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The following conventions are for general code cleanliness and readability:

An example which shows most of these conventions is:

class Internal:
    """The internal relax structural data object.

    The structural data object for this class is a container possessing a number of different arrays corresponding to different structural information.  These objects are described in the structural container docstring.
    """

    def _bonded_atom(self, attached_atom, index, mol):
        """Find the atom named attached_atom directly bonded to the atom located at the index.

        @param attached_atom:   The name of the attached atom to return.
        @type attached_atom:    str
        @param index:           The index of the atom which the attached atom is attached to.
        @type index:            int
        @param mol:             The molecule container.
        @type mol:              MolContainer instance
        @return:                A tuple of information about the bonded atom.
        @rtype:                 tuple consisting of the atom number (int), atom name (str), element name (str), and atomic position (Numeric array of len 3)
        """

        # Init.
        bonded_found = False

        # No bonded atoms, so determine the connectivities.
        if not mol.bonded[index]:
            # Determine the molecule type if needed.
            if not hasattr(mol, 'type'):
                self._mol_type(mol)



The relax user manual (PDF), created 2016-10-28.