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href="http://openbabel.org/docs/">http://openbabel.org/docs/</a></p> <div class="toctree-wrapper compound"> <ul> <li class="toctree-l1"><a class="reference internal" href="Introduction/intro.html">Introduction</a><ul> <li class="toctree-l2"><a class="reference internal" href="Introduction/goals.html">Goals of the Open Babel project</a></li> <li class="toctree-l2"><a class="reference internal" href="Introduction/faq.html">Frequently Asked Questions</a></li> <li class="toctree-l2"><a class="reference internal" href="Introduction/thanks.html">Thanks</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="Installation/install.html">Install Open Babel</a><ul> <li class="toctree-l2"><a class="reference internal" href="Installation/install.html#install-a-binary-package">Install a binary package</a></li> <li class="toctree-l2"><a class="reference internal" href="Installation/install.html#compiling-open-babel">Compiling Open Babel</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="Command-line_tools/babel.html">obabel - Convert, Filter and Manipulate Chemical Data</a><ul> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#synopsis">Synopsis</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#options">Options</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#examples">Examples</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#format-options">Format Options</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#append-property-values-to-the-title">Append property values to the title</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#generating-conformers-for-structures">Generating conformers for structures</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#filtering-molecules-from-a-multimolecule-file">Filtering molecules from a multimolecule file</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#substructure-and-similarity-searching">Substructure and similarity searching</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#sorting-molecules">Sorting molecules</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#remove-duplicate-molecules">Remove duplicate molecules</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#aliases-for-chemical-groups">Aliases for chemical groups</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#forcefield-energy-and-minimization">Forcefield energy and minimization</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#aligning-molecules-or-substructures">Aligning molecules or substructures</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/babel.html#specifying-the-speed-of-3d-coordinate-generation">Specifying the speed of 3D coordinate generation</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="GUI/GUI.html">The Open Babel GUI</a><ul> <li class="toctree-l2"><a class="reference internal" href="GUI/GUI.html#basic-operation">Basic operation</a></li> <li class="toctree-l2"><a class="reference internal" href="GUI/GUI.html#options">Options</a></li> <li class="toctree-l2"><a class="reference internal" href="GUI/GUI.html#multiple-input-files">Multiple input files</a></li> <li class="toctree-l2"><a class="reference internal" href="GUI/GUI.html#wildcards-in-filenames">Wildcards in filenames</a></li> <li class="toctree-l2"><a class="reference internal" href="GUI/GUI.html#local-input">Local input</a></li> <li class="toctree-l2"><a class="reference internal" href="GUI/GUI.html#output-file">Output file</a></li> <li class="toctree-l2"><a class="reference internal" href="GUI/GUI.html#graphical-display">Graphical display</a></li> <li class="toctree-l2"><a class="reference internal" href="GUI/GUI.html#using-a-restricted-set-of-formats">Using a restricted set of formats</a></li> <li class="toctree-l2"><a class="reference internal" href="GUI/GUI.html#other-features">Other features</a></li> <li class="toctree-l2"><a class="reference internal" href="GUI/GUI.html#example-files">Example files</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="GUITutorial/GUITutorial.html">Tutorial on using the GUI</a><ul> <li class="toctree-l2"><a class="reference internal" href="GUITutorial/Conversion.html">Converting chemical file formats</a></li> <li class="toctree-l2"><a class="reference internal" href="GUITutorial/Filtering.html">Filtering structures</a></li> <li class="toctree-l2"><a class="reference internal" href="GUITutorial/Searching.html">Substructure and similarity searching a large dataset</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="Fingerprints/intro.html">Molecular fingerprints and similarity searching</a><ul> <li class="toctree-l2"><a class="reference internal" href="Fingerprints/fingerprints.html">Fingerprint format</a></li> <li class="toctree-l2"><a class="reference internal" href="Fingerprints/spectrophore.html">Spectrophores™</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="Command-line_tools/Rosetta.html">obabel vs Chemistry Toolkit Rosetta</a><ul> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#heavy-atom-counts-from-an-sd-file">Heavy atom counts from an SD file</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#convert-a-smiles-string-to-canonical-smiles">Convert a SMILES string to canonical SMILES</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#report-how-many-sd-file-records-are-within-a-certain-molecular-weight-range">Report how many SD file records are within a certain molecular weight range</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#convert-smiles-file-to-sd-file">Convert SMILES file to SD file</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#report-the-similarity-between-two-structures">Report the similarity between two structures</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#find-the-10-nearest-neighbors-in-a-data-set">Find the 10 nearest neighbors in a data set</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#depict-a-compound-as-an-image">Depict a compound as an image</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#highlight-a-substructure-in-the-depiction">Highlight a substructure in the depiction</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#align-the-depiction-using-a-fixed-substructure">Align the depiction using a fixed substructure</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#perform-a-substructure-search-on-an-sdf-file-and-report-the-number-of-false-positives">Perform a substructure search on an SDF file and report the number of false positives</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#calculate-tpsa">Calculate TPSA</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#working-with-sd-tag-data">Working with SD tag data</a></li> <li class="toctree-l2"><a class="reference internal" href="Command-line_tools/Rosetta.html#unattempted-tasks">Unattempted tasks</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="Depiction/depiction.html">2D Depiction</a><ul> <li class="toctree-l2"><a class="reference internal" href="Depiction/depiction.html#molecular-graphics">Molecular graphics</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="3DStructureGen/Overview.html">3D Structure Generation</a><ul> <li class="toctree-l2"><a class="reference internal" href="3DStructureGen/SingleConformer.html">Generate a single conformer</a></li> <li class="toctree-l2"><a class="reference internal" href="3DStructureGen/multipleconformers.html">Generate multiple conformers</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="Forcefields/Overview.html">Molecular Mechanics and Force Fields</a><ul> <li class="toctree-l2"><a class="reference internal" href="Forcefields/gaff.html">Generalized Amber Force Field (gaff)</a></li> <li class="toctree-l2"><a class="reference internal" href="Forcefields/ghemical.html">Ghemical Force Field (ghemical)</a></li> <li class="toctree-l2"><a class="reference internal" href="Forcefields/mmff94.html">MMFF94 Force Field (mmff94)</a></li> <li class="toctree-l2"><a class="reference internal" href="Forcefields/uff.html">Universal Force Field (uff)</a></li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="UseTheLibrary/intro.html">Write software using the Open Babel library</a><ul> <li class="toctree-l2"><a class="reference internal" href="UseTheLibrary/CppAPI.html">The Open Babel API</a></li> <li class="toctree-l2"><a class="reference internal" href="UseTheLibrary/CppExamples.html">C++</a></li> <li class="toctree-l2"><a class="reference internal" href="UseTheLibrary/Python.html">Python</a></li> <li class="toctree-l2"><a class="reference internal" href="UseTheLibrary/Java.html">Java</a></li> <li class="toctree-l2"><a class="reference 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