def exclude_outliers_from_reference_restraints_selection(
pdb_hierarchy,
restraints_selection):
from mmtbx.validation.ramalyze import ramalyze
# the import below is SLOW!!!
from mmtbx.rotamer.rotamer_eval import RotamerEval
assert restraints_selection is not None
# ramachandran plot outliers
rama_outlier_selection = ramalyze(pdb_hierarchy=pdb_hierarchy,
outliers_only=False).outlier_selection()
rama_outlier_selection = flex.bool(restraints_selection.size(),
rama_outlier_selection)
# rotamer outliers
rota_outlier_selection = flex.size_t()
rotamer_manager = RotamerEval() # SLOW!!!
for model in 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()
if(rotamer_manager.evaluate_residue(residue)=="OUTLIER"):
rota_outlier_selection.extend(residue.atoms().extract_i_seq())
rota_outlier_selection = flex.bool(restraints_selection.size(),
rota_outlier_selection)
outlier_selection = rama_outlier_selection | rota_outlier_selection
return restraints_selection & (~outlier_selection)
class load(object):
def __init__(self, rotamers, residues=None):
if(residues is not None):
for i, residue in enumerate(residues):
residues[i] = residue.lower()
assert rotamers in ["favored", "favored_allowed"]
self.rotamer_evaluator = RotamerEval()
path=libtbx.env.find_in_repositories("chem_data/rotamer_chi_angles")
self.result = {}
for aa_code in aa_codes:
if(residues is not None):
if(not aa_code in residues): continue
try:
if(rotamers=="favored"):
f = "%s_favored.pkl"%aa_code
elif(rotamers=="favored_allowed"):
f = "%s_favored_allowed.pkl"%aa_code
else: raise RuntimeError("Not implemented: rotamers=%s"%rotamers)
chi_angles = easy_pickle.load(file_name = "/".join([path,f]))
except Exception:
chi_angles = None
self.result.setdefault(aa_code,[]).extend([chi_angles])
def get_chi_angles(self, resname):
resname = resname.strip().lower()
assert resname in aa_codes
return self.result[resname][0]
def rotamer(self, residue):
return self.rotamer_evaluator.evaluate_residue(residue)
class load(object):
def __init__(self, rotamers="all"):
assert rotamers in ["all", "favored", "allowed"]
self.rotamer_evaluator = RotamerEval()
path=libtbx.env.find_in_repositories("mmtbx/idealized_aa_residues/data")
self.result = {}
for aa_code in aa_codes:
try:
if( rotamers=="all"): f = "%s-coarse_step10.pickle"%aa_code
elif(rotamers=="favored"): f = "%s-coarse_step10_favored.pickle"%aa_code
else: raise RuntimeError("Not implemented: rotamers=%s"%rotamers)
chi_angles = easy_pickle.load(file_name = "/".join([path,f]))
# XXX Fix later
chi_angles_ = []
for chi in chi_angles:
chi_ = []
for ch in chi:
chi_.append(ch*math.pi/180)
chi_angles_.append(chi_)
chi_angles = chi_angles_
# XXX Fix later
except Exception:
chi_angles = None
self.result.setdefault(aa_code,[]).extend([chi_angles])
def get_chi_angles(self, resname):
resname = resname.strip().lower()
assert resname in aa_codes
return self.result[resname][0]
def rotamer(self, residue):
return self.rotamer_evaluator.evaluate_residue(residue)
class load(object):
def __init__(self):
self.rotamer_evaluator = RotamerEval()
path = libtbx.env.find_in_repositories(
"mmtbx/idealized_aa_residues/data")
self.result = {}
for aa_code in aa_codes:
try:
chi_angles = easy_pickle.load(file_name="/".join(
[path, "%s-coarse_step10.pickle" % aa_code]))
# XXX Fix later
chi_angles_ = []
for chi in chi_angles:
chi_ = []
for ch in chi:
chi_.append(ch * math.pi / 180)
chi_angles_.append(chi_)
chi_angles = chi_angles_
# XXX Fix later
except Exception:
chi_angles = None
self.result.setdefault(aa_code, []).extend([chi_angles])
def get_chi_angles(self, resname):
resname = resname.strip().lower()
assert resname in aa_codes
return self.result[resname][0]
def rotamer(self, residue):
return self.rotamer_evaluator.evaluate_residue(residue)
def show(pdb_hierarchy, tm, xrs, grm, prefix):
map = compute_map(target_map=tm, xray_structure=xrs)
cc = flex.linear_correlation(x=map.as_1d(),
y=tm.data.as_1d()).coefficient()
es = grm.energies_sites(sites_cart=xrs.sites_cart())
rmsd_a = es.angle_deviations()[2]
rmsd_b = es.bond_deviations()[2]
print "%s: overall CC: %6.4f rmsd_bonds=%6.3f rmsd_angles=%6.3f" % (
prefix, cc, rmsd_b, rmsd_a)
pdb_hierarchy.adopt_xray_structure(xrs)
rotamer_manager = RotamerEval()
for model in pdb_hierarchy.models():
for chain in model.chains():
for residue in chain.residues():
sites_cart = residue.atoms().extract_xyz()
sel = maptbx.grid_indices_around_sites(
unit_cell=xrs.unit_cell(),
fft_n_real=map.focus(),
fft_m_real=map.all(),
sites_cart=sites_cart,
site_radii=flex.double(sites_cart.size(), 2))
ccr = flex.linear_correlation(
x=map.select(sel).as_1d(),
y=tm.data.select(sel).as_1d()).coefficient()
fmt = "%s: %4s %10s CC: %6.4f"
print fmt % (prefix, residue.resname,
rotamer_manager.evaluate_residue(residue), ccr)
def exclude_outliers_from_reference_restraints_selection(
pdb_hierarchy, restraints_selection):
