Changed data model, updated GRO parser to handle velocities, arbitrary precision, multiple models

README.md

@@ -43,8 +43,4 @@
 TODO
 ----
 
-- write about unittest (AR)
-- gro reader
-  - read more than one block
-  - read velocities
-  - detect number of decimal places
+- write about unittest (AR)

package-lock.json

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+      "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-7.0.0.tgz",
+      "integrity": "sha1-jQrELxbqVd69MyyvTEA4s+P139k=",
+      "dev": true,
+      "requires": {
+        "camelcase": "4.1.0"
+      },
+      "dependencies": {
+        "camelcase": {
+          "version": "4.1.0",
+          "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-4.1.0.tgz",
+          "integrity": "sha1-1UVjW+HjPFQmScaRc+Xeas+uNN0=",
+          "dev": true
+        }
+      }
+    }
+  }
+}

package.json

@@ -15,8 +15,13 @@
     "script": "./node_modules/.bin/rollup build/js/src/script.js -e fs -f cjs -o build/js/script.js"
   },
   "jest": {
-    "moduleFileExtensions": [ "ts", "js" ],
-    "transform": { "\\.ts$": "<rootDir>/node_modules/ts-jest/preprocessor.js" },
+    "moduleFileExtensions": [
+      "ts",
+      "js"
+    ],
+    "transform": {
+      "\\.ts$": "<rootDir>/node_modules/ts-jest/preprocessor.js"
+    },
     "testRegex": "\\.spec\\.ts$"
   },
   "author": "",

src/data/data.ts → src/reader/cif/data.ts

@@ -56,9 +56,6 @@ export interface Field {
     int(row: number): number,
     float(row: number): number,
 
-    /** The 'intrinsic value' of the field, e.g., array, binary data, ... */
-    value(row: number): any,
-
     presence(row: number): ValuePresence,
 
     areValuesEqual(rowA: number, rowB: number): boolean,

src/data/schema.ts → src/reader/cif/schema.ts

@@ -67,7 +67,6 @@ export namespace Field {
     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 value<T>(spec?: Spec): Schema<T> { return createSchema(spec, Value); }
 
     function create<T>(field: Data.Field, value: (row: number) => T, toArray: Field<T>['toArray']): Field<T> {
         return { isDefined: field.isDefined, value, presence: field.presence, areValuesEqual: field.areValuesEqual, stringEquals: field.stringEquals, toArray };
@@ -76,14 +75,12 @@ export namespace Field {
     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 Value(field: Data.Field) { return create(field, field.value, () => { throw Error('not supported'); }); }
 
     const DefaultUndefined: Data.Field = {
         isDefined: false,
         str: row => null,
         int: row => 0,
         float: row => 0,
-        value: row => null,
 
         presence: row => Data.ValuePresence.NotSpecified,
         areValuesEqual: (rowA, rowB) => true,

src/reader/common/column.ts

@@ -0,0 +1,43 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export type ArrayType = string[] | number[] | Float32Array | Float64Array | Int8Array | Int16Array | Int32Array | Uint8Array | Uint16Array | Uint32Array
+export type ColumnType = typeof ColumnType.str | typeof ColumnType.int | typeof ColumnType.float
+
+export namespace ColumnType {
+    export const str = { '@type': '' as string, kind: 'str' as 'str' };
+    export const int = { '@type': 0 as number, kind: 'int' as 'int' };
+    export const float = { '@type': 0 as number, kind: 'float' as 'float' };
+}
+
+export interface Column<T> {
+    readonly isColumnDefined: boolean,
+    readonly rowCount: number,
+    value(row: number): T,
+    toArray(ctor?: (size: number) => ArrayType, startRow?: number, endRowExclusive?: number): ReadonlyArray<T>
+}
+
+export function UndefinedColumn<T extends ColumnType>(rowCount: number, type: T): Column<T['@type']> {
+    const value: Column<T['@type']>['value'] = type.kind === 'str' ? row => '' : row => 0;
+    return {
+        isColumnDefined: false,
+        rowCount,
+        value,
+        toArray(ctor, s, e) {
+            const { array } = createArray(rowCount, ctor, s, e);
+            for (let i = 0, _i = array.length; i < _i; i++) array[i] = value(0)
+            return array;
+        }
+    }
+}
+
+/** A helped function for Column.toArray */
+export function createArray(rowCount: number, ctor?: (size: number) => ArrayType, start?: number, end?: number) {
+    const c = typeof ctor !== 'undefined' ? ctor : (s: number) => new Array(s);
+    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: c(e - s) as any[], start: s, end: e };
+}

