From 609aa648b27f9a246850ea95151cb1ca5600b31e Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 5 Sep 2017 11:28:59 -0700
Subject: [PATCH] added dist files
---
dist/molio.esm.js | 641 ++++++++++++++++++++++++++++++++++++++++++++++
dist/molio.js | 1 +
2 files changed, 642 insertions(+)
create mode 100644 dist/molio.esm.js
create mode 100644 dist/molio.js
diff --git a/dist/molio.esm.js b/dist/molio.esm.js
new file mode 100644
index 000000000..572b8877b
--- /dev/null
+++ b/dist/molio.esm.js
@@ -0,0 +1,641 @@
+/*
+ * 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;
+}
+
+/**
+ * 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;
+}
+
+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 = {}));
+
+/**
+ * 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 = {}));
+
+/**
+ * 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));
+
+/**
+ * Represents a table backed by a string.
+ */
+var TextTable = function TextTable(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.
+ */
+TextTable.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;
+};
+TextTable.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( TextTable.prototype, prototypeAccessors );
+var CifTable = (function (TextTable) {
+ function CifTable () {
+ TextTable.apply(this, arguments);
+ }
+
+ if ( TextTable ) CifTable.__proto__ = TextTable;
+ CifTable.prototype = Object.create( TextTable && TextTable.prototype );
+ CifTable.prototype.constructor = CifTable;
+
+ CifTable.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;
+ };
+ CifTable.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 CifTable;
+}(TextTable));
+
+/*
+ * 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.tableMap = new Map();
+ this.tableList = [];
+};
+
+GroBlock.prototype.getTable = function getTable (name) {
+ return this.tableMap.get(name);
+};
+/**
+ * Adds a table.
+ */
+GroBlock.prototype.addTable = function addTable (table) {
+ this.tableList[this.tableList.length] = table;
+ this.tableMap.set(table.name, table);
+};
+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) {
+ 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.addTable(new TextTable(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 TextTable(state.data, 'header', headerColumns, headerTokens);
+ block.addTable(header);
+ handleTitleString(state, headerTokens);
+ handleNumberOfAtoms(state, headerTokens);
+ handleAtoms(state, block);
+ handleBoxVectors(state, headerTokens);
+ return result(file);
+}
+function parse(data) {
+ return parseInternal(data);
+}
+
+export { parse as groReader };
+//# sourceMappingURL=molio.esm.js.map
diff --git a/dist/molio.js b/dist/molio.js
new file mode 100644
index 000000000..0f83341da
--- /dev/null
+++ b/dist/molio.js
@@ -0,0 +1 @@
+!function(t,n){"object"==typeof exports&&"undefined"!=typeof module?n(exports):"function"==typeof define&&define.amd?define(["exports"],n):n(t.MOLIO={})}(this,function(t){"use strict";function n(t,n,e){var i=0,r=1;for(45===t.charCodeAt(n)&&(r=-1,n++);n<e;n++){var o=t.charCodeAt(n)-48;if(o>9||o<0)return r*i|0;i=10*i+o|0}return r*i}function e(t,e,i,r){return 43===e.charCodeAt(i)&&i++,t*Math.pow(10,n(e,i,r))}function i(t,n,i){var r=1,o=0,s=0,u=1;for(45===t.charCodeAt(n)&&(r=-1,++n);n<i;){var a=t.charCodeAt(n)-48;if(!(a>=0&&a<10)){if(-2===a){for(++n;n<i;){if(!