addAtom (
        name,
        element,
        residue,
        loc,
        serialNumber=None,
        bondedTo=None,
        )

Add an atom at the Point loc

The atom is added to the given residue (and its molecule). loc can be a sequence of Points if there are multiple coordinate sets.

bondedTo is None or an Atom. If an Atom, then the new atom inherits various attributes from that atom and a bond to that Atom is created.

Returns the new atom.

findPt (
        n1,
        n2,
        n3,
        dist,
        angle,
        dihed,
        )

addDihedralAtom (
        name,
        element,
        n1,
        n2,
        n3,
        dist,
        angle,
        dihed,
        molecule=None,
        residue=None,
        bonded=False,
        )

Add an atom given 3 Atoms/Points and angle/distance constraints

The atom is added to the given molecule. If no molecule or residue is specified, then n1/n2/n3 must be Atoms and the new atom is added to n1's molecule and residue. If just residue is specified, the new atom is added to that residue and its molecule.

n1 marks the position from which dist is measure, and in combination with n2 forms angle, and then with n3 forms dihed.

if bonded is True then n1 must be an Atom and the new atom will be bonded to it.

Returns the new atom.

addBond (
        a1,
        a2,
        drawMode=None,
        halfbond=None,
        color=None,
        )

genAtomName ( element,  residue )