def exercise_lbfgs_simple(mon_lib_srv, ener_lib, verbose=False):
# three peptides:
# 1 = poly-ALA, favored
# 2 = poly-ALA, outlier
# 3 = poly-TRP, outlier
#
# Note that the ramalyze score for the first actually gets slightly worse,
# but it's still good and we're starting from an excellent score anyway.
#
residuals = [0.00168766995882, 170.84797160, 161.5214609]
for i, peptide in enumerate([pdb1, pdb2, pdb3]):
pdb_in = iotbx.pdb.input(source_info="peptide",
lines=flex.split_lines(peptide))
log = StringIO()
pdb_hierarchy = pdb_in.construct_hierarchy()
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
gradients_fd = flex.vec3_double(sites_cart_1.size(), (0, 0, 0))
gradients_an = flex.vec3_double(sites_cart_1.size(), (0, 0, 0))
params = ramachandran.master_phil.fetch().extract(
).ramachandran_plot_restraints
rama_manager = ramachandran.ramachandran_manager(
pdb_hierarchy, params, log)
assert rama_manager.get_n_proxies() == 1
residual_an = rama_manager.target_and_gradients(
unit_cell=None,
sites_cart=sites_cart_1,
gradient_array=gradients_an)
# print "comparing", residual_an
assert approx_equal(residual_an, residuals[i], eps=0.001)
# approx_equal(residual_an, residuals[i], eps=0.001)
if verbose:
print("")
for i, peptide in enumerate([pdb1, pdb2, pdb3]):
pdb_in = iotbx.pdb.input(source_info="peptide",
lines=flex.split_lines(peptide))
o = benchmark_structure(pdb_in, mon_lib_srv, ener_lib, verbose)
phi0, psi0 = o.r0.results[0].phi, o.r0.results[0].psi
phi1, psi1 = o.r1.results[0].phi, o.r1.results[0].psi
phi2, psi2 = o.r2.results[0].phi, o.r2.results[0].psi
r0 = o.r0.results[0].score
r1 = o.r1.results[0].score
r2 = o.r2.results[0].score
if verbose:
print("peptide %d" % (i + 1))
print(" before: rmsd_bonds=%-6.4f rmsd_angles=%-6.3f" %
(o.b0, o.a0))
print(" phi=%-6.1f psi=%-6.1f score=%-.2f" %
(phi0, psi0, r0))
print(" simple: rmsd_bonds=%-6.4f rmsd_angles=%-6.3f" %
(o.b1, o.a1))
print(" phi=%-6.1f psi=%-6.1f score=%-.2f" %
(phi1, psi1, r1))
print(" + Rama: rmsd_bonds=%-6.4f rmsd_angles=%-6.3f" %
(o.b2, o.a2))
print(" phi=%-6.1f psi=%-6.1f score=%-.2f" %
(phi2, psi2, r2))
print("")
def exercise_lbfgs_simple (mon_lib_srv, ener_lib, verbose=False) :
