diff --git a/src/apps/canvas/index.ts b/src/apps/canvas/index.ts
index 1124f99841ca574dc47f6d9ebdd659eb7f6ea09d..db1a873e3f91795a36b3663e63f1417f75817cdf 100644
--- a/src/apps/canvas/index.ts
+++ b/src/apps/canvas/index.ts
@@ -26,8 +26,11 @@ if (pdbId) app.loadPdbIdOrMmcifUrl(pdbId, { assemblyId })
// 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('1lee')
+// app.loadCcp4Url('http://localhost:8091/ngl/data/1lee.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)
@@ -41,52 +44,4 @@ app.loadCcp4Url('http://localhost:8091/ngl/data/betaGal.mrc')
// 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
+// app.loadPdbIdOrMmcifUrl('http://localhost:8091/test/pdb-dev/carb/5KDS-carb.cif')
\ No newline at end of file
diff --git a/src/mol-geo/representation/volume/direct-volume.ts b/src/mol-geo/representation/volume/direct-volume.ts
index 00c62032fce172f83b57ac4974b2ab1a69228804..5819bfa9b3a6f69b2d27b7cb55c35f7cc1b0a0ec 100644
--- a/src/mol-geo/representation/volume/direct-volume.ts
+++ b/src/mol-geo/representation/volume/direct-volume.ts
@@ -114,41 +114,44 @@ function createVolumeTexture3d(volume: VolumeData) {
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) {
+ if (i < 100) {
+ console.log(get(data, x, y, z), ((get(data, x, y, z) - stats.min) / (stats.max - stats.min)) * 255)
+ }
+ 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 y = 0; y < height; ++y) {
- // for (let x = 0; x < width; ++x) {
+ // 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
- // // 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) {
+ // for (let x = 0; x < width; ++x) {
+ // for (let y = 0; y < height; ++y) {
+ // for (let z = 0; z < depth; ++z) {
// array[i + 3] = ((get(data, x, y, z) - stats.min) / (stats.max - stats.min)) * 255
// i += 4
// }
// }
// }
- let i = 0
- for (let x = 0; x < width; ++x) {
- for (let y = 0; y < height; ++y) {
- for (let z = 0; z < depth; ++z) {
- array[i + 3] = ((get(data, x, y, z) - stats.min) / (stats.max - stats.min)) * 255
- i += 4
- }
- }
- }
-
return textureVolume
}
diff --git a/src/mol-gl/shader/direct-volume.frag b/src/mol-gl/shader/direct-volume.frag
index be043efe5976a30d8fda7721da0bba2dd4e38632..6be0ab731366d502314f61722f6b124b308dc092 100644
--- a/src/mol-gl/shader/direct-volume.frag
+++ b/src/mol-gl/shader/direct-volume.frag
@@ -164,9 +164,9 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 viewDir) {
src.rgb = finalColor;
src.a = uAlpha;
- float marker = readFromTexture(tMarker, instance * float(uGroupCount) + group, uMarkerTexDim).a * 256.0;
+ float marker = readFromTexture(tMarker, instance * float(uGroupCount) + group, uMarkerTexDim).a * 255.0;
if (marker > 0.1) {
- if (mod(marker, 2.0) < 0.1) {
+ if (mod(marker, 2.0) > 0.1) {
src.rgb = mix(uHighlightColor, src.rgb, 0.3);
} else {
src.rgb = mix(uSelectColor, src.rgb, 0.3);
diff --git a/src/mol-gl/shader/direct-volume.vert b/src/mol-gl/shader/direct-volume.vert
index 3e2e594ccf0647a8251d084f8b0c15288bdefe9a..14cd4822c16de0e596a6df0e4b8fbc3fc3c86d74 100644
--- a/src/mol-gl/shader/direct-volume.vert
+++ b/src/mol-gl/shader/direct-volume.vert
@@ -26,8 +26,7 @@ uniform mat4 uProjection;
void main() {
unitCoord = aPosition + vec3(0.5);
- vec4 mvPosition = uModelView * uTransform * vec4(unitCoord * uGridDim + uBboxMin, 1.0);
- // vec4 mvPosition = uModelView * uTransform * vec4(unitCoord, 1.0);
+ vec4 mvPosition = uModelView * uTransform * vec4(unitCoord * uGridDim, 1.0);
origPos = unitCoord * uBboxSize + uBboxMin;
instance = aInstance;
gl_Position = uProjection * mvPosition;
diff --git a/src/mol-io/reader/ccp4/parser.ts b/src/mol-io/reader/ccp4/parser.ts
