def tst_02():
# Test for remove_clashes
import mmtbx.model
from mmtbx.clashes import remove_clashes
import iotbx.pdb
import sys
pdb_inp = iotbx.pdb.input(lines=pdb_poor.splitlines(), source_info='None')
model = mmtbx.model.manager(model_input=pdb_inp, )
model.set_log(log=null_out())
print "\n", "-" * 79
print " Summary of input model statistics "
print "-" * 79
model.get_restraints_manager()
geometry = model.geometry_statistics()
geometry.show(log=sys.stdout)
rc = remove_clashes(model=model)
print "\n", "-" * 79
print "Starting residues: %d " % (
rc.model.get_hierarchy().overall_counts().n_residues)
print "Side-chains removed: %d Residues removed: %d" % (
rc.side_chains_removed, rc.residues_removed)
print "Final residues: %d " % (
rc.new_model.get_hierarchy().overall_counts().n_residues)
rc.new_model.set_log(log=null_out())
rc.new_model.get_restraints_manager()
new_geometry = rc.new_model.geometry_statistics()
new_geometry.show(log=sys.stdout)
assert rc.side_chains_removed == 1
assert rc.residues_removed == 0
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_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.peptide_link.ramachandran_restraints = True
params.pdb_interpretation.peptide_link.restrain_rama_outliers = False
params.pdb_interpretation.peptide_link.restrain_rama_allowed = True
params.pdb_interpretation.peptide_link.restrain_allowed_outliers_with_emsley=True
pdb_inp = iotbx.pdb.input(file_name=file_name)
model = mmtbx.model.manager(
model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out())
grm = model.get_restraints_manager().geometry
assert grm.ramachandran_manager.get_n_proxies() == 170
assert grm.ramachandran_manager.get_n_oldfield_proxies() == 167
assert grm.ramachandran_manager.get_n_emsley_proxies() == 3
params.pdb_interpretation.peptide_link.ramachandran_restraints = True
params.pdb_interpretation.peptide_link.restrain_rama_outliers = False
params.pdb_interpretation.peptide_link.restrain_rama_allowed = False
params.pdb_interpretation.peptide_link.restrain_allowed_outliers_with_emsley=True
model.set_pdb_interpretation_params(params)
grm = model.get_restraints_manager().geometry
nprox = grm.ramachandran_manager.get_n_proxies()
assert nprox == 170
assert grm.ramachandran_manager.get_n_oldfield_proxies() == 164
assert grm.ramachandran_manager.get_n_emsley_proxies() == 6
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.peptide_link.ramachandran_restraints = True
pdb_inp = iotbx.pdb.input(file_name=file_name)
model = mmtbx.model.manager(
model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out())
grm = model.get_restraints_manager().geometry
assert grm.ramachandran_manager.get_n_proxies() == 53
# simple selection
params.pdb_interpretation.peptide_link.ramachandran_restraints = True
params.pdb_interpretation.peptide_link.rama_selection = "chain A and resid 1:7"
model.set_pdb_interpretation_params(params)
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
params.pdb_interpretation.peptide_link.ramachandran_restraints = True
params.pdb_interpretation.peptide_link.rama_selection = "chain A and resid 27:28"
model.set_pdb_interpretation_params(params)
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(pdb_str, use_ideal_bonds_angles):
# --------------------------------------------------------------
# code to switch off CDL
# --------------------------------------------------------------
#params_line = grand_master_phil_str
#params = iotbx.phil.parse(
# input_string=params_line, process_includes=True).extract()
#params.pdb_interpretation.restraints_library.cdl=False
