From 6979ae82546ac1030e45f0768651caddd9d755ee Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 3 Oct 2017 14:20:26 +0200
Subject: [PATCH] mmCIF schema
---
src/reader/cif/data-model.ts | 22 ++
src/reader/cif/index.ts | 15 ++
src/reader/cif/schema.ts | 50 ++--
src/reader/cif/schema/mmcif.ts | 246 ++++++++++++++++++
src/reader/cif/text-field.ts | 58 ++---
src/reader/cif/text-parser.ts | 10 +-
src/reader/common/column.ts | 16 +-
src/reader/common/text/column/__token.ts | 114 --------
src/reader/common/text/column/fixed.ts | 32 +--
src/reader/common/text/column/token.ts | 55 ++++
src/reader/common/text/tokenizer.ts | 61 +++--
src/reader/gro/parser.ts | 12 +-
src/reader/spec/cif.spec.ts | 4 +-
...xed-column.spec.ts => text-column.spec.ts} | 18 +-
src/script.ts | 11 +-
15 files changed, 487 insertions(+), 237 deletions(-)
create mode 100644 src/reader/cif/index.ts
delete mode 100644 src/reader/common/text/column/__token.ts
create mode 100644 src/reader/common/text/column/token.ts
rename src/reader/spec/{fixed-column.spec.ts => text-column.spec.ts} (65%)
diff --git a/src/reader/cif/data-model.ts b/src/reader/cif/data-model.ts
index 642cf5621..4033df03a 100644
--- a/src/reader/cif/data-model.ts
+++ b/src/reader/cif/data-model.ts
@@ -83,4 +83,26 @@ export function DefaultUndefinedField(rowCount: number): Field {
toIntArray: (p) => Column.createArray(rowCount, p).array,
toFloatArray: (p) => Column.createArray(rowCount, p).array
};
+}
+
+export function getMatrix(category: Category, field: string, rows: number, cols: number, row: number) {
+ const ret: number[][] = [];
+ for (let i = 0; i < rows; i++) {
+ const r: number[] = [];
+ for (let j = 0; j < cols; j++) {
+ const f = category.getField(`${field}[${i + 1}][${j + 1}]`);
+ r[j] = f ? f.float(row) : 0.0;
+ }
+ ret[i] = r;
+ }
+ return ret;
+}
+
+export function getVector(category: Category, field: string, rows: number, row: number) {
+ const ret: number[] = [];
+ for (let i = 0; i < rows; i++) {
+ const f = category.getField(`${field}[${i + 1}]`);
+ ret[i] = f ? f.float(row) : 0.0;
+ }
+ return ret;
}
\ No newline at end of file
diff --git a/src/reader/cif/index.ts b/src/reader/cif/index.ts
new file mode 100644
index 000000000..c7ba6c3d5
--- /dev/null
+++ b/src/reader/cif/index.ts
@@ -0,0 +1,15 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import parseText from './text-parser'
+import { apply as applySchema } from './schema'
+import mmCIF from './schema/mmcif'
+
+export default {
+ parseText,
+ applySchema,
+ schema: { mmCIF }
+}
\ No newline at end of file
diff --git a/src/reader/cif/schema.ts b/src/reader/cif/schema.ts
index 1244827e1..aea1576e9 100644
--- a/src/reader/cif/schema.ts
+++ b/src/reader/cif/schema.ts
@@ -6,6 +6,7 @@
import * as Data from './data-model'
import * as Column from '../common/column'
+import StringPool from '../../utils/short-string-pool'
/**
* A schema defines the shape of categories and fields.
@@ -47,27 +48,21 @@ export type Category<Fields> = Fields & {
}
export namespace Category {
- export type Schema = { '@alias'?: string } & { [field: string]: Field.Schema<any> }
+ export type Schema = { [field: string]: Field.Schema<any> }
export type Instance<T extends Schema> = Category<{ [F in keyof T]: Column.Column<T[F]['type']> }>
}
-// export interface Field<T> {
-// readonly isDefined: boolean,
-// value(row: number): T,
-// presence(row: number): Data.ValuePresence,
-// areValuesEqual(rowA: number, rowB: number): boolean,
-// stringEquals(row: number, value: string | null): boolean,
-// /** Converts the selected row range to an array. ctor might or might not be called depedning on the source data format. */
-// toArray(params?: Column.ToArrayParams): ReadonlyArray<T>
-// }
-
export namespace Field {
- export interface Schema<T> { type: T, ctor: (field: Data.Field) => Column.Column<T>, undefinedField: (c: number) => Data.Field, alias?: string };
+ export interface Schema<T> { type: T, ctor: (field: Data.Field, category: Data.Category, key: string) => Column.Column<T>, undefinedField: (c: number) => Data.Field, alias?: string };
export interface Spec { undefinedField?: (c: number) => Data.Field, alias?: string }
+ export function alias(name: string): Schema<any> { return { alias: name } as any; }
+ export function pooledStr(spec?: Spec) { return createSchema(spec, PooledStr); }
export function str(spec?: Spec) { return createSchema(spec, Str); }
