added coordinates support to model

src/mol-math/geometry/spacegroup/cell.ts

@@ -0,0 +1,23 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Vec3 } from '../../linear-algebra'
+
+export { Cell }
+
+interface Cell {
+    readonly size: Vec3
+    readonly anglesInRadians: Vec3
+}
+
+function Cell() {
+    return Cell.empty()
+}
+
+namespace Cell {
+    export function create(size: Vec3, anglesInRadians: Vec3): Cell { return { size, anglesInRadians } }
+    export function empty(): Cell { return { size: Vec3(), anglesInRadians: Vec3() } }
+}

src/mol-model/structure.ts

@@ -4,6 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
+export * from './structure/coordinates'
 export * from './structure/model'
 export * from './structure/structure'
 export * from './structure/query'

src/mol-model/structure/coordinates.ts

@@ -0,0 +1,7 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export * from './coordinates/coordinates'

src/mol-model/structure/coordinates/coordinates.ts

@@ -0,0 +1,127 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { UUID } from '../../../mol-util';
+import { Cell } from '../../../mol-math/geometry/spacegroup/cell';
+import { Model } from '../model';
+import { AtomicConformation } from '../model/properties/atomic';
+import { CustomProperties } from '../../structure';
+import { Mutable } from '../../../mol-util/type-helpers';
+import { Column } from '../../../mol-data/db';
+
+export interface Frame {
+    readonly elementCount: number
+    readonly cell: Cell
+    readonly time: Time
+
+    // positions
+    readonly x: ArrayLike<number>
+    readonly y: ArrayLike<number>
+    readonly z: ArrayLike<number>
+
+    // optional velocities
+    readonly velocities?: {
+        readonly vx: ArrayLike<number>
+        readonly vy: ArrayLike<number>
+        readonly vz: ArrayLike<number>
+    }
+
+    // optional forces
+    readonly forces?: {
+        readonly fx: ArrayLike<number>
+        readonly fy: ArrayLike<number>
+        readonly fz: ArrayLike<number>
+    }
+}
+
+//
+
+export { Time }
+
+interface Time {
+    value: number
+    unit: Time.Unit
+}
+
+function Time(value: number, unit: Time.Unit) {
+    return { value, unit }
+}
+
+namespace Time {
+    export type Unit = 'ps' | 'step'
+
+    // TODO: conversion utilities
+}
+
+//
+
+export { Coordinates }
+
+interface Coordinates {
+    readonly id: UUID
+
+    readonly frames: Frame[]
+
+    /** Number of elements (e.g. atoms) in frames */
+    readonly elementCount: number
+
+    readonly hasVelocities: boolean
+    readonly hasForces: boolean
+
+    readonly deltaTime: Time
+    readonly timeOffset: Time
+}
+
+namespace Coordinates {
+    export function create(frames: Frame[], deltaTime: Time, timeOffset: Time): Coordinates {
+        const elementCount = frames[0].elementCount
+        const hasVelocities = !!frames[0].velocities
+        const hasForces = !!frames[0].forces
+
+        return {
+            id: UUID.create22(),
+            frames,
+            elementCount,
+            hasVelocities,
+            hasForces,
+            deltaTime,
+            timeOffset
+        }
+    }
+}
+
+function getAtomicConformation(frame: Frame, atomId: Column<number>): AtomicConformation {
+    return {
+        id: UUID.create22(),
+        atomId,
+        occupancy: Column.ofConst(1, frame.elementCount, Column.Schema.int),
+        B_iso_or_equiv: Column.ofConst(0, frame.elementCount, Column.Schema.float),
+        x: frame.x,
+        y: frame.y,
+        z: frame.z,
+    }
+}
+
+export function trajectoryFromModelAndCoordinates(model: Model, coordinates: Coordinates): Model.Trajectory {
+    const trajectory: Mutable<Model.Trajectory> = []
+    const { frames } = coordinates
+    for (let i = 0, il = frames.length; i < il; ++i) {
+        const f = frames[i]
+        const m = {
+            ...model,
+            id: UUID.create22(),
+            modelNum: i,
+            atomicConformation: getAtomicConformation(f, model.atomicConformation.atomId),
+            // TODO: add support for supplying sphere and gaussian coordinates in addition to atomic coordinates
+            // coarseConformation: coarse.conformation,
+            customProperties: new CustomProperties(),
+            _staticPropertyData: Object.create(null),
+            _dynamicPropertyData: Object.create(null)
+        }
+        trajectory.push(m)
+    }
+    return trajectory
+}

src/mol-model/structure/model/model.ts

@@ -31,7 +31,12 @@ export interface Model extends Readonly<{
     /** the name of the entry/file/collection the model is part of */
     entry: string,
 
-    /** for IHM, corresponds to ihm_model_list.model_id */
+    /**
+     * corresponds to
+     * - for IHM: `ihm_model_list.model_id`
+     * - for standard mmCIF: `atom_site.pdbx_PDB_model_num`
+     * - for models from coordinates: frame index
+     */
     modelNum: number,
 
     sourceData: ModelFormat,