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Custom shapes are back
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@ceriottm
ceriottm committed Sep 18, 2023
1 parent 8716da4 commit 70c1ff3
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Showing 4 changed files with 139 additions and 28 deletions.
88 changes: 87 additions & 1 deletion python/examples/shapes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,92 @@
frames=alphaml,
properties=chemiscope.extract_properties(alphaml, only=["alpha", "alpha-vec"]),
shapes={
"cube_smooth": dict(
kind="custom",
parameters={
"global": {
"vertices": [
[0, 0, 0],
[1, 0, 0],
[0, 1, 0],
[1, 1, 0],
[0, 0, 1],
[1, 0, 1],
[0, 1, 1],
[1, 1, 1],
],
"simplices": [
[0, 2, 1],
[1, 2, 3],
[4, 6, 5],
[5, 6, 7],
[0, 1, 4],
[0, 4, 2],
[1, 3, 5],
[2, 6, 3],
[1, 5, 4],
[2, 4, 6],
[3, 7, 5],
[3, 6, 7],
],
},
"structure": [
{"position": [0, 4, 0], "color": 0xFF0000},
{"position": [3, 2, 1], "color": 0x00FF00},
],
},
),
"cube": dict(
kind="custom",
parameters={
"global": {
"vertices": [
[0, 0, 0],
[0, 1, 0],
[1, 1, 0],
[1, 0, 0],
[0, 0, 0],
[0, 0, 1],
[0, 1, 1],
[0, 1, 0],
[0, 1, 0],
[0, 1, 1],
[1, 1, 1],
[1, 1, 0],
[1, 1, 0],
[1, 1, 1],
[1, 0, 1],
[1, 0, 0],
[1, 0, 0],
[1, 0, 1],
[0, 0, 1],
[0, 0, 0],
[0, 0, 1],
[1, 0, 1],
[1, 1, 1],
[0, 1, 1],
],
"simplices": [
[0, 1, 2],
[2, 3, 0],
[4, 5, 6],
[6, 7, 4],
[8, 9, 10],
[10, 11, 8],
[12, 13, 14],
[14, 15, 12],
[16, 17, 18],
[18, 19, 16],
[20, 21, 22],
[22, 23, 20],
],
},
"structure": [
{"position": [0, 4, 0], "color": 0xFF0000},
{"position": [3, 2, 1], "color": 0x00FF00},
],
},
),
"structure_shape": dict(
kind="sphere",
parameters={
Expand Down Expand Up @@ -64,7 +150,7 @@
{
"spaceFilling": False,
"atomLabels": False,
"shape": "structure_shape",
"shape": "cube",
"axes": "off",
"keepOrientation": False,
"playbackDelay": 700,
Expand Down
32 changes: 18 additions & 14 deletions python/tests/shapes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ def test_custom_shapes(self):
numbers=[1, 1, 1], positions=[[0, 0, 0], [1, 1, 1], [2, 2, 5]]
)

#TODO re-enable after having fixed custom shapes
# TODO re-enable after having fixed custom shapes
"""
"cubes": [
[
Expand All @@ -59,21 +59,25 @@ def test_custom_shapes(self):
},
],
],"""
shapes = {
shapes = {
"spheres_structure": {
"kind" : "sphere",
"parameters" : {
"global" : {"radius": 0.1},
"structure" : [ {"position" : [1, 2, 3]} ],
}
"kind": "sphere",
"parameters": {
"global": {"radius": 0.1},
"structure": [{"position": [1, 2, 3]}],
},
},
"ellipsoids_atoms": {
"kind": "ellipsoid",
"parameters": {
"global": {"semiaxes": [0.3, 0.2, 0.1]},
"atom": [
{},
{"semiaxes": [0.1, 0.2, 0.3]},
{"orientation": [0.2, 0.3, 0.4, 1]},
],
},
},
"ellipsoids_atoms" : {
"kind" : "ellipsoid",
"parameters" : {
"global" : {"semiaxes": [0.3, 0.2, 0.1]},
"atom" : [ {}, {"semiaxes": [0.1, 0.2, 0.3]}, {"orientation": [0.2,0.3,0.4,1]}],
}
}
}

