Whitespace

The following conventions are for general code cleanliness and readability:

• Trailing whitespace is to be avoided.
• All functions should be preceded by two empty lines. The only exception is the first function of the class definition.
• Function arguments should be separated by a comma followed by a single space.
• The assignment operator should be surrounded by spaces, for example tm = 1e-8. The exception is function arguments, for example self.classic\_colour(res\_num=None, width=0.3).
• The comparison operators should also be surrounded by spaces, e.g. < , > , == , <= , => , <> , = !, is , and in .

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)