export function int(spec?: Spec) { return createSchema(spec, Int); }
export function float(spec?: Spec) { return createSchema(spec, Float); }
+ export function vector(rows: number, spec?: Spec) { return createSchema(spec, Vector(rows)); }
+ export function matrix(rows: number, cols: number, spec?: Spec) { return createSchema(spec, Matrix(rows, cols)); }
function create<T>(field: Data.Field, value: (row: number) => T, toArray: Column.Column<T>['toArray']): Column.Column<T> {
const presence = field.presence;
@@ -81,11 +76,31 @@ export namespace Field {
};
}
+ function PooledStr(field: Data.Field) {
+ const pool = StringPool.create();
+ const value = (row: number) => StringPool.get(pool, field.str(row));
+ const array = (params?: Column.ToArrayParams) => Column.createAndFillArray(field.rowCount, value, params);
+ return create<string>(field, value, array);
+ }
function Str(field: Data.Field) { return create(field, field.str, field.toStringArray); }
function Int(field: Data.Field) { return create(field, field.int, field.toIntArray); }
function Float(field: Data.Field) { return create(field, field.float, field.toFloatArray); }
- function createSchema<T>(spec: Spec | undefined, ctor: (field: Data.Field) => Column.Column<T>): Schema<T> {
+ function Vector(rows: number) {
+ return function(field: Data.Field, category: Data.Category, key: string) {
+ const value = (row: number) => Data.getVector(category, key, rows, row);
+ return create(field, value, params => Column.createAndFillArray(field.rowCount, value, params));
+ }
+ }
+
+ function Matrix(rows: number, cols: number) {
+ return function(field: Data.Field, category: Data.Category, key: string) {
+ const value = (row: number) => Data.getMatrix(category, key, rows, cols, row);
+ return create(field, value, params => Column.createAndFillArray(field.rowCount, value, params));
+ }
+ }
+
+ function createSchema<T>(spec: Spec | undefined, ctor: (field: Data.Field, category: Data.Category, key: string) => Column.Column<T>): Schema<T> {
return { type: 0 as any, ctor, undefinedField: (spec && spec.undefinedField) || Data.DefaultUndefinedField, alias: spec && spec.alias };
}
}
@@ -111,8 +126,9 @@ class _Category implements Category<any> { // tslint:disable-line:class-name
Object.defineProperty(this, k, {
get: function() {
if (cache[k]) return cache[k];
- const field = _category.getField(s.alias || k) || s.undefinedField(_category.rowCount);
- cache[k] = s.ctor(field);
+ const name = s.alias || k;
+ const field = _category.getField(name) || s.undefinedField(_category.rowCount);
+ cache[k] = s.ctor(field, _category, name);
return cache[k];
},
enumerable: true,
@@ -127,6 +143,8 @@ function createBlock(schema: Block.Schema, block: Data.Block): any {
}
function createCategory(key: string, schema: Category.Schema, block: Data.Block) {
- const cat = block.categories[schema['@alias'] || key];
+ const alias = (schema['@alias'] && schema['@alias'].alias) || key;
+ const name = alias[0] === '_' ? alias : '_' + alias;
+ const cat = block.categories[name];
return new _Category(cat || Data.Category.Empty, schema, !!cat);
}
\ No newline at end of file
diff --git a/src/reader/cif/schema/mmcif.ts b/src/reader/cif/schema/mmcif.ts
index e69de29bb..fdca87dc9 100644
--- a/src/reader/cif/schema/mmcif.ts
+++ b/src/reader/cif/schema/mmcif.ts
@@ -0,0 +1,246 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Field } from '../schema'
+
+const pooledStr = Field.pooledStr();
+const str = Field.str();
+const int = Field.int();
+const float = Field.float();
+
+const entry = {
+ id: str
+}
+
+const entity = {
+ id: str,
+ type: str as Field.Schema<'polymer' | 'non-polymer' | 'water'>,
+ src_method: str,
+ pdbx_description: str,
+ formula_weight: float,
+ pdbx_number_of_molecules: int,
+ details: str,
+ pdbx_mutation: str,
+ pdbx_fragment: str,
+ pdbx_ec: str
+}
+
+const exptl = {
+ entry_id: str,
+ method: str
+}
+
+const cell = {
+ entry_id: str,
+ length_a: float,
+ length_b: float,
+ length_c: float,
+ angle_alpha: float,
+ angle_beta: float,
+ angle_gamma: float,
+ Z_PDB: int,
+ pdbx_unique_axis: str
+}
+
+const symmetry = {
+ entry_id: str,
+ space_group_name_HM: Field.str({ alias: 'space_group_name_H-M' }),
+ pdbx_full_space_group_name_HM: Field.str({ alias: 'pdbx_full_space_group_name_H-M' }),
+ cell_setting: str,
+ Int_Tables_number: int,
+ space_group_name_Hall: str
