From e987d73d2b9e660dcf7de8a4739b9b0ff4f3e794 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 3 Oct 2017 15:39:28 +0200
Subject: [PATCH] BinaryCIF support
---
examples/1cbs_full.bcif | Bin 0 -> 66851 bytes
src/reader/cif/binary/decoder.ts | 215 ++++++++++++++++++++++++++++++
src/reader/cif/binary/encoding.ts | 152 +++++++++++++++++++++
src/reader/cif/binary/field.ts | 54 +++++++-
src/reader/cif/binary/parser.ts | 50 ++++++-
src/reader/cif/index.ts | 6 +-
src/script.ts | 55 +++++---
7 files changed, 510 insertions(+), 22 deletions(-)
create mode 100644 examples/1cbs_full.bcif
create mode 100644 src/reader/cif/binary/decoder.ts
create mode 100644 src/reader/cif/binary/encoding.ts
diff --git a/examples/1cbs_full.bcif b/examples/1cbs_full.bcif
new file mode 100644
index 0000000000000000000000000000000000000000..38628c3dafaae093d7f5f6689f4bc471ef826b27
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literal 0
HcmV?d00001
diff --git a/src/reader/cif/binary/decoder.ts b/src/reader/cif/binary/decoder.ts
new file mode 100644
index 000000000..f6c587f37
--- /dev/null
+++ b/src/reader/cif/binary/decoder.ts
@@ -0,0 +1,215 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * From CIFTools.js
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Encoding, EncodedData } from './encoding'
+
+/**
+ * Fixed point, delta, RLE, integer packing adopted from https://github.com/rcsb/mmtf-javascript/
+ * by Alexander Rose <alexander.rose@weirdbyte.de>, MIT License, Copyright (c) 2016
+ */
+
+export default function decode(data: EncodedData): any[] {
+ let current: any = data.data;
+ for (let i = data.encoding.length - 1; i >= 0; i--) {
+ current = decodeStep(current, data.encoding[i]);
+ }
+ return current as any[];
+}
+
+function decodeStep(data: any, encoding: Encoding): any {
+ switch (encoding.kind) {
+ case 'ByteArray': {
+ switch (encoding.type) {
+ case Encoding.IntDataType.Uint8: return data;
+ case Encoding.IntDataType.Int8: return int8(data);
+ case Encoding.IntDataType.Int16: return int16(data);
+ case Encoding.IntDataType.Uint16: return uint16(data);
+ case Encoding.IntDataType.Int32: return int32(data);
+ case Encoding.IntDataType.Uint32: return uint32(data);
+ case Encoding.FloatDataType.Float32: return float32(data);
+ case Encoding.FloatDataType.Float64: return float64(data);
+ default: throw new Error('Unsupported ByteArray type.')
+ }
+ }
+ case 'FixedPoint': return fixedPoint(data, encoding);
+ case 'IntervalQuantization': return intervalQuantization(data, encoding);
+ case 'RunLength': return runLength(data, encoding);
+ case 'Delta': return delta(data, encoding);
+ case 'IntegerPacking': return integerPacking(data, encoding);
+ case 'StringArray': return stringArray(data, encoding);
+ }
+}
+
+function getIntArray(type: Encoding.IntDataType, size: number) {
+ switch (type) {
+ case Encoding.IntDataType.Int8: return new Int8Array(size);
+ case Encoding.IntDataType.Int16: return new Int16Array(size);
+ case Encoding.IntDataType.Int32: return new Int32Array(size);
+ case Encoding.IntDataType.Uint8: return new Uint8Array(size);
+ case Encoding.IntDataType.Uint16: return new Uint16Array(size);
+ case Encoding.IntDataType.Uint32: return new Uint32Array(size);
+ default: throw new Error('Unsupported integer data type.');
+ }
+}
+
+function getFloatArray(type: Encoding.FloatDataType, size: number) {
+ switch (type) {
+ case Encoding.FloatDataType.Float32: return new Float32Array(size);
+ case Encoding.FloatDataType.Float64: return new Float64Array(size);
+ default: throw new Error('Unsupported floating data type.');
+ }
+}
+
+/* http://stackoverflow.com/questions/7869752/javascript-typed-arrays-and-endianness */
+const isLittleEndian = (function () {
