def __init__ (self, fmodel, pdb_hierarchy, cc_min=0.8,
molprobity_map_params=None) :
from iotbx.pdb.amino_acid_codes import one_letter_given_three_letter
from mmtbx import real_space_correlation
validation.__init__(self)
# arrays for different components
self.everything = list()
self.protein = list()
self.other = list()
self.water = list()
aa_codes = one_letter_given_three_letter.keys()
# redo real_space_corelation.simple to use map objects instead of filenames
try :
rsc_params = real_space_correlation.master_params().extract()
rsc_params.detail="residue"
rsc_params.map_1.fill_missing_reflections = False
rsc_params.map_2.fill_missing_reflections = False
if (molprobity_map_params is not None):
rsc_params.map_file_name = molprobity_map_params.map_file_name
rsc_params.map_coefficients_file_name = \
molprobity_map_params.map_coefficients_file_name
rsc_params.map_coefficients_label = \
molprobity_map_params.map_coefficients_label
rsc = real_space_correlation.simple(
fmodel=fmodel,
pdb_hierarchy=pdb_hierarchy,
params=rsc_params,
log=null_out())
except Exception, e :
raise
def __init__ (self, fmodel, pdb_hierarchy, cc_min=0.8) :
from iotbx.pdb.amino_acid_codes import one_letter_given_three_letter
from mmtbx import real_space_correlation
validation.__init__(self)
# arrays for different components
self.everything = list()
self.protein = list()
self.other = list()
self.water = list()
aa_codes = one_letter_given_three_letter.keys()
try :
rsc_params = real_space_correlation.master_params().extract()
rsc_params.detail="residue"
rsc_params.map_1.fill_missing_reflections = False
rsc_params.map_2.fill_missing_reflections = False
rsc = real_space_correlation.simple(
fmodel=fmodel,
pdb_hierarchy=pdb_hierarchy,
params=rsc_params,
log=null_out())
except Exception, e :
raise "Error: %s" % str(e)
def __init__ (self, fmodel, pdb_hierarchy, cc_min=0.8,
molprobity_map_params=None) :
from iotbx.pdb.amino_acid_codes import one_letter_given_three_letter
from mmtbx import real_space_correlation
validation.__init__(self)
# arrays for different components
self.everything = list()
self.protein = list()
self.other = list()
self.water = list()
aa_codes = one_letter_given_three_letter.keys()
# redo real_space_corelation.simple to use map objects instead of filenames
try :
rsc_params = real_space_correlation.master_params().extract()
rsc_params.detail="residue"
rsc_params.map_1.fill_missing_reflections = False
rsc_params.map_2.fill_missing_reflections = False
if (molprobity_map_params is not None):
rsc_params.map_file_name = molprobity_map_params.map_file_name
rsc_params.map_coefficients_file_name = \
molprobity_map_params.map_coefficients_file_name
rsc_params.map_coefficients_label = \
molprobity_map_params.map_coefficients_label
rsc = real_space_correlation.simple(
fmodel=fmodel,
pdb_hierarchy=pdb_hierarchy,
params=rsc_params,
log=null_out())
except Exception, e :
raise e
def __init__(self, pdb_hierarchy):
re_flip = re.compile(":FLIP")
validation.__init__(self)
in_lines = pdb_hierarchy.as_pdb_string()
reduce_out = run_reduce_with_timeout(
parameters="-BUILD -",
stdin_lines=in_lines)
check_and_report_reduce_failure(
fb_object=reduce_out,
input_lines=in_lines,
output_fname="reduce_fail.pdb")
from mmtbx.validation import utils
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
for line in reduce_out.stdout_lines:
#chain format (2-char chain)
#USER MOD Set 1.1: B 49 GLN :FLIP amide:sc= -2.7! C(o=-5.8!,f=-1.3!)
#segid format (4-char segid)
#USER MOD Set 1.1:B 49 GLN :FLIP amide:sc= -2.7! C(o=-5.8!,f=-1.3!)
if re_flip.search(line):
resid = line.split(":")[1]
#reduce has slightly different outputs using chains versus segid
if len(resid) == 15: #chain
chain_id = resid[0:2].strip()
segid = None
if (len(chain_id) == 0):
chain_id = ' '
resid_less_chain = resid[2:]
elif len(resid) == 17: #segid
#self.results = []
#return
chain_id = None
segid = resid[0:4].strip()
#chain_id = resid[0:4].strip()
resid_less_chain = resid[4:]
else:
raise Sorry("unexpected length of residue identifier in reduce USER MODs.")