+}
+
+const struct_conf = {
+ conf_type_id: str,
+ id: str,
+ pdbx_PDB_helix_id: int,
+ beg_label_comp_id: pooledStr,
+ beg_label_asym_id: pooledStr,
+ beg_label_seq_id: int,
+ pdbx_beg_PDB_ins_code: pooledStr,
+ end_label_comp_id: pooledStr,
+ end_label_asym_id: pooledStr,
+ end_label_seq_id: int,
+ pdbx_end_PDB_ins_code: pooledStr,
+ beg_auth_comp_id: pooledStr,
+ beg_auth_asym_id: pooledStr,
+ beg_auth_seq_id: int,
+ end_auth_comp_id: pooledStr,
+ end_auth_asym_id: pooledStr,
+ end_auth_seq_id: int,
+ pdbx_PDB_helix_class: int,
+ details: str,
+ pdbx_PDB_helix_length: int
+}
+
+const struct_sheet_range = {
+ sheet_id: pooledStr,
+ id: int,
+ beg_label_comp_id: pooledStr,
+ beg_label_asym_id: pooledStr,
+ beg_label_seq_id: int,
+ pdbx_beg_PDB_ins_code: pooledStr,
+ end_label_comp_id: pooledStr,
+ end_label_asym_id: pooledStr,
+ end_label_seq_id: int,
+ pdbx_end_PDB_ins_code: pooledStr,
+ beg_auth_comp_id: pooledStr,
+ beg_auth_asym_id: pooledStr,
+ beg_auth_seq_id: int,
+ end_auth_comp_id: pooledStr,
+ end_auth_asym_id: pooledStr,
+ end_auth_seq_id: int
+}
+
+type StructConnTypeId =
+ | 'covale'
+ | 'covale_base'
+ | 'covale_phosphate'
+ | 'covale_sugar'
+ | 'disulf'
+ | 'hydrog'
+ | 'metalc'
+ | 'mismat'
+ | 'modres'
+ | 'saltbr'
+
+type BondValueOrder =
+ | 'SING'
+ | 'DOUB'
+ | 'TRIP'
+ | 'QUAD'
+
+const struct_conn = {
+ id: str,
+ conn_type_id: pooledStr as Field.Schema<StructConnTypeId>,
+ pdbx_PDB_id: str,
+ ptnr1_label_asym_id: pooledStr,
+ ptnr1_label_comp_id: pooledStr,
+ ptnr1_label_seq_id: int,
+ ptnr1_label_atom_id: pooledStr,
+ pdbx_ptnr1_label_alt_id: pooledStr,
+ pdbx_ptnr1_PDB_ins_code: pooledStr,
+ pdbx_ptnr1_standard_comp_id: pooledStr,
+ ptnr1_symmetry: pooledStr,
+ ptnr2_label_asym_id: pooledStr,
+ ptnr2_label_comp_id: pooledStr,
+ ptnr2_label_seq_id: int,
+ ptnr2_label_atom_id: pooledStr,
+ pdbx_ptnr2_label_alt_id: pooledStr,
+ pdbx_ptnr2_PDB_ins_code: pooledStr,
+ ptnr1_auth_asym_id: pooledStr,
+ ptnr1_auth_comp_id: pooledStr,
+ ptnr1_auth_seq_id: int,
+ ptnr2_auth_asym_id: pooledStr,
+ ptnr2_auth_comp_id: pooledStr,
+ ptnr2_auth_seq_id: int,
+ ptnr2_symmetry: pooledStr,
+ pdbx_ptnr3_label_atom_id: pooledStr,
+ pdbx_ptnr3_label_seq_id: int,
+ pdbx_ptnr3_label_comp_id: pooledStr,
+ pdbx_ptnr3_label_asym_id: pooledStr,
+ pdbx_ptnr3_label_alt_id: pooledStr,
+ pdbx_ptnr3_PDB_ins_code: pooledStr,
+ details: pooledStr,
+ pdbx_dist_value: float,
+ pdbx_value_order: pooledStr as Field.Schema<BondValueOrder>
+}
+
+const struct_conn_type = {
+ id: str as Field.Schema<StructConnTypeId>,
+ criteria: str,
+ reference: str
+}
+
+const chem_comp_bond = {
+ comp_id: pooledStr,
+ pdbx_stereo_config: pooledStr,
+ pdbx_ordinal: int,
+ pdbx_aromatic_flag: pooledStr as Field.Schema<'Y' | 'N'>,
+ atom_id_1: pooledStr,
+ atom_id_2: pooledStr,
+ value_order: pooledStr as Field.Schema<BondValueOrder>
+}
+
+const pdbx_struct_assembly = {
+ id: str,
+ details: str,
+ method_details: str,
+ oligomeric_details: str,
+ oligomeric_count: int
+}
+
+const pdbx_struct_assembly_gen = {
+ assembly_id: str,
+ oper_expression: str,
+ asym_id_list: str
+}
+
+const pdbx_struct_oper_list = {
+ id: str,
+ type: str,
+ name: str,
+ symmetry_operation: str,
+ matrix: Field.matrix(3, 3),
+ vector: Field.vector(3)
+}
+
+const pdbx_struct_mod_residue = {
+ id: int,
+ label_asym_id: pooledStr,
+ label_seq_id: int,
+ label_comp_id: pooledStr,
+ auth_asym_id: pooledStr,
+ auth_seq_id: int,
+ auth_comp_id: pooledStr,
+ PDB_ins_code: pooledStr,
+ parent_comp_id: pooledStr,
+ details: str
+}
+
+const atom_site = {
+ group_PDB: pooledStr,
+ id: int,
+ type_symbol: pooledStr,
+ label_atom_id: pooledStr,
+ label_alt_id: pooledStr,
+ label_comp_id: pooledStr,
+ label_asym_id: pooledStr,
+ label_entity_id: pooledStr,
+ label_seq_id: int,
+ pdbx_PDB_ins_code: pooledStr,
+ pdbx_formal_charge: pooledStr,
+ Cartn_x: float,
+ Cartn_y: float,
+ Cartn_z: float,
+ occupancy: float,
+ B_iso_or_equiv: float,
+ auth_atom_id: pooledStr,
+ auth_comp_id: pooledStr,
+ auth_asym_id: pooledStr,
+ auth_seq_id: int,
+ pdbx_PDB_model_num: int
+}
+
+const schema = {
+ entry,
+ entity,
+ exptl,
+ cell,
+ symmetry,
+ struct_conf,
+ struct_sheet_range,
+ struct_conn,
+ struct_conn_type,
+ chem_comp_bond,
+ pdbx_struct_assembly,
+ pdbx_struct_assembly_gen,
+ pdbx_struct_oper_list,
+ pdbx_struct_mod_residue,
+ atom_site
+};
+export default schema;
