def exercise_02():
xs = [0, 0, 0]
ys = [0, 0, 0]
zs = [0, 0, 0]
for pdb_str in [pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]:
print(pdb_str)
for t in [
[0.05, 0.07, 0.09],
]:
tx, ty, tz = t
for x in range(3):
for y in range(3):
for z in range(3):
if (x != y and x != z and y != z):
xs_ = xs[:]
ys_ = ys[:]
zs_ = zs[:]
xs_[x] = 1
ys_[y] = 1
zs_[z] = 1
tools.u_tls_vs_u_ens(pdb_str=pdb_str,
tx=tx,
ty=ty,
tz=tz,
vx=xs_,
vy=ys_,
vz=zs_,
n_models=1000)
print()
def exercise_00():
xs = [0, 0, 0]
ys = [0, 0, 0]
zs = [0, 0, 0]
for pdb_str in [pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]:
print pdb_str
for d in [
[0.05, 0.06, 0.07],
]:
dx, dy, dz = d
for x in xrange(3):
for y in xrange(3):
for z in xrange(3):
if (x != y and x != z and y != z):
xs_ = xs[:]
ys_ = ys[:]
zs_ = zs[:]
xs_[x] = 1
ys_[y] = 1
zs_[z] = 1
tools.u_tls_vs_u_ens(pdb_str=pdb_str,
dx=dx,
dy=dy,
dz=dz,
sx=0.5,
sy=0.4,
sz=0.3,
lx=xs_,
ly=ys_,
lz=zs_)
print
def exercise_03():
sqrt = math.sqrt
vs = []
vs.append( [(sqrt(2)/2, sqrt(2)/2, 0), (-sqrt(2)/2, sqrt(2)/2, 0), (0,0,1)] )
vs.append( [(1,0,0), (0, sqrt(2)/2, sqrt(2)/2), (0, -sqrt(2)/2, sqrt(2)/2)] )
vs.append( [(sqrt(3)/2, 1/2, 0), (-1/2, sqrt(3)/2, 0), (0,0,1)] )
vs.append( [(1,0,0), (0, sqrt(3)/2, 1/2), (0, -1/2, sqrt(3)/2)] )
for pdb_str in [pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]:
for vs_ in vs:
vx,vy,vz = vs_
print vx,vy,vz
tools.u_tls_vs_u_ens(pdb_str=pdb_str,
tx=0.05,ty=0.07,tz=0.09,
vx=vx, vy=vy, vz=vz,
n_models=1000)
def exercise_01():
sqrt = math.sqrt
ls = []
ls.append( [(sqrt(2)/2, sqrt(2)/2, 0), (-sqrt(2)/2, sqrt(2)/2, 0), (0,0,1)] )
ls.append( [(1,0,0), (0, sqrt(2)/2, sqrt(2)/2), (0, -sqrt(2)/2, sqrt(2)/2)] )
ls.append( [(sqrt(3)/2, 1/2, 0), (-1/2, sqrt(3)/2, 0), (0,0,1)] )
ls.append( [(1,0,0), (0, sqrt(3)/2, 1/2), (0, -1/2, sqrt(3)/2)] )
for pdb_str in [pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]:
for ls_ in ls:
lx,ly,lz = ls_
print lx,ly,lz
tools.u_tls_vs_u_ens(pdb_str=pdb_str,
dx=0.05,dy=0.06,dz=0.07,
sx=0.5, sy=0.4, sz=0.3,
lx=lx, ly=ly, lz=lz)
def exercise_00(pdb_str, formula):
"""
TLS group 6 of 4muy.
