from mmtk import *

ff = AmberForceField()
block1 = Group('diamond111')
oh = Group('hydroxyl')
width = 39
height = 5
join = Joiner(block1)
join.repeatGroup('hookeast', 'hookwest', width)
join.repeatGroup('hooksouth', 'hooknorth', height)
join.repeatGroup('hookup', 'hookdown', 2)
result = join.getResult()

base_name = result.name
import gd
im_out=gd.image((2*width,2*height))
red = im_out.colorAllocate((255,0,0))
green = im_out.colorAllocate((0,255,0))
blue = im_out.colorAllocate((0,0,255))
im_out.string(gd.gdFontSmall, (0,0), 'Hello, world!', blue)
(maxx,maxy) = im_out.size()
count = 0
join = Joiner(result)
for y in range(maxy):
    for x in range(maxx):
	if im_out.getPixel((x,y)) > 0:
	    (xd, xm) = divmod(x, 2)
	    (yd, ym) = divmod(y, 2)
	    block_index = xd + yd*width
	    bond_index = ym + 2*xm
	    import os
	    pipe = os.popen("free")
	    print 'Free:',pipe.read()
	    print pipe.read()
	    print pipe.read()
	    print pipe.read()
	    if bond_index == 3:
		h2 = Hook((result, [result.hookup_extra[block_index][0]]))
	    else:
		h2 = Hook((result, [result.hookup[block_index][bond_index]]))
	    join.joinGroups(h2, oh.hook1, 0)
	    result = join.getIntermediateResult()
	    count = count + 1
	    result.name = '%s_%d' % (base_name,count)
result = join.getResult()
result.setPositions(ff)
result.hydrogenateDanglingBonds(ff)

#save(result,'resulthello.mmtk')
from ConfigIO import OutputFile
fmt = OutputFile('PDB/result_hello1.pdb', 'pdb.connect')
fmt.write(result)
fmt.close()

view(result)