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opensmiles.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
"http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
<head>
<meta http-equiv="Content-Type" content="application/xhtml+xml; charset=UTF-8" />
<meta name="generator" content="AsciiDoc 8.6.8" />
<title>OpenSMILES specification</title>
<style type="text/css">
/* Shared CSS for AsciiDoc xhtml11 and html5 backends */
/* Default font. */
body {
font-family: Georgia,serif;
}
/* Title font. */
h1, h2, h3, h4, h5, h6,
div.title, caption.title,
thead, p.table.header,
#toctitle,
#author, #revnumber, #revdate, #revremark,
#footer {
font-family: Arial,Helvetica,sans-serif;
}
body {
margin: 1em 5% 1em 5%;
}
a {
color: blue;
text-decoration: underline;
}
a:visited {
color: fuchsia;
}
em {
font-style: italic;
color: navy;
}
strong {
font-weight: bold;
color: #083194;
}
h1, h2, h3, h4, h5, h6 {
color: #527bbd;
margin-top: 1.2em;
margin-bottom: 0.5em;
line-height: 1.3;
}
h1, h2, h3 {
border-bottom: 2px solid silver;
}
h2 {
padding-top: 0.5em;
}
h3 {
float: left;
}
h3 + * {
clear: left;
}
h5 {
font-size: 1.0em;
}
div.sectionbody {
margin-left: 0;
}
hr {
border: 1px solid silver;
}
p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
ul, ol, li > p {
margin-top: 0;
}
ul > li { color: #aaa; }
ul > li > * { color: black; }
.monospaced, code, pre {
font-family: "Courier New", Courier, monospace;
font-size: inherit;
color: navy;
padding: 0;
margin: 0;
}
#author {
color: #527bbd;
font-weight: bold;
font-size: 1.1em;
}
#email {
}
#revnumber, #revdate, #revremark {
}
#footer {
font-size: small;
border-top: 2px solid silver;
padding-top: 0.5em;
margin-top: 4.0em;
}
#footer-text {
float: left;
padding-bottom: 0.5em;
}
#footer-badges {
float: right;
padding-bottom: 0.5em;
}
#preamble {
margin-top: 1.5em;
margin-bottom: 1.5em;
}
div.imageblock, div.exampleblock, div.verseblock,
div.quoteblock, div.literalblock, div.listingblock, div.sidebarblock,
div.admonitionblock {
margin-top: 1.0em;
margin-bottom: 1.5em;
}
div.admonitionblock {
margin-top: 2.0em;
margin-bottom: 2.0em;
margin-right: 10%;
color: #606060;
}
div.content { /* Block element content. */
padding: 0;
}
/* Block element titles. */
div.title, caption.title {
color: #527bbd;
font-weight: bold;
text-align: left;
margin-top: 1.0em;
margin-bottom: 0.5em;
}
div.title + * {
margin-top: 0;
}
td div.title:first-child {
margin-top: 0.0em;
}
div.content div.title:first-child {
margin-top: 0.0em;
}
div.content + div.title {
margin-top: 0.0em;
}
div.sidebarblock > div.content {
background: #ffffee;
border: 1px solid #dddddd;
border-left: 4px solid #f0f0f0;
padding: 0.5em;
}
div.listingblock > div.content {
border: 1px solid #dddddd;
border-left: 5px solid #f0f0f0;
background: #f8f8f8;
padding: 0.5em;
}
div.quoteblock, div.verseblock {
padding-left: 1.0em;
margin-left: 1.0em;
margin-right: 10%;
border-left: 5px solid #f0f0f0;
color: #888;
}
div.quoteblock > div.attribution {
padding-top: 0.5em;
text-align: right;
}
div.verseblock > pre.content {
font-family: inherit;
font-size: inherit;
}
div.verseblock > div.attribution {
padding-top: 0.75em;
text-align: left;
}
/* DEPRECATED: Pre version 8.2.7 verse style literal block. */
div.verseblock + div.attribution {
text-align: left;
