def tst_1():
'''
input model: bond lengths close to neutron but not quite
input grm: neutron bond lengths
'''
pdb_inp = iotbx.pdb.input(lines=pdb_str1.split("\n"), source_info=None)
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.use_neutron_distances = True
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
# request neutron bond lengths
model.set_hydrogen_bond_length(use_neutron_distances=True,
show=False,
log=sys.stdout)
model.process_input_model(make_restraints=True)
compare_XH_bond_length_to_ideal(model=model)
#STOP()
# request X-ray bond lengths
pdb_inp = iotbx.pdb.input(lines=pdb_str1.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=False)
model.set_hydrogen_bond_length(use_neutron_distances=False,
show=False,
log=sys.stdout)
compare_XH_bond_length_to_ideal(model=model)
def exercise_allowed_outliers_emsley_filling():
file_name = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/3ifk.pdb", test=os.path.isfile)
if (file_name is None):
print("Skipping test.")
return
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.ramachandran_plot_restraints.enabled = True
params.pdb_interpretation.ramachandran_plot_restraints.favored = "oldfield"
params.pdb_interpretation.ramachandran_plot_restraints.allowed = "emsley"
params.pdb_interpretation.ramachandran_plot_restraints.outlier = None
params.pdb_interpretation.ramachandran_plot_restraints.inject_emsley8k_into_oldfield_favored = False
pdb_inp = iotbx.pdb.input(file_name=file_name)
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
assert grm.ramachandran_manager.get_n_proxies() == 167
assert grm.ramachandran_manager.get_n_oldfield_proxies() == 164
assert grm.ramachandran_manager.get_n_emsley_proxies() == 3
params.pdb_interpretation.ramachandran_plot_restraints.enabled = True
params.pdb_interpretation.ramachandran_plot_restraints.favored = "oldfield"
params.pdb_interpretation.ramachandran_plot_restraints.allowed = None
params.pdb_interpretation.ramachandran_plot_restraints.outlier = None
model.set_pdb_interpretation_params(params)
model.process_input_model(make_restraints=True)
grm = model.get_restraints_manager().geometry
nprox = grm.ramachandran_manager.get_n_proxies()
assert nprox == 164
assert grm.ramachandran_manager.get_n_oldfield_proxies() == 164
assert grm.ramachandran_manager.get_n_emsley_proxies() == 0
def exercise_ramachandran_selections(mon_lib_srv, ener_lib):
# Just check overall rama proxies
file_name = libtbx.env.find_in_repositories(
# relative_path="phenix_regression/pdb/3mku.pdb",
relative_path="phenix_regression/pdb/fab_a_cut.pdb",
test=os.path.isfile)
if (file_name is None):
print("Skipping test.")
return
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.ramachandran_plot_restraints.enabled = True
params.pdb_interpretation.ramachandran_plot_restraints.inject_emsley8k_into_oldfield_favored = False
pdb_inp = iotbx.pdb.input(file_name=file_name)
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
n = grm.ramachandran_manager.get_n_proxies()
assert n == 53, n
# simple selection
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out())
params.pdb_interpretation.ramachandran_plot_restraints.enabled = True
params.pdb_interpretation.ramachandran_plot_restraints.inject_emsley8k_into_oldfield_favored = False
params.pdb_interpretation.ramachandran_plot_restraints.selection = "chain A and resid 1:7"
model.set_pdb_interpretation_params(params)
model.process_input_model(make_restraints=True)
grm = model.get_restraints_manager().geometry
nprox = grm.ramachandran_manager.get_n_proxies()
assert nprox == 5, ""+\
"Want to get 5 rama proxies, got %d" % nprox
# 7 residues: there are insertion codes
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out())
params.pdb_interpretation.ramachandran_plot_restraints.enabled = True
params.pdb_interpretation.ramachandran_plot_restraints.inject_emsley8k_into_oldfield_favored = False
