diff --git a/src/apps/render-test/state.ts b/src/apps/render-test/state.ts
index f25b0cd1fd489d2d1b3552b5c4d79456bfd059c6..a5a16bc137c074ba18a348c3a077292466b22cd6 100644
--- a/src/apps/render-test/state.ts
+++ b/src/apps/render-test/state.ts
@@ -40,8 +40,13 @@ export type ColorTheme = keyof typeof ColorTheme
export default class State {
viewer: Viewer
- pdbId = '5ire'
+ pdbId = ''
+ // pdbId = '5ire'
emdId = '8116'
+ // pdbId = '6G1K'
+ // emdId = '4339'
+ // pdbId = '4cup'
+ // emdId = ''
model = new BehaviorSubject<Model | undefined>(undefined)
volume = new BehaviorSubject<Volume | undefined>(undefined)
initialized = new BehaviorSubject<boolean>(false)
@@ -154,7 +159,10 @@ export default class State {
if (this.surfaceRepr) this.viewer.remove(this.surfaceRepr)
this.surfaceRepr = VolumeRepresentation(Surface)
- await Run(this.surfaceRepr.create(v.volume, { isoValue: VolumeIsoValue.relative(v.volume.dataStats, 1.5) }), log, 500)
+ await Run(this.surfaceRepr.create(v.volume, {
+ isoValue: VolumeIsoValue.relative(v.volume.dataStats, 3.0),
+ alpha: 0.3
+ }), log, 500)
viewer.add(this.surfaceRepr)
viewer.requestDraw()
diff --git a/src/mol-geo/representation/volume/surface.ts b/src/mol-geo/representation/volume/surface.ts
index fd22678fe086cd1068ab90e03f9dd0657a0bd77c..4815e8b5c65f48a9cd0045f5678705e64fefd71f 100644
--- a/src/mol-geo/representation/volume/surface.ts
+++ b/src/mol-geo/representation/volume/surface.ts
@@ -61,7 +61,7 @@ export default function Surface(): VolumeElementRepresentation<SurfaceProps> {
position: mesh.vertexBuffer,
normal: mesh.normalBuffer,
id: ValueCell.create(fillSerial(new Float32Array(mesh.vertexCount / 3))),
- color: createUniformColor({ value: 0x999999 }),
+ color: createUniformColor({ value: 0x7ec0ee }),
transform: ValueCell.create(new Float32Array(Mat4.identity())),
index: mesh.indexBuffer,
@@ -70,7 +70,9 @@ export default function Surface(): VolumeElementRepresentation<SurfaceProps> {
elementCount: mesh.triangleCount,
positionCount: mesh.vertexCount / 3,
- flatShaded: true
+ flatShaded: true,
+ doubleSided: true,
+ flipSided: true
})
renderObjects.push(surface)
})
diff --git a/src/mol-geo/util.ts b/src/mol-geo/util.ts
index 615b7c4f5ade78d292705741242ef3553e5009a0..0f417021677d1341368c68c8359b31c70873fe4d 100644
--- a/src/mol-geo/util.ts
+++ b/src/mol-geo/util.ts
@@ -29,8 +29,12 @@ export function transformPositionArray (t: Mat4, array: Helpers.NumberArray, off
}
}
-export function transformDirectionArray (t: Mat3, array: Helpers.NumberArray, offset: number, count: number) {
- // TODO
+export function transformDirectionArray (n: Mat3, array: Helpers.NumberArray, offset: number, count: number) {
+ for (let i = 0, il = count * 3; i < il; i += 3) {
+ Vec3.fromArray(tmpV, array, offset + i)
+ Vec3.transformMat3(tmpV, tmpV, n)
+ Vec3.toArray(tmpV, array, offset + i)
+ }
}
export function setArrayZero(array: Helpers.NumberArray) {
diff --git a/src/mol-gl/renderable/mesh.ts b/src/mol-gl/renderable/mesh.ts
index 7aa2a1eb67715ed4735c5b4a3ac7bc53c6a95c2d..91d3e432921ae39e5083be49cec733dac261beaa 100644
--- a/src/mol-gl/renderable/mesh.ts
+++ b/src/mol-gl/renderable/mesh.ts
@@ -35,12 +35,14 @@ namespace Mesh {
flatShaded?: boolean
doubleSided?: boolean
+ flipSided?: boolean
}
export function create(ctx: Context, props: Props): Renderable<Props> {
const defines = getBaseDefines(props)
if (props.flatShaded) defines.FLAT_SHADED = ''
