From af1e06203bc7562988b1c6346a1ff84e41f3389f Mon Sep 17 00:00:00 2001
From: Ke Ma <92659167+MarkMa2003@users.noreply.github.com>
Date: Sun, 5 Feb 2023 11:27:25 -0800
Subject: [PATCH] Dev focus pca (#624)
* viewer camera change based on Pca
* minor code refactor
* update author
* Update src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>
* Update src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>
* Update src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>
* Update src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>
* Update src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>
* Update src/mol-plugin-ui/structure/components.tsx
Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>
* Update src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>
* revise
* deepclone
* chunked-array
---------
Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>
---
CHANGELOG.md | 3 +
package.json | 1 +
src/mol-plugin-state/manager/camera.ts | 14 +-
.../focus-camera/focus-first-residue.ts | 147 ++++++++++++++++++
src/mol-plugin-ui/structure/components.tsx | 6 +-
5 files changed, 164 insertions(+), 7 deletions(-)
create mode 100644 src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5792f31a7..039025ad5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,9 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
+- Change the position of the camera based on the PCA of the structure and the following rules.
+ - The first residue should be in first quadrant if there is only one chain
+ - The average position of the residues of the first chain should be in the first residue if there are more than one chain.
- Add `HeadlessPluginContext` and `HeadlessScreenshotHelper` to be used in Node.js
- Add example `image-renderer`
- Fix wrong offset when rendering text with orthographic projection
diff --git a/package.json b/package.json
index 5bc2612c0..cffde8a2d 100644
--- a/package.json
+++ b/package.json
@@ -93,6 +93,7 @@
"Adam Midlik <midlik@gmail.com>",
"Koya Sakuma <koya.sakuma.work@gmail.com>",
"Gianluca Tomasello <giagitom@gmail.com>",
+ "Ke Ma <mark.ma@rcsb.org>",
"Jason Pattle <jpattle@exscientia.co.uk>",
"David Williams <dwilliams@nobiastx.com>"
],
diff --git a/src/mol-plugin-state/manager/camera.ts b/src/mol-plugin-state/manager/camera.ts
index 10f5583e7..5a3cfa940 100644
--- a/src/mol-plugin-state/manager/camera.ts
+++ b/src/mol-plugin-state/manager/camera.ts
@@ -3,6 +3,7 @@
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ke Ma <mark.ma@rcsb.org>
*/
import { Sphere3D } from '../../mol-math/geometry';
@@ -13,6 +14,8 @@ import { Loci } from '../../mol-model/loci';
import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
import { GraphicsRenderObject } from '../../mol-gl/render-object';
import { StructureElement } from '../../mol-model/structure';
+import { Vec3 } from '../../mol-math/linear-algebra/3d/vec3';
+import { pcaFocus } from './focus-camera/focus-first-residue';
// TODO: make this customizable somewhere?
const DefaultCameraFocusOptions = {
@@ -84,7 +87,7 @@ export class CameraManager {
}
}
- focusSpheres<T>(xs: ReadonlyArray<T>, sphere: (t: T) => Sphere3D | undefined, options?: Partial<CameraFocusOptions>) {
+ focusSpheres<T>(xs: ReadonlyArray<T>, sphere: (t: T) => Sphere3D | undefined, options?: Partial<CameraFocusOptions> & { principalAxes?: PrincipalAxes, positionToFlip?: Vec3 }) {
const spheres = [];
for (const x of xs) {
@@ -106,7 +109,7 @@ export class CameraManager {
this.focusSphere(this.boundaryHelper.getSphere(), options);
}
- focusSphere(sphere: Sphere3D, options?: Partial<CameraFocusOptions> & { principalAxes?: PrincipalAxes }) {
+ focusSphere(sphere: Sphere3D, options?: Partial<CameraFocusOptions> & { principalAxes?: PrincipalAxes, positionToFlip?: Vec3 }) {
const { canvas3d } = this.plugin;
if (!canvas3d) return;
@@ -114,9 +117,10 @@ export class CameraManager {