from mmtbx.validation.ramalyze import ramalyze
# the import below is SLOW!!!
from mmtbx.rotamer.rotamer_eval import RotamerEval
assert restraints_selection is not None
# ramachandran plot outliers
rama_outlier_selection = ramalyze(pdb_hierarchy=pdb_hierarchy,
outliers_only=False).outlier_selection()
rama_outlier_selection = flex.bool(restraints_selection.size(),
rama_outlier_selection)
# rotamer outliers
rota_outlier_selection = flex.size_t()
rotamer_manager = RotamerEval() # SLOW!!!
for model in 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()
if (rotamer_manager.evaluate_residue(residue) == "OUTLIER"
):
rota_outlier_selection.extend(
residue.atoms().extract_i_seq())
rota_outlier_selection = flex.bool(restraints_selection.size(),
rota_outlier_selection)
outlier_selection = rama_outlier_selection | rota_outlier_selection
return restraints_selection & (~outlier_selection)
class load(object):
def __init__(self):
self.rotamer_evaluator = RotamerEval()
path=libtbx.env.find_in_repositories("mmtbx/idealized_aa_residues/data")
self.result = {}
for aa_code in aa_codes:
try:
chi_angles = easy_pickle.load(
file_name="/".join([path,"%s-coarse_step10.pickle"%aa_code]))
# XXX Fix later
chi_angles_ = []
for chi in chi_angles:
chi_ = []
for ch in chi:
chi_.append(ch*math.pi/180)
chi_angles_.append(chi_)
chi_angles = chi_angles_
# XXX Fix later
except Exception:
chi_angles = None
self.result.setdefault(aa_code,[]).extend([chi_angles])
def get_chi_angles(self, resname):
resname = resname.strip().lower()
assert resname in aa_codes
if(resname == "mse"): return self.result["met"][0] # alias
return self.result[resname][0]
def rotamer(self, residue):
return self.rotamer_evaluator.evaluate_residue(residue)
def show(pdb_hierarchy, tm, xrs, grm, prefix):
map = compute_map(target_map=tm, xray_structure=xrs)
cc = flex.linear_correlation(
x=map.as_1d(),
y=tm.data.as_1d()).coefficient()
es = grm.energies_sites(sites_cart = xrs.sites_cart())
rmsd_a = es.angle_deviations()[2]
rmsd_b = es.bond_deviations()[2]
print "%s: overall CC: %6.4f rmsd_bonds=%6.3f rmsd_angles=%6.3f"%(
prefix, cc, rmsd_b, rmsd_a)
pdb_hierarchy.adopt_xray_structure(xrs)
rotamer_manager = RotamerEval()
for model in pdb_hierarchy.models():
for chain in model.chains():
for residue in chain.residues():
sites_cart = residue.atoms().extract_xyz()
sel = maptbx.grid_indices_around_sites(
unit_cell = xrs.unit_cell(),
fft_n_real = map.focus(),
fft_m_real = map.all(),
sites_cart = sites_cart,
site_radii = flex.double(sites_cart.size(), 2))
ccr = flex.linear_correlation(
x=map.select(sel).as_1d(),
y=tm.data.select(sel).as_1d()).coefficient()
fmt = "%s: %4s %10s CC: %6.4f"
print fmt%(prefix, residue.resname, rotamer_manager.evaluate_residue(residue),ccr)
def run(pdb_str, expected_ids):
get_class = iotbx.pdb.common_residue_names_get_class
mon_lib_srv = mmtbx.monomer_library.server.server()
rotamer_manager = RotamerEval()
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
pdb_hierarchy = pdb_inp.construct_hierarchy()
result_ids = []
for residue_group in pdb_hierarchy.residue_groups():
for conformer in residue_group.conformers():
for residue in conformer.residues():
sites_cart = residue.atoms().extract_xyz()
rotamer_name = rotamer_manager.evaluate_residue(
residue=residue)
print residue.resname, residue.resseq, rotamer_name
result_ids.append(rotamer_name)
if (get_class(residue.resname) == "common_amino_acid"):
rotamer_iterator = mon_lib_srv.rotamer_iterator(
fine_sampling=True,
comp_id=residue.resname,
atom_names=residue.atoms().extract_name(),
sites_cart=sites_cart)
if (rotamer_iterator is None
or rotamer_iterator.problem_message is not None
