diff --git a/src/apps/canvas/index.ts b/src/apps/canvas/index.ts
index c848f987e08498d97caee37b5c533be760e3c230..1124f99841ca574dc47f6d9ebdd659eb7f6ea09d 100644
--- a/src/apps/canvas/index.ts
+++ b/src/apps/canvas/index.ts
@@ -23,7 +23,11 @@ const assemblyId = urlQueryParameter('assembly')
const pdbId = urlQueryParameter('pdb')
if (pdbId) app.loadPdbIdOrMmcifUrl(pdbId, { assemblyId })
-// app.loadCcp4Url('http://localhost:8091/ngl/data/betaGal.mrc')
+// app.loadPdbIdOrMmcifUrl('3pqr')
+// app.loadCcp4Url('http://localhost:8091/ngl/data/3pqr-mode0.ccp4')
+
+app.loadPdbIdOrMmcifUrl('6DRV')
+app.loadCcp4Url('http://localhost:8091/ngl/data/betaGal.mrc')
// app.loadPdbIdOrMmcifUrl('3pqr')
// app.loadVolCifUrl('https://webchem.ncbr.muni.cz/DensityServer/x-ray/3pqr/cell?space=fractional', true)
@@ -32,4 +36,57 @@ if (pdbId) app.loadPdbIdOrMmcifUrl(pdbId, { assemblyId })
// app.loadVolcifUrl('https://webchem.ncbr.muni.cz/DensityServer/em/emd-8116/cell?space=cartesian&detail=6', true)
// app.loadPdbIdOrMmcifUrl('5gag')
-// app.loadVolcifUrl('https://webchem.ncbr.muni.cz/DensityServer/em/emd-8003/cell?detail=3', true)
\ No newline at end of file
+// app.loadVolcifUrl('https://webchem.ncbr.muni.cz/DensityServer/em/emd-8003/cell?detail=3', true)
+
+// app.loadPdbIdOrMmcifUrl('http://localhost:8091/test/pdb-dev/carb/1B5F-carb.cif')
+// app.loadPdbIdOrMmcifUrl('http://localhost:8091/test/pdb-dev/carb/2HYV-carb.cif')
+// app.loadPdbIdOrMmcifUrl('http://localhost:8091/test/pdb-dev/carb/2WMG-carb.cif')
+// app.loadPdbIdOrMmcifUrl('http://localhost:8091/test/pdb-dev/carb/5KDS-carb.cif')
+
+const basisX = [
+ h.xlen,
+ 0,
+ 0
+ ]
+
+ const basisY = [
+ h.ylen * Math.cos(Math.PI / 180.0 * h.gamma),
+ h.ylen * Math.sin(Math.PI / 180.0 * h.gamma),
+ 0
+ ]
+
+ const basisZ = [
+ h.zlen * Math.cos(Math.PI / 180.0 * h.beta),
+ h.zlen * (
+ Math.cos(Math.PI / 180.0 * h.alpha) -
+ Math.cos(Math.PI / 180.0 * h.gamma) *
+ Math.cos(Math.PI / 180.0 * h.beta)
+ ) / Math.sin(Math.PI / 180.0 * h.gamma),
+ 0
+ ]
+ basisZ[ 2 ] = Math.sqrt(
+ h.zlen * h.zlen * Math.sin(Math.PI / 180.0 * h.beta) *
+ Math.sin(Math.PI / 180.0 * h.beta) - basisZ[ 1 ] * basisZ[ 1 ]
+ )
+
+ const basis = [ 0, basisX, basisY, basisZ ]
+ const nxyz = [ 0, h.MX, h.MY, h.MZ ]
+ const mapcrs = [ 0, h.MAPC, h.MAPR, h.MAPS ]
+
+ const matrix = new Matrix4()
+
+ matrix.set(
+ basis[ mapcrs[1] ][0] / nxyz[ mapcrs[1] ],
+ basis[ mapcrs[2] ][0] / nxyz[ mapcrs[2] ],
+ basis[ mapcrs[3] ][0] / nxyz[ mapcrs[3] ],
+ 0,
+ basis[ mapcrs[1] ][1] / nxyz[ mapcrs[1] ],
+ basis[ mapcrs[2] ][1] / nxyz[ mapcrs[2] ],
+ basis[ mapcrs[3] ][1] / nxyz[ mapcrs[3] ],
+ 0,
+ basis[ mapcrs[1] ][2] / nxyz[ mapcrs[1] ],
+ basis[ mapcrs[2] ][2] / nxyz[ mapcrs[2] ],
+ basis[ mapcrs[3] ][2] / nxyz[ mapcrs[3] ],
+ 0,
+ 0, 0, 0, 1
+ )
\ No newline at end of file
diff --git a/src/apps/canvas/structure-view.ts b/src/apps/canvas/structure-view.ts
index dce28b08646960608f900b5a4ec2ba84edef3886..bd35a273e5f6cd52f55fbb6a2c7af42ad78b1ab4 100644
--- a/src/apps/canvas/structure-view.ts
+++ b/src/apps/canvas/structure-view.ts
@@ -64,15 +64,13 @@ interface StructureViewProps {
symmetryFeatureId?: number
}
-
-
export async function StructureView(app: App, viewer: Viewer, models: ReadonlyArray<Model>, props: StructureViewProps = {}): Promise<StructureView> {
const active: { [k: string]: boolean } = {
cartoon: true,
point: false,
surface: false,
ballAndStick: false,
- carbohydrate: false,
+ carbohydrate: true,
spacefill: false,
distanceRestraint: false,
symmetryAxes: false,
diff --git a/src/mol-geo/representation/volume/direct-volume.ts b/src/mol-geo/representation/volume/direct-volume.ts
