def _search_hbond(self, O_atom, C_atom, N_atom, chain_around):
def good_hbond(angle, distance):
return angle > 140 and distance < 3.8
results = []
atoms = self.model.get_atoms()
for atom in [atoms[i_seq] for i_seq in self.atoms_around]:
# no need to check the same residue, looking for N atom for bonding
if atom.parent() == O_atom.parent() or atom.parent() == N_atom.parent():
# print "skipping same residue ", atom.id_str()
continue
if atom.name.strip() == 'N':
angle = geometry_restraints.angle(
sites=[C_atom.xyz, O_atom.xyz, atom.xyz],
angle_ideal=0,
weight=1).angle_model
if good_hbond(angle, atom.distance(O_atom)):
# print "Potential bond:", atom.id_str(), atom.distance(O_atom), angle
results.append(('forward', atom.distance(O_atom), angle))
if atom.name.strip() == 'O':
# now we want to find attached N atom (another one)
another_C_atom = atom.parent().get_atom("C")
if another_C_atom is not None:
angle = geometry_restraints.angle(
sites=[another_C_atom.xyz, atom.xyz, N_atom.xyz],
angle_ideal=0,
weight=1).angle_model
if good_hbond(angle, atom.distance(N_atom)):
# print "Potential backwards bond:", atom.id_str(), atom.distance(N_atom), angle
results.append(('backward', atom.distance(N_atom), angle))
return results
def exercise_angle():
eps = 1
n_trials = 20
for i_trial in xrange(n_trials):
if (i_trial < -99):
if (i_trial == n_trials-1):
eps = 0
else:
eps *= 0.1
sites = [col(site) for site in [(-1,0,0),(0,0,0),(1,eps,0)]]
angle_ideal = 170
else:
while 1:
sites = random_sites(n_sites=3)
angle_ideal = geometry_restraints.angle(
sites, angle_ideal=0, weight=0).angle_model
if (angle_ideal > 10):
break
sigma = angle_ideal * 0.1
weight = 1 / sigma**2
residual_obj = residual_functor(
restraint_type=geometry_restraints.angle,
angle_ideal=angle_ideal,
weight=weight)
for i_pert in xrange(5):
if (i_pert == 0):
sites_mod = sites
else:
sites_mod = []
for site in sites:
shift = col([random.uniform(3,3)*sigma for i in xrange(3)])
sites_mod.append(site+shift)
a = geometry_restraints.angle(
sites=sites_mod, angle_ideal=angle_ideal, weight=weight)
if (eps != 0):
ag = a.gradients()
fg = finite_differences(sites_mod, residual_obj)
if (eps == 0):
for finite in fg:
print finite
print
else:
for analytical,finite in zip(ag,fg):
if (0):
print analytical
print finite
if (0):
for x,y in zip(analytical, finite):
if (y == 0): print None,
else: print x/y,
print
if (0):
print
assert approx_equal(analytical, finite,
eps=max(1.e-6,max(analytical)*1.e-6))
def get_angle_outliers(angle_proxies, chain, sites_cart, hierarchy):
i_seq_name_hash = build_name_hash(pdb_hierarchy=hierarchy)
kin_text = "@subgroup {geom devs} dominant\n"
for ap in angle_proxies:
restraint = geometry_restraints.angle(sites_cart=sites_cart,
proxy=ap)
res = i_seq_name_hash[ap.i_seqs[0]][5:]
altloc = i_seq_name_hash[ap.i_seqs[0]][4:5].lower()
cur_chain = i_seq_name_hash[ap.i_seqs[0]][8:10]
if chain.id.strip() is not cur_chain.strip():
continue
atom1 = i_seq_name_hash[ap.i_seqs[0]][0:4].strip()
atom2 = i_seq_name_hash[ap.i_seqs[1]][0:4].strip()
atom3 = i_seq_name_hash[ap.i_seqs[2]][0:4].strip()
if atom1[0] == "H" or atom2[0] == "H" or atom3[0] == "H":
continue
sigma = ((1/restraint.weight)**(.5))
num_sigmas = - (restraint.delta / sigma) #negative to match MolProbity direction
if abs(num_sigmas) >= 4.0:
angle_key = altloc+res[0:3].lower()+res[3:]+' '+atom1.lower()+ \
'-'+atom2.lower()+'-'+atom3.lower()
kin = add_fan(sites=restraint.sites,
delta=restraint.delta,
num_sigmas=num_sigmas,
angle_key=angle_key)
kin_text += kin
return kin_text
def angles_as_cif_loop(xray_structure, proxies):
space_group_info = sgtbx.space_group_info(
group=xray_structure.space_group())
unit_cell = xray_structure.unit_cell()
sites_cart = xray_structure.sites_cart()
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_angle_atom_site_label_1",
"_restr_angle_atom_site_label_2",
"_restr_angle_atom_site_label_3",
"_restr_angle_site_symmetry_1",
"_restr_angle_site_symmetry_2",
"_restr_angle_site_symmetry_3",
"_restr_angle_target",
"_restr_angle_target_weight_param",
"_restr_angle_diff",
))
unit_mxs = [sgtbx.rt_mx()] * 3
for proxy in proxies:
restraint = geometry_restraints.angle(unit_cell=unit_cell,
sites_cart=sites_cart,
proxy=proxy)
sym_ops = proxy.sym_ops
if sym_ops is None: sym_ops = unit_mxs
i_seqs = proxy.i_seqs
loop.add_row(
(site_labels[i_seqs[0]], site_labels[i_seqs[1]],
site_labels[i_seqs[2]],
space_group_info.cif_symmetry_code(sym_ops[0]),
space_group_info.cif_symmetry_code(sym_ops[1]),
space_group_info.cif_symmetry_code(sym_ops[2]),
fmt % restraint.angle_ideal,
fmt % math.sqrt(1 / restraint.weight), fmt % restraint.delta))
return loop
def ca_measures(protein):
for resid2 in protein:
res2 = protein[resid2] #residue n
gotall = False
if res2.prevres:
res1 = res2.prevres # n-1
if res1.prevres:
res0 = res1.prevres # n-2
if res2.nextres:
res3 = res2.nextres # n+1
if res3.nextres:
res4 = res3.nextres # n+2
gotall = True
if not gotall:
continue
CA_0 = res0.getatomxyz('CA')
CA_1 = res1.getatomxyz('CA')
CA_2 = res2.getatomxyz('CA')
CA_3 = res3.getatomxyz('CA')
CA_4 = res4.getatomxyz('CA')
if None in [CA_0,CA_1,CA_2,CA_3,CA_4]:
#getatomxyz returns either an xyz list (tuple?) or None
continue
d_in = geometry_restraints.dihedral(sites=[CA_0,CA_1,CA_2,CA_3],
angle_ideal=-40, weight=1)
d_out = geometry_restraints.dihedral(sites=[CA_1,CA_2,CA_3,CA_4],
angle_ideal=-40, weight=1)
a = geometry_restraints.angle(sites=[CA_1,CA_2,CA_3],