src/reader/common/spec/fixed-column.spec.ts

@@ -0,0 +1,50 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import FixedColumn from '../text/column/fixed'
+import { ColumnType } from '../../common/column'
+
+const lines = [
+    '1.123 abc',
+    '1.00  a',
+    '1.1    bcd   ',
+    '',
+    ' 5'
+]
+
+const data = lines.join('\n');
+
+const linesTokens = (function () {
+    const tokens: number[] = [];
+    let last = 0;
+    for (const l of lines) {
+        tokens.push(last, last + l.length);
+        last += l.length + 1;
+    }
+    if (tokens[tokens.length - 1] > data.length) tokens[tokens.length - 1] = data.length;
+    return tokens;
+}());
+
+describe('fixed text column', () => {
+    const col = FixedColumn({ data, lines: linesTokens, rowCount: lines.length });
+    const col1 = col(0, 5, ColumnType.float);
+    const col2 = col(5, 4, ColumnType.str);
+    it('number', () => {
+        expect(col1.value(0)).toBe(1.123);
+        expect(col1.value(1)).toBe(1.0);
+        expect(col1.value(2)).toBe(1.1);
+        expect(col1.value(3)).toBe(0);
+        expect(col1.value(4)).toBe(5);
+    })
+    it('str', () => {
+        expect(col2.value(0)).toBe('abc');
+        expect(col2.value(1)).toBe('a');
+        expect(col2.value(2)).toBe('bc');
+        expect(col2.value(3)).toBe('');
+        expect(col2.value(4)).toBe('');
+    })
+});

src/reader/common/text/column/__token.ts

@@ -0,0 +1,114 @@
+// /*
+//  * 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;
+//         }
+//     }
+// }

src/reader/common/text/column/fixed.ts

@@ -0,0 +1,53 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Column, ColumnType, createArray } from '../../column'
+import { trimStr } from '../tokenizer'
+import { parseIntSkipLeadingWhitespace, parseFloatSkipLeadingWhitespace } from '../number-parser'
+
+export interface FixedColumnInfo {
+    data: string,
+    lines: ArrayLike<number>,
+    rowCount: number
+}
+
+export default function FixedColumnProvider(info: FixedColumnInfo) {
+    return function<T extends ColumnType>(offset: number, width: number, type: T) {
+        return FixedColumn(info, offset, width, type);
+    }
+}
+
+function getArrayValues(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>(info: FixedColumnInfo, offset: number, width: number, type: T): Column<T['@type']> {
+    const { data, lines, rowCount } = info;
+    const { kind } = type;
+
+    const value: Column<T['@type']>['value'] = kind === 'str' ? row => {
+        let s = lines[2 * row] + offset, e = s + width, le = lines[2 * row + 1];
+        if (s >= le) return '';
+        if (e > le) e = le;
+        return trimStr(data, s, e);
+    } : kind === 'int' ? row => {
+        const s = lines[2 * row] + offset, e = s + width;
+        return parseIntSkipLeadingWhitespace(data, s, e);
+    } : row => {
+        const s = lines[2 * row] + offset, e = s + width;
+        return parseFloatSkipLeadingWhitespace(data, s, e);
+    }
+    return {
+        isColumnDefined: true,
+        rowCount,
+        value,
+        toArray(ctor, s, e) {
+            const { array, start } = createArray(rowCount, ctor, s, e);
+            return getArrayValues(value, array, start);
+        }
+    };
+}

src/reader/common/text/token-field.ts

@@ -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;
-        }
-    }
-}

src/reader/common/text/tokenizer.ts

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-export interface State<Info = any, TokenType = any> {
+export interface State<TokenType = any> {
     data: string
 
     position: number
@@ -16,12 +16,10 @@ export interface State<Info = any, TokenType = any> {
     currentTokenStart: number
     currentTokenEnd: number
 
-    currentTokenType: TokenType,
-
-    info: Info
+    currentTokenType: TokenType
 }
 
-export function State<Info, TokenType>(data: string, info?: Info, initialTokenType?: TokenType): State<Info, TokenType> {
+export function State<TokenType>(data: string, initialTokenType?: TokenType): State<TokenType> {
     return {
         data,
         position: 0,
@@ -29,37 +27,53 @@ export function State<Info, TokenType>(data: string, info?: Info, initialTokenTy
         currentLineNumber: 1,
         currentTokenStart: 0,
         currentTokenEnd: 0,
-        currentTokenType: initialTokenType!,
-        info: info!
+        currentTokenType: initialTokenType!
     };
 }
 