params.pdb_interpretation.ramachandran_plot_restraints.selection = "chain A and resid 27:28"
model.set_pdb_interpretation_params(params)
model.process_input_model(make_restraints=True)
grm = model.get_restraints_manager().geometry
nprox = grm.ramachandran_manager.get_n_proxies()
assert nprox == 5, ""+\
"Want to get 5 rama proxies, got %d" % nprox
def exercise_ss_creation_crash():
pdb_str = """
CRYST1 145.350 135.090 157.320 90.00 90.00 90.00 P 1
SCALE1 0.006880 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007402 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006356 0.00000
ATOM 1 N ASN A 1 47.095 160.279 31.220 1.00 30.00 N
ATOM 2 CA ASN A 1 65.985 120.233 34.727 1.00 30.00 C
ATOM 3 C ASN A 1 56.657 138.700 33.374 1.00 30.00 C
ATOM 4 O ASN A 1 56.353 138.977 34.561 1.00 30.00 O
ATOM 5 CB ASN A 1 65.238 120.133 36.068 1.00 30.00 C
ATOM 6 CG ASN A 1 66.087 119.360 37.057 1.00 30.00 C
ATOM 7 OD1 ASN A 1 65.746 118.217 37.441 1.00 30.00 O
ATOM 8 ND2 ASN A 1 67.240 119.920 37.395 1.00 30.00 N
ATOM 9 N ASN A 2 56.939 137.441 33.021 1.00 30.00 N
ATOM 10 CA ASN A 2 67.135 117.384 35.354 1.00 30.00 C
ATOM 11 C ASN A 2 74.935 104.398 35.546 1.00 30.00 C
ATOM 12 O ASN A 2 74.423 104.166 34.444 1.00 30.00 O
ATOM 13 CB ASN A 2 65.828 116.703 35.809 1.00 30.00 C
ATOM 14 CG ASN A 2 66.092 115.518 36.718 1.00 30.00 C
ATOM 15 OD1 ASN A 2 66.641 114.515 36.266 1.00 30.00 O
ATOM 16 ND2 ASN A 2 65.744 115.556 38.000 1.00 30.00 N
ATOM 17 N ASN A 3 76.102 103.886 35.920 1.00 30.00 N
ATOM 18 CA ASN A 3 68.960 115.076 35.163 1.00 30.00 C
ATOM 19 C ASN A 3 86.047 90.376 35.591 1.00 30.00 C
ATOM 20 O ASN A 3 87.134 90.903 35.535 1.00 30.00 O
ATOM 21 CB ASN A 3 70.251 115.882 34.903 1.00 30.00 C
ATOM 22 CG ASN A 3 71.023 116.208 36.192 1.00 30.00 C
ATOM 23 OD1 ASN A 3 70.637 117.096 36.957 1.00 30.00 O
ATOM 24 ND2 ASN A 3 72.106 115.481 36.436 1.00 30.00 N
ATOM 25 OXT ASN A 3 85.912 89.104 36.045 1.00 30.00 O
TER
END
"""
with open("exercise_ss_creation_crash_model.pdb","w") as fo:
fo.write(pdb_str)
from iotbx.data_manager import DataManager
dm=DataManager()
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.secondary_structure.enabled=True
model = dm.get_model('exercise_ss_creation_crash_model.pdb')
model.set_pdb_interpretation_params(params)
model.process_input_model(make_restraints=True)
def run_tst_grm_after_neutralize_scatterers():
# Look at nonbonded interaction CB - OE2 in Glu
# OE2 has negative charge
# vdw distance is 2.560 A when OE2 is neutral
# vdw distance is 2.752 A when OE1 has O1- charge
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_2)
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=True)
atoms = model.get_hierarchy().atoms()
grm = model.get_restraints_manager()
# with open('1.geo', 'w') as f:
# f.write(model.restraints_as_geo())
nonbonded_proxies = grm.geometry.pair_proxies().nonbonded_proxies.simple
for nb_proxy in nonbonded_proxies:
iseq, jseq = nb_proxy.i_seqs
if (iseq == 4 and jseq == 8):
vdw_distance1 = nb_proxy.vdw_distance
assert (atoms[iseq].name.strip() == 'CB')
assert (atoms[jseq].name.strip() == 'OE2')
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=False)
model.neutralize_scatterers()
model.process_input_model(make_restraints=True)
atoms2 = model.get_hierarchy().atoms()
grm2 = model.get_restraints_manager()
# with open('2.geo', 'w') as f:
# f.write(model.restraints_as_geo())
nonbonded_proxies2 = grm2.geometry.pair_proxies().nonbonded_proxies.simple
for nb_proxy in nonbonded_proxies2:
iseq, jseq = nb_proxy.i_seqs
if (iseq == 4 and jseq == 8):
vdw_distance2 = nb_proxy.vdw_distance
assert (atoms2[iseq].name.strip() == 'CB')
assert (atoms2[jseq].name.strip() == 'OE2')
assert (vdw_distance1 != vdw_distance2)
def run(args, log = sys.stdout):
if(len(args)==0):
parsed = defaults(log=log)
