def exercise_secondary_structure_from_sequence():
pdb_inp = iotbx.pdb.input(source_info=None, lines=correct_answer)
cs = pdb_inp.xray_structure_simple().crystal_symmetry()
correct_h = pdb_inp.construct_hierarchy()
test_h = ssb.secondary_structure_from_sequence(alpha_pdb_str,
sequence="ACEDGFIHKMLNQPSRTWVY")
test_h.atoms().reset_serial()
# correct_h.write_pdb_file("correct_h.pdb")
# test_h.write_pdb_file("test_h.pdb")
# why this passes...
for m1, m2 in zip(correct_h.models(), test_h.models()):
m1.is_similar_hierarchy( other=m2)
m1.is_identical_hierarchy(other=m2)
for c1, c2 in zip(m1.chains(), m2.chains()):
c1.is_similar_hierarchy( other=c2)
c1.is_identical_hierarchy(other=c2)
for rg1, rg2 in zip(c1.residue_groups(), c2.residue_groups()):
rg1.is_similar_hierarchy( other=rg2)
rg1.is_identical_hierarchy(other=rg2)
f1 = correct_h.extract_xray_structure(crystal_symmetry=cs).structure_factors(
algorithm="direct", d_min=2).f_calc().data()
f2 = test_h.extract_xray_structure(crystal_symmetry=cs).structure_factors(
algorithm="direct", d_min=2).f_calc().data()
assert approx_equal(f1, f2)
assert test_h.as_str() == correct_h.as_str()
#correct_h.write_pdb_file(file_name="tst_1_ex_last_correct.pdb")
#test_h.write_pdb_file(file_name="tst_1_ex_last_out.pdb")
# ...and this fails ?
# assert correct_h.is_similar_hierarchy(other=test_h)
assert approx_equal(test_h.atoms().extract_xyz(),
correct_h.atoms().extract_xyz(), eps=0.002)
try: ssb.secondary_structure_from_sequence(alpha_pdb_str, sequence="")
except Exception as e:
assert str(e) == "sequence should contain at least one residue."
def generate_perfect_helix(
rs_values,
ts_values,
angular_rs_values,
radial_eta,
angular_eta,
angular_zeta,
n_residues=10,
residue_code="G",
):
"""
Compute AEV values for the perfect helix.
"""
perfect_helix_ph = ssb.secondary_structure_from_sequence(
ssb.alpha_helix_str, residue_code * n_residues)
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=perfect_helix_ph.atoms().extract_xyz(), buffer_layer=5)
model = mmtbx.model.manager(model_input=None,
crystal_symmetry=box.crystal_symmetry(),
pdb_hierarchy=perfect_helix_ph,
build_grm=True,
log=null_out())
return AEV(
model=model,
rs_values=rs_values,
ts_values=ts_values,
angular_rs_values=angular_rs_values,
radial_eta=radial_eta,
angular_eta=angular_eta,
angular_zeta=angular_zeta,
).get_values()
def generate_perfect_helix(
rs_values,
ts_values,
angular_rs_values,
radial_eta,
angular_eta,
angular_zeta,
n_residues=10,
residue_code="G",
):
"""
Compute AEV values for the perfect helix.
"""
perfect_helix_ph = ssb.secondary_structure_from_sequence(
ssb.alpha_helix_str, residue_code * n_residues)
model = mmtbx.model.manager(model_input=None,
pdb_hierarchy=perfect_helix_ph,
build_grm=True,
log=null_out())
return AEV(
model=model,
rs_values=rs_values,
ts_values=ts_values,
angular_rs_values=angular_rs_values,
radial_eta=radial_eta,
angular_eta=angular_eta,
angular_zeta=angular_zeta,
).get_values()
def exercise_01(prefix="exercise_01"):
"Build poly-ALA beta strand"
ph = ssb.secondary_structure_from_sequence(
beta_strand_template, "".join(["A"]*22))
sites_1 = ph.atoms().extract_xyz()
sites_2 = iotbx.pdb.input(source_info=None,
lines=beta_strand_answer).construct_hierarchy().atoms().extract_xyz()
assert sites_1.size()==sites_2.size()
assert approx_equal(sites_1, sites_2, eps=0.002)
def generate_perfect_helix(n_residues=10, residue_code="G"):
"""
Compute AEV values for the perfect helix.
"""
perfect_helix_ph = ssb.secondary_structure_from_sequence(
ssb.alpha_helix_str, residue_code * n_residues)
model = mmtbx.model.manager(model_input=None,
pdb_hierarchy=perfect_helix_ph,
build_grm=True,
log=null_out())
return AEV(model=model).get_values()
def exercise_00(prefix="exercise_00"):
"Build poly-ALA alpha helix"
ph = ssb.secondary_structure_from_sequence(
alpha_helix_template, "".join(["A"]*12))
ph.atoms().reset_i_seq()
#ph.write_pdb_file(file_name="%s_result.pdb"%prefix)
sites_1 = ph.atoms().extract_xyz()
sites_2 = iotbx.pdb.input(source_info=None,
lines=alpha_helix_answer).construct_hierarchy().atoms().extract_xyz()
#of = open("1.pdb","w")
#print >> of, alpha_helix_answer
#of.close()
assert sites_1.size()==sites_2.size(), [sites_1.size(),sites_2.size()]
d1 = flex.sqrt((sites_1 - sites_2).dot())
rmsd = ssb.calculate_rmsd_smart(ph, iotbx.pdb.input(source_info=None,
lines=alpha_helix_answer).construct_hierarchy())
assert rmsd < 0.1, rmsd