def tst_adding_disulfur_hydrogen_atoms(switch):
element = 'H'
if switch.endswith('_D'): element = 'D'
fn = 'tst_ready_hydrogens_%s.pdb' % (switch)
f = file(fn, 'wb')
f.write(pdb_strings[switch])
del f
pdb_inp = pdb_input(fn)
hierarchy = pdb_inp.construct_hierarchy()
from mmtbx.conformation_dependent_library.testing_utils import get_geometry_restraints_manager
grm = get_geometry_restraints_manager(pdb_filename=fn)
add_disulfur_hydrogen_atoms(grm, hierarchy, element=element)
hierarchy.write_pdb_file(fn.replace('.pdb', '_updated.pdb'))
if switch == 'CYS_1':
f = file(fn.replace('.pdb', '_updated.pdb'), 'rb')
lines = f.read()
del f
assert lines.find('HG') == -1
else:
cmd = 'phenix.pdb_interpretation %s write_geo=True' % fn.replace(
'.pdb', '_updated.pdb')
print(cmd)
easy_run.go(cmd)
assert_lines_in_file(file_name='%s.geo' %
fn.replace('.pdb', '_updated.pdb'),
lines=geo_strings[switch])
def get_pdb_hierarchy_from_restraints(code):
from mmtbx.monomer_library import server
from iotbx import pdb
mon_lib_server = server.server()
path = mon_lib_server.get_comp_comp_id_direct(code, return_filename=True)
cif_obj = server.read_cif(path)
ligand_inp = pdb.pdb_input(source_info="Model from %s" % path,
lines=flex.split_lines(""))
ligand_hierarchy = ligand_inp.construct_hierarchy()
model = pdb.hierarchy.model()
chain = pdb.hierarchy.chain()
chain.id = 'Z'
rg = pdb.hierarchy.residue_group()
ag = pdb.hierarchy.atom_group()
for block, loops in cif_obj.blocks.items():
if block == 'comp_list': continue
for loop in loops.iterloops():
for row in loop.iterrows():
if '_chem_comp_atom.comp_id' not in row: break
ag.resname = row['_chem_comp_atom.comp_id']
atom = pdb.hierarchy.atom()
atom.name = row['_chem_comp_atom.atom_id']
atom.element = '%2s' % row['_chem_comp_atom.type_symbol']
atom.xyz = (
float(row['_chem_comp_atom.x']),
float(row['_chem_comp_atom.y']),
float(row['_chem_comp_atom.z']),
)
ag.append_atom(atom)
rg.append_atom_group(ag)
chain.append_residue_group(rg)
model.append_chain(chain)
ligand_hierarchy.append_model(model)
ligand_hierarchy.atoms().reset_i_seq()
return ligand_hierarchy
def exercise_line_info_exceptions():
pdb.pdb_input(source_info=None, lines=flex.std_string(["ATOM"]))
#
try:
pdb.pdb_input(source_info="some.pdb",
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
"""))
except ValueError, e:
assert not show_diff(
str(e), """\
some.pdb, line 2:
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
---------------------------------^
unexpected plus sign.""")
def exercise_line_info_exceptions():
pdb.pdb_input(source_info=None, lines=flex.std_string(["ATOM"]))
#
try:
pdb.pdb_input(
source_info="some.pdb",
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
"""))
except ValueError, e:
assert not show_diff(str(e), """\
some.pdb, line 2:
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
---------------------------------^
unexpected plus sign.""")
def exercise_BIOMT():
'''
Verifying BIOMT extraction from pdb file
'''
pdb_test_data = '''\
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 300 DETAILS: THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR
REMARK 300 ICOSAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = I).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, S
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 0.309017 -0.809017 0.500000 0.10000
REMARK 350 BIOMT2 2 0.809017 0.500000 0.309017 0.02000
REMARK 350 BIOMT3 2 -0.500000 0.309017 0.809017 0.00300
REMARK 350 BIOMT1 3 -0.809017 -0.500000 0.309017 0.00000
REMARK 350 BIOMT2 3 0.500000 -0.309017 0.809017 0.00000
REMARK 350 BIOMT3 3 -0.309017 0.809017 0.500000 0.00000
REMARK 350 BIOMT1 4 -0.809017 0.500000 -0.309017 0.00000
REMARK 350 BIOMT2 4 -0.500000 -0.309017 0.809017 0.00000
REMARK 350 BIOMT3 4 0.309017 0.809017 0.500000 0.00000
'''
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines(pdb_test_data))
mtrix_info = pdb_inp.process_BIOMT_records()
assert len(mtrix_info.r) == 4
assert approx_equal(mtrix_info.r[0], [
1.000000,0.000000,0.000000,
0.000000,1.000000,0.000000,
0.000000,0.000000,1.000000])
assert approx_equal(mtrix_info.t[0], [0.00000,0.00000,0.00000])
assert approx_equal(mtrix_info.r[1], [
0.309017,-0.809017, 0.500000,
0.809017, 0.500000, 0.309017,
-0.500000, 0.309017, 0.809017])
assert approx_equal(mtrix_info.t[1], [0.10000,0.02000,0.00300])
assert mtrix_info.serial_number == [1, 2, 3, 4]
def exercise_input_pickling():
pdb_inp = pdb.pdb_input(source_info="file/name",
lines=pdb_string_all_sections)
s = pickle.dumps(pdb_inp, 1)
l = pickle.loads(s)
assert not show_diff(l.as_pdb_string(), pdb_inp.as_pdb_string())
assert l.source_info() == "pickle"
for section in pdb.input_sections:
assert not show_diff("\n".join(getattr(l, section)()), "\n".join(
getattr(pdb_inp, section)()))
s = "\n".join(l.__getinitargs__()[1])
d = hashlib.md5(s).hexdigest()
if (pdb.hierarchy.atom.has_siguij()):
assert d == "bf987c40cc8672e2f2324d91d6de3e2b"
else:
assert d == "7375e96fd52794a785284580730de20c"
def exercise_BIOMT():
"""
Verifying BIOMT extraction from pdb file
"""
pdb_test_data = """\
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 300 DETAILS: THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR
REMARK 300 ICOSAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = I).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, S
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 0.309017 -0.809017 0.500000 0.10000
REMARK 350 BIOMT2 2 0.809017 0.500000 0.309017 0.02000
REMARK 350 BIOMT3 2 -0.500000 0.309017 0.809017 0.00300
REMARK 350 BIOMT1 3 -0.809017 -0.500000 0.309017 0.00000
REMARK 350 BIOMT2 3 0.500000 -0.309017 0.809017 0.00000
REMARK 350 BIOMT3 3 -0.309017 0.809017 0.500000 0.00000
REMARK 350 BIOMT1 4 -0.809017 0.500000 -0.309017 0.00000
REMARK 350 BIOMT2 4 -0.500000 -0.309017 0.809017 0.00000
REMARK 350 BIOMT3 4 0.309017 0.809017 0.500000 0.00000
"""
pdb_inp = pdb.pdb_input(source_info=None, lines=flex.split_lines(pdb_test_data))
mtrix_info = pdb_inp.process_BIOMT_records()
assert len(mtrix_info.r) == 4
assert approx_equal(
mtrix_info.r[0], [1.000000, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000, 0.000000, 0.000000, 1.000000]
)
assert approx_equal(mtrix_info.t[0], [0.00000, 0.00000, 0.00000])
assert approx_equal(
mtrix_info.r[1], [0.309017, -0.809017, 0.500000, 0.809017, 0.500000, 0.309017, -0.500000, 0.309017, 0.809017]
)
assert approx_equal(mtrix_info.t[1], [0.10000, 0.02000, 0.00300])
assert mtrix_info.serial_number == [1, 2, 3, 4]
def exercise_input_pickling():
pdb_inp = pdb.pdb_input(source_info="file/name", lines=pdb_string_all_sections)
for p in [pickle, cPickle]:
s = p.dumps(pdb_inp, 1)
l = p.loads(s)
assert not show_diff(l.as_pdb_string(), pdb_inp.as_pdb_string())
assert l.source_info() == "pickle"
for section in pdb.input_sections:
assert not show_diff(
"\n".join(getattr(l, section)()),
"\n".join(getattr(pdb_inp, section)()))
s = "\n".join(l.__getinitargs__()[1])
d = hashlib_md5(s).hexdigest()
if (pdb.hierarchy.atom.has_siguij()):
assert d == "bf987c40cc8672e2f2324d91d6de3e2b"
else:
assert d == "7375e96fd52794a785284580730de20c"
def tst_adding_side_chain_acid_hydrogen_atoms(switch):
element = 'H'
if switch.endswith('_D'): element = 'D'
for i in range(4):
