diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index 3e51663ac42e82effffa731e7b38529c42623d3a..05dcf0052bb191bb92370f30a54493c38ff76a79 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -21,9 +21,10 @@ import { ArrayEncoder, ArrayEncoding } from '../../common/binary-cif';
export interface Field<Key = any, Data = any> {
name: string,
type: Field.Type,
+ value(key: Key, data: Data): string | number
valueKind?: (key: Key, data: Data) => Column.ValueKind,
defaultFormat?: Field.Format,
- value(key: Key, data: Data): string | number
+ shouldInclude?: (data: Data) => boolean
}
export namespace Field {
@@ -35,31 +36,31 @@ export namespace Field {
typedArray?: ArrayEncoding.TypedArrayCtor
}
- export function getDigitCount(field: Field) {
- if (field.defaultFormat && typeof field.defaultFormat.digitCount !== 'undefined') return Math.max(0, Math.min(field.defaultFormat.digitCount, 16));
- return 6;
- }
+ export type ParamsBase<K, D> = { valueKind?: (k: K, d: D) => Column.ValueKind, encoder?: ArrayEncoder, shouldInclude?: (data: D) => boolean }
- export function str<K, D = any>(name: string, value: (k: K, d: D) => string, params?: { valueKind?: (k: K, d: D) => Column.ValueKind, encoder?: ArrayEncoder }): Field<K, D> {
- return { name, type: Type.Str, value, valueKind: params && params.valueKind, defaultFormat: params && params.encoder ? { encoder: params.encoder } : void 0 };
+ export function str<K, D = any>(name: string, value: (k: K, d: D) => string, params?: ParamsBase<K, D>): Field<K, D> {
+ return { name, type: Type.Str, value, valueKind: params && params.valueKind, defaultFormat: params && params.encoder ? { encoder: params.encoder } : void 0, shouldInclude: params && params.shouldInclude };
}
- export function int<K, D = any>(name: string, value: (k: K, d: D) => number, params?: { valueKind?: (k: K, d: D) => Column.ValueKind, encoder?: ArrayEncoder, typedArray?: ArrayEncoding.TypedArrayCtor }): Field<K, D> {
+ export function int<K, D = any>(name: string, value: (k: K, d: D) => number, params?: ParamsBase<K, D> & { typedArray?: ArrayEncoding.TypedArrayCtor }): Field<K, D> {
return {
name,
type: Type.Int,
value,
valueKind: params && params.valueKind,
- defaultFormat: params ? { encoder: params.encoder, typedArray: params.typedArray } : void 0 };
+ defaultFormat: params ? { encoder: params.encoder, typedArray: params.typedArray } : void 0,
+ shouldInclude: params && params.shouldInclude
+ };
}
- export function float<K, D = any>(name: string, value: (k: K, d: D) => number, params?: { valueKind?: (k: K, d: D) => Column.ValueKind, encoder?: ArrayEncoder, typedArray?: ArrayEncoding.TypedArrayCtor, digitCount?: number }): Field<K, D> {
+ export function float<K, D = any>(name: string, value: (k: K, d: D) => number, params?: ParamsBase<K, D> & { typedArray?: ArrayEncoding.TypedArrayCtor, digitCount?: number }): Field<K, D> {
return {
name,
type: Type.Float,
value,
valueKind: params && params.valueKind,
- defaultFormat: params ? { encoder: params.encoder, typedArray: params.typedArray, digitCount: typeof params.digitCount !== 'undefined' ? params.digitCount : void 0 } : void 0
+ defaultFormat: params ? { encoder: params.encoder, typedArray: params.typedArray, digitCount: typeof params.digitCount !== 'undefined' ? params.digitCount : void 0 } : void 0,
+ shouldInclude: params && params.shouldInclude
};
}
}
diff --git a/src/mol-io/writer/cif/encoder/binary.ts b/src/mol-io/writer/cif/encoder/binary.ts
index e10b86940a15efd63c6b0d00d1c046a185300fe0..564adbfd8059a37d877d6617be08e82ae48991e6 100644
--- a/src/mol-io/writer/cif/encoder/binary.ts
+++ b/src/mol-io/writer/cif/encoder/binary.ts
@@ -14,6 +14,7 @@ import {
} from '../../../common/binary-cif'
import { Field, Category, Encoder } from '../encoder'
import Writer from '../../writer'
+import { getIncludedFields } from './util';
export default class BinaryEncoder implements Encoder<Uint8Array> {
private data: EncodedFile;
@@ -57,12 +58,17 @@ export default class BinaryEncoder implements Encoder<Uint8Array> {
const first = categories[0]!;
const cat: EncodedCategory = { name: '_' + first.name, columns: [], rowCount: count };
const data = categories.map(c => ({ data: c.data, keys: () => c.keys ? c.keys() : Iterator.Range(0, c.rowCount - 1) }));
- for (const f of first.fields) {
+ const fields = getIncludedFields(first);
+
+ for (const f of fields) {
if (!this.filter.includeField(first.name, f.name)) continue;
const format = this.formatter.getFormat(first.name, f.name);
cat.columns.push(encodeField(f, data, count, getArrayCtor(f, format), getEncoder(f, format)));
}
+ // no columns included.
