def side_chain_placement(ag_to_place, current_reference_ag, rotamer_manager):
"""
Works with poly_gly truncated hierarchy.
Also used in fix_rama_outliers.
"""
resname = current_reference_ag.resname.upper()
c = one_three.get(resname, None)
# seems to work with unusual residues...
# if c is None:
# msg = "Only standard protein residues are currently supported.\n"
# msg += "The residue %s (chain %s, resid %s) chain is not standard." % (
# resname,
# current_reference_ag.parent().parent().id,
# current_reference_ag.parent().resid())
# raise Sorry(msg)
ag_to_place.resname = three_one.get(c,resname)
if c == 'G':
return
# align residue from ideal_res_dict to just placed ALA (ag_to_place)
# or from pdb_hierarchy_template
fixed_sites = flex.vec3_double()
moving_sites = flex.vec3_double()
reper_atoms = ["C","CA", "N"]
for (ag, arr) in [(ag_to_place, fixed_sites),
(current_reference_ag, moving_sites)]:
for a in ag.atoms():
if a.name.strip() in reper_atoms:
arr.append(a.xyz)
assert len(fixed_sites) == 3
if len(moving_sites) < 3:
error_msg = "C, CA or N atoms are absent in secondary structure element." +\
"\nPlease add them to the model and try again."
raise Sorry(error_msg)
assert len(moving_sites) == 3
lsq_fit_obj = superpose.least_squares_fit(reference_sites = fixed_sites,
other_sites = moving_sites)
ideal_correct_ag = current_reference_ag.detached_copy()
ideal_correct_ag.atoms().set_xyz(
lsq_fit_obj.r.elems*ideal_correct_ag.atoms().extract_xyz()+\
lsq_fit_obj.t.elems)
ideal_correct_ag.atoms().set_xyz(
rotamer_manager.nearest_rotamer_sites_cart(ideal_correct_ag))
if len(ideal_correct_ag.atoms()) > 4:
ag_to_place.pre_allocate_atoms(number_of_additional_atoms=\
len(ideal_correct_ag.atoms())-4)
for a in ideal_correct_ag.atoms():
if a.name.strip() not in ["N","CA","C","O"]:
at = a.detached_copy()
at.uij_erase()
ag_to_place.append_atom(atom=at)
else:
# This means something wrong with input model, e.g. only 3 atoms in
# the residue and they happened to be N, CA, C
pass
def correct_sequence(pdb_hierarchy,
sequences,
truncate_to_cbeta=False,
out=sys.stdout):
"""
Modify the sequence for the pdb hierarchy to match that of the aligned
sequence. This will remove incompatible atoms; the sidechains will still
need to be extended separated. For proteins only - mismatches in nucleic
acids will only result in a warning.
:param pdb_hierarchy: iotbx.pdb.hierarchy.root object
:param sequences: list of iotbx.bioinformatics.sequence objects
:param trucate_to_cbeta: chop off entire sidechain to C-beta (default: leave
common atoms in place)
:param out: output filehandle (default = stdout)
:returns: number of atom_group objects renamed
"""
from mmtbx.monomer_library import idealized_aa
import mmtbx.validation.sequence
from iotbx.pdb.amino_acid_codes import three_letter_given_one_letter
seq_validation = mmtbx.validation.sequence.validation(
pdb_hierarchy=pdb_hierarchy, sequences=sequences, log=out)
for chain_seq in seq_validation.chains:
if (chain_seq.chain_type == mmtbx.validation.sequence.NUCLEIC_ACID):
if (len(chain_seq.mismatch) > 0):
print(" WARNING: will skip %d mismatches in nucleic acid chain '%s'" % \
chain_seq.chain_id, file=out)
res_dict = idealized_aa.residue_dict()
expected_names = {}
for resname in res_dict.keys():
if (not "_h" in resname):
ideal_res = res_dict[resname]
expected_names[resname] = set([a.name for a in ideal_res.atoms()])
n_changed = 0
for chain in pdb_hierarchy.only_model().chains():
if (not chain.is_protein()):
continue
for chain_seq in seq_validation.chains:
if (chain.id
== chain_seq.chain_id) and (len(chain_seq.mismatch) > 0):
for residue_group in chain.residue_groups():
resid = residue_group.resid()
if (resid in chain_seq.mismatch):
idx = chain_seq.mismatch.index(resid)
new_code = chain_seq.actual_code[idx]
new_resname = three_letter_given_one_letter.get(
new_code)
if (new_resname is not None):
expected_atoms = expected_names[
new_resname.lower()]
if (truncate_to_cbeta):
expected_atoms = expected_names["ala"]
for atom_group in residue_group.atom_groups():
n_changed += 1
n_removed = 0
atom_group.resname = new_resname
for atom in atom_group.atoms():
if (not atom.name in expected_atoms):
atom_group.remove_atom(atom)
n_removed += 1
print(" chain '%s' %s %s --> %s (%d atoms removed)" % \
(chain.id, resid, residue_group.atom_groups()[0].resname,
new_resname, n_removed), file=out)
pdb_hierarchy.atoms().reset_i_seq()
return n_changed
def get_aa_parent(code):
one = modified_aa_names.lookup.get(code.upper(), False)
if not one: return code
return three_letter_given_one_letter.get(one, None)
def exercise_pdb_hierarchy_sequence_as_cif_block():
pdb_atom_site_loop_header = """\
data_mmcif
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
"""
# simple example with multiple copies of chain
input_4ehz = """\
ATOM 2 C CA . GLU A 1 6 ? -35.647 65.380 -11.775 1.00 65.78 ? ? ? ? ? ? 858 GLU A CA 1
ATOM 11 C CA . LYS A 1 7 ? -34.996 68.963 -10.712 1.00 89.52 ? ? ? ? ? ? 859 LYS A CA 1
ATOM 20 C CA . LYS A 1 8 ? -31.415 68.325 -9.529 1.00 98.54 ? ? ? ? ? ? 860 LYS A CA 1
ATOM 29 C CA . PRO A 1 9 ? -29.858 70.569 -6.813 1.00 103.45 ? ? ? ? ? ? 861 PRO A CA 1
ATOM 36 C CA . ALA A 1 10 ? -26.545 72.463 -7.079 1.00 98.87 ? ? ? ? ? ? 862 ALA A CA 1
ATOM 41 C CA . THR A 1 11 ? -23.410 70.412 -7.767 1.00 90.75 ? ? ? ? ? ? 863 THR A CA 1
ATOM 48 C CA . GLU A 1 12 ? -21.306 71.534 -4.804 1.00 75.15 ? ? ? ? ? ? 864 GLU A CA 1