# three peptides:
# 1 = poly-ALA, favored
# 2 = poly-ALA, outlier
# 3 = poly-TRP, outlier
#
# Note that the ramalyze score for the first actually gets slightly worse,
# but it's still good and we're starting from an excellent score anyway.
#
# residuals = [0.00024512, 307.616444, 294.913714]
residuals = [0.00168766995882, 186.24718562, 177.259069807]
for i, peptide in enumerate([pdb1, pdb2, pdb3]) :
pdb_in = iotbx.pdb.input(source_info="peptide",
lines=flex.split_lines(peptide))
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
log = StringIO()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
gradients_fd = flex.vec3_double(sites_cart_1.size(), (0,0,0))
gradients_an = flex.vec3_double(sites_cart_1.size(), (0,0,0))
params = ramachandran.master_phil.fetch().extract()
rama_manager = ramachandran.ramachandran_manager(
pdb_hierarchy, None, params, log)
assert rama_manager.get_n_proxies() == 1
residual_an = rama_manager.target_and_gradients(
unit_cell=None,
sites_cart=sites_cart_1,
gradient_array=gradients_an)
# print "comparing", residual_an
assert approx_equal(residual_an, residuals[i], eps=0.00001)
if verbose :
print ""
for i, peptide in enumerate([pdb1, pdb2, pdb3]) :
pdb_in = iotbx.pdb.input(source_info="peptide",
lines=flex.split_lines(peptide))
o = benchmark_structure(pdb_in, mon_lib_srv, ener_lib, verbose)
phi0, psi0 = o.r0.results[0].phi, o.r0.results[0].psi
phi1, psi1 = o.r1.results[0].phi, o.r1.results[0].psi
phi2, psi2 = o.r2.results[0].phi, o.r2.results[0].psi
r0 = o.r0.results[0].score
r1 = o.r1.results[0].score
r2 = o.r2.results[0].score
if verbose :
print "peptide %d" % (i+1)
print " before: rmsd_bonds=%-6.4f rmsd_angles=%-6.3f" % (o.b0,o.a0)
print " phi=%-6.1f psi=%-6.1f score=%-.2f" % (phi0, psi0, r0)
print " simple: rmsd_bonds=%-6.4f rmsd_angles=%-6.3f" % (o.b1,o.a1)
print " phi=%-6.1f psi=%-6.1f score=%-.2f" % (phi1, psi1, r1)
print " + Rama: rmsd_bonds=%-6.4f rmsd_angles=%-6.3f" % (o.b2,o.a2)
print " phi=%-6.1f psi=%-6.1f score=%-.2f" % (phi2, psi2, r2)
print ""
def benchmark_structure(pdb_in, mon_lib_srv, ener_lib, verbose=False, w=1.0):
log = StringIO()
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.peptide_link.ramachandran_restraints = True
params.pdb_interpretation.ramachandran_plot_restraints.inject_emsley8k_into_oldfield_favored = False
model = mmtbx.model.manager(model_input=pdb_in,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
pdb_hierarchy = model.get_hierarchy()
r0 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
sites_cart_2 = sites_cart_1.deep_copy()
assert (grm is not None)
e = grm.energies_sites(sites_cart=sites_cart_1)
b0 = e.bond_deviations()[-1]
a0 = e.angle_deviations()[-1]
flags = cctbx.geometry_restraints.flags.flags(default=True)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_1,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a1 = lbfgs.rmsd_angles
b1 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_1)
r1 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
rama_params = ramachandran.master_phil.fetch().extract(
).ramachandran_plot_restraints
rama_manager = ramachandran.ramachandran_manager(pdb_hierarchy,
rama_params, log)
grm.set_ramachandran_restraints(rama_manager)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_2,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a2 = lbfgs.rmsd_angles