# ---------------------------------------------------------------
pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=True)
pdb_hierarchy = model.get_hierarchy()
geometry_restraints = model.get_restraints_manager().geometry
xray_structure = model.get_xray_structure()
sites_cart = model.get_sites_cart()
grf = cctbx.geometry_restraints.flags.flags(default=True)
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart=sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=geometry_restraints,
geometry_restraints_flags=grf,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
xray_structure.set_sites_cart(sites_cart)
pdb_hierarchy.adopt_xray_structure(xray_structure)
atoms = pdb_hierarchy.atoms()
sites_cart = xray_structure.sites_cart()
riding_h_manager = riding.manager(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints=geometry_restraints,
use_ideal_bonds_angles=use_ideal_bonds_angles)
h_parameterization = riding_h_manager.h_parameterization
diagnostics = riding_h_manager.diagnostics(sites_cart=sites_cart,
threshold=0.05)
h_distances = diagnostics.h_distances
number_h = model.get_hd_selection().count(True)
number_h_para = len(h_parameterization) - h_parameterization.count(None)
assert (number_h_para == number_h), 'Not all H atoms are parameterized'
for ih in h_distances:
labels = atoms[ih].fetch_labels()
if use_ideal_bonds_angles:
assert (h_distances[ih] < 0.03), \
'distance too large: %s atom: %s (%s) residue: %s ' \
% (h_parameterization[ih].htype, atoms[ih].name, ih, labels.resseq.strip())
else:
assert (h_distances[ih] < 1e-7), \
'distance too large: %s atom: %s (%s) residue: %s distance %s' \
% (h_parameterization[ih].htype, atoms[ih].name, ih, labels.resseq.strip(), h_distances[ih])
def get_pdb_inputs(pdb_str):
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str.split('\n'))
model = mmtbx.model.manager(model_input=pdb_inp)
model.process(make_restraints=True)
return group_args(ph=model.get_hierarchy(),
grm=model.get_restraints_manager(),
xrs=model.get_xray_structure())
def exclude_h_on_SS(model):
rm = model.get_restraints_manager()
bond_proxies_simple, asu = rm.geometry.get_all_bond_proxies(
sites_cart=model.get_sites_cart())
els = model.get_hierarchy().atoms().extract_element()
ss_i_seqs = []
all_proxies = [p for p in bond_proxies_simple]
for proxy in asu:
all_proxies.append(proxy)
for proxy in all_proxies:
if (isinstance(proxy, ext.bond_simple_proxy)): i, j = proxy.i_seqs
elif (isinstance(proxy, ext.bond_asu_proxy)):
i, j = proxy.i_seq, proxy.j_seq
else:
assert 0 # never goes here
if ([els[i], els[j]
].count("S") == 2): # XXX may be coordinated if metal edits used
ss_i_seqs.extend([i, j])
sel_remove = flex.size_t()
for proxy in all_proxies:
if (isinstance(proxy, ext.bond_simple_proxy)): i, j = proxy.i_seqs
elif (isinstance(proxy, ext.bond_asu_proxy)):
i, j = proxy.i_seq, proxy.j_seq
else:
assert 0 # never goes here
if (els[i] in ["H", "D"] and j in ss_i_seqs): sel_remove.append(i)
if (els[j] in ["H", "D"] and i in ss_i_seqs): sel_remove.append(j)
return model.select(~flex.bool(model.size(), sel_remove))
def __init__(
self,
model,
rs_values=[2.0, 3.8, 5.2, 5.5, 6.2, 7.0, 8.6, 10.0],
# probe distances (A) for radial
radial_eta=4,
cutoff=8.1,
# radial cutoff distance
ts_values=[0.392699, 1.178097, 1.963495, 2.748894],
# probe angles (rad) for angular
angular_rs_values=[3.8, 5.2, 5.5, 6.2],
# probe distances (A) for angular
angular_eta=4,
angular_zeta=8,
# ???
):
self.hierarchy = model.get_hierarchy()