angle_ideal=120, weight=1)
res2.measures['CA_d_in'] = d_in.angle_model
res2.measures['CA_d_out'] = d_out.angle_model
res2.measures['CA_a'] = a.angle_model
def _get_angle(sites_cart, angle_proxies, i_proxy):
if i_proxy is not None:
# compute angle
angle = geometry_restraints.angle(sites_cart=sites_cart,
proxy=angle_proxies[i_proxy])
return angle
return None
def CApseudos(protein, dodihedrals=True, doangles=True):
for resid2 in protein:
res2 = protein[resid2] #residue n
gotall = False
if res2.prevres:
res1 = res2.prevres # n-1
if res1.prevres:
res0 = res1.prevres # n-2
if res2.nextres:
res3 = res2.nextres # n+1
if res3.nextres:
res4 = res3.nextres # n+2
gotall = True
if not gotall:
continue
CA_0 = res0.getatomxyz('CA')
CA_1 = res1.getatomxyz('CA')
CA_2 = res2.getatomxyz('CA')
CA_3 = res3.getatomxyz('CA')
CA_4 = res4.getatomxyz('CA')
if None in [CA_0, CA_1, CA_2, CA_3, CA_4]:
continue
if dodihedrals:
d_in = geometry_restraints.dihedral(sites=[CA_0, CA_1, CA_2, CA_3],
angle_ideal=-40,
weight=1)
d_out = geometry_restraints.dihedral(
sites=[CA_1, CA_2, CA_3, CA_4], angle_ideal=-40, weight=1)
res2.measures['CA_d_in'] = d_in.angle_model
res2.measures['CA_d_out'] = d_out.angle_model
if doangles:
a_in = geometry_restraints.angle(sites=[CA_0, CA_1, CA_2],
angle_ideal=120,
weight=1)
a = geometry_restraints.angle(sites=[CA_1, CA_2, CA_3],
angle_ideal=120,
weight=1)
a_out = geometry_restraints.angle(sites=[CA_2, CA_3, CA_4],
angle_ideal=120,
weight=1)
res2.measures['CA_a_in'] = a_in.angle_model
res2.measures['CA_a'] = a.angle_model
res2.measures['CA_a_out'] = a_out.angle_model
def CApseudos(protein, dodihedrals = True, doangles = True):
for resid2 in protein:
res2 = protein[resid2] #residue n
gotall = False
if res2.prevres:
res1 = res2.prevres # n-1
if res1.prevres:
res0 = res1.prevres # n-2
if res2.nextres:
res3 = res2.nextres # n+1
if res3.nextres:
res4 = res3.nextres # n+2
gotall = True
if not gotall:
continue
CA_0 = res0.getatomxyz('CA')
CA_1 = res1.getatomxyz('CA')
CA_2 = res2.getatomxyz('CA')
CA_3 = res3.getatomxyz('CA')
CA_4 = res4.getatomxyz('CA')
if None in [CA_0,CA_1,CA_2,CA_3,CA_4]:
continue
if dodihedrals:
d_in = geometry_restraints.dihedral(sites=[CA_0,CA_1,CA_2,CA_3],
angle_ideal=-40, weight=1)
d_out = geometry_restraints.dihedral(sites=[CA_1,CA_2,CA_3,CA_4],
angle_ideal=-40, weight=1)
res2.measures['CA_d_in'] = d_in.angle_model
res2.measures['CA_d_out'] = d_out.angle_model
if doangles:
a_in = geometry_restraints.angle(sites=[CA_0,CA_1,CA_2],
angle_ideal=120, weight=1)
a = geometry_restraints.angle(sites=[CA_1,CA_2,CA_3],
angle_ideal=120, weight=1)
a_out = geometry_restraints.angle(sites=[CA_2,CA_3,CA_4],
angle_ideal=120, weight=1)
res2.measures['CA_a_in'] = a_in.angle_model
res2.measures['CA_a'] = a.angle_model
res2.measures['CA_a_out'] = a_out.angle_model
def write_plots(method, rot_scale=2, rot_step=1, c_truncate_at=-2e4):
assert method in ["ana", "fin"]
plot_file_names = []
site0 = (-1, 0, 0)
site1 = (0, 0, 0)
axis = matrix.col((0, 0, 1))
for angle_ideal in [180, 120]:
def init_plots():
result = []
for j in range(3):
result.append([])
return result
g_plots = init_plots()
c_plots = init_plots()
for rot_deg_sc in range(90 * rot_scale, 270 * rot_scale + rot_step,
rot_step):
rot_deg = rot_deg_sc / rot_scale
r = axis.axis_and_angle_as_r3_rotation_matrix(angle=rot_deg,
deg=True)
a = angle(sites=[site0, site1, r * site0],
angle_ideal=angle_ideal,
weight=1)
if (method == "ana"):
gc = a.grads_and_curvs()
else:
gc = derivs_fd(a=a, order=1)
gc.extend(derivs_fd(a=a, order=2))
for j in range(3):
g_plots[j].append((rot_deg, gc[2][j]))
for j in range(3):
c_plots[j].append((rot_deg, gc[5][j]))
def write(deriv, plots):
file_name = "angle_%d_%s_%s.xy" % (angle_ideal, deriv, method)
plot_file_names.append(file_name)
f = open(file_name, "w")
print("@with g0", file=f)
print('@ title "%s ideal=%d method=%s"' %
(deriv, angle_ideal, method),
file=f)
for j in range(3):
print('@ s%d legend "%s"' % (j, "xyz"[j]), file=f)
for plot in plots:
for x, y in plot:
if (deriv == "curv" and y < c_truncate_at):
y = c_truncate_at
print(x, y, file=f)
print("&", file=f)
write(deriv="grad", plots=g_plots)
write(deriv="curv", plots=c_plots)
return plot_file_names
def taucalc(protein):
for resid2 in protein:
res2 = protein[resid2]
N = res2.getatomxyz('N')
CA = res2.getatomxyz('CA')
C = res2.getatomxyz('C')
if None in [N,CA,C]:
continue
tau = geometry_restraints.angle(sites=[N,CA,C], angle_ideal=120, weight=1)
res2.measures['tau'] = tau.angle_model
def taucalc(protein):
for resid2 in protein:
res2 = protein[resid2]
N = res2.getatomxyz('N')
CA = res2.getatomxyz('CA')
C = res2.getatomxyz('C')
if None in [N, CA, C]:
continue
tau = geometry_restraints.angle(sites=[N, CA, C],
angle_ideal=120,
weight=1)
res2.measures['tau'] = tau.angle_model
def write_plots(method, rot_scale=2, rot_step=1, c_truncate_at=-2e4):
assert method in ["ana", "fin"]
plot_file_names = []
site0 = (-1,0,0)
site1 = (0,0,0)
axis = matrix.col((0,0,1))
for angle_ideal in [180, 120]:
def init_plots():
result = []
for j in xrange(3):
result.append([])
return result
g_plots = init_plots()
c_plots = init_plots()
for rot_deg_sc in xrange(90*rot_scale, 270*rot_scale+rot_step, rot_step):
rot_deg = rot_deg_sc / rot_scale
r = axis.axis_and_angle_as_r3_rotation_matrix(angle=rot_deg, deg=True)
a = angle(
sites=[site0, site1, r*site0],
angle_ideal=angle_ideal,
weight=1)
if (method == "ana"):
gc = a.grads_and_curvs()