+export function getTokenString(state: State) {
+    return state.data.substring(state.currentTokenStart, state.currentTokenEnd);
+}
+
 /**
  * Eat everything until a newline occurs.
  */
 export function eatLine(state: State) {
+    const { data } = state;
     while (state.position < state.length) {
-        switch (state.data.charCodeAt(state.position)) {
+        switch (data.charCodeAt(state.position)) {
             case 10: // \n
-                state.currentTokenEnd = state.position
-                ++state.position
-                ++state.currentLineNumber
-                return
+                state.currentTokenEnd = state.position;
+                ++state.position;
+                ++state.currentLineNumber;
+                return;
             case 13: // \r
-                state.currentTokenEnd = state.position
-                ++state.position
-                ++state.currentLineNumber
-                if (state.data.charCodeAt(state.position) === 10) {
-                    ++state.position
+                state.currentTokenEnd = state.position;
+                ++state.position;
+                ++state.currentLineNumber;
+                if (data.charCodeAt(state.position) === 10) {
+                    ++state.position;
                 }
-                return
+                return;
             default:
-                ++state.position
+                ++state.position;
+                break;
         }
     }
     state.currentTokenEnd = state.position;
 }
 
+/** Sets the current token start to the current position */
+export function markStart(state: State) {
+    state.currentTokenStart = state.position;
+}
+
+/** Sets the current token start to current position and moves to the next line. */
+export function markLine(state: State) {
+    state.currentTokenStart = state.position;
+    eatLine(state);
+}
+
 /**
  * Eat everything until a whitespace/newline occurs.
  */
@@ -129,6 +143,15 @@ export function trim(state: State, start: number, end: number) {
     state.position = end;
 }
 
+export function trimStr(data: string, start: number, end: number) {
+    let s = start, e = end - 1;
+    let c = data.charCodeAt(s);
+    while ((c === 9 || c === 32) && s <= e) c = data.charCodeAt(++s);
+    c = data.charCodeAt(e);
+    while ((c === 9 || c === 32) && e >= s) c = data.charCodeAt(--e);
+    return data.substring(s, e + 1);
+}
+
 export interface Tokens {
     indicesLenMinus2: number,
     count: number,

src/reader/gro/format.ts

@@ -1,14 +0,0 @@
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import schema from './schema'
-import parse from './parser'
-
-export default {
-    parse,
-    schema
-};

src/reader/gro/parser.ts

@@ -5,77 +5,71 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { State as TokenizerState, Tokens, eatLine, skipWhitespace, eatValue, trim } from '../common/text/tokenizer'
-import { parseInt } from '../common/text/number-parser'
-import { createTokenFields } from '../common/text/token-field'
-import * as Data from '../../data/data'
+import { State as TokenizerState, Tokens, markLine, getTokenString } from '../common/text/tokenizer'
+import FixedColumn from '../common/text/column/fixed'
+import { ColumnType, UndefinedColumn } from '../common/column'
+import * as Schema from './schema'
 import Result from '../result'
 
-interface StateInfo {
-    numberOfAtoms: number
-    hasVelocities: boolean
-    numberOfDecimalPlaces: number
+interface State {
+    tokenizer: TokenizerState,
+    header: Schema.Header,
+    numberOfAtoms: number,
 }
 
-type State = TokenizerState<StateInfo>
+function createEmptyHeader(): Schema.Header {
+    return {
+        title: '',
+        timeInPs: 0,
+        hasVelocities: false,
+        precision: { position: 0, velocity: 0 },
+        box: [0, 0, 0]
+    };
+}
 
-function createState(data: string): State {
-    return TokenizerState(data, { numberOfAtoms: 0, hasVelocities: false, numberOfDecimalPlaces: 3 });
+function createState(tokenizer: TokenizerState): State {
+    return {
+        tokenizer,
+        header: createEmptyHeader(),
+        numberOfAtoms: 0
+    };
 }
 