+ const arrayBuffer = new ArrayBuffer(2);
+ const uint8Array = new Uint8Array(arrayBuffer);
+ const uint16array = new Uint16Array(arrayBuffer);
+ uint8Array[0] = 0xAA;
+ uint8Array[1] = 0xBB;
+ if (uint16array[0] === 0xBBAA) return true;
+ return false;
+})();
+
+function int8(data: Uint8Array) { return new Int8Array(data.buffer, data.byteOffset); }
+
+function flipByteOrder(data: Uint8Array, bytes: number) {
+ let buffer = new ArrayBuffer(data.length);
+ let ret = new Uint8Array(buffer);
+ for (let i = 0, n = data.length; i < n; i += bytes) {
+ for (let j = 0; j < bytes; j++) {
+ ret[i + bytes - j - 1] = data[i + j];
+ }
+ }
+ return buffer;
+}
+
+function view<T>(data: Uint8Array, byteSize: number, c: new (buffer: ArrayBuffer) => T) {
+ if (isLittleEndian) return new c(data.buffer);
+ return new c(flipByteOrder(data, byteSize));
+}
+
+function int16(data: Uint8Array) { return view(data, 2, Int16Array); }
+function uint16(data: Uint8Array) { return view(data, 2, Uint16Array); }
+function int32(data: Uint8Array) { return view(data, 4, Int32Array); }
+function uint32(data: Uint8Array) { return view(data, 4, Uint32Array); }
+function float32(data: Uint8Array) { return view(data, 4, Float32Array); }
+function float64(data: Uint8Array) { return view(data, 8, Float64Array); }
+
+function fixedPoint(data: Int32Array, encoding: Encoding.FixedPoint) {
+ let n = data.length;
+ let output = getFloatArray(encoding.srcType, n);
+ let f = 1 / encoding.factor;
+ for (let i = 0; i < n; i++) {
+ output[i] = f * data[i];
+ }
+ return output;
+}
+
+function intervalQuantization(data: Int32Array, encoding: Encoding.IntervalQuantization) {
+ let n = data.length;
+ let output = getFloatArray(encoding.srcType, n);
+ let delta = (encoding.max - encoding.min) / (encoding.numSteps - 1)
+ let min = encoding.min;
+ for (let i = 0; i < n; i++) {
+ output[i] = min + delta * data[i];
+ }
+ return output;
+}
+
+function runLength(data: Int32Array, encoding: Encoding.RunLength) {
+ let output = getIntArray(encoding.srcType, encoding.srcSize);
+ let dataOffset = 0;
+ for (let i = 0, il = data.length; i < il; i += 2) {
+ let value = data[i]; // value to be repeated
+ let length = data[i + 1]; // number of repeats
+ for (let j = 0; j < length; ++j) {
+ output[dataOffset++] = value;
+ }
+ }
+ return output;
+}
+
+function delta(data: (Int8Array | Int16Array | Int32Array), encoding: Encoding.Delta) {
+ let n = data.length;
+ let output = getIntArray(encoding.srcType, n);
+ if (!n) return output;
+ output[0] = data[0] + (encoding.origin | 0);
+ for (let i = 1; i < n; ++i) {
+ output[i] = data[i] + output[i - 1];
+ }
+ return output;
+}
+
+function integerPackingSigned(data: (Int8Array | Int16Array), encoding: Encoding.IntegerPacking) {
+ let upperLimit = encoding.byteCount === 1 ? 0x7F : 0x7FFF;
+ let lowerLimit = -upperLimit - 1;
+ let n = data.length;
+ let output = new Int32Array(encoding.srcSize);
+ let i = 0;
+ let j = 0;
+ while (i < n) {
+ let value = 0, t = data[i];
+ while (t === upperLimit || t === lowerLimit) {
+ value += t;
+ i++;
+ t = data[i];
+ }
+ value += t;
+ output[j] = value;
+ i++;
+ j++;
+ }
+ return output;
+}
+
+function integerPackingUnsigned(data: (Int8Array | Int16Array), encoding: Encoding.IntegerPacking) {
+ let upperLimit = encoding.byteCount === 1 ? 0xFF : 0xFFFF;
+ let n = data.length;
+ let output = new Int32Array(encoding.srcSize);
+ let i = 0;
+ let j = 0;
+ while (i < n) {
+ let value = 0, t = data[i];
+ while (t === upperLimit) {
+ value += t;
+ i++;
+ t = data[i];
+ }
+ value += t;
+ output[j] = value;
+ i++;
+ j++;
+ }
+ return output;
+}
+
+function integerPacking(data: (Int8Array | Int16Array), encoding: Encoding.IntegerPacking) {
