Scripts: closeatoms.py

# -----------------------------------------------------------------------------
# Draw lines between all pairs of selected atoms within a specified distance
# of each other.
#

def close_pairs(atoms, distance):
    pairs = []
    for i,a1 in enumerate(atoms):
        for a2 in atoms[i+1:]:
            d = a1.coord().distance(a2.coord())
            if d < distance:
                pairs.append((a1,a2))
    return pairs

def make_pseudobonds(atom_pairs):
    if len(atom_pairs) == 0:
        return
    from chimera import misc, OpenModels, Bond
    pg = misc.getPseudoBondGroup('closepairs', modelID = OpenModels.Default,
                                 hidden = False)
    pg.name = 'close pairs'
    for a1,a2 in atom_pairs:
        b = pg.newPseudoBond(a1,a2)
        b.drawMode = Bond.Stick
    return pg


from chimera import selection
atoms = selection.currentAtoms()
p = close_pairs(atoms, distance = 8)
make_pseudobonds(p)