else:
gc = derivs_fd(a=a, order=1)
gc.extend(derivs_fd(a=a, order=2))
for j in xrange(3):
g_plots[j].append((rot_deg, gc[2][j]))
for j in xrange(3):
c_plots[j].append((rot_deg, gc[5][j]))
def write(deriv, plots):
file_name = "angle_%d_%s_%s.xy" % (angle_ideal, deriv, method)
plot_file_names.append(file_name)
f = open(file_name, "w")
print >> f, "@with g0"
print >> f, '@ title "%s ideal=%d method=%s"' % (
deriv, angle_ideal, method)
for j in xrange(3):
print >> f, '@ s%d legend "%s"' % (j, "xyz"[j])
for plot in plots:
for x,y in plot:
if (deriv == "curv" and y < c_truncate_at): y = c_truncate_at
print >> f, x,y
print >> f, "&"
write(deriv="grad", plots=g_plots)
write(deriv="curv", plots=c_plots)
return plot_file_names
def cablam_measures(protein):
for resid2 in protein:
res2 = protein[resid2] #residue n
gotall = False
if res2.prevres:
res1 = res2.prevres # n-1
if res1.prevres:
res0 = res1.prevres # n-2
if res2.nextres:
res3 = res2.nextres # n+1
if res3.nextres:
res4 = res3.nextres # n+2
gotall = True
if not gotall:
continue
CA_0 = res0.getatomxyz('CA')
CA_1, O_1 = res1.getatomxyz('CA'), res1.getatomxyz('O')
CA_2, O_2 = res2.getatomxyz('CA'), res2.getatomxyz('O')
CA_3 = res3.getatomxyz('CA')
CA_4 = res4.getatomxyz('CA')
if None in [CA_0, CA_1, CA_2, CA_3, CA_4, O_1, O_2]:
#getatomxyz returns either an xyz list (tuple?) or None
continue
d_in = geometry_restraints.dihedral(sites=[CA_0, CA_1, CA_2, CA_3],
angle_ideal=-40,
weight=1)
d_out = geometry_restraints.dihedral(sites=[CA_1, CA_2, CA_3, CA_4],
angle_ideal=-40,
weight=1)
pseudoC_1 = perptersect(CA_1, CA_2, O_1)
pseudoC_2 = perptersect(CA_2, CA_3, O_2)
co_in = geometry_restraints.dihedral(
sites=[O_1, pseudoC_1, pseudoC_2, O_2], angle_ideal=-40, weight=1)
ca_a = geometry_restraints.angle(sites=[CA_1, CA_2, CA_3],
angle_ideal=120,
weight=1)
res2.measures['CA_d_in'] = d_in.angle_model
res2.measures['CA_d_out'] = d_out.angle_model
res2.measures['CO_d_in'] = co_in.angle_model
res2.measures['CA_a'] = ca_a.angle_model
def derivs_fd(a, order, eps=1.e-6):
result = flex.vec3_double()
sites0 = a.sites
sites = [list(site) for site in sites0]
for i_site in xrange(3):
ds = []
for i_dim in xrange(3):
samples = []
for signed_eps in [eps, -eps]:
sites[i_site][i_dim] = sites0[i_site][i_dim] + signed_eps
a_eps = angle(sites=sites, angle_ideal=a.angle_ideal, weight=a.weight)
if (order == 1):
samples.append(a_eps.residual())
elif (order == 2):
samples.append(a_eps.gradients()[i_site][i_dim])
else:
raise RuntimeError
sites[i_site][i_dim] = sites0[i_site][i_dim]
ds.append((samples[0]-samples[1])/(2*eps))
result.append(tuple(ds))
return result
def __init__(self,
pdb_hierarchy,
pdb_atoms,
geometry_restraints_manager,
outliers_only=True):
rna_geometry.__init__(self)
cutoff = 4
sites_cart = pdb_atoms.extract_xyz()
flags = geometry_restraints.flags.flags(default=True)
i_seq_name_hash = utils.build_name_hash(pdb_hierarchy=pdb_hierarchy)
for proxy in geometry_restraints_manager.angle_proxies:
restraint = geometry_restraints.angle(sites_cart=sites_cart,
proxy=proxy)
atom1 = pdb_atoms[proxy.i_seqs[0]].name
atom2 = pdb_atoms[proxy.i_seqs[1]].name
atom3 = pdb_atoms[proxy.i_seqs[2]].name
labels = pdb_atoms[proxy.i_seqs[0]].fetch_labels()
if (atom1.strip() not in rna_backbone_atoms
or atom2.strip() not in rna_backbone_atoms
or atom3.strip() not in rna_backbone_atoms):
continue
self.n_total += 1
sigma = sqrt(1 / restraint.weight)
num_sigmas = restraint.delta / sigma
is_outlier = (abs(num_sigmas) >= cutoff)
if (is_outlier or not outliers_only):
self.n_outliers += 1
self.results.append(
rna_angle(chain_id=labels.chain_id,
resseq=labels.resseq,
icode=labels.icode,
altloc=labels.altloc,
resname=labels.resname,
atoms_info=validation.get_atoms_info(
pdb_atoms, proxy.i_seqs),
sigma=sigma,
score=num_sigmas,
delta=restraint.delta,
outlier=is_outlier))
def angles_as_cif_loop(xray_structure, proxies):
space_group_info = sgtbx.space_group_info(group=xray_structure.space_group())
unit_cell = xray_structure.unit_cell()
sites_cart = xray_structure.sites_cart()
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_angle_atom_site_label_1",
"_restr_angle_atom_site_label_2",
"_restr_angle_atom_site_label_3",
"_restr_angle_site_symmetry_1",
"_restr_angle_site_symmetry_2",
"_restr_angle_site_symmetry_3",
"_restr_angle_target",
"_restr_angle_target_weight_param",
"_restr_angle_diff",
))
unit_mxs = [sgtbx.rt_mx()]*3
for proxy in proxies:
restraint = geometry_restraints.angle(
unit_cell=unit_cell,
sites_cart=sites_cart,
proxy=proxy)
sym_ops = proxy.sym_ops
if sym_ops is None: sym_ops = unit_mxs
i_seqs = proxy.i_seqs
loop.add_row((site_labels[i_seqs[0]],
site_labels[i_seqs[1]],
site_labels[i_seqs[2]],
space_group_info.cif_symmetry_code(sym_ops[0]),
space_group_info.cif_symmetry_code(sym_ops[1]),
space_group_info.cif_symmetry_code(sym_ops[2]),
fmt % restraint.angle_ideal,
fmt % math.sqrt(1/restraint.weight),
fmt % restraint.delta))
return loop
def __init__ (self, pdb_hierarchy, pdb_atoms, geometry_restraints_manager,
outliers_only=True) :
rna_geometry.__init__(self)
cutoff = 4
sites_cart = pdb_atoms.extract_xyz()
flags = geometry_restraints.flags.flags(default=True)
i_seq_name_hash = utils.build_name_hash(pdb_hierarchy=pdb_hierarchy)
for proxy in geometry_restraints_manager.angle_proxies:
restraint = geometry_restraints.angle(
sites_cart=sites_cart,
proxy=proxy)
atom1 = pdb_atoms[proxy.i_seqs[0]].name
atom2 = pdb_atoms[proxy.i_seqs[1]].name
