def exercise_cif_show():
cif_model = iotbx.cif.reader(input_string=input_1ab1).model()
builder = pdb_hierarchy_builder(cif_model["1AB1"])
hierarchy = builder.hierarchy
h_cif = hierarchy.as_cif_block()
builder = pdb_hierarchy_builder(h_cif) # this runs OK, why?
# output h_cif:
s = StringIO()
h_cif.show(out=s, align_columns=False)
builder = pdb_hierarchy_builder(h_cif) # Now it fails.
def exercise_fp_fdp():
input_anom = """\
data_anom
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.auth_asym_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.pdbx_formal_charge
_atom_site.phenix_scat_dispersion_real
_atom_site.phenix_scat_dispersion_imag
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_model_num
ATOM 47 CA . THR C 22 ? -7.12300 19.28700 -2.26800 1.000 8.32783 C ? . . B ? 11 1
ATOM 52 CA . ASN C 25 ? -11.06500 18.97000 -5.48100 1.000 8.20531 C ? . . C ? 12 1
ATOM 60 CA . VAL C 26 ? -12.16900 22.54800 -4.78000 1.000 8.45988 C ? . . C ? 13 1
HETATM 77 O . HOH S 204 ? -17.67100 15.07700 -3.15900 1.000 42.45569 O ? . . F ? 25 1
HETATM 78 CD . CD X 2 ? -14.09500 16.40900 -0.84100 1.000 5.03844 CD 2+ -0.1491 2.6871 G ? 26 1
HETATM 79 CL . CL Y 3 ? -16.37400 16.89900 -0.28500 1.000 9.96655 CL 1- 0.1114 0.3776 H ? 27 1
"""
pdb_in = iotbx.pdb.input(lines=(input_anom).splitlines(), source_info=None)
pdb_hierarchy = pdb_in.construct_hierarchy()
pdb_atoms = pdb_hierarchy.atoms()
assert approx_equal(pdb_atoms.extract_fp(), [0, 0, 0, 0, -0.1491, 0.1114])
assert approx_equal(pdb_atoms.extract_fdp(), [0, 0, 0, 0, 2.6871, 0.3776])
pdb_atoms[-1].fp = 0
pdb_atoms[-1].fdp = 0
cif_block = pdb_hierarchy.as_cif_block(
crystal_symmetry=pdb_in.crystal_symmetry())
assert "_atom_site.phenix_scat_dispersion_real" in cif_block
assert "_atom_site.phenix_scat_dispersion_imag" in cif_block
assert list(cif_block["_atom_site.phenix_scat_dispersion_real"]) == \
['.', '.', '.', '.', '-0.1491', '.']
assert list(cif_block["_atom_site.phenix_scat_dispersion_imag"]) == \
['.', '.', '.', '.', '2.6871', '.']
builder = pdb_hierarchy_builder(cif_block)
pdb_hierarchy_recycled = builder.hierarchy
pdb_atoms_recycled = pdb_hierarchy_recycled.atoms()
assert approx_equal(pdb_atoms_recycled.extract_fp(),
[0, 0, 0, 0, -0.1491, 0])
assert approx_equal(pdb_atoms_recycled.extract_fdp(),
[0, 0, 0, 0, 2.6871, 0])
def exercise_fp_fdp():
input_anom = """\
data_anom
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.auth_asym_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.pdbx_formal_charge
_atom_site.phenix_scat_dispersion_real
_atom_site.phenix_scat_dispersion_imag
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_model_num
ATOM 47 CA . THR C 22 ? -7.12300 19.28700 -2.26800 1.000 8.32783 C ? . . B ? 11 1
ATOM 52 CA . ASN C 25 ? -11.06500 18.97000 -5.48100 1.000 8.20531 C ? . . C ? 12 1
ATOM 60 CA . VAL C 26 ? -12.16900 22.54800 -4.78000 1.000 8.45988 C ? . . C ? 13 1
HETATM 77 O . HOH S 204 ? -17.67100 15.07700 -3.15900 1.000 42.45569 O ? . . F ? 25 1
HETATM 78 CD . CD X 2 ? -14.09500 16.40900 -0.84100 1.000 5.03844 CD 2+ -0.1491 2.6871 G ? 26 1
HETATM 79 CL . CL Y 3 ? -16.37400 16.89900 -0.28500 1.000 9.96655 CL 1- 0.1114 0.3776 H ? 27 1
"""
pdb_in = iotbx.pdb.input(lines=(input_anom).splitlines(), source_info=None)
