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---
title: Results - Generate TMAP
keywords: fastai
sidebar: home_sidebar
summary: "Cluster 50k reaction data set by Schneider et al. using TMAP"
description: "Cluster 50k reaction data set by Schneider et al. using TMAP"
nb_path: "nbs/05_results_generate_TMAP.ipynb"
---
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<h3 id="Load-data-and-generate-minhash-fingerprints">Load data and generate minhash fingerprints<a class="anchor-link" href="#Load-data-and-generate-minhash-fingerprints"> </a></h3>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">lf</span> <span class="o">=</span> <span class="n">tm</span><span class="o">.</span><span class="n">LSHForest</span><span class="p">(</span><span class="mi">256</span><span class="p">,</span> <span class="mi">128</span><span class="p">)</span>
<span class="n">mh_encoder</span> <span class="o">=</span> <span class="n">tm</span><span class="o">.</span><span class="n">Minhash</span><span class="p">()</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">mhfps</span> <span class="o">=</span> <span class="p">[</span><span class="n">mh_encoder</span><span class="o">.</span><span class="n">from_weight_array</span><span class="p">(</span><span class="n">fp</span><span class="o">.</span><span class="n">tolist</span><span class="p">(),</span> <span class="n">method</span><span class="o">=</span><span class="s2">"I2CWS"</span><span class="p">)</span> <span class="k">for</span> <span class="n">fp</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">ft_10k_fps</span><span class="p">)]</span>
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<pre>100%|██████████| 50000/50000 [00:15<00:00, 3213.43it/s]
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<h3 id="Calculate-rxn-properties">Calculate rxn properties<a class="anchor-link" href="#Calculate-rxn-properties"> </a></h3>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">labels</span> <span class="o">=</span> <span class="p">[]</span>
<span class="c1"># superclasses</span>
<span class="n">superclasses</span> <span class="o">=</span> <span class="p">[]</span>
<span class="c1"># product properties</span>
<span class="n">tpsa</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">logp</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">mw</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">h_acceptors</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">h_donors</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">ring_count</span> <span class="o">=</span> <span class="p">[]</span>
<span class="c1"># metals in precursors</span>
<span class="n">has_Pd</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">has_Li</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">has_Mg</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">has_Al</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">schneider_df</span><span class="o">.</span><span class="n">iterrows</span><span class="p">(),</span> <span class="n">total</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">schneider_df</span><span class="p">)):</span>
<span class="n">rxn</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s2">"rxn"</span><span class="p">]</span>
<span class="n">labels</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
<span class="nb">str</span><span class="p">(</span><span class="n">rxn</span><span class="p">)</span>
<span class="o">+</span> <span class="s2">"__"</span>
<span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">rxn</span><span class="p">)</span>
<span class="o">+</span> <span class="sa">f</span><span class="s2">"__</span><span class="si">{</span><span class="n">row</span><span class="p">[</span><span class="s1">'source'</span><span class="p">]</span><span class="si">}</span><span class="s2">"</span>
<span class="o">+</span> <span class="sa">f</span><span class="s2">"__</span><span class="si">{</span><span class="n">rxnclass2name</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s1">'rxn_class'</span><span class="p">]]</span><span class="si">}</span><span class="s2"> - </span><span class="si">{</span><span class="n">row</span><span class="p">[</span><span class="s1">'rxn_class'</span><span class="p">]</span><span class="si">}</span><span class="s2">"</span>
<span class="o">+</span> <span class="sa">f</span><span class="s2">"__</span><span class="si">{</span><span class="n">rxnclass2name</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s1">'rxn_category'</span><span class="p">]]</span><span class="si">}</span><span class="s2">"</span>
<span class="o">+</span> <span class="sa">f</span><span class="s2">"__</span><span class="si">{</span><span class="n">rxnclass2name</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="s1">'rxn_superclass'</span><span class="p">]]</span><span class="si">}</span><span class="s2">"</span>