b2 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_2)
r2 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
return group_args(a0=a0,
a1=a1,
a2=a2,
b0=b0,
b1=b1,
b2=b2,
r0=r0,
r1=r1,
r2=r2)
def benchmark_structure (pdb_in, mon_lib_srv, ener_lib, verbose=False, w=1.0) :
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
log = StringIO()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
r0 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
sites_cart_2 = sites_cart_1.deep_copy()
grm = processed_pdb_file.geometry_restraints_manager()
assert (grm is not None)
e = grm.energies_sites(sites_cart=sites_cart_1)
b0 = e.bond_deviations()[-1]
a0 = e.angle_deviations()[-1]
flags = cctbx.geometry_restraints.flags.flags(default=True)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_1,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a1 = lbfgs.rmsd_angles
b1 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_1)
r1 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
rama_params = ramachandran.master_phil.fetch().extract()
rama_manager = ramachandran.ramachandran_manager(
pdb_hierarchy, None, rama_params, log)
grm.set_ramachandran_restraints(rama_manager)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_2,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a2 = lbfgs.rmsd_angles
b2 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_2)
r2 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
return group_args(
a0=a0,
a1=a1,
a2=a2,
b0=b0,
b1=b1,
b2=b2,
r0=r0,
r1=r1,
r2=r2)
def benchmark_structure(pdb_in, mon_lib_srv, ener_lib, verbose=False, w=1.0):
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
log = StringIO()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
r0 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
sites_cart_2 = sites_cart_1.deep_copy()
grm = processed_pdb_file.geometry_restraints_manager()
assert (grm is not None)
e = grm.energies_sites(sites_cart=sites_cart_1)
b0 = e.bond_deviations()[-1]
a0 = e.angle_deviations()[-1]
flags = cctbx.geometry_restraints.flags.flags(default=True)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_1,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a1 = lbfgs.rmsd_angles
b1 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_1)
r1 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
rama_params = ramachandran.master_phil.fetch().extract()
rama_manager = ramachandran.ramachandran_manager(pdb_hierarchy, None,
rama_params, log)
grm.set_ramachandran_restraints(rama_manager)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_2,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a2 = lbfgs.rmsd_angles
b2 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_2)
r2 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
return group_args(a0=a0,
a1=a1,
a2=a2,
b0=b0,
b1=b1,
b2=b2,
r0=r0,
r1=r1,
r2=r2)
def exercise_geo_output(mon_lib_srv, ener_lib):
pdb_str = """\
CRYST1 18.879 16.714 25.616 90.00 90.00 90.00 P 1
ATOM 1 N ALA 1 13.515 7.809 20.095 1.00 0.00 N
ATOM 2 CA ALA 1 13.087 6.532 19.536 1.00 0.00 C
ATOM 3 C ALA 1 11.716 6.653 18.880 1.00 0.00 C
ATOM 4 O ALA 1 11.425 5.972 17.896 1.00 0.00 O
ATOM 5 CB ALA 1 13.065 5.461 20.616 1.00 0.00 C
