def space_group_symbol(space_group):
symbol = ccp4_symbol(space_group.info(),
lib_name="syminfo.lib",
require_at_least_one_lib=False)
if symbol != "P 1":
symbol = symbol.replace(" 1", "")
symbol = symbol.replace(" ", "")
return symbol
def space_group_symbol(space_group):
symbol = ccp4_symbol(space_group.info(),
lib_name='syminfo.lib',
require_at_least_one_lib=False)
if symbol != 'P 1':
symbol = symbol.replace(' 1', '')
symbol = symbol.replace(' ', '')
return symbol
def exercise_230():
for space_group_number in range(1, 231):
space_group_info = sgtbx.space_group_info(number=space_group_number,
table_id="A1983")
symbol = extract_from_symmetry_lib.ccp4_symbol(
space_group_info=space_group_info, lib_name="symop.lib")
if (symbol[0] == "H"):
symbol = "R" + symbol[1:] + ":H"
assert sgtbx.space_group_info(
symbol=symbol,
table_id="A1983").group() == space_group_info.group()
#
symbol = extract_from_symmetry_lib.ccp4_symbol(
space_group_info=space_group_info, lib_name="syminfo.lib")
if (symbol[0] == "H"):
symbol = "R" + symbol[1:] + ":H"
assert sgtbx.space_group_info(
symbol=symbol,
table_id="A1983").group() == space_group_info.group()
def build_ccp4_symmetry_table():
symbol_to_number = {}
ccp4_to_number = {}
# Open file
file_iter = open(op.join(
extract_from_symmetry_lib.ccp4io_lib_data, "symop.lib"))
ccp4_id_counts = libtbx.dict_with_default_0()
ccp4_symbol_counts = libtbx.dict_with_default_0()
# Run through the file
for line in file_iter:
# print "\n", line.rstrip()
flds = line.split(None, 4)
ccp4_id = flds[0]
ccp4_id_counts[ccp4_id] += 1
space_group_number = int(ccp4_id[-3:])
order_z = int(flds[1])
given_ccp4_symbol = flds[3]
symbol_to_number[given_ccp4_symbol] = space_group_number
ccp4_symbol_counts[given_ccp4_symbol] += 1
group = extract_from_symmetry_lib.collect_symops(
file_iter=file_iter, order_z=order_z)
assert group.order_z() == order_z
space_group_info = sgtbx.space_group_info(group=group)
retrieved_ccp4_symbol = extract_from_symmetry_lib.ccp4_symbol(
space_group_info=space_group_info,
lib_name="symop.lib")
# print "retrieved_ccp4_symbol", retrieved_ccp4_symbol
assert retrieved_ccp4_symbol == given_ccp4_symbol
assert space_group_info.type().number() == space_group_number
if (1):
from iotbx.pdb import format_cryst1_sgroup
sgroup = format_cryst1_sgroup(space_group_info=space_group_info)
# if (len(sgroup) > 11):
# print "ccp4 symop.lib setting leads to pdb CRYST1 overflow:",\
# ccp4_id, given_ccp4_symbol, sgroup
# print "sgroup", sgroup
ccp4_to_number[sgroup] = space_group_number
# for ccp4_id,count in ccp4_id_counts.items():
# if (count != 1):
# raise RuntimeError(
# 'ccp4 id "%s" appears %d times (should be unique).'
# % (ccp4_id, count))
# ccp4_symbol_counts = libtbx.dict_with_default_0()
# for ccp4_symbol,count in ccp4_symbol_counts.items():
# if (count != 1):
# raise RuntimeError(
# 'ccp4 symbol "%s" appears %d times (should be unique).'
# % (ccp4_symbol, count))
return (symbol_to_number, ccp4_to_number)
def build_ccp4_symmetry_table():
symbol_to_number = {}
ccp4_to_number = {}
# Open file
file_iter = open(
op.join(extract_from_symmetry_lib.ccp4io_lib_data, "symop.lib"))
ccp4_id_counts = libtbx.dict_with_default_0()
ccp4_symbol_counts = libtbx.dict_with_default_0()
# Run through the file
for line in file_iter:
# print "\n", line.rstrip()
flds = line.split(None, 4)
ccp4_id = flds[0]
ccp4_id_counts[ccp4_id] += 1
space_group_number = int(ccp4_id[-3:])
order_z = int(flds[1])
given_ccp4_symbol = flds[3]
symbol_to_number[given_ccp4_symbol] = space_group_number
ccp4_symbol_counts[given_ccp4_symbol] += 1
group = extract_from_symmetry_lib.collect_symops(file_iter=file_iter,
order_z=order_z)
assert group.order_z() == order_z
space_group_info = sgtbx.space_group_info(group=group)
retrieved_ccp4_symbol = extract_from_symmetry_lib.ccp4_symbol(
space_group_info=space_group_info, lib_name="symop.lib")
# print "retrieved_ccp4_symbol", retrieved_ccp4_symbol
assert retrieved_ccp4_symbol == given_ccp4_symbol
assert space_group_info.type().number() == space_group_number
if (1):
from iotbx.pdb import format_cryst1_sgroup
sgroup = format_cryst1_sgroup(space_group_info=space_group_info)