parsed.show(prefix=" ", out=log)
return
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(args = args,
log = sys.stdout, master_params = parsed)
processed_args.params.show()
params = processed_args.params.extract()
if(len(processed_args.pdb_file_names)==0):
raise Sorry("No PDB file found.")
if(len(processed_args.pdb_file_names)>1):
raise Sorry("More than one PDB file found.")
pdb_file_name = processed_args.pdb_file_names[0]
if(params.f_obs.f_calc.atomic_model.add_hydrogens):
pdb_file_name_r = os.path.basename(pdb_file_name)+"_reduce"
# easy_run.go("phenix.reduce %s > %s"% (pdb_file_name, pdb_file_name_r))
run_reduce_with_timeout(file_name=pdb_file_name, parameters=" > %s" % pdb_file_name_r)
pdb_file_name = pdb_file_name_r
pdbi_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
if(params.f_obs.f_calc.atomic_model.use_ramachandran_plot_restraints):
pdbi_params.pdb_interpretation.ramachandran_plot_restraints.enabled=True
model = mmtbx.model.manager(
model_input = iotbx.pdb.input(file_name = pdb_file_name),
pdb_interpretation_params = pdbi_params)
model.process_input_model(make_restraints=True)
root = iotbx.pdb.hierarchy.root()
loop_1(
params = params,
root = root,
xray_structure = model.get_xray_structure(),
pdb_hierarchy = model.get_hierarchy(),
restraints_manager = model.get_restraints_manager())
root.write_pdb_file(
file_name = params.f_obs.f_calc.atomic_model.output_file_name,
crystal_symmetry = model.crystal_symmetry())
simulate_f_obs(root=root, crystal_symmetry=model.crystal_symmetry(),
params = params)
def exercise_reference_model_restraints(mon_lib_srv, ener_lib):
# 1yjp
pdb_str = """\
CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2
ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N
ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C
ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C
ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O
ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N
ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C
ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C
ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O
ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C
ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C
ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O
ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N
ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N
ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C
ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C
ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O
ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 12.15 C
ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 12.82 C
ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.05 O
ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 13.48 N
ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00 10.29 N
ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00 10.53 C
ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00 10.24 C
ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00 8.86 O
ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00 9.80 C
ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00 10.25 C
ATOM 27 CD GLN A 4 2.504 2.044 -0.089 1.00 12.43 C
ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 1.00 14.62 O
ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 1.00 9.05 N
ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 10.38 N
ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 11.39 C
ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 11.52 C
ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 12.05 O
ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 11.96 C
ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 10.81 C
ATOM 36 CD GLN A 5 1.344 2.414 8.954 1.00 13.10 C
ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 1.00 10.65 O
ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 1.00 12.30 N
ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N
ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C
ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C
ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O
ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C
ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C
ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O
ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N
ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N
ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C
ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C
ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O
ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C
ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C
ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C
ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C
ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C
ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C
ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C
ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O
ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O
TER 60 TYR A 7
HETATM 61 O HOH A 8 -6.471 5.227 7.124 1.00 22.62 O
HETATM 62 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O
HETATM 63 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O
HETATM 64 O HOH A 11 11.808 4.179 9.970 1.00 23.99 O
HETATM 65 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O
HETATM 66 O HOH A 13 -2.749 3.429 10.024 1.00 39.15 O
HETATM 67 O HOH A 14 -1.500 0.682 10.967 1.00 43.49 O
MASTER 234 0 0 0 0 0 0 6 66 1 0 1
END """
work_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
work_params.reference_model.enabled = True
work_params.reference_model.use_starting_model_as_reference = True
model = mmtbx.model.manager(model_input=iotbx.pdb.input(
source_info=None, lines=pdb_str.split('\n')),
pdb_interpretation_params=work_params,
build_grm=True,
log=null_out())
n_ref_dih_prox = model.get_restraints_manager(
).geometry.get_n_reference_dihedral_proxies()
assert n_ref_dih_prox == 34, "expected 34, got %d" % n_ref_dih_prox
model = mmtbx.model.manager(model_input=iotbx.pdb.input(
source_info=None, lines=pdb_str.split('\n')),
pdb_interpretation_params=work_params,
build_grm=False,
log=null_out())
work_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
work_params.reference_model.enabled = True
work_params.reference_model.use_starting_model_as_reference = True
work_params.reference_model.main_chain = False
model.set_pdb_interpretation_params(work_params)
model.process_input_model(make_restraints=True)
n_ref_dih_prox = model.get_restraints_manager(
).geometry.get_n_reference_dihedral_proxies()
assert n_ref_dih_prox == 16, "expected 16, got %d" % n_ref_dih_prox
model = mmtbx.model.manager(model_input=iotbx.pdb.input(
source_info=None, lines=pdb_str.split('\n')),
pdb_interpretation_params=work_params,
build_grm=False,
log=null_out())
work_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
work_params.reference_model.enabled = True
work_params.reference_model.use_starting_model_as_reference = True
work_params.reference_model.side_chain = False
model.set_pdb_interpretation_params(work_params)
model.process_input_model(make_restraints=True)
n_ref_dih_prox = model.get_restraints_manager(
).geometry.get_n_reference_dihedral_proxies()
assert n_ref_dih_prox == 18, "expected 18, got %d" % n_ref_dih_prox
def exercise_allowed_outliers():
file_name = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/3ifk.pdb", test=os.path.isfile)
if (file_name is None):
print("Skipping test.")
return
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.ramachandran_plot_restraints.enabled = True