\ No newline at end of file
diff --git a/src/reader/cif/text-field.ts b/src/reader/cif/text-field.ts
index f09893691..c67cc8cf7 100644
--- a/src/reader/cif/text-field.ts
+++ b/src/reader/cif/text-field.ts
@@ -5,30 +5,31 @@
*/
import * as Column from '../common/column'
+import * as TokenColumn from '../common/text/column/token'
+import { Tokens } from '../common/text/tokenizer'
import * as Data from './data-model'
import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../common/text/number-parser'
-import StringPool from '../../utils/short-string-pool'
-export default function CifTextField(data: string, tokens: ArrayLike<number>, rowCount: number): Data.Field {
- const stringPool = StringPool.create();
+export default function CifTextField(tokens: Tokens, rowCount: number): Data.Field {
+ const { data, indices } = tokens;
const str: Data.Field['str'] = row => {
- const ret = StringPool.get(stringPool, data.substring(tokens[2 * row], tokens[2 * row + 1]));
+ const ret = data.substring(indices[2 * row], indices[2 * row + 1]);
if (ret === '.' || ret === '?') return '';
return ret;
};
const int: Data.Field['int'] = row => {
- return fastParseInt(data, tokens[2 * row], tokens[2 * row + 1]) || 0;
+ return fastParseInt(data, indices[2 * row], indices[2 * row + 1]) || 0;
};
const float: Data.Field['float'] = row => {
- return fastParseFloat(data, tokens[2 * row], tokens[2 * row + 1]) || 0;
+ return fastParseFloat(data, indices[2 * row], indices[2 * row + 1]) || 0;
};
const presence: Data.Field['presence'] = row => {
- const s = tokens[2 * row];
- if (tokens[2 * row + 1] - s !== 1) return Data.ValuePresence.Present;
+ const s = indices[2 * row];
+ if (indices[2 * row + 1] - s !== 1) return Data.ValuePresence.Present;
const v = data.charCodeAt(s);
if (v === 46 /* . */) return Data.ValuePresence.NotSpecified;
if (v === 63 /* ? */) return Data.ValuePresence.Unknown;
@@ -42,43 +43,20 @@ export default function CifTextField(data: string, tokens: ArrayLike<number>, ro
int,
float,
presence,
- areValuesEqual(rowA, rowB) {
- const aS = tokens[2 * rowA], bS = tokens[2 * rowB];
- const len = tokens[2 * rowA + 1] - aS;
- if (len !== tokens[2 * rowB + 1] - bS) return false;
- for (let i = 0; i < len; i++) {
- if (data.charCodeAt(i + aS) !== data.charCodeAt(i + bS)) {
- return false;
- }
- }
- return true;
- },
- stringEquals(row, value) {
- const s = tokens[2 * row];
- if (!value) return presence(row) !== Data.ValuePresence.Present;
+ areValuesEqual: TokenColumn.areValuesEqualProvider(tokens),
+ stringEquals(row, v) {
+ const s = indices[2 * row];
+ const value = v || '';
+ if (!value && presence(row) !== Data.ValuePresence.Present) return true;
const len = value.length;
- if (len !== tokens[2 * row + 1] - s) return false;
+ if (len !== indices[2 * row + 1] - s) return false;
for (let i = 0; i < len; i++) {
if (data.charCodeAt(i + s) !== value.charCodeAt(i)) return false;
}
return true;
},
- toStringArray(params) {
- const { array, start } = Column.createArray(rowCount, params);
- return fillArrayValues(str, array, start);
- },
- toIntArray(params) {
- const { array, start } = Column.createArray(rowCount, params);
- return fillArrayValues(int, array, start);
- },
- toFloatArray(params) {
- const { array, start } = Column.createArray(rowCount, params);
- return fillArrayValues(float, array, start);
- }
+ toStringArray(params) { return Column.createAndFillArray(rowCount, str, params); },
+ toIntArray(params) { return Column.createAndFillArray(rowCount, int, params); },
+ toFloatArray(params) { return Column.createAndFillArray(rowCount, float, params); }
}
-}
-
-function fillArrayValues(value: (row: number) => any, target: any[], start: number) {
- for (let i = 0, _e = target.length; i < _e; i++) target[i] = value(start + i);
- return target;
}
\ No newline at end of file
diff --git a/src/reader/cif/text-parser.ts b/src/reader/cif/text-parser.ts
index 7ea6a0d9b..4e37ddb56 100644
--- a/src/reader/cif/text-parser.ts
+++ b/src/reader/cif/text-parser.ts
@@ -24,7 +24,7 @@
import * as Data from './data-model'
import Field from './text-field'
-import { Tokens } from '../common/text/tokenizer'
+import { Tokens, TokenBuilder } from '../common/text/tokenizer'
import Result from '../result'
/**
@@ -430,7 +430,7 @@ function handleSingle(tokenizer: TokenizerState, categories: { [name: string]: D
errorMessage: 'Expected value.'