 /**
  * title string (free format string, optional time in ps after 't=')
  */
-function handleTitleString(state: State, tokens: Tokens) {
-    eatLine(state)
-    // console.log('title', state.data.substring(state.currentTokenStart, state.currentTokenEnd))
-    let start = state.currentTokenStart
-    let end = state.currentTokenEnd
-    let valueStart = state.currentTokenStart
-    let valueEnd = start
-
-    while (valueEnd < end && !isTime(state.data, valueEnd)) ++valueEnd;
+function handleTitleString(state: State) {
+    const { tokenizer, header } = state;
+    markLine(tokenizer);
 
-    if (isTime(state.data, valueEnd)) {
-        let timeStart = valueEnd + 2
+    let line = getTokenString(tokenizer);
 
-        while (valueEnd > start && isSpaceOrComma(state.data, valueEnd - 1)) --valueEnd;
-        Tokens.add(tokens, valueStart, valueEnd)  // title
+    // skip potential empty lines...
+    if (line.trim().length === 0) {
+        markLine(tokenizer);
+        line = getTokenString(tokenizer);
+    }
 
-        while (timeStart < end && state.data.charCodeAt(timeStart) === 32) ++timeStart;
-        while (valueEnd > timeStart && state.data.charCodeAt(valueEnd - 1) === 32) --valueEnd;
-        Tokens.add(tokens, timeStart, end)  // time
+    const timeOffset = line.lastIndexOf('t=');
+    if (timeOffset >= 0) {
+        header.timeInPs = parseFloat(line.substring(timeOffset + 2));
+        header.title = line.substring(0, timeOffset).trim();
+        if (header.title && header.title[header.title.length - 1] === ',') {
+            header.title = header.title.substring(0, header.title.length - 1);
+        }
     } else {
-        Tokens.add(tokens, valueStart, valueEnd)  // title
-        Tokens.add(tokens, valueEnd, valueEnd)  // empty token for time
+        header.title = line;
     }
 }
 
-function isSpaceOrComma(data: string, position: number): boolean {
-    const c = data.charCodeAt(position);
-    return c === 32 || c === 44
-}
-
-function isTime(data: string, position: number): boolean {
-    // T/t
-    const c = data.charCodeAt(position);
-    if (c !== 84 && c !== 116) return false;
-    // =
-    if (data.charCodeAt(position + 1) !== 61) return false;
-
-    return true;
-}
-
 /**
  * number of atoms (free format integer)
  */
-function handleNumberOfAtoms(state: State, tokens: Tokens) {
-    skipWhitespace(state)
-    state.currentTokenStart = state.position
-    eatValue(state)
-    state.info.numberOfAtoms = parseInt(state.data, state.currentTokenStart, state.currentTokenEnd)
-    Tokens.add(tokens, state.currentTokenStart, state.currentTokenEnd)
-    eatLine(state)
+function handleNumberOfAtoms(state: State) {
+    const { tokenizer } = state;
+    markLine(tokenizer);
+    const line = getTokenString(tokenizer);
+    state.numberOfAtoms = parseInt(line);
 }
 
 /**
@@ -94,33 +88,46 @@ function handleNumberOfAtoms(state: State, tokens: Tokens) {
  *     position (in nm, x y z in 3 columns, each 8 positions with 3 decimal places)
  *     velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4 decimal places)
  */
-function handleAtoms(state: State) {
-    const fieldSizes = [ 5, 5, 5, 5, 8, 8, 8, 8, 8, 8 ];
-    const fields = [ 'residueNumber', 'residueName', 'atomName', 'atomNumber', 'x', 'y', 'z' ]
-    if (state.info.hasVelocities) {
-        fields.push('vx', 'vy', 'vz')
-    }
-
-    const fieldCount = fields.length
-    const tokens = Tokens.create(state.info.numberOfAtoms * 2 * fieldCount)
+function handleAtoms(state: State): Schema.Atoms {
+    const { tokenizer, numberOfAtoms } = state;
+    const lineTokens = Tokens.create(numberOfAtoms * 2);
 
-    let start: number;
-    let end: number;
-
-    for (let i = 0, _i = state.info.numberOfAtoms; i < _i; ++i) {
-        state.currentTokenStart = state.position;
-        end = state.currentTokenStart;
-        for (let j = 0; j < fieldCount; ++j) {
-            start = end;
-            end = start + fieldSizes[j];
-
-            trim(state, start, end);
-            Tokens.addUnchecked(tokens, state.currentTokenStart, state.currentTokenEnd);
-        }
-        eatLine(state)
+    for (let i = 0; i < numberOfAtoms; i++) {
+        markLine(tokenizer);
+        Tokens.addUnchecked(lineTokens, tokenizer.currentTokenStart, tokenizer.currentTokenEnd);
     }
 