resname = resid_less_chain[5:8]
assert (resname in ["ASN", "GLN", "HIS"])
flip = nqh_flip(
chain_id=chain_id,
segid=segid,
resseq=resid_less_chain[0:4].strip(),
icode= resid_less_chain[4:5],
altloc=resid_less_chain[12:13],
resname=resname,
outlier=True)
flip.set_coordinates_from_hierarchy(pdb_hierarchy)
self.results.append(flip)
self.n_outliers += 1
def __init__ (self, pdb_hierarchy) :
re_flip = re.compile(":FLIP")
validation.__init__(self)
reduce_out = easy_run.fully_buffered("phenix.reduce -BUILD -",
stdin_lines=pdb_hierarchy.as_pdb_string())
for line in reduce_out.stderr_lines :
#orientation 4: A 68 HIS :FLIP no HD1: bump=-0.607, HB=0.998, total=0.390
if re_flip.search(line) :
resname = line[22:25]
assert (resname in ["ASN", "GLN", "HIS"])
flip = nqh_flip(
chain_id=line[15:17].strip(),
resseq=line[17:21].strip(),
icode=line[21],
altloc=line[29],
resname=resname)
flip.set_coordinates_from_hierarchy(pdb_hierarchy)
self.results.append(flip)
self.n_outliers += 1
def __init__(self,
pdb_atoms,
sites_cart,
energies_sites,
restraint_proxies,
unit_cell,
ignore_hd=True,
sigma_cutoff=4.0,
outliers_only=True,
use_segids_in_place_of_chainids=False):
validation.__init__(self)
self.z_min = self.z_max = self.z_mean = None
deviations_method = getattr(energies_sites,
"%s_deviations" % self.restraint_type)
self.min, self.max, self.mean = deviations_method()
target = getattr(energies_sites,
"%s_residual_sum" % self.restraint_type)
self.n_total = getattr(energies_sites,
"n_%s_proxies" % self.restraint_type)
if (self.n_total > 0):
self.target = target / self.n_total
else:
self.target = 0
deviations_z_method = getattr(energies_sites,
"%s_deviations_z" % self.restraint_type,
None)
if (deviations_z_method is not None):
deviations_z = deviations_z_method()
self.z_min, self.z_max, self.z_mean = deviations_z_method()
self.results = sorted(
self.get_outliers(
proxies=restraint_proxies,
unit_cell=unit_cell,
sites_cart=sites_cart,
pdb_atoms=pdb_atoms,
sigma_cutoff=sigma_cutoff,
outliers_only=outliers_only,
use_segids_in_place_of_chainids=use_segids_in_place_of_chainids
))
self.n_outliers = len(self.results)
def __init__ (self,
pdb_atoms,
sites_cart,
energies_sites,
restraint_proxies,
unit_cell,
ignore_hd=True,
sigma_cutoff=4.0,
outliers_only=True,
use_segids_in_place_of_chainids=False) :
validation.__init__(self)
self.z_min = self.z_max = self.z_mean = None
deviations_method = getattr(energies_sites, "%s_deviations" %
self.restraint_type)
self.min, self.max, self.mean = deviations_method()
target = getattr(energies_sites, "%s_residual_sum" %
self.restraint_type)
self.n_total = getattr(energies_sites, "n_%s_proxies" %
self.restraint_type)
if (self.n_total > 0) :
self.target = target / self.n_total
else :
self.target = 0
deviations_z_method = getattr(energies_sites, "%s_deviations_z" %
self.restraint_type, None)
if (deviations_z_method is not None) :
deviations_z = deviations_z_method()
self.z_min, self.z_max, self.z_mean = deviations_z_method()
self.results = sorted(self.get_outliers(
proxies=restraint_proxies,
unit_cell=unit_cell,
sites_cart=sites_cart,
pdb_atoms=pdb_atoms,
sigma_cutoff=sigma_cutoff,
outliers_only=outliers_only,
use_segids_in_place_of_chainids=use_segids_in_place_of_chainids))
self.n_outliers = len(self.results)
def __init__(self, pdb_hierarchy):
re_flip = re.compile(":FLIP")
validation.__init__(self)
reduce_out = easy_run.fully_buffered(
"phenix.reduce -BUILD -",
stdin_lines=pdb_hierarchy.as_pdb_string())
for line in reduce_out.stdout_lines:
#USER MOD Set 1.1: B 49 GLN :FLIP amide:sc= -2.7! C(o=-5.8!,f=-1.3!)