}
}
- fields[fieldName] = Field(tokenizer.data, [tokenizer.currentTokenStart, tokenizer.currentTokenEnd], 1);
+ fields[fieldName] = Field({ data: tokenizer.data, indices: [tokenizer.currentTokenStart, tokenizer.currentTokenEnd], count: 1 }, 1);
moveNext(tokenizer);
}
@@ -461,11 +461,11 @@ function handleLoop(tokenizer: TokenizerState, categories: { [name: string]: Dat
const rowCountEstimate = name === '_atom_site' ? (tokenizer.data.length / 100) | 0 : 32;
const tokens: Tokens[] = [];
const fieldCount = fieldNames.length;
- for (let i = 0; i < fieldCount; i++) tokens[i] = Tokens.create(rowCountEstimate);
+ for (let i = 0; i < fieldCount; i++) tokens[i] = TokenBuilder.create(tokenizer, rowCountEstimate);
let tokenCount = 0;
while (tokenizer.currentTokenType === CifTokenType.Value) {
- Tokens.add(tokens[(tokenCount++) % fieldCount], tokenizer.currentTokenStart, tokenizer.currentTokenEnd);
+ TokenBuilder.add(tokens[(tokenCount++) % fieldCount], tokenizer.currentTokenStart, tokenizer.currentTokenEnd);
moveNext(tokenizer);
}
@@ -480,7 +480,7 @@ function handleLoop(tokenizer: TokenizerState, categories: { [name: string]: Dat
const rowCount = (tokenCount / fieldCount) | 0;
const fields = Object.create(null);
for (let i = 0; i < fieldCount; i++) {
- fields[fieldNames[i]] = Field(tokenizer.data, tokens[i].indices, rowCount);
+ fields[fieldNames[i]] = Field(tokens[i], rowCount);
}
categories[name] = Data.Category(rowCount, fields);
diff --git a/src/reader/common/column.ts b/src/reader/common/column.ts
index dab5ac063..1c27a911e 100644
--- a/src/reader/common/column.ts
+++ b/src/reader/common/column.ts
@@ -53,4 +53,18 @@ export function createArray(rowCount: number, params?: ToArrayParams) {
const s = typeof start !== 'undefined' ? Math.max(Math.min(start, rowCount - 1), 0) : 0;
const e = typeof end !== 'undefined' ? Math.min(end, rowCount) : rowCount;
return { array: new c(e - s) as any[], start: s, end: e };
-}
\ No newline at end of file
+}
+
+/** A helped function for Column.toArray */
+export function fillArrayValues(value: (row: number) => any, target: any[], start: number) {
+ for (let i = 0, _e = target.length; i < _e; i++) target[i] = value(start + i);
+ return target;
+}
+
+/** A helped function for Column.toArray */
+export function createAndFillArray(rowCount: number, value: (row: number) => any, params?: ToArrayParams) {
+ const { array, start } = createArray(rowCount, params);
+ return fillArrayValues(value, array, start);
+}
+
+
diff --git a/src/reader/common/text/column/__token.ts b/src/reader/common/text/column/__token.ts
deleted file mode 100644
index 87326c26d..000000000
--- a/src/reader/common/text/column/__token.ts
+++ /dev/null
@@ -1,114 +0,0 @@
-// /*
-// * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
-// *
-// * @author David Sehnal <david.sehnal@gmail.com>
-// */
-
-// import * as Data from '../../../../data/data'
-// import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../number-parser'
-// import { Tokens } from '../tokenizer'
-// import ShortStringPool from '../../../../utils/short-string-pool'
-
-// export function createTokenFields(data: string, fields: string[], tokens: Tokens): { [name: string]: Data.Field } {
-// const fi: TokenFieldInfo = { data, fieldCount: fields.length, tokens: tokens.indices };
-// const categoryFields = Object.create(null);
-// for (let i = 0; i < fi.fieldCount; ++i) {
-// categoryFields[fields[i]] = TokenField(fi, i);
-// }
-// return categoryFields;
-// }
-
-// export interface TokenFieldInfo {
-// data: string,
-// tokens: ArrayLike<number>,
-// fieldCount: number,
-// isCif?: boolean
-// }
-
-// export function TokenField(info: TokenFieldInfo, index: number): Data.Field {
-// const { data, tokens, fieldCount, isCif = false } = info;
-// const stringPool = ShortStringPool.create();
-
-// const str: Data.Field['str'] = isCif ? row => {
-// const i = (row * fieldCount + index) * 2;
-// const ret = ShortStringPool.get(stringPool, data.substring(tokens[i], tokens[i + 1]));
-// if (ret === '.' || ret === '?') return null;
-// return ret;
-// } : row => {
-// const i = (row * fieldCount + index) * 2;
-// return ShortStringPool.get(stringPool, data.substring(tokens[i], tokens[i + 1]));
-// };
-
-// const int: Data.Field['int'] = row => {
-// const i = (row * fieldCount + index) * 2;
-// return fastParseInt(data, tokens[i], tokens[i + 1]) || 0;
-// };
-
-// const float: Data.Field['float'] = row => {
-// const i = (row * fieldCount + index) * 2;
-// return fastParseFloat(data, tokens[i], tokens[i + 1]) || 0;
-// };
-
-// const presence: Data.Field['presence'] = isCif ? row => {
-// const i = 2 * (row * fieldCount + index);
-// const s = tokens[i];
-// if (tokens[i + 1] - s !== 1) return Data.ValuePresence.Present;
-// const v = data.charCodeAt(s);
-// if (v === 46 /* . */) return Data.ValuePresence.NotSpecified;
-// if (v === 63 /* ? */) return Data.ValuePresence.Unknown;
-// return Data.ValuePresence.Present;
-// } : row => {
-// const i = 2 * (row * fieldCount + index);
-// return tokens[i] === tokens[i + 1] ? Data.ValuePresence.NotSpecified : Data.ValuePresence.Present
-// };
-
-// return {
-// isDefined: true,
-// str,
-// int,
-// float,
-// value: str,
-// presence,