atom3 = pdb_atoms[proxy.i_seqs[2]].name
labels = pdb_atoms[proxy.i_seqs[0]].fetch_labels()
if (atom1.strip() not in rna_backbone_atoms or
atom2.strip() not in rna_backbone_atoms or
atom3.strip() not in rna_backbone_atoms):
continue
self.n_total += 1
sigma = sqrt(1 / restraint.weight)
num_sigmas = restraint.delta / sigma
is_outlier = (abs(num_sigmas) >= cutoff)
if (is_outlier or not outliers_only):
self.n_outliers += 1
self.results.append(rna_angle(
chain_id=labels.chain_id,
resseq=labels.resseq,
icode=labels.icode,
altloc=labels.altloc,
resname=labels.resname,
atoms_info=validation.get_atoms_info(pdb_atoms, proxy.i_seqs),
sigma=sigma,
score=num_sigmas,
delta=restraint.delta,
outlier=is_outlier))
def run(args):
assert args in [[], ["--verbose"]]
if (len(args) == 0):
out = null_out()
else:
out = sys.stdout
#
mt = flex.mersenne_twister(seed=0)
#
for i_trial in xrange(10):
l0 = mt.random_double() + 0.5
l1 = mt.random_double() + 0.5
l2 = mt.random_double() + 0.5
angle_model = mt.random_double() * 178 + 1 \
+ 180 * (mt.random_size_t() % 3 - 1)
v = matrix.col(mt.random_double_point_on_sphere())
axis = v.ortho()
site1 = v * l1
site0 = site1 + v * l0
r = axis.axis_and_angle_as_r3_rotation_matrix(angle=angle_model, deg=True)
site2 = site1 + (r * v) * l2
a = angle(
sites=[site0, site1, site2],
angle_ideal=mt.random_double() * 720 - 360,
weight=mt.random_double() * 10 + 0.1)
assert approx_equal(min(
abs(angle_delta_deg(angle_1=a.angle_model, angle_2= angle_model)),
abs(angle_delta_deg(angle_1=a.angle_model, angle_2=-angle_model))), 0)
check_derivs(out=out, a=a)
#
for site2 in [(0,2.3,0), (0,0,2.5)]:
perm = flex.size_t([0,1,2])
while True:
a = angle(
sites=tuple(flex.vec3_double(
[(1.2,0,0), (0,0,0), site2]).select(perm)),
angle_ideal=mt.random_double() * 720 - 360,
weight=mt.random_double() * 10 + 0.1)
check_derivs(out=out, a=a)
if (not perm.next_permutation()):
break
#
for site0 in [(1,0,0),(0,1,0),(0,0,1),(1,1,1)]:
perm = flex.size_t([0,1,2])
while True:
a = angle(
sites=tuple(flex.vec3_double(
[site0, (0,0,0), -matrix.col(site0)]).select(perm)),
angle_ideal=180,
weight=1.3)
check_derivs(out=out, a=a, expect_failure=True)
if (not perm.next_permutation()):
break
#
plot_file_names = []
for method in ["ana", "fin"]:
plot_file_names.extend(write_plots(method=method))
f = open("angle_xy_as_pdf_commands", "w")
for file_name in plot_file_names:
print >> f, "ppdf %s > %s" % (file_name, file_name.replace(".xy", ".pdf"))
f.close()
#
print "OK"
def ensemble_mean_geometry_stats(self,
restraints_manager,
xray_structure,
ensemble_xray_structures,
ignore_hd = True,
verbose = False,
out = None,
return_pdb_string = False):
if (out is None): out = sys.stdout
if verbose:
utils.print_header("Ensemble mean geometry statistics", out = out)
ensemble_size = len(ensemble_xray_structures)
print("Ensemble size : ", ensemble_size, file=out)
# Dictionaries to store deltas
ensemble_bond_deltas = {}
ensemble_angle_deltas = {}
ensemble_chirality_deltas = {}
ensemble_planarity_deltas = {}
ensemble_dihedral_deltas = {}
# List to store rmsd of each model
structures_bond_rmsd = flex.double()
structures_angle_rmsd = flex.double()
structures_chirality_rmsd = flex.double()
structures_planarity_rmsd = flex.double()
structures_dihedral_rmsd = flex.double()
# Remove water and hd atoms from global restraints manager
selection = flex.bool()
for sc in xray_structure.scatterers():
if sc.label.find('HOH') > -1:
selection.append(True)
else:
selection.append(False)
if ignore_hd:
hd_selection = xray_structure.hd_selection()
assert hd_selection.size() == selection.size()
for n in range(hd_selection.size()):
if hd_selection[n] or selection[n]:
selection[n] = True
restraints_manager = restraints_manager.select(selection = ~selection)
# Get all deltas
for n, structure in enumerate(ensemble_xray_structures):
if verbose:
print("\nModel : ", n+1, file=out)
sites_cart = structure.sites_cart()
# Remove water and hd atoms from individual structures sites cart
selection = flex.bool()
for sc in structure.scatterers():
if sc.label.find('HOH') > -1:
selection.append(True)
else:
selection.append(False)
if ignore_hd:
hd_selection = structure.hd_selection()
assert hd_selection.size() == selection.size()
for n in range(hd_selection.size()):
if hd_selection[n] or selection[n]:
selection[n] = True
sites_cart = sites_cart.select(~selection)
assert sites_cart is not None
site_labels = None
energies_sites = restraints_manager.energies_sites(
sites_cart = sites_cart,
compute_gradients = False)
# Rmsd of individual model
bond_rmsd = energies_sites.geometry.bond_deviations()[2]
angle_rmsd = energies_sites.geometry.angle_deviations()[2]
chirality_rmsd = energies_sites.geometry.chirality_deviations()[2]
planarity_rmsd = energies_sites.geometry.planarity_deviations()[2]
dihedral_rmsd = energies_sites.geometry.dihedral_deviations()[2]
structures_bond_rmsd.append(bond_rmsd)
structures_angle_rmsd.append(angle_rmsd)
structures_chirality_rmsd.append(chirality_rmsd)
structures_planarity_rmsd.append(planarity_rmsd)
structures_dihedral_rmsd.append(dihedral_rmsd)
if verbose:
print(" Model RMSD", file=out)
print(" bond : %.6g" % bond_rmsd, file=out)
print(" angle : %.6g" % angle_rmsd, file=out)
print(" chirality : %.6g" % chirality_rmsd, file=out)
print(" planarity : %.6g" % planarity_rmsd, file=out)
print(" dihedral : %.6g" % dihedral_rmsd, file=out)
# Bond
pair_proxies = restraints_manager.geometry.pair_proxies(flags=None, sites_cart=sites_cart)
