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5dfd67a22a
* copy in, get building, add some basic tests * complete the testing Except for regiosiomers, which do not work * regioisomers work now * backup commit; things work * remove last of NM macros from hashfunctions.cpp * remove last of NM macros from hashfunctions.cpp * remove dependency on the abstraction layer * typo * start using namespaces clang-format * switch to using enums for the HashFunctions and StripTypes * Add initial python wrapper (and tests) * move the new hashing code to the MolHash library still may want to revise the naming of this * Setup deprecation of the older hashing code * better release notes text * change in response to review
313 lines
8.2 KiB
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313 lines
8.2 KiB
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<title>molhash application — MolHash 1.0 documentation</title>
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<a href="index.html" class="icon icon-home"> MolHash
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<img src="_static/nextmove_logo.png" class="logo" alt="Logo"/>
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1.0
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<p class="caption"><span class="caption-text">Contents</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">molhash application</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#usage">Usage</a></li>
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<div class="section" id="molhash-application">
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<h1>molhash application<a class="headerlink" href="#molhash-application" title="Permalink to this headline">¶</a></h1>
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<p>The command-line application <strong class="command">molhash</strong> can be used to generate one of a number of molecular hashes.</p>
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<div class="section" id="usage">
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<h2>Usage<a class="headerlink" href="#usage" title="Permalink to this headline">¶</a></h2>
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<ul class="simple">
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<li><code class="docutils literal notranslate"><span class="pre">molhash</span> <span class="pre">[options]</span> <span class="pre"><infile></span> <span class="pre">[<outfile>]</span></code></li>
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<li><code class="docutils literal notranslate"><span class="pre">molhash</span> <span class="pre">[options]</span> <span class="pre">-</span> <span class="pre">[<outfile>]</span></code> - read from standard input</li>
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</ul>
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<p>For example:</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ echo "c1ccccc1C(=O)Cl" | molhash -mf -
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C7H5ClO c1ccc(cc1)C(=O)Cl
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</pre></div>
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</div>
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</div>
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<div class="section" id="options">
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<h2>Options<a class="headerlink" href="#options" title="Permalink to this headline">¶</a></h2>
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<table class="docutils option-list" frame="void" rules="none">
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<col class="option" />
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<col class="description" />
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<tbody valign="top">
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<tr><td class="option-group">
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<kbd><span class="option">-a</span></kbd></td>
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<td>Process all the molecule (and not just the single largest component)</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-s<var>a</var></span></kbd></td>
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<td>Suppress atom stereo</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-s<var>b</var></span></kbd></td>
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<td>Suppress bond stereo</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-s<var>h</var></span></kbd></td>
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<td>Suppress explicit hydrogens</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-s<var>i</var></span></kbd></td>
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<td>Suppress isotopes</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-s<var>m</var></span></kbd></td>
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<td>Suppress atom maps</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-t</span></kbd></td>
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<td>Store titles only</td></tr>
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</tbody>
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</table>
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<p class="rubric">Hash Types</p>
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<table class="docutils option-list" frame="void" rules="none">
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<kbd><span class="option">-g</span></kbd></td>
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<td>anonymous graph [default]</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-e</span></kbd></td>
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<td>element graph</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-s</span></kbd></td>
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<td>canonical smiles</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-m</span></kbd></td>
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<td>Murcko scaffold</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-m<var>f</var></span></kbd></td>
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<td>molecular formula</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-m<var>e</var></span></kbd></td>
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<td>mesomer</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-h<var>t</var></span></kbd></td>
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<td>hetatom tautomer</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-h<var>p</var></span></kbd></td>
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<td>hetatom protomer</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-r<var>p</var></span></kbd></td>
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<td>redox-pair</td></tr>
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<tr><td class="option-group">
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<kbd><span class="option">-r<var>i</var></span></kbd></td>
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<td>regioisomer</td></tr>
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</tbody>
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