-// areValuesEqual: (rowA, rowB) => {
-// const aI = (rowA * fieldCount + index) * 2, aS = tokens[aI];
-// const bI = (rowB * fieldCount + index) * 2, bS = tokens[bI];
-// const len = tokens[aI + 1] - aS;
-// if (len !== tokens[bI + 1] - bS) return false;
-// for (let i = 0; i < len; i++) {
-// if (data.charCodeAt(i + aS) !== data.charCodeAt(i + bS)) {
-// return false;
-// }
-// }
-// return true;
-// },
-// stringEquals: (row, value) => {
-// const aI = (row * fieldCount + index) * 2;
-// const s = tokens[aI];
-// if (!value) return presence(row) !== Data.ValuePresence.Present;
-// const len = value.length;
-// if (len !== tokens[aI + 1] - s) return false;
-// for (let i = 0; i < len; i++) {
-// if (data.charCodeAt(i + s) !== value.charCodeAt(i)) return false;
-// }
-// return true;
-// },
-// toStringArray: (startRow, endRowExclusive, ctor) => {
-// const count = endRowExclusive - startRow;
-// const ret = ctor(count) as any;
-// for (let i = 0; i < count; i++) { ret[i] = str(startRow + i); }
-// return ret;
-// },
-// toIntArray: (startRow, endRowExclusive, ctor) => {
-// const count = endRowExclusive - startRow;
-// const ret = ctor(count) as any;
-// for (let i = 0; i < count; i++) { ret[i] = int(startRow + i); }
-// return ret;
-// },
-// toFloatArray: (startRow, endRowExclusive, ctor) => {
-// const count = endRowExclusive - startRow;
-// const ret = ctor(count) as any;
-// for (let i = 0; i < count; i++) { ret[i] = float(startRow + i); }
-// return ret;
-// }
-// }
-// }
\ No newline at end of file
diff --git a/src/reader/common/text/column/fixed.ts b/src/reader/common/text/column/fixed.ts
index bb307f969..7caf97e35 100644
--- a/src/reader/common/text/column/fixed.ts
+++ b/src/reader/common/text/column/fixed.ts
@@ -4,46 +4,41 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column, ColumnType, createArray } from '../../column'
-import { trimStr, Lines } from '../tokenizer'
+import { Column, ColumnType, createAndFillArray } from '../../column'
+import { trimStr, Tokens } from '../tokenizer'
import { parseIntSkipLeadingWhitespace, parseFloatSkipLeadingWhitespace } from '../number-parser'
import StringPool from '../../../../utils/short-string-pool'
-export default function FixedColumnProvider(lines: Lines) {
+export default function FixedColumnProvider(lines: Tokens) {
return function<T extends ColumnType>(offset: number, width: number, type: T) {
return FixedColumn(lines, offset, width, type);
}
}
-function fillArrayValues(value: (row: number) => any, target: any[], start: number) {
- for (let i = 0, _e = target.length; i < _e; i++) target[i] = value(start + i);
- return target;
-}
-
-export function FixedColumn<T extends ColumnType>(lines: Lines, offset: number, width: number, type: T): Column<T['@type']> {
- const { data, tokens, count: rowCount } = lines;
+export function FixedColumn<T extends ColumnType>(lines: Tokens, offset: number, width: number, type: T): Column<T['@type']> {
+ const { data, indices, count: rowCount } = lines;
const { kind } = type;
const pool = kind === 'pooled-str' ? StringPool.create() : void 0;
const value: Column<T['@type']>['value'] = kind === 'str' ? row => {
- let s = tokens[2 * row] + offset, le = tokens[2 * row + 1];
+ let s = indices[2 * row] + offset, le = indices[2 * row + 1];
if (s >= le) return '';
let e = s + width;
if (e > le) e = le;
return trimStr(data, s, e);
} : kind === 'pooled-str' ? row => {
- let s = tokens[2 * row] + offset, le = tokens[2 * row + 1];
+ let s = indices[2 * row] + offset, le = indices[2 * row + 1];
if (s >= le) return '';
let e = s + width;
if (e > le) e = le;
return StringPool.get(pool!, trimStr(data, s, e));
} : kind === 'int' ? row => {
- const s = tokens[2 * row] + offset;
- if (s > tokens[2 * row + 1]) return 0;
+ const s = indices[2 * row] + offset;
+ if (s > indices[2 * row + 1]) return 0;
return parseIntSkipLeadingWhitespace(data, s, s + width);
} : row => {
- const s = tokens[2 * row] + offset;
- if (s > tokens[2 * row + 1]) return 0;
+ const s = indices[2 * row] + offset;
+ if (s > indices[2 * row + 1]) return 0;
return parseFloatSkipLeadingWhitespace(data, s, s + width);
};
return {
@@ -51,10 +46,7 @@ export function FixedColumn<T extends ColumnType>(lines: Lines, offset: number,
rowCount,
value,
isValueDefined(row) { return true; },
- toArray(params) {
- const { array, start } = createArray(rowCount, params);
- return fillArrayValues(value, array, start);
- },
+ toArray(params) { return createAndFillArray(rowCount, value, params); },
areValuesEqual(rowA, rowB) {
return value(rowA) === value(rowB);
}
diff --git a/src/reader/common/text/column/token.ts b/src/reader/common/text/column/token.ts
new file mode 100644
index 000000000..c78ccc794
--- /dev/null
+++ b/src/reader/common/text/column/token.ts
@@ -0,0 +1,55 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Column, ColumnType, createAndFillArray } from '../../column'
+import { Tokens } from '../tokenizer'
+import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../number-parser'
+import StringPool from '../../../../utils/short-string-pool'
+
+export default function TokenColumnProvider(tokens: Tokens) {
+ return function<T extends ColumnType>(type: T) {