if (props.doubleSided) defines.DOUBLE_SIDED = ''
+ if (props.flipSided) defines.FLIP_SIDED = ''
const defs: RenderItemProps = {
...getBaseDefs(props),
diff --git a/src/mol-gl/shader-code.ts b/src/mol-gl/shader-code.ts
index 0777c372677928ad9cae4db2a8162b7d001d6b92..ee2779c5d08eb83f0c5f9cead8e5187fdcdf6d7a 100644
--- a/src/mol-gl/shader-code.ts
+++ b/src/mol-gl/shader-code.ts
@@ -24,7 +24,7 @@ type ShaderDefine = (
'UNIFORM_COLOR' | 'ATTRIBUTE_COLOR' | 'INSTANCE_COLOR' | 'ELEMENT_COLOR' | 'ELEMENT_INSTANCE_COLOR' |
'UNIFORM_SIZE' | 'ATTRIBUTE_SIZE' |
'POINT_SIZE_ATTENUATION' |
- 'FLAT_SHADED' | 'DOUBLE_SIDED'
+ 'FLAT_SHADED' | 'DOUBLE_SIDED' | 'FLIP_SIDED'
)
export type ShaderDefines = {
[k in ShaderDefine]?: number|string
diff --git a/src/mol-gl/shader/mesh.frag b/src/mol-gl/shader/mesh.frag
index 088812ec63079cf1aa1f9ef504fa090bc705f0a3..38e1dde57f683a4c0bafadeba55af097a46f3626 100644
--- a/src/mol-gl/shader/mesh.frag
+++ b/src/mol-gl/shader/mesh.frag
@@ -65,6 +65,7 @@ void main() {
vec3 finalColor = material * (diffuse + ambient) + specular;
// gl_FragColor.rgb = N;
+ // gl_FragColor.a = 1.0;
// gl_FragColor.rgb = vec3(1.0, 0.0, 0.0);
gl_FragColor.rgb = finalColor;
gl_FragColor.a = alpha;
diff --git a/src/mol-gl/shader/mesh.vert b/src/mol-gl/shader/mesh.vert
index 1206fda5d3df3444d79569efa04c7d705f19199c..4a8a196ac5324ca0bd41a114549868bd01066ff6 100644
--- a/src/mol-gl/shader/mesh.vert
+++ b/src/mol-gl/shader/mesh.vert
@@ -39,6 +39,10 @@ void main(){
#ifndef FLAT_SHADED
mat3 normalMatrix = transpose(inverse(mat3(modelView)));
- vNormal = normalize(normalMatrix * normal);
+ vec3 transformedNormal = normalize(normalMatrix * normal);
+ #ifdef FLIP_SIDED
+ transformedNormal = -transformedNormal;
+ #endif
+ vNormal = transformedNormal;
#endif
}
\ No newline at end of file
diff --git a/src/mol-math/linear-algebra/3d/mat3.ts b/src/mol-math/linear-algebra/3d/mat3.ts
index 937403309d7dc9d94feb7cd60d102f1e23ddfb1d..bb2d47c5efbd2925ad82157164ccf199c4f54465 100644
--- a/src/mol-math/linear-algebra/3d/mat3.ts
+++ b/src/mol-math/linear-algebra/3d/mat3.ts
@@ -17,6 +17,8 @@
* furnished to do so, subject to the following conditions:
*/
+import { Mat4 } from '../3d'
+
interface Mat3 extends Array<number> { [d: number]: number, '@type': 'mat3', length: 9 }
namespace Mat3 {
@@ -27,6 +29,33 @@ namespace Mat3 {
return ret as any;
}
+ export function identity(): Mat3 {
+ const out = zero();
+ out[0] = 1;
+ out[1] = 0;
+ out[2] = 0;
+ out[3] = 0;
+ out[4] = 1;
+ out[5] = 0;
+ out[6] = 0;
+ out[7] = 0;
+ out[8] = 1;
+ return out;
+ }
+
+ export function setIdentity(mat: Mat3): Mat3 {
+ mat[0] = 1;
+ mat[1] = 0;
+ mat[2] = 0;
+ mat[3] = 0;
+ mat[4] = 1;
+ mat[5] = 0;
+ mat[6] = 0;
+ mat[7] = 0;
+ mat[8] = 1;
+ return mat;
+ }
+
export function toArray(a: Mat3, out: Helpers.NumberArray, offset: number) {
out[offset + 0] = a[0];
out[offset + 1] = a[1];
@@ -37,9 +66,6 @@ namespace Mat3 {
out[offset + 6] = a[6];
out[offset + 7] = a[7];
out[offset + 8] = a[8];
- out[offset + 9] = a[9];
- out[offset + 10] = a[10];
- out[offset + 11] = a[11];
}
export function fromArray(a: Mat3, array: Helpers.NumberArray, offset: number) {
@@ -52,11 +78,107 @@ namespace Mat3 {
a[6] = array[offset + 6]
a[7] = array[offset + 7]
a[8] = array[offset + 8]
- a[9] = array[offset + 9]
- a[10] = array[offset + 10]
- a[11] = array[offset + 11]
return a
}
+
+ /**
+ * Copies the upper-left 3x3 values into the given mat3.