}
div.admonitionblock .icon {
vertical-align: top;
font-size: 1.1em;
font-weight: bold;
text-decoration: underline;
color: #527bbd;
padding-right: 0.5em;
}
div.admonitionblock td.content {
padding-left: 0.5em;
border-left: 3px solid #dddddd;
}
div.exampleblock > div.content {
border-left: 3px solid #dddddd;
padding-left: 0.5em;
}
div.imageblock div.content { padding-left: 0; }
span.image img { border-style: none; }
a.image:visited { color: white; }
dl {
margin-top: 0.8em;
margin-bottom: 0.8em;
}
dt {
margin-top: 0.5em;
margin-bottom: 0;
font-style: normal;
color: navy;
}
dd > *:first-child {
margin-top: 0.1em;
}
ul, ol {
list-style-position: outside;
}
ol.arabic {
list-style-type: decimal;
}
ol.loweralpha {
list-style-type: lower-alpha;
}
ol.upperalpha {
list-style-type: upper-alpha;
}
ol.lowerroman {
list-style-type: lower-roman;
}
ol.upperroman {
list-style-type: upper-roman;
}
div.compact ul, div.compact ol,
div.compact p, div.compact p,
div.compact div, div.compact div {
margin-top: 0.1em;
margin-bottom: 0.1em;
}
tfoot {
font-weight: bold;
}
td > div.verse {
white-space: pre;
}
div.hdlist {
margin-top: 0.8em;
margin-bottom: 0.8em;
}
div.hdlist tr {
padding-bottom: 15px;
}
dt.hdlist1.strong, td.hdlist1.strong {
font-weight: bold;
}
td.hdlist1 {
vertical-align: top;
font-style: normal;
padding-right: 0.8em;
color: navy;
}
td.hdlist2 {
vertical-align: top;
}
div.hdlist.compact tr {
margin: 0;
padding-bottom: 0;
}
.comment {
background: yellow;
}
.footnote, .footnoteref {
font-size: 0.8em;
}
span.footnote, span.footnoteref {
vertical-align: super;
}
#footnotes {
margin: 20px 0 20px 0;
padding: 7px 0 0 0;
}
#footnotes div.footnote {
margin: 0 0 5px 0;
}
#footnotes hr {
border: none;
border-top: 1px solid silver;
height: 1px;
text-align: left;
margin-left: 0;
width: 20%;
min-width: 100px;
}
div.colist td {
padding-right: 0.5em;
padding-bottom: 0.3em;
vertical-align: top;
}
div.colist td img {
margin-top: 0.3em;
}
@media print {
#footer-badges { display: none; }
}
#toc {
margin-bottom: 2.5em;
}
#toctitle {
color: #527bbd;
font-size: 1.1em;
font-weight: bold;
margin-top: 1.0em;
margin-bottom: 0.1em;
}
div.toclevel0, div.toclevel1, div.toclevel2, div.toclevel3, div.toclevel4 {
margin-top: 0;
margin-bottom: 0;
}
div.toclevel2 {
margin-left: 2em;
font-size: 0.9em;
}
div.toclevel3 {
margin-left: 4em;
font-size: 0.9em;
}
div.toclevel4 {
margin-left: 6em;
font-size: 0.9em;
}
span.aqua { color: aqua; }
span.black { color: black; }
span.blue { color: blue; }
span.fuchsia { color: fuchsia; }
span.gray { color: gray; }
span.green { color: green; }
span.lime { color: lime; }
span.maroon { color: maroon; }
span.navy { color: navy; }
span.olive { color: olive; }
span.purple { color: purple; }
span.red { color: red; }
span.silver { color: silver; }
span.teal { color: teal; }
span.white { color: white; }
span.yellow { color: yellow; }
span.aqua-background { background: aqua; }
span.black-background { background: black; }
span.blue-background { background: blue; }
span.fuchsia-background { background: fuchsia; }
span.gray-background { background: gray; }
span.green-background { background: green; }
span.lime-background { background: lime; }
span.maroon-background { background: maroon; }
span.navy-background { background: navy; }
