diff --git a/src/mol-data/model.ts b/src/mol-data/model.ts
index bc5a486946ba4e8f5231a1536bd8767fd58bfce7..2d238f801d6d6f23cb616599298ce088cfae6de4 100644
--- a/src/mol-data/model.ts
+++ b/src/mol-data/model.ts
@@ -5,9 +5,9 @@
*/
import * as Formats from './model/formats'
-import CommonProperties from './model/common'
-import MacromoleculeProperties from './model/macromolecule'
-import Conformation from './model/conformation'
+//import CommonProperties from './model/properties/common'
+import MacromoleculeProperties from './model/properties/macromolecule'
+import Conformation from './model/properties/conformation'
import Segmentation from '../mol-base/collections/integer/segmentation'
/**
@@ -18,9 +18,11 @@ import Segmentation from '../mol-base/collections/integer/segmentation'
interface Model extends Readonly<{
id: string,
+ model_num: number,
+
sourceData: Formats.RawData,
- common: CommonProperties,
+ //common: CommonProperties,
macromolecule: MacromoleculeProperties,
conformation: Conformation,
diff --git a/src/mol-data/model/builders/mmcif.ts b/src/mol-data/model/builders/mmcif.ts
index 9fe460f0c7bc2ec4b312b9084f30d903d9e862e4..e9a26ff171bf7d642e9467c727124489d7a362e1 100644
--- a/src/mol-data/model/builders/mmcif.ts
+++ b/src/mol-data/model/builders/mmcif.ts
@@ -5,7 +5,7 @@
*/
import { RawData } from '../formats'
-import mmCIF from '../../../mol-io/reader/cif/schema/mmcif'
+import { Frame as mmCIF } from '../../../mol-io/reader/cif/schema/mmcif'
import Model from '../../model'
import Interval from '../../../mol-base/collections/integer/interval'
import Segmentation from '../../../mol-base/collections/integer/segmentation'
@@ -57,7 +57,8 @@ function createModel(raw: RawData, data: mmCIF, bounds: Interval): Model {
return {
id: uuId(),
sourceData: raw,
- common: 0 as any,
+ model_num: 0, // TODO: fix
+ //common: 0 as any,
macromolecule: 0 as any,
conformation: 0 as any,
version: { data: 0, conformation: 0 },
diff --git a/src/mol-data/model/common.ts b/src/mol-data/model/common.ts
deleted file mode 100644
index 885f7c2f5448e89a84ea5372289cd6cccc82b35d..0000000000000000000000000000000000000000
--- a/src/mol-data/model/common.ts
+++ /dev/null
@@ -1,11 +0,0 @@
-/**
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-interface Common {
-
-}
-
-export default Common
\ No newline at end of file
diff --git a/src/mol-data/model/formats.ts b/src/mol-data/model/formats.ts
index 1f98e96f5ebc6fc2e3cf5745c27b3849800e19b3..56ec708a4d03e60e7e7578a9a405c73aac39407f 100644
--- a/src/mol-data/model/formats.ts
+++ b/src/mol-data/model/formats.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import mmCIF from '../../mol-io/reader/cif/schema/mmcif'
+import { Frame as mmCIF_Frame } from '../../mol-io/reader/cif/schema/mmcif'
export type RawData =
- | { source: 'mmCIF', data: mmCIF }
\ No newline at end of file
+ | { source: 'mmCIF', data: mmCIF_Frame }
\ No newline at end of file
diff --git a/src/mol-data/model/macromolecule.ts b/src/mol-data/model/macromolecule.ts
deleted file mode 100644
index 368d780f2d90ffef3e2e4886f0fc32d2d814db88..0000000000000000000000000000000000000000
--- a/src/mol-data/model/macromolecule.ts
+++ /dev/null
@@ -1,11 +0,0 @@
-/**
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-interface Macromolecule {
-
-}
-
-export default Macromolecule
\ No newline at end of file
diff --git a/src/mol-data/model/properties/basic.ts b/src/mol-data/model/properties/basic.ts
new file mode 100644
index 0000000000000000000000000000000000000000..1837912b6d1cdaeca9af1e182208ac4da7537b4f
--- /dev/null
+++ b/src/mol-data/model/properties/basic.ts
@@ -0,0 +1,28 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Column from '../../../mol-base/collections/column'
+
+export type Table<Data> = { [E in keyof Data]: Column<Data[E]> }
+
+export interface ElementSymbol extends String { '@type': 'element-symbol' }
+export function ElementSymbol(s: string): ElementSymbol {
+ // TODO: optimize?