fn = 'tst_ready_hydrogens_%s_%d.pdb' % (switch, i)
with open(fn, 'w') as f:
f.write(pdb_strings[switch])
pdb_inp = pdb_input(fn)
hierarchy = pdb_inp.construct_hierarchy()
add_side_chain_acid_hydrogens(hierarchy,
configuration_index=i,
element=element)
hierarchy.write_pdb_file(fn.replace('.pdb', '_updated.pdb'))
cmd = 'phenix.pdb_interpretation %s flip_sym=0 write_geo=True' % fn.replace(
'.pdb', '_updated.pdb')
print(cmd)
easy_run.go(cmd)
assert_lines_in_file(file_name='%s.geo' %
fn.replace('.pdb', '_updated.pdb'),
lines=geo_strings[switch][i])
def exercise_xray_structure_simple():
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
CRYST1 61.410 54.829 43.543 90.00 90.00 90.00 P 21 21 21 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.016284 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018239 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022966 0.00000
ATOM 1 N GLN A 3 35.299 11.075 19.070 1.00 36.89 N
ATOM 2 CA GLN A 3 34.482 9.927 18.794 0.63 37.88 C
SIGATM 2 CA GLN A 3 1.200 2.300 3.400 0.04 0.05 C
ANISOU 2 CA GLN A 3 7794 3221 3376 -1227 1064 2601 C
ATOM 3 Q GLN A 3 35.130 8.880 17.864 0.84 37.52 C
ANISOU 3 Q GLN A 3 7875 3041 3340 -981 727 2663 C
SIGUIJ 3 Q GLN A 3 75 41 40 -1 7 63 C
ATOM 4 O GLN A 3 34.548 7.819 17.724 1.00 38.54 STUV
ATOM 5 1CB AGLN A 3 32.979 10.223 18.469 1.00 37.80
HETATM 6 CA AION B 1 32.360 11.092 17.308 0.92 35.96 CA2+
HETATM 7 CA ION B 2 30.822 10.665 17.190 1.00 36.87
"""))
for use_scale_matrix_if_available in [False, True]:
xray_structure = pdb_inp.xray_structure_simple(
use_scale_matrix_if_available=use_scale_matrix_if_available)
out = StringIO()
xray_structure.show_summary(f=out)
assert not show_diff(
out.getvalue(), """\
Number of scatterers: 7
At special positions: 0
Unit cell: (61.41, 54.829, 43.543, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
""")
out = StringIO()
xray_structure.show_scatterers(f=out)
assert not show_diff(
out.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
pdb=" N GLN A 3 " N 4 ( 0.5748 0.2020 0.4380) 1.00 0.4672 [ - ]
pdb=" CA GLN A 3 " C 4 ( 0.5615 0.1811 0.4316) 0.63 [ - ] 0.4797
u_cart = 0.779 0.322 0.338 -0.123 0.106 0.260
pdb=" Q GLN A 3 " C 4 ( 0.5721 0.1620 0.4103) 0.84 [ - ] 0.4752
u_cart = 0.788 0.304 0.334 -0.098 0.073 0.266
pdb=" O GLN A 3 " segid="STUV" O 4 ( 0.5626 0.1426 0.4070)\
1.00 0.4881 [ - ]
pdb="1CB AGLN A 3 " C 4 ( 0.5370 0.1865 0.4242) 1.00 0.4787 [ - ]
pdb="CA AION B 1 " Ca2+ 4 ( 0.5270 0.2023 0.3975) 0.92 0.4554 [ - ]
pdb="CA ION B 2 " Ca 4 ( 0.5019 0.1945 0.3948) 1.00 0.4670 [ - ]
""")
#
xray_structure = pdb_inp.xray_structure_simple(
unit_cube_pseudo_crystal=True)
out = StringIO()
xray_structure.show_summary(f=out)
assert not show_diff(
out.getvalue(), """\
Number of scatterers: 7
At special positions: 0
Unit cell: (1, 1, 1, 90, 90, 90)
Space group: P 1 (No. 1)
""")
out = StringIO()
xray_structure.show_scatterers(f=out)
assert not show_diff(
out.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
pdb=" N GLN A 3 " N 1 (35.2990 11.0750 19.0700) 1.00 0.4672 [ - ]
pdb=" CA GLN A 3 " C 1 (34.4820 9.9270 18.7940) 0.63 [ - ] 0.4797
u_cart = 0.779 0.322 0.338 -0.123 0.106 0.260
pdb=" Q GLN A 3 " C 1 (35.1300 8.8800 17.8640) 0.84 [ - ] 0.4752
u_cart = 0.788 0.304 0.334 -0.098 0.073 0.266
pdb=" O GLN A 3 " segid="STUV" O 1 (34.5480 7.8190 17.7240)\
1.00 0.4881 [ - ]
pdb="1CB AGLN A 3 " C 1 (32.9790 10.2230 18.4690) 1.00 0.4787 [ - ]
pdb="CA AION B 1 " Ca2+ 1 (32.3600 11.0920 17.3080) 0.92 0.4554 [ - ]
pdb="CA ION B 2 " Ca 1 (30.8220 10.6650 17.1900) 1.00 0.4670 [ - ]
""")
#
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 1 N GLN A 3 35.299 11.075 99.070 1.00 36.89 STUV A
"""))
xray_structure = pdb_inp.xray_structure_simple(
enable_scattering_type_unknown=True)
assert xray_structure.scatterers()[0].scattering_type == "unknown"
try:
pdb_inp.xray_structure_simple()
except Sorry, e:
assert not show_diff(
str(e), """\
Unknown chemical element type:
"ATOM 1 N GLN A 3 .*.STUV A "
To resolve this problem, specify a chemical element type in
columns 77-78 of the PDB file, right justified (e.g. " C").""")
def model(self, model):
self._hierarchy_model = pdb.pdb_input(model).construct_hierarchy()
self._model = model
def exercise_pdb_input():
for i_trial in xrange(3):
pdb_inp = pdb.pdb_input(source_info=None, lines=flex.split_lines(""))
assert (pdb_inp.file_type() == "pdb")
assert pdb_inp.source_info() == ""
assert len(pdb_inp.record_type_counts()) == 0
assert pdb_inp.unknown_section().size() == 0
assert pdb_inp.title_section().size() == 0
assert pdb_inp.remark_section().size() == 0
assert pdb_inp.primary_structure_section().size() == 0
assert pdb_inp.heterogen_section().size() == 0
assert pdb_inp.secondary_structure_section().size() == 0
assert pdb_inp.connectivity_annotation_section().size() == 0
assert pdb_inp.miscellaneous_features_section().size() == 0
assert pdb_inp.crystallographic_section().size() == 0
assert len(pdb_inp.atoms_with_labels()) == 0
assert pdb_inp.atoms().size() == 0
assert pdb_inp.model_ids().size() == 0
assert pdb_inp.model_indices().size() == 0
assert pdb_inp.ter_indices().size() == 0
assert pdb_inp.chain_indices().size() == 0
assert pdb_inp.break_indices().size() == 0
assert pdb_inp.connectivity_section().size() == 0
assert pdb_inp.bookkeeping_section().size() == 0
assert pdb_inp.model_atom_counts().size() == 0
pdb_inp = pdb.pdb_input(source_info="file/name",
lines=pdb_string_all_sections)
assert pdb_inp.source_info() == "file/name"
assert pdb_inp.record_type_counts() == {
"KEYWDS": 1,
"SEQRES": 1,
"LINK ": 1,
"ORIGX1": 1,
"SITE ": 1,
"FTNOTE": 1,
"HETSYN": 1,
"SIGATM": 2,
"MTRIX2": 1,
"MTRIX3": 1,
"HELIX ": 1,
"MTRIX1": 1,
"END ": 1,
"ANISOU": 2,
"TITLE ": 1,
"SLTBRG": 1,
"REMARK": 1,
"TURN ": 1,
"SCALE1": 1,
"SCALE2": 1,
"AUTHOR": 1,
"CRYST1": 1,
"SIGUIJ": 2,
"CISPEP": 1,
"ATOM ": 4,
"ENDMDL": 2,
"ORIGX2": 1,
"MODRES": 1,
"SOURCE": 1,
"FORMUL": 1,
"MASTER": 1,
"CAVEAT": 1,
"HET ": 1,
"COMPND": 1,
"MODEL ": 2,
"REVDAT": 1,
"SSBOND": 1,
"OBSLTE": 1,
"CONECT": 1,
"JRNL ": 1,
"SPRSDE": 1,
" ": 11,
"FOOBAR": 1,
"HETNAM": 1,
"HEADER": 1,
"ORIGX3": 1,
"BREAK ": 1,
"ONHOLD": 1,
"SHEET ": 1,
"TVECT ": 1,
"HYDBND": 1,
"TER ": 2,
"DBREF ": 1,
"EXPDTA": 1,
"SCALE3": 1,
"HETATM": 2,
"SEQADV": 1,
"SPLIT ": 1,
"NUMMDL": 1,
"MDLTYP": 2,
"DBREF1": 1,
"DBREF2": 1
}
assert list(pdb_inp.unknown_section()) == ["FOOBAR BAR FOO"]
assert not show_diff(
"\n".join(pdb_inp.title_section()), """\
HEADER ISOMERASE 02-JUL-92 1FKB
ONHOLD 26-JUN-99
OBSLTE 07-DEC-04 1A0Y 1Y4P
TITLE ATOMIC STRUCTURE OF THE RAPAMYCIN HUMAN IMMUNOPHILIN FKBP-
SPLIT 2QNH 1VSP
COMPND FK506 BINDING PROTEIN (FKBP) COMPLEX WITH IMMUNOSUPPRESSANT
SOURCE HUMAN (H**O SAPIENS) RECOMBINANT FORM EXPRESSED IN
KEYWDS ISOMERASE
EXPDTA X-RAY DIFFRACTION
NUMMDL 8
MDLTYP CA ATOMS ONLY, CHAIN B, C, D, E, F, G, H, I, J, K, L, M, N,
MDLTYP 2 O, P, Q, R, S, T, U
AUTHOR G.D.VAN DUYNE,R.F.STANDAERT,S.L.SCHREIBER,J.C.CLARDY
REVDAT 1 31-OCT-93 1FKB 0
JRNL AUTH G.D.VAN DUYNE,R.F.STANDAERT,S.L.SCHREIBER,J.CLARDY
SPRSDE 02-SEP-03 1O58 1J6N
CAVEAT 1B7F INCORRECT CHIRALITY AT C1* OF U2, CHAIN Q""")
assert not show_diff(
"\n".join(pdb_inp.remark_section()), """\
REMARK 2 RESOLUTION. 1.7 ANGSTROMS.