span.olive-background { background: olive; }
span.purple-background { background: purple; }
span.red-background { background: red; }
span.silver-background { background: silver; }
span.teal-background { background: teal; }
span.white-background { background: white; }
span.yellow-background { background: yellow; }
span.big { font-size: 2em; }
span.small { font-size: 0.6em; }
span.underline { text-decoration: underline; }
span.overline { text-decoration: overline; }
span.line-through { text-decoration: line-through; }
div.unbreakable { page-break-inside: avoid; }
/*
* xhtml11 specific
*
* */
div.tableblock {
margin-top: 1.0em;
margin-bottom: 1.5em;
}
div.tableblock > table {
border: 3px solid #527bbd;
}
thead, p.table.header {
font-weight: bold;
color: #527bbd;
}
p.table {
margin-top: 0;
}
/* Because the table frame attribute is overriden by CSS in most browsers. */
div.tableblock > table[frame="void"] {
border-style: none;
}
div.tableblock > table[frame="hsides"] {
border-left-style: none;
border-right-style: none;
}
div.tableblock > table[frame="vsides"] {
border-top-style: none;
border-bottom-style: none;
}
/*
* html5 specific
*
* */
table.tableblock {
margin-top: 1.0em;
margin-bottom: 1.5em;
}
thead, p.tableblock.header {
font-weight: bold;
color: #527bbd;
}
p.tableblock {
margin-top: 0;
}
table.tableblock {
border-width: 3px;
border-spacing: 0px;
border-style: solid;
border-color: #527bbd;
border-collapse: collapse;
}
th.tableblock, td.tableblock {
border-width: 1px;
padding: 4px;
border-style: solid;
border-color: #527bbd;
}
table.tableblock.frame-topbot {
border-left-style: hidden;
border-right-style: hidden;
}
table.tableblock.frame-sides {
border-top-style: hidden;
border-bottom-style: hidden;
}
table.tableblock.frame-none {
border-style: hidden;
}
th.tableblock.halign-left, td.tableblock.halign-left {
text-align: left;
}
th.tableblock.halign-center, td.tableblock.halign-center {
text-align: center;
}
th.tableblock.halign-right, td.tableblock.halign-right {
text-align: right;
}
th.tableblock.valign-top, td.tableblock.valign-top {
vertical-align: top;
}
th.tableblock.valign-middle, td.tableblock.valign-middle {
vertical-align: middle;
}
th.tableblock.valign-bottom, td.tableblock.valign-bottom {
vertical-align: bottom;
}
/*
* manpage specific
*
* */
body.manpage h1 {
padding-top: 0.5em;
padding-bottom: 0.5em;
border-top: 2px solid silver;
border-bottom: 2px solid silver;
}
body.manpage h2 {
border-style: none;
}
body.manpage div.sectionbody {
margin-left: 3em;
}
@media print {
body.manpage div#toc { display: none; }
}
</style>
<script type="text/javascript">
/*<+'])');
// Function that scans the DOM tree for header elements (the DOM2
// nodeIterator API would be a better technique but not supported by all
// browsers).
var iterate = function (el) {
for (var i = el.firstChild; i != null; i = i.nextSibling) {
if (i.nodeType == 1 /* Node.ELEMENT_NODE */) {
var mo = re.exec(i.tagName);
if (mo && (i.getAttribute("class") || i.getAttribute("className")) != "float") {
result[result.length] = new TocEntry(i, getText(i), mo[1]-1);
}
iterate(i);
}
}
}
iterate(el);
return result;
}
var toc = document.getElementById("toc");
if (!toc) {
return;
}
// Delete existing TOC entries in case we're reloading the TOC.