ATOM 6 N ALA 2 10.876 7.524 19.431 1.00 0.00 N
ATOM 7 CA ALA 2 9.535 7.735 18.900 1.00 0.00 C
ATOM 8 C ALA 2 9.565 8.647 17.678 1.00 0.00 C
ATOM 9 O ALA 2 8.787 8.471 16.741 1.00 0.00 O
ATOM 10 CB ALA 2 8.626 8.316 19.973 1.00 0.00 C
ATOM 11 N ALA 3 10.469 9.622 17.697 1.00 0.00 N
ATOM 12 CA ALA 3 10.606 10.565 16.593 1.00 0.00 C
ATOM 13 C ALA 3 11.132 9.871 15.340 1.00 0.00 C
ATOM 14 O ALA 3 10.687 10.157 14.228 1.00 0.00 O
ATOM 15 CB ALA 3 11.520 11.714 16.987 1.00 0.00 C
ATOM 16 N ALA 4 12.081 8.960 15.530 1.00 0.00 N
ATOM 17 CA ALA 4 12.656 8.209 14.421 1.00 0.00 C
ATOM 18 C ALA 4 11.624 7.266 13.812 1.00 0.00 C
ATOM 19 O ALA 4 11.570 7.090 12.595 1.00 0.00 O
ATOM 20 CB ALA 4 13.879 7.432 14.883 1.00 0.00 C
ATOM 21 N ALA 5 10.805 6.663 14.669 1.00 0.00 N
ATOM 22 CA ALA 5 9.753 5.761 14.218 1.00 0.00 C
ATOM 23 C ALA 5 8.662 6.528 13.481 1.00 0.00 C
ATOM 24 O ALA 5 8.107 6.045 12.494 1.00 0.00 O
ATOM 25 CB ALA 5 9.165 5.000 15.396 1.00 0.00 C
ATOM 26 N ALA 6 8.360 7.728 13.967 1.00 0.00 N
ATOM 27 CA ALA 6 7.358 8.580 13.338 1.00 0.00 C
ATOM 28 C ALA 6 7.860 9.106 11.998 1.00 0.00 C
ATOM 29 O ALA 6 7.078 9.322 11.072 1.00 0.00 O
ATOM 30 CB ALA 6 6.986 9.732 14.257 1.00 0.00 C
ATOM 31 N ALA 7 9.169 9.311 11.903 1.00 0.00 N
ATOM 32 CA ALA 7 9.781 9.787 10.668 1.00 0.00 C
ATOM 33 C ALA 7 9.912 8.655 9.655 1.00 0.00 C
ATOM 34 O ALA 7 9.905 8.886 8.446 1.00 0.00 O
ATOM 35 CB ALA 7 11.141 10.405 10.952 1.00 0.00 C
ATOM 36 N ALA 8 10.030 7.429 10.157 1.00 0.00 N
ATOM 37 CA ALA 8 10.152 6.258 9.297 1.00 0.00 C
ATOM 38 C ALA 8 8.788 5.809 8.786 1.00 0.00 C
ATOM 39 O ALA 8 8.667 5.312 7.666 1.00 0.00 O
ATOM 40 CB ALA 8 10.839 5.124 10.041 1.00 0.00 C
ATOM 41 N ALA 9 7.762 5.988 9.613 1.00 0.00 N
ATOM 42 CA ALA 9 6.405 5.603 9.243 1.00 0.00 C
ATOM 43 C ALA 9 5.816 6.576 8.228 1.00 0.00 C
ATOM 44 O ALA 9 5.000 6.195 7.389 1.00 0.00 O
ATOM 45 CB ALA 9 5.521 5.526 10.478 1.00 0.00 C
ATOM 46 N ALA 10 6.235 7.835 8.309 1.00 0.00 N
ATOM 47 CA ALA 10 5.751 8.864 7.397 1.00 0.00 C
ATOM 48 C ALA 10 6.434 8.760 6.038 1.00 0.00 C
ATOM 49 O ALA 10 5.773 8.734 5.000 1.00 0.00 O
ATOM 50 CB ALA 10 5.966 10.246 7.995 1.00 0.00 C
TER
END
"""
pdb_inp = iotbx.pdb.input(source_info="peptide",lines=flex.split_lines(pdb_str))
hierarchy = pdb_inp.construct_hierarchy()
atoms = hierarchy.atoms()
sites_cart = atoms.extract_xyz()
params = ramachandran.master_phil.fetch().extract()
params.rama_potential = "emsley"
rama_manager = ramachandran.ramachandran_manager(
hierarchy, None, params, StringIO())
out = StringIO()
rama_manager.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=[a.id_str() for a in atoms],
f=out)
gv = out.getvalue()
# print out.getvalue()
# STOP()
assert gv == """\
Ramachandran plot restraints: 8
Sorted by residual:
phi-psi angles formed by residual
pdb=" C ALA 7 " 1.53e+01
pdb=" N ALA 8 "
pdb=" CA ALA 8 "
pdb=" C ALA 8 "
pdb=" N ALA 9 "
phi-psi angles formed by residual
pdb=" C ALA 1 " 1.52e+01
pdb=" N ALA 2 "
pdb=" CA ALA 2 "
pdb=" C ALA 2 "
pdb=" N ALA 3 "
phi-psi angles formed by residual
pdb=" C ALA 6 " 1.20e+01
pdb=" N ALA 7 "
pdb=" CA ALA 7 "
pdb=" C ALA 7 "
pdb=" N ALA 8 "
phi-psi angles formed by residual
pdb=" C ALA 2 " 1.14e+01
pdb=" N ALA 3 "
pdb=" CA ALA 3 "
pdb=" C ALA 3 "
pdb=" N ALA 4 "