# if (len(sgroup) > 11):
# print "ccp4 symop.lib setting leads to pdb CRYST1 overflow:",\
# ccp4_id, given_ccp4_symbol, sgroup
# print "sgroup", sgroup
ccp4_to_number[sgroup] = space_group_number
# for ccp4_id,count in ccp4_id_counts.items():
# if (count != 1):
# raise RuntimeError(
# 'ccp4 id "%s" appears %d times (should be unique).'
# % (ccp4_id, count))
# ccp4_symbol_counts = libtbx.dict_with_default_0()
# for ccp4_symbol,count in ccp4_symbol_counts.items():
# if (count != 1):
# raise RuntimeError(
# 'ccp4 symbol "%s" appears %d times (should be unique).'
# % (ccp4_symbol, count))
return (symbol_to_number, ccp4_to_number)
def exercise_230():
for space_group_number in xrange(1,231):
space_group_info = sgtbx.space_group_info(
number=space_group_number,
table_id="A1983")
symbol = extract_from_symmetry_lib.ccp4_symbol(
space_group_info=space_group_info,
lib_name="symop.lib")
if (symbol[0] == "H"):
symbol = "R" + symbol[1:] + ":H"
assert sgtbx.space_group_info(
symbol=symbol,
table_id="A1983").group() == space_group_info.group()
#
symbol = extract_from_symmetry_lib.ccp4_symbol(
space_group_info=space_group_info,
lib_name="syminfo.lib")
if (symbol[0] == "H"):
symbol = "R" + symbol[1:] + ":H"
assert sgtbx.space_group_info(
symbol=symbol,
table_id="A1983").group() == space_group_info.group()
def set_space_group_info(self, space_group_info, symbol=None):
if (symbol is None):
symbol = extract_from_symmetry_lib.ccp4_symbol(
space_group_info=space_group_info,
lib_name="symop.lib")
if (symbol is None):
symbol = "No.%d" % space_group_info.type().number()
group = space_group_info.group()
self.set_space_group_name(name=symbol)
self.set_space_group_number(number=space_group_info.type().number())
self.set_point_group_name(name=group.point_group_type())
self.set_lattice_centring_type(
symbol=group.conventional_centring_type_symbol())
if (self.lattice_centring_type() == "\0"):
self.set_lattice_centring_type(symbol="?")
self.set_space_group(space_group=space_group_info.group())
return self
def exercise_symop_lib_recycling():
file_iter = open(
op.join(extract_from_symmetry_lib.ccp4io_lib_data, "symop.lib"))
ccp4_id_counts = libtbx.dict_with_default_0()
ccp4_symbol_counts = libtbx.dict_with_default_0()
for line in file_iter:
flds = line.split(None, 4)
ccp4_id = flds[0]
ccp4_id_counts[ccp4_id] += 1
space_group_number = int(ccp4_id[-3:])
order_z = int(flds[1])
given_ccp4_symbol = flds[3]
ccp4_symbol_counts[given_ccp4_symbol] += 1
group = extract_from_symmetry_lib.collect_symops(file_iter=file_iter,
order_z=order_z)
assert group.order_z() == order_z
space_group_info = sgtbx.space_group_info(group=group)
retrieved_ccp4_symbol = extract_from_symmetry_lib.ccp4_symbol(
space_group_info=space_group_info, lib_name="symop.lib")
assert retrieved_ccp4_symbol == given_ccp4_symbol
assert space_group_info.type().number() == space_group_number
if (1):
from iotbx.pdb import format_cryst1_sgroup
sgroup = format_cryst1_sgroup(space_group_info=space_group_info)
if (len(sgroup) > 11):
print("ccp4 symop.lib setting leads to pdb CRYST1 overflow:",\
ccp4_id, given_ccp4_symbol, sgroup)
file_iter.close()
for ccp4_id, count in ccp4_id_counts.items():
if (count != 1):
raise RuntimeError(
'ccp4 id "%s" appears %d times (should be unique).' %
(ccp4_id, count))
ccp4_symbol_counts = libtbx.dict_with_default_0()
for ccp4_symbol, count in ccp4_symbol_counts.items():
if (count != 1):
raise RuntimeError(
'ccp4 symbol "%s" appears %d times (should be unique).' %
(ccp4_symbol, count))
def exercise_syminfo_lib_pdb_cryst1_recycling():
# this call is to build _syminfo_lib_cache
assert extract_from_symmetry_lib.ccp4_symbol(
space_group_info=sgtbx.space_group_info("P 1"),
lib_name="syminfo.lib") == "P 1"
#
import iotbx.pdb.cryst1_interpretation
n_need_more_special = 0
for number in range(1, 230 + 1):
for hall,ccp4_symbol in \
extract_from_symmetry_lib._syminfo_lib_cache[number]:
