#
# This MMTK/Python script is used to position a set of "Lego"-block like
# molecules as described in my paper for MNT6.
# writtern by Peter McCluskey (pcm@rahul.net)
#

from mmtk import *
import sys
import Units
import Positioner
from ConfigIO import *

ff = GenericForceField('mm3')
world = InfiniteUniverse(ff)

result = load('result.lego7.sav')

def rotate3(alist, dir):
    if dir == 0: return alist
    if dir == 120: return [alist[2]] + alist[0:2]
    return alist[1:3] + [alist[0]]	# dir is -120

world.addObject(result)
obj_list = [result]

poslist = [(120, 'hole2', 'knob1'),\
	   (-120, 'knob2', 'hole1'),\
	   (120, 'hole2', 'knob1'),\
	   (-120, 'knob2', 'hole1'),\
	   (120, 'hole2', 'knob1')]
for (dir, end1, end2) in poslist:
    obj1 = obj_list[-1]
    molecule2 = load('result.lego7.sav')
    obj2 = molecule2
    if end1[0:4] == 'knob':
	attach2 = getattr(obj2, end2)
	attach1 = rotate3(getattr(obj1, end1), dir)
    else:
	attach1 = getattr(obj1, end1)
	attach2 = rotate3(getattr(obj2, end2), dir)
    PositionAdjacent(obj1, attach1, obj2, attach2, [2*Units.Ang]*3)
    world.addObject(molecule2)
    obj_list.append(molecule2)

save(world,'legoworld.mmtk')

import RasMol
ras_session = RasMol.RasMol(world, 1)
ras_session.Interact()

from ConfigIO import OutputFile
fmt = OutputFile('PDB/legoworld.pdb', 'pdb.connect')
fmt.write(world)
fmt.close()