self.geometry_restraints_manager = model.get_restraints_manager(
).geometry
self.rs_values = rs_values
self.radial_eta = radial_eta
# NOT USED!!!
# self.Rj = Rj
self.cutoff = cutoff
self.ts_values = ts_values
self.angular_rs_values = angular_rs_values
self.angular_eta = angular_eta
self.angular_zeta = angular_zeta
self.EAEVs = format_class(length_of_radial=len(self.rs_values))
self.MAEVs = format_class(length_of_radial=len(self.rs_values))
self.BAEVs = format_class(length_of_radial=len(self.rs_values))
self.center_atom = None
self.chain_hierarchy = None
self.generate_AEV()
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 get_pdb_inputs(pdb_str):
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
model = mmtbx.model.manager(model_input = pdb_inp, log = null_out(), build_grm=True)
return group_args(
ph = model.get_hierarchy(),
grm = model.get_restraints_manager(),
xrs = model.get_xray_structure())
def run(maxnum_residues_in_cluster):
result = []
for clustering in [True, False]:
if 0: print(" clustering", clustering, "-"*30)
model = get_model()
fq = from_cctbx(restraints_manager = model.get_restraints_manager())
if(clustering):
fm = fragments(
working_folder = os.path.split("./ase/tmp_ase.pdb")[0]+ "/",
clustering_method = betweenness_centrality_clustering,
maxnum_residues_in_cluster = maxnum_residues_in_cluster,
altloc_method = "subtract",
charge_embedding = False,
two_buffers = False,
clustering = clustering,
pdb_hierarchy = model.get_hierarchy().deep_copy(),
qm_engine_name = "mopac",
fast_interaction = True,
crystal_symmetry = model.crystal_symmetry())
else:
fc = fq
fc = from_cluster(
restraints_manager = fq,
fragment_manager = fm,
parallel_params = get_master_phil().extract())
energy, gradients = fc.target_and_gradients(sites_cart=model.get_sites_cart())
gradients = gradients.as_double()
result.append(gradients.deep_copy())
diff = flex.abs(result[0] - result[1])
max_diff = flex.max(diff)
#print " max(diff_grad):", max_diff
assert max_diff < 1.e-9
def test_1_5_overlaps():
'''
Test if 1_5 overlaps are correctly identified
'''
model = obtain_model(raw_records_0)
hd_sel = model.get_hd_selection()
grm = model.get_restraints_manager().geometry
full_connectivity_table = grm.shell_sym_tables[0].full_simple_connectivity()
outstring = '1-5 Interaction test error. {}'
# check that direction of function calling does not matter
tst = pnp.check_if_1_5_interaction(21, 33,hd_sel,full_connectivity_table)
msg = 'Test results depend on atoms order'
assert(tst), msg
tst = pnp.check_if_1_5_interaction(33, 21,hd_sel,full_connectivity_table)
assert(tst), msg
# check 1-4 interaction
tst = pnp.check_if_1_5_interaction(33, 20,hd_sel,full_connectivity_table)
msg = 'Test fails on 1-4 interaction'
assert(not tst), msg
# check 1-6 interaction
tst = pnp.check_if_1_5_interaction(33, 38,hd_sel,full_connectivity_table)
msg = 'Test fails on 1-6 interaction'
assert(not tst), msg
# 1-5 interaction of atoms other than hydrogen
tst = pnp.check_if_1_5_interaction(38, 25,hd_sel,full_connectivity_table)
msg = 'Test fails on 1-5 non hydrogen interaction'
assert(not tst), msg
# 1-5 interaction of two hydrogens
tst = pnp.check_if_1_5_interaction(33, 31,hd_sel,full_connectivity_table)
msg = 'Test fails on 1-5 two hydrogen interaction'
assert(not tst), msg
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_1(prefix="tst_model_ramachandran_1"):
""" Make sure that set_ramachandran_plot_restraints() works. """
inp = iotbx.pdb.input(lines=tst_pdb_str, source_info=None)
model = mmtbx.model.manager(model_input=inp)
model.set_ramachandran_plot_restraints(rama_potential='oldfield')
n = model.get_restraints_manager(
).geometry.ramachandran_manager.get_n_oldfield_proxies()
assert n == 2
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 exercise_bond_over_symmetry(mon_lib_srv, ener_lib):
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records9)
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.restraints_library.mcl = False
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (29, 0)
h = model.get_hierarchy()
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(32, 4),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
proxy2 = geometry_restraints.bond_simple_proxy(
i_seqs=(32, 24),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
grm.add_new_bond_restraints_in_place(proxies=[proxy, proxy2],
sites_cart=h.atoms().extract_xyz())
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (30, 2)
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="")
outtxt = out.getvalue()
# print(outtxt)
#
# Not clear why ZN-NE2 bond adds as 2 bonds.
assert_lines_in_text(
outtxt, """\
bond pdb="ZN ZN A 8 "
pdb=" NE2 HIS B 304 "
ideal model delta sigma weight residual sym.op.