((a=t.charCodeAt(n)-48)>=0&&a<10))return 53===a||21===a?e(r*(o+s/u),t,n+1,i):r*(o+s/u);s=10*s+a,u*=10,++n}return r*(o+s/u)}if(53===a||21===a)return e(r*o,t,n+1,i);break}o=10*o+a,++n}return r*o}function r(t){for(;t.position<t.length;)switch(t.data.charCodeAt(t.position)){case 10:return t.currentTokenEnd=t.position,++t.position,void++t.currentLineNumber;case 13:return t.currentTokenEnd=t.position,++t.position,++t.currentLineNumber,void(10===t.data.charCodeAt(t.position)&&++t.position);default:++t.position}t.currentTokenEnd=t.position}function o(t){for(;t.position<t.length;)switch(t.data.charCodeAt(t.position)){case 9:case 10:case 13:case 32:return void(t.currentTokenEnd=t.position);default:++t.position}t.currentTokenEnd=t.position}function s(t){for(var n=10;t.position<t.length;){var e=t.data.charCodeAt(t.position);switch(e){case 9:case 32:n=e,++t.position;break;case 10:13!==n&&++t.currentLineNumber,n=e,++t.position;break;case 13:n=e,++t.position,++t.currentLineNumber;break;default:return n}}return n}function u(t){return{data:t,position:0,length:t.length,currentLineNumber:1,currentTokenStart:0,currentTokenEnd:0,numberOfAtoms:0,hasVelocities:!1,numberOfDecimalPlaces:3}}function a(t,n){r(t);for(var e=t.currentTokenStart,i=t.currentTokenEnd,o=t.currentTokenStart,s=e;s<i&&!d(t.data,s);)++s;if(d(t.data,s)){for(var u=s+2;s>e&&c(t.data,s-1);)--s;for(v.add(n,o,s);u<i&&32===t.data.charCodeAt(u);)++u;for(;s>u&&32===t.data.charCodeAt(s-1);)--s;v.add(n,u,i)}else v.add(n,o,s),v.add(n,s,s)}function c(t,n){var e=t.charCodeAt(n);return 32===e||44===e}function d(t,n){var e=t.charCodeAt(n);return(84===e||116===e)&&61===t.charCodeAt(n+1)}function h(t,e){s(t),t.currentTokenStart=t.position,o(t),t.numberOfAtoms=n(t.data,t.currentTokenStart,t.currentTokenEnd),v.add(e,t.currentTokenStart,t.currentTokenEnd),r(t)}function f(t,n){var e=["residueNumber","residueName","atomName","atomNumber","x","y","z"];t.hasVelocities&&e.push("vx","vy","vz");for(var i,o,s,u=[5,5,5,5,8,8,8,8,8,8],a=e.length,c=v.create(2*t.numberOfAtoms*a),d=t.position,h=0;h<t.numberOfAtoms;++h){t.currentTokenStart=t.position,o=t.currentTokenStart;for(var f=0;f<a;++f){for(s=i=o,d=o=i+u[f];s<d&&32===t.data.charCodeAt(s);)++s;for(;d>s&&32===t.data.charCodeAt(d-1);)--d;v.addUnchecked(c,s,d)}t.position=d,r(t)}n.addTable(new k(t.data,"atoms",e,c))}function p(t,n){for(var e=0;e<3;++e)s(t),t.currentTokenStart=t.position,o(t),v.add(n,t.currentTokenStart,t.currentTokenEnd)}function l(t){return w.success(t)}function m(t){var n=u(t),e=new E(t),i=new N(t);e.blocks.push(i);var r=["title","timeInPs","numberOfAtoms","boxX","boxY","boxZ"],o=v.create(2*r.length),s=new k(n.data,"header",r,o);return i.addTable(s),a(n,o),h(n,o),f(n,i),p(n,o),l(e)}var v;!function(t){function n(t){var n=new Int32Array(1.61*t.indices.length|0);n.set(t.indices),t.indices=n,t.indicesLenMinus2=n.length-2|0}t.add=function(t,e,i){t.count>t.indicesLenMinus2&&n(t),t.indices[t.count++]=e,t.indices[t.count++]=i},t.addUnchecked=function(t,n,e){t.indices[t.count++]=n,t.indices[t.count++]=e},t.create=function(t){return{indicesLenMinus2:t-2|0,count:0,indices:new Int32Array(t)}}}(v||(v={}));var g=function(){this.isDefined=!1};g.prototype.getString=function(t){return null},g.prototype.getInteger=function(t){return 0},g.prototype.getFloat=function(t){return 0},g.prototype.getValuePresence=function(t){return 1},g.prototype.areValuesEqual=function(t,n){return!0},g.prototype.stringEquals=function(t,n){return null===n};var b,y=new g;!function(t){t.create=function(){return Object.create(null)},t.get=function(t,n){if(n.length>6)return n;var e=t[n];return void 0!