def exercise():
space_group = "P1"
unit_cell = "100,100,100,90,90,90"
symmetry = unit_cell + "," + space_group
sp_space_group = " P 1 "
sp_symmetry = unit_cell + "," + sp_space_group
killer = "100,P1"
killer2 = space_group + "," + unit_cell
killer3 = "100 100 100 90 90 90"
killer4 = killer3 + " " + sp_space_group
cs = crystal_symmetry_from_any.from_string(space_group)
assert (cs is not None)
assert (cs.unit_cell() is None)
assert (str(cs.space_group_info()) == 'P 1')
cs = crystal_symmetry_from_any.from_string(unit_cell)
assert (cs is not None)
assert (cs.unit_cell().parameters() == (100.0, 100.0, 100.0, 90.0, 90.0,
90.0))
assert (cs.space_group_info() is None)
cs = crystal_symmetry_from_any.from_string(symmetry)
assert (cs is not None)
assert (cs.unit_cell().parameters() == (100.0, 100.0, 100.0, 90.0, 90.0,
90.0))
assert (str(cs.space_group_info()) == 'P 1')
cs = crystal_symmetry_from_any.from_string(sp_space_group)
assert (cs is not None)
assert (cs.unit_cell() is None)
assert (str(cs.space_group_info()) == 'P 1')
cs = crystal_symmetry_from_any.from_string(sp_symmetry)
assert (cs is not None)
assert (cs.unit_cell().parameters() == (100.0, 100.0, 100.0, 90.0, 90.0,
90.0))
assert (str(cs.space_group_info()) == 'P 1')
cs = crystal_symmetry_from_any.from_string(killer)
assert (cs is None)
cs = crystal_symmetry_from_any.from_string(killer2)
assert (cs is None)
cs = crystal_symmetry_from_any.from_string(killer3)
assert (cs is None)
cs = crystal_symmetry_from_any.from_string(killer4)
assert (cs is None)
print("OK")
def get_fake_symmetry(xyz_min, xyz_max):
from iotbx import crystal_symmetry_from_any
a = xyz_max[0] - xyz_min[0] + 10.0
b = xyz_max[1] - xyz_min[1] + 10.0
c = xyz_max[2] - xyz_min[2] + 10.0
combined = "%.3f,%.3f,%.3f,90,90,90,P1" % (a, b, c)
symm = crystal_symmetry_from_any.from_string(combined)
return symm
def get_fake_symmetry (xyz_min, xyz_max) : from iotbx import crystal_symmetry_from_any a = xyz_max[0] - xyz_min[0] + 10.0 b = xyz_max[1] - xyz_min[1] + 10.0 c = xyz_max[2] - xyz_min[2] + 10.0 combined = "%.3f,%.3f,%.3f,90,90,90,P1" % (a, b, c) symm = crystal_symmetry_from_any.from_string(combined) return symm
def generate_p1_box(pdb_hierarchy, buffer=10.0): sites_cart = pdb_hierarchy.atoms().extract_xyz() xyz_max = sites_cart.max() a = xyz_max[0] + buffer b = xyz_max[1] + buffer c = xyz_max[2] + buffer combined = "%.3f,%.3f,%.3f,90,90,90,P1" % (a, b, c) symm = crystal_symmetry_from_any.from_string(combined) return symm
def generate_p1_box (pdb_hierarchy, buffer=10.0) : sites_cart = pdb_hierarchy.atoms().extract_xyz() xyz_max = sites_cart.max() a = xyz_max[0] + buffer b = xyz_max[1] + buffer c = xyz_max[2] + buffer combined = "%.3f,%.3f,%.3f,90,90,90,P1" % (a, b, c) symm = crystal_symmetry_from_any.from_string(combined) return symm
def exercise(): space_group = "P1" unit_cell = "100,100,100,90,90,90" symmetry = unit_cell+","+space_group sp_space_group = " P 1 " sp_symmetry = unit_cell+","+sp_space_group killer="100,P1" killer2=space_group+","+unit_cell killer3="100 100 100 90 90 90" killer4=killer3+" "+sp_space_group cs = crystal_symmetry_from_any.from_string(space_group) assert(cs is not None) assert(cs.unit_cell() is None) assert(str(cs.space_group_info())=='P 1') cs = crystal_symmetry_from_any.from_string(unit_cell) assert(cs is not None) assert(cs.unit_cell().parameters()==(100.0,100.0,100.0,90.0,90.0,90.0)) assert(cs.space_group_info() is None) cs = crystal_symmetry_from_any.from_string(symmetry) assert(cs is not None) assert(cs.unit_cell().parameters()==(100.0,100.0,100.0,90.0,90.0,90.0)) assert(str(cs.space_group_info())=='P 1') cs = crystal_symmetry_from_any.from_string(sp_space_group) assert(cs is not None) assert(cs.unit_cell() is None) assert(str(cs.space_group_info())=='P 1') cs = crystal_symmetry_from_any.from_string(sp_symmetry) assert(cs is not None) assert(cs.unit_cell().parameters()==(100.0,100.0,100.0,90.0,90.0,90.0)) assert(str(cs.space_group_info())=='P 1') cs = crystal_symmetry_from_any.from_string(killer) assert(cs is None) cs = crystal_symmetry_from_any.from_string(killer2) assert(cs is None) cs = crystal_symmetry_from_any.from_string(killer3) assert(cs is None) cs = crystal_symmetry_from_any.from_string(killer4) assert(cs is None) print "OK"