index 1dd1e9446bcad8bab3e1f2918d6fb1acd4917277..00c62032fce172f83b57ac4974b2ab1a69228804 100644
--- a/src/mol-geo/representation/volume/direct-volume.ts
+++ b/src/mol-geo/representation/volume/direct-volume.ts
@@ -112,10 +112,37 @@ function createVolumeTexture3d(volume: VolumeData) {
const array = new Uint8Array(width * height * depth * 4)
const textureVolume = { array, width, height, depth }
+ console.log('stats', stats)
+
+ // let i = 0
+ // for (let z = 0; z < depth; ++z) {
+ // for (let y = 0; y < height; ++y) {
+ // for (let x = 0; x < width; ++x) {
+ // array[i + 3] = ((get(data, x, y, z) - stats.min) / (stats.max - stats.min)) * 255
+ // // array[i + 3] = ((get(data, x, z, y) - stats.min) / (stats.max - stats.min)) * 255
+ // // array[i + 3] = ((get(data, y, x, z) - stats.min) / (stats.max - stats.min)) * 255
+ // // array[i + 3] = ((get(data, y, z, x) - stats.min) / (stats.max - stats.min)) * 255
+ // // array[i + 3] = ((get(data, z, y, x) - stats.min) / (stats.max - stats.min)) * 255
+ // // array[i + 3] = ((get(data, z, x, y) - stats.min) / (stats.max - stats.min)) * 255
+ // i += 4
+ // }
+ // }
+ // }
+
+ // let i = 0
+ // for (let z = 0; z < depth; ++z) {
+ // for (let x = 0; x < width; ++x) {
+ // for (let y = 0; y < height; ++y) {
+ // array[i + 3] = ((get(data, x, y, z) - stats.min) / (stats.max - stats.min)) * 255
+ // i += 4
+ // }
+ // }
+ // }
+
let i = 0
- for (let z = 0; z < depth; ++z) {
+ for (let x = 0; x < width; ++x) {
for (let y = 0; y < height; ++y) {
- for (let x = 0; x < width; ++x) {
+ for (let z = 0; z < depth; ++z) {
array[i + 3] = ((get(data, x, y, z) - stats.min) / (stats.max - stats.min)) * 255
i += 4
}
@@ -129,6 +156,7 @@ export function createDirectVolume3d(ctx: RuntimeContext, webgl: Context, volume
const gridDimension = volume.data.space.dimensions as Vec3
const textureVolume = createVolumeTexture3d(volume)
const transform = VolumeData.getGridToCartesianTransform(volume)
+ // Mat4.invert(transform, transform)
const bbox = getBoundingBox(gridDimension, transform)
const texture = directVolume ? directVolume.gridTexture.ref.value : createTexture(webgl, 'volume-uint8', 'rgba', 'ubyte', 'linear')
@@ -185,6 +213,8 @@ export function DirectVolumeVisual(): VolumeVisual<DirectVolumeProps> {
// newProps.isoValueAbsolute = VolumeIsoValue.calcAbsolute(currentVolume.dataStats, props.isoValueRelative)
}
+ console.log('newProps.isoValueAbsolute', newProps.isoValueAbsolute)
+
DirectVolume.updateValues(renderObject.values, newProps)
updateRenderableState(renderObject.state, newProps)
diff --git a/src/mol-gl/shader/direct-volume.vert b/src/mol-gl/shader/direct-volume.vert
index 248ddcaebd330ef6df7264e57b211948962ff901..3e2e594ccf0647a8251d084f8b0c15288bdefe9a 100644
--- a/src/mol-gl/shader/direct-volume.vert
+++ b/src/mol-gl/shader/direct-volume.vert
@@ -18,13 +18,16 @@ varying float instance;
uniform vec3 uBboxSize;
uniform vec3 uBboxMin;
uniform vec3 uBboxMax;
+uniform vec3 uGridDim;
+uniform mat4 uTransform;
uniform mat4 uModelView;
uniform mat4 uProjection;
void main() {
unitCoord = aPosition + vec3(0.5);
- vec4 mvPosition = uModelView * vec4(unitCoord * uBboxSize + uBboxMin, 1.0);
+ vec4 mvPosition = uModelView * uTransform * vec4(unitCoord * uGridDim + uBboxMin, 1.0);
+ // vec4 mvPosition = uModelView * uTransform * vec4(unitCoord, 1.0);
origPos = unitCoord * uBboxSize + uBboxMin;
instance = aInstance;
gl_Position = uProjection * mvPosition;
diff --git a/src/mol-model/volume/data.ts b/src/mol-model/volume/data.ts
index cda1035294766b00ea4edc8970c9bee925f1b95f..ee9fd299f3920e11e2cee42f4b192b0d70a135b4 100644
--- a/src/mol-model/volume/data.ts
+++ b/src/mol-model/volume/data.ts
