def exercise_five_cc():
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
ph = pdb_inp.construct_hierarchy()
#ph.write_pdb_file(file_name="m1.pdb")
xrs = ph.extract_xray_structure(
crystal_symmetry=pdb_inp.crystal_symmetry())
f_calc = xrs.structure_factors(
d_min=2.0).f_calc() #.resolution_filter(d_max=6)
fft_map = f_calc.fft_map(resolution_factor=0.25)
m1 = fft_map.real_map_unpadded()
#
#xrs = xrs.set_b_iso(value=50)
sc = xrs.sites_cart()
#sc = sc + flex.vec3_double(sc.size(), [.5,.5,.5])
xrs = xrs.replace_sites_cart(new_sites=sc)
ph.adopt_xray_structure(xrs)
#ph.write_pdb_file(file_name="m2.pdb")
o = correlation.five_cc(map=m1,
xray_structure=xrs,
d_min=2.0,
compute_cc_box=True,
compute_cc_image=True,
box=False).result
assert approx_equal(o.cc_box, 1.0)
assert approx_equal(o.cc_image, 1.0)
assert approx_equal(o.cc_mask, 1.0)
assert approx_equal(o.cc_peaks, 1.0)
assert approx_equal(o.cc_volume, 1.0)
def initialize(self):
five_cc_o = five_cc(map=self.target_map_object.map_data,
xray_structure=self.model.get_xray_structure(),
d_min=self.target_map_object.d_min,
compute_cc_box=True,
compute_cc_image=False,
compute_cc_mask=True,
compute_cc_volume=False,
compute_cc_peaks=False).result
self.cc_mask = five_cc_o.cc_mask
self.cc_box = five_cc_o.cc_box
# XXX use model.statistics or better method of model!
if (self.model.restraints_manager_available()):
es = self.model.get_restraints_manager().geometry.energies_sites(
sites_cart=self.model.get_sites_cart())
self.rmsd_a = es.angle_deviations()[2]
self.rmsd_b = es.bond_deviations()[2]
def show_cc(map_data, xray_structure, log=None):
import mmtbx.maps.mtriage
from mmtbx.maps.correlation import five_cc
xrs = xray_structure
xrs.scattering_type_registry(table="electron")
d99 = maptbx.d99(map=map_data,
crystal_symmetry=xrs.crystal_symmetry()).result.d99
if (log is not None): print("Resolution of map is: %6.4f" % d99, file=log)
result = five_cc(map=map_data,
xray_structure=xrs,
d_min=d99,
compute_cc_box=False,
compute_cc_mask=True,
compute_cc_peaks=False,
compute_cc_volume=False).result
if (log is not None):
print("Map-model correlation coefficient (CC)", file=log)
print(" CC_mask : %6.4f" % result.cc_mask, file=log)
return result.cc_mask
def initialize(self):
self.assert_pdb_hierarchy_xray_structure_sync()
five_cc_o = five_cc(map=self.target_map_object.map_data,
xray_structure=self.xray_structure,
d_min=self.target_map_object.d_min,
compute_cc_box=True,
compute_cc_image=False,
compute_cc_mask=True,
compute_cc_volume=False,
compute_cc_peaks=False)
self.cc_mask = five_cc_o.cc_mask
self.cc_box = five_cc_o.cc_box
if (self.geometry_restraints_manager is not None):
es = self.geometry_restraints_manager.energies_sites(
sites_cart=self.xray_structure.sites_cart())
self.rmsd_a = es.angle_deviations()[2]
self.rmsd_b = es.bond_deviations()[2]
self.dist_from_start = flex.mean(
self.xray_structure_start.distances(other=self.xray_structure))
self.assert_pdb_hierarchy_xray_structure_sync()
def initialize(self):
self.assert_pdb_hierarchy_xray_structure_sync()
# residue monitors
self.residue_monitors = []
backbone_atoms = ["N", "CA", "C", "O", "CB"]
get_class = iotbx.pdb.common_residue_names_get_class
sites_cart = self.xray_structure.sites_cart()
current_map = self.compute_map(xray_structure=self.xray_structure)
for model in self.pdb_hierarchy.models():
for chain in model.chains():
for residue_group in chain.residue_groups():
conformers = residue_group.conformers()
if (len(conformers) > 1): continue
for conformer in residue_group.conformers():
residue = conformer.only_residue()
id_str = "%s%s%s" % (chain.id, residue.resname,
residue.resseq.strip())
if (get_class(residue.resname) == "common_amino_acid"):
residue_i_seqs_backbone = flex.size_t()
residue_i_seqs_sidechain = flex.size_t()
residue_i_seqs_all = flex.size_t()
residue_i_seqs_c = flex.size_t()
residue_i_seqs_n = flex.size_t()
for atom in residue.atoms():
an = atom.name.strip()
bb = an in backbone_atoms
residue_i_seqs_all.append(atom.i_seq)
if (bb):
residue_i_seqs_backbone.append(atom.i_seq)
else:
residue_i_seqs_sidechain.append(atom.i_seq)
if (an == "C"):
residue_i_seqs_c.append(atom.i_seq)
if (an == "N"):
residue_i_seqs_n.append(atom.i_seq)
sca = sites_cart.select(residue_i_seqs_all)
scs = sites_cart.select(residue_i_seqs_sidechain)
scb = sites_cart.select(residue_i_seqs_backbone)
if (scs.size() == 0): ccs = None
else:
ccs = self.map_cc(sites_cart=scs,
other_map=current_map)
if (sca.size() == 0): cca = None
else:
cca = self.map_cc(sites_cart=sca,
other_map=current_map)
if (scb.size() == 0): ccb = None
else:
ccb = self.map_cc(sites_cart=scb,
other_map=current_map)
self.residue_monitors.append(
residue_monitor(
residue=residue,
id_str=id_str,
selection_sidechain=
residue_i_seqs_sidechain,
selection_backbone=residue_i_seqs_backbone,
selection_all=residue_i_seqs_all,
selection_c=residue_i_seqs_c,
selection_n=residue_i_seqs_n,
map_cc_sidechain=ccs,
map_cc_backbone=ccb,
map_cc_all=cca,
rotamer_status=self.rotamer_manager.
evaluate_residue(residue)))
else:
residue_i_seqs_all = residue.atoms().extract_i_seq(
)
sca = sites_cart.select(residue_i_seqs_all)
cca = self.map_cc(sites_cart=sca,
other_map=current_map)
self.residue_monitors.append(
residue_monitor(
residue=residue,
id_str=id_str,
selection_all=residue_i_seqs_all,
map_cc_all=cca))
# globals
self.five_cc = five_cc(map=self.target_map_object.map_data,
xray_structure=self.xray_structure,
d_min=self.target_map_object.d_min)
self.map_cc_whole_unit_cell = self.map_cc(other_map=current_map)
self.map_cc_around_atoms = self.map_cc(other_map=current_map,
sites_cart=sites_cart)
self.map_cc_per_atom = self.map_cc(other_map=current_map,
sites_cart=sites_cart,
per_atom=True)
if (self.geometry_restraints_manager is not None):
es = self.geometry_restraints_manager.energies_sites(
sites_cart=sites_cart)
self.rmsd_a = es.angle_deviations()[2]
self.rmsd_b = es.bond_deviations()[2]
self.dist_from_start = flex.mean(
self.xray_structure_start.distances(other=self.xray_structure))
self.number_of_rotamer_outliers = 0
for r in self.residue_monitors:
if (r.rotamer_status == "OUTLIER"):
self.number_of_rotamer_outliers += 1
self.assert_pdb_hierarchy_xray_structure_sync()