params.pdb_interpretation.ramachandran_plot_restraints.inject_emsley8k_into_oldfield_favored = False
pdb_inp = iotbx.pdb.input(file_name=file_name)
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
assert grm.ramachandran_manager.get_n_proxies(
) == 170, grm.ramachandran_manager.get_n_proxies()
full_proxies_iseqs = list(
tuple(x.get_i_seqs())
for x in grm.ramachandran_manager._oldfield_proxies)
params.pdb_interpretation.ramachandran_plot_restraints.favored = "oldfield"
params.pdb_interpretation.ramachandran_plot_restraints.allowed = "oldfield"
params.pdb_interpretation.ramachandran_plot_restraints.outlier = None
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out())
model.set_pdb_interpretation_params(params)
model.process_input_model(make_restraints=True)
grm = model.get_restraints_manager().geometry
nprox = grm.ramachandran_manager.get_n_proxies()
# print "without outliers", nprox
assert nprox == 167, nprox
no_out_proxies_iseqs = list(
tuple(x.get_i_seqs())
for x in grm.ramachandran_manager._oldfield_proxies)
# assert nprox == 5, ""+\
# "Want to get 5 rama proxies, got %d" % nprox
sdif_list = sorted(
list(set(full_proxies_iseqs) - set(no_out_proxies_iseqs)))
outliers_txt_list = [
'pdb=" N THR B 5 "', 'pdb=" N GLU B 6 "',
'pdb=" N SER B 81 "'
]
# print "outliers"
for a, answer in zip(sdif_list, outliers_txt_list):
# print model.get_hierarchy().atoms()[a[1]].id_str()
assert model.get_hierarchy().atoms()[a[1]].id_str() == answer
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out())
params.pdb_interpretation.ramachandran_plot_restraints.favored = "oldfield"
params.pdb_interpretation.ramachandran_plot_restraints.allowed = None
params.pdb_interpretation.ramachandran_plot_restraints.outlier = "oldfield"
model.set_pdb_interpretation_params(params)
model.process_input_model(make_restraints=True)
grm = model.get_restraints_manager().geometry
nprox = grm.ramachandran_manager.get_n_proxies()
# print "without allowed", nprox
assert nprox == 167
no_all_proxies_iseqs = list(
tuple(x.get_i_seqs())
for x in grm.ramachandran_manager._oldfield_proxies)
sdif_list = sorted(
list(set(full_proxies_iseqs) - set(no_all_proxies_iseqs)))
allowed_txt_list = [
'pdb=" N THR A 5 "', 'pdb=" N LEU B 4 "',
'pdb=" N SER B 38 "'
]
# print "allowed"
for a, answer in zip(sdif_list, allowed_txt_list):
# print model.get_hierarchy().atoms()[a[1]].id_str()
assert model.get_hierarchy().atoms()[a[1]].id_str() == answer
params.pdb_interpretation.ramachandran_plot_restraints.favored = "oldfield"
params.pdb_interpretation.ramachandran_plot_restraints.allowed = None
params.pdb_interpretation.ramachandran_plot_restraints.outlier = None
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out())
model.set_pdb_interpretation_params(params)
model.process_input_model(make_restraints=True)
grm = model.get_restraints_manager().geometry
nprox = grm.ramachandran_manager.get_n_proxies()
# print "without both", nprox
assert nprox == 164
no_both_proxies_iseqs = list(
tuple(x.get_i_seqs())
for x in grm.ramachandran_manager._oldfield_proxies)
sdif_list = sorted(
list(set(full_proxies_iseqs) - set(no_both_proxies_iseqs)))
both_txt_list = [
'pdb=" N THR A 5 "', 'pdb=" N LEU B 4 "',
'pdb=" N THR B 5 "', 'pdb=" N GLU B 6 "',
'pdb=" N SER B 38 "', 'pdb=" N SER B 81 "'
]
# print "both"
for a, answer in zip(sdif_list, both_txt_list):
# print model.get_hierarchy().atoms()[a[1]].id_str()
assert model.get_hierarchy().atoms()[a[1]].id_str() == answer
def run(args, params=None, out=sys.stdout, log=sys.stderr):
# params keyword is for running program from GUI dialog
if (((len(args) == 0) and (params is None)) or
((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help")))):
show_usage()
return
# parse command-line arguments
if (params is None):
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="file_name")
work_params = pcl.work.extract()