ATOM 57 C CA . VAL A 1 13 ? -17.543 70.954 -4.809 1.00 49.52 ? ? ? ? ? ? 865 VAL A CA 1
ATOM 64 C CA . ASP A 1 14 ? -16.048 68.671 -2.185 1.00 26.98 ? ? ? ? ? ? 866 ASP A CA 1
ATOM 72 C CA . PRO A 1 15 ? -12.276 69.450 -2.061 1.00 27.34 ? ? ? ? ? ? 867 PRO A CA 1
ATOM 79 C CA . THR A 1 16 ? -11.669 65.942 -0.699 1.00 23.73 ? ? ? ? ? ? 868 THR A CA 1
ATOM 86 C CA . HIS A 1 17 ? -13.266 64.157 -3.671 1.00 23.80 ? ? ? ? ? ? 869 HIS A CA 1
ATOM 96 C CA . PHE A 1 18 ? -10.664 63.252 -6.277 1.00 14.88 ? ? ? ? ? ? 870 PHE A CA 1
ATOM 107 C CA . GLU A 1 19 ? -12.022 62.182 -9.666 1.00 23.47 ? ? ? ? ? ? 871 GLU A CA 1
ATOM 116 C CA . LYS A 1 20 ? -10.351 59.111 -11.117 1.00 17.57 ? ? ? ? ? ? 872 LYS A CA 1
ATOM 125 C CA . ARG A 1 21 ? -10.204 60.546 -14.661 1.00 19.09 ? ? ? ? ? ? 873 ARG A CA 1
ATOM 136 C CA . PHE A 1 22 ? -7.912 63.384 -13.545 1.00 22.03 ? ? ? ? ? ? 874 PHE A CA 1
ATOM 147 C CA . LEU A 1 23 ? -5.613 61.332 -11.271 1.00 18.20 ? ? ? ? ? ? 875 LEU A CA 1
ATOM 155 C CA . LYS A 1 24 ? -2.583 60.745 -13.513 1.00 26.05 ? ? ? ? ? ? 876 LYS A CA 1
ATOM 2365 C CA . VAL B 1 13 ? 38.084 -8.470 -5.157 1.00 57.98 ? ? ? ? ? ? 865 VAL B CA 1
ATOM 2372 C CA . ASP B 1 14 ? 36.468 -6.229 -2.536 1.00 51.96 ? ? ? ? ? ? 866 ASP B CA 1
ATOM 2380 C CA . PRO B 1 15 ? 32.749 -7.130 -2.340 1.00 48.96 ? ? ? ? ? ? 867 PRO B CA 1
ATOM 2387 C CA . THR B 1 16 ? 31.935 -3.705 -0.847 1.00 26.72 ? ? ? ? ? ? 868 THR B CA 1
ATOM 2394 C CA . HIS B 1 17 ? 33.519 -1.814 -3.754 1.00 33.15 ? ? ? ? ? ? 869 HIS B CA 1
ATOM 2404 C CA . PHE B 1 18 ? 31.094 -0.811 -6.488 1.00 26.55 ? ? ? ? ? ? 870 PHE B CA 1
ATOM 2415 C CA . GLU B 1 19 ? 32.359 0.467 -9.861 1.00 38.45 ? ? ? ? ? ? 871 GLU B CA 1
ATOM 2424 C CA . LYS B 1 20 ? 30.409 3.510 -11.036 1.00 33.69 ? ? ? ? ? ? 872 LYS B CA 1
ATOM 2433 C CA . ARG B 1 21 ? 30.400 2.430 -14.663 1.00 36.58 ? ? ? ? ? ? 873 ARG B CA 1
ATOM 2444 C CA . PHE B 1 22 ? 28.294 -0.647 -13.791 1.00 38.39 ? ? ? ? ? ? 874 PHE B CA 1
ATOM 2455 C CA . LEU B 1 23 ? 25.763 1.275 -11.703 1.00 32.87 ? ? ? ? ? ? 875 LEU B CA 1
ATOM 2463 C CA . LYS B 1 24 ? 22.588 1.723 -13.713 1.00 30.22 ? ? ? ? ? ? 876 LYS B CA 1
"""
import iotbx.bioinformatics
from iotbx.pdb.amino_acid_codes import three_letter_given_one_letter
from cctbx.array_family import flex
sequence_4ehz = iotbx.bioinformatics.sequence(
"GDIVSEKKPATEVDPTHFEKRFLK") #RIRDLGEGHF"
pdb_in = iotbx.pdb.input(lines=(pdb_atom_site_loop_header +
input_4ehz).splitlines(),
source_info=None)
model = mmtbx.model.manager(pdb_in)
model.set_sequences([sequence_4ehz])
cif_block = model._sequence_validation.sequence_as_cif_block()
sequence = ';' + sequence_4ehz.sequence + '\n;'
assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == sequence
assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][
0] == sequence
assert cif_block['_entity_poly.pdbx_strand_id'] == 'A,B'
assert approx_equal(flex.int(cif_block['_entity_poly_seq.num']),
list(range(1, 25)))
assert cif_block['_entity_poly_seq.entity_id'].all_eq('1')
assert list(cif_block['_entity_poly_seq.mon_id']) == [
three_letter_given_one_letter.get(i) for i in sequence_4ehz.sequence
]
#
# example with modified amino acid - PTR
input_3zdi = """\
ATOM 1422 C CA . ASN A 1 179 ? -11.025 -26.833 -3.747 1.00 86.68 ? ? ? ? ? ? 213 ASN A CA 1
ATOM 1430 C CA . VAL A 1 180 ? -7.831 -26.493 -1.696 1.00 82.40 ? ? ? ? ? ? 214 VAL A CA 1
ATOM 1437 C CA . SER A 1 181 ? -8.142 -28.602 1.444 1.00 89.69 ? ? ? ? ? ? 215 SER A CA 1
ATOM 1443 C CA . PTR A 1 182 ? -5.406 -26.622 3.177 1.00 88.05 ? ? ? ? ? ? 216 PTR A CA 1
ATOM 1459 C CA . ILE A 1 183 ? -7.514 -23.621 4.117 1.00 83.90 ? ? ? ? ? ? 217 ILE A CA 1
ATOM 1467 C CA . CYS A 1 184 ? -8.907 -21.533 7.009 1.00 86.39 ? ? ? ? ? ? 218 CYS A CA 1
ATOM 1473 C CA . SER A 1 185 ? -6.795 -21.356 10.148 1.00 91.03 ? ? ? ? ? ? 219 SER A CA 1
"""
sequence_3zdi = iotbx.bioinformatics.sequence("NVSYICSR")
pdb_in = iotbx.pdb.input(lines=(pdb_atom_site_loop_header +
input_3zdi).splitlines(),
source_info=None)
model = mmtbx.model.manager(pdb_in)
model.set_sequences([sequence_3zdi])
cif_block = model._sequence_validation.sequence_as_cif_block()
assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == \
';NVS(PTR)ICSR\n;'
assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == \
';' + sequence_3zdi.sequence + '\n;'
assert approx_equal(flex.int(cif_block['_entity_poly_seq.num']),
list(range(1, 9)))
assert list(cif_block['_entity_poly_seq.mon_id']) == [
'ASN', 'VAL', 'SER', 'PTR', 'ILE', 'CYS', 'SER', 'ARG'
]
#
input_4gln = """\
ATOM 2 C CA . DTH A 1 1 ? -2.916 5.861 2.629 1.00 16.39 ? ? ? ? ? ? 1 DTH D CA 1
ATOM 9 C CA . DTY A 1 2 ? 0.533 4.844 3.866 1.00 10.74 ? ? ? ? ? ? 2 DTY D CA 1
ATOM 21 C CA . DLY A 1 3 ? 3.161 3.111 1.736 1.00 8.24 ? ? ? ? ? ? 3 DLY D CA 1
ATOM 30 C CA . DLE A 1 4 ? 6.958 3.293 1.625 1.00 7.95 ? ? ? ? ? ? 4 DLE D CA 1
ATOM 38 C CA . DIL A 1 5 ? 9.053 0.443 0.257 1.00 8.44 ? ? ? ? ? ? 5 DIL D CA 1
ATOM 46 C CA . DLE A 1 6 ? 12.622 1.402 -0.674 1.00 8.62 ? ? ? ? ? ? 6 DLE D CA 1
ATOM 54 C CA A DSG A 1 7 ? 14.930 -1.609 -0.756 0.60 11.27 ? ? ? ? ? ? 7 DSG D CA 1
ATOM 55 C CA B DSG A 1 7 ? 14.934 -1.617 -0.732 0.40 11.77 ? ? ? ? ? ? 7 DSG D CA 1
ATOM 67 C CA . GLY A 1 8 ? 18.113 -0.249 -2.284 1.00 13.02 ? ? ? ? ? ? 8 GLY D CA 1
ATOM 71 C CA . DLY A 1 9 ? 21.326 -1.954 -3.288 1.00 17.83 ? ? ? ? ? ? 9 DLY D CA 1
ATOM 80 C CA . DTH A 1 10 ? 20.765 -0.934 -6.926 1.00 16.38 ? ? ? ? ? ? 10 DTH D CA 1