or rotamer_iterator.rotamer_info is None):
rotamer_iterator = None
if (rotamer_iterator is not None):
d1_min, d2_min = 1.e+9, 1.e+9
for r, rotamer_sites_cart in rotamer_iterator:
sites_cart_rot = rotamer_manager.nearest_rotamer_sites_cart(
residue=residue)
d1 = flex.mean(
flex.sqrt((sites_cart - sites_cart_rot).dot()))
d2 = flex.mean(
flex.sqrt(
(sites_cart - rotamer_sites_cart).dot()))
if (d1 < d1_min):
d1_min = d1
if (d2 < d2_min):
d2_min = d2
assert approx_equal(d1_min, d2_min)
assert result_ids == expected_ids
def run(pdb_str, expected_ids):
get_class = iotbx.pdb.common_residue_names_get_class
mon_lib_srv = mmtbx.monomer_library.server.server()
rotamer_manager = RotamerEval()
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
pdb_hierarchy = pdb_inp.construct_hierarchy()
result_ids = []
for residue_group in pdb_hierarchy.residue_groups():
for conformer in residue_group.conformers():
for residue in conformer.residues():
sites_cart = residue.atoms().extract_xyz()
rotamer_name = rotamer_manager.evaluate_residue(residue=residue)
print residue.resname, residue.resseq, rotamer_name
result_ids.append(rotamer_name)
if(get_class(residue.resname) == "common_amino_acid"):
rotamer_iterator = mon_lib_srv.rotamer_iterator(
fine_sampling = True,
comp_id = residue.resname,
atom_names = residue.atoms().extract_name(),
sites_cart = sites_cart)
if(rotamer_iterator is None or
rotamer_iterator.problem_message is not None or
rotamer_iterator.rotamer_info is None):
rotamer_iterator = None
if(rotamer_iterator is not None):
d1_min, d2_min = 1.e+9, 1.e+9
for r, rotamer_sites_cart in rotamer_iterator:
sites_cart_rot = rotamer_manager.nearest_rotamer_sites_cart(
residue=residue)
d1= flex.mean(flex.sqrt((sites_cart - sites_cart_rot).dot()))
d2= flex.mean(flex.sqrt((sites_cart - rotamer_sites_cart).dot()))
if(d1 < d1_min):
d1_min = d1
if(d2 < d2_min):
d2_min = d2
assert approx_equal(d1_min, d2_min)
assert result_ids == expected_ids
out = StringIO()
r.show_old_output(out=out, verbose=False)
assert (out.getvalue() == """\
A 47 PRO:1.00:86.4:329.3:41.3:324.9::Favored:Cg_exo
A 48 MSE:0.70:0.3:287.6:214.8:138.3::OUTLIER:OUTLIER
A 49 LYS:1.00:0.1:288.6:263.2:251.7:233.0:OUTLIER:OUTLIER
"""), out.getvalue()
try:
r = rotalyze.rotalyze(pdb_hierarchy=hierarchy, data_version="9000")
except ValueError:
pass
else:
raise Exception_expected
from mmtbx.rotamer.rotamer_eval import RotamerEval
rotamer_manager = RotamerEval()
results = []
for model in hierarchy.models():
for chain in model.chains():
for residue in chain.residues():
cur_rot = rotamer_manager.evaluate_residue(residue)
results.append(cur_rot)
assert results == ['Cg_exo', 'OUTLIER', 'OUTLIER']
if (__name__ == "__main__"):
exercise_rotalyze()
exercise_2()
print "OK"
class structure_monitor(object):
def __init__(self,
pdb_hierarchy,
xray_structure,
target_map_object=None,
geometry_restraints_manager=None):
adopt_init_args(self, locals())
self.unit_cell = self.xray_structure.unit_cell()
self.xray_structure = xray_structure.deep_copy_scatterers()
self.xray_structure_start = xray_structure.deep_copy_scatterers()
self.states_collector = mmtbx.utils.states(
pdb_hierarchy = self.pdb_hierarchy,
xray_structure = self.xray_structure,
counter = 1)
self.states_collector.add(sites_cart = self.xray_structure.sites_cart())
self.rotamer_manager = RotamerEval()
self.assert_pdb_hierarchy_xray_structure_sync()
#
self.five_cc = None
self.map_cc_whole_unit_cell = None
self.map_cc_around_atoms = None
self.map_cc_per_atom = None
self.rmsd_b = None
self.rmsd_a = None
self.dist_from_start = 0
self.dist_from_previous = 0
self.number_of_rotamer_outliers = 0
self.residue_monitors = None
self.stats_evaluations = []
#
self.initialize()