-    return Data.Category(state.info.numberOfAtoms, createTokenFields(state.data, fields, tokens));
+    const lines = lineTokens.indices;
+    const positionSample = tokenizer.data.substring(lines[0], lines[1]).substring(20);
+    const precisions = positionSample.match(/\.\d+/g)!;
+    const hasVelocities = precisions.length === 6;
+    state.header.hasVelocities = hasVelocities;
+    state.header.precision.position = precisions[0].length - 1;
+    state.header.precision.velocity = hasVelocities ? precisions[3].length - 1 : 0;
+
+    const pO = 20;
+    const pW = state.header.precision.position + 5;
+    const vO = pO + 3 * pW;
+    const vW = state.header.precision.velocity + 4;
+
+    const col = FixedColumn({ data: tokenizer.data, lines, rowCount: state.numberOfAtoms });
+    const undef = UndefinedColumn(state.numberOfAtoms, ColumnType.float);
+
+    const ret = {
+        count: state.numberOfAtoms,
+        residueNumber: col(0, 5, ColumnType.int),
+        residueName: col(5, 5, ColumnType.str),
+        atomName: col(10, 5, ColumnType.str),
+        atomNumber: col(15, 5, ColumnType.int),
+        x: col(pO, pW, ColumnType.float),
+        y: col(pO + pW, pW, ColumnType.float),
+        z: col(pO + 2 * pW, pW, ColumnType.float),
+        vx: hasVelocities ? col(vO, vW, ColumnType.float) : undef,
+        vy: hasVelocities ? col(vO + vW, vW, ColumnType.float) : undef,
+        vz: hasVelocities ? col(vO + 2 * vW, vW, ColumnType.float) : undef,
+    };
+
+    return ret;
 }
 
 /**
@@ -129,35 +136,32 @@ function handleAtoms(state: State) {
  * the last 6 values may be omitted (they will be set to zero).
  * Gromacs only supports boxes with v1(y)=v1(z)=v2(z)=0.
  */
-function handleBoxVectors(state: State, tokens: Tokens) {
-    // just read the first three values, ignore any remaining
-    for (let i = 0; i < 3; ++i) {
-        skipWhitespace(state);
-        state.currentTokenStart = state.position;
-        eatValue(state);
-        Tokens.add(tokens, state.currentTokenStart, state.currentTokenEnd);
-    }
+function handleBoxVectors(state: State) {
+    const { tokenizer } = state;
+    markLine(tokenizer);
+    const values = getTokenString(tokenizer).trim().split(/\s+/g);
+    state.header.box = [+values[0], +values[1], +values[2]];
 }
 
-function parseInternal(data: string): Result<Data.File> {
-    const state = createState(data);
-
-    const headerFields = ['title', 'timeInPs', 'numberOfAtoms', 'boxX', 'boxY', 'boxZ'];
-    const headerTokens = Tokens.create(2 * headerFields.length);
-
-    handleTitleString(state, headerTokens);
-    handleNumberOfAtoms(state, headerTokens);
-    const atoms = handleAtoms(state);
-    handleBoxVectors(state, headerTokens);
-
-    const block = Data.Block({
-        header: Data.Category(1, createTokenFields(data, headerFields, headerTokens)),
-        atoms
-    });
+function parseInternal(data: string): Result<Schema.File> {
+    const tokenizer = TokenizerState(data);
+
+    const structures: Schema.Structure[] = [];
+    while (tokenizer.position < data.length) {
+        const state = createState(tokenizer);
+        handleTitleString(state);
+        handleNumberOfAtoms(state);
+        const atoms = handleAtoms(state);
+        handleBoxVectors(state);
+        structures.push({ header: state.header, atoms });
+    }
 
-    return Result.success(Data.File([block]));
+    const result: Schema.File = { structures };
+    return Result.success(result);
 }
 