var tocEntriesToRemove = [];
var i;
for (i = 0; i < toc.childNodes.length; i++) {
var entry = toc.childNodes[i];
if (entry.nodeName.toLowerCase() == 'div'
&& entry.getAttribute("class")
&& entry.getAttribute("class").match(/^toclevel/))
tocEntriesToRemove.push(entry);
}
for (i = 0; i < tocEntriesToRemove.length; i++) {
toc.removeChild(tocEntriesToRemove[i]);
}
// Rebuild TOC entries.
var entries = tocEntries(document.getElementById("content"), toclevels);
for (var i = 0; i < entries.length; ++i) {
var entry = entries[i];
if (entry.element.id == "")
entry.element.id = "_toc_" + i;
var a = document.createElement("a");
a.href = "#" + entry.element.id;
a.appendChild(document.createTextNode(entry.text));
var div = document.createElement("div");
div.appendChild(a);
div.className = "toclevel" + entry.toclevel;
toc.appendChild(div);
}
if (entries.length == 0)
toc.parentNode.removeChild(toc);
},
/////////////////////////////////////////////////////////////////////
// Footnotes generator
/////////////////////////////////////////////////////////////////////
/* Based on footnote generation code from:
* http://www.brandspankingnew.net/archive/2005/07/format_footnote.html
*/
footnotes: function () {
// Delete existing footnote entries in case we're reloading the footnodes.
var i;
var noteholder = document.getElementById("footnotes");
if (!noteholder) {
return;
}
var entriesToRemove = [];
for (i = 0; i < noteholder.childNodes.length; i++) {
var entry = noteholder.childNodes[i];
if (entry.nodeName.toLowerCase() == 'div' && entry.getAttribute("class") == "footnote")
entriesToRemove.push(entry);
}
for (i = 0; i < entriesToRemove.length; i++) {
noteholder.removeChild(entriesToRemove[i]);
}
// Rebuild footnote entries.
var cont = document.getElementById("content");
var spans = cont.getElementsByTagName("span");
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<body class="article">
<div id="header">
<h1>OpenSMILES specification</h1>
<span id="author">Craig A. James</span><br />
<span id="revnumber">version 1.0,</span>
<span id="revdate">2013-09-06</span>
<br /><span id="revremark">Current specification</span>
</div>
<div id="content">
<div id="preamble">
<div class="sectionbody">
<div class="paragraph"><p><a href="http://www.opensmiles.org">www.opensmiles.org</a></p></div>
<div class="paragraph"><p>Copyright © 2007, Craig A. James</p></div>
<div class="paragraph"><p>Content is available under <a href="http://www.gnu.org/copyleft/fdl.html">GNU Free Documentation License 1.2</a></p></div>
<div class="paragraph"><p>Contributors: Richard Apodaca, Noel O’Boyle, Andrew Dalke, John van Drie, Peter Ertl,
Geoff Hutchison, Craig A. James, Greg Landrum, Chris Morley, Egon Willighagen, Hans De Winter,
Tim Vandermeersch</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_introduction">Introduction</h2>
<div class="sectionbody">
<div class="sidebarblock">
<div class="content">
<div class="paragraph"><p>"… we cannot improve the language of any science, without, at the
same time improving the science itself; neither can we, on the other
hand, improve a science, without improving the language or nomenclature
which belongs to it …"</p></div>
<div class="paragraph"><p><a href="http://en.wikipedia.org/wiki/Antoine_Lavoisier">Antoine Lavoiser, 1787</a></p></div>
</div></div>
<div class="sect2">
<h3 id="_purpose">Purpose</h3>
<div class="paragraph"><p>This document formally defines an
<a href="http://en.wikipedia.org/wiki/Open_specifications">open specification</a> version of the
<a href="http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification">SMILES</a>
language, a typographical <a href="http://en.wikipedia.org/wiki/Line_notation">line notation</a>
for specifying chemical structure. It is hosted under the banner of the
<a href="http://blueobelisk.sourceforge.net">Blue Obelisk</a>
project, with the intent to solicit contributions and comments from the
entire computational chemistry community.</p></div>
</div>
<div class="sect2">
<h3 id="_motivation">Motivation</h3>
<div class="paragraph"><p>SMILES was originally developed as a proprietary specification by