#
ATOM 472 C CA . GLU B 2 6 ? 15.798 -6.874 23.843 1.00 31.74 ? ? ? ? ? ? 6 GLU E CA 1
ATOM 477 C CA . VAL B 2 7 ? 16.644 -3.926 21.599 1.00 15.99 ? ? ? ? ? ? 7 VAL E CA 1
ATOM 484 C CA . VAL B 2 8 ? 13.767 -1.465 21.234 1.00 10.37 ? ? ? ? ? ? 8 VAL E CA 1
ATOM 491 C CA . LYS B 2 9 ? 12.953 -1.088 17.521 1.00 8.44 ? ? ? ? ? ? 9 LYS E CA 1
#
HETATM 2537 O O . HOH E 3 . ? 8.196 -3.708 8.277 1.00 15.02 ? ? ? ? ? ? 101 HOH D O 1
HETATM 2538 O O . HOH E 3 . ? 4.901 -4.298 5.515 1.00 13.08 ? ? ? ? ? ? 102 HOH D O 1
HETATM 2663 O O . HOH F 3 . ? 10.535 -2.721 20.049 1.00 15.44 ? ? ? ? ? ? 201 HOH E O 1
HETATM 2664 O O . HOH F 3 . ? 0.790 8.695 30.909 1.00 17.06 ? ? ? ? ? ? 202 HOH E O 1
HETATM 2795 O O . HOH G 3 . ? 11.265 2.914 43.878 1.00 13.92 ? ? ? ? ? ? 201 HOH F O 1
HETATM 2796 O O . HOH G 3 . ? 11.197 11.667 36.108 1.00 17.00 ? ? ? ? ? ? 202 HOH F O 1
"""
sequence_4gln = [
iotbx.bioinformatics.sequence("TYKLILNGKT"),
iotbx.bioinformatics.sequence("GQNHHEVVK")
]
pdb_in = iotbx.pdb.input(lines=(pdb_atom_site_loop_header +
input_4gln).splitlines(),
source_info=None)
model = mmtbx.model.manager(pdb_in)
model.set_sequences(sequence_4gln)
cif_block = model._sequence_validation.sequence_as_cif_block()
assert list(cif_block['_entity.id']) == ['1', '2']
assert approx_equal(flex.int(cif_block['_entity_poly_seq.num']),
list(range(1, 11)) + list(range(1, 10)))
assert list(cif_block['_entity_poly_seq.mon_id']) == [
'DTH', 'DTY', 'DLY', 'DLE', 'DIL', 'DLE', 'DSG', 'GLY', 'DLY', 'DTH',
'GLY', 'GLN', 'ASN', 'HIS', 'HIS', 'GLU', 'VAL', 'VAL', 'LYS'
]
assert list(cif_block['_entity_poly.pdbx_seq_one_letter_code']) == [
';(DTH)(DTY)(DLY)(DLE)(DIL)(DLE)(DSG)G(DLY)(DTH)\n;',
';' + sequence_4gln[1].sequence + '\n;'
]
assert list(cif_block['_entity_poly.pdbx_seq_one_letter_code_can']) == [
';' + sequence_4gln[0].sequence + '\n;',
';' + sequence_4gln[1].sequence + '\n;'
]
#
input_1ezu = """\
ATOM 3971 C CA . VAL D 2 16 ? 24.971 -4.493 -3.652 1.00 33.12 ? ? ? ? ? ? 731 VAL D CA 1
ATOM 3978 C CA . SER D 2 17 ? 27.194 -3.056 -0.946 1.00 35.47 ? ? ? ? ? ? 732 SER D CA 1
ATOM 3984 C CA . LEU D 2 18 ? 26.541 0.123 0.961 1.00 45.29 ? ? ? ? ? ? 733 LEU D CA 1
ATOM 3992 C CA . ASN D 2 19 ? 29.777 2.032 1.598 1.00 53.09 ? ? ? ? ? ? 734 ASN D CA 1
ATOM 4000 C CA . SER D 2 20 ? 30.737 4.963 3.775 1.00 61.92 ? ? ? ? ? ? 737 SER D CA 1
ATOM 4006 C CA . GLY D 2 21 ? 34.478 4.622 4.207 1.00 62.21 ? ? ? ? ? ? 738 GLY D CA 1
ATOM 4010 C CA . TYR D 2 22 ? 33.903 0.885 4.483 1.00 54.81 ? ? ? ? ? ? 739 TYR D CA 1
"""
sequence_1ezu = iotbx.bioinformatics.sequence('VSLNSGY')
pdb_in = iotbx.pdb.input(lines=(pdb_atom_site_loop_header +
input_1ezu).splitlines(),
source_info=None)
model = mmtbx.model.manager(pdb_in)
model.set_sequences([sequence_1ezu])
cif_block = model._sequence_validation.sequence_as_cif_block()
assert list(cif_block['_entity_poly_seq.mon_id']) == [
'VAL', 'SER', 'LEU', 'ASN', 'SER', 'GLY', 'TYR'
]
assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == \
';' + sequence_1ezu.sequence + '\n;'
assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == \
';' + sequence_1ezu.sequence + '\n;'
input_2hok = """\
ATOM 301 P P . C A 1 15 ? 15.802 44.045 80.094 1.00 59.36 ? ? ? ? ? ? 23 C A P 1
ATOM 321 P P . C A 1 16 ? 12.286 47.301 82.617 1.00 68.27 ? ? ? ? ? ? 24 C A P 1
ATOM 341 P P . U A 1 17 ? 6.815 51.648 82.739 1.00 78.03 ? ? ? ? ? ? 25 U A P 1
ATOM 361 P P . G A 1 21 ? 7.042 52.289 91.645 1.00 96.25 ? ? ? ? ? ? 29 G A P 1
ATOM 384 P P . C A 1 22 ? 7.024 46.751 90.841 1.00 84.69 ? ? ? ? ? ? 30 C A P 1
ATOM 404 P P . G A 1 23 ? 7.477 40.933 88.377 1.00 81.65 ? ? ? ? ? ? 31 G A P 1
"""
sequence_2hok = iotbx.bioinformatics.sequence("CCUUCUGCG")
pdb_in = iotbx.pdb.input(lines=(pdb_atom_site_loop_header +
input_2hok).splitlines(),
source_info=None)
model = mmtbx.model.manager(pdb_in)
model.set_sequences([sequence_2hok])
cif_block = model._sequence_validation.sequence_as_cif_block()
assert list(cif_block['_entity_poly_seq.mon_id']) == [
'C', 'C', 'U', 'U', 'C', 'U', 'G', 'C', 'G'
]
assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == \
';' + sequence_2hok.sequence + '\n;'
assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == \
';' + sequence_2hok.sequence + '\n;'
#
input_3tpy = """\
ATOM 2 CA GLN A 24 2.586 40.220 34.036 1.00 41.54 C
ATOM 8 CA LYS A 25 1.265 43.698 34.904 1.00 25.47 C
ATOM 17 CA GLN A 26 3.834 45.984 36.538 1.00 22.91 C
ATOM 26 CA PRO A 27 2.835 48.614 39.135 1.00 19.20 C
ATOM 33 CA ILE A 28 3.972 52.206 39.293 1.00 18.70 C
ATOM 41 CA SER A 29 6.403 51.332 42.097 1.00 22.63 C
TER
HETATM 852 MG MG A 999 -12.415 61.451 32.421 0.70 28.10 MG
HETATM 853 C TRS A 153 -0.078 70.151 24.773 0.33 24.86 C
HETATM 877 PA BDUP A 777 -9.339 60.563 31.137 0.70 19.64 P
HETATM 881 PB BDUP A 777 -11.768 59.969 29.491 0.70 27.76 P
HETATM 885 PG BDUP A 777 -13.098 58.529 31.620 0.70 33.91 P
HETATM 905 P AUMP A 154 -9.010 60.358 31.334 0.30 11.42 P
HETATM 909 O HOH A 155 -0.197 60.723 27.343 1.00 17.17 O
HETATM 910 O HOH A 156 -10.293 62.567 35.648 1.00 19.43 O
"""
sequence_3tpy = iotbx.bioinformatics.sequence("QKQPIS")
pdb_in = iotbx.pdb.input(lines=(input_3tpy).splitlines(), source_info=None)
model = mmtbx.model.manager(pdb_in)
model.set_sequences([sequence_3tpy])
cif_block = model.get_hierarchy().as_cif_block()
assert list(cif_block["_atom_site.label_seq_id"]) == [
'1', '2', '3', '4', '5', '6', '.', '.', '.', '.', '.', '.', '.', '.'
