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transformer_fingerprints.html
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---
title: Transformer fingerprints
keywords: fastai
sidebar: home_sidebar
summary: "RXNBERT fingerprints"
description: "RXNBERT fingerprints"
nb_path: "nbs/02_transformer_fingerprints.ipynb"
---
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<h2 id="RXNBERTFingerprintGenerator" class="doc_header"><code>class</code> <code>RXNBERTFingerprintGenerator</code><a href="https://github.com/rxn4chemistry/rxnfp/tree/master/rxnfp/transformer_fingerprints.py#L25" class="source_link" style="float:right">[source]</a></h2><blockquote><p><code>RXNBERTFingerprintGenerator</code>(<strong><code>model</code></strong>:<code>BertModel</code>, <strong><code>tokenizer</code></strong>:<a href="/rxnfp/tokenization.html#SmilesTokenizer"><code>SmilesTokenizer</code></a>, <strong><code>force_no_cuda</code></strong>=<em><code>False</code></em>) :: <a href="/rxnfp/core.html#FingerprintGenerator"><code>FingerprintGenerator</code></a></p>
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<p>Generate RXNBERT fingerprints from reaction SMILES</p>
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<h2 id="RXNBERTMinhashFingerprintGenerator" class="doc_header"><code>class</code> <code>RXNBERTMinhashFingerprintGenerator</code><a href="https://github.com/rxn4chemistry/rxnfp/tree/master/rxnfp/transformer_fingerprints.py#L72" class="source_link" style="float:right">[source]</a></h2><blockquote><p><code>RXNBERTMinhashFingerprintGenerator</code>(<strong><code>model</code></strong>:<code>BertModel</code>, <strong><code>tokenizer</code></strong>:<a href="/rxnfp/tokenization.html#SmilesTokenizer"><code>SmilesTokenizer</code></a>, <strong><code>permutations</code></strong>=<em><code>256</code></em>, <strong><code>seed</code></strong>=<em><code>42</code></em>, <strong><code>force_no_cuda</code></strong>=<em><code>False</code></em>) :: <a href="/rxnfp/core.html#FingerprintGenerator"><code>FingerprintGenerator</code></a></p>
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<p>Generate RXNBERT fingerprints from reaction SMILES</p>
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<h4 id="get_default_model_and_tokenizer" class="doc_header"><code>get_default_model_and_tokenizer</code><a href="https://github.com/rxn4chemistry/rxnfp/tree/master/rxnfp/transformer_fingerprints.py#L110" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>get_default_model_and_tokenizer</code>(<strong><code>model</code></strong>=<em><code>'bert_ft'</code></em>, <strong><code>force_no_cuda</code></strong>=<em><code>False</code></em>)</p>
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<h4 id="generate_fingerprints" class="doc_header"><code>generate_fingerprints</code><a href="https://github.com/rxn4chemistry/rxnfp/tree/master/rxnfp/transformer_fingerprints.py#L134" class="source_link" style="float:right">[source]</a></h4><blockquote><p><code>generate_fingerprints</code>(<strong><code>rxns</code></strong>:<code>List</code>[<code>str</code>], <strong><code>fingerprint_generator</code></strong>:<a href="/rxnfp/core.html#FingerprintGenerator"><code>FingerprintGenerator</code></a>, <strong><code>batch_size</code></strong>=<em><code>1</code></em>)</p>
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<h1 id="Usage">Usage<a class="anchor-link" href="#Usage"> </a></h1>
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<h2 id="Convert-reaction-to-fingerprint">Convert reaction to fingerprint<a class="anchor-link" href="#Convert-reaction-to-fingerprint"> </a></h2>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">model</span><span class="p">,</span> <span class="n">tokenizer</span> <span class="o">=</span> <span class="n">get_default_model_and_tokenizer</span><span class="p">()</span>
<span class="n">rxnfp_generator</span> <span class="o">=</span> <span class="n">RXNBERTFingerprintGenerator</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">tokenizer</span><span class="p">)</span>
<span class="n">example_rxn</span> <span class="o">=</span> <span class="s2">"Nc1cccc2cnccc12.O=C(O)c1cc([N+](=O)[O-])c(Sc2c(Cl)cncc2Cl)s1>>O=C(Nc1cccc2cnccc12)c1cc([N+](=O)[O-])c(Sc2c(Cl)cncc2Cl)s1"</span>
<span class="n">fp</span> <span class="o">=</span> <span class="n">rxnfp_generator</span><span class="o">.</span><span class="n">convert</span><span class="p">(</span><span class="n">example_rxn</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fp</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">fp</span><span class="p">[:</span><span class="mi">5</span><span class="p">])</span>
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<pre>256
[-2.0174953937530518, 1.7602049112319946, -1.3323532342910767, -1.109501838684082, 1.2254544496536255]
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<h2 id="Convert-reaction-list-to-fingerprints">Convert reaction list to fingerprints<a class="anchor-link" href="#Convert-reaction-list-to-fingerprints"> </a></h2>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">fps</span> <span class="o">=</span> <span class="n">rxnfp_generator</span><span class="o">.</span><span class="n">convert_batch</span><span class="p">([</span><span class="n">example_rxn</span><span class="p">,</span> <span class="n">example_rxn</span><span class="p">])</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fps</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">fps</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
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<pre>2 256
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<h2 id="Convert-reaction-to-minhash-fingerprint">Convert reaction to minhash fingerprint<a class="anchor-link" href="#Convert-reaction-to-minhash-fingerprint"> </a></h2>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">model</span><span class="p">,</span> <span class="n">tokenizer</span> <span class="o">=</span> <span class="n">get_default_model_and_tokenizer</span><span class="p">()</span>
<span class="n">rxnmhfp_generator</span> <span class="o">=</span> <span class="n">RXNBERTMinhashFingerprintGenerator</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">tokenizer</span><span class="p">)</span>
<span class="n">example_rxn</span> <span class="o">=</span> <span class="s2">"Nc1cccc2cnccc12.O=C(O)c1cc([N+](=O)[O-])c(Sc2c(Cl)cncc2Cl)s1>>O=C(Nc1cccc2cnccc12)c1cc([N+](=O)[O-])c(Sc2c(Cl)cncc2Cl)s1"</span>
<span class="n">fp</span> <span class="o">=</span> <span class="n">rxnmhfp_generator</span><span class="o">.</span><span class="n">convert</span><span class="p">(</span><span class="n">example_rxn</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fp</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">fp</span><span class="p">[:</span><span class="mi">5</span><span class="p">])</span>
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<pre>512
VectorUint[248, 1, 39, 1, 201]
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