<a href="http://www.daylight.com">Daylight Chemical Information Systems</a>
Since the introduction of SMILES in the late 1980’s, it has
become widely accepted as a defacto standard for exchange of molecular structures. Many independent
SMILES software packages have been written in <code>C</code>, <code>C++</code>, <code>Java</code>, <code>Python</code>, <code>LISP</code>, and probably even
<code>FORTRAN</code>.</p></div>
<div class="paragraph"><p>At this point in the history of SMILES, is appropriate for the chemistry community
to develop a new, non-proprietary specification for the SMILES language. Daylight’s
<a href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">SMILES Theory Manual</a>
has long been the "gold standard" for the SMILES language, but as a
proprietary specification, it limits the universal adoption of SMILES, and has no
mechanism for contributions from the chemistry community. We salute Daylight for
their past contributions, and the excellent SMILES documentation they provided free
of charge for the past two decades.</p></div>
</div>
<div class="sect2">
<h3 id="_audience">Audience</h3>
<div class="paragraph"><p>This document is intended for developers designing or improving a SMILES
parser or writer. <strong>Readers are expected to be acquainted with
SMILES.</strong> Due to the formality of this document, it is not a good
tutorial for those trying to learn SMILES. This document is written with
<strong>precision</strong> as the primary goal; <strong>readability</strong> is secondary.</p></div>
</div>
<div class="sect2">
<h3 id="_what_is_a_molecule_the_valence_model_of_chemistry">What is a Molecule? The Valence Model of Chemistry</h3>
<div class="paragraph"><p>Before defining the SMILES language, it is important to state the physical model on which it is
based: the valence model of chemistry, which uses a mathematician’s
<a href="http://en.wikipedia.org/wiki/Graph_%28mathematics%29">graph</a> to
represent a molecule. In a chemical graph, the <strong>nodes</strong>
are atoms, and the <strong>edges</strong> are semi-rigid bonds that can be single, double, or
triple according to the rules of
<a href="http://en.wikipedia.org/wiki/Valence_bond_theory">valence bond theory</a>.</p></div>
<div class="paragraph"><p>This simple mental model has little resemblance to the underlying quantum-mechanical reality of
electrons, protons and neutrons, yet it has proved to be a remarkably useful approximation of how
atoms behave in close proximity to one another. However, the valence model is an imperfect
representation of molecular structure, and the SMILES language inherits these imperfections.
Chemical bonds are often tautomeric, aromatic or otherwise fractional rather than neat integer
multiples. Delocalized bonds, bond-centered bonds, hydrogen bonds and various other inter-atom
forces that are well characterized by a quantum-mechanics description simply don’t fit into the
valence model.</p></div>
<div class="sidebarblock">
<div class="content">
<div class="paragraph"><p>"If you can build a molecule from a modeling kit, you can name it."</p></div>
<div class="paragraph"><p><a href="http://www.daylight.com/meetings/mug03/McLeod/MUG03McLeodPeters.pdf">McLeod Peters</a></p></div>
</div></div>
<div class="paragraph"><p>McLeod and Peters' quip captures the deficiencies of SMILES well: if you
<strong>can’t</strong> build a molecule from a modeling kit, the deficiencies of SMILES and other
connection-table formats become apparent.</p></div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_formal_grammar">Formal Grammar</h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_syntax_versus_semantics">Syntax versus Semantics</h3>
<div class="paragraph"><p>This SMILES specification is divided into two distinct parts: A
<strong>syntactic specification</strong> specifies how the atoms,
bonds, parentheses, digits and so forth are represented, and a <strong>semantic
specification</strong> that describes how those symbols are interpreted as a sensible
molecule. For example, the syntax specifies how <a href="#ringclosure">ring closures</a>
are written, but the semantics require that they come in pairs.