FTNOTE 1 CIS PEPTIDE: GLY 190 - PHE 191""")
assert not show_diff(
"\n".join(pdb_inp.primary_structure_section()), """\
DBREF 1HTQ A 601 468 SWS Q10377 GLN1_MYCTU 2 478
DBREF1 1JZX A 1 2880 GB 15805042
DBREF2 1JZX A NC_001263 2587937 2590817
SEQRES 1 A 477 THR GLU LYS THR PRO ASP ASP VAL PHE LYS LEU ALA LYS
SEQADV 1KEH ALA A 170 SWS Q9L5D6 SER 199 ENGINEERED
MODRES 6NSE CYS A 384 CYS MODIFIED BY CAD""")
assert not show_diff(
"\n".join(pdb_inp.heterogen_section()), """\
HET GLC A 810 12
HETNAM G6D 6-DEOXY-ALPHA-D-GLUCOSE
HETSYN G6D QUINOVOSE
FORMUL 2 CA 4(CA1 2+)""")
assert not show_diff(
"\n".join(pdb_inp.secondary_structure_section()), """\
HELIX 1 1 GLN A 18 GLY A 34 1 17
SHEET 1 A 7 PHE A 257 ALA A 260 0
TURN 1 T1 GLY E 2 THR E 5 BETA, TYPE II""")
assert not show_diff(
"\n".join(pdb_inp.connectivity_annotation_section()), """\
SSBOND 12 CYS B 191 CYS B 220
LINK N PRO C 61 C GLY A 9 1556
HYDBND N GLY A 148 O PHE B 41
SLTBRG N ILE A 16 OD2 ASP A 194
CISPEP 1 ALA A 183 PRO A 184 1 0.96""")
assert not show_diff(
"\n".join(pdb_inp.miscellaneous_features_section()), """\
SITE 1 CAB 3 HIS B 57 ASP B 102 SER B 195""")
assert not show_diff(
"\n".join(pdb_inp.crystallographic_section()), """\
CRYST1 45.920 49.790 89.880 90.00 97.34 90.00 P 1 21 1 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.021777 0.000000 0.002805 0.00000
SCALE2 0.000000 0.020084 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011218 0.00000
MTRIX1 1 0.739109 0.012922 -0.673462 17.07460 1
MTRIX2 1 0.015672 -0.999875 -0.001986 21.64730 1
MTRIX3 1 -0.673404 -0.009087 -0.739219 44.75290 1
TVECT 1 0.00000 0.00000 20.42000""")
assert len(pdb_inp.atoms_with_labels()) == 6
assert [atom.serial for atom in pdb_inp.atoms()] \
== [" 1", " 2", " 3", " 4", " 9", " 10"]
assert [atom.element for atom in pdb_inp.atoms()] \
== [" N", " C", " C", " O", " ", " "]
assert list(pdb_inp.model_ids()) == [" 1", " 3"]
assert list(pdb_inp.model_indices()) == [4, 6]
assert list(pdb_inp.ter_indices()) == [5, 6]
assert [list(v) for v in pdb_inp.chain_indices()] == [[4], [5, 6]]
assert list(pdb_inp.break_indices()) == [2]
assert not show_diff("\n".join(pdb_inp.connectivity_section()), """\
CONECT 5332 5333 5334 5335 5336""")
assert not show_diff(
"\n".join(pdb_inp.bookkeeping_section()), """\
MASTER 81 0 0 7 3 0 0 645800 20 0 12
END""")
assert list(pdb_inp.model_atom_counts()) == [4, 2]
#
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 1 CB LYS 109 16.113 7.345 47.084 1.00 20.00 A
ATOM 2 CG LYS 109 17.058 6.315 47.703 1.00 20.00 A
ATOM 3 CB LYS 109 26.721 1.908 15.275 1.00 20.00 B
ATOM 4 CG LYS 109 27.664 2.793 16.091 1.00 20.00 B
"""))
expected_id_strs = """\
pdb=" CB LYS 109 " segid="A "
pdb=" CG LYS 109 " segid="A "
pdb=" CB LYS 109 " segid="B "
pdb=" CG LYS 109 " segid="B "
""".splitlines()
for awl, eids in zip(pdb_inp.atoms_with_labels(), expected_id_strs):
assert not show_diff(awl.id_str(), eids)
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdefS123E1C1
HETATM12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdefS123E1C1
"""))
for awl in pdb_inp.atoms_with_labels():
assert awl.name == "N123"
assert awl.altloc == "A"
assert awl.resname == "R12"
assert awl.chain_id == "C"
assert awl.resseq == "1234"
assert awl.icode == "I"
assert awl.segid == "S123"
assert awl.id_str() == 'pdb="N123AR12 C1234I" segid="S123"'
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdef E1C1
HETATM12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdef E1C1
"""))
for awl in pdb_inp.atoms_with_labels():
assert awl.name == "N123"
assert awl.altloc == "A"
assert awl.resname == "R12"
assert awl.chain_id == "C"
assert awl.resseq == "1234"
assert awl.icode == "I"
assert awl.segid == " "
assert awl.id_str() == 'pdb="N123AR12 C1234I"'
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM
HETATM
"""))
for awl in pdb_inp.atoms_with_labels():
assert awl.name == " "
assert awl.altloc == " "
assert awl.resname == " "
assert awl.chain_id == " "
assert awl.resseq == " "
assert awl.icode == " "
assert awl.segid == " "
assert awl.id_str() == 'pdb=" "'
#
pdb_inp = pdb.pdb_input(source_info=None, lines=flex.split_lines("""\
"""))
assert list(pdb_inp.model_indices()) == []
assert list(pdb_inp.chain_indices()) == []
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM
"""))
assert list(pdb_inp.model_indices()) == [1]
assert [list(v) for v in pdb_inp.chain_indices()] == [[1]]
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [0]
assert [list(v) for v in pdb_inp.chain_indices()] == [[]]
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ATOM
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [1]
assert [list(v) for v in pdb_inp.chain_indices()] == [[1]]
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
MODEL 2
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [0, 0]
assert [list(v) for v in pdb_inp.chain_indices()] == [[], []]
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
MODEL 2
ATOM
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [0, 1]
assert [list(v) for v in pdb_inp.chain_indices()] == [[], [1]]
try:
pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
ATOM
"""))
except ValueError, e:
assert not show_diff(
str(e), """\
input line 3:
ATOM
^
ATOM or HETATM record is outside MODEL/ENDMDL block.""")
def target(self, target):
self._hierarchy_target = pdb.pdb_input(target).construct_hierarchy()
self._target = target
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
"""))
except ValueError, e:
assert not show_diff(
str(e), """\
some.pdb, line 2:
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
---------------------------------^
unexpected plus sign.""")
else:
raise Exception_expected
try:
pdb.pdb_input(source_info="some.pdb",
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
"""),
raise_sorry_if_format_error=True)
except Sorry:
pass
else:
raise Exception_expected
try:
pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 84- 848 848 0 0 0
"""))
except ValueError, e:
assert not show_diff(
def exercise_xray_structure_simple():
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
CRYST1 61.410 54.829 43.543 90.00 90.00 90.00 P 21 21 21 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.016284 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018239 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022966 0.00000
ATOM 1 N GLN A 3 35.299 11.075 19.070 1.00 36.89 N
ATOM 2 CA GLN A 3 34.482 9.927 18.794 0.63 37.88 C
SIGATM 2 CA GLN A 3 1.200 2.300 3.400 0.04 0.05 C
ANISOU 2 CA GLN A 3 7794 3221 3376 -1227 1064 2601 C
ATOM 3 Q GLN A 3 35.130 8.880 17.864 0.84 37.52 C
ANISOU 3 Q GLN A 3 7875 3041 3340 -981 727 2663 C
SIGUIJ 3 Q GLN A 3 75 41 40 -1 7 63 C
ATOM 4 O GLN A 3 34.548 7.819 17.724 1.00 38.54 STUV
ATOM 5 1CB AGLN A 3 32.979 10.223 18.469 1.00 37.80
HETATM 6 CA AION B 1 32.360 11.092 17.308 0.92 35.96 CA2+
HETATM 7 CA ION B 2 30.822 10.665 17.190 1.00 36.87
"""))
for use_scale_matrix_if_available in [False, True]:
xray_structure = pdb_inp.xray_structure_simple(
use_scale_matrix_if_available=use_scale_matrix_if_available)
out = StringIO()
xray_structure.show_summary(f=out)
assert not show_diff(
out.getvalue(), """\
Number of scatterers: 7
At special positions: 0
Unit cell: (61.41, 54.829, 43.543, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
""")
out = StringIO()
xray_structure.show_scatterers(f=out)
assert not show_diff(
out.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
pdb=" N GLN A 3 " N 4 ( 0.5748 0.2020 0.4380) 1.00 0.4672 [ - ]
pdb=" CA GLN A 3 " C 4 ( 0.5615 0.1811 0.4316) 0.63 [ - ] 0.4797
u_cart = 0.779 0.322 0.338 -0.123 0.106 0.260
pdb=" Q GLN A 3 " C 4 ( 0.5721 0.1620 0.4103) 0.84 [ - ] 0.4752
u_cart = 0.788 0.304 0.334 -0.098 0.073 0.266
pdb=" O GLN A 3 " segid="STUV" O 4 ( 0.5626 0.1426 0.4070)\
1.00 0.4881 [ - ]
pdb="1CB AGLN A 3 " C 4 ( 0.5370 0.1865 0.4242) 1.00 0.4787 [ - ]
pdb="CA AION B 1 " Ca2+ 4 ( 0.5270 0.2023 0.3975) 0.92 0.4554 [ - ]
pdb="CA ION B 2 " Ca 4 ( 0.5019 0.1945 0.3948) 1.00 0.4670 [ - ]
""")
#
xray_structure = pdb_inp.xray_structure_simple(
unit_cube_pseudo_crystal=True)
out = StringIO()
xray_structure.show_summary(f=out)
assert not show_diff(
out.getvalue(), """\
Number of scatterers: 7
At special positions: 0
Unit cell: (1, 1, 1, 90, 90, 90)
Space group: P 1 (No. 1)
""")
out = StringIO()
xray_structure.show_scatterers(f=out)
assert not show_diff(
out.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
pdb=" N GLN A 3 " N 1 (35.2990 11.0750 19.0700) 1.00 0.4672 [ - ]
pdb=" CA GLN A 3 " C 1 (34.4820 9.9270 18.7940) 0.63 [ - ] 0.4797
u_cart = 0.779 0.322 0.338 -0.123 0.106 0.260
pdb=" Q GLN A 3 " C 1 (35.1300 8.8800 17.8640) 0.84 [ - ] 0.4752
u_cart = 0.788 0.304 0.334 -0.098 0.073 0.266
pdb=" O GLN A 3 " segid="STUV" O 1 (34.5480 7.8190 17.7240)\
1.00 0.4881 [ - ]
pdb="1CB AGLN A 3 " C 1 (32.9790 10.2230 18.4690) 1.00 0.4787 [ - ]
pdb="CA AION B 1 " Ca2+ 1 (32.3600 11.0920 17.3080) 0.92 0.4554 [ - ]
pdb="CA ION B 2 " Ca 1 (30.8220 10.6650 17.1900) 1.00 0.4670 [ - ]
""")
#
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 1 N GLN A 3 35.299 11.075 99.070 1.00 36.89 STUV A
"""))
xray_structure = pdb_inp.xray_structure_simple(
enable_scattering_type_unknown=True)
assert xray_structure.scatterers()[0].scattering_type == "unknown"
try:
pdb_inp.xray_structure_simple()
except Sorry as e:
assert not show_diff(
str(e), """\
Unknown chemical element type:
"ATOM 1 N GLN A 3 .*.STUV A "
To resolve this problem, specify a chemical element type in
columns 77-78 of the PDB file, right justified (e.g. " C").""")