# or use parameters defined by GUI
else:
work_params = params
pdb_files = work_params.file_name
work_params.secondary_structure.enabled = True
assert work_params.format in [
"phenix", "phenix_refine", "phenix_bonds", "pymol", "refmac",
"kinemage", "pdb", 'csv'
]
if work_params.quiet:
out = StringIO()
pdb_combined = iotbx.pdb.combine_unique_pdb_files(file_names=pdb_files)
pdb_structure = iotbx.pdb.input(source_info=None,
lines=flex.std_string(
pdb_combined.raw_records))
cs = pdb_structure.crystal_symmetry()
corrupted_cs = False
if cs is not None:
if [cs.unit_cell(), cs.space_group()].count(None) > 0:
corrupted_cs = True
cs = None
elif cs.unit_cell().volume() < 10:
corrupted_cs = True
cs = None
if cs is None:
if corrupted_cs:
print("Symmetry information is corrupted, ", file=out)
else:
print("Symmetry information was not found, ", file=out)
print("putting molecule in P1 box.", file=out)
from cctbx import uctbx
atoms = pdb_structure.atoms()
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=atoms.extract_xyz(), buffer_layer=3)
atoms.set_xyz(new_xyz=box.sites_cart)
cs = box.crystal_symmetry()
defpars = mmtbx.model.manager.get_default_pdb_interpretation_params()
defpars.pdb_interpretation.automatic_linking.link_carbohydrates = False
defpars.pdb_interpretation.c_beta_restraints = False
defpars.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
model = mmtbx.model.manager(model_input=pdb_structure,
crystal_symmetry=cs,
pdb_interpretation_params=defpars,
stop_for_unknowns=False)
pdb_hierarchy = model.get_hierarchy()
geometry = None
if pdb_hierarchy.contains_nucleic_acid():
model.process_input_model(make_restraints=True)
geometry = model.get_restraints_manager().geometry
if len(pdb_hierarchy.models()) != 1:
raise Sorry("Multiple models not supported.")
ss_from_file = None
if (hasattr(pdb_structure, "extract_secondary_structure")
and not work_params.ignore_annotation_in_file):
ss_from_file = pdb_structure.extract_secondary_structure()
m = manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry,
sec_str_from_pdb_file=ss_from_file,
params=work_params.secondary_structure,
verbose=work_params.verbose)
# bp_p = nucleic_acids.get_basepair_plane_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair,
# geometry)
# st_p = nucleic_acids.get_stacking_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.stacking_pair,
# geometry)
# hb_b, hb_a = nucleic_acids.get_basepair_hbond_proxies(pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair)
result_out = StringIO()
# prefix_scope="refinement.pdb_interpretation"
# prefix_scope=""
prefix_scope = ""
if work_params.format == "phenix_refine":
prefix_scope = "refinement.pdb_interpretation"
elif work_params.format == "phenix":
prefix_scope = "pdb_interpretation"
ss_phil = None
working_phil = m.as_phil_str(master_phil=sec_str_master_phil)
phil_diff = sec_str_master_phil.fetch_diff(source=working_phil)
if work_params.format in ["phenix", "phenix_refine"]:
comment = "\n".join([
"# These parameters are suitable for use in e.g. phenix.real_space_refine",
"# or geometry_minimization. To use them in phenix.refine add ",
"# 'refinement.' if front of pdb_interpretation."
])
if work_params.format == "phenix_refine":
comment = "\n".join([
"# These parameters are suitable for use in phenix.refine only.",
"# To use them in other Phenix tools remove ",
"# 'refinement.' if front of pdb_interpretation."
])
print(comment, file=result_out)
if (prefix_scope != ""):
print("%s {" % prefix_scope, file=result_out)
if work_params.show_all_params:
working_phil.show(prefix=" ", out=result_out)
else:
phil_diff.show(prefix=" ", out=result_out)
if (prefix_scope != ""):
print("}", file=result_out)
elif work_params.format == "pdb":
print(m.actual_sec_str.as_pdb_str(), file=result_out)
elif work_params.format == "phenix_bonds":
raise Sorry("Not yet implemented.")