"""
pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str)
pdb_hierarchy = pdb_inp.construct_hierarchy()
asc = pdb_hierarchy.atom_selection_cache()
cs = pdb_inp.crystal_symmetry_from_cryst1()
tls_extract = mmtbx.tls.tools.tls_from_pdb_inp(
remark_3_records = pdb_inp.extract_remark_iii_records(3),
pdb_hierarchy = pdb_hierarchy)
#
deg_to_rad_scale = math.pi/180
tls_params_one_group = tls_extract.tls_params[0]
T = matrix.sym(sym_mat3=tls_params_one_group.t)
L = matrix.sym(sym_mat3=tls_params_one_group.l)
S = matrix.sqr(tls_params_one_group.s)
origin = tls_params_one_group.origin
tlso = tools.tlso(
t = T.as_sym_mat3(),
l = L.as_sym_mat3(),
s = S,
origin = origin)
log = open("analysis.log","w")
r = analysis.run(T=T, L=L*(deg_to_rad_scale**2), S=S*deg_to_rad_scale,
log=log, find_t_S_using_formula=formula).self_check(show=False)
log.close()
#
rs = flex.double()
for trial in xrange(10):
o = tools.u_tls_vs_u_ens(pdb_str=pdb_str,
dx = r.dx,
dy = r.dy,
dz = r.dz,
sx = r.sx,
sy = r.sy,
sz = r.sz,
lx = r.l_x,
ly = r.l_y,
lz = r.l_z,
tx = r.tx,
ty = r.ty,
tz = r.tz,
vx = r.v_x,
vy = r.v_y,
vz = r.v_z,
w_M_lx = r.w_M_lx,
w_M_ly = r.w_M_ly,
w_M_lz = r.w_M_lz,
origin = origin,
n_models = 10000,
assert_similarity=False)
rs.append(o.r)
return flex.mean(rs)
def exercise_03():
sqrt = math.sqrt
vs = []
vs.append([(sqrt(2) / 2, sqrt(2) / 2, 0), (-sqrt(2) / 2, sqrt(2) / 2, 0),
(0, 0, 1)])
vs.append([(1, 0, 0), (0, sqrt(2) / 2, sqrt(2) / 2),
(0, -sqrt(2) / 2, sqrt(2) / 2)])
vs.append([(sqrt(3) / 2, 1 / 2, 0), (-1 / 2, sqrt(3) / 2, 0), (0, 0, 1)])
vs.append([(1, 0, 0), (0, sqrt(3) / 2, 1 / 2), (0, -1 / 2, sqrt(3) / 2)])
for pdb_str in [pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]:
for vs_ in vs:
vx, vy, vz = vs_
print(vx, vy, vz)
tools.u_tls_vs_u_ens(pdb_str=pdb_str,
tx=0.05,
ty=0.07,
tz=0.09,
vx=vx,
vy=vy,
vz=vz,
n_models=1000)
def exercise_00():
xs=[0,0,0]
ys=[0,0,0]
zs=[0,0,0]
for pdb_str in [pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]:
print pdb_str
for d in [[0.05,0.06,0.07], ]:
dx,dy,dz = d
for x in xrange(3):
for y in xrange(3):
for z in xrange(3):
if(x!=y and x!=z and y!=z):
xs_ = xs[:]
ys_ = ys[:]
zs_ = zs[:]
xs_[x]=1
ys_[y]=1
zs_[z]=1
tools.u_tls_vs_u_ens(pdb_str=pdb_str,
dx=dx,dy=dy,dz=dz, sx=0.5,sy=0.4,sz=0.3, lx=xs_,ly=ys_,lz=zs_)
print
def exercise_04():
sqrt = math.sqrt
ls = []
ls.append( [(sqrt(2)/2, sqrt(2)/2, 0), (-sqrt(2)/2, sqrt(2)/2, 0), (0,0,1)] )
