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index.js
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// WHEN REPLACING, CHECK FOR:
// KEEP THIS WHEN REGENERATING THE PARSER !!
/*
* Generated by PEG.js 0.10.0.
*
* http://pegjs.org/
*/
function peg$subclass(child, parent) {
function ctor() {
this.constructor = child;
}
ctor.prototype = parent.prototype;
child.prototype = new ctor();
}
function peg$SyntaxError(message, expected, found, location) {
this.message = message;
this.expected = expected;
this.found = found;
this.location = location;
this.name = "SyntaxError";
if (typeof Error.captureStackTrace === "function") {
Error.captureStackTrace(this, peg$SyntaxError);
}
}
peg$subclass(peg$SyntaxError, Error);
peg$SyntaxError.buildMessage = function (expected, found) {
var DESCRIBE_EXPECTATION_FNS = {
literal: function (expectation) {
return "\"" + literalEscape(expectation.text) + "\"";
},
"class": function (expectation) {
var escapedParts = "",
i;
for (i = 0; i < expectation.parts.length; i++) {
escapedParts += expectation.parts[i] instanceof Array ?
classEscape(expectation.parts[i][0]) + "-" + classEscape(expectation.parts[i][1]) :
classEscape(expectation.parts[i]);
}
return "[" + (expectation.inverted ? "^" : "") + escapedParts + "]";
},
any: function (expectation) {
return "any character";
},
end: function (expectation) {
return "end of input";
},
other: function (expectation) {
return expectation.description;
}
};
function hex(ch) {
return ch.charCodeAt(0).toString(16).toUpperCase();
}
function literalEscape(s) {
return s
.replace(/\\/g, '\\\\')
.replace(/"/g, '\\"')
.replace(/\0/g, '\\0')
.replace(/\t/g, '\\t')
.replace(/\n/g, '\\n')
.replace(/\r/g, '\\r')
.replace(/[\x00-\x0F]/g, function (ch) {
return '\\x0' + hex(ch);
})
.replace(/[\x10-\x1F\x7F-\x9F]/g, function (ch) {
return '\\x' + hex(ch);
});
}
function classEscape(s) {
return s
.replace(/\\/g, '\\\\')
.replace(/\]/g, '\\]')
.replace(/\^/g, '\\^')
.replace(/-/g, '\\-')
.replace(/\0/g, '\\0')
.replace(/\t/g, '\\t')
.replace(/\n/g, '\\n')
.replace(/\r/g, '\\r')
.replace(/[\x00-\x0F]/g, function (ch) {
return '\\x0' + hex(ch);
})
.replace(/[\x10-\x1F\x7F-\x9F]/g, function (ch) {
return '\\x' + hex(ch);
});
}
function describeExpectation(expectation) {
return DESCRIBE_EXPECTATION_FNS[expectation.type](expectation);
}
function describeExpected(expected) {
var descriptions = new Array(expected.length),
i, j;
for (i = 0; i < expected.length; i++) {
descriptions[i] = describeExpectation(expected[i]);
}
descriptions.sort();
if (descriptions.length > 0) {
for (i = 1, j = 1; i < descriptions.length; i++) {
if (descriptions[i - 1] !== descriptions[i]) {
descriptions[j] = descriptions[i];
j++;
}
}
descriptions.length = j;
}
switch (descriptions.length) {
case 1:
return descriptions[0];
case 2:
return descriptions[0] + " or " + descriptions[1];
default:
return descriptions.slice(0, -1).join(", ") +
", or " +
descriptions[descriptions.length - 1];
}
}
function describeFound(found) {
return found ? "\"" + literalEscape(found) + "\"" : "end of input";
}
return "Expected " + describeExpected(expected) + " but " + describeFound(found) + " found.";
};
function peg$parse(input, options) {
options = options !== void 0 ? options : {};
// KEEP THIS WHEN REGENERATING THE PARSER !!
var nOpenParentheses = input.split('(').length - 1;
var nCloseParentheses = input.split(')').length - 1;
if (nOpenParentheses !== nCloseParentheses) {
throw peg$buildSimpleError('The number of opening parentheses does not match the number of closing parentheses.', 0);
}
// KEEP THIS WHEN REGENERATING THE PARSER !!
