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update selections.rst
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IAlibay committed Jun 1, 2022
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13 changes: 7 additions & 6 deletions package/doc/sphinx/source/documentation_pages/selections.rst
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Expand Up @@ -173,12 +173,13 @@ smarts *SMARTS-query*
RDKit's `GetSubstructMatches
<https://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html#rdkit.Chem.rdchem.Mol.GetSubstructMatches>`_.
By default, the `useChirality` kwarg in ``rdkit_kwargs`` is set to true
and maxMatches in ``smarts_kwargs`` is ``10 * len(AtomGroup)`` or
``10 * len(Universe.atoms)``, whichever is applicable.
Note that the number of matches can occasionally exceed the default
value of maxMatches, causing too few atoms to be returned. If this
occurs, a warning will be issued. The problem can be fixed by increasing
the value of maxMatches. This behavior may be updated in the future.
and maxMatches in ``smarts_kwargs`` is ``max(1000, 10 * n_atoms)``, where
``n_atoms`` is either ``len(AtomGroup)`` or ``len(Universe.atoms)``,
whichever is applicable. Note that the number of matches can occasionally
exceed the default value of maxMatches, causing too few atoms to be
returned. If this occurs, a warning will be issued. The problem can be
fixed by increasing the value of maxMatches. This behavior may be updated
in the future

chiral *R | S*
select a particular stereocenter. e.g. ``name C and chirality S``
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