from mmtk import *
import string

ff = AmberForceField()
world = InfiniteUniverse(ff)
layer = Group('kaehler_a_layer')
join = Joiner(layer)
join.joinGroups(layer.hookup, layer.hookdown)
join.joinGroups(join.getIntermediateResult().hookup, layer.hookdown)
join.joinGroups(join.getIntermediateResult().hookup, layer.hookdown)
join.joinGroups(join.getIntermediateResult().hookup, layer.hookdown)
result = join.getResult()
try:
    result.setPositions(ff)
except ConformationError, msg:
    print 'ConformationError',msg

world.group = result
#minimizer = ConjugateGradientMinimizer(world, log = (0, None, 50, stdout,
#						     ("energy",)))
#minimizer(convergence = 1.e-3, steps = 25)
world.removeObject(result)


hpairs = [[result.findAtomByName('kaehler_a_layer.kaehler_a_layer1.H4'),\
	   result.findAtomByName('kaehler_a_layer.kaehler_a_layer2.H5')],\
	  [result.findAtomByName('kaehler_a_layer.kaehler_a_layer1.H6'),\
	   result.findAtomByName('kaehler_a_layer.kaehler_a_layer2.H1')],\
	  [result.findAtomByName('kaehler_a_layer.kaehler_a_layer2.H2'),\
	   result.findAtomByName('kaehler_a_layer.kaehler_a_layer3.H3')],\
	  [result.findAtomByName('kaehler_a_layer.kaehler_a_layer2.H4'),\
	   result.findAtomByName('kaehler_a_layer.kaehler_a_layer3.H5')],\
  'kaehler_a_layer.kaehler_a_layer2.H3','kaehler_a_layer.kaehler_a_layer2.H6',\
  'kaehler_a_layer.kaehler_a_layer1.C2','kaehler_a_layer.kaehler_a_layer3.C1']
print hpairs
oxygens = [result.generateNewAtom('O'), result.generateNewAtom('O'),\
	   result.generateNewAtom('O'), result.generateNewAtom('O'),\
	   result.generateNewAtom('F'), result.generateNewAtom('F'),\
	   result.generateNewAtom('Si'), result.generateNewAtom('Si')]

result.replaceAtoms(hpairs, oxygens)

result.calcDanglingBonds(ff)
result.positionDanglingBonds(ff)
result.labelDanglingBonds()

world.group = result

#save(result,'resultk.mmtk')
from ConfigIO import OutputFile
fmt = OutputFile('PDB/resultk.pdb')
fmt.write(result)
fmt.close()

if 1:
    import RasMol
    ras_session = RasMol.RasMol(result, 1)
    ras_session.RefreshScreen()
    ras_session.Interact()