def __init__(self, s):
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
self.type = r_info.type()
self.ev = r_info.ev()
self.trans = t_info.intrinsic_part()
def __init__(self, s ):
r_info = sgtbx.rot_mx_info( s.r() )
t_info = sgtbx.translation_part_info( s )
self.type = r_info.type()
self.ev = r_info.ev()
self.trans= t_info.intrinsic_part()
def rt_mx_analysis(s):
print "<tr>"
print "<td><tt>" + str(s) + "</tt>"
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
if (r_info.type() == 1):
print "<td>1<td>-<td>-<td>-"
elif (r_info.type() == -1):
print "<td>%d<td>-<td>-<td>%s" % (
r_info.type(),
str(t_info.origin_shift()))
elif (abs(r_info.type()) == 2):
print "<td>%d<td>%s<td>%s<td>%s" % (
r_info.type(),
str_ev(r_info.ev()),
str(t_info.intrinsic_part()),
str(t_info.origin_shift()))
else:
print "<td>%d^%d<td>%s<td>%s<td>%s" % (
r_info.type(),
r_info.sense(),
str_ev(r_info.ev()),
str(t_info.intrinsic_part()),
str(t_info.origin_shift()))
print "</tr>"
def change_origin(self, origin): o = self.raw_origin - origin t_l = self.one_minus_r*o t_l = sgtbx.tr_vec((sg_t_den*t_l).as_int(), tr_den=sg_t_den) self.rt = sgtbx.rt_mx(self.r, self.t_i.plus(t_l).new_denominator(sg_t_den)) tr_info = sgtbx.translation_part_info(self.rt) self.origin = tr_info.origin_shift() self.t_i = tr_info.intrinsic_part()
def change_origin(self, origin): o = self.raw_origin - origin t_l = self.one_minus_r*o t_l = sgtbx.tr_vec((sg_t_den*t_l).as_int(), tr_den=sg_t_den) self.rt = sgtbx.rt_mx(self.r, self.t_i.plus(t_l).new_denominator(sg_t_den)) tr_info = sgtbx.translation_part_info(self.rt) self.origin = tr_info.origin_shift() self.t_i = tr_info.intrinsic_part()
def browse(self):
for self.symbol in sgtbx.space_group_symbol_iterator():
self.sg = sgtbx.space_group(self.symbol.hall()).make_tidy()
self.z2p_op = self.sg.z2p_op()
self.sg_p = self.sg.change_basis(self.z2p_op)
self.on_new_space_group()
for self.op in self.sg_p:
self.rot_info = self.op.r().info()
self.tr_info = sgtbx.translation_part_info(self.op)
if self.tr_info.origin_shift().is_zero(): continue
self.on_new_symmetry()
def browse(self):
for self.symbol in sgtbx.space_group_symbol_iterator():
self.sg = sgtbx.space_group(self.symbol.hall()).make_tidy()
self.z2p_op = self.sg.z2p_op()
self.sg_p = self.sg.change_basis(self.z2p_op)
self.on_new_space_group()
for self.op in self.sg_p:
self.rot_info = self.op.r().info()
self.tr_info = sgtbx.translation_part_info(self.op)
if self.tr_info.origin_shift().is_zero(): continue
self.on_new_symmetry()
def rt_mx_analysis(s):
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
t_intrinsic = str(t_info.intrinsic_part().mod_positive())
t_shift = str(t_info.origin_shift().mod_positive())
if (r_info.type() == 1):
return ("1", "-", "-", "-")
if (r_info.type() == -1):
return (str(r_info.type()), "-", "-", "(%s)" % (t_shift, ))
if (abs(r_info.type()) == 2):
return (str(r_info.type()), str_ev(r_info.ev()),
"(%s)" % (t_intrinsic, ), "(%s)" % (t_shift, ))
return (str(r_info.type()), str_ev(r_info.ev()), "(%s)" % (t_intrinsic, ),
"(%s)" % (t_shift, ))
def rt_mx_analysis(s):
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
t_intrinsic = str(t_info.intrinsic_part().mod_positive())
t_shift = str(t_info.origin_shift().mod_positive())
if (r_info.type() == 1):
return ("1", "-", "-", "-")
if (r_info.type() == -1):
return (str(r_info.type()), "-", "-", "location=(%s)" % (t_shift, ))
if (abs(r_info.type()) == 2):
return (str(r_info.type()), "axis=" + str_ev(r_info.ev()),
"(%s)" % (t_intrinsic, ), "location=(%s)" % (t_shift, ))
sense = "+"
if (r_info.sense() < 0):
sense = "-"
return (str(r_info.type()) + sense, "axis=" + str_ev(r_info.ev()),
"(%s)" % (t_intrinsic, ), "location=(%s)" % (t_shift, ))
def rt_mx_analysis(s):
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
t_intrinsic = str(t_info.intrinsic_part().mod_positive())
