Molecule.part_angle¶

Molecule.part_angle(bond_a, bond_b, atoms, angle, zero)¶

Change the bond angle of two bond vectors. Variable atoms specifies which atoms or rather which part of the molecule needs to be rotated in order to change the specified bond angle. First however the system needs to be set to zero. Therefore, the atom id to define the new coordinate system must be given for the set of specified atoms. Normally this is the atom that touches the angle.

The rotation axis is determined by creating the cross product of the two bond vectors. Thus, getting the normal vector of a surface that contains both bond vectors.

Parameters:

bond_alist: First bond vector given as a list of two atom ids
bond_blist: Second bond vector given as a list of two atom ids
atomsinteger, list: List of atoms to be rotated (can also be one id)
anglefloat: Rotation angle
zerointeger: Atom id to define zero point of the new coordinate system

Examples

mol.part_angle([0, 1], [1, 2], [1, 2, 3], 90, 1)