]
#
input_3tgr = """\
ATOM 2449 CA GLY A 459 -17.536 10.137 41.979 1.00181.52 C
ATOM 2453 CA GLN A 460 -15.862 12.780 44.128 1.00192.51 C
ATOM 2462 CA ASN A 463 -19.198 8.054 50.455 1.00180.96 C
ATOM 2470 CA ASP A 464 -19.235 4.661 52.197 1.00143.07 C
ATOM 2478 CA THR A 465 -20.893 2.988 49.198 1.00 91.96 C
"""
sequence_3tgr = iotbx.bioinformatics.sequence("DGGQSNETNDTET")
pdb_in = iotbx.pdb.input(lines=(input_3tgr).splitlines(), source_info=None)
model = mmtbx.model.manager(pdb_in)
model.set_sequences([sequence_3tgr])
cif_block = model._sequence_validation.sequence_as_cif_block()
assert cif_block["_entity_poly.pdbx_seq_one_letter_code"][0] == \
';DGGQSNETNDNET\n;'
input_2im9 = """\
ATOM 2423 CA PRO A 345 2.114 16.158 0.161 1.00 29.14 C
ATOM 2430 CA VAL A 346 -1.223 17.837 0.938 1.00 31.05 C
ATOM 2437 CA CYS A 349 -4.081 15.852 7.014 0.50 28.57 C
ATOM 2443 CA GLN A 350 -6.176 14.041 9.639 0.50 30.62 C
ATOM 2452 CA LEU A 351 -6.631 10.729 7.797 0.50 31.53 C
ATOM 2460 CA PHE A 352 -5.220 9.172 4.620 0.50 31.95 C
"""
sequence_2im9 = iotbx.bioinformatics.sequence(
"SSPTIKGINIQVVLPEKPVSNGCQLFDIR")
pdb_in = iotbx.pdb.input(lines=(input_2im9).splitlines(), source_info=None)
model = mmtbx.model.manager(pdb_in)
model.set_sequences([sequence_2im9])
cif_block = model._sequence_validation.sequence_as_cif_block()
assert list(cif_block["_entity_poly_seq.mon_id"]) == [
'SER', 'SER', 'PRO', 'THR', 'ILE', 'LYS', 'GLY', 'ILE', 'ASN', 'ILE',
'GLN', 'VAL', 'VAL', 'LEU', 'PRO', 'GLU', 'LYS', 'PRO', 'VAL', 'SER',
'ASN', 'GLY', 'CYS', 'CYS', 'GLN', 'LEU', 'ASP', 'ILE', 'ARG'
]
def sequence_as_cif_block(self, custom_residues=None):
"""
Export sequence information as mmCIF block
Version 5.0 of mmCIF/PDBx dictionary
Parameters
----------
custom_residues: list of str
List of custom 3-letter residues to keep in pdbx_one_letter_sequence
The 3-letter residue must exist in the model. If None, the value
from self.custom_residues is used.
Returns
-------
cif_block: iotbx.cif.model.block
"""
if custom_residues is None:
custom_residues = self.custom_residues
dna = set(['DA', 'DT', 'DC', 'DG', 'DI'])
rna = set(['A', 'U', 'C', 'G'])
rna_to_dna = {'A': 'DA', 'U': 'DT', 'T': 'DT', 'C': 'DC', 'G': 'DG',
'I': 'DI'}
modified_dna = set()
modified_rna = set()
for key in modified_rna_dna_names.lookup.keys():
value = modified_rna_dna_names.lookup[key]
if value in dna:
modified_dna.add(key)
elif value in rna:
modified_rna.add(key)
# http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity.html
entity_loop = iotbx.cif.model.loop(header=(
'_entity.id',
'_entity.pdbx_description'
))
# http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity_poly.html
entity_poly_loop = iotbx.cif.model.loop(header=(
'_entity_poly.entity_id',
'_entity_poly.nstd_linkage',
'_entity_poly.nstd_monomer',
'_entity_poly.pdbx_seq_one_letter_code',
'_entity_poly.pdbx_seq_one_letter_code_can',
'_entity_poly.pdbx_strand_id',
'_entity_poly.pdbx_target_identifier',
'_entity_poly.type',
))
# http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity_poly_seq.html
entity_poly_seq_loop = iotbx.cif.model.loop(header=(
'_entity_poly_seq.entity_id',
'_entity_poly_seq.num',
'_entity_poly_seq.mon_id',
'_entity_poly_seq.hetero',
))
# http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ref.html
struct_ref_loop = iotbx.cif.model.loop(header=(
'_struct_ref.id',
'_struct_ref.db_code',
'_struct_ref.db_name',
'_struct_ref.entity_id',
'_struct_ref.pdbx_align_begin',
'_struct_ref.pdbx_db_accession',
'_struct_ref.pdbx_db_isoform',
'_struct_ref.pdbx_seq_one_letter_code',
))
# http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ref_seq.html
struct_ref_seq_loop = iotbx.cif.model.loop(header=(
'_struct_ref_seq.align_id',
'_struct_ref_seq.db_align_beg',
'_struct_ref_seq.db_align_end',
'_struct_ref_seq.pdbx_PDB_id_code',
'_struct_ref_seq.pdbx_auth_seq_align_beg',
'_struct_ref_seq.pdbx_auth_seq_align_end',
'_struct_ref_seq.pdbx_db_accession',
'_struct_ref_seq.pdbx_db_align_beg_ins_code',
'_struct_ref_seq.pdbx_db_align_end_ins_code',
'_struct_ref_seq.pdbx_seq_align_beg_ins_code',
'_struct_ref_seq.pdbx_seq_align_end_ins_code',
'_struct_ref_seq.pdbx_strand_id',
'_struct_ref_seq.ref_id',
'_struct_ref_seq.seq_align_beg',
'_struct_ref_seq.seq_align_end',
))
entity_id = 0
# entity_poly
sequence_to_entity_id = dict()
nstd_linkage = dict()
nstd_monomer = dict()
seq_one_letter_code = dict()
seq_one_letter_code_can = dict()
strand_id = dict()
target_identifier = dict()
sequence_type = dict()
# entity_poly_seq
num = dict()
mon_id = dict()
hetero = dict()
# struct_ref (work in progress)
chain_id = dict()
db_code = '?'
db_name = '?'
align_begin = '?'
db_accession = '?'
db_isoform = '?'
# struct_ref_seq (work in progress)
db_align_beg = '?'
db_align_end = '?'
PDB_id_code = '?'
align_beg_ins_code = '?'
align_end_ins_code = '?'
for i_chain, chain in enumerate(self.chains):
seq_can = chain.alignment.b
# entity_id
if seq_can not in sequence_to_entity_id:
entity_id += 1
sequence_to_entity_id[seq_can] = entity_id
else:
# subsequent matches just add strand_id
entity_id = sequence_to_entity_id[seq_can]
strand_id[entity_id].append(chain.chain_id)
continue
# entity_poly items
# nstd_linkage (work in progress)
if entity_id not in nstd_linkage:
nstd_linkage[entity_id] = 'no'
# nstd_monomer
if entity_id not in nstd_monomer:
nstd_monomer[entity_id] = 'no'
# pdbx_seq_one_letter_code
if entity_id not in seq_one_letter_code:
seq_one_letter_code[entity_id] = list()
# type (work in progress)
if entity_id not in sequence_type:
sequence_type[entity_id] = '?'
