diff --git a/LICENSE b/LICENSE
index c4c761c0706abd3eaa70951fcebed56e40f9a6bd..28cd5a5a9fa4ddcf561eaab15bfcd47b0d0b71cc 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
The MIT License
- Copyright (c) 2017, Mol* contributors
+ Copyright (c) 2017 - now, Mol* contributors
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index cdd07586a73e4fe45a7b945006a3b6ff1f3e1027..a2370eef7653f00cabd92b4acb089fe19bf54bc5 100644
--- a/README.md
+++ b/README.md
@@ -1,56 +1,47 @@
+[](./LICENSE)
+# Mol*
-[](https://github.com/arose/molio/blob/master/LICENSE)
+The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that will serve as basis for the next-generation data delivery and analysis tools for macromolecular structure data. This is a collaboration between PDBe and RCSB PDB teams and the development will be open source and available to anyone who wants to use it for developing visualisation tools for macromolecular structure data available from [PDB](https://www.wwpdb.org/) and other institutions.
-- general, non-opinionated library for reading and writing molecular structure related file formats
-- extending on the ideas of the CIFTools.js library
+This particular project is a prototype implementation of this technology (still under development).
+## Project Overview
-## Module Overview
+The core of Mol* currently consists of these modules:
- `mol-task` Computation abstraction with progress tracking and cancellation support.
-- `mol-data` Collections (integer based sets, inteface to columns/tables, etc.)
+- `mol-data` Collections (integer based sets, interface to columns/tables, etc.)
- `mol-math` Math related (loosely) algorithms and data structures.
-- `mol-io` Parsing library. Each format is parsed into an interface that corresponds to the data stored by it.
-- `mol-model` Data structures and algorithms (such as querying) for representing molecular data.
-- `mol-ql` Mapping of `mol-model` to the MolQL query language spec.
+- `mol-io` Parsing library. Each format is parsed into an interface that corresponds to the data stored by it. Support for common coordinate, experimental/map, and annotation data formats.
+- `mol-model` Data structures and algorithms (such as querying) for representing molecular data (including coordinate, experimental/map, and annotation data).
+- `mol-ql` Mapping of `mol-model` to the [MolQL query language](https://molql.github.io) spec.
- `mol-util` Useful things that do not fit elsewhere.
+The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `apps` (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
+
+## Previous Work
+This project builds on experience from previous solutions:
+- [LiteMol Suite](https://www.litemol.org)
+- [WebChemistry](https://webchem.ncbr.muni.cz)
+- [NGL Viewer](http://nglviewer.org/)
+- [MolQL](https://molql.github.io)
+- [PDB Component Library](https://www.ebi.ac.uk/pdbe/pdb-component-library/)
+- And many others (list will be continuously expanded).
+
## Building & Running
### Build:
-
- npm install
- npm run build
+ npm install
+ npm run build
### Build automatically on file save:
+ npm run watch
- npm run watch
-
-### Bundle with rollup (UMD and ES6)
-
- npm run bundle
-
-### Make distribution files
-
- npm run dist
-
-### Build everything above
-
- npm run-script build && npm run-script bundle && npm run-script dist
-
-
-## Example script
-
-### Build
-
- npm run script
-
-### Run
-
- node ./build/js/script.js
-
+### Run test script from src/script.ts
+ npm run script
-TODO
-----
+## Contributing
+Just open an issue or make a pull request. All contributions are welcome.
-- write about unittest (AR)
\ No newline at end of file
+## Roadmap
+Continually develop this prototype project. As individual modules become stable, make them into standalone libraries.
diff --git a/dist/molio.esm.js b/dist/molio.esm.js
deleted file mode 100644
index cce873658043fbb596eeee573c00706e62ac2a4c..0000000000000000000000000000000000000000
--- a/dist/molio.esm.js
+++ /dev/null
@@ -1,681 +0,0 @@
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * from https://github.com/dsehnal/CIFTools.js
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-/**
- * Efficient integer and float parsers.