<span class="p">)</span>
<span class="n">superclasses</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s2">"rxn_superclass"</span><span class="p">]))</span>
<span class="n">precursors</span><span class="p">,</span> <span class="n">products</span> <span class="o">=</span> <span class="n">rxn</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'>>'</span><span class="p">)</span>
<span class="n">mol</span> <span class="o">=</span> <span class="n">Chem</span><span class="o">.</span><span class="n">MolFromSmiles</span><span class="p">(</span><span class="n">products</span><span class="p">)</span>
<span class="n">tpsa</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Descriptors</span><span class="o">.</span><span class="n">TPSA</span><span class="p">(</span><span class="n">mol</span><span class="p">))</span>
<span class="n">logp</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Descriptors</span><span class="o">.</span><span class="n">MolLogP</span><span class="p">(</span><span class="n">mol</span><span class="p">))</span>
<span class="n">mw</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Descriptors</span><span class="o">.</span><span class="n">MolWt</span><span class="p">(</span><span class="n">mol</span><span class="p">))</span>
<span class="n">h_acceptors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Descriptors</span><span class="o">.</span><span class="n">NumHAcceptors</span><span class="p">(</span><span class="n">mol</span><span class="p">))</span>
<span class="n">h_donors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Descriptors</span><span class="o">.</span><span class="n">NumHDonors</span><span class="p">(</span><span class="n">mol</span><span class="p">))</span>
<span class="n">ring_count</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Descriptors</span><span class="o">.</span><span class="n">RingCount</span><span class="p">(</span><span class="n">mol</span><span class="p">))</span>
<span class="n">has_Pd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">'Pd'</span> <span class="ow">in</span> <span class="n">precursors</span><span class="p">)</span>
<span class="n">has_Li</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">'Li'</span> <span class="ow">in</span> <span class="n">precursors</span><span class="p">)</span>
<span class="n">has_Mg</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">'Mg'</span> <span class="ow">in</span> <span class="n">precursors</span><span class="p">)</span>
<span class="n">has_Al</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">'Al'</span> <span class="ow">in</span> <span class="n">precursors</span><span class="p">)</span>
<span class="n">tpsa_ranked</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">rankdata</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">tpsa</span><span class="p">)</span> <span class="o">/</span> <span class="nb">max</span><span class="p">(</span><span class="n">tpsa</span><span class="p">))</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">tpsa</span><span class="p">)</span>
<span class="n">logp_ranked</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">rankdata</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">logp</span><span class="p">)</span> <span class="o">/</span> <span class="nb">max</span><span class="p">(</span><span class="n">logp</span><span class="p">))</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">logp</span><span class="p">)</span>
<span class="n">mw_ranked</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">rankdata</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">mw</span><span class="p">)</span> <span class="o">/</span> <span class="nb">max</span><span class="p">(</span><span class="n">mw</span><span class="p">))</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">mw</span><span class="p">)</span>
<span class="n">h_acceptors_ranked</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">rankdata</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">h_acceptors</span><span class="p">)</span> <span class="o">/</span> <span class="nb">max</span><span class="p">(</span><span class="n">h_acceptors</span><span class="p">))</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span>
<span class="n">h_acceptors</span>
<span class="p">)</span>
<span class="n">h_donors_ranked</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">rankdata</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">h_donors</span><span class="p">)</span> <span class="o">/</span> <span class="nb">max</span><span class="p">(</span><span class="n">h_donors</span><span class="p">))</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">h_donors</span><span class="p">)</span>