if re_flip.search(line):
resid = line.split(":")[1]
chain_id = resid[0:2].strip()
if (len(chain_id) == 0):
chain_id = ' '
resname = resid[7:10]
assert (resname in ["ASN", "GLN", "HIS"])
flip = nqh_flip(chain_id=chain_id,
resseq=resid[2:6].strip(),
icode=resid[6:7],
altloc=resid[14:15],
resname=resname,
outlier=True)
flip.set_coordinates_from_hierarchy(pdb_hierarchy)
self.results.append(flip)
self.n_outliers += 1
def __init__ (self, pdb_hierarchy) :
re_flip = re.compile(":FLIP")
validation.__init__(self)
reduce_out = easy_run.fully_buffered("phenix.reduce -BUILD -",
stdin_lines=pdb_hierarchy.as_pdb_string())
for line in reduce_out.stdout_lines:
#USER MOD Set 1.1: B 49 GLN :FLIP amide:sc= -2.7! C(o=-5.8!,f=-1.3!)
if re_flip.search(line) :
resid = line.split(":")[1]
chain_id = resid[0:2].strip()
if (len(chain_id) == 0):
chain_id = ' '
resname = resid[7:10]
assert (resname in ["ASN", "GLN", "HIS"])
flip = nqh_flip(
chain_id=chain_id,
resseq=resid[2:6].strip(),
icode=resid[6:7],
altloc=resid[14:15],
resname=resname,
outlier=True)
flip.set_coordinates_from_hierarchy(pdb_hierarchy)
self.results.append(flip)
self.n_outliers += 1
def __init__(self,
pdb_hierarchy,
xray_structure,
ignore_hd=True,
collect_outliers=True):
for name in self.__slots__:
setattr(self, name, None)
validation.__init__(self)
assert len(xray_structure.scatterers()) != 0
from cctbx import adptbx
from scitbx.array_family import flex
xrs = xray_structure
self.n_total = xrs.scatterers().size() # always include H/D
self.results = None
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
hd_selection = xrs.hd_selection()
subtract_hd = True
self.n_all = hd_selection.size()
self.n_hd = hd_selection.count(True)
if (ignore_hd) and (0 < self.n_hd < self.n_all):
xrs = xrs.select(~hd_selection)
subtract_hd = False
u_isos = xrs.extract_u_iso_or_u_equiv()
occ = xrs.scatterers().extract_occupancies()
self.n_atoms = xrs.scatterers().size()
self.n_non_hd = self.n_all - self.n_hd
self.n_aniso = xrs.use_u_aniso().count(True)
self.n_aniso_h = (xray_structure.use_u_aniso()
& hd_selection).count(True)
self.n_npd = xrs.is_positive_definite_u().count(False)
self.n_zero_b = (u_isos == 0).count(True)
self.n_zero_occ = (occ == 0).count(True)
u_cutoff_high = sys.maxsize
u_cutoff_low = 0
u_non_zero = u_isos.select(u_isos > 0)
if (len(u_non_zero) > 1):
mv = flex.mean_and_variance(u_non_zero)
sigma = mv.unweighted_sample_standard_deviation()
u_cutoff_high = mv.mean() + (4.0 * sigma)
u_cutoff_low = mv.mean() - (4.0 * sigma)
self.b_mean = adptbx.u_as_b(flex.mean(u_isos))
self.b_min = adptbx.u_as_b(flex.min(u_isos))
self.b_max = adptbx.u_as_b(flex.max(u_isos))
self.o_mean = flex.mean(occ)
self.o_min = flex.min(occ)
self.o_max = flex.max(occ)
self.n_outliers = self.n_aniso_h + self.n_npd
self.zero_occ = []
self.partial_occ = []
self.different_occ = []
self.bad_adps = []
self.b_histogram = None # TODO
def is_u_iso_outlier(u):
return (u < u_cutoff_low) or (u > u_cutoff_high) or (u <= 0)