- *
- * For the purposes of parsing numbers from the mmCIF data representations,
- * up to 4 times faster than JS parseInt/parseFloat.
- */
-
-function parseInt(str, start, end) {
- var ret = 0, neg = 1;
- if (str.charCodeAt(start) === 45 /* - */) {
- neg = -1;
- start++;
- }
- for (; start < end; start++) {
- var c = str.charCodeAt(start) - 48;
- if (c > 9 || c < 0)
- { return (neg * ret) | 0; }
- else
- { ret = (10 * ret + c) | 0; }
- }
- return neg * ret;
-}
-function parseScientific(main, str, start, end) {
- // handle + in '1e+1' separately.
- if (str.charCodeAt(start) === 43 /* + */)
- { start++; }
- return main * Math.pow(10.0, parseInt(str, start, end));
-}
-
-function parseFloat(str, start, end) {
- var neg = 1.0, ret = 0.0, point = 0.0, div = 1.0;
- if (str.charCodeAt(start) === 45) {
- neg = -1.0;
- ++start;
- }
- while (start < end) {
- var c = str.charCodeAt(start) - 48;
- if (c >= 0 && c < 10) {
- ret = ret * 10 + c;
- ++start;
- }
- else if (c === -2) {
- ++start;
- while (start < end) {
- c = str.charCodeAt(start) - 48;
- if (c >= 0 && c < 10) {
- point = 10.0 * point + c;
- div = 10.0 * div;
- ++start;
- }
- else if (c === 53 || c === 21) {
- return parseScientific(neg * (ret + point / div), str, start + 1, end);
- }
- else {
- return neg * (ret + point / div);
- }
- }
- return neg * (ret + point / div);
- }
- else if (c === 53 || c === 21) {
- return parseScientific(neg * ret, str, start + 1, end);
- }
- else
- { break; }
- }
- return neg * ret;
-}
-
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * from https://github.com/dsehnal/CIFTools.js
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-/**
- * Eat everything until a newline occurs.
- */
-function eatLine(state) {
- while (state.position < state.length) {
- switch (state.data.charCodeAt(state.position)) {
- case 10:// \n
- 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;
- }
- return;
- default:
- ++state.position;
- }
- }
- state.currentTokenEnd = state.position;
-}
-/**
- * Eat everything until a whitespace/newline occurs.
- */
-function eatValue(state) {
- while (state.position < state.length) {
- switch (state.data.charCodeAt(state.position)) {
- case 9: // \t
- case 10: // \n
- case 13: // \r
- case 32:// ' '
- state.currentTokenEnd = state.position;
- return;
- default:
- ++state.position;
- break;
- }
- }
- state.currentTokenEnd = state.position;
-}
-/**
- * Skips all the whitespace - space, tab, newline, CR
- * Handles incrementing line count.
- */
-function skipWhitespace(state) {
- var prev = 10;
- while (state.position < state.length) {
- var c = state.data.charCodeAt(state.position);
- switch (c) {
- case 9: // '\t'
- case 32:// ' '
- prev = c;
- ++state.position;
- break;
- case 10:// \n
- // handle \r\n
- if (prev !== 13) {
- ++state.currentLineNumber;
- }
- prev = c;
- ++state.position;
- break;
- case 13:// \r
- prev = c;
- ++state.position;
- ++state.currentLineNumber;
- break;
- default:
- return prev;
- }
- }
- return prev;
-}
-
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * from https://github.com/dsehnal/CIFTools.js
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-var Tokens;
-(function (Tokens) {
- function resize(tokens) {
- // scale the size using golden ratio, because why not.