t_shift = str(t_info.origin_shift().mod_positive())
if (r_info.type() == 1):
return ("1", "-", "-", "-")
if (r_info.type() == -1):
return (str(r_info.type()), "-", "-", "(%s)" % (t_shift,))
if (abs(r_info.type()) == 2):
return (str(r_info.type()),
str_ev(r_info.ev()),
"(%s)" % (t_intrinsic,),
"(%s)" % (t_shift,))
return (str(r_info.type()),
str_ev(r_info.ev()),
"(%s)" % (t_intrinsic,),
"(%s)" % (t_shift,))
def rt_mx_analysis(s):
print("<tr>")
print("<td><tt>" + str(s) + "</tt>")
r_info = sgtbx.rot_mx_info(s.r())
t_info = sgtbx.translation_part_info(s)
if (r_info.type() == 1):
print("<td>1<td>-<td>-<td>-")
elif (r_info.type() == -1):
print("<td>%d<td>-<td>-<td>%s" %
(r_info.type(), str(t_info.origin_shift())))
elif (abs(r_info.type()) == 2):
print("<td>%d<td>%s<td>%s<td>%s" %
(r_info.type(), str_ev(r_info.ev()), str(
t_info.intrinsic_part()), str(t_info.origin_shift())))
else:
print("<td>%d^%d<td>%s<td>%s<td>%s" %
(r_info.type(), r_info.sense(), str_ev(r_info.ev()),
str(t_info.intrinsic_part()), str(t_info.origin_shift())))
print("</tr>")
status.in_table = False
print
print "Additional generators of Euclidean normalizer:"
ss = sgtbx.structure_seminvariants(sg)
ss_vm = ss.vectors_and_moduli()
print " Number of structure-seminvariant vectors and moduli:", len(ss_vm)
if (len(ss_vm)):
print " Vector Modulus"
for vm in ss_vm: print " ", vm.v, vm.m
k2l = sg_type.addl_generators_of_euclidean_normalizer(True, False)
l2n = sg_type.addl_generators_of_euclidean_normalizer(False, True)
if (len(k2l)):
print " Inversion through a centre at:",
assert len(k2l) == 1
print sgtbx.translation_part_info(k2l[0]).origin_shift()
if (len(l2n)):
print " Further generators:"
print "</pre><table border=2 cellpadding=2>"
status.in_table = True
rt_mx_analysis_header()
for s in l2n: rt_mx_analysis(s)
print "</table><pre>"
status.in_table = False
print
print "Grid factors implied by symmetries:"
grid_sg = sg.gridding()
grid_ss = ss.gridding()
eucl_sg = sg_type.expand_addl_generators_of_euclidean_normalizer(True,True)
grid_eucl = eucl_sg.refine_gridding(grid_ss)
def run(server_info, inp, status):
print("<pre>")
symbols_inp = None
lookup_symbol = inp.sgsymbol
if (lookup_symbol == ""): lookup_symbol = "P 1"
if (inp.convention == "Hall"):
hall_symbol = lookup_symbol
else:
symbols_inp = sgtbx.space_group_symbols(lookup_symbol, inp.convention)
hall_symbol = symbols_inp.hall()
if (symbols_inp.number() == 0):
symbols_inp = None
inp.convention = "Hall"
else:
print("Result of symbol lookup:")
show_symbols(symbols_inp)
print()
try:
ps = sgtbx.parse_string(hall_symbol)
sg = sgtbx.space_group(ps)
except RuntimeError as e:
print("-->" + ps.string() + "<--")
print(("-" * (ps.where() + 3)) + "^")
raise
io_utils.show_input_symbol(inp.sgsymbol, inp.convention)
if (len(inp.shelx_latt) != 0):
for n_fld in inp.shelx_latt:
expand_shelx_latt(sg, n_fld)
if (len(inp.symxyz) != 0):
print("Addition of symmetry operations:")
print("</pre><table border=2 cellpadding=2>")
status.in_table = True
rt_mx_analysis_header()
for s in inp.symxyz:
ps = sgtbx.parse_string(s)
try:
s = sgtbx.rt_mx(ps)
except RuntimeError as e:
print("</table><pre>")
status.in_table = False
print("-->" + ps.string() + "<--")
print(("-" * (ps.where() + 3)) + "^")
raise
rt_mx_analysis(s)
sg.expand_smx(s)
print("</table><pre>")
status.in_table = False
print()
sg_type = sg.type()
show_group_generic(sg_type, status)
if (inp.convention == "Hall" or len(inp.shelx_latt) != 0
or len(inp.symxyz) != 0):
symbols_match = sg.match_tabulated_settings()
if (symbols_match.number() != 0):
if (symbols_inp is None or symbols_inp.universal_hermann_mauguin()
!= symbols_match.universal_hermann_mauguin()):
print("Symmetry operations match:")
show_symbols(symbols_match)
print()
else:
print("Additional symmetry operations are redundant.")