else:
raise Exception_expected
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 1 1A GLN A 3 35.299 11.075 99.070 1.00 36.89
"""))
xray_structure = pdb_inp.xray_structure_simple(
enable_scattering_type_unknown=True)
assert xray_structure.scatterers()[0].scattering_type == "unknown"
try:
pdb_inp.xray_structure_simple()
except Sorry as e:
assert not show_diff(
str(e), """\
Unknown chemical element type:
"ATOM 1 1A GLN A 3 .*. "
To resolve this problem, specify a chemical element type in
columns 77-78 of the PDB file, right justified (e.g. " C").""")
else:
raise Exception_expected
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 1 N GLN A 3 35.299 11.075 99.070 1.00 36.89 Bx5
"""))
xray_structure = pdb_inp.xray_structure_simple(
enable_scattering_type_unknown=True)
assert xray_structure.scatterers()[0].scattering_type == "unknown"
try:
pdb_inp.xray_structure_simple()
except Sorry as e:
assert not show_diff(
str(e), '''\
Unknown charge:
"ATOM 1 N GLN A 3 .*. Bx5"
^^''')
else:
raise Exception_expected
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 1 N GLN A 3 35.299 11.075 99.070 1.00 36.89 Cs3-
"""))
xray_structure = pdb_inp.xray_structure_simple()
assert xray_structure.scatterers()[0].scattering_type == "Cs"
xray_structure = pdb_inp.xray_structure_simple(
scattering_type_exact=True, enable_scattering_type_unknown=True)
assert xray_structure.scatterers()[0].scattering_type == "unknown"
out = StringIO()
xray_structure.scattering_type_registry().show(out=out)
assert not show_diff(
out.getvalue(), """\
Number of scattering types: 1
Type Number sf(0) Gaussians
unknown 1 None None
sf(0) = scattering factor at diffraction angle 0.
""")
try:
pdb_inp.xray_structure_simple(scattering_type_exact=True)
except Sorry as e:
assert not show_diff(
str(e), '''\
Unknown scattering type:
"ATOM 1 N GLN A 3 .*. Cs3-"
^^^^ ^^^^''')
else:
raise Exception_expected
#
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ATOM 1 N GLN A 3 35.299 11.075 19.070 1.00 36.89
ATOM 2 CA GLN A 3 34.482 9.927 18.794 0.63 37.88
ENDMDL
MODEL 2
ATOM 1 N GLN A 3 25.299 1.075 9.070 0.54 26.89
ATOM 2 CA GLN A 3 24.482 -1.927 8.794 1.00 27.88
ENDMDL
"""))
xray_structure = pdb_inp.xray_structure_simple(
unit_cube_pseudo_crystal=True)
out = StringIO()
xray_structure.show_scatterers(f=out)
assert not show_diff(
out.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
model=" 1" pdb=" N GLN A 3 " N 1 (35.2990 11.0750 19.0700)\
1.00 0.4672 [ - ]
model=" 1" pdb=" CA GLN A 3 " C 1 (34.4820 9.9270 18.7940)\
0.63 0.4798 [ - ]
model=" 2" pdb=" N GLN A 3 " N 1 (25.2990 1.0750 9.0700)\
0.54 0.3406 [ - ]
model=" 2" pdb=" CA GLN A 3 " C 1 (24.4820 -1.9270 8.7940)\
1.00 0.3531 [ - ]
""")
xray_structures = pdb_inp.xray_structures_simple(
unit_cube_pseudo_crystal=True)
assert len(xray_structures) == 2
out = StringIO()
xray_structures[0].show_scatterers(f=out)
assert not show_diff(
out.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
model=" 1" pdb=" N GLN A 3 " N 1 (35.2990 11.0750 19.0700)\
1.00 0.4672 [ - ]
model=" 1" pdb=" CA GLN A 3 " C 1 (34.4820 9.9270 18.7940)\
0.63 0.4798 [ - ]
""")
out = StringIO()
xray_structures[1].show_scatterers(f=out)
assert not show_diff(
out.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
model=" 2" pdb=" N GLN A 3 " N 1 (25.2990 1.0750 9.0700)\
0.54 0.3406 [ - ]
model=" 2" pdb=" CA GLN A 3 " C 1 (24.4820 -1.9270 8.7940)\
1.00 0.3531 [ - ]
""")
#
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 369 PEAK PEAK 1 61.114 12.134 8.619 1.00 20.00 PEAK
ATOM 504 SITE SITE 2 67.707 2.505 14.951 1.00 20.00 SITE
"""))
xray_structure = pdb_inp.xray_structure_simple()
assert xray_structure.scattering_type_registry().type_index_pairs_as_dict() \
== {"const": 0}
assert list(xray_structure.scattering_type_registry().unique_counts) == [2]
#
pdb_inp = pdb.pdb_input(source_info=None, lines=flex.split_lines("""\
"""))
assert pdb_inp.xray_structure_simple().scatterers().size() == 0
assert len(pdb_inp.xray_structures_simple()) == 1
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
"""))
assert pdb_inp.xray_structure_simple().scatterers().size() == 0
assert len(pdb_inp.xray_structures_simple()) == 1
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
MODEL 2
ENDMDL
"""))
assert pdb_inp.xray_structure_simple().scatterers().size() == 0
assert len(pdb_inp.xray_structures_simple()) == 2
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ATOM 1 N GLN A 3 35.299 11.075 99.070 1.00 36.89 O-2
ENDMDL
MODEL 2
ENDMDL
"""))
assert pdb_inp.xray_structure_simple().scatterers().size() == 1
xray_structures = pdb_inp.xray_structures_simple()
assert len(xray_structures) == 2
assert xray_structures[0].scatterers().size() == 1
assert xray_structures[1].scatterers().size() == 0
assert xray_structures[0].scatterers()[0].scattering_type == "O2-"
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
MODEL 2
ATOM 1 N GLN A 3 35.299 11.075 99.070 1.00 36.89 Fe+3
ENDMDL
"""))
assert pdb_inp.xray_structure_simple().scatterers().size() == 1
xray_structures = pdb_inp.xray_structures_simple()
assert len(xray_structures) == 2
assert xray_structures[0].scatterers().size() == 0
assert xray_structures[1].scatterers().size() == 1
assert xray_structures[1].scatterers()[0].scattering_type == "Fe3+"
input_pdb_string = """\
ATOM 1 N GLN A 3 35.299 11.075 19.070 1.00 36.89 N
ATOM 2 CA GLN A 3 34.482 9.927 18.794 0.63 37.88 C0
ATOM 3 C GLN A 3 35.130 8.880 17.864 0.84 37.52 C 0
ATOM 4 O GLN A 3 34.548 7.819 17.724 1.00 38.54 O00
ATOM 5 1CB GLN A 3 32.979 10.223 18.469 1.00 37.80 C 1
HETATM 6 CA ION B 1 32.360 11.092 17.308 0.92 35.96 X
HETATM 7 CA ION B 2 30.822 10.665 17.190 1.00 36.87 FE4+
ATOM 8 O MET A 5 6.215 22.789 24.067 1.00 0.00 -2
"""
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines(input_pdb_string))
assert [scatterer.scattering_type
for scatterer in pdb_inp.xray_structure_simple(
scattering_type_exact=True,
enable_scattering_type_unknown=True).scatterers()] \
== ["N", "C", "C", "O", "unknown", "unknown", "unknown", "O2-"]
#
cs1 = crystal.symmetry(unit_cell=(3.113, 3.444, 2.572, 90, 90, 90),
space_group_symbol="P1")
cs2 = crystal.symmetry(unit_cell=(10, 20, 30, 80, 85, 95),
space_group_symbol="P-1")
input_pdb_string = """\
ATOM 1 N GLN A 3 35.299 11.075 19.070 1.00 36.89 N
ATOM 2 CA GLN A 3 34.482 9.927 18.794 0.63 37.88 C
"""
pdb_inp = pdb.pdb_input(source_info=None, lines=input_pdb_string)
xs = pdb_inp.xray_structure_simple()
assert xs.is_similar_symmetry(cs1)
xs = pdb_inp.xray_structure_simple(crystal_symmetry=cs2)
assert xs.is_similar_symmetry(cs2)
input_pdb_string = """\
CRYST1 10.000 20.000 30.000 80.00 85.00 95.00
ATOM 1 N GLN A 3 35.299 11.075 19.070 1.00 36.89 N
ATOM 2 CA GLN A 3 34.482 9.927 18.794 0.63 37.88 C
"""
pdb_inp = pdb.pdb_input(source_info=None, lines=input_pdb_string)
xs = pdb_inp.xray_structure_simple()
assert xs.is_similar_symmetry(
cs1.customized_copy(unit_cell=cs2.unit_cell()))
xs = pdb_inp.xray_structure_simple(crystal_symmetry=cs2)
assert xs.is_similar_symmetry(cs2)
input_pdb_string = """\
CRYST1 P -1
ATOM 1 N GLN A 3 35.299 11.075 19.070 1.00 36.89 N
ATOM 2 CA GLN A 3 34.482 9.927 18.794 0.63 37.88 C
"""
pdb_inp = pdb.pdb_input(source_info=None, lines=input_pdb_string)
xs = pdb_inp.xray_structure_simple()
assert xs.is_similar_symmetry(
cs1.customized_copy(space_group_info=cs2.space_group_info()))
xs = pdb_inp.xray_structure_simple(crystal_symmetry=cs2)
assert xs.is_similar_symmetry(cs2)
input_pdb_string = """\
CRYST1 10.000 20.000 30.000 80.00 85.00 95.00 P -1
ATOM 1 N GLN A 3 35.299 11.075 19.070 1.00 36.89 N
ATOM 2 CA GLN A 3 34.482 9.927 18.794 0.63 37.88 C
"""
pdb_inp = pdb.pdb_input(source_info=None, lines=input_pdb_string)
xs = pdb_inp.xray_structure_simple()
assert xs.is_similar_symmetry(cs2)
xs = pdb_inp.xray_structure_simple(crystal_symmetry=cs1)
assert xs.is_similar_symmetry(cs1)
def exercise_pdb_input():
for i_trial in range(3):
pdb_inp = pdb.pdb_input(source_info=None, lines=flex.split_lines(""))
assert (pdb_inp.file_type() == "pdb")
assert pdb_inp.source_info() == ""
assert len(pdb_inp.record_type_counts()) == 0
