Molecule.add¶

Molecule.add(atom_type, pos, bond=[], r=0, theta=0, phi=0, is_deg=True, name='', residue=0)¶

Add a new atom in polar coordinates. The pos input is either an atom id, that determines is the bond-start, or a vector for a specific position.

If the polar coordinates are dependent on a bond vector as an axis, the bond variable must be set. The coordinate system is then transformed to the bond axis. If this variable is set to an empty list, then the given coordinates are assumed to be dependent on the z-axis.

Parameters:

atom_typestring: Atom type
posinteger, list: Position of the atom
bondlist, optional: Bond axis
rfloat, optional: Bond length
thetafloat, optional: Azimuthal angle
phifloat, optional: Polar angle
is_degbool, optional: True if the input of the angles in degree
namestring, optional: Optionally set a unique atom name
residueinteger, optional: Residue number

Examples

mol.add("C", [0, 0, 0])
mol.add("C", 0, r=0.153, theta=-135)
mol.add("C", 1, [0, 1], r=0.153, theta= 135)