pdb_hierarchy = pdb_in.construct_hierarchy()
pdb_atoms = pdb_hierarchy.atoms()
assert approx_equal(pdb_atoms.extract_fp(), [0, 0, 0, 0, -0.1491, 0.1114])
assert approx_equal(pdb_atoms.extract_fdp(), [0, 0, 0, 0, 2.6871, 0.3776])
pdb_atoms[-1].fp = 0
pdb_atoms[-1].fdp = 0
cif_block = pdb_hierarchy.as_cif_block(
crystal_symmetry=pdb_in.crystal_symmetry())
assert "_atom_site.phenix_scat_dispersion_real" in cif_block
assert "_atom_site.phenix_scat_dispersion_imag" in cif_block
assert list(cif_block["_atom_site.phenix_scat_dispersion_real"]) == \
['.', '.', '.', '.', '-0.1491', '.']
assert list(cif_block["_atom_site.phenix_scat_dispersion_imag"]) == \
['.', '.', '.', '.', '2.6871', '.']
builder = pdb_hierarchy_builder(cif_block)
pdb_hierarchy_recycled = builder.hierarchy
pdb_atoms_recycled = pdb_hierarchy_recycled.atoms()
assert approx_equal(
pdb_atoms_recycled.extract_fp(), [0, 0, 0, 0, -0.1491, 0])
assert approx_equal(
pdb_atoms_recycled.extract_fdp(), [0, 0, 0, 0, 2.6871, 0])
def exercise_pdb_hierachy_builder():
cif_model = iotbx.cif.reader(input_string=input_1ab1).model()
builder = pdb_hierarchy_builder(cif_model["1AB1"])
#assert builder.crystal_symmetry is None
hierarchy = builder.hierarchy
atoms = hierarchy.atoms()
assert atoms[0].segid == " " # some code relies on this
s = StringIO()
hierarchy.show(out=s)
assert not show_diff(
s.getvalue(), """\
model id="" #chains=1
chain id="A" #residue_groups=2
resid=" 2 " #atom_groups=3
altloc="" resname="THR" #atoms=4
" C "
" O "
" H "
" HA "
altloc="A" resname="THR" #atoms=8
" CA "
" CB "
" OG1"
" CG2"
" HB "
"HG21"
"HG22"
"HG23"
altloc="B" resname="THR" #atoms=8
" CA "
" CB "
" OG1"
" CG2"
" HB "
"HG21"
"HG22"
"HG23"
resid=" 66 " #atom_groups=2
altloc="A" resname="EOH" #atoms=3
" C1 "
" C2 "
" O "
altloc="B" resname="EOH" #atoms=3
" C1 "
" C2 "
" O "
""")
cif_block = hierarchy.as_cif_block()
builder = pdb_hierarchy_builder(cif_block)
hierarchy_recycled = builder.hierarchy
s1 = StringIO()
hierarchy_recycled.show(out=s1)
assert not show_diff(s.getvalue(), s1.getvalue())
#
input_missing_mandatory_items = """\
data_1AB1
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.occupancy
_atom_site.B_iso_or_equiv
ATOM 17 C A THR A 1 2 0.70 2.98
ATOM 18 C B THR A 1 2 0.30 5.01
ATOM 19 C . THR A 1 2 1.00 2.92
ATOM 20 O . THR A 1 2 1.00 3.70
"""
cif_model = iotbx.cif.reader(
input_string=input_missing_mandatory_items).model()
try:
pdb_hierarchy_builder(cif_model["1AB1"])
except AssertionError as e:
pass
else:
# TODO: raise a better error here
raise Exception_expected
input_4edr = """\
data_4EDR
_cell.length_a 150.582
_cell.length_b 150.582
_cell.length_c 38.633
_cell.angle_alpha 90.000
_cell.angle_beta 90.000
_cell.angle_gamma 120.000
#
_symmetry.space_group_name_H-M 'P 61'
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 1 N N . SER A 1 1 21.138 -69.073 17.360 1.00 23.68 108 SER A N 1
ATOM 2 C CA . SER A 1 1 22.164 -68.793 18.358 1.00 22.98 108 SER A CA 1
ATOM 3 C C . SER A 1 1 23.173 -67.799 17.805 1.00 21.13 108 SER A C 1
ATOM 4 O O . SER A 1 1 23.251 -67.594 16.595 1.00 19.34 108 SER A O 1
ATOM 5 C CB . SER A 1 1 22.882 -70.080 18.766 1.00 22.68 108 SER A CB 1
ATOM 6 O OG . SER A 1 1 23.683 -70.569 17.703 1.00 24.00 108 SER A OG 1