has_protein = False
has_rna = False
has_dna = False
has_sugar = False
is_d = False
# chain.alignment.a is the model
# chain.alignment.b is the sequence
for i_a, i_b in zip(chain.alignment.i_seqs_a, chain.alignment.i_seqs_b):
# sequence does not have residue in model
if i_b is None:
continue
# model does not have residue in sequence
if i_a is None or chain.resnames[i_a] is None:
letter = seq_can[i_b]
else:
resname = chain.resnames[i_a].strip()
# check for modified residues
if (resname in modified_aa_names.lookup or
resname in modified_rna_dna_names.lookup or
resname in custom_residues):
letter = '({resname})'.format(resname=resname)
nstd_monomer[entity_id] = 'yes'
elif resname in three_letter_l_given_three_letter_d:
letter = '({resname})'.format(resname=resname)
nstd_monomer[entity_id] = 'yes'
# check for nucleic acid
elif resname in dna:
letter = '({resname})'.format(resname=resname)
elif resname in rna:
letter = resname
# regular protein
else:
letter = one_letter_given_three_letter.get(resname)
if letter is None:
letter = 'X'
# check for protein
if (resname in one_letter_given_three_letter or
resname in modified_aa_names.lookup):
has_protein = True
# check for DNA
# hybrid protein/DNA/RNA chains are not allowed
if resname in dna or resname in modified_dna:
has_dna = True
has_protein = False
# check for RNA
# does not handle hybrid DNA/RNA chains
if resname in rna or resname in modified_rna:
has_rna = True
has_dna = False
has_protein = False
# check chirality
# hybrid D/L handed chains are not allowed
if resname in three_letter_l_given_three_letter_d:
is_d = True
# pdbx_seq_one_letter_code
seq_one_letter_code[entity_id].append(letter)
# pdbx_seq_one_letter_code_can
seq_one_letter_code_can[entity_id] = seq_can.replace('-', '')
# strand_id
if entity_id not in strand_id:
strand_id[entity_id] = list()
strand_id[entity_id].append(chain.chain_id)
# target_identifier (work in progress)
if entity_id not in target_identifier:
target_identifier[entity_id] = '?'
# type
# polypeptide(L)
# polypeptide(D)
# polydeoxyribonucleotide,
# polyribonucleotide
# missing
# cyclic-psuedo-peptide
# other
# peptide nucleic acid
# polydeoxyribonucleotide/polyribonucleotide
# polysaccharide(D)
# polysaccahride(L)
if has_protein:
choice = 'polypeptide'
if is_d:
choice += '(D)'
else:
choice += '(L)'
if has_dna:
choice = 'polydeoxyribonucleotide'
if has_rna:
choice = 'polyribonucleotide'
sequence_type[entity_id] = choice
# entity_poly_seq items
if entity_id not in mon_id:
mon_id[entity_id] = list()
if entity_id not in num:
num[entity_id] = list()
if entity_id not in hetero:
hetero[entity_id] = list()
# struct_ref items
if entity_id not in chain_id:
chain_id[entity_id] = i_chain + 1
for i_a, i_b in zip(chain.alignment.i_seqs_a, chain.alignment.i_seqs_b):
# sequence does not have residue in model
if i_b is None:
continue
seq_resname = None
if has_protein:
seq_resname = three_letter_given_one_letter.get(seq_can[i_b])
if has_dna:
seq_resname = rna_to_dna.get(seq_can[i_b])
if has_rna:
seq_resname = seq_can[i_b]
if seq_resname is None:
seq_resname = 'UNK'
# model does not have residue in sequence
if i_a is None or chain.resnames[i_a] is None:
resname = seq_resname
else:
resname = chain.resnames[i_a]
mon_id[entity_id].append(resname.strip())
if len(num[entity_id]) == 0:
num[entity_id].append(1)
else:
num[entity_id].append(num[entity_id][-1] + 1)
hetero[entity_id].append('no')
# build loops
ids = list(sequence_to_entity_id.values())
ids.sort()
align_id = 1
for entity_id in ids:
# construct entity_poly loop
if len(strand_id[entity_id]) == 1:
chains = strand_id[entity_id][0]
else:
chains = strand_id[entity_id]
#chains.sort()
chains = ','.join(chains)
entity_poly_loop.add_row((
entity_id,
nstd_linkage[entity_id],
nstd_monomer[entity_id],
';' + ''.join(seq_one_letter_code[entity_id]) + '\n;',
';' + seq_one_letter_code_can[entity_id] + '\n;',
chains,
target_identifier[entity_id],
sequence_type[entity_id]
))
# construct entity loop
entity_loop.add_row((
entity_id,
'Chains: ' + chains
))
# construct entity_poly_seq loop
chain_length = len(mon_id[entity_id])
for i in range(chain_length):
entity_poly_seq_loop.add_row((
entity_id,
num[entity_id][i],
mon_id[entity_id][i],
hetero[entity_id][i]
))
# construct struct_ref loop
struct_ref_loop.add_row((
chain_id[entity_id],
db_code,
db_name,
entity_id,
align_begin,
db_accession,
db_isoform,
';' + seq_one_letter_code_can[entity_id] + '\n;'
))
# construct struct_ref_seq loop
for chain in strand_id[entity_id]:
struct_ref_seq_loop.add_row((
align_id,
db_align_beg,
db_align_end,
PDB_id_code,
'1',
len(seq_one_letter_code_can[entity_id]) - 1,
db_accession,
align_beg_ins_code,
align_end_ins_code,
align_beg_ins_code,
align_end_ins_code,
chain,
chain_id[entity_id],
'1',
len(seq_one_letter_code_can[entity_id]) - 1
))
# construct block
cif_block = iotbx.cif.model.block()
cif_block.add_loop(entity_loop)
cif_block.add_loop(entity_poly_loop)
cif_block.add_loop(entity_poly_seq_loop)
cif_block.add_loop(struct_ref_loop)
cif_block.add_loop(struct_ref_seq_loop)
return cif_block
def exercise_pdb_hierarchy_sequence_as_cif_block():
pdb_atom_site_loop_header = """\
data_mmcif
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
"""
# simple example with multiple copies of chain
input_4ehz = """\
ATOM 2 C CA . GLU A 1 6 ? -35.647 65.380 -11.775 1.00 65.78 ? ? ? ? ? ? 858 GLU A CA 1
ATOM 11 C CA . LYS A 1 7 ? -34.996 68.963 -10.712 1.00 89.52 ? ? ? ? ? ? 859 LYS A CA 1
ATOM 20 C CA . LYS A 1 8 ? -31.415 68.325 -9.529 1.00 98.54 ? ? ? ? ? ? 860 LYS A CA 1
ATOM 29 C CA . PRO A 1 9 ? -29.858 70.569 -6.813 1.00 103.45 ? ? ? ? ? ? 861 PRO A CA 1
ATOM 36 C CA . ALA A 1 10 ? -26.545 72.463 -7.079 1.00 98.87 ? ? ? ? ? ? 862 ALA A CA 1
ATOM 41 C CA . THR A 1 11 ? -23.410 70.412 -7.767 1.00 90.75 ? ? ? ? ? ? 863 THR A CA 1
ATOM 48 C CA . GLU A 1 12 ? -21.306 71.534 -4.804 1.00 75.15 ? ? ? ? ? ? 864 GLU A CA 1