phi-psi angles formed by residual
pdb=" C ALA 8 " 1.06e+01
pdb=" N ALA 9 "
pdb=" CA ALA 9 "
pdb=" C ALA 9 "
pdb=" N ALA 10 "
phi-psi angles formed by residual
pdb=" C ALA 4 " 1.06e+01
pdb=" N ALA 5 "
pdb=" CA ALA 5 "
pdb=" C ALA 5 "
pdb=" N ALA 6 "
phi-psi angles formed by residual
pdb=" C ALA 3 " 1.03e+01
pdb=" N ALA 4 "
pdb=" CA ALA 4 "
pdb=" C ALA 4 "
pdb=" N ALA 5 "
phi-psi angles formed by residual
pdb=" C ALA 5 " 7.58e+00
pdb=" N ALA 6 "
pdb=" CA ALA 6 "
pdb=" C ALA 6 "
pdb=" N ALA 7 "
"""
params.rama_potential = "oldfield"
rama_manager = ramachandran.ramachandran_manager(
hierarchy, None, params, StringIO())
out = StringIO()
rama_manager.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=[a.id_str() for a in atoms],
f=out)
gv = out.getvalue()
# print out.getvalue()
# STOP()
assert not show_diff(gv, """\
Ramachandran plot restraints: 8
Sorted by residual:
phi-psi angles formed by residual
pdb=" C ALA 7 " 1.52e-01
pdb=" N ALA 8 "
pdb=" CA ALA 8 "
pdb=" C ALA 8 "
pdb=" N ALA 9 "
phi-psi angles formed by residual
pdb=" C ALA 4 " 1.28e-01
pdb=" N ALA 5 "
pdb=" CA ALA 5 "
pdb=" C ALA 5 "
pdb=" N ALA 6 "
phi-psi angles formed by residual
pdb=" C ALA 6 " 5.19e-02
pdb=" N ALA 7 "
pdb=" CA ALA 7 "
pdb=" C ALA 7 "
pdb=" N ALA 8 "
phi-psi angles formed by residual
pdb=" C ALA 5 " 3.46e-02
pdb=" N ALA 6 "
pdb=" CA ALA 6 "
pdb=" C ALA 6 "
pdb=" N ALA 7 "
phi-psi angles formed by residual
pdb=" C ALA 2 " 2.54e-02
pdb=" N ALA 3 "
pdb=" CA ALA 3 "
pdb=" C ALA 3 "
pdb=" N ALA 4 "
phi-psi angles formed by residual
pdb=" C ALA 8 " 2.00e-02
pdb=" N ALA 9 "
pdb=" CA ALA 9 "
pdb=" C ALA 9 "
pdb=" N ALA 10 "
phi-psi angles formed by residual
pdb=" C ALA 1 " 1.21e-02
pdb=" N ALA 2 "
pdb=" CA ALA 2 "
pdb=" C ALA 2 "
pdb=" N ALA 3 "
phi-psi angles formed by residual
pdb=" C ALA 3 " 9.28e-03
pdb=" N ALA 4 "
pdb=" CA ALA 4 "
pdb=" C ALA 4 "
pdb=" N ALA 5 "
""")
def exercise_manager_selection(mon_lib_srv, ener_lib):
pdb_inp = iotbx.pdb.input(source_info="peptide",
lines=flex.split_lines(pdb_str))
hierarchy = pdb_inp.construct_hierarchy()
atoms = hierarchy.atoms()
sites_cart = atoms.extract_xyz()
params = ramachandran.master_phil.fetch().extract()
params = params.ramachandran_plot_restraints
params.favored = 'emsley'
params.allowed = 'emsley'
params.outlier = 'emsley'
params.inject_emsley8k_into_oldfield_favored = False
rama_manager = ramachandran.ramachandran_manager(hierarchy, params,
StringIO())
out = StringIO()
s_out = StringIO()
rama_manager.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=[a.id_str() for a in atoms],
f=out)
selected_m = rama_manager.proxy_select(n_seq=hierarchy.atoms_size(),
iselection=flex.size_t(range(40)))
selected_m.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=[a.id_str() for a in atoms],
f=s_out)
assert not show_diff(
s_out.getvalue(), """\
Ramachandran plot restraints (Oldfield): 0
Sorted by residual:
Ramachandran plot restraints (Emsley): 6
Sorted by residual:
phi-psi angles formed by residual
pdb=" C ALA 1 " 1.52e+01
pdb=" N ALA 2 "
pdb=" CA ALA 2 "
pdb=" C ALA 2 "
pdb=" N ALA 3 "
phi-psi angles formed by residual
pdb=" C ALA 6 " 1.20e+01
pdb=" N ALA 7 "
pdb=" CA ALA 7 "
pdb=" C ALA 7 "
pdb=" N ALA 8 "
phi-psi angles formed by residual
pdb=" C ALA 2 " 1.14e+01
