From b84bbdace2210ee5b7bb26e021fce61eba2b5aaf Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 5 Feb 2023 15:08:17 -0800
Subject: [PATCH] refactor PCA focus some more
---
CHANGELOG.md | 2 +-
.../focus-camera/focus-first-residue.ts | 100 ++++++++----------
2 files changed, 45 insertions(+), 57 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1ce156f55..77d620edb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,7 @@ 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:
+- Improve Component camera focus 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 quadrant if there is more than one chain
- Add `HeadlessPluginContext` and `HeadlessScreenshotHelper` to be used in Node.js
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
index 529fe6fe3..f96529512 100644
--- a/src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
+++ b/src/mol-plugin-state/manager/focus-camera/focus-first-residue.ts
@@ -1,8 +1,9 @@
/**
- * Copyright (c) 2022-23 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Ke Ma <mark.ma@rcsb.org>
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Structure } from '../../../mol-model/structure';
import { Vec3 } from '../../..//mol-math/linear-algebra/3d/vec3';
@@ -11,23 +12,18 @@ import { PrincipalAxes } from '../../../mol-math/linear-algebra/matrix/principal
import { StructureComponentRef } from '../structure/hierarchy-state';
import { Camera } from '../../../mol-canvas3d/camera';
-
-function getPolymerPositions(structure: Structure): Float32Array | undefined {
+function getPolymerResiduePositions(structure: Structure): Float32Array | undefined {
if (structure.atomicResidueCount === 1) return undefined;
- let polymerElementCount = 0;
- for (const unit of structure.units) {
- polymerElementCount += unit.props.polymerElements?.length ?? 0;
- }
+ const { polymerResidueCount } = structure;
+ if (polymerResidueCount <= 1) return undefined;
- if (polymerElementCount <= 1) return undefined;
-
- const stride = 2 ** Math.max(Math.ceil(Math.log10(polymerElementCount / 1000)), 0);
+ const stride = 2 ** Math.max(Math.ceil(Math.log10(polymerResidueCount / 1000)), 0);
const size = stride === 1
- ? polymerElementCount
- : Math.ceil(polymerElementCount / stride) + structure.units.length;
+ ? polymerResidueCount
+ : Math.ceil(polymerResidueCount / stride) + structure.units.length;
- const tmpPos = Vec3.zero();
+ const tmpPos = Vec3();
const positions = new Float32Array(3 * size);
let o = 0;
for (const unit of structure.units) {
@@ -41,8 +37,8 @@ function getPolymerPositions(structure: Structure): Float32Array | undefined {
}
}
}
- if (positions.length !== o) return positions.slice(0, 3 * o);
- return positions;
+
+ return positions.length !== o ? positions.slice(0, 3 * o) : positions;
}
function calculateDisplacement(position: Vec3, origin: Vec3, normalDir: Vec3) {
@@ -70,21 +66,20 @@ function getAxesToFlip(position: Vec3, origin: Vec3, up: Vec3, normalDir: Vec3)
function getFirstResidueOrAveragePosition(structure: Structure, polymerPositions: Float32Array): Vec3 {
if (structure.units.length === 1) {
- // if only one chain => first residue coordinates
+ // if only one chain, return the coordinates of the first residue
return Vec3.create(polymerPositions[0], polymerPositions[1], polymerPositions[2]);
} else {
- // if more than one chain => average of coordinates of the first chain
- const polymerElements = structure.units.find(u => u.props.polymerElements)?.props.polymerElements;
- if (polymerElements?.length) {
- const pos = Vec3.zero();
- const center = Vec3.zero();
- const { position } = structure.units[0].conformation;
- for (let i = 0; i < polymerElements.length; i++) {
+ // if more than one chain, return average of the coordinates of the first polymer chain