<span class="n">ring_count_ranked</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">rankdata</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">ring_count</span><span class="p">)</span> <span class="o">/</span> <span class="nb">max</span><span class="p">(</span><span class="n">ring_count</span><span class="p">))</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span>
<span class="n">ring_count</span>
<span class="p">)</span>
<span class="n">labels_groups</span><span class="p">,</span> <span class="n">groups</span> <span class="o">=</span> <span class="n">Faerun</span><span class="o">.</span><span class="n">create_categories</span><span class="p">(</span><span class="n">superclasses</span><span class="p">)</span>
<span class="n">labels_groups</span> <span class="o">=</span> <span class="p">[(</span><span class="n">label</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">label</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s2"> - </span><span class="si">{</span><span class="n">rxnclass2name</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">label</span><span class="p">[</span><span class="mi">1</span><span class="p">])]</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span> <span class="k">for</span> <span class="n">label</span> <span class="ow">in</span> <span class="n">labels_groups</span><span class="p">]</span>
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<h3 id="Configure-LSH-forest">Configure LSH forest<a class="anchor-link" href="#Configure-LSH-forest"> </a></h3>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">lf</span><span class="o">.</span><span class="n">batch_add</span><span class="p">(</span><span class="n">mhfps</span><span class="p">)</span>
<span class="n">lf</span><span class="o">.</span><span class="n">index</span><span class="p">()</span>
<span class="c1"># Layout</span>
<span class="n">cfg</span> <span class="o">=</span> <span class="n">tm</span><span class="o">.</span><span class="n">LayoutConfiguration</span><span class="p">()</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">k</span> <span class="o">=</span> <span class="mi">50</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">kc</span> <span class="o">=</span> <span class="mi">50</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">sl_scaling_min</span> <span class="o">=</span> <span class="mf">1.0</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">sl_scaling_max</span> <span class="o">=</span> <span class="mf">1.0</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">sl_repeats</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">sl_extra_scaling_steps</span> <span class="o">=</span> <span class="mi">2</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">placer</span> <span class="o">=</span> <span class="n">tm</span><span class="o">.</span><span class="n">Placer</span><span class="o">.</span><span class="n">Barycenter</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">merger</span> <span class="o">=</span> <span class="n">tm</span><span class="o">.</span><span class="n">Merger</span><span class="o">.</span><span class="n">LocalBiconnected</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">merger_factor</span> <span class="o">=</span> <span class="mf">2.0</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">merger_adjustment</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">fme_iterations</span> <span class="o">=</span> <span class="mi">1000</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">sl_scaling_type</span> <span class="o">=</span> <span class="n">tm</span><span class="o">.</span><span class="n">ScalingType</span><span class="o">.</span><span class="n">RelativeToDesiredLength</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">node_size</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="mi">37</span>
<span class="n">cfg</span><span class="o">.</span><span class="n">mmm_repeats</span> <span class="o">=</span> <span class="mi">1</span>
<span class="c1"># Define colormaps</span>
<span class="n">set1</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">"Set1"</span><span class="p">)</span><span class="o">.</span><span class="n">colors</span>
<span class="n">rainbow</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">"rainbow"</span><span class="p">)</span>
<span class="n">colors</span> <span class="o">=</span> <span class="n">rainbow</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">groups</span><span class="p">))))[:,</span> <span class="p">:</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
<span class="n">custom_cm</span> <span class="o">=</span> <span class="n">LinearSegmentedColormap</span><span class="o">.</span><span class="n">from_list</span><span class="p">(</span><span class="s2">"my_map"</span><span class="p">,</span> <span class="n">colors</span><span class="p">,</span> <span class="n">N</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">colors</span><span class="p">))</span>