2.900 2.969 -0.069 5.00e-02 4.00e+02 1.92e+00 -x-1/2,y+1/2,-z+3/4
""")
assert_lines_in_text(
outtxt, """\
bond pdb=" NE2 HIS B 304 "
pdb="ZN ZN A 8 "
ideal model delta sigma weight residual sym.op.
2.900 2.969 -0.069 5.00e-02 4.00e+02 1.92e+00 -x-1/2,y-1/2,-z+3/4
""")
def exercise_bond_near_symmetry3(mon_lib_srv, ener_lib):
""" Since neighbors_fast_pair_generator for non-symmetry interactions
provides only (i,j) pair and not (j,i), and there's no sorting involved
(no way to guess what to check), there was a bug where non-symmetry interaction
was missed in add_new_bond_restraints_in_place.
Actually testing that both bonds are added without symmetry operators.
"""
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records8)
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
h = model.get_hierarchy()
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(64, 37),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
proxy2 = geometry_restraints.bond_simple_proxy(
i_seqs=(72, 37),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
grm.add_new_hbond_restraints_in_place(
proxies=[proxy, proxy2],
sites_cart=h.atoms().extract_xyz(),
max_distance_between_connecting_atoms=10)
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="",
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
outtxt = out.getvalue()
assert not show_diff(
outtxt, """\
Bond restraints: 2
Sorted by residual:
bond pdb=" O ARG A 25 "
pdb=" N AASN A 29 "
ideal model delta sigma weight residual
2.900 2.934 -0.034 5.00e-02 4.00e+02 4.53e-01
bond pdb=" O ARG A 25 "
pdb=" N BASN A 29 "
ideal model delta sigma weight residual
2.900 2.888 0.012 5.00e-02 4.00e+02 5.59e-02
""")
def exercise_dihedral_edits_change():
edits = """\
geometry_restraints.edits {
dihedral {
action = *change
atom_selection_1 = resid 1 and name CA
atom_selection_2 = resid 1 and name C
atom_selection_3 = resid 2 and name N
atom_selection_4 = resid 2 and name CA
angle_ideal = 100.00
alt_angle_ideals = 90,110
sigma = 2
periodicity = 2
}
}"""
def_params = mmtbx.model.manager.get_default_pdb_interpretation_scope()
edits_phil = iotbx.phil.parse(edits)
working_phil = def_params.fetch(edits_phil)
params = working_phil.extract()
inp = iotbx.pdb.input(lines=raw_records2, source_info=None)
model = mmtbx.model.manager(model_input=inp)
model.process(make_restraints=True)
grm = model.get_restraints_manager().geometry
assert grm.dihedral_proxies.size() == 9
dih1 = grm.dihedral_proxies.proxy_select(n_seq=model.get_number_of_atoms(),
iselection=flex.size_t(
[1, 2, 5, 6]))
assert dih1.size() == 1
dp1 = dih1[0]
assert approx_equal(dp1.angle_ideal, 180)
assert dp1.alt_angle_ideals == None
assert dp1.origin_id == 0
assert dp1.periodicity == 0
assert dp1.slack == 0
assert not dp1.top_out
assert approx_equal(dp1.weight, 0.04)
# Now with modifications
inp = iotbx.pdb.input(lines=raw_records2, source_info=None)
model2 = mmtbx.model.manager(model_input=inp)
model2.process(pdb_interpretation_params=params, make_restraints=True)
grm2 = model2.get_restraints_manager().geometry
assert grm2.dihedral_proxies.size() == 9
dih2 = grm2.dihedral_proxies.proxy_select(
n_seq=model2.get_number_of_atoms(),
iselection=flex.size_t([1, 2, 5, 6]))
assert dih2.size() == 1
dp2 = dih2[0]
assert approx_equal(dp2.angle_ideal, 100)
assert dp2.alt_angle_ideals == (90, 110)
assert dp2.origin_id == origin_ids.get_origin_id('edits')
assert dp2.periodicity == 2
assert dp2.slack == 0
assert not dp2.top_out
assert approx_equal(dp2.weight, 0.25)
def run(args):
assert len(args) == 1
# Read file into pdb_input class
inp = iotbx.pdb.input(file_name=args[0])