const radius = Math.max(sphere.radius + extraRadius, minRadius);
if (options?.principalAxes) {
- const { origin, dirA, dirC } = options?.principalAxes.boxAxes;
- const snapshot = canvas3d.camera.getFocus(origin, radius, dirA, dirC);
- canvas3d.requestCameraReset({ durationMs, snapshot });
+ this.plugin.canvas3d?.camera.setState(Camera.createDefaultSnapshot());
+ const { origin, dirA, dirC } = pcaFocus(this.plugin, options);
+ const snapshot = this.plugin.canvas3d?.camera.getFocus(origin, radius, dirA, dirC);
+ this.plugin.canvas3d?.requestCameraReset({ durationMs, snapshot });
} else {
const snapshot = canvas3d.camera.getFocus(sphere.center, radius);
canvas3d.requestCameraReset({ durationMs, snapshot });
diff --git a/src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts b/src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
new file mode 100644
index 000000000..545d9b76b
--- /dev/null
+++ b/src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
@@ -0,0 +1,147 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Ke Ma <mark.ma@rcsb.org>
+ */
+import { Structure } from '../../../mol-model/structure';
+import { Vec3 } from '../../..//mol-math/linear-algebra/3d/vec3';
+import { PluginContext } from '../../../mol-plugin/context';
+import { CameraFocusOptions } from '../camera';
+import { PrincipalAxes } from '../../../mol-math/linear-algebra/matrix/principal-axes';
+import { StructureComponentRef } from '../structure/hierarchy-state';
+import { deepClone } from '../../../mol-util/object';
+import { ChunkedArray } from '../../../mol-data/util/chunked-array';
+
+
+export function getPolymerPositions(polymerStructure: Structure): Float32Array {
+ const tmpMatrix = Vec3.zero();
+ const cAdd3 = ChunkedArray.add3;
+ const positions = ChunkedArray.create(Float32Array, 3, 1024, polymerStructure.atomicResidueCount);
+ for (let i = 0; i < polymerStructure.units.length; i++) {
+ const unit = polymerStructure.units[i];
+ const { polymerElements } = unit.props;
+ const readPosition = unit.conformation.position;
+ if (polymerElements) {
+ for (let j = 0; j < polymerElements.length; j++) {
+ readPosition(polymerElements[j], tmpMatrix);
+ cAdd3(positions, tmpMatrix[0], tmpMatrix[1], tmpMatrix[2]);
+ }
+ }
+ }
+ return ChunkedArray.compact(positions) as Float32Array;
+}
+export function calculateDisplacement(position: Vec3, origin: Vec3, normalDir: Vec3) {
+ const A = normalDir[0];
+ const B = normalDir[1];
+ const C = normalDir[2];
+ const D = -A * origin[0] - B * origin[1] - C * origin[2];
+
+ const x = position[0];
+ const y = position[1];
+ const z = position[2];
+
+ const displacement = (A * x + B * y + C * z + D) / Math.sqrt(A * A + B * B + C * C);
+ return displacement;
+}
+
+export function getAxesToFlip(position: Vec3, origin: Vec3, up: Vec3, normalDir: Vec3) {
+ const toYAxis = calculateDisplacement(position, origin, normalDir);
+ const toXAxis = calculateDisplacement(position, origin, up);
+ const axes: ('aroundX' | 'aroundY')[] = [];
+ if (toYAxis < 0) axes.push('aroundY');
+ if (toXAxis < 0) axes.push('aroundX');
+ return axes;
+}
+
+export function getFirstResidueOrAveragePosition(structure: Structure, caPositions: Float32Array): Vec3 {
+ if (structure.units.length === 1) {
+ // if only one chain => first residue coordinates
+ return Vec3.create(caPositions[0], caPositions[1], caPositions[2]);
+ } else {
+ // if more than one chain => average of coordinates of the first chain
+ const tmpMatrixPos = Vec3.zero();
+ const atomIndices = structure.units[0].props.polymerElements;
+ const firstChainPositions = [];
+ if (atomIndices) {
+ for (let i = 0; i < atomIndices.length; i++) {
+ const coordinates = structure.units[0].conformation.position(atomIndices[i], tmpMatrixPos);
+ for (let j = 0; j < coordinates.length; j++) {
+ firstChainPositions.push(coordinates[j]);
+ }
+ }
+ let sumX = 0;
+ let sumY = 0;