+ return encoding.isUnsigned ? integerPackingUnsigned(data, encoding) : integerPackingSigned(data, encoding);
+}
+
+function stringArray(data: Uint8Array, encoding: Encoding.StringArray) {
+ let str = encoding.stringData;
+ let offsets = decode({ encoding: encoding.offsetEncoding, data: encoding.offsets });
+ let indices = decode({ encoding: encoding.dataEncoding, data });
+ let cache: any = Object.create(null);
+ let result = new Array(indices.length);
+ let offset = 0;
+ for (let i of indices) {
+ if (i < 0) {
+ result[offset++] = null;
+ continue;
+ }
+ let v = cache[i];
+ if (v === void 0) {
+ v = str.substring(offsets[i], offsets[i + 1]);
+ cache[i] = v;
+ }
+ result[offset++] = v;
+ }
+ return result;
+}
\ No newline at end of file
diff --git a/src/reader/cif/binary/encoding.ts b/src/reader/cif/binary/encoding.ts
new file mode 100644
index 000000000..c9369e964
--- /dev/null
+++ b/src/reader/cif/binary/encoding.ts
@@ -0,0 +1,152 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * From CIFTools.js
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export const VERSION = '0.3.0';
+
+export type Encoding =
+ | Encoding.ByteArray
+ | Encoding.FixedPoint
+ | Encoding.RunLength
+ | Encoding.Delta
+ | Encoding.IntervalQuantization
+ | Encoding.IntegerPacking
+ | Encoding.StringArray;
+
+export interface EncodedFile {
+ version: string,
+ encoder: string,
+ dataBlocks: EncodedDataBlock[]
+}
+
+export interface EncodedDataBlock {
+ header: string,
+ categories: EncodedCategory[],
+}
+
+export interface EncodedCategory {
+ name: string,
+ rowCount: number,
+ columns: EncodedColumn[],
+}
+
+export interface EncodedColumn {
+ name: string,
+ data: EncodedData,
+
+ /**
+ * The mask represents the presence or absent of particular "CIF value".
+ * If the mask is not set, every value is present.
+ *
+ * 0 = Value is present
+ * 1 = . = value not specified
+ * 2 = ? = value unknown
+ */
+ mask?: EncodedData
+}
+
+export interface EncodedData {
+ encoding: Encoding[],
+ data: Uint8Array
+}
+
+export namespace Encoding {
+
+ export const enum IntDataType {
+ Int8 = 1,
+ Int16 = 2,
+ Int32 = 3,
+ Uint8 = 4,
+ Uint16 = 5,
+ Uint32 = 6,
+ }
+
+ export const enum FloatDataType {
+ Float32 = 32,
+ Float64 = 33
+ }
+
+ export type DataType = IntDataType | FloatDataType
+
+ export type IntArray = Int8Array | Int16Array | Int32Array | Uint8Array | Uint16Array | Uint32Array
+ export type FloatArray = Float32Array | Float64Array
+
+ export function getDataType(data: IntArray | FloatArray): DataType {
+ let srcType: DataType;
+ if (data instanceof Int8Array) srcType = Encoding.IntDataType.Int8;
+ else if (data instanceof Int16Array) srcType = Encoding.IntDataType.Int16;
+ else if (data instanceof Int32Array) srcType = Encoding.IntDataType.Int32;
+ else if (data instanceof Uint8Array) srcType = Encoding.IntDataType.Uint8;
+ else if (data instanceof Uint16Array) srcType = Encoding.IntDataType.Uint16;
+ else if (data instanceof Uint32Array) srcType = Encoding.IntDataType.Uint32;
+ else if (data instanceof Float32Array) srcType = Encoding.FloatDataType.Float32;
+ else if (data instanceof Float64Array) srcType = Encoding.FloatDataType.Float64;
+ else throw new Error('Unsupported integer data type.');
+ return srcType;
+ }
+
+ export function isSignedIntegerDataType(data: IntArray) {
+ return data instanceof Int8Array || data instanceof Int16Array || data instanceof Int32Array;
+ }
+
+ // type[] -> Uint8[]
+ export interface ByteArray {
+ kind: 'ByteArray',
+ type: DataType
+ }
+
+ // (Float32 | Float64)[] -> Int32[]
+ export interface FixedPoint {
+ kind: 'FixedPoint',
+ factor: number,
+ srcType: FloatDataType
+ }
+
+ // (Float32|Float64)[] -> Int32
+ export interface IntervalQuantization {