# create a model manager
# Catch Sorry about MTRIX here.
model = mmtbx.model.manager(
model_input=inp,
restraint_objects=
None, # these are ligands if any [('fname', cif_object), ()]
log=null_out(),
)
print("=" * 80)
print("number of atoms with MTRIX multiplication:",
model.get_number_of_atoms())
show_ss_counts(model)
# Expand with BIOMT if needed. MTRIX are already expanded by default
# Catch case when both MTRIX and BIOMT present, or other Sorry raised by
# BIOMT handling.
# LIMITATION: this should be done before any selections made on model.manager
double_counter = 0
try:
model.expand_with_BIOMT_records()
except Sorry as e:
if str(e).startswith("Model has been already expanded"):
double_counter += 1
print("=" * 80)
print("number of atoms with BIOMT multiplication:",
model.get_number_of_atoms())
show_ss_counts(model)
# Get default params
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params(
)
# Set whatever you want
pdb_int_params.pdb_interpretation.secondary_structure.protein.enabled = True
pdb_int_params.pdb_interpretation.ncs_search.enabled = True
pdb_int_params.pdb_interpretation.ncs_search.residue_match_radius = 999
pdb_int_params.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
#pdb_int_params.pdb_interpretation.nonbonded_weight = None
# set the params. Note, that GRM would be dropped, even if it was already
# constructed. In this example it is not yet constructed.
model.set_pdb_interpretation_params(params=pdb_int_params)
grm = model.get_restraints_manager()
# Not clear which one should be used at the moment
gs = model.geometry_statistics()
gs.show()
# The second way
msi = model.get_model_statistics_info()
msi.show_remark_3()
def exercise_1(prefix="tst_model_ramachandran_1"):
""" Make sure that set_ramachandran_plot_restraints() works. """
inp = iotbx.pdb.input(lines=tst_pdb_str, source_info=None)
model = mmtbx.model.manager(model_input=inp)
rama_params = master_phil.fetch().extract().ramachandran_plot_restraints
rama_params.favored = 'oldfield'
rama_params.allowed = 'oldfield'
rama_params.outlier = 'oldfield'
model.set_ramachandran_plot_restraints(rama_params=rama_params)
n = model.get_restraints_manager(
).geometry.ramachandran_manager.get_n_oldfield_proxies()
assert n == 2
rama_params.favored = 'emsley'
rama_params.allowed = 'emsley'
rama_params.outlier = 'emsley'
model.set_ramachandran_plot_restraints(rama_params=rama_params)
n = model.get_restraints_manager(
).geometry.ramachandran_manager.get_n_emsley_proxies()
assert n == 2
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 compare_XH_bond_length_to_ideal(model):
geometry = model.get_restraints_manager().geometry
atoms = model.get_hierarchy().atoms()
sites_cart = model.get_sites_cart()
bond_proxies_simple, asu = \
geometry.get_all_bond_proxies(sites_cart = sites_cart)
hd_selection = model.get_hd_selection()
for bp in bond_proxies_simple:
i, j = bp.i_seqs
if hd_selection[i] or hd_selection[j]:
assert approx_equal(atoms[i].distance(atoms[j]),
bp.distance_ideal,
eps=0.001)
def get_CNCO_bond_angle(model):
geometry = model.get_restraints_manager()
bond_proxies_simple, asu = geometry.geometry.get_all_bond_proxies(
sites_cart=model.get_sites_cart())
bps_dict = {}
