def run(self):
xrs = self.pdb_hierarchy.extract_xray_structure(
crystal_symmetry=self.crystal_symmetry)
xrs.scattering_type_registry(table=self.params.scattering_table)
soin = maptbx.shift_origin_if_needed(
map_data=self.map_data,
sites_cart=xrs.sites_cart(),
crystal_symmetry=self.crystal_symmetry)
map_data = soin.map_data
xrs.set_sites_cart(soin.sites_cart)
self.five_cc_result = mmtbx.maps.correlation.five_cc(
map=map_data,
xray_structure=xrs,
d_min=self.params.resolution,
compute_cc_mask=self.params.compute_cc_mask,
compute_cc_volume=self.params.compute_cc_volume,
compute_cc_peaks=self.params.compute_cc_peaks)
# Atom radius
self.atom_radius = mtriage.get_atom_radius(
xray_structure=xrs,
d_min=self.params.resolution,
map_data=map_data,
crystal_symmetry=self.crystal_symmetry,
radius=self.params.atom_radius)
# Model-map FSC
if (self.params.compute_fsc):
mtriage_params = mtriage.master_params().extract()
mtriage_params.scattering_table = self.params.scattering_table
mtriage_params.compute_d_model = False
mtriage_params.compute_d99 = False
mtriage_params.radius_smooth = self.atom_radius
self.fsc = mtriage.mtriage(
map_data=self.map_data,
pdb_hierarchy=self.pdb_hierarchy,
crystal_symmetry=self.crystal_symmetry,
params=mtriage_params).run().get_results().fsc_curve_model.fsc
#
cc_calculator = mmtbx.maps.correlation.from_map_and_xray_structure_or_fmodel(
xray_structure=xrs,
map_data=map_data,
d_min=self.params.resolution)
#
def get_common_data(atoms, atom_radius):
sel = atoms.extract_i_seq()
return group_args(b_iso_mean=flex.mean(atoms.extract_b()),
occ_mean=flex.mean(atoms.extract_occ()),
n_atoms=atoms.size(),
cc=cc_calculator.cc(selection=sel,
atom_radius=atom_radius),
xyz_mean=atoms.extract_xyz().mean())
# CC per chain
if (self.params.compute_cc_per_chain):
for chain in self.pdb_hierarchy.chains():
cd = get_common_data(atoms=chain.atoms(),
atom_radius=self.atom_radius)
self.cc_per_chain.append(
group_args(chain_id=chain.id,
b_iso_mean=cd.b_iso_mean,
occ_mean=cd.occ_mean,
n_atoms=cd.n_atoms,
cc=cd.cc))
# CC per residue
if (self.params.compute_cc_per_residue):
for rg in self.pdb_hierarchy.residue_groups():
for conformer in rg.conformers():
for residue in conformer.residues():
cd = get_common_data(atoms=residue.atoms(),
atom_radius=self.atom_radius)
self.cc_per_residue.append(
group_args(
chain_id=rg.parent().id,
resname=residue.resname,
resseq=residue.resseq,
icode=residue.icode,
b_iso_mean=cd.b_iso_mean,
occ_mean=cd.occ_mean,
n_atoms=cd.n_atoms,
cc=cd.cc,
xyz_mean=cd.xyz_mean,
residue=residue)) # for compatibility with GUI
def run(self):
xrs = self.pdb_hierarchy.extract_xray_structure(
crystal_symmetry=self.crystal_symmetry)
xrs.scattering_type_registry(table = self.params.scattering_table)
soin = maptbx.shift_origin_if_needed(
map_data = self.map_data,
sites_cart = xrs.sites_cart(),
crystal_symmetry = self.crystal_symmetry)
map_data = soin.map_data
xrs.set_sites_cart(soin.sites_cart)
self.five_cc = mmtbx.maps.correlation.five_cc(
map = map_data,
xray_structure = xrs,
keep_map_calc = self.params.keep_map_calc,
d_min = self.params.resolution,
compute_cc_mask = self.params.compute.cc_mask,
compute_cc_volume = self.params.compute.cc_volume,
compute_cc_peaks = self.params.compute.cc_peaks,
compute_cc_box = self.params.compute.cc_box,
compute_cc_image = self.params.compute.cc_image)
# Atom radius
self.atom_radius = mtriage.get_atom_radius(
xray_structure = xrs,
resolution = self.params.resolution,
radius = self.params.atom_radius)
#
cc_calculator = mmtbx.maps.correlation.from_map_and_xray_structure_or_fmodel(
xray_structure = xrs,
map_data = map_data,
d_min = self.params.resolution)
#
def get_common_data(atoms, atom_radius):
sel = atoms.extract_i_seq()
cc = cc_calculator.cc(selection = sel, atom_radius = atom_radius)
return group_args(
b_iso_mean = flex.mean(atoms.extract_b()),
occ_mean = flex.mean(atoms.extract_occ()),
n_atoms = atoms.size(),
cc = cc,
xyz_mean = atoms.extract_xyz().mean())
# CC per chain
if(self.params.compute.cc_per_chain):
for chain in self.pdb_hierarchy.chains():
cd = get_common_data(atoms=chain.atoms(), atom_radius=self.atom_radius)
self.cc_per_chain.append(group_args(
chain_id = chain.id,
b_iso_mean = cd.b_iso_mean,
occ_mean = cd.occ_mean,
n_atoms = cd.n_atoms,
cc = cd.cc))
# CC per residue
if(self.params.compute.cc_per_residue):
for rg in self.pdb_hierarchy.residue_groups():
for conformer in rg.conformers():
for residue in conformer.residues():
cd = get_common_data(
atoms = residue.atoms(),
atom_radius = self.atom_radius)
self.cc_per_residue.append(group_args(
chain_id = rg.parent().id,
resname = residue.resname,
resseq = residue.resseq,
icode = residue.icode,
b_iso_mean = cd.b_iso_mean,
occ_mean = cd.occ_mean,
n_atoms = cd.n_atoms,
cc = cd.cc,
xyz_mean = cd.xyz_mean))
# Side chain
sel_mc_str = "protein and (name C or name N or name CA or name O or name CB)"
asc = self.pdb_hierarchy.atom_selection_cache()
sel_mc = asc.selection(sel_mc_str)
sel_sc = ~sel_mc
if(sel_mc.count(True)>0):
self.cc_main_chain = get_common_data(
atoms = self.pdb_hierarchy.select(sel_mc).atoms(),
atom_radius = self.atom_radius)
if(sel_sc.count(True)>0):
self.cc_side_chain = get_common_data(
atoms = self.pdb_hierarchy.select(sel_sc).atoms(),
atom_radius = self.atom_radius)