From a61f3c401df03584fc85ce6b5518fc5ce50953e6 Mon Sep 17 00:00:00 2001
From: Michele Ceriotti <michele.ceriotti@gmail.com>
Date: Wed, 20 Sep 2023 14:06:54 -0700
Subject: [PATCH] Few tweaks - mostly scale as a global parameter

---
 src/structure/shapes.ts | 20 ++++++++++++--------
 src/structure/viewer.ts | 22 ----------------------
 2 files changed, 12 insertions(+), 30 deletions(-)

diff --git a/src/structure/shapes.ts b/src/structure/shapes.ts
index 91e9b8adf..31357b931 100644
--- a/src/structure/shapes.ts
+++ b/src/structure/shapes.ts
@@ -27,6 +27,7 @@ export interface XYZ {
 export interface BaseShapeData {
     position: [number, number, number];
     orientation?: [number, number, number, number];
+    scale?: number;
     color?: ColorSpec;
 }
 
@@ -158,6 +159,8 @@ export class Shape {
     public position: XYZ;
     /// orientation of the particle
     public orientation: Quaternion;
+    /// scaling factor
+    public scale: number;
 
     // orientation is passed to 3dmol in the (x, y, z, w) convention
     constructor(data: Partial<SphereData>) {
@@ -165,6 +168,7 @@ export class Shape {
         this.orientation = new Quaternion(qx, qy, qz, qw);
         const [x, y, z] = data.position || [0, 0, 0];
         this.position = { x, y, z };
+        this.scale = data.scale || 1.0;
     }
 
     // disabling eslint because it complains parameters is never used
@@ -265,8 +269,8 @@ export class Sphere extends Shape {
     public radius: number;
 
     constructor(data: Partial<SphereData>) {
-        super({ position: data.position });
-        this.radius = data.radius || 1.0;
+        super(data);
+        this.radius = (data.radius || 1.0) * this.scale;
     }
 
     public static validateParameters(parameters: Record<string, unknown>): string {
@@ -321,7 +325,7 @@ export class Ellipsoid extends Shape {
     constructor(data: Partial<EllipsoidData>) {
         super(data);
         assert(data.semiaxes);
-        this.semiaxes = data.semiaxes;
+        this.semiaxes = [ this.scale * data.semiaxes[0], this.scale * data.semiaxes[1], this.scale * data.semiaxes[2] ];
     }
 
     public static validateParameters(parameters: Record<string, unknown>): string {
@@ -481,10 +485,10 @@ export class Arrow extends Shape {
     constructor(data: Partial<ArrowData>) {
         super(data);
         assert(data.vector);
-        this.vector = data.vector;
-        this.base_radius = data.base_radius || 0.1;
-        this.head_radius = data.head_radius || 0.15;
-        this.head_length = data.head_length || 0.2;
+        this.vector = [this.scale*data.vector[0], this.scale*data.vector[1], this.scale*data.vector[2] ];
+        this.base_radius = this.scale*(data.base_radius || 0.1);
+        this.head_radius = this.scale*(data.head_radius || 0.15);
+        this.head_length = this.scale*(data.head_length || 0.2);
     }
 
     public static validateParameters(parameters: Record<string, unknown>): string {
@@ -548,7 +552,7 @@ export class CustomShape extends Shape {
 
         this.vertices = [];
         for (const v of data.vertices) {
-            this.vertices.push({ x: v[0], y: v[1], z: v[2] });
+            this.vertices.push({ x: v[0]*this.scale, y: v[1]*this.scale, z: v[2]*this.scale });
         }
         this.simplices = data.simplices;
     }
diff --git a/src/structure/viewer.ts b/src/structure/viewer.ts
index 6accf4987..a6d3f70e8 100644
--- a/src/structure/viewer.ts
+++ b/src/structure/viewer.ts
@@ -1003,28 +1003,6 @@ export class MoleculeViewer {
                                         shape.outputTo3Dmol(shape_data.color || 0xffffff)
                                     );
                                 }
-                                /*
-                                if (current_shape[i].kind === 'ellipsoid') {
-                                    const data = current_shape[i] as unknown as EllipsoidData;
-                                    const shape = new Ellipsoid(position, data);
-                                    this._viewer.addCustom(
-                                        shape.outputTo3Dmol($3Dmol.elementColors.Jmol[name] || 0x000000)
-                                    );
-                                } else if (current_shape[i].kind === 'custom') {
-                                    const data = current_shape[i] as unknown as CustomShapeData;
-                                    const shape = new CustomShape(position, data);
-                                    this._viewer.addCustom(
-                                        shape.outputTo3Dmol($3Dmol.elementColors.Jmol[name] || 0x000000)
-                                    );
-                                } else {
-                                    assert(current_shape[i].kind === 'sphere');
-                                    const data = current_shape[i] as unknown as SphereData;
-                                    const shape = new Sphere(position, data);
-                                    this._viewer.addCustom(
-                                        shape.outputTo3Dmol($3Dmol.elementColors.Jmol[name] || 0x000000)
-                                    );
-                                }
-                                */
                             }
                         } else {
                             // the shape is defined only at the structure level