<span class="n">bin_cmap</span> <span class="o">=</span> <span class="n">ListedColormap</span><span class="p">([</span><span class="n">set1</span><span class="p">[</span><span class="mi">8</span><span class="p">],</span> <span class="s2">"#5400F6"</span><span class="p">],</span> <span class="n">name</span><span class="o">=</span><span class="s2">"bin_cmap"</span><span class="p">)</span>
<span class="c1"># Get tree coordinates</span>
<span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">s</span><span class="p">,</span> <span class="n">t</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">tm</span><span class="o">.</span><span class="n">layout_from_lsh_forest</span><span class="p">(</span><span class="n">lf</span><span class="p">,</span> <span class="n">config</span><span class="o">=</span><span class="n">cfg</span><span class="p">)</span>
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<h3 id="Create-Fearun-plot">Create Fearun plot<a class="anchor-link" href="#Create-Fearun-plot"> </a></h3>
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<div class="input">
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">f</span> <span class="o">=</span> <span class="n">Faerun</span><span class="p">(</span><span class="n">clear_color</span><span class="o">=</span><span class="s2">"#ffffff"</span><span class="p">,</span> <span class="n">coords</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">view</span><span class="o">=</span><span class="s2">"front"</span><span class="p">,)</span>
<span class="n">f</span><span class="o">.</span><span class="n">add_scatter</span><span class="p">(</span>
<span class="s2">"ReactionAtlas"</span><span class="p">,</span>
<span class="p">{</span>
<span class="s2">"x"</span><span class="p">:</span> <span class="n">x</span><span class="p">,</span> <span class="s2">"y"</span><span class="p">:</span> <span class="n">y</span><span class="p">,</span>
<span class="s2">"c"</span><span class="p">:</span> <span class="p">[</span>
<span class="n">groups</span><span class="p">,</span> <span class="c1"># superclasses</span>
<span class="n">has_Pd</span><span class="p">,</span>
<span class="n">has_Li</span><span class="p">,</span>
<span class="n">has_Mg</span><span class="p">,</span>
<span class="n">has_Al</span><span class="p">,</span>
<span class="n">tpsa_ranked</span><span class="p">,</span>
<span class="n">logp_ranked</span><span class="p">,</span>
<span class="n">mw_ranked</span><span class="p">,</span>
<span class="n">h_acceptors_ranked</span><span class="p">,</span>
<span class="n">h_donors_ranked</span><span class="p">,</span>
<span class="n">ring_count_ranked</span><span class="p">,</span>
<span class="p">],</span>
<span class="s2">"labels"</span><span class="p">:</span> <span class="n">labels</span>
<span class="p">},</span>
<span class="n">shader</span><span class="o">=</span><span class="s2">"smoothCircle"</span><span class="p">,</span>
<span class="n">colormap</span><span class="o">=</span><span class="p">[</span>
<span class="n">custom_cm</span><span class="p">,</span>
<span class="n">bin_cmap</span><span class="p">,</span>
<span class="n">bin_cmap</span><span class="p">,</span>
<span class="n">bin_cmap</span><span class="p">,</span>
<span class="n">bin_cmap</span><span class="p">,</span>
<span class="s2">"rainbow"</span><span class="p">,</span>
<span class="s2">"rainbow"</span><span class="p">,</span>
<span class="s2">"rainbow"</span><span class="p">,</span>
<span class="s2">"rainbow"</span><span class="p">,</span>
<span class="s2">"rainbow"</span><span class="p">,</span>
<span class="s2">"rainbow"</span><span class="p">,</span>
<span class="p">],</span>
<span class="n">point_scale</span><span class="o">=</span><span class="mf">2.0</span><span class="p">,</span>
<span class="n">categorical</span><span class="o">=</span><span class="p">[</span>
<span class="kc">True</span><span class="p">,</span>
<span class="kc">True</span><span class="p">,</span>
<span class="kc">True</span><span class="p">,</span>
<span class="kc">True</span><span class="p">,</span>
<span class="kc">True</span><span class="p">,</span>
<span class="kc">False</span><span class="p">,</span>
<span class="kc">False</span><span class="p">,</span>
<span class="kc">False</span><span class="p">,</span>
<span class="kc">False</span><span class="p">,</span>
<span class="kc">False</span><span class="p">,</span>
<span class="kc">False</span><span class="p">,</span>
<span class="p">],</span>
<span class="n">has_legend</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
<span class="n">legend_labels</span><span class="o">=</span><span class="p">[</span>
<span class="n">labels_groups</span><span class="p">,</span>
<span class="p">[(</span><span class="mi">0</span><span class="p">,</span> <span class="s2">"No"</span><span class="p">),</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s2">"Yes"</span><span class="p">)],</span>
