2.2 Find analogs for target
===============================

.. code:: ipython3

    from marsi.nearest_neighbors import search_closest_compounds


.. parsed-literal::

    Looking for local setup.cfg
    Not available [Errno 2] No such file or directory: 'setup.cfg'



.. raw:: html

    





.. raw:: html

    




.. parsed-literal::

    /Users/joaca/Documents/repositories/marsi/marsi/chemistry/rdkit.py:25 DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead.


.. code:: ipython3

    from marsi.chemistry.common import dynamic_fingerprint_cut

.. code:: ipython3

    glucose_inchi = "InChI=1/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1"

.. code:: ipython3

    from marsi.chemistry.molecule import Molecule

.. code:: ipython3

    glucose_molecule = Molecule.from_inchi(glucose_inchi)

.. code:: ipython3

    glucose_molecule




.. raw:: html

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    <title> - Open Babel Depiction</title>
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.. code:: ipython3

    cutoff = dynamic_fingerprint_cut(glucose_molecule.num_atoms); cutoff




.. parsed-literal::

    0.439615



.. code:: ipython3

    hits = search_closest_compounds(molecule=glucose_molecule, fp_cut=cutoff)


.. parsed-literal::

    /usr/local/miniconda3/envs/marsi/lib/python3.5/site-packages/sklearn/utils/validation.py:475 DataConversionWarning: Data with input dtype int32 was converted to bool by check_pairwise_arrays.



.. raw:: html

    <p>Failed to display Jupyter Widget of type <code>HBox</code>.</p>
    <p>
      If you're reading this message in Jupyter Notebook or JupyterLab, it may mean
      that the widgets JavaScript is still loading. If this message persists, it
      likely means that the widgets JavaScript library is either not installed or
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    <p>
      If you're reading this message in another notebook frontend (for example, a static
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      it may mean that your frontend doesn't currently support widgets.
    </p>



.. parsed-literal::

    /Users/joaca/Documents/repositories/marsi/marsi/chemistry/rdkit.py:258 DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead.


.. code:: ipython3

    hits.sort_values('structural_score', ascending=False).head(15)




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          <th>bonds</th>
          <th>tanimoto_similarity</th>
          <th>structural_score</th>
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          <th>BQCCAEOLPYCBAE-UKFBFLRUSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.777778</td>
          <td>0.96</td>
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          <th>MSWZFWKMSRAUBD-RDQKPOQOSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.777778</td>
          <td>0.96</td>
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          <th>MSWZFWKMSRAUBD-UKFBFLRUSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.777778</td>
          <td>0.96</td>
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          <th>WCWOEQFAYSXBRK-GKFJPSPNSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.692308</td>
          <td>0.96</td>
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          <th>WCWOEQFAYSXBRK-FPRJBGLDSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.692308</td>
          <td>0.96</td>
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          <th>WCWOEQFAYSXBRK-FQJSGBEDSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.692308</td>
          <td>0.96</td>
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          <th>MSWZFWKMSRAUBD-FQJSGBEDSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.777778</td>
          <td>0.96</td>
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          <th>WCWOEQFAYSXBRK-QBFJYBIGSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.692308</td>
          <td>0.96</td>
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        <tr>
          <th>WCWOEQFAYSXBRK-DVKNGEFBSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.692308</td>
          <td>0.96</td>
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          <th>MSWZFWKMSRAUBD-TVIMKVIFSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.777778</td>
          <td>0.96</td>
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          <th>WCWOEQFAYSXBRK-BYIBVSMXSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.692308</td>
          <td>0.96</td>
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          <th>MSWZFWKMSRAUBD-HGVZOGFYSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.777778</td>
          <td>0.96</td>
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          <th>WCWOEQFAYSXBRK-RWOPYEJCSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
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          <td>0.96</td>
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          <th>MSWZFWKMSRAUBD-PHYPRBDBSA-N</th>
          <td>C6H13NO5</td>
          <td>25</td>
          <td>25</td>
          <td>0.777778</td>
          <td>0.96</td>
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          <td>C6H13NO5</td>
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          <td>0.96</td>
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.. code:: ipython3

    from marsi.io.db import Metabolite

.. code:: ipython3

    Metabolite.get('WCWOEQFAYSXBRK-FPRJBGLDSA-N')




.. raw:: html

    
    <table>
        <tbody>
            <tr><td><strong>Formula</strong></td><td>C6H13NO5</td></tr>
            <tr><td><strong>InChi</strong></td><td>InChI=1S/C6H13NO5/c7-6-5(11)4(10)3(9)2(1-8)12-6/h2-6,8-11H,1,7H2/t2-,3+,4+,5-,6-/m1/s1</td></tr>
            <tr><td><strong>InChi Key</strong></td><td>WCWOEQFAYSXBRK-FPRJBGLDSA-N</td></tr>
            <tr><td><strong>Structure</strong></td><td><?xml version="1.0"?>
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    <text x="32.500000" y="88.000000" fill="rgb(12,12,255)"  stroke="rgb(12,12,255)" stroke-width="1" font-size="16" >N</text>
    <text x="103.282032" y="48.000000" fill="rgb(255,12,12)"  stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >OH</text>
    <text x="172.564065" y="88.000000" fill="rgb(255,12,12)"  stroke="rgb(255,12,12)" stroke-width="1" font-size="16" >OH</text>
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            <tr><td><strong>DBs</strong></td><td>zinc: ZINC13544123</td></tr>
            <tr><td><strong>Synonyms</strong></td><td></td></tr>
        </tbody>
    </table>



.. code:: ipython3

    Metabolite.get('WCWOEQFAYSXBRK-QBFJYBIGSA-N')




.. raw:: html

    
    <table>
        <tbody>
            <tr><td><strong>Formula</strong></td><td>C6H13NO5</td></tr>
            <tr><td><strong>InChi</strong></td><td>InChI=1S/C6H13NO5/c7-6-5(11)4(10)3(9)2(1-8)12-6/h2-6,8-11H,1,7H2/t2-,3+,4+,5+,6-/m1/s1</td></tr>
            <tr><td><strong>InChi Key</strong></td><td>WCWOEQFAYSXBRK-QBFJYBIGSA-N</td></tr>
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    <text x="32.500000" y="88.000000" fill="rgb(12,12,255)"  stroke="rgb(12,12,255)" stroke-width="1" font-size="16" >N</text>
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            <tr><td><strong>DBs</strong></td><td>zinc: ZINC22059796</td></tr>
            <tr><td><strong>Synonyms</strong></td><td></td></tr>
        </tbody>
    </table>



.. code:: ipython3

    Metabolite.get('BQCCAEOLPYCBAE-UKFBFLRUSA-N')




.. raw:: html

    
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        <tbody>
            <tr><td><strong>Formula</strong></td><td>C6H13NO5</td></tr>
            <tr><td><strong>InChi</strong></td><td>InChI=1S/C6H13NO5/c7-3-4(9)2(1-8)12-6(11)5(3)10/h2-6,8-11H,1,7H2/t2-,3-,4-,5-,6+/m1/s1</td></tr>
            <tr><td><strong>InChi Key</strong></td><td>BQCCAEOLPYCBAE-UKFBFLRUSA-N</td></tr>
            <tr><td><strong>Structure</strong></td><td><?xml version="1.0"?>
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    <title> - Open Babel Depiction</title>
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            <tr><td><strong>DBs</strong></td><td>zinc: ZINC83295854</td></tr>
            <tr><td><strong>Synonyms</strong></td><td></td></tr>
        </tbody>
    </table>