sgi_hall = sgtbx.space_group_info(symbol="Hall: " + hall)
if (sgi_hall.group().is_centric()):
continue
sgroup = iotbx.pdb.format_cryst1_sgroup(space_group_info=sgi_hall)
if (len(sgroup) > 11):
print("ccp4 syminfo.lib setting leads to pdb CRYST1 overflow:",\
ccp4_symbol, sgroup)
cs = sgi_hall.any_compatible_crystal_symmetry(volume=1000)
pdb_str = iotbx.pdb.format_cryst1_record(crystal_symmetry=cs)
cs2 = iotbx.pdb.cryst1_interpretation.crystal_symmetry(
cryst1_record=pdb_str)
if (cs2.space_group_info() is None):
if (n_need_more_special == 0): print()
print('"%s": "Hall: %s",' %
(ccp4_symbol.replace(" ", "").upper(), hall))
n_need_more_special += 1
else:
assert cs2.is_similar_symmetry(other=cs)
if (ccp4io_adaptbx is not None):
exercise_mmdb_cryst1_interpretation(sgi_hall=sgi_hall,
pdb_str=pdb_str)
if (n_need_more_special != 0):
print()
from libtbx.utils import plural_s
raise RuntimeError("""\
Please edit iotbx/pdb/cryst1_interpretation.py:
Add the %d line%s above with "Hall:" to the "special" dictionary.
""" % plural_s(n_need_more_special))
def exercise_symop_lib_recycling():
file_iter = open(op.join(
extract_from_symmetry_lib.ccp4io_lib_data, "symop.lib"))
ccp4_id_counts = libtbx.dict_with_default_0()
ccp4_symbol_counts = libtbx.dict_with_default_0()
for line in file_iter:
flds = line.split(None, 4)
ccp4_id = flds[0]
ccp4_id_counts[ccp4_id] += 1
space_group_number = int(ccp4_id[-3:])
order_z = int(flds[1])
given_ccp4_symbol = flds[3]
ccp4_symbol_counts[given_ccp4_symbol] += 1
group = extract_from_symmetry_lib.collect_symops(
file_iter=file_iter, order_z=order_z)
assert group.order_z() == order_z
space_group_info = sgtbx.space_group_info(group=group)
retrieved_ccp4_symbol = extract_from_symmetry_lib.ccp4_symbol(
space_group_info=space_group_info,
lib_name="symop.lib")
assert retrieved_ccp4_symbol == given_ccp4_symbol
assert space_group_info.type().number() == space_group_number
if (1):
from iotbx.pdb import format_cryst1_sgroup
sgroup = format_cryst1_sgroup(space_group_info=space_group_info)
if (len(sgroup) > 11):
print "ccp4 symop.lib setting leads to pdb CRYST1 overflow:",\
ccp4_id, given_ccp4_symbol, sgroup
for ccp4_id,count in ccp4_id_counts.items():
if (count != 1):
raise RuntimeError(
'ccp4 id "%s" appears %d times (should be unique).'
% (ccp4_id, count))
ccp4_symbol_counts = libtbx.dict_with_default_0()
for ccp4_symbol,count in ccp4_symbol_counts.items():
if (count != 1):
raise RuntimeError(
'ccp4 symbol "%s" appears %d times (should be unique).'
% (ccp4_symbol, count))
def exercise_syminfo_lib_pdb_cryst1_recycling():
# this call is to build _syminfo_lib_cache
assert extract_from_symmetry_lib.ccp4_symbol(
space_group_info=sgtbx.space_group_info("P 1"),
lib_name="syminfo.lib") == "P 1"
#
import iotbx.pdb.cryst1_interpretation
n_need_more_special = 0
for number in xrange(1,230+1):
for hall,ccp4_symbol in \
extract_from_symmetry_lib._syminfo_lib_cache[number]:
sgi_hall = sgtbx.space_group_info(symbol="Hall: "+hall)
if (sgi_hall.group().is_centric()):
continue
sgroup = iotbx.pdb.format_cryst1_sgroup(space_group_info=sgi_hall)
if (len(sgroup) > 11):
print "ccp4 syminfo.lib setting leads to pdb CRYST1 overflow:",\
ccp4_symbol, sgroup
cs = sgi_hall.any_compatible_crystal_symmetry(volume=1000)
pdb_str = iotbx.pdb.format_cryst1_record(crystal_symmetry=cs)
cs2 = iotbx.pdb.cryst1_interpretation.crystal_symmetry(
cryst1_record=pdb_str)
if (cs2.space_group_info() is None):
if (n_need_more_special == 0): print
print '"%s": "Hall: %s",' % (
ccp4_symbol.replace(" ", "").upper(), hall)
n_need_more_special += 1
else:
assert cs2.is_similar_symmetry(other=cs)
if (ccp4io_adaptbx is not None):
exercise_mmdb_cryst1_interpretation(
sgi_hall=sgi_hall, pdb_str=pdb_str)
if (n_need_more_special != 0):
print
from libtbx.utils import plural_s
raise RuntimeError("""\
Please edit iotbx/pdb/cryst1_interpretation.py:
Add the %d line%s above with "Hall:" to the "special" dictionary.
