespace Schema {
export interface FloatPrecision {
@@ -48,7 +47,7 @@ namespace Column {
full: number
}
- export type Scalar<T = any> = Schema.Str | Schema.Int | Schema.Float | Schema.Coordinate| Schema.Aliased<T>
+ export type Scalar<T = any> = Schema.Str | Schema.Int | Schema.Float | Schema.Coordinate | Schema.Aliased<T>
export function FP(full: number, acceptable: number, low: number): FloatPrecision { return { low, full, acceptable }; }
@@ -57,8 +56,7 @@ namespace Column {
export type Float = { '@type': 'float', T: number, kind: 'float', precision: FloatPrecision }
export type Coordinate = { '@type': 'coord', T: number, kind: 'float' }
- export type Vector = { '@type': 'vector', T: number[], dim: number, kind: 'vector' };
- export type Matrix = { '@type': 'matrix', T: number[][], rows: number, cols: number, kind: 'matrix' };
+ export type Tensor = { '@type': 'tensor', T: Tensors, space: Tensors.Space, kind: 'tensor' };
export type Aliased<T> = { '@type': 'aliased', T: T } & { kind: 'str' | 'int' | 'float' }
export const str: Str = { '@type': 'str', T: '', kind: 'str' };
@@ -66,8 +64,9 @@ namespace Column {
export const coord: Coordinate = { '@type': 'coord', T: 0, kind: 'float' };
export function float(precision: FloatPrecision): Float { return { '@type': 'float', T: 0, kind: 'float', precision } };
- export function vector(dim: number): Vector { return { '@type': 'vector', T: [] as number[], dim, kind: 'vector' }; }
- export function matrix(rows: number, cols: number): Matrix { return { '@type': 'matrix', T: [] as number[][], rows, cols, kind: 'matrix' }; }
+ export function tensor(space: Tensors.Space): Tensor { return { '@type': 'tensor', T: space.create(), space, kind: 'tensor' }; }
+ export function vector(dim: number): Tensor { return tensor(Tensors.Vector(dim)); }
+ export function matrix(rows: number, cols: number): Tensor { return tensor(Tensors.ColumnMajorMatrix(rows, cols)); }
export function aliased<T>(t: Schema): Aliased<T> { return t as any as Aliased<T>; }
}
diff --git a/src/mol-base/math/tensor.ts b/src/mol-base/math/tensor.ts
index b4d89187e84b8f88ea324cfdb1545ac2b007b9ba..d77c82b054ef106fcaaa57c4ac2c6e3fd7165ede 100644
--- a/src/mol-base/math/tensor.ts
+++ b/src/mol-base/math/tensor.ts
@@ -10,6 +10,7 @@ namespace Tensor {
export type ArrayCtor = { new (size: number): ArrayLike<number> }
export interface Space {
+ readonly rank: number,
readonly dimensions: ReadonlyArray<number>,
readonly axisOrderSlowToFast: ReadonlyArray<number>,
create(array?: ArrayCtor): Tensor,
@@ -19,7 +20,6 @@ namespace Tensor {
interface Layout {
dimensions: number[],
- // slowest to fastest changing
axisOrderSlowToFast: number[],
axisOrderFastToSlow: number[],
accessDimensions: number[],
@@ -40,7 +40,7 @@ namespace Tensor {
export function Space(dimensions: number[], axisOrderSlowToFast: number[], ctor?: ArrayCtor): Space {
const layout = Layout(dimensions, axisOrderSlowToFast, ctor);
const { get, set } = accessors(layout);
- return { dimensions: [...dimensions], axisOrderSlowToFast: [...axisOrderSlowToFast], create: creator(layout), get, set };
+ return { rank: dimensions.length, dimensions, axisOrderSlowToFast, create: creator(layout), get, set };
}
export function Vector(d: number, ctor?: ArrayCtor) { return Space([d], [0], ctor); }