[bps_dict.setdefault(p.i_seqs, True) for p in bond_proxies_simple]
hierarchy = model.get_hierarchy()
atom1s = []
atom2s = []
atom3s = []
results = []
for a in hierarchy.atoms():
if (not a.parent().resname == "MTN"): continue
if a.element.strip().upper() == "C":
atom1s.append(a)
if a.element.strip().upper() == "N":
atom2s.append(a)
if a.element.strip().upper() == "O":
atom3s.append(a)
for i, a1 in enumerate(atom1s):
for a2 in atom2s:
if (not a1.is_in_same_conformer_as(a2)): continue
if (not is_bonded(a1, a2, bps_dict)): continue
for j, a4 in enumerate(atom1s):
if (j <= i): continue
if (not a4.is_in_same_conformer_as(a2)): continue
if (not is_bonded(a4, a2, bps_dict)): continue
if (not a1.is_in_same_conformer_as(a4)): continue
if (is_bonded(a1, a4, bps_dict)): continue
for a3 in atom3s:
if (not a2.is_in_same_conformer_as(a3)): continue
if (not is_bonded(a3, a2, bps_dict)): continue
d12 = a1.distance(a2)
d23 = a2.distance(a3)
d24 = a2.distance(a4)
angle123 = a2.angle(a1, a3, deg=True)
angle124 = a2.angle(a1, a4, deg=True)
angle324 = a2.angle(a3, a4, deg=True)
result = group_args(atom_1=a1,
atom_2=a2,
atom_3=a3,
atom_4=a4,
d_C_L_N=d12,
d_O_N=d23,
d_C_R_N=d24,
a_C_L_N_O=angle123,
a_C_N_C=angle124,
a_C_R_N_O=angle324)
if (result is not None): results.append(result)
return results
def tst_1(prefix="gm_ncs_constr_tst1"):
log = sys.stdout
pdb_in = iotbx.pdb.input(source_info=None, lines=pdb_string1.split('\n'))
# print dir(pdb_in)
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params(
)
pdb_int_params.pdb_interpretation.ncs_search.enabled = True
model = mmtbx.model.manager(model_input=pdb_in,
pdb_interpretation_params=pdb_int_params,
build_grm=True)
ncs_obj = iotbx.ncs.input(hierarchy=model.get_hierarchy())
original_ncs_transform = ncs_obj.ncs_transform
ncs_restraints_group_list = ncs_obj.get_ncs_restraints_group_list()
ncs_obj.show(format='phil')
grm = model.get_restraints_manager()
tmp_xrs = model.get_xray_structure().deep_copy_scatterers()
refine_selection = flex.size_t(xrange(model.get_number_of_atoms()))
# print "refining sites"
cycle = 0
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_geometry_minimization(
xray_structure=tmp_xrs,
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=refine_selection,
restraints_manager=grm.geometry,
refine_sites=True,
refine_transformations=False,
)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object=tfg_obj,
xray_structure=tmp_xrs,
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=refine_selection,
finite_grad_differences_test=False,
max_iterations=100,
refine_sites=True,
refine_transformations=False)
refined_pdb_h = model.get_hierarchy().deep_copy()
refined_pdb_h.adopt_xray_structure(tmp_xrs)
refined_pdb_h.write_pdb_file("refined_%d.pdb" % cycle)
new_ncs_obj = iotbx.ncs.input(hierarchy=refined_pdb_h)
new_ncs_transform = new_ncs_obj.ncs_transform
spec = new_ncs_obj.get_ncs_info_as_spec()
for k, v in original_ncs_transform.iteritems():
assert approx_equal(v.r.elems, new_ncs_transform[k].r.elems)
assert approx_equal(v.t, new_ncs_transform[k].t)
overall_rmsd_after = spec.overall_rmsd()
assert overall_rmsd_after < 1e-6
def run(prefix):
"""
Exercise combined energy and gradients from cluster qm.
