disty = min(math.fabs(pcy-boty), math.fabs(pcy-topy))
distz = min(math.fabs(pcz-botz), math.fabs(pcz-topz))
#print min(distx, disty, distz), 2.0 * common.R
if (min(distx, disty, distz) > (2.0 * common.R)):
nanoparticles.append(nanop)
print >> sys.stderr, "Near done"
radius = {'O':0.60, 'Ti':1.40}
for selectedid in range(len(nanoparticles)):
nanop = nanoparticles[selectedid]
pcx, pcy, pcz = nanop.get_center()
nearnanop, neardst = nanoparticle.get_near_nanoparticle (nanoparticles, \
pcx, pcy, pcz, (2.0 * nanop.get_max_sphere()))
count = 1
for a in range(len(nearnanop)):
for b in range(len(nearnanop)):
if (a != b):
xlistnew, ylistnew, zlistnew = return_rototransl_xyz(nearnanop[a], xlist, ylist, zlist)
n = len(nearnanop)
print "running ", count , " of ", n**2-n
todo = False
xlistnewa = []
ylistnewa = []
zlistnewa = []
topx = max(scx)
topy = max(scy)
topz = max(scz)
if (botx >= topx) or (boty >= topy) or \
(boty >= topy):
print "Error Invalid BOX"
exit()
if (selected_nanaop >= len(scx)):
print "error invalid particle selected "
exit()
dist = 0.0
selected, distance = nanoparticle.get_near_nanoparticle(nanoparticles, \
scx[selected_nanaop], scy[selected_nanaop], \
scz[selected_nanaop], dist)
minbox_x = 100000.0
maxbox_x = -100000.0
minbox_y = 100000.0
maxbox_y = -100000.0
minbox_z = 100000.0
maxbox_z = -100000.0
i = 0
for nanop in selected:
cx, cy, cz = nanop.get_center()
A, B, H = nanop.get_dimensions()
#nanop.is_point_inside([cx, cy, cz+0.5])