+ return TokenColumn(tokens, type);
+ }
+}
+
+export function TokenColumn<T extends ColumnType>(tokens: Tokens, type: T): Column<T['@type']> {
+ const { data, indices, count: rowCount } = tokens;
+ const { kind } = type;
+ const pool = kind === 'pooled-str' ? StringPool.create() : void 0;
+
+ const value: Column<T['@type']>['value'] =
+ kind === 'str'
+ ? row => data.substring(indices[2 * row], indices[2 * row + 1])
+ : kind === 'pooled-str'
+ ? row => StringPool.get(pool!, data.substring(indices[2 * row], indices[2 * row + 1]))
+ : kind === 'int'
+ ? row => fastParseInt(data, indices[2 * row], indices[2 * row + 1]) || 0
+ : row => fastParseFloat(data, indices[2 * row], indices[2 * row + 1]) || 0;
+
+ return {
+ isDefined: true,
+ rowCount,
+ value,
+ isValueDefined(row) { return true; },
+ toArray(params) { return createAndFillArray(rowCount, value, params); },
+ areValuesEqual: areValuesEqualProvider(tokens)
+ };
+}
+
+export function areValuesEqualProvider(tokens: Tokens) {
+ const { data, indices } = tokens;
+ return function(rowA: number, rowB: number) {
+ const aS = indices[2 * rowA], bS = indices[2 * rowB];
+ const len = indices[2 * rowA + 1] - aS;
+ if (len !== indices[2 * rowB + 1] - bS) return false;
+ for (let i = 0; i < len; i++) {
+ if (data.charCodeAt(i + aS) !== data.charCodeAt(i + bS)) {
+ return false;
+ }
+ }
+ return true;
+ }
+}
\ No newline at end of file
diff --git a/src/reader/common/text/tokenizer.ts b/src/reader/common/text/tokenizer.ts
index 97fb00ef7..326497591 100644
--- a/src/reader/common/text/tokenizer.ts
+++ b/src/reader/common/text/tokenizer.ts
@@ -17,10 +17,10 @@ export interface Tokenizer {
currentTokenEnd: number
}
-export interface Lines {
+export interface Tokens {
data: string,
count: number,
- tokens: ArrayLike<number>
+ indices: ArrayLike<number>
}
export function Tokenizer(data: string): Tokenizer {
@@ -80,15 +80,21 @@ export namespace Tokenizer {
}
/** Advance the state by the given number of lines and return line starts/ends as tokens. */
- export function readLines(state: Tokenizer, count: number): Lines {
- const lineTokens = Tokens.create(count * 2);
+ export function readLine(state: Tokenizer): string {
+ markLine(state);
+ return getTokenString(state);
+ }
+
+ /** Advance the state by the given number of lines and return line starts/ends as tokens. */
+ export function readLines(state: Tokenizer, count: number): Tokens {
+ const lineTokens = TokenBuilder.create(state, count * 2);
for (let i = 0; i < count; i++) {
markLine(state);
- Tokens.addUnchecked(lineTokens, state.currentTokenStart, state.currentTokenEnd);
+ TokenBuilder.addUnchecked(lineTokens, state.currentTokenStart, state.currentTokenEnd);
}
- return { data: state.data, count, tokens: lineTokens.indices };
+ return { data: state.data, count, indices: lineTokens.indices };
}
/**
@@ -170,38 +176,43 @@ export function trimStr(data: string, start: number, end: number) {
return data.substring(s, e + 1);
}
-export interface Tokens {
- indicesLenMinus2: number,
- count: number,
- indices: Uint32Array
-}
+export namespace TokenBuilder {
+ interface Builder extends Tokens {
+ offset: number,
+ indices: Uint32Array,
+ indicesLenMinus2: number
+ }
-export namespace Tokens {
- function resize(tokens: Tokens) {
+ function resize(builder: Builder) {
// scale the size using golden ratio, because why not.
- const newBuffer = new Uint32Array((1.61 * tokens.indices.length) | 0);
- newBuffer.set(tokens.indices);
- tokens.indices = newBuffer;
- tokens.indicesLenMinus2 = (newBuffer.length - 2) | 0;
+ const newBuffer = new Uint32Array((1.61 * builder.indices.length) | 0);
+ newBuffer.set(builder.indices);
+ builder.indices = newBuffer;
+ builder.indicesLenMinus2 = (newBuffer.length - 2) | 0;
}
export function add(tokens: Tokens, start: number, end: number) {
- if (tokens.count > tokens.indicesLenMinus2) {
- resize(tokens);
+ const builder = tokens as Builder;
+ if (builder.offset > builder.indicesLenMinus2) {
+ resize(builder);
}
- tokens.indices[tokens.count++] = start;
- tokens.indices[tokens.count++] = end;
+ builder.indices[builder.offset++] = start;
+ builder.indices[builder.offset++] = end;
+ tokens.count++;
}
export function addUnchecked(tokens: Tokens, start: number, end: number) {
- tokens.indices[tokens.count++] = start;
- tokens.indices[tokens.count++] = end;
+ (tokens as Builder).indices[(tokens as Builder).offset++] = start;
+ (tokens as Builder).indices[(tokens as Builder).offset++] = end;
+ tokens.count++;
}
- export function create(size: number): Tokens {
- return {
+ export function create(tokenizer: Tokenizer, size: number): Tokens {
+ return <Builder>{
+ data: tokenizer.data,
indicesLenMinus2: (size - 2) | 0,
count: 0,
+ offset: 0,
indices: new Uint32Array(size)
}
}
diff --git a/src/reader/gro/parser.ts b/src/reader/gro/parser.ts
index bca4df98a..28a1e26ca 100644
--- a/src/reader/gro/parser.ts
+++ b/src/reader/gro/parser.ts
@@ -40,14 +40,11 @@ function State(tokenizer: Tokenizer): State {
*/
function handleTitleString(state: State) {
const { tokenizer, header } = state;
- Tokenizer.markLine(tokenizer);
-
- let line = Tokenizer.getTokenString(tokenizer);
+ let line = Tokenizer.readLine(tokenizer);
// skip potential empty lines...
