chemcoord.zmat_functions.CleanDihedralOrientation

class chemcoord.zmat_functions.CleanDihedralOrientation(clean_dihedral_orientation, cls=None)

Clean the orientation of dihedral references.

It can sometimes be, that a change in a Z-matrix coordinate flips the orientation of a dihedral reference lateron in the molecule. Note that there is an implicit dependence on the previous state of the Z-matrix that could still be transformed to cartesian coordinates, since a smooth trajectory forms a reference frame for the next step by itself. Hence, this problem can be altogether generally avoided by applying smaller steps, i.e. instead of changing zmat_1.loc[1, 'angle'] = 170 in one step, it is better to increment/decrement the angle in steps.

If this does not help, one can use this contextmanager to clean the orientation:

with CleanDihedralOrientation(True):
    zmat_1.loc[1, 'angle'] = 170

Even then it is advised to apply small steps changes.

Parameters:

clean_dihedral_orientation (bool)

__init__(clean_dihedral_orientation, cls=None)

Parameters:

clean_dihedral_orientation (bool)

Return type:

None

Methods

__init__(clean_dihedral_orientation[, cls])