- var newBuffer = new Int32Array((1.61 * tokens.indices.length) | 0);
- newBuffer.set(tokens.indices);
- tokens.indices = newBuffer;
- tokens.indicesLenMinus2 = (newBuffer.length - 2) | 0;
- }
- function add(tokens, start, end) {
- if (tokens.count > tokens.indicesLenMinus2) {
- resize(tokens);
- }
- tokens.indices[tokens.count++] = start;
- tokens.indices[tokens.count++] = end;
- }
- Tokens.add = add;
- function addUnchecked(tokens, start, end) {
- tokens.indices[tokens.count++] = start;
- tokens.indices[tokens.count++] = end;
- }
- Tokens.addUnchecked = addUnchecked;
- function create(size) {
- return {
- indicesLenMinus2: (size - 2) | 0,
- count: 0,
- indices: new Int32Array(size)
- };
- }
- Tokens.create = create;
-})(Tokens || (Tokens = {}));
-
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * from https://github.com/dsehnal/CIFTools.js
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-/**
- * Represents a column that is not present.
- */
-var _UndefinedColumn = function _UndefinedColumn() {
- this.isDefined = false;
-};
-_UndefinedColumn.prototype.getString = function getString (row) { return null; };
-
-_UndefinedColumn.prototype.getInteger = function getInteger (row) { return 0; };
-_UndefinedColumn.prototype.getFloat = function getFloat (row) { return 0.0; };
-_UndefinedColumn.prototype.getValuePresence = function getValuePresence (row) { return 1 /* NotSpecified */; };
-_UndefinedColumn.prototype.areValuesEqual = function areValuesEqual (rowA, rowB) { return true; };
-_UndefinedColumn.prototype.stringEquals = function stringEquals (row, value) { return value === null; };
-var UndefinedColumn = new _UndefinedColumn();
-
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * from https://github.com/dsehnal/CIFTools.js
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-var ShortStringPool;
-(function (ShortStringPool) {
- function create() { return Object.create(null); }
- ShortStringPool.create = create;
- function get(pool, str) {
- if (str.length > 6)
- { return str; }
- var value = pool[str];
- if (value !== void 0)
- { return value; }
- pool[str] = str;
- return str;
- }
- ShortStringPool.get = get;
-})(ShortStringPool || (ShortStringPool = {}));
-
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * from https://github.com/dsehnal/CIFTools.js
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-/**
- * Represents a single column.
- */
-var TextColumn = function TextColumn(table, data, name, index) {
- this.data = data;
- this.name = name;
- this.index = index;
- this.stringPool = ShortStringPool.create();
- this.isDefined = true;
- this.indices = table.indices;
- this.columnCount = table.columnCount;
-};
-/**
- * Returns the string value at given row.
- */
-TextColumn.prototype.getString = function getString (row) {
- var i = (row * this.columnCount + this.index) * 2;
- return ShortStringPool.get(this.stringPool, this.data.substring(this.indices[i], this.indices[i + 1]));
-};
-/**
- * Returns the integer value at given row.
- */
-TextColumn.prototype.getInteger = function getInteger (row) {
- var i = (row * this.columnCount + this.index) * 2;
- return parseInt(this.data, this.indices[i], this.indices[i + 1]);
-};
-/**
- * Returns the float value at given row.
- */
-TextColumn.prototype.getFloat = function getFloat (row) {
- var i = (row * this.columnCount + this.index) * 2;
- return parseFloat(this.data, this.indices[i], this.indices[i + 1]);
-};
-/**
- * Returns true if the token has the specified string value.
- */
-TextColumn.prototype.stringEquals = function stringEquals (row, value) {
- var this$1 = this;
-
- var aIndex = (row * this.columnCount + this.index) * 2, s = this.indices[aIndex], len = value.length;
- if (len !== this.indices[aIndex + 1] - s)
- { return false; }
- for (var i = 0; i < len; i++) {
- if (this$1.data.charCodeAt(i + s) !== value.charCodeAt(i))
- { return false; }
- }
- return true;
-};
-/**
- * Determines if values at the given rows are equal.