+ return s.toUpperCase() as any;
+}
+
+
+export interface Atoms extends Table<{
+ name: string,
+ elementSymbol: ElementSymbol,
+
+}> { }
+
+interface Common {
+
+}
+
+export default Common
\ No newline at end of file
diff --git a/src/mol-data/model/conformation.ts b/src/mol-data/model/properties/conformation.ts
similarity index 100%
rename from src/mol-data/model/conformation.ts
rename to src/mol-data/model/properties/conformation.ts
diff --git a/src/mol-data/model/properties/macromolecule.ts b/src/mol-data/model/properties/macromolecule.ts
new file mode 100644
index 0000000000000000000000000000000000000000..1285ba4d37c384f9e1a42ed08f3a12f36e763162
--- /dev/null
+++ b/src/mol-data/model/properties/macromolecule.ts
@@ -0,0 +1,72 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Column from '../../../mol-base/collections/column'
+import { Shape as mmCIF } from '../../../mol-io/reader/cif/schema/mmcif'
+
+export type Table<Data> = { [E in keyof Data]: Column<Data[E]> }
+
+export interface ElementSymbol extends String { '@type': 'element-symbol' }
+export function ElementSymbol(s: string): ElementSymbol {
+ // TODO: optimize?
+ return s.toUpperCase() as any;
+}
+
+export interface Atoms extends Table<{
+ // unique number for each atom
+ key: number,
+
+ id: number,
+ type_symbol: ElementSymbol,
+ label_atom_id: string,
+ auth_atom_id: string,
+ label_alt_id: string,
+ auth_alt_id: string,
+ pdbx_formal_charge: string,
+ occupancy: number,
+ B_iso_or_equiv: number
+}> { }
+
+export interface Residues extends Table<{
+ // unique number for each residue
+ key: number,
+
+ group_PDB: string,
+
+ label_comp_id: string,
+ auth_comp_id: string,
+ label_seq_id: number,
+ auth_seq_id: number,
+ pdbx_PDB_ins_code: string
+}> { }
+
+export interface Chains extends Table<{
+ // unique number for each chain
+ key: number,
+
+ label_asym_id: string,
+ auth_asym_id: string
+}> { }
+
+export interface Entities extends Table<{
+ // unique number for each entity
+ // row index to the EntityData table
+ key: number,
+ label_entity_id: string,
+ pdbx_PDB_model_num: number
+}> { }
+
+type _EntityData = mmCIF['entity']
+export interface EntityData extends _EntityData { }
+
+export interface Macromolecule {
+ atoms: Atoms,
+ residues: Residues,
+ chains: Chains,
+ entities: Entities
+}
+
+export default Macromolecule
\ No newline at end of file
diff --git a/src/mol-data/model/properties/symmetry.ts b/src/mol-data/model/properties/symmetry.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/mol-io/reader/cif.ts b/src/mol-io/reader/cif.ts
index 0d44a5482dab5a2fda4b3e08860233c9c856adbe..29a734f04605785d2f8fc49a5e3d2a6b4b6db60a 100644
--- a/src/mol-io/reader/cif.ts
+++ b/src/mol-io/reader/cif.ts
@@ -6,16 +6,16 @@
import parseText from './cif/text/parser'
import parseBinary from './cif/binary/parser'
-import { Block } from './cif/data-model'
+import { Frame } from './cif/data-model'
import { toTypedFrame as applySchema } from './cif/schema'
-import mmCIF from './cif/schema/mmcif'
+import { Schema as mmCIF_Schema, Frame as mmCIF_Frame } from './cif/schema/mmcif'
export default {
parseText,
parseBinary,
applySchema,
schema: {
- mmCIF: (block: Block) => applySchema(mmCIF, block)
