Here is some test code for the cover bonds score state. I forgot to include it before.
Index: kernel/test/states/test_cover_bonds.py =================================================================== --- kernel/test/states/test_cover_bonds.py (revision 0) +++ kernel/test/states/test_cover_bonds.py (revision 0) @@ -0,0 +1,71 @@ +import unittest +import IMP +import IMP.test + +rk = IMP.FloatKey("radius") + +class TestBondCover(IMP.test.TestCase): + """Tests for BondCover""" + + def _set_up_stuff(self, n): + # return [model, particles, bonds] + m= IMP.Model() + ps= IMP.Particles() + for i in range(0,n): + p= IMP.Particle() + m.add_particle(p) + d= IMP.XYZDecorator.create(p) + d.randomize_in_box(IMP.Vector3D(0,0,0), + IMP.Vector3D(10,10,10)) + ps.append(p) + bds= [] + for i in range(1,n): + ba= IMP.BondedDecorator.create(ps[i-1]) + bb= IMP.BondedDecorator.create(ps[i]) + bds.append(IMP.custom_bond(ba, bb, 10, 1)) + bl= IMP.BondDecoratorListScoreState(ps) + ss= IMP.CoverBondsScoreState(bl, rk) + m.add_score_state(bl) + m.add_score_state(ss) + return [m, ps, bds] + + + + + def test_set_position(self): + """Make sure that bond cover coordinates are correct""" + IMP.set_log_level(IMP.VERBOSE) + [m,ps, bds]= self._set_up_stuff(10) + m.evaluate(False) + for b in bds: + b.get_particle().show() + ba= b.get_bonded(0) + bb= b.get_bonded(1) + da= IMP.XYZDecorator.cast(ba.get_particle()) + db= IMP.XYZDecorator.cast(bb.get_particle()) + dc= IMP.XYZDecorator.cast(b.get_particle()) + center= [(da.get_x()+ db.get_x()) /2.0, + (da.get_y()+ db.get_y()) /2.0, + (da.get_z()+ db.get_z()) /2.0] + r= ((center[0]- da.get_x())**2 + +(center[1]- da.get_y())**2 + +(center[2]- da.get_z())**2)**.5 + print r + print center + da.show() + db.show() + dc.show() + self.assertInTolerance(r, b.get_particle().get_value(rk), r*.1, + "Radius is not close enough") + self.assertInTolerance(center[0], dc.get_x(), .1, + "X is not close enough") + self.assertInTolerance(center[1], dc.get_y(), .1, + "Y is not close enough") + self.assertInTolerance(center[2], dc.get_z(), .1, + "Z is not close enough") + + + + +if __name__ == '__main__': + unittest.main()