From 53c12b748c2fd06016222e5047f48800fa833a84 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 5 Jul 2018 11:42:55 +0200
Subject: [PATCH] wip, mmCIF exporter
---
src/mol-io/writer/cif/encoder.ts | 12 ++++++++----
src/mol-io/writer/cif/encoder/binary.ts | 2 +-
src/mol-io/writer/cif/encoder/text.ts | 10 ++++++----
.../structure/export/categories/atom_site.ts | 2 +-
src/mol-model/structure/export/mmcif.ts | 7 ++++++-
5 files changed, 22 insertions(+), 11 deletions(-)
diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index 05dcf0052..174ea0f89 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -21,7 +21,7 @@ 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
+ value(key: Key, data: Data, index: number): string | number
valueKind?: (key: Key, data: Data) => Column.ValueKind,
defaultFormat?: Field.Format,
shouldInclude?: (data: Data) => boolean
@@ -38,11 +38,11 @@ export namespace Field {
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?: ParamsBase<K, D>): Field<K, D> {
+ export function str<K, D = any>(name: string, value: (k: K, d: D, index: number) => 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?: ParamsBase<K, D> & { typedArray?: ArrayEncoding.TypedArrayCtor }): Field<K, D> {
+ export function int<K, D = any>(name: string, value: (k: K, d: D, index: number) => number, params?: ParamsBase<K, D> & { typedArray?: ArrayEncoding.TypedArrayCtor }): Field<K, D> {
return {
name,
type: Type.Int,
@@ -53,7 +53,7 @@ export namespace Field {
};
}
- 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> {
+ export function float<K, D = any>(name: string, value: (k: K, d: D, index: number) => number, params?: ParamsBase<K, D> & { typedArray?: ArrayEncoding.TypedArrayCtor, digitCount?: number }): Field<K, D> {
return {
name,
type: Type.Float,
@@ -63,6 +63,10 @@ export namespace Field {
shouldInclude: params && params.shouldInclude
};
}
+
+ export function index(name: string) {
+ return int(name, (e, d, i) => i + 1, { typedArray: Int32Array, encoder: ArrayEncoding.by(ArrayEncoding.delta).and(ArrayEncoding.runLength).and(ArrayEncoding.integerPacking) })
+ }
}
export interface Category<Key = any, Data = any> {
diff --git a/src/mol-io/writer/cif/encoder/binary.ts b/src/mol-io/writer/cif/encoder/binary.ts
index 564adbfd8..01e07965d 100644
--- a/src/mol-io/writer/cif/encoder/binary.ts
+++ b/src/mol-io/writer/cif/encoder/binary.ts
@@ -141,7 +141,7 @@ function encodeField(field: Field, data: { data: any, keys: () => Iterator<any>
allPresent = false;
} else {
mask[offset] = Column.ValueKind.Present;
- array[offset] = getter(key, d);
+ array[offset] = getter(key, d, offset);
}
offset++;
}
diff --git a/src/mol-io/writer/cif/encoder/text.ts b/src/mol-io/writer/cif/encoder/text.ts
index 55ec8ec85..a19162728 100644
--- a/src/mol-io/writer/cif/encoder/text.ts
+++ b/src/mol-io/writer/cif/encoder/text.ts
@@ -73,14 +73,14 @@ export default class TextEncoder implements Encoder<string> {
}
}
-function writeValue(builder: StringBuilder, data: any, key: any, f: Field<any, any>, floatPrecision: number): boolean {
+function writeValue(builder: StringBuilder, data: any, key: any, f: Field<any, any>, floatPrecision: number, index: number): boolean {
const kind = f.valueKind;
const p = kind ? kind(key, data) : Column.ValueKind.Present;
if (p !== Column.ValueKind.Present) {
if (p === Column.ValueKind.NotPresent) writeNotPresent(builder);
else writeUnknown(builder);
} else {
- const val = f.value(key, data);
+ const val = f.value(key, data, index);
const t = f.type;
if (t === Field.Type.Str) {
if (isMultiline(val as string)) {
@@ -127,7 +127,7 @@ function writeCifSingleRecord(category: Category<any>, builder: StringBuilder, f
if (!filter.includeField(category.name, f.name)) continue;
StringBuilder.writePadRight(builder, `_${category.name}.${f.name}`, width);
- const multiline = writeValue(builder, data, key, f, precisions[_f]);
+ const multiline = writeValue(builder, data, key, f, precisions[_f], 0);
if (!multiline) StringBuilder.newline(builder);
}
StringBuilder.write(builder, '#\n');
@@ -147,6 +147,7 @@ function writeCifLoop(categories: Category[], builder: StringBuilder, filter: Ca
writeLine(builder, `_${first.name}.${fields[i].name}`);
}
+ let index = 0;
for (let _c = 0; _c < categories.length; _c++) {
const category = categories[_c];
const data = category.data;
@@ -159,9 +160,10 @@ function writeCifLoop(categories: Category[], builder: StringBuilder, filter: Ca
let multiline = false;
for (let _f = 0; _f < fieldCount; _f++) {
- multiline = writeValue(builder, data, key, fields[_f], precisions[_f]);
+ multiline = writeValue(builder, data, key, fields[_f], precisions[_f], index);
}
if (!multiline) StringBuilder.newline(builder);
+ index++;
}
}
StringBuilder.write(builder, '#\n');
diff --git a/src/mol-model/structure/export/categories/atom_site.ts b/src/mol-model/structure/export/categories/atom_site.ts
index 7ee771645..c5b1fab70 100644
--- a/src/mol-model/structure/export/categories/atom_site.ts
+++ b/src/mol-model/structure/export/categories/atom_site.ts
@@ -14,7 +14,7 @@ import E = CifWriter.Encodings
const atom_site_fields: CifField<Element.Location>[] = [
CifField.str('group_PDB', P.residue.group_PDB),
- CifField.int('id', P.atom.id, { encoder: E.deltaRLE }),
+ CifField.index('id'),
CifField.str('type_symbol', P.atom.type_symbol as any),
CifField.str('label_atom_id', P.atom.label_atom_id),
CifField.str('label_alt_id', P.atom.label_alt_id),
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index eca4f961e..3a5f900c8 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -35,10 +35,15 @@ function _entity({ model, structure }: CifExportContext): CifCategory {
const Categories = [
copy_mmCif_category('entry'),
copy_mmCif_category('exptl'),
+ _entity,
copy_mmCif_category('cell'),
copy_mmCif_category('symmetry'),
+ copy_mmCif_category('pdbx_struct_assembly'),
+ copy_mmCif_category('pdbx_struct_assembly_gen'),
+ copy_mmCif_category('pdbx_struct_oper_list'),
+ // TODO: filter for actual present residues?
copy_mmCif_category('chem_comp'),
- _entity,
+ copy_mmCif_category('atom_sites'),
_atom_site
];
--
GitLab