Scripts: placeatom.py

# -----------------------------------------------------------------------------
# Place a new atom some distance past a specified atom along a ray from the
# center of mass of the molecule.
#
def place_atom(near_atom, distance, element,
               atom_name, residue_name, residue_number):

    m = near_atom.molecule
    
    d = near_atom.coord() - center_of_mass(m)  # Vector from center to atom
    d.normalize()

    xyz = near_atom.coord() + distance*d

    from chimera import MolResId
    a = m.newAtom(atom_name, element)
    r = m.newResidue(residue_name, MolResId(residue_number))
    r.addAtom(a)

    a.setCoord(xyz)            # Set atom coordinates
    a.drawMode = a.Sphere     # Set display style to sphere

# -----------------------------------------------------------------------------
#
def center_of_mass(molecule):

    from Measure.inertia import atoms_inertia
    c = atoms_inertia(molecule.atoms)[2]       # Center of mass coordinates
    from chimera import Point
    p = Point(*c)
    # Transform from global coordinates to molecule coordinate system.
    pm = molecule.openState.xform.inverse().apply(p)

    return pm

# -----------------------------------------------------------------------------
# Place a helium atom 2A past a selected atom along a ray from the center of
# mass of the molecule.
#
from chimera import selection
atoms = selection.currentAtoms()
if len(atoms) != 1:
    from chimera.replyobj import error
    error("Need to select exactly one atom")
else:
    from chimera import elements
    place_atom(atoms[0], 2, elements.He, 'X', 'R1', 1000)