assert pdb_inp.unknown_section().size() == 0
assert pdb_inp.title_section().size() == 0
assert pdb_inp.remark_section().size() == 0
assert pdb_inp.primary_structure_section().size() == 0
assert pdb_inp.heterogen_section().size() == 0
assert pdb_inp.secondary_structure_section().size() == 0
assert pdb_inp.connectivity_annotation_section().size() == 0
assert pdb_inp.miscellaneous_features_section().size() == 0
assert pdb_inp.crystallographic_section().size() == 0
assert len(pdb_inp.atoms_with_labels()) == 0
assert pdb_inp.atoms().size() == 0
assert pdb_inp.model_ids().size() == 0
assert pdb_inp.model_indices().size() == 0
assert pdb_inp.ter_indices().size() == 0
assert pdb_inp.chain_indices().size() == 0
assert pdb_inp.break_indices().size() == 0
assert pdb_inp.connectivity_section().size() == 0
assert pdb_inp.bookkeeping_section().size() == 0
assert pdb_inp.model_atom_counts().size() == 0
pdb_inp = pdb.pdb_input(source_info="file/name",
lines=pdb_string_all_sections)
assert pdb_inp.source_info() == "file/name"
assert pdb_inp.record_type_counts() == {
"KEYWDS": 1,
"SEQRES": 1,
"LINK ": 1,
"ORIGX1": 1,
"SITE ": 1,
"FTNOTE": 1,
"HETSYN": 1,
"SIGATM": 2,
"MTRIX2": 1,
"MTRIX3": 1,
"HELIX ": 1,
"MTRIX1": 1,
"END ": 1,
"ANISOU": 2,
"TITLE ": 1,
"SLTBRG": 1,
"REMARK": 1,
"TURN ": 1,
"SCALE1": 1,
"SCALE2": 1,
"AUTHOR": 1,
"CRYST1": 1,
"SIGUIJ": 2,
"CISPEP": 1,
"ATOM ": 4,
"ENDMDL": 2,
"ORIGX2": 1,
"MODRES": 1,
"SOURCE": 1,
"FORMUL": 1,
"MASTER": 1,
"CAVEAT": 1,
"HET ": 1,
"COMPND": 1,
"MODEL ": 2,
"REVDAT": 1,
"SSBOND": 1,
"OBSLTE": 1,
"CONECT": 1,
"JRNL ": 1,
"SPRSDE": 1,
" ": 11,
"FOOBAR": 1,
"HETNAM": 1,
"HEADER": 1,
"ORIGX3": 1,
"BREAK ": 1,
"ONHOLD": 1,
"SHEET ": 1,
"TVECT ": 1,
"HYDBND": 1,
"TER ": 2,
"DBREF ": 1,
"EXPDTA": 1,
"SCALE3": 1,
"HETATM": 2,
"SEQADV": 1,
"SPLIT ": 1,
"NUMMDL": 1,
"MDLTYP": 2,
"DBREF1": 1,
"DBREF2": 1
}
assert list(pdb_inp.unknown_section()) == ["FOOBAR BAR FOO"]
assert not show_diff(
"\n".join(pdb_inp.title_section()), """\
HEADER ISOMERASE 02-JUL-92 1FKB
ONHOLD 26-JUN-99
OBSLTE 07-DEC-04 1A0Y 1Y4P
TITLE ATOMIC STRUCTURE OF THE RAPAMYCIN HUMAN IMMUNOPHILIN FKBP-
SPLIT 2QNH 1VSP
COMPND FK506 BINDING PROTEIN (FKBP) COMPLEX WITH IMMUNOSUPPRESSANT
SOURCE HUMAN (H**O SAPIENS) RECOMBINANT FORM EXPRESSED IN
KEYWDS ISOMERASE
EXPDTA X-RAY DIFFRACTION
NUMMDL 8
MDLTYP CA ATOMS ONLY, CHAIN B, C, D, E, F, G, H, I, J, K, L, M, N,
MDLTYP 2 O, P, Q, R, S, T, U
AUTHOR G.D.VAN DUYNE,R.F.STANDAERT,S.L.SCHREIBER,J.C.CLARDY
REVDAT 1 31-OCT-93 1FKB 0
JRNL AUTH G.D.VAN DUYNE,R.F.STANDAERT,S.L.SCHREIBER,J.CLARDY
SPRSDE 02-SEP-03 1O58 1J6N
CAVEAT 1B7F INCORRECT CHIRALITY AT C1* OF U2, CHAIN Q""")
assert not show_diff(
"\n".join(pdb_inp.remark_section()), """\
REMARK 2 RESOLUTION. 1.7 ANGSTROMS.
FTNOTE 1 CIS PEPTIDE: GLY 190 - PHE 191""")
assert not show_diff(
"\n".join(pdb_inp.primary_structure_section()), """\
DBREF 1HTQ A 601 468 SWS Q10377 GLN1_MYCTU 2 478
DBREF1 1JZX A 1 2880 GB 15805042
DBREF2 1JZX A NC_001263 2587937 2590817
SEQRES 1 A 477 THR GLU LYS THR PRO ASP ASP VAL PHE LYS LEU ALA LYS
SEQADV 1KEH ALA A 170 SWS Q9L5D6 SER 199 ENGINEERED
MODRES 6NSE CYS A 384 CYS MODIFIED BY CAD""")
assert not show_diff(
"\n".join(pdb_inp.heterogen_section()), """\
HET GLC A 810 12
HETNAM G6D 6-DEOXY-ALPHA-D-GLUCOSE
HETSYN G6D QUINOVOSE
FORMUL 2 CA 4(CA1 2+)""")
assert not show_diff(
"\n".join(pdb_inp.secondary_structure_section()), """\
HELIX 1 1 GLN A 18 GLY A 34 1 17
SHEET 1 A 7 PHE A 257 ALA A 260 0
TURN 1 T1 GLY E 2 THR E 5 BETA, TYPE II""")
assert not show_diff(
"\n".join(pdb_inp.connectivity_annotation_section()), """\
SSBOND 12 CYS B 191 CYS B 220
LINK N PRO C 61 C GLY A 9 1556
HYDBND N GLY A 148 O PHE B 41
SLTBRG N ILE A 16 OD2 ASP A 194
CISPEP 1 ALA A 183 PRO A 184 1 0.96""")
assert not show_diff(
"\n".join(pdb_inp.miscellaneous_features_section()), """\
SITE 1 CAB 3 HIS B 57 ASP B 102 SER B 195""")
assert not show_diff(
"\n".join(pdb_inp.crystallographic_section()), """\
CRYST1 45.920 49.790 89.880 90.00 97.34 90.00 P 1 21 1 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.021777 0.000000 0.002805 0.00000
SCALE2 0.000000 0.020084 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011218 0.00000
MTRIX1 1 0.739109 0.012922 -0.673462 17.07460 1
MTRIX2 1 0.015672 -0.999875 -0.001986 21.64730 1
MTRIX3 1 -0.673404 -0.009087 -0.739219 44.75290 1
TVECT 1 0.00000 0.00000 20.42000""")
assert len(pdb_inp.atoms_with_labels()) == 6
assert [atom.serial for atom in pdb_inp.atoms()] \
== [" 1", " 2", " 3", " 4", " 9", " 10"]
assert [atom.element for atom in pdb_inp.atoms()] \
== [" N", " C", " C", " O", " ", " "]
assert list(pdb_inp.model_ids()) == [" 1", " 3"]
assert list(pdb_inp.model_indices()) == [4, 6]
assert list(pdb_inp.ter_indices()) == [5, 6]
assert [list(v) for v in pdb_inp.chain_indices()] == [[4], [5, 6]]
assert list(pdb_inp.break_indices()) == [2]
assert not show_diff("\n".join(pdb_inp.connectivity_section()), """\
CONECT 5332 5333 5334 5335 5336""")
assert not show_diff(
"\n".join(pdb_inp.bookkeeping_section()), """\
MASTER 81 0 0 7 3 0 0 645800 20 0 12
END""")
assert list(pdb_inp.model_atom_counts()) == [4, 2]
#
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 1 CB LYS 109 16.113 7.345 47.084 1.00 20.00 A
ATOM 2 CG LYS 109 17.058 6.315 47.703 1.00 20.00 A
ATOM 3 CB LYS 109 26.721 1.908 15.275 1.00 20.00 B
ATOM 4 CG LYS 109 27.664 2.793 16.091 1.00 20.00 B
"""))
expected_id_strs = """\
pdb=" CB LYS 109 " segid="A "
pdb=" CG LYS 109 " segid="A "
pdb=" CB LYS 109 " segid="B "
pdb=" CG LYS 109 " segid="B "
""".splitlines()
for awl, eids in zip(pdb_inp.atoms_with_labels(), expected_id_strs):
assert not show_diff(awl.id_str(), eids)
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdefS123E1C1
HETATM12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdefS123E1C1
"""))
for awl in pdb_inp.atoms_with_labels():
assert awl.name == "N123"
assert awl.altloc == "A"
assert awl.resname == "R12"
assert awl.chain_id == "C"
assert awl.resseq == "1234"
assert awl.icode == "I"
assert awl.segid == "S123"
assert awl.id_str() == 'pdb="N123AR12 C1234I" segid="S123"'
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM 12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdef E1C1
HETATM12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdef E1C1
"""))
for awl in pdb_inp.atoms_with_labels():
assert awl.name == "N123"
assert awl.altloc == "A"
assert awl.resname == "R12"
assert awl.chain_id == "C"
assert awl.resseq == "1234"
assert awl.icode == "I"
assert awl.segid == " "
assert awl.id_str() == 'pdb="N123AR12 C1234I"'
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM
HETATM
"""))
for awl in pdb_inp.atoms_with_labels():
assert awl.name == " "
assert awl.altloc == " "
assert awl.resname == " "
assert awl.chain_id == " "
assert awl.resseq == " "
assert awl.icode == " "
assert awl.segid == " "
assert awl.id_str() == 'pdb=" "'
#
pdb_inp = pdb.pdb_input(source_info=None, lines=flex.split_lines("""\
"""))
assert list(pdb_inp.model_indices()) == []
assert list(pdb_inp.chain_indices()) == []
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM
"""))
assert list(pdb_inp.model_indices()) == [1]
assert [list(v) for v in pdb_inp.chain_indices()] == [[1]]
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [0]
assert [list(v) for v in pdb_inp.chain_indices()] == [[]]
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ATOM
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [1]
assert [list(v) for v in pdb_inp.chain_indices()] == [[1]]
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
MODEL 2
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [0, 0]
assert [list(v) for v in pdb_inp.chain_indices()] == [[], []]
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
MODEL 2
ATOM
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [0, 1]
assert [list(v) for v in pdb_inp.chain_indices()] == [[], [1]]
try:
pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
ATOM
"""))
except ValueError as e:
assert not show_diff(
str(e), """\
input line 3:
ATOM
^
ATOM or HETATM record is outside MODEL/ENDMDL block.""")