Likewise, the syntax specifies how <a href="#atomicsymbol">atomic elements</a>
are written, but the semantics determines whether a particular ring system
is actually aromatic.</p></div>
<div class="paragraph"><p>For this specification, the syntax and semantics are explained
separately; in practice, the syntax and semantics are usually mixed
together in the code that implements a SMILES parser. This chapter is only
concerned with syntax.</p></div>
</div>
<div class="sect2">
<h3 id="_grammar">Grammar</h3>
<div class="tableblock">
<table rules="rows"
width="100%"
frame="hsides"
cellspacing="0" cellpadding="4">
<col width="20%" />
<col width="80%" />
<thead>
<tr>
<th align="left" valign="top"> Section </th>
<th align="left" valign="top"> Formal Grammar</th>
</tr>
</thead>
<tbody>
<tr>
<td colspan="2" align="left" valign="top"><p class="table"><strong>ATOMS</strong></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><a href="#inatoms">Atoms</a></p></td>
<td align="left" valign="top"><p class="table"><em>atom</em> ::= <em>bracket_atom</em> | <em>aliphatic_organic</em> | <em>aromatic_organic</em> | <code>'*'</code></p></td>
</tr>
<tr>
<td colspan="2" align="left" valign="top"><p class="table"><strong>ORGANIC SUBSET ATOMS</strong></p></td>
</tr>
<tr>
<td rowspan="2" align="left" valign="top"><p class="table"><a href="#orgsbst">Organic Subset</a></p></td>
<td align="left" valign="top"><p class="table"><em>aliphatic_organic</em> ::= <code>'B'</code> | <code>'C'</code> | <code>'N'</code> | <code>'O'</code> | <code>'S'</code> | <code>'P'</code> | <code>'F'</code> | <code>'Cl'</code> | <code>'Br'</code> | <code>'I'</code></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>aromatic_organic</em> ::= <code>'b'</code> | <code>'c'</code> | <code>'n'</code> | <code>'o'</code> | <code>'s'</code> | <code>'p'</code></p></td>
</tr>
<tr>
<td colspan="2" align="left" valign="top"><p class="table"><strong>BRACKET ATOMS</strong></p></td>
</tr>
<tr>
<td rowspan="5" align="left" valign="top"><p class="table"><a href="#inatoms">Bracket Atoms</a></p></td>
<td align="left" valign="top"><p class="table"><em>bracket_atom</em> ::= <code>'['</code> <em>isotope</em>? <em>symbol</em> <em>chiral</em>? <em>hcount</em>? <em>charge</em>? <em>class</em>? <code>']'</code></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>symbol</em> ::= <em>element_symbols</em> | <em>aromatic_symbols</em> | <code>'*'</code></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>isotope</em> ::= <em>NUMBER</em></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>element_symbols</em> ::= <code>'H'</code> | <code>'He'</code> | <code>'Li'</code> | <code>'Be'</code> | <code>'B'</code> | <code>'C'</code> | <code>'N'</code> | <code>'O'</code> | <code>'F'</code> | <code>'Ne'</code> | <code>'Na'</code> | <code>'Mg'</code> | <code>'Al'</code> | <code>'Si'</code> | <code>'P'</code> | <code>'S'</code> | <code>'Cl'</code> | <code>'Ar'</code> | <code>'K'</code> | <code>'Ca'</code> | <code>'Sc'</code> | <code>'Ti'</code> | <code>'V'</code> | <code>'Cr'</code> | <code>'Mn'</code> | <code>'Fe'</code> | <code>'Co'</code> | <code>'Ni'</code> | <code>'Cu'</code> | <code>'Zn'</code> | <code>'Ga'</code> | <code>'Ge'</code> | <code>'As'</code> | <code>'Se'</code> | <code>'Br'</code> | <code>'Kr'</code> | <code>'Rb'</code> | <code>'Sr'</code> | <code>'Y'</code> | <code>'Zr'</code> | <code>'Nb'</code> | <code>'Mo'</code> | <code>'Tc'</code> | <