def assert_pdb_hierarchy_xray_structure_sync(self):
return #XXX
sc1 = self.xray_structure.sites_cart()
sc2 = self.pdb_hierarchy.atoms().extract_xyz()
assert approx_equal(sc1, sc2, 1.e-3)
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()
def compute_map(self, xray_structure):
self.assert_pdb_hierarchy_xray_structure_sync()
mc = self.target_map_object.miller_array.structure_factors_from_scatterers(
xray_structure = xray_structure).f_calc()
fft_map = miller.fft_map(
crystal_gridding = self.target_map_object.crystal_gridding,
fourier_coefficients = mc)
fft_map.apply_sigma_scaling()
return fft_map.real_map_unpadded()
def map_cc_histogram_per_atom(self, radius=2, n_slots=10):
self.assert_pdb_hierarchy_xray_structure_sync()
from mmtbx.maps import correlation
current_map = self.compute_map(xray_structure = self.xray_structure)
return correlation.histogram_per_atom(
map_1 = current_map,
map_2 = self.target_map_object.map_data,
sites_cart = self.xray_structure.sites_cart(),
unit_cell = self.xray_structure.unit_cell(),
radius = radius,
n_slots = n_slots)
def map_cc(self, other_map, sites_cart=None, atom_radius=2, per_atom=False):
self.assert_pdb_hierarchy_xray_structure_sync()
from mmtbx.maps import correlation
if(sites_cart is not None):
if(per_atom):
result = correlation.from_map_map_atoms_per_atom(
map_1 = other_map,
map_2 = self.target_map_object.map_data,
sites_cart = sites_cart,
unit_cell = self.xray_structure.unit_cell(),
radius = atom_radius)
else:
result = correlation.from_map_map_atoms(
map_1 = other_map,
map_2 = self.target_map_object.map_data,
sites_cart = sites_cart,
unit_cell = self.xray_structure.unit_cell(),
radius = atom_radius)
else:
result = correlation.from_map_map(
map_1 = other_map,
map_2 = self.target_map_object.map_data)
return result
def show(self, prefix="", log=None):
self.assert_pdb_hierarchy_xray_structure_sync()
if(log is None): log = sys.stdout
fmt = """%s CC_mask: %-6.3f
%s CC_volume: %-6.3f
%s CC_peaks: %-6.3f
%s rmsd (bonds): %-s
%s rmsd (angles): %-s
%s Dist. moved from start: %-6.3f
%s Dist. moved from previous: %-6.3f
%s All-atom clashscore %-s
%s Ramachandran plot:
%s outliers: %-s %%
%s allowed: %-s %%
%s favored: %-s %%
%s Omega angle:
%s cis-proline: %-s %%
%s twisted proline: %-s %%
%s cis-general: %-s %%
%s twisted-general: %-s %%
%s CaBLAM analysis:
%s outliers: %-s %%
%s disfavored: %-s %%
%s ca outliers: %-s %%
%s Rotamer outliers: %-s %%
%s C-beta deviations: %-s %%
"""
mso = None
try:
if self.geometry_restraints_manager is not None and False:
# XXX False at the end is intentional, because currently I want to
# disable this 'if' branch. Reason is - nothing from extended
# model_statistics (with GRM) is being used, so no reason to spend
# time calculating statistics over various restraints.
mso = mmtbx.model.statistics.geometry(
pdb_hierarchy = self.pdb_hierarchy,
molprobity_scores = libtbx.env.has_module("probe"),
restraints_manager = self.geometry_restraints_manager)
else:
mso = mmtbx.model.statistics.geometry_no_grm(
pdb_hierarchy = self.pdb_hierarchy,
molprobity_scores = libtbx.env.has_module("probe"))
except Exception:
# some part of validation failed
pass
self.stats_evaluations.append(
group_args(
cc = group_args(
cc_mask = self.five_cc.result.cc_mask,
cc_volume = self.five_cc.result.cc_volume,
cc_peaks = self.five_cc.result.cc_peaks),
geometry = mso,
rmsd_a = self.rmsd_a,
rmsd_b = self.rmsd_b))
if mso is not None and self.five_cc is not None:
print(fmt%(
# prefix, self.map_cc_whole_unit_cell,
# prefix, self.map_cc_around_atoms,
prefix, self.five_cc.cc_mask,
prefix, self.five_cc.cc_volume,
prefix, self.five_cc.cc_peaks,