var peg$FAILED = {},
peg$startRuleFunctions = {
chain: peg$parsechain
},
peg$startRuleFunction = peg$parsechain,
peg$c0 = function (s) {
var branches = [];
var rings = [];
for (var i = 0; i < s[1].length; i++) {
branches.push(s[1][i]);
}
for (var i = 0; i < s[2].length; i++) {
var bond = (s[2][i][0]) ? s[2][i][0] : '-';
rings.push({
'bond': bond,
'id': s[2][i][1]
});
}
for (var i = 0; i < s[3].length; i++) {
branches.push(s[3][i]);
}
for (var i = 0; i < s[6].length; i++) {
branches.push(s[6][i]);
}
return {
'atom': s[0],
'isBracket': s[0].element ? true : false,
'branches': branches,
'branchCount': branches.length,
'ringbonds': rings,
'ringbondCount': rings.length,
'bond': s[4] ? s[4] : '-',
'next': s[5],
'hasNext': s[5] ? true : false
}
return s;
},
peg$c1 = "(",
peg$c2 = peg$literalExpectation("(", false),
peg$c3 = ")",
peg$c4 = peg$literalExpectation(")", false),
peg$c5 = function (b) {
var bond = (b[1]) ? b[1] : '-';
b[2].branchBond = bond;
return b[2]
},
peg$c6 = function (a) {
return a;
},
peg$c7 = /^[\-=#$:\/\\.]/,
peg$c8 = peg$classExpectation(["-", "=", "#", "$", ":", "/", "\\", "."], false, false),
peg$c9 = function (b) {
return b;
},
peg$c10 = "[",
peg$c11 = peg$literalExpectation("[", false),
peg$c12 = "se",
peg$c13 = peg$literalExpectation("se", false),
peg$c14 = "as",
peg$c15 = peg$literalExpectation("as", false),
peg$c16 = "]",
peg$c17 = peg$literalExpectation("]", false),
peg$c18 = function (b) {
return {
'isotope': b[1],
'element': b[2],
'chirality': b[3],
'hcount': b[4],
'charge': b[5],
'class': b[6]
}
},
peg$c19 = "B",
peg$c20 = peg$literalExpectation("B", false),
peg$c21 = "r",
peg$c22 = peg$literalExpectation("r", false),
peg$c23 = "C",
peg$c24 = peg$literalExpectation("C", false),
peg$c25 = "l",
peg$c26 = peg$literalExpectation("l", false),
peg$c27 = /^[NOPSFI]/,
peg$c28 = peg$classExpectation(["N", "O", "P", "S", "F", "I"], false, false),
peg$c29 = function (o) {
if (o.length > 1) return o.join('');
return o;
},
peg$c30 = /^[bcnops]/,
peg$c31 = peg$classExpectation(["b", "c", "n", "o", "p", "s"], false, false),
peg$c32 = "*",
peg$c33 = peg$literalExpectation("*", false),
peg$c34 = function (w) {
return w;
},
peg$c35 = /^[A-Z]/,
peg$c36 = peg$classExpectation([
["A", "Z"]
], false, false),
peg$c37 = /^[a-z]/,
peg$c38 = peg$classExpectation([
["a", "z"]
], false, false),
peg$c39 = function (e) {
return e.join('');
},
peg$c40 = "%",
peg$c41 = peg$literalExpectation("%", false),
peg$c42 = /^[1-9]/,
peg$c43 = peg$classExpectation([
["1", "9"]
], false, false),
peg$c44 = /^[0-9]/,
peg$c45 = peg$classExpectation([
["0", "9"]
], false, false),
peg$c46 = function (r) {
if (r.length == 1) return Number(r);
return Number(r.join('').replace('%', ''));
},
peg$c47 = "@",
peg$c48 = peg$literalExpectation("@", false),
peg$c49 = "TH",
peg$c50 = peg$literalExpectation("TH", false),
peg$c51 = /^[12]/,
peg$c52 = peg$classExpectation(["1", "2"], false, false),
peg$c53 = "AL",
peg$c54 = peg$literalExpectation("AL", false),
peg$c55 = "SP",
peg$c56 = peg$literalExpectation("SP", false),
peg$c57 = /^[1-3]/,
peg$c58 = peg$classExpectation([
["1", "3"]
], false, false),
peg$c59 = "TB",
peg$c60 = peg$literalExpectation("TB", false),
peg$c61 = "OH",
peg$c62 = peg$literalExpectation("OH", false),
peg$c63 = function (c) {
if (!c[1]) return '@';
if (c[1] == '@') return '@@';
return c[1].join('').replace(',', '');
},
peg$c64 = function (c) {
return c;
},
peg$c65 = "+",