ATOM 57 C CA . VAL A 1 13 ? -17.543 70.954 -4.809 1.00 49.52 ? ? ? ? ? ? 865 VAL A CA 1
ATOM 64 C CA . ASP A 1 14 ? -16.048 68.671 -2.185 1.00 26.98 ? ? ? ? ? ? 866 ASP A CA 1
ATOM 72 C CA . PRO A 1 15 ? -12.276 69.450 -2.061 1.00 27.34 ? ? ? ? ? ? 867 PRO A CA 1
ATOM 79 C CA . THR A 1 16 ? -11.669 65.942 -0.699 1.00 23.73 ? ? ? ? ? ? 868 THR A CA 1
ATOM 86 C CA . HIS A 1 17 ? -13.266 64.157 -3.671 1.00 23.80 ? ? ? ? ? ? 869 HIS A CA 1
ATOM 96 C CA . PHE A 1 18 ? -10.664 63.252 -6.277 1.00 14.88 ? ? ? ? ? ? 870 PHE A CA 1
ATOM 107 C CA . GLU A 1 19 ? -12.022 62.182 -9.666 1.00 23.47 ? ? ? ? ? ? 871 GLU A CA 1
ATOM 116 C CA . LYS A 1 20 ? -10.351 59.111 -11.117 1.00 17.57 ? ? ? ? ? ? 872 LYS A CA 1
ATOM 125 C CA . ARG A 1 21 ? -10.204 60.546 -14.661 1.00 19.09 ? ? ? ? ? ? 873 ARG A CA 1
ATOM 136 C CA . PHE A 1 22 ? -7.912 63.384 -13.545 1.00 22.03 ? ? ? ? ? ? 874 PHE A CA 1
ATOM 147 C CA . LEU A 1 23 ? -5.613 61.332 -11.271 1.00 18.20 ? ? ? ? ? ? 875 LEU A CA 1
ATOM 155 C CA . LYS A 1 24 ? -2.583 60.745 -13.513 1.00 26.05 ? ? ? ? ? ? 876 LYS A CA 1
ATOM 2365 C CA . VAL B 1 13 ? 38.084 -8.470 -5.157 1.00 57.98 ? ? ? ? ? ? 865 VAL B CA 1
ATOM 2372 C CA . ASP B 1 14 ? 36.468 -6.229 -2.536 1.00 51.96 ? ? ? ? ? ? 866 ASP B CA 1
ATOM 2380 C CA . PRO B 1 15 ? 32.749 -7.130 -2.340 1.00 48.96 ? ? ? ? ? ? 867 PRO B CA 1
ATOM 2387 C CA . THR B 1 16 ? 31.935 -3.705 -0.847 1.00 26.72 ? ? ? ? ? ? 868 THR B CA 1
ATOM 2394 C CA . HIS B 1 17 ? 33.519 -1.814 -3.754 1.00 33.15 ? ? ? ? ? ? 869 HIS B CA 1
ATOM 2404 C CA . PHE B 1 18 ? 31.094 -0.811 -6.488 1.00 26.55 ? ? ? ? ? ? 870 PHE B CA 1
ATOM 2415 C CA . GLU B 1 19 ? 32.359 0.467 -9.861 1.00 38.45 ? ? ? ? ? ? 871 GLU B CA 1
ATOM 2424 C CA . LYS B 1 20 ? 30.409 3.510 -11.036 1.00 33.69 ? ? ? ? ? ? 872 LYS B CA 1
ATOM 2433 C CA . ARG B 1 21 ? 30.400 2.430 -14.663 1.00 36.58 ? ? ? ? ? ? 873 ARG B CA 1
ATOM 2444 C CA . PHE B 1 22 ? 28.294 -0.647 -13.791 1.00 38.39 ? ? ? ? ? ? 874 PHE B CA 1
ATOM 2455 C CA . LEU B 1 23 ? 25.763 1.275 -11.703 1.00 32.87 ? ? ? ? ? ? 875 LEU B CA 1
ATOM 2463 C CA . LYS B 1 24 ? 22.588 1.723 -13.713 1.00 30.22 ? ? ? ? ? ? 876 LYS B CA 1
"""
import iotbx.bioinformatics
from iotbx.pdb.amino_acid_codes import three_letter_given_one_letter
from cctbx.array_family import flex
sequence_4ehz = iotbx.bioinformatics.sequence("GDIVSEKKPATEVDPTHFEKRFLK")#RIRDLGEGHF"
pdb_in = iotbx.pdb.input(
lines=(pdb_atom_site_loop_header+input_4ehz).splitlines(),
source_info=None)
pdb_hierarchy = pdb_in.construct_hierarchy()
cif_block = pdb_hierarchy.as_cif_block_with_sequence(
sequences=[sequence_4ehz],
crystal_symmetry=pdb_in.crystal_symmetry())
assert cif_block['_entity.id'][0] == '1'
assert cif_block['_entity.type'][0] == 'polymer'
assert cif_block['_entity.pdbx_number_of_molecules'][0] == '2'
assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == sequence_4ehz.sequence
assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == sequence_4ehz.sequence
assert cif_block['_entity_poly.pdbx_strand_id'] == 'A,B'
assert approx_equal(flex.int(cif_block['_entity_poly_seq.num']), range(1, 25))
assert cif_block['_entity_poly_seq.entity_id'].all_eq('1')
assert list(cif_block['_entity_poly_seq.mon_id']) == [
three_letter_given_one_letter.get(i) for i in sequence_4ehz.sequence]
#
# example with modified amino acid - PTR
input_3zdi = """\
ATOM 1422 C CA . ASN A 1 179 ? -11.025 -26.833 -3.747 1.00 86.68 ? ? ? ? ? ? 213 ASN A CA 1
ATOM 1430 C CA . VAL A 1 180 ? -7.831 -26.493 -1.696 1.00 82.40 ? ? ? ? ? ? 214 VAL A CA 1
ATOM 1437 C CA . SER A 1 181 ? -8.142 -28.602 1.444 1.00 89.69 ? ? ? ? ? ? 215 SER A CA 1
ATOM 1443 C CA . PTR A 1 182 ? -5.406 -26.622 3.177 1.00 88.05 ? ? ? ? ? ? 216 PTR A CA 1
ATOM 1459 C CA . ILE A 1 183 ? -7.514 -23.621 4.117 1.00 83.90 ? ? ? ? ? ? 217 ILE A CA 1
ATOM 1467 C CA . CYS A 1 184 ? -8.907 -21.533 7.009 1.00 86.39 ? ? ? ? ? ? 218 CYS A CA 1
ATOM 1473 C CA . SER A 1 185 ? -6.795 -21.356 10.148 1.00 91.03 ? ? ? ? ? ? 219 SER A CA 1
"""
sequence_3zdi = iotbx.bioinformatics.sequence("NVSYICSR")
pdb_in = iotbx.pdb.input(
lines=(pdb_atom_site_loop_header+input_3zdi).splitlines(),
source_info=None)
pdb_hierarchy = pdb_in.construct_hierarchy()
cif_block = pdb_hierarchy.as_cif_block_with_sequence(
sequences=[sequence_3zdi],
crystal_symmetry=pdb_in.crystal_symmetry())
assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == 'NVS(PTR)ICSR'
assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == sequence_3zdi.sequence
assert approx_equal(flex.int(cif_block['_entity_poly_seq.num']), range(1, 9))
assert list(cif_block['_entity_poly_seq.mon_id']) == [
'ASN', 'VAL', 'SER', 'PTR', 'ILE', 'CYS', 'SER', 'ARG']
#
input_4gln = """\
ATOM 2 C CA . DTH A 1 1 ? -2.916 5.861 2.629 1.00 16.39 ? ? ? ? ? ? 1 DTH D CA 1
ATOM 9 C CA . DTY A 1 2 ? 0.533 4.844 3.866 1.00 10.74 ? ? ? ? ? ? 2 DTY D CA 1
ATOM 21 C CA . DLY A 1 3 ? 3.161 3.111 1.736 1.00 8.24 ? ? ? ? ? ? 3 DLY D CA 1
ATOM 30 C CA . DLE A 1 4 ? 6.958 3.293 1.625 1.00 7.95 ? ? ? ? ? ? 4 DLE D CA 1
ATOM 38 C CA . DIL A 1 5 ? 9.053 0.443 0.257 1.00 8.44 ? ? ? ? ? ? 5 DIL D CA 1
ATOM 46 C CA . DLE A 1 6 ? 12.622 1.402 -0.674 1.00 8.62 ? ? ? ? ? ? 6 DLE D CA 1
ATOM 54 C CA A DSG A 1 7 ? 14.930 -1.609 -0.756 0.60 11.27 ? ? ? ? ? ? 7 DSG D CA 1
ATOM 55 C CA B DSG A 1 7 ? 14.934 -1.617 -0.732 0.40 11.77 ? ? ? ? ? ? 7 DSG D CA 1
ATOM 67 C CA . GLY A 1 8 ? 18.113 -0.249 -2.284 1.00 13.02 ? ? ? ? ? ? 8 GLY D CA 1
ATOM 71 C CA . DLY A 1 9 ? 21.326 -1.954 -3.288 1.00 17.83 ? ? ? ? ? ? 9 DLY D CA 1
ATOM 80 C CA . DTH A 1 10 ? 20.765 -0.934 -6.926 1.00 16.38 ? ? ? ? ? ? 10 DTH D CA 1
#
ATOM 472 C CA . GLU B 2 6 ? 15.798 -6.874 23.843 1.00 31.74 ? ? ? ? ? ? 6 GLU E CA 1
ATOM 477 C CA . VAL B 2 7 ? 16.644 -3.926 21.599 1.00 15.99 ? ? ? ? ? ? 7 VAL E CA 1
ATOM 484 C CA . VAL B 2 8 ? 13.767 -1.465 21.234 1.00 10.37 ? ? ? ? ? ? 8 VAL E CA 1
ATOM 491 C CA . LYS B 2 9 ? 12.953 -1.088 17.521 1.00 8.44 ? ? ? ? ? ? 9 LYS E CA 1
