From eea59e9e75051c391c1c998d13c0c2d3d6a918a1 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 9 Apr 2018 18:47:18 -0700
Subject: [PATCH] wip, point repr
---
src/apps/render-test/state.ts | 33 ++++-----
src/mol-geo/representation/structure/point.ts | 67 +++++++++++++++++++
2 files changed, 84 insertions(+), 16 deletions(-)
create mode 100644 src/mol-geo/representation/structure/point.ts
diff --git a/src/apps/render-test/state.ts b/src/apps/render-test/state.ts
index d0304a83d..0a65fce44 100644
--- a/src/apps/render-test/state.ts
+++ b/src/apps/render-test/state.ts
@@ -12,14 +12,20 @@ import { createColorTexture } from 'mol-gl/util';
import Icosahedron from 'mol-geo/primitive/icosahedron'
import Box from 'mol-geo/primitive/box'
import Spacefill from 'mol-geo/representation/structure/spacefill'
+import Point from 'mol-geo/representation/structure/point'
import CIF from 'mol-io/reader/cif'
import { Run, Progress } from 'mol-task'
-import { ElementSet, Structure } from 'mol-model/structure'
+import { Structure } from 'mol-model/structure'
+
+function log(progress: Progress) {
+ const p = progress.root.progress
+ console.log(`${p.message} ${(p.current/p.max*100).toFixed(2)}%`)
+}
async function parseCif(data: string|Uint8Array) {
const comp = CIF.parse(data)
- const parsed = await Run(comp);
+ const parsed = await Run(comp, log, 100);
if (parsed.isError) throw parsed;
return parsed
}
@@ -117,21 +123,16 @@ export default class State {
const mesh2 = makeCubesMesh();
renderer.add(mesh2)
- function log(progress: Progress) {
- const p = progress.root.progress
- console.log(`${p.message} ${(p.current/p.max*100).toFixed(2)}%`)
- }
+ const structures = await getPdb('4v99')
+ const { elements, units } = structures[0];
- async function createSpacefills (structure: Structure) {
- const spacefills: RenderObject[] = []
- const { elements, units } = structure;
- const spacefill = Spacefill()
- spacefills.push(...await Run(spacefill.create(units, elements), log, 100))
- return spacefills
- }
- const structures = await getPdb('3pqr')
- const spacefills = await createSpacefills(structures[0])
- spacefills.forEach(renderer.add)
+ // const spacefill = Spacefill()
+ // const spacefills = await Run(spacefill.create(units, elements), log, 100)
+ // spacefills.forEach(renderer.add)
+
+ const point = Point()
+ const points = await Run(point.create(units, elements), log, 100)
+ points.forEach(renderer.add)
renderer.frame()
}
diff --git a/src/mol-geo/representation/structure/point.ts b/src/mol-geo/representation/structure/point.ts
new file mode 100644
index 000000000..af7aaa05c
--- /dev/null
+++ b/src/mol-geo/representation/structure/point.ts
@@ -0,0 +1,67 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ValueCell } from 'mol-util/value-cell'
+
+import { createRenderObject, RenderObject } from 'mol-gl/renderer'
+import { createColorTexture } from 'mol-gl/util';
+import { Mat4 } from 'mol-math/linear-algebra'
+import { OrderedSet } from 'mol-data/int'
+import { ChunkedArray } from 'mol-data/util';
+import { Element, Unit, ElementSet } from 'mol-model/structure';
+import P from 'mol-model/structure/query/properties';
+import { RepresentationProps, UnitRepresentation } from './index';
+import { Task } from 'mol-task'
+
+
+export default function Point(): UnitRepresentation {
+ const renderObjects: RenderObject[] = []
+ const vertices = ChunkedArray.create(Float32Array, 3, 1024, 2048);
+
+ return {
+ create: (units: ReadonlyArray<Unit>, elements: ElementSet, props: Partial<RepresentationProps> = {}) => Task.create('Spacefill', async ctx => {
+ const l = Element.Location();
+
+ const unitIds = ElementSet.unitIds(elements);
+ for (let i = 0, _i = unitIds.length; i < _i; i++) {
+ const unitId = unitIds[i];
+ const unit = units[unitId];
+ const elementGroup = ElementSet.unitGetByIndex(elements, i);
+ const elementCount = OrderedSet.size(elementGroup.elements)
+ l.unit = unit;
+
+ for (let i = 0; i < elementCount; i++) {
+ l.element = OrderedSet.getAt(elementGroup.elements, i)
+ ChunkedArray.add3(vertices, P.atom.x(l), P.atom.y(l), P.atom.z(l))
+ }
+
+ if (i % 10 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Point', current: i, max: _i });
+ }
+ }
+
+ const transformArray = new Float32Array(32)
+ const m4 = Mat4.identity()
+ Mat4.toArray(m4, transformArray, 0)
+
+ const color = ValueCell.create(createColorTexture(1))
+ color.ref.value.set([ 0, 0, 255 ])
+
+ const points = createRenderObject('point', {
+ position: ValueCell.create(ChunkedArray.compact(vertices, true) as Float32Array),
+ color,
+ transform: ValueCell.create(transformArray),
+
+ instanceCount: transformArray.length / 16,
+ positionCount: vertices.elementCount
+ }, {})
+ renderObjects.push(points)
+
+ return renderObjects
+ }),
+ update: (props: RepresentationProps) => false
+ }
+}
--
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