From d7f7770b7ce62431f08a07117251ed12be892bc2 Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Fri, 7 Jun 2019 11:49:31 -0700
Subject: [PATCH] drops browser test, creates spec
---
src/mol-io/writer/_spec/cif.spec.ts | 98 ++++++++++++++++++++++++++++-
1 file changed, 96 insertions(+), 2 deletions(-)
diff --git a/src/mol-io/writer/_spec/cif.spec.ts b/src/mol-io/writer/_spec/cif.spec.ts
index efd8eac6e..7231c5d82 100644
--- a/src/mol-io/writer/_spec/cif.spec.ts
+++ b/src/mol-io/writer/_spec/cif.spec.ts
@@ -1,6 +1,15 @@
+import * as Data from '../../reader/cif/data-model'
import { CifWriter } from '../cif';
+import decodeMsgPack from '../../common/msgpack/decode'
+import { EncodedFile, EncodedCategory } from '../../common/binary-cif';
+import Field from '../../reader/cif/binary/field'
+
+const cartn_x = Data.CifField.ofNumbers([1.001, 1.002, 1.003, 1.004, 1.005, 1.006, 1.007, 1.008, 1.009]);
+const cartn_y = Data.CifField.ofNumbers([-3.0, -2.666, -2.3333, -2.0, -1.666, -1.333, -1.0, -0.666, -0.333]);
+const cartn_z = Data.CifField.ofNumbers([1, 2, 3, 4, 5, 6, 7, 8, 9].map(i => Math.sqrt(i)));
+const label_seq_id = Data.CifField.ofNumbers([1, 2, 3, 6, 11, 23, 47, 106, 235]);
+const atom_site = Data.CifCategory.ofFields('atom_site', { 'Cartn_x': cartn_x, 'Cartn_y': cartn_y, 'Cartn_z': cartn_z, 'label_seq_id': label_seq_id });
-const cif = await downloadFromPdb('1brr')
const encoder = CifWriter.createEncoder({
binary: true,
encoderName: 'mol*',
@@ -24,4 +33,89 @@ const encoder = CifWriter.createEncoder({
'encoding': 'delta-rle'
}
])
-});
\ No newline at end of file
+});
+
+function getCategoryInstanceProvider(cat: Data.CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
+ return {
+ name: cat.name,
+ instance: () => CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount })
+ };
+}
+
+function wrap(name: string, field: Data.CifField): CifWriter.Field {
+ const type = Data.getCifFieldType(field);
+ if (type['@type'] === 'str') {
+ return { name, type: CifWriter.Field.Type.Str, value: field.str, valueKind: field.valueKind };
+ } else if (type['@type'] === 'float') {
+ return { name, type: CifWriter.Field.Type.Float, value: field.float, valueKind: field.valueKind };
+ } else {
+ return { name, type: CifWriter.Field.Type.Int, value: field.int, valueKind: field.valueKind };
+ }
+}
+
+function Category(data: EncodedCategory): Data.CifCategory {
+ const map = Object.create(null);
+ const cache = Object.create(null);
+ for (const col of data.columns) map[col.name] = col;
+ return {
+ rowCount: data.rowCount,
+ name: data.name.substr(1),
+ fieldNames: data.columns.map(c => c.name),
+ getField(name) {
+ const col = map[name];
+ if (!col) return void 0;
+ if (!!cache[name]) return cache[name];
+ cache[name] = Field(col);
+ return cache[name];
+ }
+ }
+}
+describe('config', () => {
+ encoder.startDataBlock('test');
+ const fields: CifWriter.Field[] = [];
+ for (const f of atom_site.fieldNames) {
+ fields.push(wrap(f, atom_site.getField(f)!))
+ }
+
+ encoder.writeCategory(getCategoryInstanceProvider(atom_site, fields));
+ const encoded = encoder.getData() as Uint8Array;
+
+ const unpacked = decodeMsgPack(encoded) as EncodedFile;
+ const decoded = Data.CifFile(unpacked.dataBlocks.map(block => {
+ const cats = Object.create(null);
+ for (const cat of block.categories) cats[cat.name.substr(1)] = Category(cat);
+ return Data.CifBlock(block.categories.map(c => c.name.substr(1)), cats, block.header);
+ }));
+
+ const decoded_atom_site = decoded.blocks[0].categories['atom_site'];
+ const decoded_cartn_x = decoded_atom_site.getField('Cartn_x')!;
+ const decoded_cartn_y = decoded_atom_site.getField('Cartn_y')!;
+ const decoded_cartn_z = decoded_atom_site.getField('Cartn_z')!;
+ const decoded_label_seq_id = decoded_atom_site.getField('label_seq_id')!;
+
+ const delta = 0.001;
+ function assert(e: ArrayLike<number>, a: ArrayLike<number>) {
+ expect(e.length).toBe(a.length);
+ for (let i = 0; i < e.length; i++) {
+ expect(Math.abs(e[i] - a[i])).toBeLessThan(delta);
+ }
+ }
+
+ function join(field: Data.CifField) {
+ return field.binaryEncoding!.map(e => e.kind).join();
+ }
+
+ it('strategy', () => {
+ expect(join(decoded_cartn_x)).toBe('FixedPoint,Delta,IntegerPacking,ByteArray');
+ expect(join(decoded_cartn_y)).toBe('FixedPoint,RunLength,IntegerPacking,ByteArray');
+ expect(join(decoded_cartn_z)).toBe('FixedPoint,Delta,IntegerPacking,ByteArray');
+ expect(join(decoded_label_seq_id)).toBe('Delta,RunLength,IntegerPacking,ByteArray');
+ });
+
+ it('precision', () => {
+ assert(decoded_cartn_x.toFloatArray(), cartn_x.toFloatArray());
+ assert(decoded_cartn_y.toFloatArray(), cartn_y.toFloatArray().map(d => Math.round(d)));
+ assert(decoded_cartn_z.toFloatArray(), cartn_z.toFloatArray().map(d => Math.round(d * 10) / 10));
+ assert(decoded_label_seq_id.toIntArray(), label_seq_id.toIntArray());
+ });
+})
\ No newline at end of file
--
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