pdb=" N ALA 3 "
pdb=" CA ALA 3 "
pdb=" C ALA 3 "
pdb=" N ALA 4 "
phi-psi angles formed by residual
pdb=" C ALA 4 " 1.06e+01
pdb=" N ALA 5 "
pdb=" CA ALA 5 "
pdb=" C ALA 5 "
pdb=" N ALA 6 "
phi-psi angles formed by residual
pdb=" C ALA 3 " 1.03e+01
pdb=" N ALA 4 "
pdb=" CA ALA 4 "
pdb=" C ALA 4 "
pdb=" N ALA 5 "
phi-psi angles formed by residual
pdb=" C ALA 5 " 7.58e+00
pdb=" N ALA 6 "
pdb=" CA ALA 6 "
pdb=" C ALA 6 "
pdb=" N ALA 7 "
Ramachandran plot restraints (emsley8k): 0
Sorted by residual:
Ramachandran plot restraints (phi/psi/2): 0
Sorted by residual:
""")
def exercise_geo_output(mon_lib_srv, ener_lib):
pdb_inp = iotbx.pdb.input(source_info="peptide",
lines=flex.split_lines(pdb_str))
hierarchy = pdb_inp.construct_hierarchy()
atoms = hierarchy.atoms()
sites_cart = atoms.extract_xyz()
params = ramachandran.master_phil.fetch().extract()
params = params.ramachandran_plot_restraints
params.favored = 'emsley'
params.allowed = 'emsley'
params.outlier = 'emsley'
params.inject_emsley8k_into_oldfield_favored = False
rama_manager = ramachandran.ramachandran_manager(hierarchy, params,
StringIO())
out = StringIO()
rama_manager.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=[a.id_str() for a in atoms],
f=out)
gv = out.getvalue()
assert not show_diff(
gv, """\
Ramachandran plot restraints (Oldfield): 0
Sorted by residual:
Ramachandran plot restraints (Emsley): 8
Sorted by residual:
phi-psi angles formed by residual
pdb=" C ALA 7 " 1.53e+01
pdb=" N ALA 8 "
pdb=" CA ALA 8 "
pdb=" C ALA 8 "
pdb=" N ALA 9 "
phi-psi angles formed by residual
pdb=" C ALA 1 " 1.52e+01
pdb=" N ALA 2 "
pdb=" CA ALA 2 "
pdb=" C ALA 2 "
pdb=" N ALA 3 "
phi-psi angles formed by residual
pdb=" C ALA 6 " 1.20e+01
pdb=" N ALA 7 "
pdb=" CA ALA 7 "
pdb=" C ALA 7 "
pdb=" N ALA 8 "
phi-psi angles formed by residual
pdb=" C ALA 2 " 1.14e+01
pdb=" N ALA 3 "
pdb=" CA ALA 3 "
pdb=" C ALA 3 "
pdb=" N ALA 4 "
phi-psi angles formed by residual
pdb=" C ALA 8 " 1.06e+01
pdb=" N ALA 9 "
pdb=" CA ALA 9 "
pdb=" C ALA 9 "
pdb=" N ALA 10 "
phi-psi angles formed by residual
pdb=" C ALA 4 " 1.06e+01
pdb=" N ALA 5 "
pdb=" CA ALA 5 "
pdb=" C ALA 5 "
pdb=" N ALA 6 "
phi-psi angles formed by residual
pdb=" C ALA 3 " 1.03e+01
pdb=" N ALA 4 "
pdb=" CA ALA 4 "
pdb=" C ALA 4 "
pdb=" N ALA 5 "
phi-psi angles formed by residual
pdb=" C ALA 5 " 7.58e+00
pdb=" N ALA 6 "
pdb=" CA ALA 6 "
pdb=" C ALA 6 "
pdb=" N ALA 7 "
Ramachandran plot restraints (emsley8k): 0
Sorted by residual:
Ramachandran plot restraints (phi/psi/2): 0
Sorted by residual:
""")
params.favored = 'oldfield'
params.allowed = 'oldfield'
params.outlier = 'oldfield'
params.inject_emsley8k_into_oldfield_favored = False
rama_manager = ramachandran.ramachandran_manager(hierarchy, params,
StringIO())
out = StringIO()
rama_manager.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=[a.id_str() for a in atoms],
f=out)
gv = out.getvalue()
#print(gv)
#STOP()
assert not show_diff(
gv, """\
Ramachandran plot restraints (Oldfield): 8
Sorted by residual:
phi-psi angles formed by residual
pdb=" C ALA 5 " 3.46e-02
pdb=" N ALA 6 "
pdb=" CA ALA 6 "
pdb=" C ALA 6 "
pdb=" N ALA 7 "
phi-psi angles formed by residual
pdb=" C ALA 6 " 2.86e-02
pdb=" N ALA 7 "
pdb=" CA ALA 7 "
pdb=" C ALA 7 "
pdb=" N ALA 8 "