assert pair_proxies is not None
if verbose:
pair_proxies.bond_proxies.show_histogram_of_deltas(
sites_cart = sites_cart,
n_slots = 10,
f = out)
for proxy in pair_proxies.bond_proxies.simple:
bond_simple_proxy = geometry_restraints.bond(
sites_cart = sites_cart,
proxy = proxy)
if proxy.i_seqs in ensemble_bond_deltas:
ensemble_bond_deltas[proxy.i_seqs][0]+=bond_simple_proxy.delta
ensemble_bond_deltas[proxy.i_seqs][1]+=1
else:
ensemble_bond_deltas[proxy.i_seqs] = [bond_simple_proxy.delta, 1]
if verbose:
print("bond simple :", proxy.i_seqs, file=out)
print(" distance_ideal : %.6g" % proxy.distance_ideal, file=out)
print(" distance_model : %.6g" % bond_simple_proxy.distance_model, file=out)
print(" detla : %.6g" % bond_simple_proxy.delta, file=out)
if (pair_proxies.bond_proxies.asu.size() > 0):
asu_mappings = pair_proxies.bond_proxies.asu_mappings()
for proxy in pair_proxies.bond_proxies.asu:
rt_mx = asu_mappings.get_rt_mx_ji(pair=proxy)
bond_asu_proxy = geometry_restraints.bond(
sites_cart = sites_cart,
asu_mappings = asu_mappings,
proxy = proxy)
proxy_i_seqs = (proxy.i_seq, proxy.j_seq)
if proxy_i_seqs in ensemble_bond_deltas:
ensemble_bond_deltas[proxy_i_seqs][0]+=bond_asu_proxy.delta
ensemble_bond_deltas[proxy_i_seqs][1]+=1
else:
ensemble_bond_deltas[proxy_i_seqs] = [bond_asu_proxy.delta, 1]
if verbose:
print("bond asu :", (proxy.i_seq, proxy.j_seq), rt_mx, file=out)
print(" distance_ideal : %.6g" % proxy.distance_ideal, file=out)
print(" distance_model : %.6g" % bond_asu_proxy.distance_model, file=out)
print(" delta : %.6g" % bond_asu_proxy.delta, file=out)
# Angle
if verbose:
restraints_manager.geometry.angle_proxies.show_histogram_of_deltas(
sites_cart = sites_cart,
n_slots = 10,
f = out)
for proxy in restraints_manager.geometry.angle_proxies:
angle_proxy = geometry_restraints.angle(
sites_cart = sites_cart,
proxy = proxy)
if proxy.i_seqs in ensemble_angle_deltas:
ensemble_angle_deltas[proxy.i_seqs][0]+=angle_proxy.delta
ensemble_angle_deltas[proxy.i_seqs][1]+=1
else:
ensemble_angle_deltas[proxy.i_seqs] = [angle_proxy.delta, 1]
if verbose:
print("angle : ", proxy.i_seqs, file=out)
print(" angle_ideal : %.6g" % proxy.angle_ideal, file=out)
print(" angle_model : %.6g" % angle_proxy.angle_model, file=out)
print(" delta : %.6g" % angle_proxy.delta, file=out)
# Chirality
if verbose:
restraints_manager.geometry.chirality_proxies.show_histogram_of_deltas(
sites_cart = sites_cart,
n_slots = 10,
f = out)
for proxy in restraints_manager.geometry.chirality_proxies:
chirality_proxy = geometry_restraints.chirality(
sites_cart = sites_cart,
proxy = proxy)
if proxy.i_seqs in ensemble_chirality_deltas:
ensemble_chirality_deltas[proxy.i_seqs][0]+=chirality_proxy.delta
ensemble_chirality_deltas[proxy.i_seqs][1]+=1
else:
ensemble_chirality_deltas[proxy.i_seqs] = [chirality_proxy.delta, 1]
if verbose:
print("chirality : ", proxy.i_seqs, file=out)
print(" chirality_ideal : %.6g" % proxy.volume_ideal, file=out)
print(" chirality_model : %.6g" % chirality_proxy.volume_model, file=out)
print(" chirality : %.6g" % chirality_proxy.delta, file=out)
# Planarity
for proxy in restraints_manager.geometry.planarity_proxies:
planarity_proxy = geometry_restraints.planarity(
sites_cart = sites_cart,
proxy = proxy)
proxy_i_seqs = []
for i_seq in proxy.i_seqs:
proxy_i_seqs.append(i_seq)
proxy_i_seqs = tuple(proxy_i_seqs)
if proxy_i_seqs in ensemble_planarity_deltas:
ensemble_planarity_deltas[proxy_i_seqs][0]+=planarity_proxy.rms_deltas()
ensemble_planarity_deltas[proxy_i_seqs][1]+=1
else:
ensemble_planarity_deltas[proxy_i_seqs] = [planarity_proxy.rms_deltas(), 1]
if verbose:
print("planarity : ", proxy_i_seqs, file=out)
print(" planarity rms_deltas : %.6g" % planarity_proxy.rms_deltas(), file=out)
# Dihedral
if verbose:
restraints_manager.geometry.dihedral_proxies.show_histogram_of_deltas(
sites_cart = sites_cart,
n_slots = 10,
f = out)
for proxy in restraints_manager.geometry.dihedral_proxies:
dihedral_proxy = geometry_restraints.dihedral(
sites_cart = sites_cart,
proxy = proxy)
if proxy.i_seqs in ensemble_dihedral_deltas:
ensemble_dihedral_deltas[proxy.i_seqs][0]+=dihedral_proxy.delta
ensemble_dihedral_deltas[proxy.i_seqs][1]+=1
else:
ensemble_dihedral_deltas[proxy.i_seqs] = [dihedral_proxy.delta, 1]
if verbose:
print("dihedral : ", proxy.i_seqs, file=out)
print(" dihedral_ideal : %.6g" % proxy.angle_ideal, file=out)
print(" periodicity : %.6g" % proxy.periodicity, file=out)
print(" dihedral_model : %.6g" % dihedral_proxy.angle_model, file=out)
print(" delta : %.6g" % dihedral_proxy.delta, file=out)
# Calculate RMSDs for ensemble model
# Bond
mean_bond_delta = flex.double()
for proxy, info in six.iteritems(ensemble_bond_deltas):
# assert info[1] == ensemble_size
if info[1]!=ensemble_size:
print('skipping bond RMSD calns of ensemble %s' % info, file=out)
continue
mean_delta = info[0] / info[1]
mean_bond_delta.append(mean_delta)
bond_delta_sq = mean_bond_delta * mean_bond_delta
ensemble_bond_rmsd = math.sqrt(flex.mean_default(bond_delta_sq, 0))
# Angle
mean_angle_delta = flex.double()
for proxy, info in six.iteritems(ensemble_angle_deltas):
assert info[1] == ensemble_size
mean_delta = info[0] / info[1]
mean_angle_delta.append(mean_delta)
angle_delta_sq = mean_angle_delta * mean_angle_delta
ensemble_angle_rmsd = math.sqrt(flex.mean_default(angle_delta_sq, 0))
# Chirality
mean_chirality_delta = flex.double()