HETATM 2650 MN MN . MN F 4 . 9.296 -44.783 -6.320 1.00 44.18 505 MN A MN 1
#
loop_
_atom_site_anisotrop.id
_atom_site_anisotrop.type_symbol
_atom_site_anisotrop.pdbx_label_atom_id
_atom_site_anisotrop.pdbx_label_alt_id
_atom_site_anisotrop.pdbx_label_comp_id
_atom_site_anisotrop.pdbx_label_asym_id
_atom_site_anisotrop.pdbx_label_seq_id
_atom_site_anisotrop.U[1][1]
_atom_site_anisotrop.U[2][2]
_atom_site_anisotrop.U[3][3]
_atom_site_anisotrop.U[1][2]
_atom_site_anisotrop.U[1][3]
_atom_site_anisotrop.U[2][3]
1 N N . SER A 1 0.4097 0.2916 0.1984 0.1130 0.0328 0.0375
2 C CA . SER A 1 0.4035 0.2848 0.1847 0.1242 0.0297 0.0347
3 C C . SER A 1 0.3744 0.2637 0.1648 0.1278 0.0215 0.0258
4 O O . SER A 1 0.3494 0.2393 0.1463 0.1236 0.0185 0.0236
5 C CB . SER A 1 0.4085 0.2738 0.1795 0.1267 0.0311 0.0373
6 O OG . SER A 1 0.4276 0.2843 0.1998 0.1252 0.0273 0.0344
"""
cif_model = iotbx.cif.reader(input_string=input_4edr).model()
cif_block = cif_model["4EDR"]
builder = pdb_hierarchy_builder(cif_block)
assert approx_equal(builder.crystal_symmetry.unit_cell().parameters(),
(150.582, 150.582, 38.633, 90, 90, 120))
assert builder.crystal_symmetry.space_group_info().symbol_and_number() == \
'P 61 (No. 169)'
hierarchy = builder.hierarchy
s = StringIO()
hierarchy.show(out=s)
assert not show_diff(
s.getvalue(), """\
model id="" #chains=1
chain id="A" #residue_groups=2
resid=" 108 " #atom_groups=1
altloc="" resname="SER" #atoms=6
" N "
" CA "
" C "
" O "
" CB "
" OG "
resid=" 505 " #atom_groups=1
altloc="" resname="MN" #atoms=1
"MN "
""")
cif_block = hierarchy.as_cif_block(
crystal_symmetry=builder.crystal_symmetry)
assert "_space_group_symop.operation_xyz" in cif_block
assert "_cell.length_a" in cif_block
builder = pdb_hierarchy_builder(cif_block)
hierarchy_recycled = builder.hierarchy
s1 = StringIO()
hierarchy_recycled.show(out=s1)
assert not show_diff(s.getvalue(), s1.getvalue())
for hierarchy in (hierarchy, hierarchy_recycled):
residue_group = next(hierarchy.residue_groups())
assert residue_group.resseq == ' 108'
assert residue_group.resseq_as_int() == 108
atoms = hierarchy.atoms()
assert atoms[0].serial == ' 1'
assert atoms[0].name == ' N '
assert atoms[0].b == 23.68
assert atoms[0].uij_is_defined()
assert approx_equal(atoms[0].uij,
(0.4097, 0.2916, 0.1984, 0.113, 0.0328, 0.0375))
assert atoms[1].serial == ' 2'
assert atoms[1].name == ' CA '
assert atoms[1].b == 22.98
assert atoms[1].uij_is_defined()
assert approx_equal(atoms[1].uij,
(0.4035, 0.2848, 0.1847, 0.1242, 0.0297, 0.0347))
assert not atoms[6].uij_is_defined()
assert atoms[6].serial == ' 2650'
assert atoms[6].name == 'MN '
assert atoms[6].b == 44.18
assert approx_equal(atoms[6].uij, (-1, -1, -1, -1, -1, -1))
#
input_1ezu = """\
data_1EZU
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 3422 N N . GLY C 2 164 ? -25.713 -9.765 41.937 1.00 38.56 584 GLY C N 1
ATOM 3423 C CA . GLY C 2 164 ? -27.027 -9.485 41.364 1.00 38.07 584 GLY C CA 1
ATOM 3424 C C . GLY C 2 164 ? -27.645 -10.541 40.476 1.00 35.83 584 GLY C C 1
ATOM 3425 O O . GLY C 2 164 ? -27.554 -11.745 40.752 1.00 35.99 584 GLY C O 1
ATOM 3426 N N . PHE C 2 165 A -28.265 -10.093 39.385 1.00 34.13 584 PHE C N 1