#
HETATM 2537 O O . HOH E 3 . ? 8.196 -3.708 8.277 1.00 15.02 ? ? ? ? ? ? 101 HOH D O 1
HETATM 2538 O O . HOH E 3 . ? 4.901 -4.298 5.515 1.00 13.08 ? ? ? ? ? ? 102 HOH D O 1
HETATM 2663 O O . HOH F 3 . ? 10.535 -2.721 20.049 1.00 15.44 ? ? ? ? ? ? 201 HOH E O 1
HETATM 2664 O O . HOH F 3 . ? 0.790 8.695 30.909 1.00 17.06 ? ? ? ? ? ? 202 HOH E O 1
HETATM 2795 O O . HOH G 3 . ? 11.265 2.914 43.878 1.00 13.92 ? ? ? ? ? ? 201 HOH F O 1
HETATM 2796 O O . HOH G 3 . ? 11.197 11.667 36.108 1.00 17.00 ? ? ? ? ? ? 202 HOH F O 1
"""
sequence_4gln = [iotbx.bioinformatics.sequence("TYKLILNGKT"),
iotbx.bioinformatics.sequence("GQNHHEVVK")]
pdb_in = iotbx.pdb.input(
lines=(pdb_atom_site_loop_header+input_4gln).splitlines(),
source_info=None)
pdb_hierarchy = pdb_in.construct_hierarchy()
cif_block = pdb_hierarchy.as_cif_block_with_sequence(
sequences=sequence_4gln,
crystal_symmetry=pdb_in.crystal_symmetry())
assert list(cif_block['_entity.id']) == ['1', '2', '3']
assert list(cif_block['_entity.type']) == ['polymer', 'polymer', 'water']
assert approx_equal(flex.int(cif_block['_entity_poly_seq.num']),
range(1, 11)+range(1, 10))
assert list(cif_block['_entity_poly_seq.mon_id']) == [
'DTH', 'DTY', 'DLY', 'DLE', 'DIL', 'DLE', 'DSG', 'GLY', 'DLY', 'DTH',
'GLY', 'GLN', 'ASN', 'HIS', 'HIS', 'GLU', 'VAL', 'VAL', 'LYS']
assert list(cif_block['_entity_poly.pdbx_seq_one_letter_code']) == [
'(DTH)(DTY)(DLY)(DLE)(DIL)(DLE)(DSG)G(DLY)(DTH)', sequence_4gln[1].sequence]
assert list(cif_block['_entity_poly.pdbx_seq_one_letter_code_can']) == [
sequence_4gln[0].sequence, sequence_4gln[1].sequence]
assert approx_equal(flex.int(cif_block['_atom_site.label_entity_id']),
[1]*11 + [2]*4 + [3]*6)
assert list(cif_block['_atom_site.label_seq_id']) == [
'1', '2', '3', '4', '5', '6', '7', '7', '8', '9', '10', '6', '7', '8', '9',
'.', '.', '.', '.', '.', '.']
#
input_1ezu = """\
ATOM 3971 C CA . VAL D 2 16 ? 24.971 -4.493 -3.652 1.00 33.12 ? ? ? ? ? ? 731 VAL D CA 1
ATOM 3978 C CA . SER D 2 17 ? 27.194 -3.056 -0.946 1.00 35.47 ? ? ? ? ? ? 732 SER D CA 1
ATOM 3984 C CA . LEU D 2 18 ? 26.541 0.123 0.961 1.00 45.29 ? ? ? ? ? ? 733 LEU D CA 1
ATOM 3992 C CA . ASN D 2 19 ? 29.777 2.032 1.598 1.00 53.09 ? ? ? ? ? ? 734 ASN D CA 1
ATOM 4000 C CA . SER D 2 20 ? 30.737 4.963 3.775 1.00 61.92 ? ? ? ? ? ? 737 SER D CA 1
ATOM 4006 C CA . GLY D 2 21 ? 34.478 4.622 4.207 1.00 62.21 ? ? ? ? ? ? 738 GLY D CA 1
ATOM 4010 C CA . TYR D 2 22 ? 33.903 0.885 4.483 1.00 54.81 ? ? ? ? ? ? 739 TYR D CA 1
"""
sequence_1ezu = iotbx.bioinformatics.sequence('VSLNSGY')
pdb_in = iotbx.pdb.input(
lines=(pdb_atom_site_loop_header+input_1ezu).splitlines(),
source_info=None)
pdb_hierarchy = pdb_in.construct_hierarchy()
cif_block = pdb_hierarchy.as_cif_block_with_sequence(
sequences=[sequence_1ezu])
assert list(cif_block['_entity_poly_seq.mon_id']) == [
'VAL', 'SER', 'LEU', 'ASN', 'SER', 'GLY', 'TYR']
assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == sequence_1ezu.sequence
assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == sequence_1ezu.sequence
assert list(cif_block['_atom_site.auth_seq_id']) == [
'731', '732', '733', '734', '737', '738', '739']
assert list(cif_block['_atom_site.label_seq_id']) == [
'1', '2', '3', '4', '5', '6', '7']
input_2hok = """\
ATOM 301 P P . C A 1 15 ? 15.802 44.045 80.094 1.00 59.36 ? ? ? ? ? ? 23 C A P 1
ATOM 321 P P . C A 1 16 ? 12.286 47.301 82.617 1.00 68.27 ? ? ? ? ? ? 24 C A P 1
ATOM 341 P P . U A 1 17 ? 6.815 51.648 82.739 1.00 78.03 ? ? ? ? ? ? 25 U A P 1
ATOM 361 P P . G A 1 21 ? 7.042 52.289 91.645 1.00 96.25 ? ? ? ? ? ? 29 G A P 1
ATOM 384 P P . C A 1 22 ? 7.024 46.751 90.841 1.00 84.69 ? ? ? ? ? ? 30 C A P 1
ATOM 404 P P . G A 1 23 ? 7.477 40.933 88.377 1.00 81.65 ? ? ? ? ? ? 31 G A P 1
"""
sequence_2hok = iotbx.bioinformatics.sequence("CCUUCUGCG")
pdb_in = iotbx.pdb.input(
lines=(pdb_atom_site_loop_header+input_2hok).splitlines(),
source_info=None)
pdb_hierarchy = pdb_in.construct_hierarchy()
cif_block = pdb_hierarchy.as_cif_block_with_sequence(
sequences=[sequence_2hok])
assert list(cif_block['_entity_poly_seq.mon_id']) == [
'C', 'C', 'U', 'U', 'C', 'U', 'G', 'C', 'G']
assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == sequence_2hok.sequence
assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == sequence_2hok.sequence
assert list(cif_block['_atom_site.auth_seq_id']) == [
'23', '24', '25', '29', '30', '31']
assert list(cif_block['_atom_site.label_seq_id']) == [
'1', '2', '3', '7', '8', '9']
#
input_3tpy = """\
ATOM 2 CA GLN A 24 2.586 40.220 34.036 1.00 41.54 C
ATOM 8 CA LYS A 25 1.265 43.698 34.904 1.00 25.47 C
ATOM 17 CA GLN A 26 3.834 45.984 36.538 1.00 22.91 C
ATOM 26 CA PRO A 27 2.835 48.614 39.135 1.00 19.20 C
ATOM 33 CA ILE A 28 3.972 52.206 39.293 1.00 18.70 C
ATOM 41 CA SER A 29 6.403 51.332 42.097 1.00 22.63 C
TER
HETATM 852 MG MG A 999 -12.415 61.451 32.421 0.70 28.10 MG
HETATM 853 C TRS A 153 -0.078 70.151 24.773 0.33 24.86 C
HETATM 877 PA BDUP A 777 -9.339 60.563 31.137 0.70 19.64 P
HETATM 881 PB BDUP A 777 -11.768 59.969 29.491 0.70 27.76 P
HETATM 885 PG BDUP A 777 -13.098 58.529 31.620 0.70 33.91 P
HETATM 905 P AUMP A 154 -9.010 60.358 31.334 0.30 11.42 P
HETATM 909 O HOH A 155 -0.197 60.723 27.343 1.00 17.17 O
HETATM 910 O HOH A 156 -10.293 62.567 35.648 1.00 19.43 O
"""
sequence_3tpy = iotbx.bioinformatics.sequence("QKQPIS")
pdb_in = iotbx.pdb.input(lines=(input_3tpy).splitlines(), source_info=None)
pdb_hierarchy = pdb_in.construct_hierarchy()
cif_block = pdb_hierarchy.as_cif_block_with_sequence(
sequences=[sequence_3tpy])
assert list(cif_block["_entity.type"]) == [
'polymer', 'non-polymer', 'non-polymer', 'non-polymer', 'non-polymer', 'water']
assert list(cif_block["_atom_site.label_entity_id"]) == [
'1', '1', '1', '1', '1', '1', '2', '3', '4', '4', '4', '5', '6', '6']
assert list(cif_block["_atom_site.label_seq_id"]) == [
'1', '2', '3', '4', '5', '6', '.', '.', '.', '.', '.', '.', '.', '.']
