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Co-authored-by: Rocco Meli <[email protected]>
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doc/source/formats/guessers/default.rst

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@@ -57,6 +57,10 @@ Aromaticities
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These are guessed using the :ref:`RDKit <RDKit-format>` converter by using the ``GetIsAromatic`` method.
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.. note::
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RDKit needs to have been installed for aromaticity guessing to be available.
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RDKit is always installed when MDAnalysis was installed with conda-forge packages
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but this may not be the case when using other installation paths.
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-----------------------------------
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Bonds, Angles, Dihedrals, Impropers
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d < f \cdot (R_1 + R_2)
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of each other, where :math:`R_1` and :math:`R_2` are the VdW radii
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of the atoms and :math:`f` is an ad-hoc *fudge_factor*. This is
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of each other, where :math:`R_1` and :math:`R_2` are the van der Waals radii
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of the atoms and :math:`f` is an ad-hoc *fudge factor*. This is
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the `same algorithm that VMD uses`_.
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.. note::

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