else:
raise Exception_expected
try:
pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
MODEL 2
"""))
except ValueError as e:
assert not show_diff(
str(e), """\
input line 2:
MODEL 2
^
Missing ENDMDL for previous MODEL record.""")
else:
raise Exception_expected
try:
pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM
MODEL 1
"""))
except ValueError as e:
assert not show_diff(
str(e), """\
input line 2:
MODEL 1
^
MODEL record must appear before any ATOM or HETATM records.""")
else:
raise Exception_expected
try:
pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
ATOM
ENDMDL
"""))
except ValueError as e:
assert not show_diff(
str(e), """\
input line 2:
ENDMDL
^
No matching MODEL record.""")
else:
raise Exception_expected
#
for record_name in ["SIGATM", "ANISOU", "SIGUIJ"]:
try:
pdb.pdb_input(source_info=None,
lines=flex.std_string([record_name]))
except ValueError as e:
assert not show_diff(
str(e), """\
input line 1:
%s
^
no matching ATOM or HETATM record.""" % record_name)
else:
raise Exception_expected
#
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
MODEL 1
ATOM C
ATOM C
ATOM D
ATOM E
ATOM E
ENDMDL
MODEL 2
ATOM C
ATOM C
ATOM D
ATOM D
ATOM E
ENDMDL
MODEL 3
ATOM C
ATOM D
ATOM D
ATOM E X
ATOM E
ENDMDL
MODEL 4
ATOM C
ATOM D
ATOM C
ATOM E X
ATOM E
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [5, 10, 15, 20]
assert [list(v) for v in pdb_inp.chain_indices()] \
== [[2,3,5],[7,9,10],[11,13,15], [18,20]]
#
f = open("tmp.pdb", "w")
f.close()
pdb_inp = pdb.pdb_input(file_name="tmp.pdb")
assert pdb_inp.source_info() == "file tmp.pdb"
with open("tmp.pdb", "w") as f:
f.write("""\
ATOM 1 CA SER 1 1.212 -12.134 3.757 1.00 0.00
ATOM 2 CA LEU 2 1.118 -9.777 0.735 1.00 0.00
""")
pdb_inp = pdb.pdb_input(file_name="tmp.pdb")
try:
pdb.pdb_input(file_name="")
except IOError as e:
assert str(e).startswith('Cannot open file for reading: ""')
else:
raise Exception_expected
#
assert "HIS" in pdb.common_residue_names_amino_acid
assert "TRO" in pdb.common_residue_names_modified_amino_acid
assert "GUA" in pdb.common_residue_names_rna_dna
assert "2MA" in pdb.common_residue_names_modified_rna_dna
assert "CD " in pdb.common_residue_names_ccp4_mon_lib_rna_dna
assert "HOH" in pdb.common_residue_names_water
assert "SO4" in pdb.common_residue_names_small_molecule
assert " FE" in pdb.common_residue_names_element
get_class = pdb.common_residue_names_get_class
assert get_class(name="ALA") == "common_amino_acid"
assert get_class(name="0AF") == "modified_amino_acid"
assert get_class(name="TRQ") == "modified_amino_acid"
assert get_class(name=" U") == "common_rna_dna"
assert get_class(name="2MA") == "modified_rna_dna"
assert get_class(name="HOH") == "common_water"
assert get_class(name="SO4") == "common_small_molecule"
assert get_class(name="CL ") == "common_element"
assert get_class(name="ABC") == "other"
assert get_class(name="CD ") == "common_element"
assert get_class(name="CD ", consider_ccp4_mon_lib_rna_dna=True) \
== "ccp4_mon_lib_rna_dna"
#
assert pdb.rna_dna_reference_residue_name(common_name="ALA") is None
for common_names in [
pdb.common_residue_names_rna_dna,
pdb.common_residue_names_ccp4_mon_lib_rna_dna
]:
for n in common_names:
r = pdb.rna_dna_reference_residue_name(common_name=n)
assert r is not None
assert pdb.rna_dna_reference_residue_name(common_name=" " +
n.lower() + " ") == r
#
for line in """\
CRYST1 61.410 54.829 43.543 90.00 90.00 90.00 P 21 21 21 8
REMARK sg= P2(1)2(1)2(1) a= 61.410 b= 54.829 c= 43.543 alpha= 90 beta= 90 gamma= 90
""".splitlines():
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.std_string([line]))
cs = pdb_inp.crystal_symmetry()
assert str(cs.unit_cell()) == "(61.41, 54.829, 43.543, 90, 90, 90)"
assert str(cs.space_group_info()) == "P 21 21 21"
sps = pdb_inp.special_position_settings()
assert sps.is_similar_symmetry(cs)
assert approx_equal(sps.min_distance_sym_equiv(), 0.5)
for weak_symmetry in [False, True]:
cs = pdb_inp.crystal_symmetry(
crystal_symmetry=crystal.symmetry(unit_cell=(10, 10, 10, 90,
90, 90)),
weak_symmetry=weak_symmetry)
if (weak_symmetry):
assert str(
cs.unit_cell()) == "(61.41, 54.829, 43.543, 90, 90, 90)"
else:
assert str(cs.unit_cell()) == "(10, 10, 10, 90, 90, 90)"
assert str(cs.space_group_info()) == "P 21 21 21"
sps = pdb_inp.special_position_settings(
special_position_settings=cs.special_position_settings(
min_distance_sym_equiv=3),
weak_symmetry=weak_symmetry)
assert sps.is_similar_symmetry(cs)
assert approx_equal(sps.min_distance_sym_equiv(), 3)
#
assert pdb_inp.extract_header_year() is None
assert pdb_inp.extract_remark_iii_records(iii=2) == []
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
HEADER 02-JUL-92
REMARK 2 RESOLUTION. 1.7 ANGSTROMS.
"""))
assert pdb_inp.extract_header_year() == 1992
assert pdb_inp.extract_remark_iii_records(iii=2) \
== ['REMARK 2 RESOLUTION. 1.7 ANGSTROMS.']
# extract_connectivity
pdb_inp = pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
HETATM 1 C ACT 1428 -0.014 0.010 0.027 1.00 20.00
HETATM 2 O ACT 1428 -0.480 -1.088 -0.009 1.00 20.00
HETATM 3 OXT ACT 1428 -0.744 0.936 -0.009 1.00 20.00
HETATM 4 CH3 ACT 1428 1.238 0.142 -0.009 1.00 20.00
CONECT 1 2 3 4
CONECT 4 1
"""))
bonds = pdb_inp.extract_connectivity()
assert (len(bonds) == 4)
assert (list(bonds[0]) == [1, 2, 3]) and (list(bonds[3]) == [0])
assert (list(bonds[1]) == list(bonds[2]) == [])
def exercise_line_info_exceptions():
pdb.pdb_input(source_info=None, lines=flex.std_string(["ATOM"]))
#
try:
pdb.pdb_input(source_info="some.pdb",
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
"""))
except ValueError as e:
assert not show_diff(
str(e), """\
some.pdb, line 2:
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
---------------------------------^
unexpected plus sign.""")
else:
raise Exception_expected
try:
pdb.pdb_input(source_info="some.pdb",
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
"""),
raise_sorry_if_format_error=True)
except Sorry:
pass
else:
raise Exception_expected
try:
pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 84- 848 848 0 0 0
"""))
except ValueError as e:
assert not show_diff(
str(e), """\
input line 3:
ANISOU 9 2H3 MPR B 5 84- 848 848 0 0 0
----------------------------------^
unexpected minus sign.""")
else:
raise Exception_expected
try:
pdb.pdb_input(source_info=None,
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 c 848 848 0 0 0
"""))
except ValueError as e:
assert not show_diff(
str(e), """\
input line 2:
ANISOU 9 2H3 MPR B 5 c 848 848 0 0 0
------------------------------^
unexpected character.""")