#
input_3tgr = """\
ATOM 2449 CA GLY A 459 -17.536 10.137 41.979 1.00181.52 C
ATOM 2453 CA GLN A 460 -15.862 12.780 44.128 1.00192.51 C
ATOM 2462 CA ASN A 463 -19.198 8.054 50.455 1.00180.96 C
ATOM 2470 CA ASP A 464 -19.235 4.661 52.197 1.00143.07 C
ATOM 2478 CA THR A 465 -20.893 2.988 49.198 1.00 91.96 C
"""
sequence_3tgr = iotbx.bioinformatics.sequence("DGGQSNETNDTET")
pdb_in = iotbx.pdb.input(lines=(input_3tgr).splitlines(), source_info=None)
pdb_hierarchy = pdb_in.construct_hierarchy()
cif_block = pdb_hierarchy.as_cif_block_with_sequence(
sequences=[sequence_3tgr])
assert list(cif_block["_entity_poly_seq.mon_id"]) == [
'ASP', 'GLY', 'GLY', 'GLN', 'SER', 'ASN', 'GLU', 'THR', 'ASN', 'ASP', 'THR',
'GLU', 'THR']
assert list(cif_block["_atom_site.label_comp_id"]) == [
'GLY', 'GLN', 'ASN', 'ASP', 'THR']
assert list(cif_block["_atom_site.label_seq_id"]) == ['3', '4', '9', '10', '11']
assert cif_block["_entity_poly.pdbx_seq_one_letter_code"][0] == 'DGGQSNETNDTET'
input_2im9 = """\
ATOM 2423 CA PRO A 345 2.114 16.158 0.161 1.00 29.14 C
ATOM 2430 CA VAL A 346 -1.223 17.837 0.938 1.00 31.05 C
ATOM 2437 CA CYS A 349 -4.081 15.852 7.014 0.50 28.57 C
ATOM 2443 CA GLN A 350 -6.176 14.041 9.639 0.50 30.62 C
ATOM 2452 CA LEU A 351 -6.631 10.729 7.797 0.50 31.53 C
ATOM 2460 CA PHE A 352 -5.220 9.172 4.620 0.50 31.95 C
"""
sequence_2im9 = iotbx.bioinformatics.sequence("SSPTIKGINIQVVLPEKPVSNGCQLFDIR")
pdb_in = iotbx.pdb.input(lines=(input_2im9).splitlines(), source_info=None)
pdb_hierarchy = pdb_in.construct_hierarchy()
cif_block = pdb_hierarchy.as_cif_block_with_sequence(
sequences=[sequence_2im9])
assert list(cif_block["_entity_poly_seq.mon_id"]) == [
'SER', 'SER', 'PRO', 'THR', 'ILE', 'LYS', 'GLY', 'ILE', 'ASN', 'ILE', 'GLN',
'VAL', 'VAL', 'LEU', 'PRO', 'GLU', 'LYS', 'PRO', 'VAL', 'SER', 'ASN', 'GLY',
'CYS', 'GLN', 'LEU', 'PHE', 'ASP', 'ILE', 'ARG']
assert list(cif_block["_atom_site.label_seq_id"]) == [
'18', '19', '23', '24', '25', '26']
def correct_sequence (pdb_hierarchy,
sequences,
truncate_to_cbeta=False,
out=sys.stdout) :
"""
Modify the sequence for the pdb hierarchy to match that of the aligned
sequence. This will remove incompatible atoms; the sidechains will still
need to be extended separated. For proteins only - mismatches in nucleic
acids will only result in a warning.
:param pdb_hierarchy: iotbx.pdb.hierarchy.root object
:param sequences: list of iotbx.bioinformatics.sequence objects
:param trucate_to_cbeta: chop off entire sidechain to C-beta (default: leave
common atoms in place)
:param out: output filehandle (default = stdout)
:returns: number of atom_group objects renamed
"""
from mmtbx.monomer_library import idealized_aa
import mmtbx.validation.sequence
from iotbx.pdb.amino_acid_codes import three_letter_given_one_letter
seq_validation = mmtbx.validation.sequence.validation(
pdb_hierarchy=pdb_hierarchy,
sequences=sequences,
log=out)
for chain_seq in seq_validation.chains :
if (chain_seq.chain_type == mmtbx.validation.sequence.NUCLEIC_ACID) :
if (len(chain_seq.mismatch) > 0) :
print >> out, \
" WARNING: will skip %d mismatches in nucleic acid chain '%s'" % \
chain_seq.chain_id
res_dict = idealized_aa.residue_dict()
expected_names = {}
for resname in res_dict.keys() :
if (not "_h" in resname) :
ideal_res = res_dict[resname]
expected_names[resname] = set([ a.name for a in ideal_res.atoms() ])
n_changed = 0
for chain in pdb_hierarchy.only_model().chains() :
if (not chain.is_protein()) :
continue
for chain_seq in seq_validation.chains :
if (chain.id == chain_seq.chain_id) and (len(chain_seq.mismatch) > 0) :
for residue_group in chain.residue_groups() :
resid = residue_group.resid()
if (resid in chain_seq.mismatch) :
idx = chain_seq.mismatch.index(resid)
new_code = chain_seq.actual_code[idx]
new_resname = three_letter_given_one_letter.get(new_code)
if (new_resname is not None) :
expected_atoms = expected_names[new_resname.lower()]
if (truncate_to_cbeta) :
expected_atoms = expected_names["ala"]
for atom_group in residue_group.atom_groups() :
n_changed += 1
n_removed = 0
atom_group.resname = new_resname
for atom in atom_group.atoms() :
if (not atom.name in expected_atoms) :
atom_group.remove_atom(atom)
n_removed += 1
print >> out, " chain '%s' %s %s --> %s (%d atoms removed)" % \
(chain.id, resid, residue_group.atom_groups()[0].resname,
new_resname, n_removed)
pdb_hierarchy.atoms().reset_i_seq()
return n_changed