==e?e:(t[n]=n,n)}}(b||(b={}));var C=function(t,n,e,i){this.data=n,this.name=e,this.index=i,this.stringPool=b.create(),this.isDefined=!0,this.indices=t.indices,this.columnCount=t.columnCount};C.prototype.getString=function(t){var n=2*(t*this.columnCount+this.index);return b.get(this.stringPool,this.data.substring(this.indices[n],this.indices[n+1]))},C.prototype.getInteger=function(t){var e=2*(t*this.columnCount+this.index);return n(this.data,this.indices[e],this.indices[e+1])},C.prototype.getFloat=function(t){var n=2*(t*this.columnCount+this.index);return i(this.data,this.indices[n],this.indices[n+1])},C.prototype.stringEquals=function(t,n){var e=this,i=2*(t*this.columnCount+this.index),r=this.indices[i],o=n.length;if(o!==this.indices[i+1]-r)return!1;for(var s=0;s<o;s++)if(e.data.charCodeAt(s+r)!==n.charCodeAt(s))return!1;return!0},C.prototype.areValuesEqual=function(t,n){var e=this,i=2*(t*this.columnCount+this.index),r=2*(n*this.columnCount+this.index),o=this.indices[i],s=this.indices[r],u=this.indices[i+1]-o;if(u!==this.indices[r+1]-s)return!1;for(var a=0;a<u;a++)if(e.data.charCodeAt(a+o)!==e.data.charCodeAt(a+s))return!1;return!0},C.prototype.getValuePresence=function(t){var n=2*(t*this.columnCount+this.index);return this.indices[n]===this.indices[n+1]?1:0};var A=function(t){function n(){t.apply(this,arguments)}return t&&(n.__proto__=t),n.prototype=Object.create(t&&t.prototype),n.prototype.constructor=n,n.prototype.getString=function(n){var e=t.prototype.getString.call(this,n);return"."===e||"?"===e?null:e},n.prototype.getValuePresence=function(t){var n=2*(t*this.columnCount+this.index),e=this.indices[n];if(this.indices[n+1]-e!=1)return 0;var i=this.data.charCodeAt(e);return 46===i?1:63===i?2:0},n}(C),k=function(t,n,e,i){this.name=n,this.indices=i.indices,this.data=t,this.columnCount=e.length,this.rowCount=i.count/2/e.length|0,this.initColumns(e)},T={columnNames:{}};T.columnNames.get=function(){return this.columnNameList},k.prototype.getColumn=function(t){var n=this.columnIndices.get(t);return void 0!==n?new C(this,this.data,t,n):y},k.prototype.initColumns=function(t){var n=this;this.columnIndices=new Map,this.columnNameList=[];for(var e=0;e<t.length;e++)n.columnIndices.set(t[e],e),n.columnNameList.push(t[e])},Object.defineProperties(k.prototype,T);var w;!function(t){function n(){t.apply(this,arguments)}t&&(n.__proto__=t),n.prototype=Object.create(t&&t.prototype),n.prototype.constructor=n,n.prototype.getColumn=function(t){var n=this.columnIndices.get(t);return void 0!==n?new A(this,this.data,t,n):y},n.prototype.initColumns=function(t){var n=this;this.columnIndices=new Map,this.columnNameList=[];for(var e=0;e<t.length;e++){var i=t[e].substr(n.name.length+1);n.columnIndices.set(i,e),n.columnNameList.push(i)}}}(k);!function(t){t.error=function(t,n){return void 0===n&&(n=-1),new L(t,n)},t.success=function(t,n){return void 0===n&&(n=[]),new x(t,n)}}(w||(w={}));var L=function(t,n){this.message=t,this.line=n,this.isError=!0};L.prototype.toString=function(){return this.line>=0?"[Line "+this.line+"] "+this.message:this.message};var x=function(t,n){this.result=t,this.warnings=n,this.isError=!1},E=function(t){this.blocks=[],this.data=t},N=function(t){this.data=t,this.tableMap=new Map,this.tableList=[]};N.prototype.getTable=function(t){return this.tableMap.get(t)},N.prototype.addTable=function(t){this.tableList[this.tableList.length]=t,this.tableMap.set(t.name,t)},t.groReader=function(t){return m(t)},Object.defineProperty(t,"__esModule",{value:!0})});
--
GitLab