for proxy, info in six.iteritems(ensemble_chirality_deltas):
assert info[1] == ensemble_size
mean_delta = info[0] / info[1]
mean_chirality_delta.append(mean_delta)
chirality_delta_sq = mean_chirality_delta * mean_chirality_delta
ensemble_chirality_rmsd = math.sqrt(flex.mean_default(chirality_delta_sq, 0))
# Planarity
mean_planarity_delta = flex.double()
for proxy, info in six.iteritems(ensemble_planarity_deltas):
assert info[1] == ensemble_size
mean_delta = info[0] / info[1]
mean_planarity_delta.append(mean_delta)
planarity_delta_sq = mean_planarity_delta * mean_planarity_delta
ensemble_planarity_rmsd = math.sqrt(flex.mean_default(planarity_delta_sq, 0))
# Dihedral
mean_dihedral_delta = flex.double()
for proxy, info in six.iteritems(ensemble_dihedral_deltas):
assert info[1] == ensemble_size
mean_delta = info[0] / info[1]
mean_dihedral_delta.append(mean_delta)
dihedral_delta_sq = mean_dihedral_delta * mean_dihedral_delta
ensemble_dihedral_rmsd = math.sqrt(flex.mean_default(dihedral_delta_sq, 0))
# Calculate <structure rmsd>
assert ensemble_size == structures_bond_rmsd
assert ensemble_size == structures_angle_rmsd
assert ensemble_size == structures_chirality_rmsd
assert ensemble_size == structures_planarity_rmsd
assert ensemble_size == structures_dihedral_rmsd
structure_bond_rmsd_mean = structures_bond_rmsd.min_max_mean().mean
structure_angle_rmsd_mean = structures_angle_rmsd.min_max_mean().mean
structure_chirality_rmsd_mean = structures_chirality_rmsd.min_max_mean().mean
structure_planarity_rmsd_mean = structures_planarity_rmsd.min_max_mean().mean
structure_dihedral_rmsd_mean = structures_dihedral_rmsd.min_max_mean().mean
# Show summary
utils.print_header("Ensemble RMSD summary", out = out)
print(" RMSD (mean delta per restraint)", file=out)
print(" bond : %.6g" % ensemble_bond_rmsd, file=out)
print(" angle : %.6g" % ensemble_angle_rmsd, file=out)
print(" chirality : %.6g" % ensemble_chirality_rmsd, file=out)
print(" planarity : %.6g" % ensemble_planarity_rmsd, file=out)
print(" dihedral : %.6g" % ensemble_dihedral_rmsd, file=out)
print(" RMSD (mean RMSD per structure)", file=out)
print(" bond : %.6g" % structure_bond_rmsd_mean, file=out)
print(" angle : %.6g" % structure_angle_rmsd_mean, file=out)
print(" chirality : %.6g" % structure_chirality_rmsd_mean, file=out)
print(" planarity : %.6g" % structure_planarity_rmsd_mean, file=out)
print(" dihedral : %.6g" % structure_dihedral_rmsd_mean, file=out)
if ignore_hd:
print("\n Calculated excluding H/D", file=out)
else:
print("\n Calculated including H/D", file=out)
if return_pdb_string:
ens_geo_pdb_string = "REMARK 3"
ens_geo_pdb_string += "\nREMARK 3 NUMBER STRUCTURES IN ENSEMBLE : {0:5d}".format(ensemble_size)
if ignore_hd:
ens_geo_pdb_string += "\nREMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (EXCLUDING H/D)"
else:
ens_geo_pdb_string += "\nREMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (INCLUDING H/D)"
ens_geo_pdb_string += "\nREMARK 3 RMSD (MEAN DELTA PER RESTRAINT)"
ens_geo_pdb_string += "\nREMARK 3 BOND : {0:5.3f}".format(ensemble_bond_rmsd)
ens_geo_pdb_string += "\nREMARK 3 ANGLE : {0:5.3f}".format(ensemble_angle_rmsd)
ens_geo_pdb_string += "\nREMARK 3 CHIRALITY : {0:5.3f}".format(ensemble_chirality_rmsd)
ens_geo_pdb_string += "\nREMARK 3 PLANARITY : {0:5.3f}".format(ensemble_planarity_rmsd)
ens_geo_pdb_string += "\nREMARK 3 DIHEDRAL : {0:5.2f}".format(ensemble_dihedral_rmsd)
ens_geo_pdb_string += "\nREMARK 3 RMSD (MEAN RMSD PER STRUCTURE)"
ens_geo_pdb_string += "\nREMARK 3 BOND : {0:5.3f}".format(structure_bond_rmsd_mean)
ens_geo_pdb_string += "\nREMARK 3 ANGLE : {0:5.3f}".format(structure_angle_rmsd_mean)
ens_geo_pdb_string += "\nREMARK 3 CHIRALITY : {0:5.3f}".format(structure_chirality_rmsd_mean)
ens_geo_pdb_string += "\nREMARK 3 PLANARITY : {0:5.3f}".format(structure_planarity_rmsd_mean)
ens_geo_pdb_string += "\nREMARK 3 DIHEDRAL : {0:5.2f}".format(structure_dihedral_rmsd_mean)
ens_geo_pdb_string += "\nREMARK 3"
return ens_geo_pdb_string
def _get_angle(sites_cart, angle_proxies, i_proxy):
if i_proxy is not None:
# compute angle
angle = geometry_restraints.angle(sites_cart=sites_cart, proxy=angle_proxies[i_proxy])
return angle
return None
def ensemble_mean_geometry_stats(self,
restraints_manager,
xray_structure,
ensemble_xray_structures,
ignore_hd = True,
verbose = False,
out = None,
return_pdb_string = False):
if (out is None): out = sys.stdout
if verbose:
utils.print_header("Ensemble mean geometry statistics", out = out)
ensemble_size = len(ensemble_xray_structures)
print >> out, "Ensemble size : ", ensemble_size
# Dictionaries to store deltas
ensemble_bond_deltas = {}
ensemble_angle_deltas = {}
ensemble_chirality_deltas = {}
ensemble_planarity_deltas = {}
ensemble_dihedral_deltas = {}
# List to store rmsd of each model
structures_bond_rmsd = flex.double()
structures_angle_rmsd = flex.double()
structures_chirality_rmsd = flex.double()
structures_planarity_rmsd = flex.double()
structures_dihedral_rmsd = flex.double()
# Remove water and hd atoms from global restraints manager
selection = flex.bool()
for sc in xray_structure.scatterers():
if sc.label.find('HOH') > -1:
selection.append(True)
else:
selection.append(False)
if ignore_hd:
hd_selection = xray_structure.hd_selection()
assert hd_selection.size() == selection.size()
for n in xrange(hd_selection.size()):
if hd_selection[n] or selection[n]:
selection[n] = True
restraints_manager = restraints_manager.select(selection = ~selection)