peg$c66 = peg$literalExpectation("+", false),
peg$c67 = function (c) {
if (!c[1]) return 1;
if (c[1] != '+') return Number(c[1].join(''));
return 2;
},
peg$c68 = "-",
peg$c69 = peg$literalExpectation("-", false),
peg$c70 = function (c) {
if (!c[1]) return -1;
if (c[1] != '-') return -Number(c[1].join(''));
return -2;
},
peg$c71 = "H",
peg$c72 = peg$literalExpectation("H", false),
peg$c73 = function (h) {
if (h[1]) return Number(h[1]);
return 1;
},
peg$c74 = ":",
peg$c75 = peg$literalExpectation(":", false),
peg$c76 = /^[0]/,
peg$c77 = peg$classExpectation(["0"], false, false),
peg$c78 = function (c) {
return Number(c[1][0] + c[1][1].join(''));
},
peg$c79 = function (i) {
return Number(i.join(''));
},
peg$currPos = 0,
peg$savedPos = 0,
peg$posDetailsCache = [{
line: 1,
column: 1
}],
peg$maxFailPos = 0,
peg$maxFailExpected = [],
peg$silentFails = 0,
peg$result;
if ("startRule" in options) {
if (!(options.startRule in peg$startRuleFunctions)) {
throw new Error("Can't start parsing from rule \"" + options.startRule + "\".");
}
peg$startRuleFunction = peg$startRuleFunctions[options.startRule];
}
function text() {
return input.substring(peg$savedPos, peg$currPos);
}
function location() {
return peg$computeLocation(peg$savedPos, peg$currPos);
}
function expected(description, location) {
location = location !== void 0 ? location : peg$computeLocation(peg$savedPos, peg$currPos)
throw peg$buildStructuredError(
[peg$otherExpectation(description)],
input.substring(peg$savedPos, peg$currPos),
location
);
}
function error(message, location) {
location = location !== void 0 ? location : peg$computeLocation(peg$savedPos, peg$currPos)
throw peg$buildSimpleError(message, location);
}
function peg$literalExpectation(text, ignoreCase) {
return {
type: "literal",
text: text,
ignoreCase: ignoreCase
};
}
function peg$classExpectation(parts, inverted, ignoreCase) {
return {
type: "class",
parts: parts,
inverted: inverted,
ignoreCase: ignoreCase
};
}
function peg$anyExpectation() {
return {
type: "any"
};
}
function peg$endExpectation() {
return {
type: "end"
};
}
function peg$otherExpectation(description) {
return {
type: "other",
description: description
};
}
function peg$computePosDetails(pos) {
var details = peg$posDetailsCache[pos],
p;
if (details) {
return details;
} else {
p = pos - 1;
while (!peg$posDetailsCache[p]) {
p--;
}
details = peg$posDetailsCache[p];
details = {
line: details.line,
column: details.column
};
while (p < pos) {
if (input.charCodeAt(p) === 10) {
details.line++;
details.column = 1;
} else {
details.column++;
}
p++;
}
peg$posDetailsCache[pos] = details;
return details;
}
}
function peg$computeLocation(startPos, endPos) {
var startPosDetails = peg$computePosDetails(startPos),
endPosDetails = peg$computePosDetails(endPos);
return {
start: {
offset: startPos,
line: startPosDetails.line,
column: startPosDetails.column
},
end: {
offset: endPos,
line: endPosDetails.line,
column: endPosDetails.column
}
};
}
function peg$fail(expected) {
if (peg$currPos < peg$maxFailPos) {
return;
}
if (peg$currPos > peg$maxFailPos) {
peg$maxFailPos = peg$currPos;
peg$maxFailExpected = [];
}
peg$maxFailExpected.push(expected);
}
function peg$buildSimpleError(message, location) {
return new peg$SyntaxError(message, null, null, location);
}
function peg$buildStructuredError(expected, found, location) {
return new peg$SyntaxError(
peg$SyntaxError.buildMessage(expected, found),
expected,
found,