ls.append( [(1,0,0), (0, sqrt(2)/2, sqrt(2)/2), (0, -sqrt(2)/2, sqrt(2)/2)] )
ls.append( [(sqrt(3)/2, 1/2, 0), (-1/2, sqrt(3)/2, 0), (0,0,1)] )
ls.append( [(1,0,0), (0, sqrt(3)/2, 1/2), (0, -1/2, sqrt(3)/2)] )
vs = ls[:]
vs.reverse()
for pdb_str in [pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]:
for ls_, vs_ in zip(ls,vs):
lx,ly,lz = ls_
vx,vy,vz = vs_
print lx,ly,lz
print vx,vy,vz
tools.u_tls_vs_u_ens(pdb_str=pdb_str,
dx=0.05,dy=0.06,dz=0.07,
sx=0.3, sy=0.2, sz=0.1,
lx=lx, ly=ly, lz=lz,
tx=0.06,ty=0.08,tz=0.09,
vx=vx, vy=vy, vz=vz,
w_M_lx=[0.1,0.2,0.3], w_M_ly=[-0.4,-0.3,-0.1], w_M_lz=[-0.2,0.1,0.3])
def exercise_02():
xs=[0,0,0]
ys=[0,0,0]
zs=[0,0,0]
for pdb_str in [pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]:
print pdb_str
for t in [[0.05,0.07,0.09], ]:
tx,ty,tz = t
for x in xrange(3):
for y in xrange(3):
for z in xrange(3):
if(x!=y and x!=z and y!=z):
xs_ = xs[:]
ys_ = ys[:]
zs_ = zs[:]
xs_[x]=1
ys_[y]=1
zs_[z]=1
tools.u_tls_vs_u_ens(pdb_str=pdb_str,
tx=tx,ty=ty,tz=tz, vx=xs_,vy=ys_,vz=zs_,
n_models=1000)
print
def exercise_01():
sqrt = math.sqrt
ls = []
ls.append([(sqrt(2) / 2, sqrt(2) / 2, 0), (-sqrt(2) / 2, sqrt(2) / 2, 0),
(0, 0, 1)])
ls.append([(1, 0, 0), (0, sqrt(2) / 2, sqrt(2) / 2),
(0, -sqrt(2) / 2, sqrt(2) / 2)])
ls.append([(sqrt(3) / 2, 1 / 2, 0), (-1 / 2, sqrt(3) / 2, 0), (0, 0, 1)])
ls.append([(1, 0, 0), (0, sqrt(3) / 2, 1 / 2), (0, -1 / 2, sqrt(3) / 2)])
for pdb_str in [pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]:
for ls_ in ls:
lx, ly, lz = ls_
print(lx, ly, lz)
tools.u_tls_vs_u_ens(pdb_str=pdb_str,
dx=0.05,
dy=0.06,
dz=0.07,
sx=0.5,
sy=0.4,
sz=0.3,
lx=lx,
ly=ly,
lz=lz)
def exercise_04():
sqrt = math.sqrt
ls = []
ls.append([(sqrt(2) / 2, sqrt(2) / 2, 0), (-sqrt(2) / 2, sqrt(2) / 2, 0),
(0, 0, 1)])
ls.append([(1, 0, 0), (0, sqrt(2) / 2, sqrt(2) / 2),
(0, -sqrt(2) / 2, sqrt(2) / 2)])
ls.append([(sqrt(3) / 2, 1 / 2, 0), (-1 / 2, sqrt(3) / 2, 0), (0, 0, 1)])
ls.append([(1, 0, 0), (0, sqrt(3) / 2, 1 / 2), (0, -1 / 2, sqrt(3) / 2)])
vs = ls[:]
vs.reverse()
for pdb_str in [pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]:
for ls_, vs_ in zip(ls, vs):
lx, ly, lz = ls_
vx, vy, vz = vs_
print lx, ly, lz
print vx, vy, vz
tools.u_tls_vs_u_ens(pdb_str=pdb_str,
dx=0.05,
dy=0.06,
dz=0.07,
sx=0.3,
sy=0.2,
sz=0.1,
lx=lx,
ly=ly,
lz=lz,
tx=0.06,
ty=0.08,
tz=0.09,
vx=vx,
vy=vy,
vz=vz,
w_M_lx=[0.1, 0.2, 0.3],
w_M_ly=[-0.4, -0.3, -0.1],
w_M_lz=[-0.2, 0.1, 0.3])