"""
for restraints in ["cctbx", "qm"]:
if 0:
print("Using restraints:", restraints)
result = []
for clustering in [True, False]:
if 0:
print(" clustering", clustering, "-" * 30)
model = get_model()
if (restraints == "qm"):
fq = from_qm(pdb_hierarchy=model.get_hierarchy(),
qm_engine_name="mopac",
method="PM3",
crystal_symmetry=model.crystal_symmetry(),
clustering=clustering)
else:
fq = from_cctbx(
restraints_manager=model.get_restraints_manager())
if (clustering):
fm = fragments(
working_folder=os.path.split("./ase/tmp_ase.pdb")[0] + "/",
clustering_method=betweenness_centrality_clustering,
maxnum_residues_in_cluster=8,
charge_embedding=False,
two_buffers=False,
fast_interaction=True,
pdb_hierarchy=model.get_hierarchy().deep_copy(
), # deep copy just in case
qm_engine_name="mopac",
crystal_symmetry=model.crystal_symmetry())
fc = from_cluster(restraints_manager=fq,
fragment_manager=fm,
parallel_params=get_master_phil().extract())
else:
fc = fq
energy, gradients = fc.target_and_gradients(
sites_cart=model.get_sites_cart())
if (restraints == "qm"):
energy = energy * (kcal / mol) * (kcal / mol) / Hartree
gradients = gradients * (kcal / mol) * (kcal / mol) * (Bohr /
Hartree)
gradients = gradients.as_double()
result.append(gradients.deep_copy())
#
diff = flex.abs(result[0] - result[1])
max_diff = flex.max(diff)
def exercise_adopting_coord_restraints():
inp_1 = iotbx.pdb.input(lines=pdb_str_h, source_info=None)
h_model = mmtbx.model.manager(model_input=inp_1)
inp_2 = iotbx.pdb.input(lines=pdb_str, source_info=None)
model = mmtbx.model.manager(model_input=inp_2)
# case 1: big model adopting small model.
h_model.set_reference_coordinate_restraints(ref_model=model)
# print h_model.restraints_as_geo()
rcp = h_model.get_restraints_manager(
).geometry.reference_coordinate_proxies
assert len(rcp) == 59
# Note iseqs, hydrogens are skipped
answer = [[(0, ), (-9.009, 4.612, 6.102), 25.0],
[(1, ), (-9.052, 4.207, 4.651), 25.0],
[(2, ), (-8.015, 3.14, 4.419), 25.0],
[(3, ), (-7.523, 2.521, 5.381), 25.0],
[(9, ), (-7.656, 2.923, 3.155), 25.0],
[(10, ), (-6.522, 2.038, 2.831), 25.0]]
# for p in rcp:
# print p.i_seqs, p.ref_sites, p.weight
for i in range(6):
assert rcp[i].i_seqs == answer[i][0], "%s %s" % (rcp[i].i_seqs,
answer[i][0])
assert approx_equal(rcp[i].ref_sites, answer[i][1])
assert approx_equal(
rcp[i].weight,
answer[i][2]), "%s, %s" % (rcp[i].weight, answer[i][2])
# case 2: small model adopting big model.
model.set_reference_coordinate_restraints(ref_model=h_model)
rcp = model.get_restraints_manager().geometry.reference_coordinate_proxies
assert len(rcp) == 59
# Note iseqs, hydrogens are skipped
answer = [[(0, ), (-9.009, 4.612, 6.102), 25.0],
[(1, ), (-9.052, 4.207, 4.651), 25.0],
[(2, ), (-8.015, 3.14, 4.419), 25.0],
[(3, ), (-7.523, 2.521, 5.381), 25.0],
[(4, ), (-7.656, 2.923, 3.155), 25.0],
[(5, ), (-6.522, 2.038, 2.831), 25.0]]
for i in range(6):
assert rcp[i].i_seqs == answer[i][0]
assert approx_equal(rcp[i].ref_sites, answer[i][1])
assert approx_equal(
rcp[i].weight,
answer[i][2]), "%s, %s" % (rcp[i].weight, answer[i][2])
def exercise_1():
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1)
model = mmtbx.model.manager(
model_input = inp,
log = null_out())
assert model.get_number_of_atoms() == 21
assert model.get_hierarchy().atoms_size() == 21
assert model.get_xray_structure().scatterers().size() == 21
ss = model.get_ss_annotation()