phi-psi angles formed by residual
pdb=" C ALA 2 " 2.54e-02
pdb=" N ALA 3 "
pdb=" CA ALA 3 "
pdb=" C ALA 3 "
pdb=" N ALA 4 "
phi-psi angles formed by residual
pdb=" C ALA 8 " 2.00e-02
pdb=" N ALA 9 "
pdb=" CA ALA 9 "
pdb=" C ALA 9 "
pdb=" N ALA 10 "
phi-psi angles formed by residual
pdb=" C ALA 1 " 1.21e-02
pdb=" N ALA 2 "
pdb=" CA ALA 2 "
pdb=" C ALA 2 "
pdb=" N ALA 3 "
phi-psi angles formed by residual
pdb=" C ALA 4 " 1.00e-02
pdb=" N ALA 5 "
pdb=" CA ALA 5 "
pdb=" C ALA 5 "
pdb=" N ALA 6 "
phi-psi angles formed by residual
pdb=" C ALA 3 " 9.28e-03
pdb=" N ALA 4 "
pdb=" CA ALA 4 "
pdb=" C ALA 4 "
pdb=" N ALA 5 "
phi-psi angles formed by residual
pdb=" C ALA 7 " 3.90e-03
pdb=" N ALA 8 "
pdb=" CA ALA 8 "
pdb=" C ALA 8 "
pdb=" N ALA 9 "
Ramachandran plot restraints (Emsley): 0
Sorted by residual:
Ramachandran plot restraints (emsley8k): 0
Sorted by residual:
Ramachandran plot restraints (phi/psi/2): 0
Sorted by residual:
""")
def exercise_geo_output(mon_lib_srv, ener_lib):
pdb_str = """\
CRYST1 18.879 16.714 25.616 90.00 90.00 90.00 P 1
ATOM 1 N ALA 1 13.515 7.809 20.095 1.00 0.00 N
ATOM 2 CA ALA 1 13.087 6.532 19.536 1.00 0.00 C
ATOM 3 C ALA 1 11.716 6.653 18.880 1.00 0.00 C
ATOM 4 O ALA 1 11.425 5.972 17.896 1.00 0.00 O
ATOM 5 CB ALA 1 13.065 5.461 20.616 1.00 0.00 C
ATOM 6 N ALA 2 10.876 7.524 19.431 1.00 0.00 N
ATOM 7 CA ALA 2 9.535 7.735 18.900 1.00 0.00 C
ATOM 8 C ALA 2 9.565 8.647 17.678 1.00 0.00 C
ATOM 9 O ALA 2 8.787 8.471 16.741 1.00 0.00 O
ATOM 10 CB ALA 2 8.626 8.316 19.973 1.00 0.00 C
ATOM 11 N ALA 3 10.469 9.622 17.697 1.00 0.00 N
ATOM 12 CA ALA 3 10.606 10.565 16.593 1.00 0.00 C
ATOM 13 C ALA 3 11.132 9.871 15.340 1.00 0.00 C
ATOM 14 O ALA 3 10.687 10.157 14.228 1.00 0.00 O
ATOM 15 CB ALA 3 11.520 11.714 16.987 1.00 0.00 C
ATOM 16 N ALA 4 12.081 8.960 15.530 1.00 0.00 N
ATOM 17 CA ALA 4 12.656 8.209 14.421 1.00 0.00 C
ATOM 18 C ALA 4 11.624 7.266 13.812 1.00 0.00 C
ATOM 19 O ALA 4 11.570 7.090 12.595 1.00 0.00 O
ATOM 20 CB ALA 4 13.879 7.432 14.883 1.00 0.00 C
ATOM 21 N ALA 5 10.805 6.663 14.669 1.00 0.00 N
ATOM 22 CA ALA 5 9.753 5.761 14.218 1.00 0.00 C
ATOM 23 C ALA 5 8.662 6.528 13.481 1.00 0.00 C
ATOM 24 O ALA 5 8.107 6.045 12.494 1.00 0.00 O
ATOM 25 CB ALA 5 9.165 5.000 15.396 1.00 0.00 C
ATOM 26 N ALA 6 8.360 7.728 13.967 1.00 0.00 N
ATOM 27 CA ALA 6 7.358 8.580 13.338 1.00 0.00 C
ATOM 28 C ALA 6 7.860 9.106 11.998 1.00 0.00 C
ATOM 29 O ALA 6 7.078 9.322 11.072 1.00 0.00 O
ATOM 30 CB ALA 6 6.986 9.732 14.257 1.00 0.00 C
ATOM 31 N ALA 7 9.169 9.311 11.903 1.00 0.00 N
ATOM 32 CA ALA 7 9.781 9.787 10.668 1.00 0.00 C
ATOM 33 C ALA 7 9.912 8.655 9.655 1.00 0.00 C
ATOM 34 O ALA 7 9.905 8.886 8.446 1.00 0.00 O
ATOM 35 CB ALA 7 11.141 10.405 10.952 1.00 0.00 C
ATOM 36 N ALA 8 10.030 7.429 10.157 1.00 0.00 N
ATOM 37 CA ALA 8 10.152 6.258 9.297 1.00 0.00 C
ATOM 38 C ALA 8 8.788 5.809 8.786 1.00 0.00 C
ATOM 39 O ALA 8 8.667 5.312 7.666 1.00 0.00 O
ATOM 40 CB ALA 8 10.839 5.124 10.041 1.00 0.00 C
ATOM 41 N ALA 9 7.762 5.988 9.613 1.00 0.00 N
ATOM 42 CA ALA 9 6.405 5.603 9.243 1.00 0.00 C
ATOM 43 C ALA 9 5.816 6.576 8.228 1.00 0.00 C
ATOM 44 O ALA 9 5.000 6.195 7.389 1.00 0.00 O
ATOM 45 CB ALA 9 5.521 5.526 10.478 1.00 0.00 C
ATOM 46 N ALA 10 6.235 7.835 8.309 1.00 0.00 N
ATOM 47 CA ALA 10 5.751 8.864 7.397 1.00 0.00 C