location
);
}
function peg$parsechain() {
var s0, s1, s2, s3, s4, s5, s6, s7, s8, s9;
s0 = peg$currPos;
s1 = peg$currPos;
s2 = peg$parseatom();
if (s2 !== peg$FAILED) {
s3 = [];
s4 = peg$parsebranch();
while (s4 !== peg$FAILED) {
s3.push(s4);
s4 = peg$parsebranch();
}
if (s3 !== peg$FAILED) {
s4 = [];
s5 = peg$currPos;
s6 = peg$parsebond();
if (s6 === peg$FAILED) {
s6 = null;
}
if (s6 !== peg$FAILED) {
s7 = peg$parsering();
if (s7 !== peg$FAILED) {
s6 = [s6, s7];
s5 = s6;
} else {
peg$currPos = s5;
s5 = peg$FAILED;
}
} else {
peg$currPos = s5;
s5 = peg$FAILED;
}
while (s5 !== peg$FAILED) {
s4.push(s5);
s5 = peg$currPos;
s6 = peg$parsebond();
if (s6 === peg$FAILED) {
s6 = null;
}
if (s6 !== peg$FAILED) {
s7 = peg$parsering();
if (s7 !== peg$FAILED) {
s6 = [s6, s7];
s5 = s6;
} else {
peg$currPos = s5;
s5 = peg$FAILED;
}
} else {
peg$currPos = s5;
s5 = peg$FAILED;
}
}
if (s4 !== peg$FAILED) {
s5 = [];
s6 = peg$parsebranch();
while (s6 !== peg$FAILED) {
s5.push(s6);
s6 = peg$parsebranch();
}
if (s5 !== peg$FAILED) {
s6 = peg$parsebond();
if (s6 === peg$FAILED) {
s6 = null;
}
if (s6 !== peg$FAILED) {
s7 = peg$parsechain();
if (s7 === peg$FAILED) {
s7 = null;
}
if (s7 !== peg$FAILED) {
s8 = [];
s9 = peg$parsebranch();
while (s9 !== peg$FAILED) {
s8.push(s9);
s9 = peg$parsebranch();
}
if (s8 !== peg$FAILED) {
s2 = [s2, s3, s4, s5, s6, s7, s8];
s1 = s2;
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
if (s1 !== peg$FAILED) {
peg$savedPos = s0;
s1 = peg$c0(s1);
}
s0 = s1;
return s0;
}
function peg$parsebranch() {
var s0, s1, s2, s3, s4, s5;
s0 = peg$currPos;
s1 = peg$currPos;
if (input.charCodeAt(peg$currPos) === 40) {
s2 = peg$c1;
peg$currPos++;
} else {
s2 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c2);
}
}
if (s2 !== peg$FAILED) {
s3 = peg$parsebond();
if (s3 === peg$FAILED) {
s3 = null;
}
if (s3 !== peg$FAILED) {
s4 = peg$parsechain();
if (s4 !== peg$FAILED) {
if (input.charCodeAt(peg$currPos) === 41) {
s5 = peg$c3;
peg$currPos++;
} else {
s5 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c4);
}
}
if (s5 !== peg$FAILED) {
s2 = [s2, s3, s4, s5];
s1 = s2;
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
if (s1 !== peg$FAILED) {
peg$savedPos = s0;
s1 = peg$c5(s1);
}
s0 = s1;
return s0;
}
function peg$parseatom() {
var s0, s1;
s0 = peg$currPos;
s1 = peg$parseorganicsymbol();
if (s1 === peg$FAILED) {
s1 = peg$parsearomaticsymbol();
if (s1 === peg$FAILED) {
s1 = peg$parsebracketatom();
if (s1 === peg$FAILED) {
s1 = peg$parsewildcard();
}
}
}
if (s1 !== peg$FAILED) {
peg$savedPos = s0;
s1 = peg$c6(s1);
}
s0 = s1;
return s0;
}
function peg$parsebond() {
var s0, s1;
s0 = peg$currPos;
if (peg$c7.test(input.charAt(peg$currPos))) {
s1 = input.charAt(peg$currPos);
peg$currPos++;
} else {
s1 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c8);
}
}
if (s1 !== peg$FAILED) {
peg$savedPos = s0;
s1 = peg$c9(s1);
}
s0 = s1;
return s0;
}
function peg$parsebracketatom() {
var s0, s1, s2, s3, s4, s5, s6, s7, s8, s9;
s0 = peg$currPos;
s1 = peg$currPos;
if (input.charCodeAt(peg$currPos) === 91) {
s2 = peg$c10;
peg$currPos++;
} else {
s2 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c11);
}
}
if (s2 !== peg$FAILED) {
s3 = peg$parseisotope();
if (s3 === peg$FAILED) {
s3 = null;
}
if (s3 !== peg$FAILED) {
if (input.substr(peg$currPos, 2) === peg$c12) {
s4 = peg$c12;
peg$currPos += 2;
} else {
s4 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c13);
}
}