diff --git a/src/mol-io/reader/cif/data-model.ts b/src/mol-io/reader/cif/data-model.ts
index 6f1422206212a952051022a3b12620551e516a2d..75805537f0a87a192fb3d14df5d06965675e6922 100644
--- a/src/mol-io/reader/cif/data-model.ts
+++ b/src/mol-io/reader/cif/data-model.ts
@@ -5,6 +5,7 @@
*/
import { Column } from 'mol-base/collections/database'
+import Tensor from 'mol-base/math/tensor'
export interface File {
readonly name?: string,
@@ -76,24 +77,32 @@ export interface Field {
toFloatArray(params?: Column.ToArrayParams<number>): ReadonlyArray<number>
}
-export function getMatrix(category: Category, field: string, rows: number, cols: number, row: number) {
- const ret: number[][] = [];
- for (let i = 0; i < rows; i++) {
- const r: number[] = [];
- for (let j = 0; j < cols; j++) {
- const f = category.getField(`${field}[${i + 1}][${j + 1}]`);
- r[j] = f ? f.float(row) : 0.0;
+export function getTensor(category: Category, field: string, space: Tensor.Space, row: number): Tensor {
+ const ret = space.create();
+ if (space.rank === 1) {
+ const rows = space.dimensions[0];
+ for (let i = 0; i < rows; i++) {
+ const f = category.getField(`${field}[${i + 1}]`);
+ space.set(ret, i, !!f ? f.float(row) : 0.0);
}
- ret[i] = r;
- }
- return ret;
-}
-
-export function getVector(category: Category, field: string, rows: number, row: number) {
- const ret: number[] = [];
- for (let i = 0; i < rows; i++) {
- const f = category.getField(`${field}[${i + 1}]`);
- ret[i] = f ? f.float(row) : 0.0;
- }
+ } else if (space.rank === 2) {
+ const rows = space.dimensions[0], cols = space.dimensions[1];
+ for (let i = 0; i < rows; i++) {
+ for (let j = 0; j < cols; j++) {
+ const f = category.getField(`${field}[${i + 1}][${j + 1}]`);
+ space.set(ret, i, j, !!f ? f.float(row) : 0.0);
+ }
+ }
+ } else if (space.rank === 3) {
+ const d0 = space.dimensions[0], d1 = space.dimensions[1], d2 = space.dimensions[2];
+ 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}]`);
+ space.set(ret, i, j, k, !!f ? f.float(row) : 0.0);
+ }
+ }
+ }
+ } else throw new Error('Tensors with rank > 3 currently not supported.');
return ret;
}
\ No newline at end of file
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index 3c8c4021434c60aca2d9bf70da56a47a35c2be1a..441f4082c7d1c13b06604092f792c940cd12f2ad 100644
--- a/src/mol-io/reader/cif/schema.ts
+++ b/src/mol-io/reader/cif/schema.ts
@@ -22,14 +22,9 @@ function getColumnCtor(t: Column.Schema): ColumnCtor {
case 'str': return (f, c, k) => createColumn(Column.Type.str, f, f.str, f.toStringArray);
case 'int': return (f, c, k) => createColumn(Column.Type.int, f, f.int, f.toIntArray);
case 'float': return (f, c, k) => createColumn(Column.Type.float, f, f.float, f.toFloatArray);
- case 'vector': return (f, c, k) => {
- const dim = t.dim;
- const value = (row: number) => Data.getVector(c, k, dim, row);
- return createColumn(t, f, value, params => ColumnHelpers.createAndFillArray(f.rowCount, value, params));
- }
- case 'matrix': return (f, c, k) => {
- const rows = t.rows, cols = t.cols;
- const value = (row: number) => Data.getMatrix(c, k, rows, cols, row);
+ case 'tensor': return (f, c, k) => {
+ const space = t.space;
+ const value = (row: number) => Data.getTensor(c, k, space, row);
return createColumn(t, f, value, params => ColumnHelpers.createAndFillArray(f.rowCount, value, params));
}
}