-export default function parse(data: string) {
+export function parse(data: string) {
     return parseInternal(data);
-}
+}
+
+export default parse;

src/reader/gro/schema.d.ts

@@ -0,0 +1,40 @@
+/*
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Column } from '../common/column'
+
+export interface Header {
+    title: string,
+    timeInPs: number,
+    /** number of decimal places */
+    precision: { position: number, velocity: number },
+    hasVelocities: boolean,
+    box: [number, number, number]
+}
+
+export interface Atoms {
+    count: number,
+    residueNumber: Column<number>,
+    residueName: Column<string>,
+    atomName: Column<string>,
+    atomNumber: Column<number>,
+    x: Column<number>,
+    y: Column<number>,
+    z: Column<number>,
+    vx: Column<number>,
+    vy: Column<number>,
+    vz: Column<number>
+}
+
+export interface Structure {
+    header: Readonly<Header>,
+    atoms: Readonly<Atoms>
+}
+
+export interface File {
+    structures: Structure[]
+}

src/reader/gro/schema.ts

@@ -1,40 +0,0 @@
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import * as Schema from '../../data/schema'
-import * as Data from '../../data/data'
-
-const str = Schema.Field.str()
-const int = Schema.Field.int()
-const float = Schema.Field.float()
-
-const header = {
-    'title': str,
-    'timeInPs': float,
-    'numberOfAtoms': int,
-    'boxX': float,
-    'boxY': float,
-    'boxZ': float
-}
-
-const atoms = {
-    'residueNumber': int,
-    'residueName': str,
-    'atomName': str,
-    'atomNumber': int,
-    'x': float,
-    'y': float,
-    'z': float,
-    'vx': float,
-    'vy': float,
-    'vz': float
-}
-
-const schema = { header, atoms };
-export default function (block: Data.Block) {
-    return Schema.apply(schema, block);
-}

src/data/spec/schema.spec.ts → src/reader/spec/cif.spec.ts

@@ -4,8 +4,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as Data from '../data'
-import * as Schema from '../schema'
+import * as Data from '../cif/data'
+import * as Schema from '../cif/schema'
 
 function Field(values: any[]): Data.Field {
     return {
@@ -13,7 +13,6 @@ function Field(values: any[]): Data.Field {
         str: row => '' + values[row],
         int: row => +values[row] || 0,
         float: row => +values[row] || 0,
-        value: row => values[row],
 
         presence: row => Data.ValuePresence.Present,
         areValuesEqual: (rowA, rowB) => values[rowA] === values[rowB],

src/reader/spec/gro.spec.ts

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import Gro from '../gro/format'
+import Gro from '../gro/parser'
 
 const groString = `MD of 2 waters, t= 4.2
     6
@@ -15,82 +15,77 @@ const groString = `MD of 2 waters, t= 4.2
     2WATER  OW1    4   1.275   0.053   0.622  0.2519  0.3140 -0.1734
     2WATER  HW2    5   1.337   0.002   0.680 -1.0641 -1.1349  0.0257
     2WATER  HW3    6   1.326   0.120   0.568  1.9427 -0.8216 -0.0244
-   1.82060   1.82060   1.82060`
+   1.82060   2.82060   3.82060`
 
 const groStringHighPrecision = `Generated by trjconv : 2168 system t=  15.00000
     3
     1ETH     C1    1   2.735383   2.672010   1.450194  0.2345 -0.1622 0.2097
     1ETH    H11    2   0.015804   2.716597   1.460588  0.8528 -0.7984 0.6605
     1ETH    H12    3   2.744822   2.565544   1.409227 -2.3812  2.8618 1.8101
-   1.82060   1.82060   1.82060`
+   1.82060   2.82060   3.82060`
 
 describe('gro reader', () => {
     it('basic', () => {
-        const parsed = Gro.parse(groString)
+        const parsed = Gro(groString)
 