@@ -25,7 +25,10 @@ namespace VolumeData {
export function getGridToCartesianTransform(volume: VolumeData) {
const { data: { space } } = volume;
const scale = Mat4.fromScaling(_scale, Vec3.div(Vec3.zero(), Box3D.size(Vec3.zero(), volume.fractionalBox), Vec3.ofArray(space.dimensions)));
+ const scale1 = Mat4.getScaling(Vec3.zero(), scale)
+ console.log('scale1', scale1)
const translate = Mat4.fromTranslation(_translate, volume.fractionalBox.min);
+ console.log('translate1', translate)
return Mat4.mul3(Mat4.zero(), volume.cell.fromFractional, translate, scale);
}
}
diff --git a/src/mol-model/volume/formats/ccp4.ts b/src/mol-model/volume/formats/ccp4.ts
index eaa685c1eebd53312011f299bded0c7081b686a4..34af61067270113deebf14a8e78ba7582457ec37 100644
--- a/src/mol-model/volume/formats/ccp4.ts
+++ b/src/mol-model/volume/formats/ccp4.ts
@@ -7,7 +7,7 @@
import { VolumeData } from '../data'
import { Task } from 'mol-task';
import { SpacegroupCell, Box3D } from 'mol-math/geometry';
-import { Tensor, Vec3 } from 'mol-math/linear-algebra';
+import { Tensor, Vec3, Mat4 } from 'mol-math/linear-algebra';
import { Ccp4File } from 'mol-io/reader/ccp4/schema';
import { degToRad } from 'mol-math/misc';
@@ -28,7 +28,7 @@ import { degToRad } from 'mol-math/misc';
function volumeFromCcp4(source: Ccp4File): Task<VolumeData> {
return Task.create<VolumeData>('Parse Volume Data', async ctx => {
const { header, values } = source;
-
+ console.log('header', header)
const cell = SpacegroupCell.create(
header.ISPG,
Vec3.create(header.xLength, header.yLength, header.zLength),
@@ -41,9 +41,9 @@ function volumeFromCcp4(source: Ccp4File): Task<VolumeData> {
const grid = [header.NX, header.NY, header.NZ];
const extent = normalizeOrder([header.NC, header.NR, header.NS]);
- const gridOrigin: number[] = normalizeOrder([header.NCSTART, header.NRSTART, header.NSSTART]);
+ const gridOrigin = normalizeOrder([header.NCSTART, header.NRSTART, header.NSSTART]);
- // TODO: this is code from LiteMol, but not sure about the part based on originXYZ. The
+ // TODO: this is code from LiteMol, but not sure about the part based on originXYZ. The
// if (header.originX === 0.0 && header.originY === 0.0 && header.originZ === 0.0) {
// gridOrigin = normalizeOrder([header.NCSTART, header.NRSTART, header.NSSTART]);
// } else {
@@ -58,6 +58,13 @@ function volumeFromCcp4(source: Ccp4File): Task<VolumeData> {
const origin_frac = Vec3.create(gridOrigin[0] / grid[0], gridOrigin[1] / grid[1], gridOrigin[2] / grid[2]);
const dimensions_frac = Vec3.create(extent[0] / grid[0], extent[1] / grid[1], extent[2] / grid[2]);
+ console.log('length', header.xLength, header.yLength, header.zLength)
+ console.log('grid', grid)
+ console.log('extent', extent)
+ console.log('gridOrigin', gridOrigin)
+ console.log('origin_frac', origin_frac)
+ console.log('dimensions_frac', dimensions_frac)
+
const space = Tensor.Space(extent, Tensor.invertAxisOrder(axis_order_fast_to_slow), header.MODE === 0 ? Int8Array : Float32Array);
const data = Tensor.create(space, Tensor.Data1(values));
@@ -65,7 +72,7 @@ function volumeFromCcp4(source: Ccp4File): Task<VolumeData> {
// Min/max/mean are reliable (based on LiteMol/DensityServer usage)
// These, however, calculate sigma, so no data on that.
- return {
+ const vd = {
cell,
fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)),
data,
@@ -76,6 +83,12 @@ function volumeFromCcp4(source: Ccp4File): Task<VolumeData> {
sigma: header.ARMS
}
};
+
+ const transform = VolumeData.getGridToCartesianTransform(vd);
+ const scale = Mat4.getScaling(Vec3.zero(), transform)
+ console.log('transform', transform)
+ console.log('scale', scale)
+ return vd
});
}