ATOM 3427 C CA . PHE C 2 165 A -28.937 -11.016 38.471 1.00 36.09 584 PHE C CA 1
ATOM 3428 C C . PHE C 2 165 A -28.697 -10.685 37.018 1.00 36.74 584 PHE C C 1
ATOM 3429 O O . PHE C 2 165 A -28.853 -9.536 36.627 1.00 39.19 584 PHE C O 1
ATOM 3430 C CB . PHE C 2 165 A -30.444 -10.982 38.748 1.00 35.84 584 PHE C CB 1
ATOM 3431 C CG . PHE C 2 165 A -30.802 -11.298 40.174 1.00 39.04 584 PHE C CG 1
ATOM 3432 C CD1 . PHE C 2 165 A -30.914 -10.282 41.119 1.00 39.32 584 PHE C CD1 1
ATOM 3433 C CD2 . PHE C 2 165 A -30.983 -12.614 40.579 1.00 36.86 584 PHE C CD2 1
ATOM 3434 C CE1 . PHE C 2 165 A -31.203 -10.572 42.458 1.00 35.08 584 PHE C CE1 1
ATOM 3435 C CE2 . PHE C 2 165 A -31.271 -12.924 41.904 1.00 32.57 584 PHE C CE2 1
ATOM 3436 C CZ . PHE C 2 165 A -31.379 -11.898 42.850 1.00 32.97 584 PHE C CZ 1
"""
cif_model = iotbx.cif.reader(input_string=input_1ezu).model()
cif_block = cif_model["1EZU"]
builder = pdb_hierarchy_builder(cif_block)
hierarchy = builder.hierarchy
residue_groups = list(hierarchy.residue_groups())
assert residue_groups[0].icode == " "
assert residue_groups[1].icode == "A"
s = StringIO()
hierarchy.show(out=s)
assert not show_diff(
s.getvalue(), """\
model id="" #chains=1
chain id="C" #residue_groups=2
resid=" 584 " #atom_groups=1
altloc="" resname="GLY" #atoms=4
" N "
" CA "
" C "
" O "
resid=" 584A" #atom_groups=1
altloc="" resname="PHE" #atoms=11
" N "
" CA "
" C "
" O "
" CB "
" CG "
" CD1"
" CD2"
" CE1"
" CE2"
" CZ "
""")
cif_block = hierarchy.as_cif_block()
builder = pdb_hierarchy_builder(cif_block)
hierarchy_recycled = builder.hierarchy
s1 = StringIO()
hierarchy_recycled.show(out=s1)
assert not show_diff(s.getvalue(), s1.getvalue())
input_charges = """\
data_charges
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x_esd
_atom_site.Cartn_y_esd
_atom_site.Cartn_z_esd
_atom_site.occupancy_esd
_atom_site.B_iso_or_equiv_esd
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
HETATM 2932 CA CA . CA J 2 . ? 221.154 27.397 60.094 1.00 49.40 ? ? ? ? ? 2 1123 CA C CA 1
HETATM 2996 O O1S . MES D 4 . ? 47.470 -6.157 23.319 1.00 13.84 ? ? ? ? ? -1 1653 MES F O1S 1
HETATM 2997 O O2S . MES D 4 . ? 47.327 -5.296 20.939 1.00 15.26 ? ? ? ? ? 1- 1653 MES F O2S 1
"""
hierarchy = iotbx.pdb.input(lines=input_charges.splitlines(),
source_info=None).construct_hierarchy()
atoms = hierarchy.atoms()
assert atoms[0].charge == "2+"
assert atoms[1].charge == "1-"
assert atoms[2].charge == "1-"
s = StringIO()
hierarchy.show(out=s)
assert not show_diff(
s.getvalue(), """\
model id="" #chains=2
chain id="C" #residue_groups=1
resid="1123 " #atom_groups=1
altloc="" resname="CA" #atoms=1
"CA "
chain id="F" #residue_groups=1
resid="1653 " #atom_groups=1
altloc="" resname="MES" #atoms=2
" O1S"
" O2S"
""")
cif_block = hierarchy.as_cif_block()
builder = pdb_hierarchy_builder(cif_block)
hierarchy_recycled = builder.hierarchy
s1 = StringIO()
hierarchy_recycled.show(out=s1)
assert not show_diff(s.getvalue(), s1.getvalue())
atoms = hierarchy.atoms()
assert atoms[0].charge == "2+"
assert atoms[1].charge == "1-"
assert atoms[2].charge == "1-"
def exercise_pdb_hierachy_builder():
input_1ab1 = """\
data_1AB1
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 17 C CA A THR A 1 2 13.800 11.354 5.944 0.70 2.98 2 THR A CA 1