print()
else:
print("Space group number:", sg_type.number())
print("Conventional Hermann-Mauguin symbol:", \
sgtbx.space_group_symbols(sg_type.number()) \
.universal_hermann_mauguin())
print("Universal Hermann-Mauguin symbol:", \
sg_type.universal_hermann_mauguin_symbol())
print("Hall symbol:", sg_type.hall_symbol())
print("Change-of-basis matrix:", sg_type.cb_op().c())
print(" Inverse:", sg_type.cb_op().c_inv())
print()
wyckoff_table = sgtbx.wyckoff_table(sg_type)
print("List of Wyckoff positions:")
print("</pre><table border=2 cellpadding=2>")
status.in_table = True
print("<tr>")
print("<th>Wyckoff letter")
print("<th>Multiplicity")
print("<th>Site symmetry<br>point group type")
print("<th>Representative special position operator")
print("</tr>")
for i_position in range(wyckoff_table.size()):
position = wyckoff_table.position(i_position)
print("<tr>")
print("<td>%s<td>%d<td>%s<td><tt>%s</tt>" %
(position.letter(), position.multiplicity(),
position.point_group_type(),
str(position.special_op_simplified())))
print("</tr>")
print("</table><pre>")
status.in_table = False
print()
print("Harker planes:")
print("</pre><table border=2 cellpadding=2>")
status.in_table = True
print("<tr>")
print("<th>Algebraic")
print("<th>Normal vector")
print("<th>A point in the plane")
print("</tr>")
planes = harker.planes_fractional(sg)
for plane in planes.list:
print("<tr>")
print("<td><tt>%s</tt><td>%s<td>%s" %
(plane.algebraic(), str_ev(plane.n), str(plane.p)))
print("</tr>")
print("</table><pre>")
status.in_table = False
print()
print("Additional generators of Euclidean normalizer:")
ss = sgtbx.structure_seminvariants(sg)
ss_vm = ss.vectors_and_moduli()
print(" Number of structure-seminvariant vectors and moduli:", len(ss_vm))
if (len(ss_vm)):
print(" Vector Modulus")
for vm in ss_vm:
print(" ", vm.v, vm.m)
k2l = sg_type.addl_generators_of_euclidean_normalizer(True, False)
l2n = sg_type.addl_generators_of_euclidean_normalizer(False, True)
if (len(k2l)):
print(" Inversion through a centre at:", end=' ')
assert len(k2l) == 1
print(sgtbx.translation_part_info(k2l[0]).origin_shift())
if (len(l2n)):
print(" Further generators:")
print("</pre><table border=2 cellpadding=2>")
status.in_table = True
rt_mx_analysis_header()
for s in l2n:
rt_mx_analysis(s)
print("</table><pre>")
status.in_table = False
print()
print("Grid factors implied by symmetries:")
grid_sg = sg.gridding()
grid_ss = ss.gridding()
eucl_sg = sg_type.expand_addl_generators_of_euclidean_normalizer(
True, True)
grid_eucl = eucl_sg.refine_gridding(grid_ss)
print(" Space group:", grid_sg)
print(" Structure-seminvariant vectors and moduli:", grid_ss)
print(" Euclidean normalizer:", grid_eucl)
print()
print(" All points of a grid over the unit cell are mapped")
print(" exactly onto other grid points only if the factors")
print(" shown above are factors of the grid.")