code>'Ru'</code> | <code>'Rh'</code> | <code>'Pd'</code> | <code>'Ag'</code> | <code>'Cd'</code> | <code>'In'</code> | <code>'Sn'</code> | <code>'Sb'</code> | <code>'Te'</code> | <code>'I'</code> | <code>'Xe'</code> | <code>'Cs'</code> | <code>'Ba'</code> | <code>'Hf'</code> | <code>'Ta'</code> | <code>'W'</code> | <code>'Re'</code> | <code>'Os'</code> | <code>'Ir'</code> | <code>'Pt'</code> | <code>'Au'</code> | <code>'Hg'</code> | <code>'Tl'</code> | <code>'Pb'</code> | <code>'Bi'</code> | <code>'Po'</code> | <code>'At'</code> | <code>'Rn'</code> | <code>'Fr'</code> | <code>'Ra'</code> | <code>'Rf'</code> | <code>'Db'</code> | <code>'Sg'</code> | <code>'Bh'</code> | <code>'Hs'</code> | <code>'Mt'</code> | <code>'Ds'</code> | <code>'Rg'</code> | <code>'Cn'</code> | <code>'Fl'</code> | <code>'Lv'</code> | <code>'La'</code> | <code>'Ce'</code> | <code>'Pr'</code> | <code>'Nd'</code> | <code>'Pm'</code> | <code>'Sm'</code> | <code>'Eu'</code> | <code>'Gd'</code> | <code>'Tb'</code> | <code>'Dy'</code> | <code>'Ho'</code> | <code>'Er'</code> | <code>'Tm'</code> | <code>'Yb'</code> | <code>'Lu'</code> | <code>'Ac'</code> | <code>'Th'</code> | <code>'Pa'</code> | <code>'U'</code> | <code>'Np'</code> | <code>'Pu'</code> | <code>'Am'</code> | <code>'Cm'</code> | <code>'Bk'</code> | <code>'Cf'</code> | <code>'Es'</code> | <code>'Fm'</code> | <code>'Md'</code> | <code>'No'</code> | <code>'Lr'</code></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>aromatic_symbols</em> ::= <code>'b'</code> | <code>'c'</code> | <code>'n'</code> | <code>'o'</code> | <code>'p'</code> | <code>'s'</code> | <code>'se'</code> | <code>'as'</code></p></td>
</tr>
<tr>
<td colspan="2" align="left" valign="top"><p class="table"><strong>CHIRALITY</strong></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><a href="#chirality">Chirality</a></p></td>
<td align="left" valign="top"><p class="table"><em>chiral</em> ::= <code>'@'</code> | <code>'@@'</code> | <code>'@TH1'</code> | <code>'@TH2'</code> | <code>'@AL1'</code> | <code>'@AL2'</code> | <code>'@SP1'</code> | <code>'@SP2'</code> | <code>'@SP3'</code> | <code>'@TB1'</code> | <code>'@TB2'</code> | <code>'@TB3'</code> | … | <code>'@TB20'</code> | <code>'@OH1'</code> | <code>'@OH2'</code> | <code>'@OH3'</code> | … | <code>'@OH30'</code> | <code>'@TB'</code> <em>DIGIT</em> <em>DIGIT</em> | <code>'@OH'</code> <em>DIGIT</em> <em>DIGIT</em></p></td>
</tr>
<tr>
<td colspan="2" align="left" valign="top"><p class="table"><strong>HYDROGENS</strong></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><a href="#hydrogens">Hydrogens</a></p></td>
<td align="left" valign="top"><p class="table"><em>hcount</em> ::= <code>'H'</code> | <code>'H'</code> <em>DIGIT</em></p></td>
</tr>
<tr>
<td colspan="2" align="left" valign="top"><p class="table"><strong>CHARGES</strong></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><a href="#charge">Charge</a></p></td>
<td align="left" valign="top"><p class="table"><em>charge</em> ::= <code>'-'</code> | <code>'-'</code> <em>DIGIT</em>? <em>DIGIT</em> | <code>'+'</code> | <code>'+'</code> <em>DIGIT</em>? <em>DIGIT</em> | <code>'--'</code> <strong>deprecated</strong> | <code>'++'</code> <strong>deprecated</strong></p></td>
</tr>
<tr>
<td colspan="2" align="left" valign="top"><p class="table"><strong>ATOM CLASS</strong></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><a href="#atomclass">Atom Class</a></p></td>