ATOM 48 C ALA 10 6.434 8.760 6.038 1.00 0.00 C
ATOM 49 O ALA 10 5.773 8.734 5.000 1.00 0.00 O
ATOM 50 CB ALA 10 5.966 10.246 7.995 1.00 0.00 C
TER
END
"""
pdb_inp = iotbx.pdb.input(source_info="peptide",lines=flex.split_lines(pdb_str))
hierarchy = pdb_inp.construct_hierarchy()
atoms = hierarchy.atoms()
sites_cart = atoms.extract_xyz()
params = ramachandran.master_phil.fetch().extract()
params.rama_potential = "emsley"
rama_manager = ramachandran.ramachandran_manager(
hierarchy, params, StringIO())
out = StringIO()
rama_manager.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=[a.id_str() for a in atoms],
f=out)
gv = out.getvalue()
# print out.getvalue()
# STOP()
assert not show_diff(gv, """\
Ramachandran plot restraints (Oldfield): 0
Sorted by residual:
Ramachandran plot restraints (Emsley): 8
Sorted by residual:
phi-psi angles formed by residual
pdb=" C ALA 7 " 1.53e+01
pdb=" N ALA 8 "
pdb=" CA ALA 8 "
pdb=" C ALA 8 "
pdb=" N ALA 9 "
phi-psi angles formed by residual
pdb=" C ALA 1 " 1.52e+01
pdb=" N ALA 2 "
pdb=" CA ALA 2 "
pdb=" C ALA 2 "
pdb=" N ALA 3 "
phi-psi angles formed by residual
pdb=" C ALA 6 " 1.20e+01
pdb=" N ALA 7 "
pdb=" CA ALA 7 "
pdb=" C ALA 7 "
pdb=" N ALA 8 "
phi-psi angles formed by residual
pdb=" C ALA 2 " 1.14e+01
pdb=" N ALA 3 "
pdb=" CA ALA 3 "
pdb=" C ALA 3 "
pdb=" N ALA 4 "
phi-psi angles formed by residual
pdb=" C ALA 8 " 1.06e+01
pdb=" N ALA 9 "
pdb=" CA ALA 9 "
pdb=" C ALA 9 "
pdb=" N ALA 10 "
phi-psi angles formed by residual
pdb=" C ALA 4 " 1.06e+01
pdb=" N ALA 5 "
pdb=" CA ALA 5 "
pdb=" C ALA 5 "
pdb=" N ALA 6 "
phi-psi angles formed by residual
pdb=" C ALA 3 " 1.03e+01
pdb=" N ALA 4 "
pdb=" CA ALA 4 "
pdb=" C ALA 4 "
pdb=" N ALA 5 "
phi-psi angles formed by residual
pdb=" C ALA 5 " 7.58e+00
pdb=" N ALA 6 "
pdb=" CA ALA 6 "
pdb=" C ALA 6 "
pdb=" N ALA 7 "
""")
params.rama_potential = "oldfield"
rama_manager = ramachandran.ramachandran_manager(
hierarchy, params, StringIO())
out = StringIO()
rama_manager.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=[a.id_str() for a in atoms],
f=out)
gv = out.getvalue()
assert not show_diff(gv, """\
Ramachandran plot restraints (Oldfield): 8
Sorted by residual:
phi-psi angles formed by residual
pdb=" C ALA 5 " 3.46e-02
pdb=" N ALA 6 "
pdb=" CA ALA 6 "
pdb=" C ALA 6 "
pdb=" N ALA 7 "
phi-psi angles formed by residual
pdb=" C ALA 6 " 2.86e-02
pdb=" N ALA 7 "
pdb=" CA ALA 7 "
pdb=" C ALA 7 "
pdb=" N ALA 8 "
phi-psi angles formed by residual
pdb=" C ALA 2 " 2.54e-02
pdb=" N ALA 3 "
pdb=" CA ALA 3 "
pdb=" C ALA 3 "
pdb=" N ALA 4 "
phi-psi angles formed by residual
pdb=" C ALA 8 " 2.00e-02
pdb=" N ALA 9 "
pdb=" CA ALA 9 "
pdb=" C ALA 9 "
pdb=" N ALA 10 "
phi-psi angles formed by residual
pdb=" C ALA 1 " 1.21e-02
pdb=" N ALA 2 "
pdb=" CA ALA 2 "
pdb=" C ALA 2 "
pdb=" N ALA 3 "
phi-psi angles formed by residual
pdb=" C ALA 4 " 1.00e-02
pdb=" N ALA 5 "
pdb=" CA ALA 5 "
pdb=" C ALA 5 "
pdb=" N ALA 6 "
phi-psi angles formed by residual
pdb=" C ALA 3 " 9.28e-03
pdb=" N ALA 4 "
pdb=" CA ALA 4 "
pdb=" C ALA 4 "
pdb=" N ALA 5 "
phi-psi angles formed by residual
pdb=" C ALA 7 " 3.90e-03
pdb=" N ALA 8 "
pdb=" CA ALA 8 "
pdb=" C ALA 8 "
pdb=" N ALA 9 "
Ramachandran plot restraints (Emsley): 0
Sorted by residual:
""")