print()
print("</pre>")
print
print "Additional generators of Euclidean normalizer:"
ss = sgtbx.structure_seminvariants(sg)
ss_vm = ss.vectors_and_moduli()
print " Number of structure-seminvariant vectors and moduli:", len(ss_vm)
if (len(ss_vm)):
print " Vector Modulus"
for vm in ss_vm:
print " ", vm.v, vm.m
k2l = sg_type.addl_generators_of_euclidean_normalizer(True, False)
l2n = sg_type.addl_generators_of_euclidean_normalizer(False, True)
if (len(k2l)):
print " Inversion through a centre at:",
assert len(k2l) == 1
print sgtbx.translation_part_info(k2l[0]).origin_shift()
if (len(l2n)):
print " Further generators:"
print "</pre><table border=2 cellpadding=2>"
status.in_table = True
rt_mx_analysis_header()
for s in l2n:
rt_mx_analysis(s)
print "</table><pre>"
status.in_table = False
print
print "Grid factors implied by symmetries:"
grid_sg = sg.gridding()
grid_ss = ss.gridding()
eucl_sg = sg_type.expand_addl_generators_of_euclidean_normalizer(
def rlc_RTMxAnalysis(M):
r_info = sgtbx.rot_mx_info(M.r())
t_info = sgtbx.translation_part_info(M)
t_intrinsic = t_info.intrinsic_part().mod_positive().as_double()
t_shift = t_info.origin_shift().mod_positive().as_double()
#End = list_plus(Start + map(None,r_info.ev()))
####debug
### trans = 0
### length = 0
####debug
#if (r_info.type() == 1):
if (r_info.type() < 2):
#(rt, start, end) = ('1',(0,0,0),(0,0,0))
return None
#elif (r_info.type() == -1):
# (rt, start, end) = (str(r_info.type()),t_shift,())
elif (abs(r_info.type()) == 2):
trans = reduce(lambda x,y:x+y,t_intrinsic)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r)))
#(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type())+"^1",t_shift,tuple(list_plus(t_shift,r)))
#(rt, start, end) = (str(r_info.type())+"^1",t_shift,tuple(list_plus(t_shift,r_info.ev())))
elif (r_info.type() == 3):
if (r_info.sense() >= 0) :
# ignore opposite sense of rotation axes since they superimpose
trans = N.sqrt(reduce(lambda x,y:x+y,(map(lambda x,y:(y-x)*(y-x),(0,0,0),t_intrinsic))))
# trans = N.sqrt(t_intrinsic[0]**2 + t_intrinsic[1]**2 + t_intrinsic[2]**2)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
# fudge to make sure that PyMOL actually draws the axis (move it slightly off [1,-1,1]) !!!
r[0] = r[0]*1.000001
(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r)))
#(rt, start, end) = (str(r_info.type()),t_shift, tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
#(rt, start, end) = (str(r_info.type())+ "^" + subscript ,t_shift,tuple(list_plus(t_shift,r)))
(start, end) = (t_shift,tuple(list_plus(t_shift,r)))
length = N.sqrt(reduce(lambda x,y:x+y,(map(lambda x,y:(y-x)*(y-x),start, end))))
# r_info.sense() for 3^1 and 3^2 seems always to be "1" ???
# if r_info.sense() < 0:
# subscript = str(1-r_info.sense())
# else:
# subscript = str(r_info.sense())
# use ratio of trans to length to get the correct axis symbol:
# fudged the value to get the right numbers. (using length/2., rather than length/3.)
if trans < length*0.5 :
subscript = '1'
else:
subscript = '2'
rt = str(r_info.type())+ "^" + subscript
#(rt, start, end) = (str(r_info.type()) + "^" + subscript,t_shift, tuple(list_plus(t_shift,r_info.ev())))
### print "Type, sense, Start, End, length, trans", rt, r_info.sense(), start, end, length, trans
# print "type: %s, sense: %s, trans: %s, length: %s," % (r_info.type(), r_info.sense(), trans, length)
# print "(rt, start, end)", (rt,start,end)
else:
return None
#return (r_info.type(),r_info.ev(), t_intrinsic, t_shift)
elif (r_info.sense() > 0):
# ignore opposite sense of rotation axes since they superimpose
trans = reduce(lambda x,y:x+y,t_intrinsic)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r)))
#(rt, start, end) = (str(r_info.type()),t_shift, tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x)/maxr for x in r_info.ev()]
subscript = str(int(trans*r_info.type()+.5)) # add 0.5 to fix rounding errors
(rt, start, end) = (str(r_info.type())+ "^" + subscript ,t_shift,tuple(list_plus(t_shift,r)))
#(rt, start, end) = (str(r_info.type()) + "^" + subscript,t_shift, tuple(list_plus(t_shift,r_info.ev())))
#return (r_info.type(),r_info.ev(), t_intrinsic, t_shift)