- */
-TextColumn.prototype.areValuesEqual = function areValuesEqual (rowA, rowB) {
- var this$1 = this;
-
- var aIndex = (rowA * this.columnCount + this.index) * 2;
- var bIndex = (rowB * this.columnCount + this.index) * 2;
- var aS = this.indices[aIndex];
- var bS = this.indices[bIndex];
- var len = this.indices[aIndex + 1] - aS;
- if (len !== this.indices[bIndex + 1] - bS)
- { return false; }
- for (var i = 0; i < len; i++) {
- if (this$1.data.charCodeAt(i + aS) !== this$1.data.charCodeAt(i + bS)) {
- return false;
- }
- }
- return true;
-};
-TextColumn.prototype.getValuePresence = function getValuePresence (row) {
- var index = 2 * (row * this.columnCount + this.index);
- if (this.indices[index] === this.indices[index + 1]) {
- return 1 /* NotSpecified */;
- }
- return 0 /* Present */;
-};
-var CifColumn = (function (TextColumn) {
- function CifColumn () {
- TextColumn.apply(this, arguments);
- }
-
- if ( TextColumn ) CifColumn.__proto__ = TextColumn;
- CifColumn.prototype = Object.create( TextColumn && TextColumn.prototype );
- CifColumn.prototype.constructor = CifColumn;
-
- CifColumn.prototype.getString = function getString (row) {
- var ret = TextColumn.prototype.getString.call(this, row);
- if (ret === '.' || ret === '?')
- { return null; }
- return ret;
- };
- /**
- * Returns true if the value is not defined (. or ? token).
- */
- CifColumn.prototype.getValuePresence = function getValuePresence (row) {
- var index = 2 * (row * this.columnCount + this.index);
- var s = this.indices[index];
- if (this.indices[index + 1] - s !== 1)
- { return 0 /* Present */; }
- var v = this.data.charCodeAt(s);
- if (v === 46 /* . */)
- { return 1 /* NotSpecified */; }
- if (v === 63 /* ? */)
- { return 2 /* Unknown */; }
- return 0 /* Present */;
- };
-
- return CifColumn;
-}(TextColumn));
-
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * from https://github.com/dsehnal/CIFTools.js
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-/**
- * Represents a category backed by a string.
- */
-var TextCategory = function TextCategory(data, name, columns, tokens) {
- this.name = name;
- this.indices = tokens.indices;
- this.data = data;
- this.columnCount = columns.length;
- this.rowCount = (tokens.count / 2 / columns.length) | 0;
- this.initColumns(columns);
-};
-
-var prototypeAccessors = { columnNames: {} };
-
-prototypeAccessors.columnNames.get = function () {
- return this.columnNameList;
-};
-/**
- * Get a column object that makes accessing data easier.
- */
-TextCategory.prototype.getColumn = function getColumn (name) {
- var i = this.columnIndices.get(name);
- if (i !== void 0)
- { return new TextColumn(this, this.data, name, i); }
- return UndefinedColumn;
-};
-TextCategory.prototype.initColumns = function initColumns (columns) {
- var this$1 = this;
-
- this.columnIndices = new Map();
- this.columnNameList = [];
- for (var i = 0; i < columns.length; i++) {
- this$1.columnIndices.set(columns[i], i);
- this$1.columnNameList.push(columns[i]);
- }
-};
-
-Object.defineProperties( TextCategory.prototype, prototypeAccessors );
-var CifCategory = (function (TextCategory) {
- function CifCategory () {
- TextCategory.apply(this, arguments);
- }
-
- if ( TextCategory ) CifCategory.__proto__ = TextCategory;
- CifCategory.prototype = Object.create( TextCategory && TextCategory.prototype );
- CifCategory.prototype.constructor = CifCategory;
-
- CifCategory.prototype.getColumn = function getColumn (name) {
- var i = this.columnIndices.get(name);
- if (i !== void 0)
- { return new CifColumn(this, this.data, name, i); }
- return UndefinedColumn;
- };
- CifCategory.prototype.initColumns = function initColumns (columns) {
- var this$1 = this;
-
- this.columnIndices = new Map();
- this.columnNameList = [];
- for (var i = 0; i < columns.length; i++) {
- var colName = columns[i].substr(this$1.name.length + 1);
- this$1.columnIndices.set(colName, i);
- this$1.columnNameList.push(colName);
- }
- };
-
- return CifCategory;
-}(TextCategory));
-
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * from https://github.com/dsehnal/CIFTools.js