ATOM 18 C CA B THR A 1 2 13.872 10.918 5.772 0.30 5.01 2 THR A CA 1
ATOM 19 C C . THR A 1 2 14.118 10.664 7.274 1.00 2.92 2 THR A C 1
ATOM 20 O O . THR A 1 2 15.013 9.787 7.376 1.00 3.70 2 THR A O 1
ATOM 21 C CB A THR A 1 2 12.784 10.610 5.099 0.70 4.35 2 THR A CB 1
ATOM 22 C CB B THR A 1 2 12.938 9.905 5.108 0.30 1.07 2 THR A CB 1
ATOM 23 O OG1 A THR A 1 2 13.364 9.360 4.756 0.70 5.60 2 THR A OG1 1
ATOM 24 O OG1 B THR A 1 2 12.559 10.450 3.917 0.30 5.43 2 THR A OG1 1
ATOM 25 C CG2 A THR A 1 2 12.451 11.323 3.797 0.70 7.65 2 THR A CG2 1
ATOM 26 C CG2 B THR A 1 2 11.642 9.729 5.862 0.30 2.71 2 THR A CG2 1
ATOM 27 H H . THR A 1 2 15.500 10.728 5.006 1.00 1.74 2 THR A H 1
ATOM 28 H HA . THR A 1 2 13.437 12.241 6.128 1.00 4.09 2 THR A HA 1
ATOM 29 H HB A THR A 1 2 11.947 10.457 5.635 0.70 1.11 2 THR A HB 1
ATOM 30 H HB B THR A 1 2 13.426 9.030 5.019 0.30 4.20 2 THR A HB 1
ATOM 31 H HG21 A THR A 1 2 13.241 11.856 3.510 0.70 1.00 2 THR A HG21 1
ATOM 32 H HG21 B THR A 1 2 11.196 10.615 5.970 0.30 2.01 2 THR A HG21 1
ATOM 33 H HG22 A THR A 1 2 12.211 10.692 3.092 0.70 5.54 2 THR A HG22 1
ATOM 34 H HG22 B THR A 1 2 11.027 9.120 5.405 0.30 10.62 2 THR A HG22 1
ATOM 35 H HG23 A THR A 1 2 11.693 11.979 3.928 0.70 9.26 2 THR A HG23 1
ATOM 36 H HG23 B THR A 1 2 11.801 9.381 6.801 0.30 8.15 2 THR A HG23 1
# ...trunacted...
HETATM 679 C C1 A EOH B 2 . 16.083 0.909 12.713 0.60 15.95 66 EOH A C1 1
HETATM 680 C C1 B EOH B 2 . 15.565 1.042 13.226 0.40 14.21 66 EOH A C1 1
HETATM 681 C C2 A EOH B 2 . 15.130 -0.269 13.016 0.60 14.85 66 EOH A C2 1
HETATM 682 C C2 B EOH B 2 . 14.830 -0.303 13.058 0.40 15.17 66 EOH A C2 1
HETATM 683 O O A EOH B 2 . 15.378 1.984 12.104 0.60 12.07 66 EOH A O 1
HETATM 684 O O B EOH B 2 . 14.811 2.078 12.602 0.40 5.53 66 EOH A O 1
"""
cif_model = iotbx.cif.reader(input_string=input_1ab1).model()
builder = pdb_hierarchy_builder(cif_model["1AB1"])
#assert builder.crystal_symmetry is None
hierarchy = builder.hierarchy
atoms = hierarchy.atoms()
assert atoms[0].segid == " " # some code relies on this
s = StringIO()
hierarchy.show(out=s)
assert not show_diff(
s.getvalue(), """\
model id="" #chains=2
chain id="A" #residue_groups=1 ### WARNING: duplicate chain id ###
resid=" 2 " #atom_groups=3
altloc="" resname="THR" #atoms=4
" C "
" O "
" H "
" HA "
altloc="A" resname="THR" #atoms=8