+ mmCIF: (frame: Frame) => applySchema<typeof mmCIF_Schema, mmCIF_Frame>(mmCIF_Schema, frame)
}
}
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index 7d603fc73f3710f279c20c33c7952860768b5087..368aaa11098108cc7ce99677d0a764eee09b22f2 100644
--- a/src/mol-io/reader/cif/schema.ts
+++ b/src/mol-io/reader/cif/schema.ts
@@ -24,8 +24,8 @@ import Column, { createAndFillArray } from '../../../mol-base/collections/column
//////////////////////////////////////////////
-export function toTypedFrame<Schema extends FrameSchema>(schema: Schema, frame: Data.Frame): TypedFrame<Schema> {
- return createTypedFrame(schema, frame) as TypedFrame<Schema>;
+export function toTypedFrame<Schema extends FrameSchema, Frame extends TypedFrame<Schema> = TypedFrame<Schema>>(schema: Schema, frame: Data.Frame): Frame {
+ return createTypedFrame(schema, frame) as Frame;
}
export function toTypedCategory<Schema extends CategorySchema>(schema: Schema, category: Data.Category): TypedCategory<Schema> {
@@ -33,13 +33,14 @@ export function toTypedCategory<Schema extends CategorySchema>(schema: Schema, c
}
export type FrameSchema = { [category: string]: CategorySchema }
+export type TypedFrameShape<Schema extends FrameSchema> = { [C in keyof Schema]: TypedCategoryShape<Schema[C]> }
export type TypedFrame<Schema extends FrameSchema> = {
readonly _header?: string,
readonly _frame: Data.Frame
} & { [C in keyof Schema]: TypedCategory<Schema[C]> }
-
export type CategorySchema = { [field: string]: Field.Schema<any> }
+export type TypedCategoryShape<Schema extends CategorySchema> = { [F in keyof Schema]: Column<Schema[F]['T']> }
export type TypedCategory<Schema extends CategorySchema> = {
readonly _rowCount: number,
readonly _isDefined: boolean,
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index b317a628481b7292b353517ebdc4f9f04c47b42d..a5d3ba1567e63dc17b42123231f1e3195c2a3141 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Field, TypedFrame } from '../schema'
+import { Field, TypedFrame, TypedFrameShape } from '../schema'
const str = Field.str();
const int = Field.int();
@@ -14,9 +14,11 @@ const entry = {
id: str
}
+type EntityType = 'polymer' | 'non-polymer' | 'water'
+
const entity = {
id: str,
- type: str as Field.Schema<'polymer' | 'non-polymer' | 'water'>,
+ type: str as Field.Schema<EntityType>,
src_method: str,
pdbx_description: str,
formula_weight: float,
@@ -225,7 +227,7 @@ const atom_site = {
pdbx_PDB_model_num: int
}
-const mmCIF = {
+export const Schema = {
entry,
entity,
exptl,
@@ -242,5 +244,6 @@ const mmCIF = {
pdbx_struct_mod_residue,
atom_site
};
-type mmCIF = TypedFrame<typeof mmCIF>
-export default mmCIF;
\ No newline at end of file
+
+export interface Frame extends TypedFrame<typeof Schema> { }
+export interface Shape extends TypedFrameShape<typeof Schema> { }
\ No newline at end of file
diff --git a/src/script.ts b/src/script.ts
index e05c5e817689fb20e596e8d8abfe004ff89846c2..dbe952e166678bedb9cb3ed5eba471aa1d4fc768 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -117,7 +117,7 @@ async function runCIF(input: string | Uint8Array) {
console.time('createModels');
const models = buildModels(mmcif);
console.timeEnd('createModels');
- console.log(models[0].common);
+ console.log(models[0].id);
// const schema = await _dic()
// if (schema) {