+ if (!cat.columns.length) return;
+
this.dataBlocks[this.dataBlocks.length - 1].categories.push(cat);
}
diff --git a/src/mol-io/writer/cif/encoder/text.ts b/src/mol-io/writer/cif/encoder/text.ts
index 7352dbace857d189afe873ffd3677c8bf5c35e22..55ec8ec85db359d964f72526ba0813de77fe9be5 100644
--- a/src/mol-io/writer/cif/encoder/text.ts
+++ b/src/mol-io/writer/cif/encoder/text.ts
@@ -11,6 +11,7 @@ import { Column } from 'mol-data/db'
import StringBuilder from 'mol-util/string-builder'
import { Category, Field, Encoder } from '../encoder'
import Writer from '../../writer'
+import { getFieldDigitCount, getIncludedFields } from './util';
export default class TextEncoder implements Encoder<string> {
private builder = StringBuilder.create();
@@ -102,13 +103,13 @@ function getFloatPrecisions(categoryName: string, fields: Field[], formatter: Ca
for (const f of fields) {
const format = formatter.getFormat(categoryName, f.name);
if (format && typeof format.digitCount !== 'undefined') ret[ret.length] = f.type === Field.Type.Float ? Math.pow(10, Math.max(0, Math.min(format.digitCount, 15))) : 0;
- else ret[ret.length] = f.type === Field.Type.Float ? Math.pow(10, Field.getDigitCount(f)) : 0;
+ else ret[ret.length] = f.type === Field.Type.Float ? Math.pow(10, getFieldDigitCount(f)) : 0;
}
return ret;
}
function writeCifSingleRecord(category: Category<any>, builder: StringBuilder, filter: Category.Filter, formatter: Category.Formatter) {
- const fields = category.fields;
+ const fields = getIncludedFields(category);
const data = category.data;
let width = fields.reduce((w, f) => filter.includeField(category.name, f.name) ? Math.max(w, f.name.length) : 0, 0);
@@ -134,8 +135,11 @@ function writeCifSingleRecord(category: Category<any>, builder: StringBuilder, f
function writeCifLoop(categories: Category[], builder: StringBuilder, filter: Category.Filter, formatter: Category.Formatter) {
const first = categories[0];
- const fields = filter === Category.DefaultFilter ? first.fields : first.fields.filter(f => filter.includeField(first.name, f.name));
+ const fieldSource = getIncludedFields(first);
+ const fields = filter === Category.DefaultFilter ? fieldSource : fieldSource.filter(f => filter.includeField(first.name, f.name));
const fieldCount = fields.length;
+ if (fieldCount === 0) return;
+
const precisions = getFloatPrecisions(first.name, fields, formatter);
writeLine(builder, 'loop_');
diff --git a/src/mol-io/writer/cif/encoder/util.ts b/src/mol-io/writer/cif/encoder/util.ts
new file mode 100644
index 0000000000000000000000000000000000000000..af8b3369f61d11939cca26f24b3bae02a0de4a6a
--- /dev/null
+++ b/src/mol-io/writer/cif/encoder/util.ts
@@ -0,0 +1,18 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Field, Category } from '../encoder';
+
+export function getFieldDigitCount(field: Field) {
+ if (field.defaultFormat && typeof field.defaultFormat.digitCount !== 'undefined') return Math.max(0, Math.min(field.defaultFormat.digitCount, 16));
+ return 6;
+}
+
+export function getIncludedFields(category: Category<any, any>) {
+ return category.fields.some(f => !!f.shouldInclude)
+ ? category.fields.filter(f => !f.shouldInclude || f.shouldInclude(category.data))
+ : category.fields;
+}
\ No newline at end of file
diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index 8f9cac24028275ce2a8882e3859e1bd8c8e63c87..2e9776d8dd50ad3a642d1a08266ae4ced996bed2 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -18,7 +18,7 @@ interface SymmetryOperator {
}
namespace SymmetryOperator {
- export const DefaultName = 'identity'
+ export const DefaultName = '1_555'
export const Default: SymmetryOperator = create(DefaultName, Mat4.identity());
const RotationEpsilon = 0.0001;
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index 0a522303c91d4d124a9260cbb0c2031fed8d6e75..ea699f649fe5e900813d315af5cad2717b39bbb5 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -47,7 +47,9 @@ const atom_site_fields: CifField<Element.Location>[] = [
CifField.str('auth_asym_id', P.chain.auth_asym_id),
CifField.int('pdbx_PDB_model_num', P.unit.model_num, { encoder: E.deltaRLE }),
- CifField.str('operator_name', P.unit.operator_name)
+ CifField.str<Element.Location, Structure>('operator_name', P.unit.operator_name, {
+ shouldInclude: structure => structure.units.some(u => !u.conformation.operator.isIdentity)
+ })
];
function copy_mmCif_cat(name: keyof mmCIF_Schema) {
@@ -66,7 +68,7 @@ function _entity({ model, structure }: Context): CifCategory {
function _atom_site({ structure }: Context): CifCategory {
return {
- data: void 0,
+ data: structure,
name: 'atom_site',
fields: atom_site_fields,
rowCount: structure.elementCount,