+ */
+ export function fromMat4(out: Mat3, a: Mat4) {
+ out[0] = a[0];
+ out[1] = a[1];
+ out[2] = a[2];
+ out[3] = a[4];
+ out[4] = a[5];
+ out[5] = a[6];
+ out[6] = a[8];
+ out[7] = a[9];
+ out[8] = a[10];
+ return out;
+ }
+
+ /**
+ * Creates a new Mat3 initialized with values from an existing matrix
+ */
+ export function clone(a: Mat3) {
+ return Mat3.copy(Mat3.zero(), a);
+ }
+
+ /**
+ * Copy the values from one Mat3 to another
+ */
+ export function copy(out: Mat3, a: Mat3) {
+ out[0] = a[0];
+ out[1] = a[1];
+ out[2] = a[2];
+ out[3] = a[3];
+ out[4] = a[4];
+ out[5] = a[5];
+ out[6] = a[6];
+ out[7] = a[7];
+ out[8] = a[8];
+ return out;
+ }
+
+ /**
+ * Transpose the values of a Mat3
+ */
+ export function transpose(out: Mat3, a: Mat3) {
+ // If we are transposing ourselves we can skip a few steps but have to cache some values
+ if (out === a) {
+ const a01 = a[1], a02 = a[2], a12 = a[5];
+ out[1] = a[3];
+ out[2] = a[6];
+ out[3] = a01;
+ out[5] = a[7];
+ out[6] = a02;
+ out[7] = a12;
+ } else {
+ out[0] = a[0];
+ out[1] = a[3];
+ out[2] = a[6];
+ out[3] = a[1];
+ out[4] = a[4];
+ out[5] = a[7];
+ out[6] = a[2];
+ out[7] = a[5];
+ out[8] = a[8];
+ }
+ return out;
+ }
+
+ /**
+ * Inverts a Mat3
+ */
+ export function invert(out: Mat3, a: Mat3): Mat3 {
+ const a00 = a[0], a01 = a[1], a02 = a[2];
+ const a10 = a[3], a11 = a[4], a12 = a[5];
+ const a20 = a[6], a21 = a[7], a22 = a[8];
+
+ const b01 = a22 * a11 - a12 * a21;
+ const b11 = -a22 * a10 + a12 * a20;
+ const b21 = a21 * a10 - a11 * a20;
+
+ // Calculate the determinant
+ let det = a00 * b01 + a01 * b11 + a02 * b21;
+
+ if (!det) {
+ console.warn('non-invertible matrix.', a);
+ return out;
+ }
+ det = 1.0 / det;
+
+ out[0] = b01 * det;
+ out[1] = (-a22 * a01 + a02 * a21) * det;
+ out[2] = (a12 * a01 - a02 * a11) * det;
+ out[3] = b11 * det;
+ out[4] = (a22 * a00 - a02 * a20) * det;
+ out[5] = (-a12 * a00 + a02 * a10) * det;
+ out[6] = b21 * det;
+ out[7] = (-a21 * a00 + a01 * a20) * det;
+ out[8] = (a11 * a00 - a01 * a10) * det;
+ return out;
+ }
}
export default Mat3
\ No newline at end of file
diff --git a/src/mol-math/linear-algebra/3d/vec3.ts b/src/mol-math/linear-algebra/3d/vec3.ts
index 7fb5b67350fe47e9c0019fc6a86293b579b81f27..bc44e7e6e7f9a41a855f179f6b8fd4b824c17dfc 100644
--- a/src/mol-math/linear-algebra/3d/vec3.ts
+++ b/src/mol-math/linear-algebra/3d/vec3.ts
@@ -18,7 +18,7 @@
*/
import Mat4 from './mat4';
-import { Quat } from '../3d';
+import { Quat, Mat3 } from '../3d';
interface Vec3 extends Array<number> { [d: number]: number, '@type': 'vec3', length: 3 }
@@ -265,7 +265,18 @@ namespace Vec3 {
return out;
}
- /** Transforms the vec3 with a quat */
+ /**
+ * Transforms the Vec3 with a Mat3.
+ */
+ export function transformMat3(out: Vec3, a: Vec3, m: Mat3) {
+ const x = a[0], y = a[1], z = a[2];
+ out[0] = x * m[0] + y * m[3] + z * m[6];
+ out[1] = x * m[1] + y * m[4] + z * m[7];
+ out[2] = x * m[2] + y * m[5] + z * m[8];
+ return out;
+ }
+
+ /** Transforms the Vec3 with a quat */
export function transformQuat(out: Vec3, a: Vec3, q: Quat) {
// benchmarks: http://jsperf.com/quaternion-transform-vec3-implementations
diff --git a/src/mol-view/viewer.ts b/src/mol-view/viewer.ts
index 48ff8e3d4bcbdc838f932feed804449c6cd22b66..54a908c04b77f1c801dd93b806f6eccc0d56e0c9 100644
--- a/src/mol-view/viewer.ts
+++ b/src/mol-view/viewer.ts
@@ -65,7 +65,7 @@ namespace Viewer {
})
const gl = getWebGLContext(canvas, {
- alpha: true,
+ alpha: false,
antialias: true,
depth: true,
preserveDrawingBuffer: true