shnitsel.geo.nonred
===================

.. py:module:: shnitsel.geo.nonred


Functions
---------

.. autoapisummary::

   shnitsel.geo.nonred.get_smiles_order_ignoring_h
   shnitsel.geo.nonred.flag_nonredundant


Module Contents
---------------

.. py:function:: get_smiles_order_ignoring_h(mol)

   Returns the order in which atoms would appear in the canonical SMILES of
   ``mol``, ignoring hydrogens

   :param mol: An ``rdkit.Chem.Mol`` object

   :returns: * A list of integers representing indices of the original ``mol`` object (as opposed
             * *to the integers assigned to the copy stripped of hydrogens)*


.. py:function:: flag_nonredundant(mol, include_h = True)

   Compute a non-redundant set of bonds, angles, and dihedrals
   sufficient to uniquely determine the atoms of the input,
   given a fixed centre and whole-molecular orientation.

   :param mol: Molecule under study.
   :type mol: rdkit.Chem.rdchem.Mol
   :param include_h: Whether to include internal coordinates for hydrogen atoms
   :type include_h: bool

   :returns:

             {
                 'bonds':      [...],
                 'angles':     [...],
                 'dihedrals':  [...]
             }
   :rtype: dict