def get_origin_translation(asu_prmtop_file_name, asu_rst7_file_name):
rst7 = raf.rst7(asu_rst7_file_name)
coords = rst7.Get_Coords()
UCbox = rst7.Get_Box()
u, invu = raf.CompXfrm(UCbox)
masses = raf.prmtop(asu_prmtop_file_name).Get_Masses()
com = raf.COM(coords, masses)
frac_com = dot(u, com)
origin_translation = array([0.5, 0.5, 0.5]) - frac_com
return u, origin_translation
op = 0
for line in symops.splitlines():
line = line.split('\'')[-1].split()
for i in range(3):
for j in range(3):
Rf[op][i][j] = line[i * 3 + j + 1]
try:
Tf[op][i] = float(line[((i * 2) - 1 + 11)]) / float(line[(
(i * 2) + 11)])
except ZeroDivisionError:
Tf[op][i] = 0.0
op += 1
pdbf = raf.pdb(pdbfile)
box = pdbf.Get_Box()
u, invu = raf.CompXfrm(box)
print "================================"
Tc = zeros(shape(Tf))
for i in range(numops):
Tc[i] = dot(invu, Tf[i]).astype(float32)
#~ print Tc
print "================================"
Rc = zeros(shape(Rf))
for i in range(numops):
Rc[i] = dot(dot(invu, Rf[i]), u)
#~ print Rc
print "================================"
for op in range(numops):
def get_U_invU(asu_rst7_file_name):
rst7 = Rst7.open(asu_rst7_file_name)
UCbox = rst7.box
U, invU = raf.CompXfrm(UCbox)
return U, invU, UCbox