+ kind: 'IntervalQuantization',
+ min: number,
+ max: number,
+ numSteps: number,
+ srcType: FloatDataType
+ }
+
+ // (Uint8 | Int8 | Int16 | Int32)[] -> Int32[]
+ export interface RunLength {
+ kind: 'RunLength',
+ srcType: IntDataType,
+ srcSize: number
+ }
+
+ // T=(Int8Array | Int16Array | Int32Array)[] -> T[]
+ export interface Delta {
+ kind: 'Delta',
+ origin: number,
+ srcType: IntDataType
+ }
+
+ // Int32[] -> (Int8 | Int16 | Uint8 | Uint16)[]
+ export interface IntegerPacking {
+ kind: 'IntegerPacking',
+ byteCount: number,
+ isUnsigned: boolean,
+ srcSize: number
+ }
+
+ // string[] -> Uint8[]
+ // stores 0 and indices of ends of strings:
+ // stringData = '123456'
+ // offsets = [0,2,5,6]
+ // encodes ['12','345','6']
+ export interface StringArray {
+ kind: 'StringArray',
+ dataEncoding: Encoding[],
+ stringData: string,
+ offsetEncoding: Encoding[],
+ offsets: Uint8Array
+ }
+
+}
\ No newline at end of file
diff --git a/src/reader/cif/binary/field.ts b/src/reader/cif/binary/field.ts
index 0ffdd02fc..974dd522b 100644
--- a/src/reader/cif/binary/field.ts
+++ b/src/reader/cif/binary/field.ts
@@ -1 +1,53 @@
-// TODO
\ No newline at end of file
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as Column from '../../common/column'
+import * as Data from '../data-model'
+import { EncodedColumn } from './encoding'
+import decode from './decoder'
+import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../../common/text/number-parser'
+
+export default function Field(column: EncodedColumn): Data.Field {
+ const mask = column.mask ? decode(column.mask) as number[] : void 0;
+ const data = decode(column.data);
+ const isNumeric = (data as any).buffer && (data as any).byteLength && (data as any).BYTES_PER_ELEMENT;
+
+ const str: Data.Field['str'] = isNumeric
+ ? mask
+ ? row => mask[row] === Data.ValuePresence.Present ? '' + data[row] : ''
+ : row => '' + data[row]
+ : mask
+ ? row => mask[row] === Data.ValuePresence.Present ? data[row] : ''
+ : row => data[row];
+
+ const int: Data.Field['int'] = isNumeric
+ ? row => data[row]
+ : row => { const v = data[row]; return fastParseInt(v, 0, v.length); };
+
+ const float: Data.Field['float'] = isNumeric
+ ? row => data[row]
+ : row => { const v = data[row]; return fastParseFloat(v, 0, v.length); };
+
+ const presence: Data.Field['presence'] = mask
+ ? row => mask[row]
+ : row => Data.ValuePresence.Present;
+
+ const rowCount = data.length;
+
+ return {
+ isDefined: true,
+ rowCount,
+ str,
+ int,
+ float,
+ presence,
+ areValuesEqual: (rowA, rowB) => data[rowA] === data[rowB],
+ stringEquals(row, v) { return str(row) === v; },
+ toStringArray(params) { return Column.createAndFillArray(rowCount, str, params); },
+ toIntArray(params) { return Column.createAndFillArray(rowCount, int, params); },
+ toFloatArray(params) { return Column.createAndFillArray(rowCount, float, params); }
+ };
+}
\ No newline at end of file
diff --git a/src/reader/cif/binary/parser.ts b/src/reader/cif/binary/parser.ts
index 0ffdd02fc..1cdbd04b1 100644
--- a/src/reader/cif/binary/parser.ts
+++ b/src/reader/cif/binary/parser.ts
@@ -1 +1,49 @@
-// TODO
\ No newline at end of file
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as Data from '../data-model'
+import * as Encoding from './encoding'
+import Field from './field'
+import Result from '../../result'
+import decodeMsgPack from '../../../utils/msgpack/decode'
+
+function checkVersions(min: number[], current: number[]) {
+ for (let i = 0; i < 2; i++) {
+ if (min[i] > current[i]) return false;
+ }
+ return true;
+}
+
+function Category(data: Encoding.EncodedCategory): Data.Category {
+ const map = Object.create(null);
+ for (const col of data.columns) map[col.name] = col;