if (line.trim().length === 0) {
- Tokenizer.markLine(tokenizer);
- line = Tokenizer.getTokenString(tokenizer);
+ line = Tokenizer.readLine(tokenizer);
}
const timeOffset = line.lastIndexOf('t=');
@@ -92,7 +89,7 @@ function handleAtoms(state: State): Schema.Atoms {
const { tokenizer, numberOfAtoms } = state;
const lines = Tokenizer.readLines(tokenizer, numberOfAtoms);
- const positionSample = tokenizer.data.substring(lines.tokens[0], lines.tokens[1]).substring(20);
+ const positionSample = tokenizer.data.substring(lines.indices[0], lines.indices[1]).substring(20);
const precisions = positionSample.match(/\.\d+/g)!;
const hasVelocities = precisions.length === 6;
@@ -133,8 +130,7 @@ function handleAtoms(state: State): Schema.Atoms {
*/
function handleBoxVectors(state: State) {
const { tokenizer } = state;
- Tokenizer.markLine(tokenizer);
- const values = Tokenizer.getTokenString(tokenizer).trim().split(/\s+/g);
+ const values = Tokenizer.readLine(tokenizer).trim().split(/\s+/g);
state.header.box = [+values[0], +values[1], +values[2]];
}
diff --git a/src/reader/spec/cif.spec.ts b/src/reader/spec/cif.spec.ts
index 80b4c1388..87950cf64 100644
--- a/src/reader/spec/cif.spec.ts
+++ b/src/reader/spec/cif.spec.ts
@@ -10,8 +10,8 @@ import * as Schema from '../cif/schema'
const columnData = `123abc`;
-const intField = TextField(columnData, [0, 1, 1, 2, 2, 3], 3);
-const strField = TextField(columnData, [3, 4, 4, 5, 5, 6], 3);
+const intField = TextField({ data: columnData, indices: [0, 1, 1, 2, 2, 3], count: 3 }, 3);
+const strField = TextField({ data: columnData, indices: [3, 4, 4, 5, 5, 6], count: 3 }, 3);
const testBlock = Data.Block({
'atoms': Data.Category(3, {
diff --git a/src/reader/spec/fixed-column.spec.ts b/src/reader/spec/text-column.spec.ts
similarity index 65%
rename from src/reader/spec/fixed-column.spec.ts
rename to src/reader/spec/text-column.spec.ts
index c91bfb742..e37d18d6a 100644
--- a/src/reader/spec/fixed-column.spec.ts
+++ b/src/reader/spec/text-column.spec.ts
@@ -6,6 +6,7 @@
*/
import FixedColumn from '../common/text/column/fixed'
+import TokenColumn from '../common/text/column/token'
import { ColumnType } from '../common/column'
const lines = [
@@ -16,7 +17,7 @@ const lines = [
' 5'
]
-const data = lines.join('\n');
+const linesData = lines.join('\n');
const linesTokens = (function () {
const tokens: number[] = [];
@@ -25,12 +26,12 @@ const linesTokens = (function () {
tokens.push(last, last + l.length);
last += l.length + 1;
}
- if (tokens[tokens.length - 1] > data.length) tokens[tokens.length - 1] = data.length;
+ if (tokens[tokens.length - 1] > linesData.length) tokens[tokens.length - 1] = linesData.length;
return tokens;
}());
describe('fixed text column', () => {
- const col = FixedColumn({ data, tokens: linesTokens, count: lines.length });
+ const col = FixedColumn({ data: linesData, indices: linesTokens, count: lines.length });
const col1 = col(0, 5, ColumnType.float);
const col2 = col(5, 4, ColumnType.str);
it('number', () => {
@@ -48,3 +49,14 @@ describe('fixed text column', () => {
expect(col2.value(4)).toBe('');
})
});
+
+describe('token text column', () => {
+ const tokensData = '321';
+ const col = TokenColumn({ data: tokensData, indices: [0, 1, 1, 2, 2, 3], count: 3 });
+ const col1 = col(ColumnType.int);
+ it('number', () => {
+ expect(col1.value(0)).toBe(3);
+ expect(col1.value(1)).toBe(2);
+ expect(col1.value(2)).toBe(1);
+ })
+});
diff --git a/src/script.ts b/src/script.ts
index ea36fe76a..06615a362 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -8,7 +8,7 @@
import * as fs from 'fs'
import Gro from './reader/gro/parser'
-import CIF from './reader/cif/text-parser'
+import CIF from './reader/cif/index'
// const file = '1crn.gro'
// const file = 'water.gro'
@@ -81,7 +81,7 @@ export function _cif() {
}
console.time('parseCIF');
- const parsed = CIF(input);
+ const parsed = CIF.parseText(input);
console.timeEnd('parseCIF');
if (parsed.isError) {
console.log(parsed);
@@ -92,7 +92,12 @@ export function _cif() {
const atom_site = data.categories._atom_site;
console.log(atom_site.getField('Cartn_x')!.float(0));
- console.log(atom_site.getField('label_atom_id')!.toStringArray());
+ //console.log(atom_site.getField('label_atom_id')!.toStringArray());
+
+ const mmcif = CIF.applySchema(CIF.schema.mmCIF, data);
+ console.log(mmcif.atom_site.Cartn_x.value(0));
+ console.log(mmcif.entity.type.toArray());
+ console.log(mmcif.pdbx_struct_oper_list.matrix.value(0));
});
}
--
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