         if (parsed.isError) {
             console.log(parsed)
-        } else {
-            const groFile = parsed.result;
-            const data = Gro.schema(groFile.blocks[0]);
-
-            const { header, atoms } = data;
-            if (header._isDefined) {
-                expect(header.title.value(0)).toBe('MD of 2 waters')
-                expect(header.timeInPs.value(0)).toBeCloseTo(4.2)
-                expect(header.numberOfAtoms.value(0)).toBe(6)
-
-                expect(header.boxX.value(0)).toBeCloseTo(1.82060)
-                expect(header.boxY.value(0)).toBeCloseTo(1.82060)
-                expect(header.boxZ.value(0)).toBeCloseTo(1.82060)
-            } else {
-                console.error('no header')
-            }
-
-            if (atoms._rowCount === 6)  {
-                expect(atoms.x.value(0)).toBeCloseTo(0.126);
-                expect(atoms.y.value(0)).toBeCloseTo(1.624);
-                expect(atoms.z.value(0)).toBeCloseTo(1.679);
-
-                // TODO: check velocities when they are parsed.
-            } else {
-                console.error('no atoms');
-            }
+            return;
         }
-    })
+
+        const groFile = parsed.result;
+        const data = groFile.structures[0];
+
+        const { header, atoms } = data;
+        expect(header.title).toBe('MD of 2 waters')
+        expect(header.timeInPs).toBeCloseTo(4.2)
+        expect(header.hasVelocities).toBe(true);
+        expect(header.precision.position).toBe(3);
+        expect(header.precision.velocity).toBe(4);
+        expect(header.box[0]).toBeCloseTo(1.82060, 0.00001)
+        expect(header.box[1]).toBeCloseTo(2.82060, 0.00001)
+        expect(header.box[2]).toBeCloseTo(3.82060, 0.00001)
+
+        expect(atoms.count).toBe(6);
+
+        expect(atoms.x.value(0)).toBeCloseTo(0.126, 0.001);
+        expect(atoms.y.value(0)).toBeCloseTo(1.624, 0.001);
+        expect(atoms.z.value(0)).toBeCloseTo(1.679, 0.001);
+
+        expect(atoms.vx.value(5)).toBeCloseTo(1.9427, 0.0001);
+        expect(atoms.vy.value(5)).toBeCloseTo(-0.8216, 0.0001);
+        expect(atoms.vz.value(5)).toBeCloseTo(-0.0244, 0.0001);
+    });
 
     it('high precision', () => {
-        const parsed = Gro.parse(groStringHighPrecision)
+        const parsed = Gro(groStringHighPrecision);
 
         if (parsed.isError) {
             console.log(parsed)
-        } else {
-            const groFile = parsed.result;
-            const data = Gro.schema(groFile.blocks[0]);
-
-            const { header, atoms } = data;
-            if (header._isDefined) {
-                expect(header.title.value(0)).toBe('Generated by trjconv : 2168 system')
-                expect(header.timeInPs.value(0)).toBeCloseTo(15)
-                expect(header.numberOfAtoms.value(0)).toBe(3)
-
-                expect(header.boxX.value(0)).toBeCloseTo(1.82060)
-                expect(header.boxY.value(0)).toBeCloseTo(1.82060)
-                expect(header.boxZ.value(0)).toBeCloseTo(1.82060)
-            } else {
-                console.error('no header')
-            }
-
-            if (atoms._rowCount === 3)  {
-                // TODO: test when high-prec parser is available
-                // expect(atoms.x.value(1)).toBeCloseTo(0.015804, 0.00001);
-                // expect(atoms.y.value(1)).toBeCloseTo(2.716597, 0.00001);
-                // expect(atoms.z.value(1)).toBeCloseTo(1.460588, 0.00001);
-
-                // TODO: check velocities when they are parsed.
-            } else {
-                console.error('no atoms');
-            }
+            return;
         }
-    })
+
+        const groFile = parsed.result;
+        const data = groFile.structures[0];
+
+        const { header, atoms } = data;
+        expect(header.title).toBe('Generated by trjconv : 2168 system')
+        expect(header.timeInPs).toBeCloseTo(15)
+        expect(header.hasVelocities).toBe(true);
+        expect(header.precision.position).toBe(6);
+        expect(header.precision.velocity).toBe(4);
+        expect(header.box[0]).toBeCloseTo(1.82060, 0.00001)
+        expect(header.box[1]).toBeCloseTo(2.82060, 0.00001)
+        expect(header.box[2]).toBeCloseTo(3.82060, 0.00001)
+
+        expect(atoms.count).toBe(3);
+
+        expect(atoms.x.value(1)).toBeCloseTo(0.015804, 0.000001);
+        expect(atoms.y.value(1)).toBeCloseTo(2.716597, 0.000001);
+        expect(atoms.z.value(1)).toBeCloseTo(1.460588, 0.000001);
+
+        expect(atoms.vx.value(0)).toBeCloseTo(0.2345, 0.0001);
+        expect(atoms.vy.value(0)).toBeCloseTo(-0.1622, 0.0001);
+        expect(atoms.vz.value(0)).toBeCloseTo(0.2097, 0.0001);
+    });
 });

src/script.ts

@@ -7,72 +7,64 @@
 // import * as util from 'util'
 import * as fs from 'fs'
 
-import Gro from './reader/gro/format'
+import Gro from './reader/gro/parser'
 