index 087b7ffc0711d5c37e63c89365ff138b341a981c..30e7c9e9db807ed6210956cdd1f2599e7cdbb976 100644
--- a/src/mol-io/reader/ccp4/parser.ts
+++ b/src/mol-io/reader/ccp4/parser.ts
@@ -104,6 +104,18 @@ async function parseInternal(file: FileHandle, ctx: RuntimeContext): Promise<Res
return Result.error(`ccp4 mode '${header.MODE}' unsupported`);
}
+ // if the file was converted by mapmode2to0 - scale the data
+ // based on uglymol (https://github.com/uglymol/uglymol) by Marcin Wojdyr (wojdyr)
+ if (intView[39] === -128 && intView[40] === 127) {
+ values = new Float32Array(values)
+ // scaling f(x)=b1*x+b0 such that f(-128)=min and f(127)=max
+ const b1 = (header.AMAX - header.AMIN) / 255.0
+ const b0 = 0.5 * (header.AMIN + header.AMAX + b1)
+ for (let j = 0, jl = values.length; j < jl; ++j) {
+ values[j] = b1 * values[j] + b0
+ }
+ }
+
const result: Schema.Ccp4File = { header, values };
return Result.success(result);
}
diff --git a/src/mol-math/geometry/spacegroup/construction.ts b/src/mol-math/geometry/spacegroup/construction.ts
index 2acdb5287eb62b96c24ee3a4617a5f742b04bc63..fad17c498cd7dbd95736c5e5d6b912e2caf8ee4d 100644
--- a/src/mol-math/geometry/spacegroup/construction.ts
+++ b/src/mol-math/geometry/spacegroup/construction.ts
@@ -26,10 +26,10 @@ interface Spacegroup {
}
namespace SpacegroupCell {
- // Create a 'P 1' with cellsize [1, 1, 1]
+ /** Create a 'P 1' with cellsize [1, 1, 1] */
export const Zero: SpacegroupCell = create('P 1', Vec3.create(1, 1, 1), Vec3.create(Math.PI / 2, Math.PI / 2, Math.PI / 2));
- // True if 'P 1' with cellsize [1, 1, 1]
+ /** True if 'P 1' with cellsize [1, 1, 1] */
export function isZero(cell: SpacegroupCell) {
return cell.index === 0 && cell.size[0] === 1 && cell.size[1] === 1 && cell.size[1] === 1;
}
@@ -37,7 +37,10 @@ namespace SpacegroupCell {
// returns Zero cell if the spacegroup does not exist
export function create(nameOrNumber: number | string | SpacegroupName, size: Vec3, anglesInRadians: Vec3): SpacegroupCell {
const index = getSpacegroupIndex(nameOrNumber);
- if (index < 0) return Zero;
+ if (index < 0) {
+ console.warn(`Unknown spacegroup '${nameOrNumber}', returning a 'P 1' with cellsize [1, 1, 1]`)
+ return Zero;
+ }
const alpha = anglesInRadians[0];
const beta = anglesInRadians[1];
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index e97ee8a4178fdc19f29ebe9b008514918704b5eb..414de8fbcc6f287ccbb7548428ba18437a852848 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -27,7 +27,7 @@ import { ChemicalComponent, ChemicalComponentMap } from '../properties/chemical-
import { ComponentType, getMoleculeType } from '../types';
import mmCIF_Format = Format.mmCIF
-import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, UnknownSaccharideComponent, SaccharideCompIdMap } from 'mol-model/structure/structure/carbohydrates/constants';
+import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap } from 'mol-model/structure/structure/carbohydrates/constants';
type AtomSite = mmCIF_Database['atom_site']
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 6048fc52c8665aca7b3b77359107f9c9c758f031..729e7bb56c1b38207f8297e19a457212eec0cd27 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -17,7 +17,7 @@ import { getAtomicMoleculeType, getPositionMatrix } from '../../util';
import StructureElement from '../element';
import Structure from '../structure';
import Unit from '../unit';
-import { SaccharideCompIdMap, UnknownSaccharideComponent, SaccharideComponent, SaccharidesSnfgMap } from './constants';
+import { UnknownSaccharideComponent, SaccharideComponent } from './constants';