+ const firstPolymerUnit = structure.units.find(u => u.props.polymerElements);
+ if (firstPolymerUnit) {
+ const pos = Vec3();
+ const center = Vec3();
+ const { polymerElements, conformation: { position } } = firstPolymerUnit;
+ for (let i = 0, il = polymerElements.length; i < il; i++) {
position(polymerElements[i], pos);
Vec3.add(center, center, pos);
}
- Vec3.scale(center, center, 1 / polymerElements.length);
- return center;
+ return Vec3.scale(center, center, 1 / polymerElements.length);
} else {
return Vec3.create(polymerPositions[0], polymerPositions[1], polymerPositions[2]);
}
@@ -92,16 +87,16 @@ function getFirstResidueOrAveragePosition(structure: Structure, polymerPositions
}
export function pcaFocus(plugin: PluginContext, radius: number, options: { principalAxes: PrincipalAxes, positionToFlip?: Vec3 }) {
- const { origin, dirB } = options.principalAxes.boxAxes;
- let { dirA: up, dirC: dir } = options.principalAxes.boxAxes;
+ if (!plugin.canvas3d) return;
+
+ const { origin, dirA, dirB, dirC } = options.principalAxes.boxAxes;
+
+ const up = Vec3.clone(dirA);
+ const dir = Vec3.clone(dirC);
if (options.positionToFlip) {
const { aroundX, aroundY } = getAxesToFlip(options.positionToFlip, origin, up, dirB);
- // Clone the up and dir since we will be mutating them below
- up = Vec3.clone(up);
- dir = Vec3.clone(dir);
-
if (aroundX) {
Vec3.negate(dir, dir);
Vec3.negate(up, up);
@@ -111,46 +106,39 @@ export function pcaFocus(plugin: PluginContext, radius: number, options: { princ
}
}
- if (plugin.canvas3d) {
- const position = Vec3();
- // NOTE: the below Vec3.scale is simplification of
- // Vec3.scaleAndAdd(position, position, origin, 100);
- // plugin.canvas3d.camera.setState({ position }, 0);
- // const deltaDistance = Vec3();
- // Vec3.negate(deltaDistance, position);
- // from the original code.
- Vec3.scale(position, origin, -100);
- if (Vec3.dot(position, up) <= 0) {
- Vec3.negate(dir, dir);
- }
- const upY = Vec3.create(0, 1, 0);
- if (Vec3.dot(upY, dir) <= 0) {
- Vec3.negate(up, up);
- }
+ const position = Vec3.scale(Vec3(), origin, -100);
+ if (Vec3.dot(position, up) <= 0) {
+ Vec3.negate(dir, dir);
+ }
+ if (Vec3.dot(Vec3.unitY, dir) <= 0) {
+ Vec3.negate(up, up);
}
- return plugin.canvas3d?.camera.getFocus(origin, radius, up, dir, Camera.createDefaultSnapshot());
+ return plugin.canvas3d.camera.getFocus(origin, radius, up, dir, Camera.createDefaultSnapshot());
}
-export interface PCAFocusInfo {
+interface PcaTransformData {
principalAxes: PrincipalAxes;
positionToFlip: Vec3;
}
-export function getPcaTransform(group: StructureComponentRef[]): PCAFocusInfo | undefined {
+export function getPcaTransform(group: StructureComponentRef[]): PcaTransformData | undefined {
const structure = group[0].cell.obj?.data;
- if (!structure) {
- return undefined;
- }
+ if (!structure) return undefined;
+
if ('_pcaTransformData' in structure.currentPropertyData) {
return structure.currentPropertyData._pcaTransformData;
}
- const positions = getPolymerPositions(structure);
+ const positions = getPolymerResiduePositions(structure);
if (!positions) {
structure.currentPropertyData._pcaTransformData = undefined;
return undefined;
}
const positionToFlip = getFirstResidueOrAveragePosition(structure, positions);
- structure.currentPropertyData._pcaTransformData = { principalAxes: PrincipalAxes.ofPositions(positions), positionToFlip } as PCAFocusInfo;
- return structure.currentPropertyData._pcaTransformData;
+ const pcaTransfromData: PcaTransformData = {
+ principalAxes: PrincipalAxes.ofPositions(positions),
+ positionToFlip
+ };
+ structure.currentPropertyData._pcaTransformData = pcaTransfromData;
+ return pcaTransfromData;
}
--
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