 //const file = '1crn.gro'
 // const file = 'water.gro'
 // const file = 'test.gro'
 const file = 'md_1u19_trj.gro'
 
-fs.readFile(`./examples/${file}`, 'utf8', function (err,data) {
+fs.readFile(`./examples/${file}`, 'utf8', function (err,input) {
     if (err) {
         return console.log(err);
     }
     // console.log(data);
 
     console.time('parse')
-    const parsed = Gro.parse(data)
+    const parsed = Gro(input)
     console.timeEnd('parse')
     if (parsed.isError) {
         console.log(parsed)
-    } else {
-        const groFile = parsed.result
-        const data = Gro.schema(groFile.blocks[0])
+        return;
+    }
 
-        // const header = groFile.blocks[0].getCategory('header')
-        const { header, atoms } = data;
-        if (header._rowCount !== 1) {
-            console.log('title', header.title.value(0))
-            console.log('timeInPs', header.timeInPs.value(0))
-            console.log('numberOfAtoms', header.numberOfAtoms.value(0))
-            console.log('boxX', header.boxX.value(0))
-            console.log('boxY', header.boxY.value(0))
-            console.log('boxZ', header.boxZ.value(0))
-        } else {
-            console.error('no header')
-        }
+    const groFile = parsed.result
 
-        if (atoms._rowCount > 0) {
-            console.log(`'${atoms.residueNumber.value(1)}'`)
-            console.log(`'${atoms.residueName.value(1)}'`)
-            console.log(`'${atoms.atomName.value(1)}'`)
-            console.log(atoms.z.value(1))
-            console.log(`'${atoms.z.value(1)}'`)
+    console.log('structure count: ', groFile.structures.length);
 
-            const n = atoms._rowCount
-            console.log('rowCount', n)
+    const data = groFile.structures[0];
 
-            console.time('getFloatArray x')
-            const x = atoms.x.toArray(0, n, x => new Float32Array(x))!
-            console.timeEnd('getFloatArray x')
-            console.log(x.length, x[0], x[x.length-1])
+    // const header = groFile.blocks[0].getCategory('header')
+    const { header, atoms } = data;
+    console.log(JSON.stringify(header, null, 2));
+    console.log('number of atoms:', atoms.count);
 
-            console.time('getFloatArray y')
-            const y = atoms.y.toArray(0, n, x => new Float32Array(x))!
-            console.timeEnd('getFloatArray y')
-            console.log(y.length, y[0], y[y.length-1])
+    console.log(`'${atoms.residueNumber.value(1)}'`)
+    console.log(`'${atoms.residueName.value(1)}'`)
+    console.log(`'${atoms.atomName.value(1)}'`)
+    console.log(atoms.z.value(1))
+    console.log(`'${atoms.z.value(1)}'`)
 
-            console.time('getFloatArray z')
-            const z = atoms.z.toArray(0, n, x => new Float32Array(x))!
-            console.timeEnd('getFloatArray z')
-            console.log(z.length, z[0], z[z.length-1])
+    const n = atoms.count;
+    console.log('rowCount', n)
 
-            console.time('getIntArray residueNumber')
-            const residueNumber = atoms.residueNumber.toArray(0, n, x => new Int32Array(x))!
-            console.timeEnd('getIntArray residueNumber')
-            console.log(residueNumber.length, residueNumber[0], residueNumber[residueNumber.length-1])
-        } else {
-            console.error('no atoms')
-        }
-    }
+    console.time('getFloatArray x')
+    const x = atoms.x.toArray(x => new Float32Array(x))!
+    console.timeEnd('getFloatArray x')
+    console.log(x.length, x[0], x[x.length-1])
+
+    console.time('getFloatArray y')
+    const y = atoms.y.toArray(x => new Float32Array(x))!
+    console.timeEnd('getFloatArray y')
+    console.log(y.length, y[0], y[y.length-1])
+
+    console.time('getFloatArray z')
+    const z = atoms.z.toArray(x => new Float32Array(x))!
+    console.timeEnd('getFloatArray z')
+    console.log(z.length, z[0], z[z.length-1])
+
+    console.time('getIntArray residueNumber')
+    const residueNumber = atoms.residueNumber.toArray(x => new Int32Array(x))!
+    console.timeEnd('getIntArray residueNumber')
+    console.log(residueNumber.length, residueNumber[0], residueNumber[residueNumber.length-1])
 });