" CA "
" CB "
" OG1"
" CG2"
" HB "
"HG21"
"HG22"
"HG23"
altloc="B" resname="THR" #atoms=8
" CA "
" CB "
" OG1"
" CG2"
" HB "
"HG21"
"HG22"
"HG23"
chain id="A" #residue_groups=1 ### WARNING: duplicate chain id ###
resid=" 66 " #atom_groups=2
altloc="A" resname="EOH" #atoms=3
" C1 "
" C2 "
" O "
altloc="B" resname="EOH" #atoms=3
" C1 "
" C2 "
" O "
""")
cif_block = hierarchy.as_cif_block()
builder = pdb_hierarchy_builder(cif_block)
hierarchy_recycled = builder.hierarchy
s1 = StringIO()
hierarchy_recycled.show(out=s1)
assert not show_diff(s.getvalue(), s1.getvalue())
#
input_missing_mandatory_items = """\
data_1AB1
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.occupancy
_atom_site.B_iso_or_equiv
ATOM 17 C A THR A 1 2 0.70 2.98
ATOM 18 C B THR A 1 2 0.30 5.01
ATOM 19 C . THR A 1 2 1.00 2.92
ATOM 20 O . THR A 1 2 1.00 3.70
"""
cif_model = iotbx.cif.reader(
input_string=input_missing_mandatory_items).model()
try:
pdb_hierarchy_builder(cif_model["1AB1"])
except AssertionError, e:
pass
_atom_site_anisotrop.U[2][2]
_atom_site_anisotrop.U[3][3]
_atom_site_anisotrop.U[1][2]
_atom_site_anisotrop.U[1][3]
_atom_site_anisotrop.U[2][3]
1 N N . SER A 1 0.4097 0.2916 0.1984 0.1130 0.0328 0.0375
2 C CA . SER A 1 0.4035 0.2848 0.1847 0.1242 0.0297 0.0347
3 C C . SER A 1 0.3744 0.2637 0.1648 0.1278 0.0215 0.0258
4 O O . SER A 1 0.3494 0.2393 0.1463 0.1236 0.0185 0.0236
5 C CB . SER A 1 0.4085 0.2738 0.1795 0.1267 0.0311 0.0373
6 O OG . SER A 1 0.4276 0.2843 0.1998 0.1252 0.0273 0.0344
"""
cif_model = iotbx.cif.reader(input_string=input_4edr).model()
cif_block = cif_model["4EDR"]
builder = pdb_hierarchy_builder(cif_block)
assert approx_equal(builder.crystal_symmetry.unit_cell().parameters(),
(150.582, 150.582, 38.633, 90, 90, 120))
assert builder.crystal_symmetry.space_group_info().symbol_and_number() == \
'P 61 (No. 169)'
hierarchy = builder.hierarchy
s = StringIO()
hierarchy.show(out=s)
assert not show_diff(
s.getvalue(), """\
model id="" #chains=2
chain id="A" #residue_groups=1 ### WARNING: duplicate chain id ###
resid=" 108 " #atom_groups=1
altloc="" resname="SER" #atoms=6
" N "
" CA "
def exercise_pdb_hierachy_builder():
input_1ab1 = """\
data_1AB1
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 17 C CA A THR A 1 2 13.800 11.354 5.944 0.70 2.98 2 THR A CA 1