prefix, format_value("%-6.2f", self.rmsd_b).strip(),
prefix, format_value("%-6.2f", self.rmsd_a).strip(),
prefix, self.dist_from_start,
prefix, self.dist_from_previous,
prefix, format_value("%-6.2f", mso.clashscore),
prefix,
prefix, format_value("%-5.2f", mso.ramachandran_outliers),
prefix, format_value("%-5.2f", mso.ramachandran_allowed),
prefix, format_value("%-5.2f", mso.ramachandran_favored),
prefix,
prefix, format_value("%-5.2f", mso.cis_proline),
prefix, format_value("%-5.2f", mso.twisted_proline),
prefix, format_value("%-5.2f", mso.cis_general),
prefix, format_value("%-5.2f", mso.twisted_general),
prefix,
prefix, format_value("%-5.2f", mso.cablam_outliers),
prefix, format_value("%-5.2f", mso.cablam_disfavored),
prefix, format_value("%-5.2f", mso.cablam_ca_outliers),
prefix, format_value("%6.2f", mso.rotamer_outliers).strip(),
prefix, format_value("%-5.2f", mso.c_beta_dev_percent)), file=log)
def show_residues(self, map_cc_all=0.8, map_cc_sidechain=0.8, log=None):
self.assert_pdb_hierarchy_xray_structure_sync()
if(log is None): log = sys.stdout
header_printed = True
for r in self.residue_monitors:
i1=r.map_cc_all < map_cc_all
i2=r.rotamer_status == "OUTLIER"
i4=r.map_cc_sidechain is not None and r.map_cc_sidechain<map_cc_sidechain
if([i1,i2,i4].count(True)>0):
if(header_printed):
print("Residue CC CC CC Rotamer", file=log)
print(" id all backbone sidechain id", file=log)
header_printed = False
print(r.format_info_string(), file=log)
def update(self, xray_structure, accept_as_is=True):
if(not accept_as_is):
current_map = self.compute_map(xray_structure = xray_structure)
sites_cart = xray_structure.sites_cart()
sites_cart_ = self.xray_structure.sites_cart()
for r in self.residue_monitors:
sca = sites_cart.select(r.selection_all)
scs = sites_cart.select(r.selection_sidechain)
scb = sites_cart.select(r.selection_backbone)
map_cc_all = self.map_cc(sites_cart = sca, other_map = current_map)
map_cc_sidechain = self.map_cc(sites_cart = scs, other_map = current_map)
map_cc_backbone = self.map_cc(sites_cart = scb, other_map = current_map)
flag = map_cc_all >= r.map_cc_all and \
map_cc_backbone >= r.map_cc_backbone and \
map_cc_sidechain>= r.map_cc_sidechain
if(flag):
residue_sites_cart_new = sites_cart.select(r.selection_all)
sites_cart_ = sites_cart_.set_selected(r.selection_all,
residue_sites_cart_new)
xray_structure = xray_structure.replace_sites_cart(sites_cart_)
# re-initialize monitor
self.dist_from_previous = flex.mean(self.xray_structure.distances(
other = xray_structure))
self.xray_structure = xray_structure
self.pdb_hierarchy.adopt_xray_structure(xray_structure)
self.initialize()
self.states_collector.add(sites_cart = xray_structure.sites_cart())
self.assert_pdb_hierarchy_xray_structure_sync()
def exercise_2():
pdb_str = """\
ATOM 2527 N LEU A 261 -31.022 -24.808 107.479 1.00 28.22 N
ATOM 2528 CA LEU A 261 -30.054 -23.719 107.237 1.00 21.77 C
ATOM 2529 C LEU A 261 -30.582 -22.773 106.168 1.00 27.64 C
ATOM 2530 O LEU A 261 -29.841 -21.977 105.561 1.00 26.70 O
ATOM 2531 CB LEU A 261 -28.696 -24.276 106.874 1.00 22.58 C
ATOM 2532 CG LEU A 261 -28.135 -25.066 108.060 1.00 40.89 C
ATOM 2533 CD1 LEU A 261 -26.892 -25.858 107.664 1.00 46.72 C
ATOM 2534 CD2 LEU A 261 -27.806 -24.109 109.202 1.00 38.88 C
ATOM 2535 H LEU A 261 -31.201 -25.277 106.781 1.00 33.87 H
ATOM 2536 HA LEU A 261 -29.950 -23.204 108.064 1.00 26.12 H
ATOM 2537 HB2 LEU A 261 -28.781 -24.874 106.115 1.00 27.10 H
ATOM 2538 HB3 LEU A 261 -28.088 -23.548 106.670 1.00 27.10 H
ATOM 2539 HG LEU A 261 -28.806 -25.693 108.373 1.00 49.07 H
ATOM 2540 HD11 LEU A 261 -26.570 -26.338 108.430 1.00 56.07 H
ATOM 2541 HD12 LEU A 261 -27.124 -26.473 106.965 1.00 56.07 H
