From 088e61bccffe4cad07fbaa01c8f85399eb649048 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Sun, 5 Nov 2017 18:47:10 +0100
Subject: [PATCH] include float precision in table schemas
---
src/apps/domain-annotation-server/schemas.ts | 2 +-
.../collections/database/_spec/table.spec.ts | 8 +--
src/mol-base/collections/database/column.ts | 29 +++++++++++
src/mol-base/collections/database/table.ts | 2 +-
.../structure/model/properties/hierarchy.ts | 2 +-
src/mol-io/reader/_spec/cif.spec.ts | 2 +-
src/mol-io/reader/cif/schema.ts | 2 +-
src/mol-io/reader/cif/schema/dic.ts | 9 ++--
src/mol-io/reader/cif/schema/mmcif.ts | 52 ++++++++++---------
9 files changed, 70 insertions(+), 38 deletions(-)
diff --git a/src/apps/domain-annotation-server/schemas.ts b/src/apps/domain-annotation-server/schemas.ts
index 34f17d566..90bbcba97 100644
--- a/src/apps/domain-annotation-server/schemas.ts
+++ b/src/apps/domain-annotation-server/schemas.ts
@@ -6,7 +6,7 @@
import { Column } from 'mol-base/collections/database'
-import Type = Column.Type
+import Type = Column.Schema
export const Sources = {
id: Type.str,
diff --git a/src/mol-base/collections/database/_spec/table.spec.ts b/src/mol-base/collections/database/_spec/table.spec.ts
index 69e534231..9f61d1baf 100644
--- a/src/mol-base/collections/database/_spec/table.spec.ts
+++ b/src/mol-base/collections/database/_spec/table.spec.ts
@@ -53,8 +53,8 @@ describe('column', () => {
describe('table', () => {
const schema = {
- x: Column.Type.int,
- n: Column.Type.str
+ x: Column.Schema.int,
+ n: Column.Schema.str
};
it('ofRows', () => {
@@ -89,7 +89,7 @@ describe('table', () => {
x: Column.ofArray({ array: [10, -1], type: Column.Type.int }),
n: Column.ofArray({ array: ['row1', 'row2'], type: Column.Type.str }),
});
- const s = { x: Column.Type.int, y: Column.Type.int };
+ const s = { x: Column.Schema.int, y: Column.Schema.int };
const picked = Table.pickColumns(s, t, { y: Column.ofArray({ array: [3, 4], type: Column.Type.int })});
expect(picked._columns).toEqual(['x', 'y']);
expect(picked._rowCount).toEqual(2);
@@ -102,7 +102,7 @@ describe('table', () => {
x: Column.ofArray({ array: [10, -1], type: Column.Type.int }),
n: Column.ofArray({ array: ['row1', 'row2'], type: Column.Type.str }),
});
- const s = { x: Column.Type.int };
+ const s = { x: Column.Schema.int };
const view = Table.view(t, s, [1]);
expect(view._columns).toEqual(['x']);
expect(view._rowCount).toEqual(1);
diff --git a/src/mol-base/collections/database/column.ts b/src/mol-base/collections/database/column.ts
index 80b9fc94c..a6110269f 100644
--- a/src/mol-base/collections/database/column.ts
+++ b/src/mol-base/collections/database/column.ts
@@ -39,6 +39,35 @@ 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 namespace Schema {
+ export interface FloatPrecision {
+ low: number,
+ acceptable: number,
+ full: number
+ }
+
+ export type Scalar = Schema.Str | Schema.Int | Schema.Float
+
+ 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 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 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 function aliased<T>(t: Schema): Aliased<T> { return t as any as Aliased<T>; }
+ }
+
