get_bonds

Cartesian.get_bonds(modified_properties=None, maximum_edge_length=25, difference_edge=6, use_valency=False, use_lookup=False, set_lookup=True, divide_et_impera=True, atomic_radius_data='atomic_radius_cc')[source]

Returns a dictionary representing the bonds.

Warning

This function is not sideeffect free, since it assigns the output to a variable self.__bond_dic if set_lookup is True (which is the default). This is necessary for performance reasons.

The Cartesian().get_bonds() method will use or not use a lookup
depending on use_lookup. Greatly increases performance if True, but could introduce bugs in certain situations.

Just imagine a situation where the Cartesian().frame is changed manually. If you apply lateron a method e.g. to_zmat() that makes use of get_bonds() the dictionary of the bonds may not represent the actual situation anymore.

You have two possibilities to cope with this problem. Either you just re-execute get_bonds on your specific instance, or you change the internally_use_lookup option in the settings submodule. Please note that the internal use of the lookup variable greatly improves performance.

Parameters:
  • modified_properties (dic) –

    If you want to change the van der Vaals radius or valency of one or more specific atoms, pass a dictionary that looks like:

    modified_properties = {index1 :
    {'atomic_radius' : 1.5, 'valency' : 8}, ...}

    For global changes use the constants.py module.

  • maximum_edge_length (float) – Maximum length of one edge of a
  • if divide_et_impera is True. (cuboid) –
  • difference_edge (float) –
  • use_valency (bool) – If True atoms can’t have more bonds than their valency. This means that the bonds, exceeding the number of valency, with lowest overlap will be cut, although the van der Waals radii overlap.
  • use_lookup (bool) –
  • set_lookup (bool) –
  • divide_et_impera (bool) – Since the calculation of overlaps or distances between atoms scale with O(n^2), it is recommended to split the molecule in smaller cuboids and calculate the bonds in each cuboid. The scaling becomes then O(n\log(n)). This approach can lead to problems if use_valency is True. Bonds from one cuboid to another can not be counted for the valency.. This means that in certain situations some atoms can be oversaturated, although use_valency is True.
  • atomic_radius_data (str) – Defines which column of constants.elements is used. The default is atomic_radius_cc and can be changed with settings.atomic_radius_data. Compare with add_data().
Returns:

Dictionary mapping from an atom index to the indices of atoms bonded to.
Return type:

dict