+ return {
+ rowCount: data.rowCount,
+ getField(name) {
+ const col = map[name];
+ return col ? Field(col) : Data.DefaultUndefinedField(data.rowCount);
+ }
+ }
+}
+
+export default function parse(data: Uint8Array): Result<Data.File> {
+ const minVersion = [0, 3];
+
+ try {
+ const unpacked = decodeMsgPack(data) as Encoding.EncodedFile;
+ if (!checkVersions(minVersion, unpacked.version.match(/(\d)\.(\d)\.\d/)!.slice(1).map(v => +v))) {
+ return Result.error<Data.File>(`Unsupported format version. Current ${unpacked.version}, required ${minVersion.join('.')}.`);
+ }
+ const file = Data.File(unpacked.dataBlocks.map(block => {
+ const cats = Object.create(null);
+ for (const cat of block.categories) cats[cat.name] = Category(cat);
+ return Data.Block(cats, block.header);
+ }));
+ return Result.success(file);
+ } catch (e) {
+ return Result.error<Data.File>('' + e);
+ }
+}
\ No newline at end of file
diff --git a/src/reader/cif/index.ts b/src/reader/cif/index.ts
index c3882b9e8..e7dcc0f88 100644
--- a/src/reader/cif/index.ts
+++ b/src/reader/cif/index.ts
@@ -5,14 +5,18 @@
*/
import parseText from './text/parser'
+import parseBinary from './binary/parser'
import { Block } from './data-model'
import { apply as applySchema } from './schema'
import mmCIF from './schema/mmcif'
export default {
parseText,
+ parseBinary,
applySchema,
schema: {
mmCIF: (block: Block) => applySchema(mmCIF, block)
}
-}
\ No newline at end of file
+}
+
+export * from './data-model'
\ No newline at end of file
diff --git a/src/script.ts b/src/script.ts
index 0ac94deb9..ba82c95d2 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -72,32 +72,49 @@ export function _gro() {
});
}
+function runCIF(input: string | Uint8Array) {
+ console.time('parseCIF');
+ const parsed = typeof input === 'string' ? CIF.parseText(input) : CIF.parseBinary(input);
+ console.timeEnd('parseCIF');
+ if (parsed.isError) {
+ console.log(parsed);
+ return;
+ }
+
+ const data = parsed.result.blocks[0];
+ const atom_site = data.categories._atom_site;
+ console.log(atom_site.getField('Cartn_x')!.float(0));
+ //console.log(atom_site.getField('label_atom_id')!.toStringArray());
+
+ const mmcif = CIF.schema.mmCIF(data);
+ console.log(mmcif.atom_site.Cartn_x.value(0));
+ console.log(mmcif.entity.type.toArray());
+ console.log(mmcif.pdbx_struct_oper_list.matrix.value(0));
+}
+
export function _cif() {
- const path = `./examples/1cbs_updated.cif`;
- //const path = 'c:/test/quick/3j3q.cif';
+ let path = `./examples/1cbs_updated.cif`;
+ //path = 'c:/test/quick/3j3q.cif';
fs.readFile(path, 'utf8', function (err, input) {
if (err) {
return console.log(err);
}
+ console.log('------------------');
+ console.log('Text CIF:');
+ runCIF(input);
+ });
- console.time('parseCIF');
- const parsed = CIF.parseText(input);
- console.timeEnd('parseCIF');
- if (parsed.isError) {
- console.log(parsed);
- return;
+ path = `./examples/1cbs_full.bcif`;
+ //const path = 'c:/test/quick/3j3q.cif';
+ fs.readFile(path, function (err, input) {
+ if (err) {
+ return console.log(err);
}
-
- const data = parsed.result.blocks[0];
-
- const atom_site = data.categories._atom_site;
- console.log(atom_site.getField('Cartn_x')!.float(0));
- //console.log(atom_site.getField('label_atom_id')!.toStringArray());
-
- const mmcif = CIF.schema.mmCIF(data);
- console.log(mmcif.atom_site.Cartn_x.value(0));
- console.log(mmcif.entity.type.toArray());
- console.log(mmcif.pdbx_struct_oper_list.matrix.value(0));
+ console.log('------------------');
+ console.log('BinaryCIF:');
+ const data = new Uint8Array(input.byteLength);
+ for (let i = 0; i < input.byteLength; i++) data[i] = input[i];
+ runCIF(input);
});
}
--
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