ATOM 18 C CA B THR A 1 2 13.872 10.918 5.772 0.30 5.01 2 THR A CA 1
ATOM 19 C C . THR A 1 2 14.118 10.664 7.274 1.00 2.92 2 THR A C 1
ATOM 20 O O . THR A 1 2 15.013 9.787 7.376 1.00 3.70 2 THR A O 1
ATOM 21 C CB A THR A 1 2 12.784 10.610 5.099 0.70 4.35 2 THR A CB 1
ATOM 22 C CB B THR A 1 2 12.938 9.905 5.108 0.30 1.07 2 THR A CB 1
ATOM 23 O OG1 A THR A 1 2 13.364 9.360 4.756 0.70 5.60 2 THR A OG1 1
ATOM 24 O OG1 B THR A 1 2 12.559 10.450 3.917 0.30 5.43 2 THR A OG1 1
ATOM 25 C CG2 A THR A 1 2 12.451 11.323 3.797 0.70 7.65 2 THR A CG2 1
ATOM 26 C CG2 B THR A 1 2 11.642 9.729 5.862 0.30 2.71 2 THR A CG2 1
ATOM 27 H H . THR A 1 2 15.500 10.728 5.006 1.00 1.74 2 THR A H 1
ATOM 28 H HA . THR A 1 2 13.437 12.241 6.128 1.00 4.09 2 THR A HA 1
ATOM 29 H HB A THR A 1 2 11.947 10.457 5.635 0.70 1.11 2 THR A HB 1
ATOM 30 H HB B THR A 1 2 13.426 9.030 5.019 0.30 4.20 2 THR A HB 1
ATOM 31 H HG21 A THR A 1 2 13.241 11.856 3.510 0.70 1.00 2 THR A HG21 1
ATOM 32 H HG21 B THR A 1 2 11.196 10.615 5.970 0.30 2.01 2 THR A HG21 1
ATOM 33 H HG22 A THR A 1 2 12.211 10.692 3.092 0.70 5.54 2 THR A HG22 1
ATOM 34 H HG22 B THR A 1 2 11.027 9.120 5.405 0.30 10.62 2 THR A HG22 1
ATOM 35 H HG23 A THR A 1 2 11.693 11.979 3.928 0.70 9.26 2 THR A HG23 1
ATOM 36 H HG23 B THR A 1 2 11.801 9.381 6.801 0.30 8.15 2 THR A HG23 1
# ...trunacted...
HETATM 679 C C1 A EOH B 2 . 16.083 0.909 12.713 0.60 15.95 66 EOH A C1 1
HETATM 680 C C1 B EOH B 2 . 15.565 1.042 13.226 0.40 14.21 66 EOH A C1 1
HETATM 681 C C2 A EOH B 2 . 15.130 -0.269 13.016 0.60 14.85 66 EOH A C2 1
HETATM 682 C C2 B EOH B 2 . 14.830 -0.303 13.058 0.40 15.17 66 EOH A C2 1
HETATM 683 O O A EOH B 2 . 15.378 1.984 12.104 0.60 12.07 66 EOH A O 1
HETATM 684 O O B EOH B 2 . 14.811 2.078 12.602 0.40 5.53 66 EOH A O 1
"""
cif_model = iotbx.cif.reader(input_string=input_1ab1).model()
builder = pdb_hierarchy_builder(cif_model["1AB1"])
#assert builder.crystal_symmetry is None
hierarchy = builder.hierarchy
atoms = hierarchy.atoms()
assert atoms[0].segid == " " # some code relies on this
s = StringIO()
hierarchy.show(out=s)
assert not show_diff(s.getvalue(), """\
model id="" #chains=2
chain id="A" #residue_groups=1 ### WARNING: duplicate chain id ###
resid=" 2 " #atom_groups=3