else:
return None
# print "type: %s, sense: %s, trans: %s, length: %s," % (r_info.type(), r_info.sense(), trans, length),
# print "(rt, start, end)", (rt,start,end)
return (rt, start, end)
def __init__(self,symop): self.symop = symop # an instance of rt_mx from cctbx import sgtbx self.r_info = sgtbx.rot_mx_info(self.symop.r()) self.t_info = sgtbx.translation_part_info(self.symop)
def rlc_RTMxAnalysis(M):
r_info = sgtbx.rot_mx_info(M.r())
t_info = sgtbx.translation_part_info(M)
t_intrinsic = t_info.intrinsic_part().mod_positive().as_double()
t_shift = t_info.origin_shift().mod_positive().as_double()
#End = list_plus(Start + map(None,r_info.ev()))
####debug
### trans = 0
### length = 0
####debug
#if r_info.type() == 1:
if r_info.type() < 2:
#(rt, start, end) = ('1',(0,0,0),(0,0,0))
return None
#elif r_info.type() == -1:
# (rt, start, end) = (str(r_info.type()),t_shift,())
elif abs(r_info.type()) == 2:
trans = sum(t_intrinsic)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type()), t_shift,
tuple(list_plus(t_shift, r)))
#(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type()) + "^1", t_shift,
tuple(list_plus(t_shift, r)))
#(rt, start, end) = (str(r_info.type())+"^1",t_shift,tuple(list_plus(t_shift,r_info.ev())))
elif r_info.type() == 3:
if r_info.sense() >= 0:
# ignore opposite sense of rotation axes since they superimpose
trans = N.sqrt(
sum((map(lambda x, y: (y - x) * (y - x), (0, 0, 0),
t_intrinsic))))
# trans = N.sqrt(t_intrinsic[0]**2 + t_intrinsic[1]**2 + t_intrinsic[2]**2)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
# fudge to make sure that PyMOL actually draws the axis (move it slightly off [1,-1,1]) !!!
r[0] = r[0] * 1.000001
(rt, start, end) = (str(r_info.type()), t_shift,
tuple(list_plus(t_shift, r)))
#(rt, start, end) = (str(r_info.type()),t_shift, tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
#(rt, start, end) = (str(r_info.type())+ "^" + subscript ,t_shift,tuple(list_plus(t_shift,r)))
(start, end) = (t_shift, tuple(list_plus(t_shift, r)))
length = N.sqrt(
sum((map(lambda x, y: (y - x) * (y - x), start, end))))
# r_info.sense() for 3^1 and 3^2 seems always to be "1" ???
# if r_info.sense() < 0:
# subscript = str(1-r_info.sense())
# else:
# subscript = str(r_info.sense())
# use ratio of trans to length to get the correct axis symbol:
# fudged the value to get the right numbers. (using length/2., rather than length/3.)
if trans < length * 0.5:
subscript = '1'
else:
subscript = '2'
rt = str(r_info.type()) + "^" + subscript
#(rt, start, end) = (str(r_info.type()) + "^" + subscript,t_shift, tuple(list_plus(t_shift,r_info.ev())))
### print "Type, sense, Start, End, length, trans", rt, r_info.sense(), start, end, length, trans
# print "type: %s, sense: %s, trans: %s, length: %s," % (r_info.type(), r_info.sense(), trans, length)
# print "(rt, start, end)", (rt,start,end)
else:
return None
#return (r_info.type(),r_info.ev(), t_intrinsic, t_shift)
elif r_info.sense() > 0:
# ignore opposite sense of rotation axes since they superimpose
trans = sum(t_intrinsic)
if trans == 0:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
(rt, start, end) = (str(r_info.type()), t_shift,
tuple(list_plus(t_shift, r)))
#(rt, start, end) = (str(r_info.type()),t_shift, tuple(list_plus(t_shift,r_info.ev())))
else:
maxr = max([abs(x) for x in r_info.ev()])
r = [float(x) / maxr for x in r_info.ev()]
subscript = str(int(trans * r_info.type() +
.5)) # add 0.5 to fix rounding errors
(rt, start, end) = (str(r_info.type()) + "^" + subscript, t_shift,
tuple(list_plus(t_shift, r)))
#(rt, start, end) = (str(r_info.type()) + "^" + subscript,t_shift, tuple(list_plus(t_shift,r_info.ev())))
#return (r_info.type(),r_info.ev(), t_intrinsic, t_shift)
else:
return None
# print "type: %s, sense: %s, trans: %s, length: %s," % (r_info.type(), r_info.sense(), trans, length),
# print "(rt, start, end)", (rt,start,end)
return (rt, start, end)
def __init__(self, symop):
self.symop = symop # an instance of rt_mx
from cctbx import sgtbx
self.r_info = sgtbx.rot_mx_info(self.symop.r())
self.t_info = sgtbx.translation_part_info(self.symop)