else:
raise Exception_expected
#
try:
pdb.pdb_input(
source_info="some.pdb",
lines=flex.std_string([
"ATOM 1045 O HOH 30 x 0.530 42.610 45.267 1.00 33.84"
]))
except ValueError as e:
assert not show_diff(
str(e), """\
some.pdb, line 1:
ATOM 1045 O HOH 30 x 0.530 42.610 45.267 1.00 33.84
------------------------------^
not a floating-point number.""")
else:
raise Exception_expected
try:
pdb.pdb_input(
source_info="some.pdb",
lines=flex.std_string([
"ATOM 1045 O HOH 30 x 0.530 42.610 45.267 1.00 33.84"
]))
except ValueError as e:
assert not show_diff(
str(e), """\
some.pdb, line 1:
ATOM 1045 O HOH 30 x 0.530 42.610 45.267 1.00 33.84
-------------------------------^
not a floating-point number.""")
else:
raise Exception_expected
try:
pdb.pdb_input(
source_info="some.pdb",
lines=flex.std_string([
"HETATM 4160 O HOH S 272 nan 0.000 0.000 1.00 54.72"
]))
except ValueError as e:
assert not show_diff(
str(e), """\
some.pdb, line 1:
HETATM 4160 O HOH S 272 nan 0.000 0.000 1.00 54.72
-----------------------------------^
not a floating-point number.""")
else:
raise Exception_expected
try:
pdb.pdb_input(
source_info="some.pdb",
lines=flex.std_string([
"ATOM 1045 O HOH 30 0x530 42.610 45.267 1.00 33.84"
]))
except ValueError as e:
assert not show_diff(
str(e), """\
some.pdb, line 1:
ATOM 1045 O HOH 30 0x530 42.610 45.267 1.00 33.84
----------------------------------^
unexpected character.""")
else:
raise Exception_expected
def exercise_xray_structure_simple():
pdb_inp = pdb.pdb_input(source_info=None, lines=flex.split_lines("""\
CRYST1 61.410 54.829 43.543 90.00 90.00 90.00 P 21 21 21 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.016284 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018239 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022966 0.00000
ATOM 1 N GLN A 3 35.299 11.075 19.070 1.00 36.89 N
ATOM 2 CA GLN A 3 34.482 9.927 18.794 0.63 37.88 C
SIGATM 2 CA GLN A 3 1.200 2.300 3.400 0.04 0.05 C
ANISOU 2 CA GLN A 3 7794 3221 3376 -1227 1064 2601 C
ATOM 3 Q GLN A 3 35.130 8.880 17.864 0.84 37.52 C
ANISOU 3 Q GLN A 3 7875 3041 3340 -981 727 2663 C
SIGUIJ 3 Q GLN A 3 75 41 40 -1 7 63 C
ATOM 4 O GLN A 3 34.548 7.819 17.724 1.00 38.54 STUV
ATOM 5 1CB AGLN A 3 32.979 10.223 18.469 1.00 37.80
HETATM 6 CA AION B 1 32.360 11.092 17.308 0.92 35.96 CA2+
HETATM 7 CA ION B 2 30.822 10.665 17.190 1.00 36.87
"""))
for use_scale_matrix_if_available in [False, True]:
xray_structure = pdb_inp.xray_structure_simple(
use_scale_matrix_if_available=use_scale_matrix_if_available)
out = StringIO()
xray_structure.show_summary(f=out)
assert not show_diff(out.getvalue(), """\
Number of scatterers: 7
At special positions: 0
Unit cell: (61.41, 54.829, 43.543, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
""")
out = StringIO()
xray_structure.show_scatterers(f=out)
assert not show_diff(out.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
pdb=" N GLN A 3 " N 4 ( 0.5748 0.2020 0.4380) 1.00 0.4672 [ - ]
pdb=" CA GLN A 3 " C 4 ( 0.5615 0.1811 0.4316) 0.63 [ - ] 0.4797
u_cart = 0.779 0.322 0.338 -0.123 0.106 0.260
pdb=" Q GLN A 3 " C 4 ( 0.5721 0.1620 0.4103) 0.84 [ - ] 0.4752
u_cart = 0.788 0.304 0.334 -0.098 0.073 0.266
pdb=" O GLN A 3 " segid="STUV" O 4 ( 0.5626 0.1426 0.4070)\
1.00 0.4881 [ - ]
pdb="1CB AGLN A 3 " C 4 ( 0.5370 0.1865 0.4242) 1.00 0.4787 [ - ]
pdb="CA AION B 1 " Ca2+ 4 ( 0.5270 0.2023 0.3975) 0.92 0.4554 [ - ]
pdb="CA ION B 2 " Ca 4 ( 0.5019 0.1945 0.3948) 1.00 0.4670 [ - ]
""")
#
xray_structure = pdb_inp.xray_structure_simple(unit_cube_pseudo_crystal=True)
out = StringIO()
xray_structure.show_summary(f=out)
assert not show_diff(out.getvalue(), """\
Number of scatterers: 7
At special positions: 0
Unit cell: (1, 1, 1, 90, 90, 90)
Space group: P 1 (No. 1)
""")
out = StringIO()
xray_structure.show_scatterers(f=out)
assert not show_diff(out.getvalue(), """\
Label, Scattering, Multiplicity, Coordinates, Occupancy, Uiso, Ustar as Uiso
pdb=" N GLN A 3 " N 1 (35.2990 11.0750 19.0700) 1.00 0.4672 [ - ]
pdb=" CA GLN A 3 " C 1 (34.4820 9.9270 18.7940) 0.63 [ - ] 0.4797
u_cart = 0.779 0.322 0.338 -0.123 0.106 0.260
pdb=" Q GLN A 3 " C 1 (35.1300 8.8800 17.8640) 0.84 [ - ] 0.4752
u_cart = 0.788 0.304 0.334 -0.098 0.073 0.266
pdb=" O GLN A 3 " segid="STUV" O 1 (34.5480 7.8190 17.7240)\
1.00 0.4881 [ - ]
pdb="1CB AGLN A 3 " C 1 (32.9790 10.2230 18.4690) 1.00 0.4787 [ - ]
pdb="CA AION B 1 " Ca2+ 1 (32.3600 11.0920 17.3080) 0.92 0.4554 [ - ]
pdb="CA ION B 2 " Ca 1 (30.8220 10.6650 17.1900) 1.00 0.4670 [ - ]
""")
#
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
ATOM 1 N GLN A 3 35.299 11.075 99.070 1.00 36.89 STUV A
"""))
xray_structure = pdb_inp.xray_structure_simple(
enable_scattering_type_unknown=True)
assert xray_structure.scatterers()[0].scattering_type == "unknown"
try:
pdb_inp.xray_structure_simple()
except Sorry, e:
assert not show_diff(str(e), """\
Unknown chemical element type:
"ATOM 1 N GLN A 3 .*.STUV A "
To resolve this problem, specify a chemical element type in
columns 77-78 of the PDB file, right justified (e.g. " C").""")
Args:
ideal_hierarchy (pdb_hierarchy): Ideal ligand
poor_hierarchy (pdb_hierarchy): Poor ligand with correct c.o.m. and same
atom names in order. Could become more sophisticated.
"""
sites_moving = flex.vec3_double()
sites_fixed = flex.vec3_double()
for atom1, atom2 in zip(ideal_hierarchy.atoms(), poor_hierarchy.atoms()):
assert atom1.name == atom2.name, '%s!=%s' % (atom1.quote(),
atom2.quote())
sites_moving.append(atom1.xyz)
sites_fixed.append(atom2.xyz)
lsq_fit = superpose.least_squares_fit(reference_sites=sites_fixed,
other_sites=sites_moving)
sites_new = ideal_hierarchy.atoms().extract_xyz()
sites_new = lsq_fit.r.elems * sites_new + lsq_fit.t.elems
# rmsd = sites_fixed.rms_difference(lsq_fit.other_sites_best_fit())
ideal_hierarchy.atoms().set_xyz(sites_new)
return ideal_hierarchy
if __name__ == "__main__":
from iotbx import pdb
ideal_inp = pdb.pdb_input(sys.argv[1])
ideal_hierarchy = ideal_inp.construct_hierarchy()
poor_inp = pdb.pdb_input(sys.argv[2])
poor_hierarchy = poor_inp.construct_hierarchy()
ideal_hierarchy = superpose_ideal_ligand_on_poor_ligand(
ideal_hierarchy, poor_hierarchy)
ideal_hierarchy.write_pdb_file('new.pdb')
def exercise_pdb_input():
for i_trial in xrange(3):
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines(""))
assert (pdb_inp.file_type() == "pdb")
assert pdb_inp.source_info() == ""
assert len(pdb_inp.record_type_counts()) == 0
assert pdb_inp.unknown_section().size() == 0
assert pdb_inp.title_section().size() == 0
assert pdb_inp.remark_section().size() == 0
assert pdb_inp.primary_structure_section().size() == 0
assert pdb_inp.heterogen_section().size() == 0
assert pdb_inp.secondary_structure_section().size() == 0
assert pdb_inp.connectivity_annotation_section().size() == 0
assert pdb_inp.miscellaneous_features_section().size() == 0
assert pdb_inp.crystallographic_section().size() == 0
assert len(pdb_inp.atoms_with_labels()) == 0
assert pdb_inp.atoms().size() == 0
assert pdb_inp.model_ids().size() == 0
assert pdb_inp.model_indices().size() == 0
assert pdb_inp.ter_indices().size() == 0
assert pdb_inp.chain_indices().size() == 0
assert pdb_inp.break_indices().size() == 0
assert pdb_inp.connectivity_section().size() == 0
assert pdb_inp.bookkeeping_section().size() == 0
assert pdb_inp.model_atom_counts().size() == 0
pdb_inp = pdb.pdb_input(
source_info="file/name",
lines=pdb_string_all_sections)
assert pdb_inp.source_info() == "file/name"
assert pdb_inp.record_type_counts() == {
"KEYWDS": 1, "SEQRES": 1, "LINK ": 1, "ORIGX1": 1, "SITE ": 1,
"FTNOTE": 1, "HETSYN": 1, "SIGATM": 2, "MTRIX2": 1, "MTRIX3": 1,
"HELIX ": 1, "MTRIX1": 1, "END ": 1, "ANISOU": 2, "TITLE ": 1,
"SLTBRG": 1, "REMARK": 1, "TURN ": 1, "SCALE1": 1, "SCALE2": 1,
"AUTHOR": 1, "CRYST1": 1, "SIGUIJ": 2, "CISPEP": 1, "ATOM ": 4,
"ENDMDL": 2, "ORIGX2": 1, "MODRES": 1, "SOURCE": 1, "FORMUL": 1,
"MASTER": 1, "CAVEAT": 1, "HET ": 1, "COMPND": 1, "MODEL ": 2,
"REVDAT": 1, "SSBOND": 1, "OBSLTE": 1, "CONECT": 1, "JRNL ": 1,
"SPRSDE": 1, " ":11, "FOOBAR": 1, "HETNAM": 1, "HEADER": 1,
"ORIGX3": 1, "BREAK ": 1, "ONHOLD": 1, "SHEET ": 1, "TVECT ": 1,
"HYDBND": 1, "TER ": 2, "DBREF ": 1, "EXPDTA": 1, "SCALE3": 1,
"HETATM": 2, "SEQADV": 1, "SPLIT ": 1, "NUMMDL": 1, "MDLTYP": 2,
"DBREF1": 1, "DBREF2": 1}
assert list(pdb_inp.unknown_section()) == ["FOOBAR BAR FOO"]
assert not show_diff("\n".join(pdb_inp.title_section()), """\
HEADER ISOMERASE 02-JUL-92 1FKB
ONHOLD 26-JUN-99
OBSLTE 07-DEC-04 1A0Y 1Y4P
TITLE ATOMIC STRUCTURE OF THE RAPAMYCIN HUMAN IMMUNOPHILIN FKBP-
SPLIT 2QNH 1VSP
COMPND FK506 BINDING PROTEIN (FKBP) COMPLEX WITH IMMUNOSUPPRESSANT
SOURCE HUMAN (H**O SAPIENS) RECOMBINANT FORM EXPRESSED IN
KEYWDS ISOMERASE
EXPDTA X-RAY DIFFRACTION
NUMMDL 8
MDLTYP CA ATOMS ONLY, CHAIN B, C, D, E, F, G, H, I, J, K, L, M, N,
MDLTYP 2 O, P, Q, R, S, T, U
AUTHOR G.D.VAN DUYNE,R.F.STANDAERT,S.L.SCHREIBER,J.C.CLARDY
REVDAT 1 31-OCT-93 1FKB 0
JRNL AUTH G.D.VAN DUYNE,R.F.STANDAERT,S.L.SCHREIBER,J.CLARDY
SPRSDE 02-SEP-03 1O58 1J6N
CAVEAT 1B7F INCORRECT CHIRALITY AT C1* OF U2, CHAIN Q""")
assert not show_diff("\n".join(pdb_inp.remark_section()), """\
REMARK 2 RESOLUTION. 1.7 ANGSTROMS.