elif work_params.format in ["pymol", "refmac", "kinemage", 'csv']:
m.show_summary(log=out)
model.process_input_model(make_restraints=True)
(hb_proxies, hb_angle_proxies, planarity_proxies,
parallelity_proxies) = m.create_all_new_restraints(
pdb_hierarchy=pdb_hierarchy,
grm=model.get_restraints_manager().geometry,
log=out)
if hb_proxies.size() > 0:
if work_params.format == "pymol":
file_load_add = "load %s" % work_params.file_name[0]
# surprisingly, pymol handles filenames with whitespaces without quotes...
print(file_load_add, file=result_out)
bonds_in_format = hb_proxies.as_pymol_dashes(
pdb_hierarchy=pdb_hierarchy)
elif work_params.format == "kinemage":
bonds_in_format = hb_proxies.as_kinemage(
pdb_hierarchy=pdb_hierarchy)
elif work_params.format == "csv":
bonds_in_format = hb_proxies.as_csv(
pdb_hierarchy=pdb_hierarchy)
else:
bonds_in_format = hb_proxies.as_refmac_restraints(
pdb_hierarchy=pdb_hierarchy)
print(bonds_in_format, file=result_out)
if hb_angle_proxies.size() > 0:
if work_params.format == "pymol":
angles_in_format = hb_angle_proxies.as_pymol_dashes(
pdb_hierarchy=pdb_hierarchy)
print(angles_in_format, file=result_out)
result = result_out.getvalue()
out_prefix = os.path.basename(work_params.file_name[0])
if work_params.output_prefix is not None:
out_prefix = work_params.output_prefix
filename = "%s_ss.eff" % out_prefix
if work_params.format == "pymol":
filename = "%s_ss.pml" % out_prefix
outf = open(filename, "w")
outf.write(result)
outf.close()
print(result, file=out)
return os.path.abspath(filename)
def stats(model, prefix, no_ticks=True):
# Get rid of H, multi-model, no-protein and single-atom residue models
if (model.percent_of_single_atom_residues() > 20):
return None
sel = model.selection(string="protein")
if (sel.count(True) == 0):
return None
ssr = "protein and not (element H or element D or resname UNX or resname UNK or resname UNL)"
sel = model.selection(string=ssr)
model = model.select(sel)
if (len(model.get_hierarchy().models()) > 1):
return None
# Add H; this looses CRYST1 !
rr = run_reduce_with_timeout(
stdin_lines=model.get_hierarchy().as_pdb_string().splitlines(),
file_name=None,
parameters="-oh -his -flip -keep -allalt -pen9999 -",
override_auto_timeout_with=None)
# Create model; this is a single-model pure protein with new H added
pdb_inp = iotbx.pdb.input(source_info=None, lines=rr.stdout_lines)
model = mmtbx.model.manager(
model_input=pdb_inp,
#build_grm = True,
#pdb_hierarchy = pdb_inp.construct_hierarchy(),
#process_input = True,
log=null_out())
if (model.crystal_symmetry() is None):
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=model.get_sites_cart(), buffer_layer=5)
model.set_sites_cart(box.sites_cart)
model._crystal_symmetry = box.crystal_symmetry()
model.process_input_model(make_restraints=True)
#
N = 10
#
import cctbx.geometry_restraints.process_nonbonded_proxies as pnp
h_bond_params = pnp.h_bond()
h_bond_params.a_DHA_cutoff = 90
#
SS = get_ss_selections(hierarchy=model.get_hierarchy())
HB_all = find(model=model.select(flex.bool(model.size(), True)),
h_bond_params=h_bond_params).get_params_as_arrays(
replace_with_empty_threshold=N)
HB_alpha = find(model=model.select(SS.both.h_sel),
h_bond_params=h_bond_params).get_params_as_arrays(
