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<div class="title">Getting Started</div> </div>
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<h3><a class="anchor" id="intro"></a>Introduction to Open Babel API</h3><div class="textblock"><p>Open Babel is a full chemical software toolbox. In addition to converting file formats, it offers a complete programming library for developing chemistry software. The library is written primarily in C++ and also offers interfaces to other languages (e.g., Perl and Python) using essentially the same API.</p>
<p>The heart of Open Babel lies in the <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml">OBAtom</a>, and <a class="el" href="classOpenBabel_1_1OBBond.shtml">OBBond</a> classes, which handle operations on atoms, bonds and molecules. Newcomers should start with looking at the <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> class, designed to store the basic information in a molecule and to perceive information about a molecule.</p>
<h2><a class="anchor" id="Lazy"></a>
Evaluation</h2>
<p>One of the key philosophies in the code is that transformations and automatic perception of properties are performed in a <a href="http://en.wikipedia.org/wiki/Lazy_evaluation">"lazy"</a> manner. That is, until you call for partial atomic charges, no charges are calculated. This ensures faster transformations of chemical data -- properties that are not needed for your code will typically not be calculated. When such data is needed, appropriate routines are called, and a "flag" is set (e.g., via <a class="el" href="classOpenBabel_1_1OBMol.shtml#adcdab8f96dc4fdc2940749e527087245">OBMol::SetFlag</a> or <a class="el" href="classOpenBabel_1_1OBAtom.shtml#adcdab8f96dc4fdc2940749e527087245" title="Sets the bitwise flag.">OBAtom::SetFlag</a> etc.) so that the code is only run once.</p>
<h2><a class="anchor" id="Arbitrary"></a>
Data</h2>
<p>Arbitrary custom data and text descriptors can be stored in any atom, bond, molecule, or residue using the <a class="el" href="classOpenBabel_1_1OBGenericData.shtml">OBGenericData</a> or <a class="el" href="classOpenBabel_1_1OBPairData.shtml">OBPairData</a> classes.</p>
<p>Conversion between various chemical file formats is accomplished through the <a class="el" href="classOpenBabel_1_1OBConversion.shtml">OBConversion</a> and <a class="el" href="classOpenBabel_1_1OBFormat.shtml">OBFormat</a> classes, often through use of the <a class="el" href="classOpenBabel_1_1OBMoleculeFormat.shtml">OBMoleculeFormat</a> subclass which is designed for easy read/write access to one or more <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> objects. The philosophy of the file format codes is to parse as much chemical information from a given file as possible (no data left behind) and ideally any perception or transformations will occur when writing to some other format later. </p>
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<h3><a class="anchor" id="start"></a>Getting Started</h3><div class="textblock"><p>Not surprisingly, the Open Babel library is a full chemical toolbox. So to start out, the first example is to read in molecular file data and uses the <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a>, and <a class="el" href="classOpenBabel_1_1OBConversion.shtml">OBConversion</a> classes. The <a class="el" href="classOpenBabel_1_1OBMol.shtml">former</a> is designed to store the basic information in a molecule and to perceive information and chemical properties. The <a class="el" href="classOpenBabel_1_1OBConversion.shtml">latter</a> is designed to handle conversion of a variety of data (i.e., not just molecules) and import and export.</p>
<p>This example program shows how to read in a molecule, check the number of atoms, and write a SMILES string. </p>
<div class="fragment"><pre class="fragment"><span class="preprocessor"> #include <iostream.h></span>
<span class="comment">// Include Open Babel classes for OBMol and OBConversion</span>
<span class="preprocessor"> #include <<a class="code" href="mol_8h.shtml" title="Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue. (the main header for Open Babel)...">openbabel/mol.h</a>></span>
<span class="preprocessor"> #include <<a class="code" href="obconversion_8h.shtml" title="Handle file conversions. Declaration of OBFormat, OBConversion.">openbabel/obconversion.h</a>></span>
<span class="keywordtype">int</span> main(<span class="keywordtype">int</span> argc,<span class="keywordtype">char</span> **argv)
{
<span class="comment">// Read from STDIN (cin) and Write to STDOUT (cout)</span>
OBConversion conv(&cin,&cout);
<span class="comment">// Try to set input format to MDL SD file</span>
<span class="comment">// and output to SMILES</span>
<span class="keywordflow">if</span>(conv.SetInAndOutFormats(<span class="stringliteral">"SDF"</span>,<span class="stringliteral">"SMI"</span>))
{
OBMol mol;
<span class="keywordflow">if</span>(conv.Read(&mol))
{
<span class="comment">// ...manipulate molecule</span>
cerr << <span class="stringliteral">" Molecule has: "</span> << mol.NumAtoms()
<< <span class="stringliteral">" atoms."</span> << endl;
}
<span class="comment">// Write SMILES to the standard output</span>
conv->Write(&mol);
}
<span class="keywordflow">return</span> 0; <span class="comment">// exit with success</span>
}
</pre></div><p>All of the <a class="el" href="mainclasses.shtml">main classes</a>, including <a class="el" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> and <a class="el" href="classOpenBabel_1_1OBConversion.shtml" title="Class to convert from one format to another.">OBConversion</a>, include example code designed to facilitate using the Open Babel code in real-world chemistry. Complete examples are provided in the doc/examples directory and <a href="examples.shtml">all these examples are included in the documentation</a>.</p>
<p>For a further list of example code, see the <a href="http://openbabel.org/wiki/Developer:Tutorial">developer tutorials</a>. This section includes examples in C++, Perl, Python, and other programming languages.</p>
<p>Also, the <code>tools</code> directory of the Open Babel source releases include a variety of programs which are intended to be more advanced examples (although usually still under 300 lines of code).</p>
<p>Please e-mail the <a href="mailto:openbabel-discuss@lists.sourceforge.net">openbabel-discuss@lists.sourceforge.net</a> mailing list if you have more questions! </p>
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<h3><a class="anchor" id="other"></a>Further Information</h3><div class="textblock"><p>Open Babel is a community project. In addition to this API documentation, the website offers a variety of up-to-date and useful information for developing with the library.</p>
<p>Open Babel homepage:</p>
<ul>
<li><a href="http://openbabel.org/wiki/Develop">Developing with Open Babel</a></li>
<li><a href="http://openbabel.org/wiki/Developer:Tutorial">Developer tutorials</a></li>
<li><a href="http://openbabel.org/wiki/Contribute">Contributing to the Open Babel project</a></li>
</ul>
<p>SourceForge project pages:</p>
<ul>
<li><a href="http://sourceforge.net/projects/openbabel/">Open Babel project page</a></li>
<li><a href="http://sourceforge.net/tracker/?group_id=40728&atid=428740">Bug reporter</a></li>
<li><a href="http://sourceforge.net/tracker/?group_id=40728&atid=428743">Feature requests</a></li>
<li><a href="http://sourceforge.net/tracker/?group_id=40728&atid=447448">File format requests</a></li>
<li><a href="http://sourceforge.net/tracker/?group_id=40728&atid=428743">Mailing lists and archives</a> </li>
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