altloc="" resname="THR" #atoms=4
" C "
" O "
" H "
" HA "
altloc="A" resname="THR" #atoms=8
" CA "
" CB "
" OG1"
" CG2"
" HB "
"HG21"
"HG22"
"HG23"
altloc="B" resname="THR" #atoms=8
" CA "
" CB "
" OG1"
" CG2"
" HB "
"HG21"
"HG22"
"HG23"
chain id="A" #residue_groups=1 ### WARNING: duplicate chain id ###
resid=" 66 " #atom_groups=2
altloc="A" resname="EOH" #atoms=3
" C1 "
" C2 "
" O "
altloc="B" resname="EOH" #atoms=3
" C1 "
" C2 "
" O "
""")
cif_block = hierarchy.as_cif_block()
builder = pdb_hierarchy_builder(cif_block)
hierarchy_recycled = builder.hierarchy
s1 = StringIO()
hierarchy_recycled.show(out=s1)
assert not show_diff(s.getvalue(), s1.getvalue())
#
input_missing_mandatory_items = """\
data_1AB1
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.occupancy
_atom_site.B_iso_or_equiv
ATOM 17 C A THR A 1 2 0.70 2.98
ATOM 18 C B THR A 1 2 0.30 5.01
ATOM 19 C . THR A 1 2 1.00 2.92
ATOM 20 O . THR A 1 2 1.00 3.70
"""
cif_model = iotbx.cif.reader(input_string=input_missing_mandatory_items).model()
try: pdb_hierarchy_builder(cif_model["1AB1"])
except AssertionError, e: pass
else:
_atom_site_anisotrop.U[2][2]
_atom_site_anisotrop.U[3][3]
_atom_site_anisotrop.U[1][2]
_atom_site_anisotrop.U[1][3]
_atom_site_anisotrop.U[2][3]
1 N N . SER A 1 0.4097 0.2916 0.1984 0.1130 0.0328 0.0375
2 C CA . SER A 1 0.4035 0.2848 0.1847 0.1242 0.0297 0.0347
3 C C . SER A 1 0.3744 0.2637 0.1648 0.1278 0.0215 0.0258
4 O O . SER A 1 0.3494 0.2393 0.1463 0.1236 0.0185 0.0236
5 C CB . SER A 1 0.4085 0.2738 0.1795 0.1267 0.0311 0.0373
6 O OG . SER A 1 0.4276 0.2843 0.1998 0.1252 0.0273 0.0344
"""
cif_model = iotbx.cif.reader(input_string=input_4edr).model()
cif_block = cif_model["4EDR"]
builder = pdb_hierarchy_builder(cif_block)
assert approx_equal(builder.crystal_symmetry.unit_cell().parameters(),
(150.582, 150.582, 38.633, 90, 90, 120))
assert builder.crystal_symmetry.space_group_info().symbol_and_number() == \
'P 61 (No. 169)'
hierarchy = builder.hierarchy
s = StringIO()
hierarchy.show(out=s)
assert not show_diff(s.getvalue(), """\
model id="" #chains=2
chain id="A" #residue_groups=1 ### WARNING: duplicate chain id ###
resid=" 108 " #atom_groups=1
altloc="" resname="SER" #atoms=6
" N "
" CA "
" C "