ATOM 2542 HD13 LEU A 261 -26.219 -25.247 107.353 1.00 56.07 H
ATOM 2543 HD21 LEU A 261 -28.608 -23.653 109.468 1.00 46.66 H
ATOM 2544 HD22 LEU A 261 -27.455 -24.612 109.941 1.00 46.66 H
ATOM 2545 HD23 LEU A 261 -27.153 -23.474 108.899 1.00 46.66 H
ATOM 2546 N GLY A 262 -31.887 -22.863 105.948 1.00 23.68 N
ATOM 2547 CA GLY A 262 -32.572 -21.935 105.075 1.00 21.87 85 C
ATOM 2548 C GLY A 262 -33.718 -22.620 104.386 1.00 27.32 C
ATOM 2549 O GLY A 262 -33.943 -23.822 104.556 1.00 23.10 O
ATOM 2550 H GLY A 262 -32.399 -23.459 106.298 1.00 28.42 H
ATOM 2551 HA2 GLY A 262 -32.916 -21.189 105.591 1.00 26.25 85 H
ATOM 2552 HA3 GLY A 262 -31.958 -21.598 104.405 1.00 26.25 85 H
ATOM 2553 N SER A 263 -34.460 -21.830 103.628 1.00 24.62 N
ATOM 2554 CA SER A 263 -35.631 -22.290 102.921 1.00 27.15 C
ATOM 2555 C SER A 263 -35.594 -21.761 101.492 1.00 22.14 C
ATOM 2556 O SER A 263 -34.723 -20.945 101.159 1.00 21.01 O
ATOM 2557 CB SER A 263 -36.839 -21.713 103.619 1.00 25.73 C
ATOM 2558 OG SER A 263 -36.907 -22.232 104.922 1.00 26.84 O
ATOM 2559 H SER A 263 -34.296 -20.995 103.507 1.00 29.54 H
ATOM 2560 HA SER A 263 -35.680 -23.269 102.917 1.00 32.58 H
ATOM 2561 HB2 SER A 263 -36.754 -20.747 103.661 1.00 30.87 H
ATOM 2562 HB3 SER A 263 -37.641 -21.960 103.132 1.00 30.87 H
ATOM 2563 HG SER A 263 -37.560 -21.925 105.312 1.00 32.20 H
"""
pdb_str2 = """
ATOM 453 N PRO A 47 8.633 6.370 5.022 1.00 13.79 N
ATOM 454 CA PRO A 47 7.915 7.571 5.496 1.00 14.61 C
ATOM 455 C PRO A 47 7.612 7.481 6.994 1.00 15.06 C
ATOM 456 O PRO A 47 7.289 6.377 7.439 1.00 14.39 O
ATOM 457 CB PRO A 47 6.639 7.559 4.651 1.00 16.24 C
ATOM 458 CG PRO A 47 7.089 6.901 3.338 1.00 15.52 C
ATOM 459 CD PRO A 47 7.990 5.773 3.833 1.00 14.40 C
ATOM 460 N MSE A 48 7.754 8.528 7.779 1.00 15.13 N
ATOM 461 CA MSE A 48 7.482 8.456 9.201 1.00 16.17 C
ATOM 462 C MSE A 48 6.040 8.750 9.517 1.00 15.23 C
ATOM 463 O MSE A 48 5.417 9.418 8.735 1.00 14.77 O
ATOM 464 CB MSE A 48 8.165 9.538 10.023 1.00 19.62 C
ATOM 465 CG MSE A 48 9.630 9.466 10.238 1.00 21.70 C
ATOM 466 SE MSE A 48 10.022 10.161 12.050 0.70 37.95 SE
ATOM 467 CE MSE A 48 11.268 8.720 12.235 1.00 28.72 C
ATOM 468 N LYS A 49 5.519 8.291 10.645 1.00 13.93 N
ATOM 469 CA LYS A 49 4.167 8.624 11.045 1.00 13.79 C
ATOM 470 C LYS A 49 4.022 10.138 11.202 1.00 14.66 C
ATOM 471 O LYS A 49 5.011 10.853 11.351 1.00 15.69 O
ATOM 472 CB LYS A 49 3.797 7.915 12.349 1.00 13.33 C
ATOM 473 CG LYS A 49 3.593 6.416 12.204 1.00 14.35 C
ATOM 474 CD LYS A 49 2.121 6.071 12.044 1.00 16.45 C
ATOM 475 CE LYS A 49 1.571 5.402 13.292 1.00 18.19 C
ATOM 476 NZ LYS A 49 0.899 4.110 12.980 1.00 19.97 N
"""
pdb_io = pdb.input(source_info=None, lines=pdb_str)
hierarchy = pdb_io.construct_hierarchy()
try :
rotalyze.rotalyze(pdb_hierarchy=hierarchy)
except Sorry as e :
assert ("GLY A 262" in str(e))
else :
raise Exception_expected
pdb_io = pdb.input(source_info=None, lines=pdb_str2)
hierarchy = pdb_io.construct_hierarchy()
r = rotalyze.rotalyze(pdb_hierarchy=hierarchy)
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue()
assert output == """\
A 47 PRO:1.00:86.4:329.3:41.3:324.9::Favored:Cg_exo
A 48 MSE:0.70:0.3:287.6:214.8:138.3::OUTLIER:OUTLIER
A 49 LYS:1.00:0.1:288.6:263.2:251.7:233.0:OUTLIER:OUTLIER
""", output
r = rotalyze.rotalyze(pdb_hierarchy=hierarchy,
data_version="8000")
out = StringIO()
r.show_old_output(out=out, verbose=False)
assert (out.getvalue() == """\
A 47 PRO:1.00:86.4:329.3:41.3:324.9::Favored:Cg_exo
A 48 MSE:0.70:0.3:287.6:214.8:138.3::OUTLIER:OUTLIER
A 49 LYS:1.00:0.1:288.6:263.2:251.7:233.0:OUTLIER:OUTLIER
"""), out.getvalue()
try :
r = rotalyze.rotalyze(pdb_hierarchy=hierarchy,
data_version="9000")
except ValueError :