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-var ParserResult;
-(function (ParserResult) {
- function error(message, line) {
- if ( line === void 0 ) line = -1;
-
- return new ParserError(message, line);
- }
- ParserResult.error = error;
- function success(result, warnings) {
- if ( warnings === void 0 ) warnings = [];
-
- return new ParserSuccess(result, warnings);
- }
- ParserResult.success = success;
-})(ParserResult || (ParserResult = {}));
-var ParserError = function ParserError(message, line) {
- this.message = message;
- this.line = line;
- this.isError = true;
-};
-ParserError.prototype.toString = function toString () {
- if (this.line >= 0) {
- return ("[Line " + (this.line) + "] " + (this.message));
- }
- return this.message;
-};
-var ParserSuccess = function ParserSuccess(result, warnings) {
- this.result = result;
- this.warnings = warnings;
- this.isError = false;
-};
-
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-var GroFile = function GroFile(data) {
- this.blocks = [];
- this.data = data;
-};
-var GroBlock = function GroBlock(data) {
- this.data = data;
- this.categoryMap = new Map();
- this.categoryList = [];
-};
-
-GroBlock.prototype.getCategory = function getCategory (name) {
- return this.categoryMap.get(name);
-};
-/**
- * Adds a category.
- */
-GroBlock.prototype.addCategory = function addCategory (category) {
- this.categoryList[this.categoryList.length] = category;
- this.categoryMap.set(category.name, category);
-};
-function createTokenizer(data) {
- return {
- data: data,
- position: 0,
- length: data.length,
- currentLineNumber: 1,
- currentTokenStart: 0,
- currentTokenEnd: 0,
- numberOfAtoms: 0,
- hasVelocities: false,
- numberOfDecimalPlaces: 3
- };
-}
-/**
- * title string (free format string, optional time in ps after 't=')
- */
-function handleTitleString(state, tokens) {
- eatLine(state);
- // console.log('title', state.data.substring(state.currentTokenStart, state.currentTokenEnd))
- var start = state.currentTokenStart;
- var end = state.currentTokenEnd;
- var valueStart = state.currentTokenStart;
- var valueEnd = start;
- while (valueEnd < end && !isTime(state.data, valueEnd))
- { ++valueEnd; }
- if (isTime(state.data, valueEnd)) {
- var timeStart = valueEnd + 2;
- while (valueEnd > start && isSpaceOrComma(state.data, valueEnd - 1))
- { --valueEnd; }
- Tokens.add(tokens, valueStart, valueEnd); // title
- 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
- }
- else {
- Tokens.add(tokens, valueStart, valueEnd); // title
- Tokens.add(tokens, valueEnd, valueEnd); // empty token for time
- }
-}
-function isSpaceOrComma(data, position) {
- var c = data.charCodeAt(position);
- return c === 32 || c === 44;
-}
-function isTime(data, position) {
- // T/t
- var c = data.charCodeAt(position);
- if (c !== 84 && c !== 116)
- { return false; }
- // =
- if (data.charCodeAt(position + 1) !== 61)
- { return false; }
- return true;
-}
-// function isDot(state: TokenizerState): boolean {
-// // .
-// if (state.data.charCodeAt(state.currentTokenStart) !== 46) return false;
-// return true;
-// }
-// function numberOfDecimalPlaces (state: TokenizerState) {
-// // var ndec = firstLines[ 2 ].length - firstLines[ 2 ].lastIndexOf('.') - 1
-// const start = state.currentTokenStart
-// const end = state.currentTokenEnd
-// for (let i = end; start < i; --i) {
-// // .
-// if (state.data.charCodeAt(i) === 46) return end - start - i
-// }
-// throw new Error('Could not determine number of decimal places')
-// }
-/**
- * number of atoms (free format integer)
- */
-function handleNumberOfAtoms(state, tokens) {
- skipWhitespace(state);
- state.currentTokenStart = state.position;
- eatValue(state);
- state.numberOfAtoms = parseInt(state.data, state.currentTokenStart, state.currentTokenEnd);
- Tokens.add(tokens, state.currentTokenStart, state.currentTokenEnd);
- eatLine(state);
-}
-// function checkForVelocities (state: GroState) {
-// }
-/**
- * This format is fixed, ie. all columns are in a fixed position.