<span class="p">[(</span><span class="mi">0</span><span class="p">,</span> <span class="s2">"No"</span><span class="p">),</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s2">"Yes"</span><span class="p">)],</span>
<span class="p">[(</span><span class="mi">0</span><span class="p">,</span> <span class="s2">"No"</span><span class="p">),</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s2">"Yes"</span><span class="p">)],</span>
<span class="p">[(</span><span class="mi">0</span><span class="p">,</span> <span class="s2">"No"</span><span class="p">),</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s2">"Yes"</span><span class="p">)],</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="p">],</span>
<span class="n">selected_labels</span><span class="o">=</span><span class="p">[</span><span class="s2">"SMILES"</span><span class="p">,</span> <span class="s2">"SMILES"</span><span class="p">,</span> <span class="s2">"Patent ID"</span><span class="p">,</span> <span class="s2">"Named Reaction"</span><span class="p">,</span> <span class="s2">"Category"</span><span class="p">,</span> <span class="s2">"Superclass"</span><span class="p">],</span>
<span class="n">series_title</span><span class="o">=</span><span class="p">[</span>
<span class="s2">"Superclass"</span><span class="p">,</span>
<span class="s2">"Pd"</span><span class="p">,</span>
<span class="s2">"Li"</span><span class="p">,</span>
<span class="s2">"Mg"</span><span class="p">,</span>
<span class="s2">"Al"</span><span class="p">,</span>
<span class="s2">"TPSA"</span><span class="p">,</span>
<span class="s2">"logP"</span><span class="p">,</span>
<span class="s2">"Mol Weight"</span><span class="p">,</span>
<span class="s2">"H Acceptors"</span><span class="p">,</span>
<span class="s2">"H Donors"</span><span class="p">,</span>
<span class="s2">"Ring Count"</span><span class="p">,</span>
<span class="p">],</span>
<span class="n">max_legend_label</span><span class="o">=</span><span class="p">[</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">tpsa</span><span class="p">))),</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">logp</span><span class="p">))),</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">mw</span><span class="p">))),</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">h_acceptors</span><span class="p">))),</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">h_donors</span><span class="p">))),</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">ring_count</span><span class="p">))),</span>
<span class="p">],</span>
<span class="n">min_legend_label</span><span class="o">=</span><span class="p">[</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">tpsa</span><span class="p">))),</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">logp</span><span class="p">))),</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">mw</span><span class="p">))),</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">h_acceptors</span><span class="p">))),</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">h_donors</span><span class="p">))),</span>
<span class="nb">str</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">ring_count</span><span class="p">))),</span>
<span class="p">],</span>
<span class="n">title_index</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
<span class="n">legend_title</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span>
<span class="p">)</span>
<span class="n">f</span><span class="o">.</span><span class="n">add_tree</span><span class="p">(</span><span class="s2">"reactiontree"</span><span class="p">,</span> <span class="p">{</span><span class="s2">"from"</span><span class="p">:</span> <span class="n">s</span><span class="p">,</span> <span class="s2">"to"</span><span class="p">:</span> <span class="n">t</span><span class="p">},</span> <span class="n">point_helper</span><span class="o">=</span><span class="s2">"ReactionAtlas"</span><span class="p">)</span>
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<h3 id="Result">Result<a class="anchor-link" href="#Result"> </a></h3><p>The result of running <code>f.plot("ft_10k_schneider_50k", template="reaction_smiles")</code> is:</p>
<div style="text-align: center">
{% include image.html width="800" max-width="800" file="/rxnfp/images/sample_tmap.jpg" %}
<p style="text-align: center;"> <b>Figure:</b> Reaction atlas of 50k Schneider data set. Product and precursor properties are highlighted in the different layers. </p>
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<h3 id="Interative-version">Interative version<a class="anchor-link" href="#Interative-version"> </a></h3><p>An interactive reaction atlas made from the same data set and fingerprint can be found here (<strong><a href="../tmaps/tmap_ft_10k.html">link</a></strong>).</p>
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