FTNOTE 1 CIS PEPTIDE: GLY 190 - PHE 191""")
assert not show_diff("\n".join(pdb_inp.primary_structure_section()), """\
DBREF 1HTQ A 601 468 SWS Q10377 GLN1_MYCTU 2 478
DBREF1 1JZX A 1 2880 GB 15805042
DBREF2 1JZX A NC_001263 2587937 2590817
SEQRES 1 A 477 THR GLU LYS THR PRO ASP ASP VAL PHE LYS LEU ALA LYS
SEQADV 1KEH ALA A 170 SWS Q9L5D6 SER 199 ENGINEERED
MODRES 6NSE CYS A 384 CYS MODIFIED BY CAD""")
assert not show_diff("\n".join(pdb_inp.heterogen_section()), """\
HET GLC A 810 12
HETNAM G6D 6-DEOXY-ALPHA-D-GLUCOSE
HETSYN G6D QUINOVOSE
FORMUL 2 CA 4(CA1 2+)""")
assert not show_diff("\n".join(pdb_inp.secondary_structure_section()), """\
HELIX 1 1 GLN A 18 GLY A 34 1 17
SHEET 1 A 7 PHE A 257 ALA A 260 0
TURN 1 T1 GLY E 2 THR E 5 BETA, TYPE II""")
assert not show_diff(
"\n".join(pdb_inp.connectivity_annotation_section()), """\
SSBOND 12 CYS B 191 CYS B 220
LINK N PRO C 61 C GLY A 9 1556
HYDBND N GLY A 148 O PHE B 41
SLTBRG N ILE A 16 OD2 ASP A 194
CISPEP 1 ALA A 183 PRO A 184 1 0.96""")
assert not show_diff(
"\n".join(pdb_inp.miscellaneous_features_section()), """\
SITE 1 CAB 3 HIS B 57 ASP B 102 SER B 195""")
assert not show_diff("\n".join(pdb_inp.crystallographic_section()), """\
CRYST1 45.920 49.790 89.880 90.00 97.34 90.00 P 1 21 1 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.021777 0.000000 0.002805 0.00000
SCALE2 0.000000 0.020084 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011218 0.00000
MTRIX1 1 0.739109 0.012922 -0.673462 17.07460 1
MTRIX2 1 0.015672 -0.999875 -0.001986 21.64730 1
MTRIX3 1 -0.673404 -0.009087 -0.739219 44.75290 1
TVECT 1 0.00000 0.00000 20.42000""")
assert len(pdb_inp.atoms_with_labels()) == 6
assert [atom.serial for atom in pdb_inp.atoms()] \
== [" 1", " 2", " 3", " 4", " 9", " 10"]
assert [atom.element for atom in pdb_inp.atoms()] \
== [" N", " C", " C", " O", " ", " "]
assert list(pdb_inp.model_ids()) == [" 1", " 3"]
assert list(pdb_inp.model_indices()) == [4,6]
assert list(pdb_inp.ter_indices()) == [5,6]
assert [list(v) for v in pdb_inp.chain_indices()] == [[4],[5,6]]
assert list(pdb_inp.break_indices()) == [2]
assert not show_diff("\n".join(pdb_inp.connectivity_section()), """\
CONECT 5332 5333 5334 5335 5336""")
assert not show_diff("\n".join(pdb_inp.bookkeeping_section()), """\
MASTER 81 0 0 7 3 0 0 645800 20 0 12
END""")
assert list(pdb_inp.model_atom_counts()) == [4,2]
#
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
ATOM 1 CB LYS 109 16.113 7.345 47.084 1.00 20.00 A
ATOM 2 CG LYS 109 17.058 6.315 47.703 1.00 20.00 A
ATOM 3 CB LYS 109 26.721 1.908 15.275 1.00 20.00 B
ATOM 4 CG LYS 109 27.664 2.793 16.091 1.00 20.00 B
"""))
expected_id_strs = """\
pdb=" CB LYS 109 " segid="A "
pdb=" CG LYS 109 " segid="A "
pdb=" CB LYS 109 " segid="B "
pdb=" CG LYS 109 " segid="B "
""".splitlines()
for awl,eids in zip(pdb_inp.atoms_with_labels(), expected_id_strs):
assert not show_diff(awl.id_str(), eids)
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
ATOM 12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdefS123E1C1
HETATM12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdefS123E1C1
"""))
for awl in pdb_inp.atoms_with_labels():
assert awl.name == "N123"
assert awl.altloc == "A"
assert awl.resname == "R12"
assert awl.chain_id == "C"
assert awl.resseq == "1234"
assert awl.icode == "I"
assert awl.segid == "S123"
assert awl.id_str() == 'pdb="N123AR12 C1234I" segid="S123"'
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
ATOM 12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdef E1C1
HETATM12345qN123AR12 C1234Ixyz1234.6781234.6781234.678123.56213.56abcdef E1C1
"""))
for awl in pdb_inp.atoms_with_labels():
assert awl.name == "N123"
assert awl.altloc == "A"
assert awl.resname == "R12"
assert awl.chain_id == "C"
assert awl.resseq == "1234"
assert awl.icode == "I"
assert awl.segid == " "
assert awl.id_str() == 'pdb="N123AR12 C1234I"'
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
ATOM
HETATM
"""))
for awl in pdb_inp.atoms_with_labels():
assert awl.name == " "
assert awl.altloc == " "
assert awl.resname == " "
assert awl.chain_id == " "
assert awl.resseq == " "
assert awl.icode == " "
assert awl.segid == " "
assert awl.id_str() == 'pdb=" "'
#
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
"""))
assert list(pdb_inp.model_indices()) == []
assert list(pdb_inp.chain_indices()) == []
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
ATOM
"""))
assert list(pdb_inp.model_indices()) == [1]
assert [list(v) for v in pdb_inp.chain_indices()] == [[1]]
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [0]
assert [list(v) for v in pdb_inp.chain_indices()] == [[]]
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
MODEL 1
ATOM
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [1]
assert [list(v) for v in pdb_inp.chain_indices()] == [[1]]
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
MODEL 2
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [0,0]
assert [list(v) for v in pdb_inp.chain_indices()] == [[],[]]
pdb_inp = pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
MODEL 2
ATOM
ENDMDL
"""))
assert list(pdb_inp.model_indices()) == [0,1]
assert [list(v) for v in pdb_inp.chain_indices()] == [[],[1]]
try:
pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
MODEL 1
ENDMDL
ATOM
"""))
except ValueError, e:
assert not show_diff(str(e), """\
input line 3:
ATOM
^
ATOM or HETATM record is outside MODEL/ENDMDL block.""")
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
"""))
except ValueError, e:
assert not show_diff(str(e), """\
some.pdb, line 2:
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
---------------------------------^
unexpected plus sign.""")
else: raise Exception_expected
try :
pdb.pdb_input(
source_info="some.pdb",
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 8+8 848 848 0 0 0
"""),
raise_sorry_if_format_error=True)
except Sorry :
pass
else: raise Exception_expected
try:
pdb.pdb_input(
source_info=None,
lines=flex.split_lines("""\
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08
ANISOU 9 2H3 MPR B 5 84- 848 848 0 0 0
"""))
except ValueError, e: