def exercise_1():
pdb_inp = iotbx.pdb.input(lines=flex.std_string(pdb_str_1.splitlines()),
source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp)
model.process(make_restraints=True)
grm = model.get_restraints_manager().geometry
pdb_hierarchy = model.get_hierarchy()
sites_cart = model.get_sites_cart()
# c-beta restraints are added by default!!!
assert len(grm.get_c_beta_torsion_proxies()) == 4
#test global selection and removing c-beta restraints
tst_boolsel = pdb_hierarchy.atom_selection_cache().selection("resname TYR")
tst_iselection = tst_boolsel.iselection()
#test global selection
grm2 = grm.select(iselection=tst_iselection)
assert len(grm2.get_c_beta_torsion_proxies()) == 2
grm2 = grm.select(selection=tst_boolsel)
assert len(grm2.get_c_beta_torsion_proxies()) == 2
#remove a selection
grm.remove_c_beta_torsion_restraints_in_place(selection=tst_iselection)
assert len(grm.get_c_beta_torsion_proxies()) == 2
#add a selection
grm.remove_c_beta_torsion_restraints_in_place()
assert len(grm.get_c_beta_torsion_proxies()) == 0
c_beta_torsion_proxies = c_beta.get_c_beta_torsion_proxies(
pdb_hierarchy, selection=tst_iselection, sigma=2.5)
assert len(c_beta_torsion_proxies) == 2
def exercise_4():
"""
Testing UNK to be equivalent to ALA
"""
pdb_h = iotbx.pdb.input(source_info=None,
lines=pdb_str_7).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert c_beta_restrs.size() == 10
assert c_beta_skip == {}
#
pdb_h = iotbx.pdb.input(source_info=None,
lines=pdb_str_7.replace(
"UNK", "ALA")).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert c_beta_restrs.size() == 10
assert c_beta_skip == {}
def exercise_1():
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = server.server(),
ener_lib = server.ener_lib(),
raw_records = flex.std_string(pdb_str_1.splitlines()),
strict_conflict_handling = True,
force_symmetry = True,
log = None)
grm = processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
sites_cart = pdb_hierarchy.atoms().extract_xyz()
# c-beta restraints are added by default!!!
assert len(grm.get_c_beta_torsion_proxies()) == 4
#test global selection and removing c-beta restraints
tst_boolsel = pdb_hierarchy.atom_selection_cache().selection("resname TYR")
tst_iselection = tst_boolsel.iselection()
#test global selection
grm2 = grm.select(iselection=tst_iselection)
assert len(grm2.get_c_beta_torsion_proxies()) == 2
grm2 = grm.select(selection=tst_boolsel)
assert len(grm2.get_c_beta_torsion_proxies()) == 2
#remove a selection
grm.remove_c_beta_torsion_restraints_in_place(selection=tst_iselection)
assert len(grm.get_c_beta_torsion_proxies()) == 2
#add a selection
grm.remove_c_beta_torsion_restraints_in_place()
assert len(grm.get_c_beta_torsion_proxies()) == 0
c_beta_torsion_proxies = c_beta.get_c_beta_torsion_proxies(
pdb_hierarchy,
selection=tst_iselection,
sigma=2.5)
assert len(c_beta_torsion_proxies) == 2
def exercise_1():
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = server.server(),
ener_lib = server.ener_lib(),
raw_records = flex.std_string(pdb_str_1.splitlines()),
strict_conflict_handling = True,
force_symmetry = True,
log = None)
grm = processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
sites_cart = pdb_hierarchy.atoms().extract_xyz()
# c-beta restraints are added by default!!!
assert len(grm.get_c_beta_torsion_proxies()) == 4
#test global selection and removing c-beta restraints
tst_boolsel = pdb_hierarchy.atom_selection_cache().selection("resname TYR")
tst_iselection = tst_boolsel.iselection()
#test global selection
grm2 = grm.select(iselection=tst_iselection)
assert len(grm2.get_c_beta_torsion_proxies()) == 2
grm2 = grm.select(selection=tst_boolsel)
assert len(grm2.get_c_beta_torsion_proxies()) == 2
#remove a selection
grm.remove_c_beta_torsion_restraints_in_place(selection=tst_iselection)
assert len(grm.get_c_beta_torsion_proxies()) == 2
#add a selection
grm.remove_c_beta_torsion_restraints_in_place()
assert len(grm.get_c_beta_torsion_proxies()) == 0
c_beta_torsion_proxies = c_beta.get_c_beta_torsion_proxies(
pdb_hierarchy,
selection=tst_iselection,
sigma=2.5)
assert len(c_beta_torsion_proxies) == 2
def exercise_3():
"""
Testing d-peptide
"""
pdb_h = iotbx.pdb.input(source_info=None,
lines=pdb_str_5).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert len(c_beta_restrs) == 0
assert len(c_beta_skip.get("d-peptide", [])) == 1
assert len(c_beta_skip.get("-ve", [])) == 0
pdb_h = iotbx.pdb.input(source_info=None,
lines=pdb_str_6).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert len(c_beta_restrs) == 0
assert len(c_beta_skip.get("d-peptide", [])) == 0
assert len(c_beta_skip.get("-ve", [])) == 1
def exercise_4():
"""
Testing UNK to be equivalent to ALA
"""
pdb_h = iotbx.pdb.input(
source_info=None,
lines=pdb_str_7).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert c_beta_restrs.size()==10
assert c_beta_skip == {}
#
pdb_h = iotbx.pdb.input(
source_info=None,
lines=pdb_str_7.replace("UNK","ALA")).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert c_beta_restrs.size()==10
assert c_beta_skip == {}
def exercise_2():
"""
Testing with ACs
"""
pdb_h = iotbx.pdb.input(source_info=None,
lines=pdb_str_2).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert len(c_beta_restrs) == 2
pdb_h = iotbx.pdb.input(source_info=None,
lines=pdb_str_3).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert len(c_beta_restrs) == 4
pdb_h = iotbx.pdb.input(source_info=None,
lines=pdb_str_4).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert len(c_beta_restrs) == 2
def exercise_3():
"""
Testing d-peptide
"""
pdb_h = iotbx.pdb.input(
source_info=None,
lines=pdb_str_5).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert len(c_beta_restrs) == 0
assert len(c_beta_skip.get("d-peptide", []))==1
assert len(c_beta_skip.get("-ve", []))==0
pdb_h = iotbx.pdb.input(
source_info=None,
lines=pdb_str_6).construct_hierarchy()
c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert len(c_beta_restrs) == 0
assert len(c_beta_skip.get("d-peptide", []))==0
assert len(c_beta_skip.get("-ve", []))==1
def exercise_2():
"""
Testing with ACs
"""
pdb_h = iotbx.pdb.input(
source_info=None,
lines=pdb_str_2).construct_hierarchy()
c_beta_restrs = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert len(c_beta_restrs) == 2
pdb_h = iotbx.pdb.input(
source_info=None,
lines=pdb_str_3).construct_hierarchy()
c_beta_restrs = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert len(c_beta_restrs) == 4
pdb_h = iotbx.pdb.input(
source_info=None,
lines=pdb_str_4).construct_hierarchy()
c_beta_restrs = c_beta.get_c_beta_torsion_proxies(pdb_h)
assert len(c_beta_restrs) == 2
