diff --git a/src/mol-io/reader/ccp4/parser.ts b/src/mol-io/reader/ccp4/parser.ts
index 488ca23311375f5ac452e7a2a233b74fec102891..629303b84d2858f57fc18d19b4550f274176c228 100644
--- a/src/mol-io/reader/ccp4/parser.ts
+++ b/src/mol-io/reader/ccp4/parser.ts
@@ -8,7 +8,6 @@ import { Task, RuntimeContext } from 'mol-task';
import * as Schema from './schema'
import Result from '../result'
import { FileHandle } from '../../common/file-handle';
-import { flipByteOrder } from '../../common/binary';
async function parseInternal(file: FileHandle, ctx: RuntimeContext): Promise<Result<Schema.Ccp4File>> {
await ctx.update({ message: 'Parsing CCP4 file...' });
@@ -32,9 +31,12 @@ async function parseInternal(file: FileHandle, ctx: RuntimeContext): Promise<Res
// 54 MACHST Machine stamp indicating machine type which wrote file
// 17 and 17 for big-endian or 68 and 65 for little-endian
const MACHST = [ dv.getUint8(53 * 4), dv.getUint8(53 * 4 + 1) ]
-
- if (MACHST[ 0 ] === 17 && MACHST[ 1 ] === 17) {
- flipByteOrder(buffer, buffer.length)
+ // found MRC files that don't have the MACHST stamp set and are big-endian
+ if (MACHST[0] !== 68 && MACHST[1] !== 65) {
+ // flip byte order in-place
+ for (let i = 0, il = bin.byteLength; i < il; i += 4) {
+ dv.setFloat32(i, dv.getFloat32(i), true)
+ }
}
const header: Schema.Ccp4Header = {
@@ -91,17 +93,13 @@ async function parseInternal(file: FileHandle, ctx: RuntimeContext): Promise<Res
// TODO bytes 57-256 LABEL
}
+ const offset = 256 * 4 + header.NSYMBT
+ const count = header.NC * header.NR * header.NS
let values
if (header.MODE === 2) {
- values = new Float32Array(
- bin, 256 * 4 + header.NSYMBT,
- header.NX * header.NY * header.NZ
- )
+ values = new Float32Array(bin, offset, count)
} else if (header.MODE === 0) {
- values = new Float32Array(new Int8Array(
- bin, 256 * 4 + header.NSYMBT,
- header.NX * header.NY * header.NZ
- ))
+ values = new Int8Array(bin, offset, count)
} else {
return Result.error(`ccp4 mode '${header.MODE}' unsupported`);
}
diff --git a/src/mol-io/reader/ccp4/schema.ts b/src/mol-io/reader/ccp4/schema.ts
index 12b23631614eff9db792686a495c68e4a83e14f0..0ef828cf3b26e05ea79d7ce954f3f610770fa9cc 100644
--- a/src/mol-io/reader/ccp4/schema.ts
+++ b/src/mol-io/reader/ccp4/schema.ts
@@ -6,11 +6,11 @@
*/
export interface Ccp4Header {
- /** columns (fastest changing) */
+ /** number of columns (fastest changing) */
NC: number
- /** rows */
+ /** number of rows */
NR: number
- /** sections (slowest changing) */
+ /** number of sections (slowest changing) */
NS: number
/**
* 0 image : signed 8-bit bytes range -128 to 127
@@ -49,11 +49,11 @@ export interface Ccp4Header {
beta: number
/** gamma cell angle (Degrees) */
gamma: number
- /** axis corresponds for columns (1,2,3 for X,Y,Z) */
+ /** axis corresponds to columns (1,2,3 for X,Y,Z) */
MAPC: number
- /** axis corresponds for rows (1,2,3 for X,Y,Z) */
+ /** axis corresponds to rows (1,2,3 for X,Y,Z) */
MAPR: number
- /** axis corresponds for sections (1,2,3 for X,Y,Z) */
+ /** axis corresponds to sections (1,2,3 for X,Y,Z) */
MAPS: number
/** minimum density value */
AMIN: number
@@ -67,8 +67,8 @@ export interface Ccp4Header {
NSYMBT: number
/** flag for skew transformation, =0 none, =1 if foll */
LSKFLG: number
- /** Skew matrix S (in order S11, S12, S13, S21 etc) if LSKFLG .ne. 0
- *
+ /**
+ * Skew matrix S (in order S11, S12, S13, S21 etc) if LSKFLG .ne. 0
* May be used in CCP4 but not in MRC
*/
SKWMAT: number[]
diff --git a/src/mol-model/volume/data.ts b/src/mol-model/volume/data.ts
index 05e85eba318b1d8eec28f77ec161f0589524fefd..cda1035294766b00ea4edc8970c9bee925f1b95f 100644
--- a/src/mol-model/volume/data.ts
+++ b/src/mol-model/volume/data.ts
@@ -7,8 +7,8 @@
import { SpacegroupCell, Box3D } from 'mol-math/geometry'
import { Tensor, Mat4, Vec3 } from 'mol-math/linear-algebra'
+/** The basic unit cell that contains the data. */
interface VolumeData {
- // The basic unit cell that contains the data.
readonly cell: SpacegroupCell,
readonly fractionalBox: Box3D,
readonly data: Tensor,
diff --git a/src/mol-model/volume/formats/density-server.ts b/src/mol-model/volume/formats/density-server.ts
index 300d7039c56e329b2eea986c2753b9499225d5c1..0b1cb234dc0be00610f1636bfc5dded5ad3698e6 100644
--- a/src/mol-model/volume/formats/density-server.ts
+++ b/src/mol-model/volume/formats/density-server.ts
@@ -13,14 +13,17 @@ import { Tensor, Vec3 } from 'mol-math/linear-algebra';
function parseDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
return Task.create<VolumeData>('Parse Volume Data', async ctx => {
const { volume_data_3d_info: info, volume_data_3d: values } = source;
- const cell = SpacegroupCell.create(info.spacegroup_number.value(0),
+ const cell = SpacegroupCell.create(
+ info.spacegroup_number.value(0),
Vec3.ofArray(info.spacegroup_cell_size.value(0)),
- Vec3.scale(Vec3.zero(), Vec3.ofArray(info.spacegroup_cell_angles.value(0)), Math.PI / 180));
+ Vec3.scale(Vec3.zero(), Vec3.ofArray(info.spacegroup_cell_angles.value(0)), Math.PI / 180)
+ );
const tensorSpace = Tensor.Space(info.sample_count.value(0), info.axis_order.value(0), Float32Array);
const data = Tensor.create(tensorSpace, Tensor.Data1(values.values.toArray()));
- const origin = Vec3.ofArray(info.origin.value(0)), dimensions = Vec3.ofArray(info.dimensions.value(0));
+ const origin = Vec3.ofArray(info.origin.value(0))
+ const dimensions = Vec3.ofArray(info.dimensions.value(0));
return {
cell,