pass
else :
raise Exception_expected
from mmtbx.rotamer.rotamer_eval import RotamerEval
rotamer_manager = RotamerEval()
results = []
for model in hierarchy.models():
for chain in model.chains():
for residue in chain.residues():
cur_rot = rotamer_manager.evaluate_residue(residue)
results.append(cur_rot)
assert results == ['Cg_exo', 'OUTLIER', 'OUTLIER']
out = StringIO()
r.show_old_output(out=out, verbose=False)
assert (out.getvalue() == """\
A 47 PRO:1.00:86.4:329.3:41.3:324.9::Favored:Cg_exo
A 48 MSE:0.70:0.3:287.6:214.8:138.3::OUTLIER:OUTLIER
A 49 LYS:1.00:0.1:288.6:263.2:251.7:233.0:OUTLIER:OUTLIER
"""), out.getvalue()
try :
r = rotalyze.rotalyze(pdb_hierarchy=hierarchy,
data_version="9000")
except ValueError :
pass
else :
raise Exception_expected
from mmtbx.rotamer.rotamer_eval import RotamerEval
rotamer_manager = RotamerEval()
results = []
for model in hierarchy.models():
for chain in model.chains():
for residue in chain.residues():
cur_rot = rotamer_manager.evaluate_residue(residue)
results.append(cur_rot)
assert results == ['Cg_exo', 'OUTLIER', 'OUTLIER']
if (__name__ == "__main__") :
exercise_rotalyze()
exercise_2()
print "OK"
class structure_monitor(object):
def __init__(self,
pdb_hierarchy,
xray_structure,
target_map_object=None,
geometry_restraints_manager=None):
adopt_init_args(self, locals())
self.unit_cell = self.xray_structure.unit_cell()
self.xray_structure = xray_structure.deep_copy_scatterers()
self.xray_structure_start = xray_structure.deep_copy_scatterers()
self.states_collector = mmtbx.utils.states(
pdb_hierarchy = self.pdb_hierarchy,
xray_structure = self.xray_structure,
counter = 1)
self.states_collector.add(sites_cart = self.xray_structure.sites_cart())
self.rotamer_manager = RotamerEval()
self.assert_pdb_hierarchy_xray_structure_sync()
#
self.map_cc_whole_unit_cell = None
self.map_cc_around_atoms = None
self.map_cc_per_atom = None
self.rmsd_b = None
self.rmsd_a = None
self.dist_from_start = 0
self.dist_from_previous = 0
self.number_of_rotamer_outliers = 0
self.residue_monitors = None
#
self.initialize()
def assert_pdb_hierarchy_xray_structure_sync(self):
return #XXX
sc1 = self.xray_structure.sites_cart()
sc2 = self.pdb_hierarchy.atoms().extract_xyz()
assert approx_equal(sc1, sc2, 1.e-3)
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.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()
def compute_map(self, xray_structure):
self.assert_pdb_hierarchy_xray_structure_sync()
mc = self.target_map_object.miller_array.structure_factors_from_scatterers(
xray_structure = xray_structure).f_calc()
fft_map = miller.fft_map(
crystal_gridding = self.target_map_object.crystal_gridding,
fourier_coefficients = mc)
fft_map.apply_sigma_scaling()
return fft_map.real_map_unpadded()
def map_cc_histogram_per_atom(self, radius=2, n_slots=10):
self.assert_pdb_hierarchy_xray_structure_sync()
from mmtbx.maps import correlation
current_map = self.compute_map(xray_structure = self.xray_structure)
return correlation.histogram_per_atom(
map_1 = current_map,
map_2 = self.target_map_object.map_data,
sites_cart = self.xray_structure.sites_cart(),
unit_cell = self.xray_structure.unit_cell(),
radius = radius,
n_slots = n_slots)
def map_cc(self, other_map, sites_cart=None, atom_radius=2, per_atom=False):
self.assert_pdb_hierarchy_xray_structure_sync()
from mmtbx.maps import correlation
if(sites_cart is not None):
if(per_atom):
result = correlation.from_map_map_atoms_per_atom(
map_1 = other_map,
map_2 = self.target_map_object.map_data,
sites_cart = sites_cart,
unit_cell = self.xray_structure.unit_cell(),
radius = atom_radius)
else:
result = correlation.from_map_map_atoms(
map_1 = other_map,
