Scripts: dipole.py

from chimera import Point, openModels, Molecule, Vector, UserError

showVector = True  # change to "False" to hide dipole vector
vectorScale = 1  # may want to increase/decrease for better presentation

def centerOfMass(model):
        return Point([a.coord() for a in model.atoms],
                [a.element.mass for a in model.atoms])

# calculation method conscripted from:
#       A server and database for dipole moments of proteins
#       Nucleic Acids Res. 2007 Jul;35(Web Server issue):W512-21
#       doi:10.1093/nar/gkm307
for m in openModels.list(modelTypes=[Molecule]):
        com = centerOfMass(m)
        dipole = Vector()
        for a in m.atoms:
                try:
                        dipole += a.charge * (a.coord() - com)
                except AttributeError:
                        raise UserError("No charge assigned to %s" % a)
        # 4.803 is conversion factor to Debyes for angstrom measurements
        print "Dipole moment for %s %s: %.3f" % (m, m.name, 4.803 * dipole.length)
        if showVector:
                v = com + vectorScale * dipole
                bildString = ".arrow %g %g %g %g %g %g .1 .2 .9" % (
                        com[0], com[1], com[2], v[0], v[1], v[2])
                from StringIO import StringIO
                bild = StringIO(bildString)
                openModels.open(bild, type="Bild", identifyAs="%s dipole" % m.name, sameAs=m)