- * Optionally (for now only yet with trjconv) you can write gro files
- * with any number of decimal places, the format will then be n+5
- * positions with n decimal places (n+1 for velocities) in stead
- * of 8 with 3 (with 4 for velocities). Upon reading, the precision
- * will be inferred from the distance between the decimal points
- * (which will be n+5). Columns contain the following information
- * (from left to right):
- * residue number (5 positions, integer)
- * residue name (5 characters)
- * atom name (5 characters)
- * atom number (5 positions, integer)
- * 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, block) {
- console.log('MOINMOIN');
- var name = 'atoms';
- var columns = ['residueNumber', 'residueName', 'atomName', 'atomNumber', 'x', 'y', 'z'];
- if (state.hasVelocities) {
- columns.push('vx', 'vy', 'vz');
- }
- var fieldSizes = [5, 5, 5, 5, 8, 8, 8, 8, 8, 8];
- var columnCount = columns.length;
- var tokens = Tokens.create(state.numberOfAtoms * 2 * columnCount);
- var start;
- var end;
- var valueStart;
- var valueEnd = state.position;
- for (var i = 0; i < state.numberOfAtoms; ++i) {
- state.currentTokenStart = state.position;
- end = state.currentTokenStart;
- for (var j = 0; j < columnCount; ++j) {
- start = end;
- end = start + fieldSizes[j];
- // trim
- valueStart = start;
- valueEnd = end;
- while (valueStart < valueEnd && state.data.charCodeAt(valueStart) === 32)
- { ++valueStart; }
- while (valueEnd > valueStart && state.data.charCodeAt(valueEnd - 1) === 32)
- { --valueEnd; }
- Tokens.addUnchecked(tokens, valueStart, valueEnd);
- }
- state.position = valueEnd;
- eatLine(state);
- }
- block.addCategory(new TextCategory(state.data, name, columns, tokens));
-}
-/**
- * box vectors (free format, space separated reals), values:
- * v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y),
- * 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, tokens) {
- // just read the first three values, ignore any remaining
- for (var i = 0; i < 3; ++i) {
- skipWhitespace(state);
- state.currentTokenStart = state.position;
- eatValue(state);
- Tokens.add(tokens, state.currentTokenStart, state.currentTokenEnd);
- }
-}
-/**
- * Creates an error result.
- */
-// function error(line: number, message: string) {
-// return ParserResult.error<GroFile>(message, line);
-// }
-/**
- * Creates a data result.
- */
-function result(data) {
- return ParserResult.success(data);
-}
-function parseInternal(data) {
- var state = createTokenizer(data);
- var file = new GroFile(data);
- var block = new GroBlock(data);
- file.blocks.push(block);
- var headerColumns = ['title', 'timeInPs', 'numberOfAtoms', 'boxX', 'boxY', 'boxZ'];
- var headerTokens = Tokens.create(2 * headerColumns.length);
- var header = new TextCategory(state.data, 'header', headerColumns, headerTokens);
- block.addCategory(header);
- handleTitleString(state, headerTokens);
- handleNumberOfAtoms(state, headerTokens);
- handleAtoms(state, block);
- handleBoxVectors(state, headerTokens);
- return result(file);
-}
-function parse(data) {
- return parseInternal(data);
-}
-
-/*
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-export { parse as groReader };
-//# sourceMappingURL=molio.esm.js.map
diff --git a/dist/molio.js b/dist/molio.js
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/molio.sublime-project b/molio.sublime-project
deleted file mode 100644
index 24db30311b340c8d78001f0fb705810ab77a8c38..0000000000000000000000000000000000000000
--- a/molio.sublime-project
+++ /dev/null
@@ -1,8 +0,0 @@
-{
- "folders":
- [
- {
- "path": "."
