chemcoord.Cartesian.get_zmat¶

Cartesian.
get_zmat
(construction_table=None, use_lookup=None)¶ Transform to internal coordinates.
Transforming to internal coordinates involves basically three steps:
1. Define an order of how to build and define for each atom the used reference atoms.
2. Check for problematic local linearity. In this algorithm an angle with
170 < angle < 10
is assumed to be linear. This is not the mathematical definition, but makes it safer against “floating point noise”3. Calculate the bond lengths, angles and dihedrals using the references defined in step 1 and 2.
In the first two steps a so called
construction_table
is created. This is basically a Zmatrix without the values for the bonds, angles and dihedrals hence containing only the information about the used references. ChemCoord uses apandas.DataFrame
with the columns['b', 'a', 'd']
. Look intoget_construction_table()
for more information.It is important to know, that calculating the construction table is a very costly step since the algoritym tries to make some guesses based on connectivity to create a “chemical” zmatrix.
If you create several zmatrices based on the same references you can obtain the construction table of a zmatrix with
Zmat_instance.loc[:, ['b', 'a', 'd']]
If you then pass the buildlist as argument togive_zmat
, the algorithm directly starts with step 3 (which is much faster).If a
construction_table
is passed intoget_zmat()
the check for pathological linearity is not performed! So if aconstruction_table
is either manually created, or obtained fromget_construction_table()
under the optionperform_checks = False
, it is recommended to use the following methods:If you want to check for problematic indices in order to solve the invalid references yourself, use the following methods:
Parameters:  construction_table (pandas.DataFrame) –
 use_lookup (bool) – Use a lookup variable for
get_bonds()
. The default is specified insettings['defaults']['use_lookup']
Returns: A new instance of
Zmat
.Return type: