"coord" column schema

src/mol-base/collections/database/column.ts

@@ -39,7 +39,7 @@ namespace Column {
         export function aliased<T>(t: Type): Aliased<T> { return t as any as Aliased<T>; }
     }
 
-    export type Schema<T = any> = Schema.Scalar | Schema.Vector | Schema.Matrix | Schema.Aliased<T>
+    export type Schema<T = any> = Schema.Scalar<T> | Schema.Vector | Schema.Matrix
 
     export namespace Schema {
         export interface FloatPrecision {
@@ -48,23 +48,26 @@ namespace Column {
             full: number
         }
 
-        export type Scalar = Schema.Str | Schema.Int | Schema.Float
+        export type Scalar<T = any> = Schema.Str | Schema.Int | Schema.Float | Schema.Coordinate| Schema.Aliased<T>
 
         export function FP(full: number, acceptable: number, low: number): FloatPrecision { return { low, full, acceptable }; }
 
-        export type Str = { '@type': 'schema', T: string, kind: 'str' }
-        export type Int = { '@type': 'schema', T: number, kind: 'int' }
-        export type Float = { '@type': 'schema', T: number, kind: 'float', precision: FloatPrecision }
-        export type Vector = { '@type': 'schema', T: number[], dim: number, kind: 'vector' };
-        export type Matrix = { '@type': 'schema', T: number[][], rows: number, cols: number, kind: 'matrix' };
-        export type Aliased<T> = { '@type': 'schema', T: T } & { kind: 'str' | 'int' | 'float' }
+        export type Str = { '@type': 'str', T: string, kind: 'str' }
+        export type Int = { '@type': 'int', T: number, kind: 'int' }
+        export type Float = { '@type': 'float', T: number, kind: 'float', precision: FloatPrecision }
+        export type Coordinate = { '@type': 'coord', T: number, kind: 'float' }
 
-        export const str: Str = { '@type': 'schema', T: '', kind: 'str' };
-        export const int: Int = { '@type': 'schema', T: 0, kind: 'int' };
-        export function float(precision: FloatPrecision): Float { return { '@type': 'schema', T: 0, kind: 'float', precision } };
+        export type Vector = { '@type': 'vector', T: number[], dim: number, kind: 'vector' };
+        export type Matrix = { '@type': 'matrix', T: number[][], rows: number, cols: number, kind: 'matrix' };
+        export type Aliased<T> = { '@type': 'aliased', T: T } & { kind: 'str' | 'int' | 'float' }
 
-        export function vector(dim: number): Vector { return { '@type': 'schema', T: [] as number[], dim, kind: 'vector' }; }
-        export function matrix(rows: number, cols: number): Matrix { return { '@type': 'schema', T: [] as number[][], rows, cols, kind: 'matrix' }; }
+        export const str: Str = { '@type': 'str', T: '', kind: 'str' };
+        export const int: Int = { '@type': 'int', T: 0, kind: 'int' };
+        export const coord: Coordinate = { '@type': 'coord', T: 0, kind: 'float' };
+        export function float(precision: FloatPrecision): Float { return { '@type': 'float', T: 0, kind: 'float', precision } };
+
+        export function vector(dim: number): Vector { return { '@type': 'vector', T: [] as number[], dim, kind: 'vector' }; }
+        export function matrix(rows: number, cols: number): Matrix { return { '@type': 'matrix', T: [] as number[][], rows, cols, kind: 'matrix' }; }
         export function aliased<T>(t: Schema): Aliased<T> { return t as any as Aliased<T>; }
     }
 

src/mol-io/reader/cif/schema/mmcif.ts

@@ -218,9 +218,9 @@ const atom_site = {
     label_seq_id: int,
     pdbx_PDB_ins_code: str,
     pdbx_formal_charge: str,
-    Cartn_x: float(FP(6, 3, 1)),
-    Cartn_y: float(FP(6, 3, 1)),
-    Cartn_z: float(FP(6, 3, 1)),
+    Cartn_x: Schema.coord,
+    Cartn_y: Schema.coord,
+    Cartn_z: Schema.coord,
     occupancy: float(FP(2, 2, 1)),
     B_iso_or_equiv: float(FP(2, 2, 1)),
     auth_atom_id: str,

src/mol-io/writer/cif/encoder.ts

@@ -7,7 +7,10 @@
 import Iterator from 'mol-base/collections/iterator'
 import { Column } from 'mol-base/collections/database'
 import Encoder from '../encoder'
-//import { ArrayEncoder, ArrayEncoding as E } from '../../common/binary-cif'
+
+// TODO: support for "coordinate fields", make "coordinate precision" a parameter of the encoder
+// TODO: automatically detect "precision" of floating point arrays.
+// TODO: automatically detect "best encoding" for integer arrays. This could be used for "fixed-point" as well.
 
 export const enum FieldType {
     Str, Int, Float
@@ -26,7 +29,7 @@ export type FieldDefinition<Key = any, Data = any> =
     | FieldDefinitionBase<Key, Data> & { type: FieldType.Float, value(key: Key, data: Data): number }
 
 export interface FieldFormat {
-    // TODO
+    // TODO: do we actually need this?
     // textDecimalPlaces: number,
     // stringEncoder: ArrayEncoder,
     // numericEncoder: ArrayEncoder,