def exercise_3():
#test torsion restraints
for use_reference in ['True', 'False', 'top_out', 'None']:
pdb_inp = iotbx.pdb.input(
lines=flex.std_string(pdb_str_2.splitlines()), source_info=None)
model = manager(
model_input=pdb_inp,
log=null_out())
grm = model.get_restraints_manager().geometry
xrs2 = model.get_xray_structure()
awl2 = model.get_hierarchy().atoms_with_labels()
pdb2 = model.get_hierarchy()
pdb_inp3 = iotbx.pdb.input(source_info=None, lines=pdb_str_3)
xrs3 = pdb_inp3.xray_structure_simple()
ph3 = pdb_inp3.construct_hierarchy()
ph3.atoms().reset_i_seq()
awl3 = ph3.atoms_with_labels()
sites_cart_reference = flex.vec3_double()
selection = flex.size_t()
min_selection = flex.size_t()
reference_names = ["N", "CA", "CB", "CG", "CD", "NE", "CZ", "NH1", "NH2"]
minimize_names = ["CG", "CD", "NE", "CZ", "NH1", "NH2"]
for a2,a3 in zip(tuple(awl2), tuple(awl3)):
assert a2.resname == a3.resname
assert a2.name == a3.name
assert a2.i_seq == a3.i_seq
if(a2.resname == "ARG" and a2.name.strip() in reference_names):
selection.append(a2.i_seq)
sites_cart_reference.append(a3.xyz)
if a2.name.strip() in minimize_names:
min_selection.append(a2.i_seq)
assert selection.size() == len(reference_names)
selection_bool = flex.bool(xrs2.scatterers().size(), min_selection)
if(use_reference == 'True'):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart_reference,
selection = selection,
sigma = 2.5)
elif(use_reference == 'top_out'):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart_reference,
selection = selection,
sigma = 2.5,
limit = 180.0,
top_out_potential=True)
elif(use_reference == 'None'):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart_reference,
selection = selection,
sigma = 2.5)
grm.remove_chi_torsion_restraints_in_place(
selection = selection)
d1 = flex.mean(flex.sqrt((xrs2.sites_cart().select(min_selection) -
xrs3.sites_cart().select(min_selection)).dot()))
print("distance start (use_reference: %s): %6.4f"%(str(use_reference), d1))
assert d1>4.0
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
from cctbx import geometry_restraints
import mmtbx.refinement.geometry_minimization
import scitbx.lbfgs
grf = geometry_restraints.flags.flags(default=True)
grf.nonbonded = False
sites_cart = xrs2.sites_cart()
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager = grm,
sites_cart_selection = flex.bool(sites_cart.size(), min_selection),
geometry_restraints_flags = grf,
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=5000))
xrs2.set_sites_cart(sites_cart = sites_cart)
d2 = flex.mean(flex.sqrt((xrs2.sites_cart().select(min_selection) -
xrs3.sites_cart().select(min_selection)).dot()))
print("distance final (use_reference: %s): %6.4f"%(str(use_reference), d2))
if (use_reference in ['True', 'top_out']):
assert d2<0.3, "%s, %f" % (use_reference, d2)
else:
assert d2>4.0, d2
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
#test torsion manipulation
grm.remove_chi_torsion_restraints_in_place()
grm.remove_chi_torsion_restraints_in_place()
sites_cart_reference = []
selections_reference = []
for model in pdb2.models():
for chain in model.chains():
for residue in chain.residues():
sites_cart_reference.append(residue.atoms().extract_xyz())
selections_reference.append(residue.atoms().extract_i_seq())
#one residue at a time (effectively chi angles only)
for sites_cart, selection in zip(sites_cart_reference, selections_reference):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart,
selection = selection)
assert grm.get_n_chi_torsion_proixes() == 6
grm.remove_chi_torsion_restraints_in_place()
#all sites at once, chi angles only
sites_cart = xrs2.sites_cart()
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart,
selection = None,
chi_angles_only = True)
assert grm.get_n_chi_torsion_proixes() == 6
#all sites at once, all torsions
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart,
selection = None,
chi_angles_only = False)
# grm.get_chi_torsion_proxies().show_sorted(
# by_value='residual',
# sites_cart=sites_cart,
# site_labels=[atom.id_str() for atom in pdb2.atoms()])
assert grm.get_n_chi_torsion_proixes() == 12, grm.get_n_chi_torsion_proixes()
def exercise_2():
for use_reference in [True, False, None]:
pdb_inp = iotbx.pdb.input(
lines=flex.std_string(pdb_str_2.splitlines()), source_info=None)
model = manager(
model_input=pdb_inp,
log=null_out())
grm = model.get_restraints_manager().geometry
xrs2 = model.get_xray_structure()
awl2 = model.get_hierarchy().atoms_with_labels()
pdb_inp3 = iotbx.pdb.input(source_info=None, lines=pdb_str_3)
xrs3 = pdb_inp3.xray_structure_simple()
ph3 = pdb_inp3.construct_hierarchy()
ph3.atoms().reset_i_seq()
awl3 = ph3.atoms_with_labels()
sites_cart_reference = flex.vec3_double()
selection = flex.size_t()
reference_names = ["CG", "CD", "NE", "CZ", "NH1", "NH2"]
for a2,a3 in zip(tuple(awl2), tuple(awl3)):
assert a2.resname == a3.resname
assert a2.name == a3.name
assert a2.i_seq == a3.i_seq
if(a2.resname == "ARG" and a2.name.strip() in reference_names):
selection.append(a2.i_seq)
sites_cart_reference.append(a3.xyz)
assert selection.size() == len(reference_names)
selection_bool = flex.bool(xrs2.scatterers().size(), selection)
if(use_reference):
grm.adopt_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = sites_cart_reference,
selection = selection,
sigma = 0.01))
elif(use_reference is None):
grm.adopt_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = sites_cart_reference,
selection = selection,
sigma = 0.01))
grm.remove_reference_coordinate_restraints_in_place(
selection = selection)
d1 = flex.mean(flex.sqrt((xrs2.sites_cart().select(selection) -
xrs3.sites_cart().select(selection)).dot()))
print("distance start (use_reference: %s): %6.4f"%(str(use_reference), d1))
assert d1>4.0
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
from cctbx import geometry_restraints
import mmtbx.refinement.geometry_minimization
import scitbx.lbfgs
grf = geometry_restraints.flags.flags(default=True)
sites_cart = xrs2.sites_cart()
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager = grm,
sites_cart_selection = flex.bool(sites_cart.size(), selection),
geometry_restraints_flags = grf,
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=5000))
xrs2.set_sites_cart(sites_cart = sites_cart)
d2 = flex.mean(flex.sqrt((xrs2.sites_cart().select(selection) -
xrs3.sites_cart().select(selection)).dot()))
print("distance final (use_reference: %s): %6.4f"%(str(use_reference), d2))
if(use_reference): assert d2<0.005, "failed: %f<0.05" % d2
else: assert d2>4.0, d2
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)