<td align="left" valign="top"><p class="table"><em>class</em> ::= <code>':'</code> <em>NUMBER</em></p></td>
</tr>
<tr>
<td colspan="2" align="left" valign="top"><p class="table"><strong>BONDS AND CHAINS</strong></p></td>
</tr>
<tr>
<td rowspan="6" align="left" valign="top"><p class="table"><a href="#bonds">Bonds</a></p></td>
<td align="left" valign="top"><p class="table"><em>bond</em> ::= <code>'-'</code> | <code>'='</code> | <code>'#'</code> | <code>'$'</code> | <code>':'</code> | <code>'/'</code> | <code>'\'</code></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>ringbond</em> ::= <em>bond</em>? <em>DIGIT</em> | <em>bond</em>? <code>'%'</code> <em>DIGIT</em> <em>DIGIT</em></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>branched_atom</em> ::= <em>atom</em> <em>ringbond</em>* <em>branch</em>*</p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>branch</em> ::= <code>'('</code> <em>chain</em> <code>')'</code> | <code>'('</code> <em>bond</em> <em>chain</em> <code>')'</code> | <code>'('</code> <em>dot</em> <em>chain</em> <code>')'</code></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>chain</em> ::= <em>branched_atom</em> | <em>chain</em> <em>branched_atom</em> | <em>chain</em> <em>bond</em> <em>branched_atom</em> | <em>chain</em> <em>dot</em> <em>branched_atom</em></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>dot</em> ::= <code>'.'</code></p></td>
</tr>
<tr>
<td colspan="2" align="left" valign="top"><p class="table"><strong>SMILES STRINGS</strong></p></td>
</tr>
<tr>
<td rowspan="2" align="left" valign="top"><p class="table"></p></td>
<td align="left" valign="top"><p class="table"><em>smiles</em> ::= <em>terminator</em> | <em>chain</em> <em>terminator</em></p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><em>terminator</em> ::= <em>SPACE</em> | <em>TAB</em> | <em>LINEFEED</em> | <em>CARRIAGE_RETURN</em> | <em>END_OF_STRING</em></p></td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_reading_smiles">Reading SMILES</h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="inatoms">Atoms</h3>
<div class="sect3">
<h4 id="atomicsymbol">Atomic Symbol</h4>
<div class="paragraph"><p>An atom is represented by its atomic symbol, enclosed in square brackets, <code>[]</code>.
The first character of the symbol is uppercase and the second (if any) is lowercase,
except that for aromatic atoms (see below), the first character is lowercase. There are
<a href="http://www.iupac.org/reports/provisional/abstract04/RB-prs310804/TableI-3.04.pdf">114 valid atomic symbols</a>
, as defined by <a href="http://www.iupac.org">IUPAC</a> (see also
<a href="http://www.webelements.com">Web Elements</a>).</p></div>
<div class="paragraph"><p>The symbol <code>'*'</code> is also accepted as a valid atomic symbol, and represents a "wildcard" or unknown atom.</p></div>
<div class="paragraph"><p>Examples:</p></div>
<div class="tableblock">
<table rules="rows"
width="30%"
frame="hsides"
cellspacing="0" cellpadding="4">
<col width="33%" />
<col width="66%" />
<thead>
<tr>
<th align="left" valign="top"> SMILES </th>
<th align="left" valign="top"> Atomic Symbol</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left" valign="top"><p class="table"><code>[U]</code></p></td>
<td align="left" valign="top"><p class="table">Uranium</p></td>
</tr>
<tr>
<td align="left" valign="top"><p class="table"><code>[Pb]</code></p></td>
<td align="left" valign="top"><p class="table">Lead</p></td>
</tr>
<tr>