if (s4 === peg$FAILED) {
if (input.substr(peg$currPos, 2) === peg$c14) {
s4 = peg$c14;
peg$currPos += 2;
} else {
s4 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c15);
}
}
if (s4 === peg$FAILED) {
s4 = peg$parsearomaticsymbol();
if (s4 === peg$FAILED) {
s4 = peg$parseelementsymbol();
if (s4 === peg$FAILED) {
s4 = peg$parsewildcard();
}
}
}
}
if (s4 !== peg$FAILED) {
s5 = peg$parsechiral();
if (s5 === peg$FAILED) {
s5 = null;
}
if (s5 !== peg$FAILED) {
s6 = peg$parsehcount();
if (s6 === peg$FAILED) {
s6 = null;
}
if (s6 !== peg$FAILED) {
s7 = peg$parsecharge();
if (s7 === peg$FAILED) {
s7 = null;
}
if (s7 !== peg$FAILED) {
s8 = peg$parseclass();
if (s8 === peg$FAILED) {
s8 = null;
}
if (s8 !== peg$FAILED) {
if (input.charCodeAt(peg$currPos) === 93) {
s9 = peg$c16;
peg$currPos++;
} else {
s9 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c17);
}
}
if (s9 !== peg$FAILED) {
s2 = [s2, s3, s4, s5, s6, s7, s8, s9];
s1 = s2;
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
if (s1 !== peg$FAILED) {
peg$savedPos = s0;
s1 = peg$c18(s1);
}
s0 = s1;
return s0;
}
function peg$parseorganicsymbol() {
var s0, s1, s2, s3;
s0 = peg$currPos;
s1 = peg$currPos;
if (input.charCodeAt(peg$currPos) === 66) {
s2 = peg$c19;
peg$currPos++;
} else {
s2 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c20);
}
}
if (s2 !== peg$FAILED) {
if (input.charCodeAt(peg$currPos) === 114) {
s3 = peg$c21;
peg$currPos++;
} else {
s3 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c22);
}
}
if (s3 === peg$FAILED) {
s3 = null;
}
if (s3 !== peg$FAILED) {
s2 = [s2, s3];
s1 = s2;
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
if (s1 === peg$FAILED) {
s1 = peg$currPos;
if (input.charCodeAt(peg$currPos) === 67) {
s2 = peg$c23;
peg$currPos++;
} else {
s2 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c24);
}
}
if (s2 !== peg$FAILED) {
if (input.charCodeAt(peg$currPos) === 108) {
s3 = peg$c25;
peg$currPos++;
} else {
s3 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c26);
}
}
if (s3 === peg$FAILED) {
s3 = null;
}
if (s3 !== peg$FAILED) {
s2 = [s2, s3];
s1 = s2;
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
} else {
peg$currPos = s1;
s1 = peg$FAILED;
}
if (s1 === peg$FAILED) {
if (peg$c27.test(input.charAt(peg$currPos))) {
s1 = input.charAt(peg$currPos);
peg$currPos++;
} else {
s1 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c28);
}
}
}
}
if (s1 !== peg$FAILED) {
peg$savedPos = s0;
s1 = peg$c29(s1);
}
s0 = s1;
return s0;
}
function peg$parsearomaticsymbol() {
var s0, s1;
s0 = peg$currPos;
if (peg$c30.test(input.charAt(peg$currPos))) {
s1 = input.charAt(peg$currPos);
peg$currPos++;
} else {
s1 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c31);
}
}
if (s1 !== peg$FAILED) {
peg$savedPos = s0;
s1 = peg$c6(s1);
}
s0 = s1;
return s0;
}
function peg$parsewildcard() {
var s0, s1;
s0 = peg$currPos;
if (input.charCodeAt(peg$currPos) === 42) {
s1 = peg$c32;
peg$currPos++;
} else {
s1 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c33);
}
}
if (s1 !== peg$FAILED) {
peg$savedPos = s0;
s1 = peg$c34(s1);
}
s0 = s1;
return s0;
}
function peg$parseelementsymbol() {
var s0, s1, s2, s3;
s0 = peg$currPos;
s1 = peg$currPos;
if (peg$c35.test(input.charAt(peg$currPos))) {
s2 = input.charAt(peg$currPos);
peg$currPos++;
} else {
s2 = peg$FAILED;
if (peg$silentFails === 0) {
peg$fail(peg$c36);
}
}
if (s2 !== peg$FAILED) {
if (peg$c37.test(input.charAt(peg$currPos))) {