- }
- ]
-}
diff --git a/package-lock.json b/package-lock.json
index 047413021a6fd3733756bae612ac80c1eb74a9cd..2c12def033f6ca417d7e46fcde7469950e725e06 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index 59f858186b753055f38774f3514554ec03fe15ee..dcda720c213899e898360d787fe52476cc6de098 100644
--- a/package.json
+++ b/package.json
@@ -1,19 +1,13 @@
{
- "name": "mol-star",
+ "name": "mol-star-proto",
"version": "0.1.0",
"description": "Comprehensive molecular library.",
- "main": "dist/molio.js",
- "module": "dist/molio.esm.js",
- "types": "src/index.d.ts",
"scripts": {
"lint": "./node_modules/.bin/tslint src/**/*.ts",
"build": "./node_modules/.bin/tsc",
"watch": "./node_modules/.bin/tsc -watch",
- "bundle": "./node_modules/.bin/rollup -c",
"test": "./node_modules/.bin/jest",
- "dist": "./node_modules/.bin/uglifyjs build/js/molio.dev.js -cm > dist/molio.js && cp build/js/molio.esm.js dist/molio.esm.js",
- "script": "./node_modules/.bin/rollup build/node_modules/script.js -e fs -f cjs -o build/js/script.js",
- "runscript": "node build/node_modules/script.js",
+ "script": "node build/node_modules/script.js",
"download-dics": "./node_modules/.bin/download -o build/dics http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic && ./node_modules/.bin/download -o build/dics http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ddl.dic"
},
"jest": {
@@ -34,9 +28,9 @@
"license": "MIT",
"devDependencies": {
"@types/benchmark": "^1.0.31",
- "@types/express": "^4.0.39",
- "@types/jest": "^21.1.8",
- "@types/node": "^8.0.56",
+ "@types/express": "^4.11.0",
+ "@types/jest": "^21.1.10",
+ "@types/node": "^8.5.8",
"@types/node-fetch": "^1.6.7",
"benchmark": "^2.1.4",
"download-cli": "^1.0.5",
@@ -45,12 +39,12 @@
"rollup-plugin-buble": "^0.16.0",
"rollup-plugin-commonjs": "^8.2.6",
"rollup-plugin-json": "^2.3.0",
- "rollup-plugin-node-resolve": "^3.0.0",
+ "rollup-plugin-node-resolve": "^3.0.2",
"rollup-watch": "^4.3.1",
"ts-jest": "^21.2.4",
- "tslint": "^5.8.0",
+ "tslint": "^5.9.1",
"typescript": "^2.6.2",
- "uglify-js": "^3.2.1",
+ "uglify-js": "^3.3.7",
"util.promisify": "^1.0.0"
},
"dependencies": {
diff --git a/rollup.config.js b/rollup.config.js
deleted file mode 100644
index cae10ad5d9564a165d3f79716974e314de857041..0000000000000000000000000000000000000000
--- a/rollup.config.js
+++ /dev/null
@@ -1,40 +0,0 @@
-// import buble from 'rollup-plugin-buble';
-import json from 'rollup-plugin-json';
-import resolve from 'rollup-plugin-node-resolve';
-import commonjs from 'rollup-plugin-commonjs';
-
-var path = require('path');
-var pkg = require('./package.json');
-var external = Object.keys(pkg.dependencies);
-
-export default {
- input: 'build/js/src/index.js',
- plugins: [
- resolve({
- jsnext: true,
- main: true
- }),
- commonjs(),
- json(),
- // buble()
- ],
- output: [
- {
- file: "build/js/molio.dev.js",
- format: 'umd',
- name: 'MOLIO',
- sourcemap: false
- },
- // {
- // file: "build/js/molio.esm.js",
- // format: 'es',
- // sourcemap: false
- // }
- ],
- external: external,
- sourcemap: false,
- onwarn(warning, warn) {
- if (warning.code === 'THIS_IS_UNDEFINED') return;
- warn(warning); // this requires Rollup 0.46
- }
-};
\ No newline at end of file