replace_with_empty_threshold=N)
HB_beta = find(model=model.select(SS.both.s_sel),
h_bond_params=h_bond_params).get_params_as_arrays(
replace_with_empty_threshold=N)
print(HB_all.d_HA.size())
result_dict = {}
result_dict["all"] = HB_all
result_dict["alpha"] = HB_alpha
result_dict["beta"] = HB_beta
# result_dict["loop"] = get_selected(sel=loop_sel)
# Load histograms for reference high-resolution d_HA and a_DHA
pkl_fn = libtbx.env.find_in_repositories(
relative_path="mmtbx") + "/nci/d_HA_and_a_DHA_high_res.pkl"
assert os.path.isfile(pkl_fn)
ref = easy_pickle.load(pkl_fn)
#
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(10, 10))
kwargs = dict(histtype='bar', bins=20, range=[1.6, 3.0], alpha=.8)
for j, it in enumerate([["alpha", 1], ["beta", 3], ["all", 5]]):
key, i = it
ax = plt.subplot(int("32%d" % i))
if (no_ticks):
#ax.set_xticks([])
ax.set_yticks([])
if (j in [0, 1]):
ax.tick_params(bottom=False)
ax.set_xticklabels([])
ax.tick_params(axis="x", labelsize=12)
ax.tick_params(axis="y", labelsize=12, left=False, pad=-2)
ax.text(0.98,
0.92,
key,
size=12,
horizontalalignment='right',
transform=ax.transAxes)
HB = result_dict[key]
if HB is None: continue
w1 = np.ones_like(HB.d_HA) / HB.d_HA.size()
ax.hist(HB.d_HA, color="orangered", weights=w1, rwidth=0.3, **kwargs)
#
start, end1, end2 = 0, max(ref.distances[key].vals), \
round(max(ref.distances[key].vals),2)
if (not no_ticks):
plt.yticks([0.01, end1], ["0", end2],
visible=True,
rotation="horizontal")
if (key == "alpha"): plt.ylim(0, end2 + 0.02)
elif (key == "beta"): plt.ylim(0, end2 + 0.02)
elif (key == "all"): plt.ylim(0, end2 + 0.02)
else: assert 0
#
if (j == 0): ax.set_title("Distance", size=15)
bins = list(flex.double(ref.distances[key].bins))
ax.bar(bins, ref.distances[key].vals, alpha=.3, width=0.07)
#
kwargs = dict(histtype='bar', bins=20, range=[90, 180], alpha=.8)
for j, it in enumerate([["alpha", 2], ["beta", 4], ["all", 6]]):
key, i = it
ax = plt.subplot(int("32%d" % i))
if (j in [0, 1]):
ax.tick_params(bottom=False)
ax.set_xticklabels([])
if (no_ticks):
#ax.set_xticks([])
ax.set_yticks([])
ax.tick_params(axis="x", labelsize=12)
ax.tick_params(axis="y", labelsize=12, left=False, pad=-2)
ax.text(0.98,
0.92,
key,
size=12,
horizontalalignment='right',
transform=ax.transAxes)
ax.text(0.98,
0.92,
key,
size=12,
horizontalalignment='right',
transform=ax.transAxes)
#if(j in [0,1]): ax.plot_params(bottom=False)
HB = result_dict[key]
if HB is None: continue
w1 = np.ones_like(HB.a_DHA) / HB.a_DHA.size()
ax.hist(HB.a_DHA, color="orangered", weights=w1, rwidth=0.3, **kwargs)
#
start, end1, end2 = 0, max(ref.angles[key].vals), \
round(max(ref.angles[key].vals),2)
if (not no_ticks):
plt.yticks([0.01, end1], ["0", end2],
visible=True,
rotation="horizontal")
if (key == "alpha"): plt.ylim(0, end2 + 0.02)
elif (key == "beta"): plt.ylim(0, end2 + 0.02)
elif (key == "all"): plt.ylim(0, end2 + 0.02)
else: assert 0
#
if (j == 0): ax.set_title("Angle", size=15)
ax.bar(ref.angles[key].bins, ref.angles[key].vals, width=4.5, alpha=.3)
plt.subplots_adjust(wspace=0.12, hspace=0.025)
if (no_ticks):
plt.subplots_adjust(wspace=0.025, hspace=0.025)
#fig.savefig("%s.png"%prefix, dpi=1000)
fig.savefig("%s.pdf" % prefix)