import { CarbohydrateElement, CarbohydrateLink, Carbohydrates, CarbohydrateTerminalLink, PartialCarbohydrateElement } from './data';
import { UnitRings, UnitRing } from '../unit/rings';
import { ElementIndex } from '../../model/indexing';
diff --git a/src/mol-model/volume/data.ts b/src/mol-model/volume/data.ts
index ee9fd299f3920e11e2cee42f4b192b0d70a135b4..cda1035294766b00ea4edc8970c9bee925f1b95f 100644
--- a/src/mol-model/volume/data.ts
+++ b/src/mol-model/volume/data.ts
@@ -25,10 +25,7 @@ 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 34af61067270113deebf14a8e78ba7582457ec37..febb0fc604f172b4a7195b0b0bc06e5492657403 100644
--- a/src/mol-model/volume/formats/ccp4.ts
+++ b/src/mol-model/volume/formats/ccp4.ts
@@ -7,33 +7,17 @@
import { VolumeData } from '../data'
import { Task } from 'mol-task';
import { SpacegroupCell, Box3D } from 'mol-math/geometry';
-import { Tensor, Vec3, Mat4 } from 'mol-math/linear-algebra';
+import { Tensor, Vec3 } from 'mol-math/linear-algebra';
import { Ccp4File } from 'mol-io/reader/ccp4/schema';
import { degToRad } from 'mol-math/misc';
-// TODO implement voxelSize parameter
-
-// TODO support for rescaling of values
-// based on uglymol (https://github.com/uglymol/uglymol) by Marcin Wojdyr (wojdyr)
-// if the file was converted by mapmode2to0 - scale the data
-// if (intView[ 39 ] === -128 && intView[ 40 ] === 127) {
-// // scaling f(x)=b1*x+b0 such that f(-128)=min and f(127)=max
-// const b1 = (header.DMAX - header.DMIN) / 255.0
-// const b0 = 0.5 * (header.DMIN + header.DMAX + b1)
-// for (let j = 0, jl = data.length; j < jl; ++j) {
-// data[ j ] = b1 * data[ j ] + b0
-// }
-// }
-
-function volumeFromCcp4(source: Ccp4File): Task<VolumeData> {
+function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3 }): 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),
- Vec3.create(degToRad(header.alpha), degToRad(header.beta), degToRad(header.gamma))
- );
+ const size = Vec3.create(header.xLength, header.yLength, header.zLength)
+ if (params && params.voxelSize) Vec3.mul(size, size, params.voxelSize)
+ const angles = Vec3.create(degToRad(header.alpha), degToRad(header.beta), degToRad(header.gamma))
+ const cell = SpacegroupCell.create(header.ISPG || 'P 1', size, angles);
const axis_order_fast_to_slow = Vec3.create(header.MAPC - 1, header.MAPR - 1, header.MAPS - 1);
const normalizeOrder = Tensor.convertToCanonicalAxisIndicesFastToSlow(axis_order_fast_to_slow);
@@ -41,30 +25,17 @@ 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 = normalizeOrder([header.NCSTART, header.NRSTART, header.NSSTART]);
-
- // 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 {
- // // Use ORIGIN records rather than old n[xyz]start records
- // // http://www2.mrc-lmb.cam.ac.uk/image2000.html
- // // XXX the ORIGIN field is only used by the EM community, and
- // // has undefined meaning for non-orthogonal maps and/or
- // // non-cubic voxels, etc.
- // gridOrigin = [header.originX, header.originY, header.originZ];
- // }
+ let gridOrigin: number[]
+ if (header.originX === 0.0 && header.originY === 0.0 && header.originZ === 0.0) {
+ gridOrigin = normalizeOrder([header.NCSTART, header.NRSTART, header.NSSTART]);
+ } else {
+ // When available (e.g. in MRC files) use ORIGIN records instead of N[CRS]START
+ gridOrigin = [header.originX, header.originY, header.originZ];
+ }
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));
@@ -72,7 +43,7 @@ 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.
- const vd = {
+ return {
cell,
fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)),
data,
@@ -83,12 +54,6 @@ 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
});
}