# Get all deltas
for n, structure in enumerate(ensemble_xray_structures):
if verbose:
print >> out, "\nModel : ", n+1
sites_cart = structure.sites_cart()
# Remove water and hd atoms from individual structures sites cart
selection = flex.bool()
for sc in structure.scatterers():
if sc.label.find('HOH') > -1:
selection.append(True)
else:
selection.append(False)
if ignore_hd:
hd_selection = structure.hd_selection()
assert hd_selection.size() == selection.size()
for n in xrange(hd_selection.size()):
if hd_selection[n] or selection[n]:
selection[n] = True
sites_cart = sites_cart.select(~selection)
assert sites_cart is not None
site_labels = None
energies_sites = restraints_manager.energies_sites(
sites_cart = sites_cart,
compute_gradients = False)
# Rmsd of individual model
bond_rmsd = energies_sites.geometry.bond_deviations()[2]
angle_rmsd = energies_sites.geometry.angle_deviations()[2]
chirality_rmsd = energies_sites.geometry.chirality_deviations()[2]
planarity_rmsd = energies_sites.geometry.planarity_deviations()[2]
dihedral_rmsd = energies_sites.geometry.dihedral_deviations()[2]
structures_bond_rmsd.append(bond_rmsd)
structures_angle_rmsd.append(angle_rmsd)
structures_chirality_rmsd.append(chirality_rmsd)
structures_planarity_rmsd.append(planarity_rmsd)
structures_dihedral_rmsd.append(dihedral_rmsd)
if verbose:
print >> out, " Model RMSD"
print >> out, " bond : %.6g" % bond_rmsd
print >> out, " angle : %.6g" % angle_rmsd
print >> out, " chirality : %.6g" % chirality_rmsd
print >> out, " planarity : %.6g" % planarity_rmsd
print >> out, " dihedral : %.6g" % dihedral_rmsd
# Bond
pair_proxies = restraints_manager.geometry.pair_proxies(flags=None, sites_cart=sites_cart)
assert pair_proxies is not None
if verbose:
pair_proxies.bond_proxies.show_histogram_of_deltas(
sites_cart = sites_cart,
n_slots = 10,
f = out)
for proxy in pair_proxies.bond_proxies.simple:
bond_simple_proxy = geometry_restraints.bond(
sites_cart = sites_cart,
proxy = proxy)
if proxy.i_seqs in ensemble_bond_deltas:
ensemble_bond_deltas[proxy.i_seqs][0]+=bond_simple_proxy.delta
ensemble_bond_deltas[proxy.i_seqs][1]+=1
else:
ensemble_bond_deltas[proxy.i_seqs] = [bond_simple_proxy.delta, 1]
if verbose:
print >> out, "bond simple :", proxy.i_seqs
print >> out, " distance_ideal : %.6g" % proxy.distance_ideal
print >> out, " distance_model : %.6g" % bond_simple_proxy.distance_model
print >> out, " detla : %.6g" % bond_simple_proxy.delta
if (pair_proxies.bond_proxies.asu.size() > 0):
asu_mappings = pair_proxies.bond_proxies.asu_mappings()
for proxy in pair_proxies.bond_proxies.asu:
rt_mx = asu_mappings.get_rt_mx_ji(pair=proxy)
bond_asu_proxy = geometry_restraints.bond(
sites_cart = sites_cart,
asu_mappings = asu_mappings,
proxy = proxy)
proxy_i_seqs = (proxy.i_seq, proxy.j_seq)
if proxy_i_seqs in ensemble_bond_deltas:
ensemble_bond_deltas[proxy_i_seqs][0]+=bond_asu_proxy.delta
ensemble_bond_deltas[proxy_i_seqs][1]+=1
else:
ensemble_bond_deltas[proxy_i_seqs] = [bond_asu_proxy.delta, 1]
if verbose:
print >> out, "bond asu :", (proxy.i_seq, proxy.j_seq), rt_mx
print >> out, " distance_ideal : %.6g" % proxy.distance_ideal
print >> out, " distance_model : %.6g" % bond_asu_proxy.distance_model
print >> out, " delta : %.6g" % bond_asu_proxy.delta
# Angle
if verbose:
restraints_manager.geometry.angle_proxies.show_histogram_of_deltas(
sites_cart = sites_cart,
n_slots = 10,
f = out)
for proxy in restraints_manager.geometry.angle_proxies:
angle_proxy = geometry_restraints.angle(
sites_cart = sites_cart,
proxy = proxy)
if proxy.i_seqs in ensemble_angle_deltas:
ensemble_angle_deltas[proxy.i_seqs][0]+=angle_proxy.delta
ensemble_angle_deltas[proxy.i_seqs][1]+=1
else:
ensemble_angle_deltas[proxy.i_seqs] = [angle_proxy.delta, 1]
if verbose:
print >> out, "angle : ", proxy.i_seqs
print >> out, " angle_ideal : %.6g" % proxy.angle_ideal
print >> out, " angle_model : %.6g" % angle_proxy.angle_model
print >> out, " delta : %.6g" % angle_proxy.delta
# Chirality
if verbose:
restraints_manager.geometry.chirality_proxies.show_histogram_of_deltas(
sites_cart = sites_cart,
n_slots = 10,
f = out)
for proxy in restraints_manager.geometry.chirality_proxies:
chirality_proxy = geometry_restraints.chirality(
sites_cart = sites_cart,
proxy = proxy)
if proxy.i_seqs in ensemble_chirality_deltas:
ensemble_chirality_deltas[proxy.i_seqs][0]+=chirality_proxy.delta
ensemble_chirality_deltas[proxy.i_seqs][1]+=1
else:
ensemble_chirality_deltas[proxy.i_seqs] = [chirality_proxy.delta, 1]
if verbose:
print >> out, "chirality : ", proxy.i_seqs
print >> out, " chirality_ideal : %.6g" % proxy.volume_ideal
print >> out, " chirality_model : %.6g" % chirality_proxy.volume_model
print >> out, " chirality : %.6g" % chirality_proxy.delta
# Planarity
for proxy in restraints_manager.geometry.planarity_proxies:
planarity_proxy = geometry_restraints.planarity(
sites_cart = sites_cart,
proxy = proxy)
proxy_i_seqs = []
for i_seq in proxy.i_seqs:
proxy_i_seqs.append(i_seq)
proxy_i_seqs = tuple(proxy_i_seqs)
if proxy_i_seqs in ensemble_planarity_deltas:
ensemble_planarity_deltas[proxy_i_seqs][0]+=planarity_proxy.rms_deltas()
ensemble_planarity_deltas[proxy_i_seqs][1]+=1
else:
ensemble_planarity_deltas[proxy_i_seqs] = [planarity_proxy.rms_deltas(), 1]
if verbose:
print >> out, "planarity : ", proxy_i_seqs
print >> out, " planarity rms_deltas : %.6g" % planarity_proxy.rms_deltas()
# Dihedral
if verbose:
restraints_manager.geometry.dihedral_proxies.show_histogram_of_deltas(
sites_cart = sites_cart,
n_slots = 10,
f = out)
for proxy in restraints_manager.geometry.dihedral_proxies:
dihedral_proxy = geometry_restraints.dihedral(
sites_cart = sites_cart,
proxy = proxy)
if proxy.i_seqs in ensemble_dihedral_deltas:
ensemble_dihedral_deltas[proxy.i_seqs][0]+=dihedral_proxy.delta
ensemble_dihedral_deltas[proxy.i_seqs][1]+=1
else:
ensemble_dihedral_deltas[proxy.i_seqs] = [dihedral_proxy.delta, 1]
if verbose:
print >> out, "dihedral : ", proxy.i_seqs
print >> out, " dihedral_ideal : %.6g" % proxy.angle_ideal
print >> out, " periodicity : %.6g" % proxy.periodicity
print >> out, " dihedral_model : %.6g" % dihedral_proxy.angle_model
print >> out, " delta : %.6g" % dihedral_proxy.delta
# Calculate RMSDs for ensemble model
# Bond
mean_bond_delta = flex.double()
for proxy, info in ensemble_bond_deltas.iteritems():
assert info[1] == ensemble_size
mean_delta = info[0] / info[1]
mean_bond_delta.append(mean_delta)
bond_delta_sq = mean_bond_delta * mean_bond_delta
ensemble_bond_rmsd = math.sqrt(flex.mean_default(bond_delta_sq, 0))
# Angle
mean_angle_delta = flex.double()
for proxy, info in ensemble_angle_deltas.iteritems():
assert info[1] == ensemble_size
mean_delta = info[0] / info[1]
mean_angle_delta.append(mean_delta)
angle_delta_sq = mean_angle_delta * mean_angle_delta
ensemble_angle_rmsd = math.sqrt(flex.mean_default(angle_delta_sq, 0))
# Chirality
mean_chirality_delta = flex.double()
for proxy, info in ensemble_chirality_deltas.iteritems():
assert info[1] == ensemble_size
mean_delta = info[0] / info[1]
mean_chirality_delta.append(mean_delta)
chirality_delta_sq = mean_chirality_delta * mean_chirality_delta
ensemble_chirality_rmsd = math.sqrt(flex.mean_default(chirality_delta_sq, 0))
# Planarity
mean_planarity_delta = flex.double()
for proxy, info in ensemble_planarity_deltas.iteritems():
assert info[1] == ensemble_size
mean_delta = info[0] / info[1]
mean_planarity_delta.append(mean_delta)
planarity_delta_sq = mean_planarity_delta * mean_planarity_delta
ensemble_planarity_rmsd = math.sqrt(flex.mean_default(planarity_delta_sq, 0))
# Dihedral
mean_dihedral_delta = flex.double()
for proxy, info in ensemble_dihedral_deltas.iteritems():
assert info[1] == ensemble_size
mean_delta = info[0] / info[1]
mean_dihedral_delta.append(mean_delta)
dihedral_delta_sq = mean_dihedral_delta * mean_dihedral_delta
ensemble_dihedral_rmsd = math.sqrt(flex.mean_default(dihedral_delta_sq, 0))
# Calculate <structure rmsd>
assert ensemble_size == structures_bond_rmsd
assert ensemble_size == structures_angle_rmsd
assert ensemble_size == structures_chirality_rmsd
assert ensemble_size == structures_planarity_rmsd
assert ensemble_size == structures_dihedral_rmsd
structure_bond_rmsd_mean = structures_bond_rmsd.min_max_mean().mean
structure_angle_rmsd_mean = structures_angle_rmsd.min_max_mean().mean
structure_chirality_rmsd_mean = structures_chirality_rmsd.min_max_mean().mean
structure_planarity_rmsd_mean = structures_planarity_rmsd.min_max_mean().mean
structure_dihedral_rmsd_mean = structures_dihedral_rmsd.min_max_mean().mean
# Show summary
utils.print_header("Ensemble RMSD summary", out = out)
print >> out, " RMSD (mean delta per restraint)"
print >> out, " bond : %.6g" % ensemble_bond_rmsd
print >> out, " angle : %.6g" % ensemble_angle_rmsd
print >> out, " chirality : %.6g" % ensemble_chirality_rmsd
print >> out, " planarity : %.6g" % ensemble_planarity_rmsd
print >> out, " dihedral : %.6g" % ensemble_dihedral_rmsd
print >> out, " RMSD (mean RMSD per structure)"
print >> out, " bond : %.6g" % structure_bond_rmsd_mean
print >> out, " angle : %.6g" % structure_angle_rmsd_mean
print >> out, " chirality : %.6g" % structure_chirality_rmsd_mean
print >> out, " planarity : %.6g" % structure_planarity_rmsd_mean
print >> out, " dihedral : %.6g" % structure_dihedral_rmsd_mean
if ignore_hd:
print >> out, "\n Calculated excluding H/D"
else:
print >> out, "\n Calculated including H/D"
if return_pdb_string:
ens_geo_pdb_string = "REMARK 3"
ens_geo_pdb_string += "\nREMARK 3 NUMBER STRUCTURES IN ENSEMBLE : {0:5d}".format(ensemble_size)
if ignore_hd:
ens_geo_pdb_string += "\nREMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (EXCLUDING H/D)"
else:
ens_geo_pdb_string += "\nREMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (INCLUDING H/D)"
ens_geo_pdb_string += "\nREMARK 3 RMSD (MEAN DELTA PER RESTRAINT)"
ens_geo_pdb_string += "\nREMARK 3 BOND : {0:5.3f}".format(ensemble_bond_rmsd)
ens_geo_pdb_string += "\nREMARK 3 ANGLE : {0:5.3f}".format(ensemble_angle_rmsd)
ens_geo_pdb_string += "\nREMARK 3 CHIRALITY : {0:5.3f}".format(ensemble_chirality_rmsd)
ens_geo_pdb_string += "\nREMARK 3 PLANARITY : {0:5.3f}".format(ensemble_planarity_rmsd)
ens_geo_pdb_string += "\nREMARK 3 DIHEDRAL : {0:5.2f}".format(ensemble_dihedral_rmsd)
ens_geo_pdb_string += "\nREMARK 3 RMSD (MEAN RMSD PER STRUCTURE)"
ens_geo_pdb_string += "\nREMARK 3 BOND : {0:5.3f}".format(structure_bond_rmsd_mean)
ens_geo_pdb_string += "\nREMARK 3 ANGLE : {0:5.3f}".format(structure_angle_rmsd_mean)
ens_geo_pdb_string += "\nREMARK 3 CHIRALITY : {0:5.3f}".format(structure_chirality_rmsd_mean)
ens_geo_pdb_string += "\nREMARK 3 PLANARITY : {0:5.3f}".format(structure_planarity_rmsd_mean)
ens_geo_pdb_string += "\nREMARK 3 DIHEDRAL : {0:5.2f}".format(structure_dihedral_rmsd_mean)
ens_geo_pdb_string += "\nREMARK 3"
return ens_geo_pdb_string