""" % plural_s(n_need_more_special))
def write_par_file(file_name, experiment):
from scitbx import matrix
from dxtbx.model.crystal import crystal_model
from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
from iotbx.mtz.extract_from_symmetry_lib import ccp4_symbol
imageset = experiment.imageset
detector = imageset.get_detector()
goniometer = imageset.get_goniometer()
beam = imageset.get_beam()
scan = imageset.get_scan()
R_to_mosflm = align_reference_frame(
beam.get_s0(), (1.0, 0.0, 0.0),
goniometer.get_rotation_axis(), (0.0, 0.0, 1.0))
cryst = experiment.crystal
cryst = cryst.change_basis(
cryst.get_space_group().info()\
.change_of_basis_op_to_reference_setting())
A = cryst.get_A()
A_inv = A.inverse()
real_space_a = R_to_mosflm * A_inv.elems[:3]
real_space_b = R_to_mosflm * A_inv.elems[3:6]
real_space_c = R_to_mosflm * A_inv.elems[6:9]
cryst_mosflm = crystal_model(
real_space_a, real_space_b, real_space_c,
space_group=cryst.get_space_group(),
mosaicity=cryst.get_mosaicity())
A_mosflm = cryst_mosflm.get_A()
U_mosflm = cryst_mosflm.get_U()
B_mosflm = cryst_mosflm.get_B()
UB_mosflm = U_mosflm * B_mosflm
uc_params = cryst_mosflm.get_unit_cell().parameters()
assert U_mosflm.is_r3_rotation_matrix(), U_mosflm
symmetry = cryst_mosflm.get_space_group().type().number()
beam_centre = tuple(reversed(detector[0].get_beam_centre(beam.get_s0())))
distance = detector[0].get_directed_distance()
polarization = R_to_mosflm * matrix.col(beam.get_polarization_normal())
rotation = matrix.col(goniometer.get_rotation_axis())
if (rotation.angle(matrix.col(detector[0].get_fast_axis())) <
rotation.angle(matrix.col(detector[0].get_slow_axis()))):
direction = 'FAST'
else:
direction = 'SLOW'
rotation = R_to_mosflm * rotation
with open(file_name, 'wb') as f:#
print >> f, '# parameter file for BEST'
print >> f, 'TITLE From DIALS'
print >> f, 'DETECTOR PILA'
print >> f, 'SITE Not set'
print >> f, 'DIAMETER %6.2f' %(max(detector[0].get_image_size()) * detector[0].get_pixel_size()[0])
print >> f, 'PIXEL %s' %detector[0].get_pixel_size()[0]
print >> f, 'ROTAXIS %4.2f %4.2f %4.2f' %rotation.elems, direction
print >> f, 'POLAXIS %4.2f %4.2f %4.2f' %polarization.elems
print >> f, 'GAIN 1.00' # correct for Pilatus images
print >> f, 'CMOSAIC %.2f' %experiment.profile.sigma_m()
print >> f, 'PHISTART %.2f' %scan.get_oscillation_range()[0]
print >> f, 'PHIWIDTH %.2f' %scan.get_oscillation()[1]
print >> f, 'DISTANCE %7.2f' %distance
print >> f, 'WAVELENGTH %.5f' %beam.get_wavelength()
print >> f, 'POLARISATION %7.5f' %beam.get_polarization_fraction()
print >> f, 'SYMMETRY %s' %ccp4_symbol(
cryst.get_space_group().info(), lib_name='syminfo.lib',
require_at_least_one_lib=False).replace(' ', '')
print >> f, 'UB %9.6f %9.6f %9.6f' %UB_mosflm[:3]
print >> f, ' %9.6f %9.6f %9.6f' %UB_mosflm[3:6]
print >> f, ' %9.6f %9.6f %9.6f' %UB_mosflm[6:]
print >> f, 'CELL %8.2f %8.2f %8.2f %6.2f %6.2f %6.2f' %uc_params
print >> f, 'RASTER 13 13 7 3 4'
print >> f, 'SEPARATION 2.960 2.960'
print >> f, 'BEAM %8.3f %8.3f' %beam_centre
print >> f, '# end of parameter file for BEST'