# print ss.as_pdb_str()
# STOP()
assert ss.get_n_helices() == 3
# because the second strand contains chain B which is not in ATOM records
# whole sheet got discarded.
assert ss.get_n_sheets() == 0
rm = model.get_restraints_manager()
assert rm.geometry.pair_proxies().bond_proxies.simple.size() == 6
# since No NCS was set, these functions return the whole thing and no
# master selection
assert model.get_master_hierarchy().atoms_size() == 21
assert model.get_master_selection().size() == 0
# print model.model_as_pdb()
# print "="*40
# Here we set NCS constraints
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1)
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
pdb_int_params.pdb_interpretation.ncs_search.enabled=True
model = mmtbx.model.manager(
model_input = inp,
pdb_interpretation_params = pdb_int_params,
process_input=True,
log = null_out())
# model.get_xray_structure()
assert not model.ncs_constraints_present()
assert model.get_ncs_obj() is not None
model.setup_ncs_constraints_groups()
# print model.get_ncs_obj()
assert model.ncs_constraints_present()
assert model.get_master_hierarchy().atoms_size() == 7
# print model.get_master_hierarchy().as_pdb_string()
# print list(model.get_master_selection())
assert list(model.get_master_selection()).count(True) == 7
def exclude_h_on_coordinated_S(model): # XXX if edits used it should be like in exclude_h_on_SS
rm = model.get_restraints_manager().geometry
els = model.get_hierarchy().atoms().extract_element()
# Find possibly coordinated S
exclusion_list = ["H","D","T","S","O","P","N","C","SE"]
sel_s = []
for proxy in rm.pair_proxies().nonbonded_proxies.simple:
i,j = proxy.i_seqs
if(els[i] == "S" and not els[j] in exclusion_list): sel_s.append(i)
if(els[j] == "S" and not els[i] in exclusion_list): sel_s.append(j)
# Find H attached to possibly coordinated S
bond_proxies_simple, asu = rm.get_all_bond_proxies(
sites_cart = model.get_sites_cart())
sel_remove = flex.size_t()
for proxy in bond_proxies_simple:
i,j = proxy.i_seqs
if(els[i] in ["H","D"] and j in sel_s): sel_remove.append(i)
if(els[j] in ["H","D"] and i in sel_s): sel_remove.append(j)
return model.select(~flex.bool(model.size(), sel_remove))
def get_dihedrals_and_phi_psi(model):
from cctbx.geometry_restraints import dihedral_proxy_registry
dihedral_registry = dihedral_proxy_registry(strict_conflict_handling=True)
dihedral_registry.initialize_table()
from mmtbx.conformation_dependent_library import generate_protein_threes
grm = None
try:
grm = model._processed_pdb_file.geometry_restraints_manager()
except AttributeError:
grm = model.get_restraints_manager().geometry
assert grm is not None
dihedral_proxies = grm.get_dihedral_proxies().deep_copy()
for p in dihedral_proxies:
dihedral_registry.add_if_not_duplicated(p)
for three in generate_protein_threes(hierarchy=model.get_hierarchy(),
geometry=None):
proxies = three.get_dummy_dihedral_proxies(only_psi_phi_pairs=False)
for p in proxies:
dihedral_registry.add_if_not_duplicated(p)
return dihedral_registry.proxies
def validate(pdb_str, threshold_bonds=0.02 * 4, threshold_angles=2.5 * 4):
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.use_neutron_distances = True
params.pdb_interpretation.restraints_library.cdl = False
model = mmtbx.model.manager(
model_input=pdb_inp,
build_grm=True,
stop_for_unknowns=True, #False,
pdb_interpretation_params=params,
log=null_out())
grm = model.get_restraints_manager().geometry
sites_cart = model.get_sites_cart()
b_deltas = flex.abs(
grm.get_all_bond_proxies()[0].deltas(sites_cart=sites_cart))
b_outl = b_deltas.select(b_deltas > threshold_bonds)
if (b_outl.size() > 0): return None
a_deltas = flex.abs(
grm.get_all_angle_proxies().deltas(sites_cart=sites_cart))
a_outl = a_deltas.select(a_deltas > threshold_angles)
if (a_outl.size() > 0): return None
return pdb_str