export interface ToArrayParams<T> {
array?: ArrayCtor<T>,
start?: number,
diff --git a/src/mol-base/collections/database/table.ts b/src/mol-base/collections/database/table.ts
index fa701fa39..a7178bc1c 100644
--- a/src/mol-base/collections/database/table.ts
+++ b/src/mol-base/collections/database/table.ts
@@ -16,7 +16,7 @@ type Table<Schema extends Table.Schema> = {
/** An immutable table */
namespace Table {
- export type Schema = { [field: string]: Column.Type }
+ export type Schema = { [field: string]: Column.Schema }
export type Columns<S extends Schema> = { [C in keyof S]: Column<S[C]['T']> }
export type Row<S extends Schema> = { [C in keyof S]: S[C]['T'] }
export type Arrays<S extends Schema> = { [C in keyof S]: ArrayLike<S[C]['T']> }
diff --git a/src/mol-data/structure/model/properties/hierarchy.ts b/src/mol-data/structure/model/properties/hierarchy.ts
index fa647d207..a19de7fd5 100644
--- a/src/mol-data/structure/model/properties/hierarchy.ts
+++ b/src/mol-data/structure/model/properties/hierarchy.ts
@@ -10,7 +10,7 @@ import { mmCIF_Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
import { ElementSymbol} from '../types'
export const AtomsSchema = {
- type_symbol: Column.Type.aliased<ElementSymbol>(mmCIF.atom_site.type_symbol),
+ type_symbol: Column.Schema.aliased<ElementSymbol>(mmCIF.atom_site.type_symbol),
label_atom_id: mmCIF.atom_site.label_atom_id,
auth_atom_id: mmCIF.atom_site.auth_atom_id,
label_alt_id: mmCIF.atom_site.label_alt_id,
diff --git a/src/mol-io/reader/_spec/cif.spec.ts b/src/mol-io/reader/_spec/cif.spec.ts
index b2309f006..856e1e16f 100644
--- a/src/mol-io/reader/_spec/cif.spec.ts
+++ b/src/mol-io/reader/_spec/cif.spec.ts
@@ -22,7 +22,7 @@ const testBlock = Data.Block(['atoms'], {
}, 'test');
namespace TestSchema {
- export const atoms = { x: Column.Type.int, name: Column.Type.str }
+ export const atoms = { x: Column.Schema.int, name: Column.Schema.str }
export const schema = { atoms }
}
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index ee788fdfd..3c8c40214 100644
--- a/src/mol-io/reader/cif/schema.ts
+++ b/src/mol-io/reader/cif/schema.ts
@@ -17,7 +17,7 @@ export function toTable<Schema extends Table.Schema, R extends Table<Schema> = T
type ColumnCtor = (field: Data.Field, category: Data.Category, key: string) => Column<any>
-function getColumnCtor(t: Column.Type): ColumnCtor {
+function getColumnCtor(t: Column.Schema): ColumnCtor {
switch (t.kind) {
case 'str': return (f, c, k) => createColumn(Column.Type.str, f, f.str, f.toStringArray);
case 'int': return (f, c, k) => createColumn(Column.Type.int, f, f.int, f.toIntArray);
diff --git a/src/mol-io/reader/cif/schema/dic.ts b/src/mol-io/reader/cif/schema/dic.ts
index 09e0d5b60..f9a934abd 100644
--- a/src/mol-io/reader/cif/schema/dic.ts
+++ b/src/mol-io/reader/cif/schema/dic.ts
@@ -5,11 +5,12 @@
*/
import { Database, Column } from 'mol-base/collections/database'
-import Types = Column.Type
+import Schema = Column.Schema
+import FP = Schema.FP
-const str = Types.str
-const float = Types.float
+const str = Schema.str;
+const float = Schema.float;
const datablock = {
id: str,
@@ -55,7 +56,7 @@ const item_units_conversion = {
from_code: str,