map_2 = self.target_map_object.map_data,
sites_cart = sites_cart,
unit_cell = self.xray_structure.unit_cell(),
radius = atom_radius)
else:
result = correlation.from_map_map(
map_1 = other_map,
map_2 = self.target_map_object.map_data)
return result
def show(self, prefix="", log=None):
self.assert_pdb_hierarchy_xray_structure_sync()
if(log is None): log = sys.stdout
fmt = """%s Map CC (whole unit cell): %-6.3f
%s Map CC (around atoms): %-6.3f
%s rmsd (bonds): %-s
%s rmsd (angles): %-s
%s Dist. moved from start: %-6.3f
%s Dist. moved from previous: %-6.3f
%s All-atom clashscore %-s
%s Ramachandran plot:
%s outliers: %-s %%
%s allowed: %-s %%
%s favored: %-s %%
%s Rotamer outliers: %-s %%
%s C-beta deviations: %-s
"""
if(self.geometry_restraints_manager is not None):
mso = model_statistics.geometry(
pdb_hierarchy = self.pdb_hierarchy,
molprobity_scores = libtbx.env.has_module("probe"),
restraints_manager = self.geometry_restraints_manager)
print >> log, fmt%(
prefix, self.map_cc_whole_unit_cell,
prefix, self.map_cc_around_atoms,
prefix, format_value("%-6.2f", self.rmsd_b).strip(),
prefix, format_value("%-6.2f", self.rmsd_a).strip(),
prefix, self.dist_from_start,
prefix, self.dist_from_previous,
prefix, format_value("%-6.2f", mso.clashscore),
prefix,
prefix, format_value("%-5.2f", mso.ramachandran_outliers),
prefix, format_value("%-5.2f", mso.ramachandran_allowed),
prefix, format_value("%-5.2f", mso.ramachandran_favored),
prefix, format_value("%6.2f", mso.rotamer_outliers).strip(),
prefix, format_value("%-3d", mso.c_beta_dev))
else:
print >> log, fmt%(
prefix, self.map_cc_whole_unit_cell,
prefix, self.map_cc_around_atoms,
prefix, "None",
prefix, "None",
prefix, self.dist_from_start,
prefix, self.dist_from_previous,
prefix, "None",
prefix,
prefix, "None",
prefix, "None",
prefix, "None",
prefix, "None",
prefix, "None")
def show_residues(self, map_cc_all=0.8, map_cc_sidechain=0.8, log=None):
self.assert_pdb_hierarchy_xray_structure_sync()
if(log is None): log = sys.stdout
header_printed = True
for r in self.residue_monitors:
i1=r.map_cc_all < map_cc_all
i2=r.rotamer_status == "OUTLIER"
i4=r.map_cc_sidechain is not None and r.map_cc_sidechain<map_cc_sidechain
if([i1,i2,i4].count(True)>0):
if(header_printed):
print >> log, "Residue CC CC CC Rotamer"
print >> log, " id all backbone sidechain id"
header_printed = False
print >> log, r.format_info_string()
def update(self, xray_structure, accept_as_is=True):
if(not accept_as_is):
current_map = self.compute_map(xray_structure = xray_structure)
sites_cart = xray_structure.sites_cart()
sites_cart_ = self.xray_structure.sites_cart()
for r in self.residue_monitors:
sca = sites_cart.select(r.selection_all)
scs = sites_cart.select(r.selection_sidechain)
scb = sites_cart.select(r.selection_backbone)
map_cc_all = self.map_cc(sites_cart = sca, other_map = current_map)
map_cc_sidechain = self.map_cc(sites_cart = scs, other_map = current_map)
map_cc_backbone = self.map_cc(sites_cart = scb, other_map = current_map)
flag = map_cc_all >= r.map_cc_all and \
map_cc_backbone >= r.map_cc_backbone and \
map_cc_sidechain>= r.map_cc_sidechain
if(flag):
residue_sites_cart_new = sites_cart.select(r.selection_all)
sites_cart_ = sites_cart_.set_selected(r.selection_all,
residue_sites_cart_new)
xray_structure = xray_structure.replace_sites_cart(sites_cart_)
# re-initialize monitor
self.dist_from_previous = flex.mean(self.xray_structure.distances(
other = xray_structure))
self.xray_structure = xray_structure
self.pdb_hierarchy.adopt_xray_structure(xray_structure)
self.initialize()
self.states_collector.add(sites_cart = xray_structure.sites_cart())
self.assert_pdb_hierarchy_xray_structure_sync()