data = chemiscope.create_input(frames=[frame], shapes=shapes)
Expand Down
34 changes: 21 additions & 13 deletions src/structure/shapes.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -60,15 +60,17 @@ export interface EllipsoidParameters extends BaseShapeParameters<EllipsoidData>
// Interface for polytope data, where
// orientation is stored in the (w, x, y, z) convention
// and simplices refers to the indices of the facets
export interface CustomShapeData {
kind: 'custom';
export interface CustomShapeData extends BaseShapeData {
vertices: [number, number, number][];
simplices: [number, number, number][];
orientation?: [number, number, number, number];
}

export type ShapeData = SphereData | EllipsoidData; // | CustomShapeData;
export type ShapeParameters = SphereParameters | EllipsoidParameters;
export interface CustomShapeParameters extends BaseShapeParameters<CustomShapeData> {
kind: 'custom';
}

export type ShapeData = SphereData | EllipsoidData | CustomShapeData;
export type ShapeParameters = SphereParameters | EllipsoidParameters | CustomShapeParameters;

function addXYZ(a: XYZ, b: XYZ): XYZ {
return { x: a.x + b.x, y: a.y + b.y, z: a.z + b.z };
Expand Down Expand Up @@ -335,12 +337,16 @@ export class Ellipsoid extends Shape {
vertices.push(newVertex);

// the normal to the ellipsoid surface is best computed in the original
// coordinate system, and then rotated in place
const newNormal: XYZ = rotateAndPlace({
x: v.x / Math.pow(this.semiaxes[0], 2.0),
y: v.y / Math.pow(this.semiaxes[1], 2.0),
z: v.z / Math.pow(this.semiaxes[2], 2.0),
}, this.orientation, {x:0, y:0, z:0});
// coordinate system, and then rotated in place
const newNormal: XYZ = rotateAndPlace(
{
x: v.x / Math.pow(this.semiaxes[0], 2.0),
y: v.y / Math.pow(this.semiaxes[1], 2.0),
z: v.z / Math.pow(this.semiaxes[2], 2.0),
},
this.orientation,
{ x: 0, y: 0, z: 0 }
);

normals.push(newNormal);
}
Expand All @@ -357,8 +363,10 @@ export class CustomShape extends Shape {
public vertices: XYZ[];
public simplices: [number, number, number][];

constructor(position: [number, number, number] = [0, 0, 0], data: CustomShapeData) {
super({}); //position, data.orientation);
constructor(data: Partial<CustomShapeData>) {
super(data);
assert(data.vertices);
assert(data.simplices);

this.vertices = [];
for (const v of data.vertices) {
Expand Down
13 changes: 13 additions & 0 deletions src/structure/viewer.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -990,6 +990,12 @@ export class MoleculeViewer {
this._viewer.addCustom(
shape.outputTo3Dmol(shape_data.color || 0xffffff)
);
} else {
assert(current_shape.kind === 'custom');
const shape = new CustomShape(shape_data);
this._viewer.addCustom(
shape.outputTo3Dmol(shape_data.color || 0xffffff)
);
}
/*
if (current_shape[i].kind === 'ellipsoid') {
Expand Down Expand Up @@ -1026,6 +1032,13 @@ export class MoleculeViewer {
this._viewer.addCustom(
shape.outputTo3Dmol(shape_data.color || 0xffffff)
);
} else {
assert(current_shape.kind === 'custom');
console.log(shape_data);

Check failure on line 1037 in src/structure/viewer.ts

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GitHub Actions / npm-test (18.x) 

Unexpected console statement
const shape = new CustomShape(shape_data);
this._viewer.addCustom(
shape.outputTo3Dmol(shape_data.color || 0xffffff)
);
}
}
}
Expand Down

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