to_code: str,
operator: str,
- factor: float
+ factor: float(FP(6, 6, 6))
}
// TODO save frame dic schema
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 42aabd396..939c9039e 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -5,11 +5,13 @@
*/
import { Database, Column } from 'mol-base/collections/database'
-import Types = Column.Type
-const str = Types.str;
-const int = Types.int;
-const float = Types.float;
+import Schema = Column.Schema
+import FP = Schema.FP
+
+const str = Schema.str;
+const int = Schema.int;
+const float = Schema.float;
const entry = {
id: str
@@ -19,10 +21,10 @@ type EntityType = 'polymer' | 'non-polymer' | 'water' | 'macrolide'
const entity = {
id: str,
- type: Types.aliased<EntityType>(str),
+ type: Schema.aliased<EntityType>(str),
src_method: str,
pdbx_description: str,
- formula_weight: float,
+ formula_weight: float(FP(6, 3, 1)),
pdbx_number_of_molecules: int,
details: str,
pdbx_mutation: str,
@@ -37,12 +39,12 @@ const exptl = {
const cell = {
entry_id: str,
- length_a: float,
- length_b: float,
- length_c: float,
- angle_alpha: float,
- angle_beta: float,
- angle_gamma: float,
+ length_a: float(FP(6, 6, 6)),
+ length_b: float(FP(6, 6, 6)),
+ length_c: float(FP(6, 6, 6)),
+ angle_alpha: float(FP(6, 6, 6)),
+ angle_beta: float(FP(6, 6, 6)),
+ angle_gamma: float(FP(6, 6, 6)),
Z_PDB: int,
pdbx_unique_axis: str
}
@@ -118,7 +120,7 @@ type BondValueOrder =
const struct_conn = {
id: str,
- conn_type_id: Types.aliased<StructConnTypeId>(str),
+ conn_type_id: Schema.aliased<StructConnTypeId>(str),
pdbx_PDB_id: str,
ptnr1_label_asym_id: str,
ptnr1_label_comp_id: str,
@@ -148,12 +150,12 @@ const struct_conn = {
pdbx_ptnr3_label_alt_id: str,
pdbx_ptnr3_PDB_ins_code: str,
details: str,
- pdbx_dist_value: float,
- pdbx_value_order: Types.aliased<BondValueOrder>(str)
+ pdbx_dist_value: float(FP(6, 3, 3)),
+ pdbx_value_order: Schema.aliased<BondValueOrder>(str)
}
const struct_conn_type = {
- id: Types.aliased<StructConnTypeId>(str),
+ id: Schema.aliased<StructConnTypeId>(str),
criteria: str,
reference: str
}
@@ -162,10 +164,10 @@ const chem_comp_bond = {
comp_id: str,
pdbx_stereo_config: str,
pdbx_ordinal: int,
- pdbx_aromatic_flag: Types.aliased<'Y' | 'N'>(str),
+ pdbx_aromatic_flag: Schema.aliased<'Y' | 'N'>(str),
atom_id_1: str,
atom_id_2: str,
- value_order: Types.aliased<BondValueOrder>(str)
+ value_order: Schema.aliased<BondValueOrder>(str)
}
const pdbx_struct_assembly = {
@@ -187,8 +189,8 @@ const pdbx_struct_oper_list = {
type: str,
name: str,
symmetry_operation: str,
- matrix: Types.matrix(3, 3),
- vector: Types.vector(3)
+ matrix: Schema.matrix(3, 3),
+ vector: Schema.vector(3)
}
const pdbx_struct_mod_residue = {
@@ -216,11 +218,11 @@ const atom_site = {
label_seq_id: int,
pdbx_PDB_ins_code: str,
pdbx_formal_charge: str,
- Cartn_x: float,
- Cartn_y: float,
- Cartn_z: float,
- occupancy: float,
- B_iso_or_equiv: float,
+ Cartn_x: float(FP(6, 3, 1)),
+ Cartn_y: float(FP(6, 3, 1)),
+ Cartn_z: float(FP(6, 3, 1)),
+ occupancy: float(FP(2, 2, 1)),
+ B_iso_or_equiv: float(FP(2, 2, 1)),
auth_atom_id: str,
auth_comp_id: str,
auth_asym_id: str,
--
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