+ let sumZ = 0;
+ for (let i = 0; i < firstChainPositions.length; i += 3) {
+ sumX += firstChainPositions[i];
+ sumY += firstChainPositions[i + 1];
+ sumZ += firstChainPositions[i + 2];
+ }
+ const averagePosition = Vec3.zero();
+ averagePosition[0] = sumX / atomIndices.length;
+ averagePosition[1] = sumY / atomIndices.length;
+ averagePosition[2] = sumZ / atomIndices.length;
+ return averagePosition;
+ } else {
+ return Vec3.create(caPositions[0], caPositions[1], caPositions[2]);
+ }
+ }
+
+}
+
+export function pcaFocus(plugin: PluginContext, options: Partial<CameraFocusOptions> & { principalAxes?: PrincipalAxes, positionToFlip?: Vec3 }) {
+ if (options?.principalAxes) {
+ const { origin, dirA, dirB, dirC } = options.principalAxes.boxAxes;
+ let toFlip: ('aroundX' | 'aroundY')[] = [];
+ if (options.positionToFlip) {
+ toFlip = getAxesToFlip(options.positionToFlip, origin, dirA, dirB);
+ }
+ toFlip.forEach((axis)=>{
+ if (axis === 'aroundY') {
+ Vec3.negate(dirC, dirC);
+ } else if (axis === 'aroundX') {
+ Vec3.negate(dirA, dirA);
+ Vec3.negate(dirC, dirC);
+ }
+ });
+ if (plugin.canvas3d) {
+ const position = Vec3();
+ Vec3.scaleAndAdd(position, position, origin, 100);
+ plugin.canvas3d.camera.setState({ position }, 0);
+ const deltaDistance = Vec3();
+ Vec3.negate(deltaDistance, position);
+ if (Vec3.dot(deltaDistance, dirC) <= 0) {
+ Vec3.negate(plugin.canvas3d.camera.position, position);
+ }
+ const up = Vec3.create(0, 1, 0);
+ if (Vec3.dot(up, dirA) <= 0) {
+ Vec3.negate(plugin.canvas3d?.camera.up, plugin.canvas3d.camera.up);
+ }
+ }
+ return { origin, dirA, dirB, dirC };
+ }
+ return {
+ origin: Vec3.zero(),
+ dirA: Vec3.zero(),
+ dirB: Vec3.zero(),
+ dirC: Vec3.zero()
+ };
+}
+
+export function getPcaTransform(group: StructureComponentRef[]): { principalAxes?: PrincipalAxes, positionToFlip?: Vec3 } | undefined {
+ const polymerStructure = group[0].cell.obj?.data;
+ if (!polymerStructure) {
+ return undefined;
+ }
+ if ('_pcaTransformData' in polymerStructure.currentPropertyData) {
+ return deepClone(polymerStructure.currentPropertyData._pcaTransformData);
+ }
+ if (!polymerStructure.units[0]?.props.polymerElements?.length) {
+ polymerStructure.currentPropertyData._pcaTransformData = undefined;
+ return undefined;
+ }
+ const positions = getPolymerPositions(polymerStructure);
+ const positionToFlip = getFirstResidueOrAveragePosition(polymerStructure, positions);
+ polymerStructure.currentPropertyData._pcaTransformData = { principalAxes: PrincipalAxes.ofPositions(positions), positionToFlip };
+ return deepClone(polymerStructure.currentPropertyData._pcaTransformData);
+}
diff --git a/src/mol-plugin-ui/structure/components.tsx b/src/mol-plugin-ui/structure/components.tsx
index 0454a5772..d15b498e4 100644
--- a/src/mol-plugin-ui/structure/components.tsx
+++ b/src/mol-plugin-ui/structure/components.tsx
@@ -1,12 +1,14 @@
/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 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>
+ * @author Ke Ma <mark.ma@rcsb.org>
*/
import * as React from 'react';
import { getStructureThemeTypes } from '../../mol-plugin-state/helpers/structure-representation-params';
+import { getPcaTransform } from '../../mol-plugin-state/manager/focus-camera/focus-first-residue';
import { StructureComponentManager } from '../../mol-plugin-state/manager/structure/component';
import { StructureHierarchyManager } from '../../mol-plugin-state/manager/structure/hierarchy';
import { StructureComponentRef, StructureRepresentationRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
@@ -315,7 +317,7 @@ class StructureComponentGroup extends PurePluginUIComponent<{ group: StructureCo
this.plugin.managers.camera.focusSpheres(this.props.group, e => {
if (e.cell.state.isHidden) return;
return e.cell.obj?.data.boundary.sphere;
- });
+ }, getPcaTransform(this.props.group));
};
get reprLabel() {
--
GitLab