# these statistics cover all atoms!
occupancies = xray_structure.scatterers().extract_occupancies()
u_isos = xray_structure.extract_u_iso_or_u_equiv()
collected = flex.bool(occupancies.size(), False)
if (collect_outliers):
for i_seq, occ in enumerate(occupancies):
if (hd_selection[i_seq] and ignore_hd) or collected[i_seq]:
continue
pdb_atom = pdb_atoms[i_seq]
parent = pdb_atom.parent()
if (occ <= 0):
group_atoms = parent.atoms()
labels = pdb_atom.fetch_labels()
if (len(group_atoms) >
1) and (group_atoms.extract_occ().all_eq(0)):
i_seqs = group_atoms.extract_i_seq()
b_mean = adptbx.u_as_b(flex.mean(
u_isos.select(i_seqs)))
outlier = residue_occupancy(
chain_id=labels.chain_id,
resseq=labels.resseq,
icode=labels.icode,
altloc=labels.altloc,
resname=labels.resname,
occupancy=occ,
outlier=True,
xyz=group_atoms.extract_xyz().mean(),
b_iso=b_mean)
self.zero_occ.append(outlier)
self.n_outliers += 1
collected.set_selected(i_seqs, True)
else:
assert (pdb_atom.occ == occ), "%s: %s <--> %s" % (
pdb_atom.id_str(), pdb_atom.occ, occ)
outlier = atom_occupancy(pdb_atom=pdb_atom,
occupancy=occ,
b_iso=adptbx.u_as_b(
u_isos[i_seq]),
xyz=pdb_atom.xyz,
outlier=True)
self.zero_occ.append(outlier)
self.n_outliers += 1
elif is_u_iso_outlier(u_isos[i_seq]):
# zero displacements will always be recorded on a per-atom basis
if (u_isos[i_seq] <= 0):
outlier = atom_bfactor(pdb_atom=pdb_atom,
occupancy=occ,
b_iso=adptbx.u_as_b(
u_isos[i_seq]),
xyz=pdb_atom.xyz,
outlier=True)
self.bad_adps.append(outlier)
self.n_outliers += 1
else:
# if the average displacement for the entire residue falls outside
# the cutoffs, save as a single residue outlier
group_atoms = parent.atoms()
i_seqs = group_atoms.extract_i_seq()
u_mean = flex.mean(u_isos.select(i_seqs))
if is_u_iso_outlier(u_mean):
labels = pdb_atom.fetch_labels()
outlier = residue_bfactor(
chain_id=labels.chain_id,
resseq=labels.resseq,
icode=labels.icode,
altloc=labels.altloc,
resname=labels.resname,
occupancy=occ,
outlier=True,
xyz=group_atoms.extract_xyz().mean(),
b_iso=adptbx.u_as_b(u_mean))
self.bad_adps.append(outlier)
self.n_outliers += 1
collected.set_selected(i_seqs, True)
# otherwise, just save this atom
else:
outlier = atom_bfactor(pdb_atom=pdb_atom,
occupancy=occ,
b_iso=adptbx.u_as_b(
u_isos[i_seq]),
xyz=pdb_atom.xyz,
outlier=True)
self.bad_adps.append(outlier)
self.n_outliers += 1
# analyze occupancies for first model
model = pdb_hierarchy.models()[0]
for chain in model.chains():
residue_groups = chain.residue_groups()
for residue_group in chain.residue_groups():
# get unique set of atom names
atom_names = set()
for atom in residue_group.atoms():
atom_names.add(atom.name.strip())
# check total occupancy for each atom
for name in atom_names:
occupancy = 0.0
atoms = list()
for atom_group in residue_group.atom_groups():
atom = atom_group.get_atom(name)
if (atom is not None):
occupancy += atom.occ
atoms.append(atom)
if (not approx_equal(
occupancy, 1.0, out=None, eps=1.0e-3)):
for atom in atoms:
outlier = atom_occupancy(pdb_atom=atom,
occupancy=atom.occ,
b_iso=adptbx.u_as_b(
atom.b),
xyz=atom.xyz,
outlier=True)
self.partial_occ.append(outlier)
self.n_outliers += 1
# check that atoms in an atom group have the same occupancy
for atom_group in residue_group.atom_groups():
residue_is_okay = True
base_occupancy = atom_group.atoms()[0].occ
for atom in atom_group.atoms():
if (not approx_equal(
base_occupancy, atom.occ, out=None,
eps=1.0e-3)):
labels = atom.fetch_labels()
i_seqs = atom_group.atoms().extract_i_seq()
b_mean = adptbx.u_as_b(
flex.mean(u_isos.select(i_seqs)))
outlier = residue_occupancy(
chain_id=labels.chain_id,
resseq=labels.resseq,
icode=labels.icode,
altloc=labels.altloc,
resname=labels.resname,
occupancy=occ,
outlier=True,
xyz=atom_group.atoms().extract_xyz().mean(
),
b_iso=b_mean)
self.different_occ.append(outlier)
self.n_outliers += 1
residue_is_okay = False
break
if (not residue_is_okay):
break
def __init__(self,
pdb_hierarchy,
nontrans_only=False,
out=sys.stdout,
quiet=True):
validation.__init__(self)
self.residue_count = [0, 0]
#[OMEGA_GENERAL, OMEGA_PRO]
self.omega_count = [[0,0,0], [0,0,0]]
#[OMEGA_GENERAL, OMEGA_PRO], then
#[OMEGALYZE_TRANS, OMEGALYZE_CIS, OMEGALYZE_TWISTED]
from mmtbx.validation import utils
from scitbx.array_family import flex
self._outlier_i_seqs = flex.size_t()
pdb_atoms = pdb_hierarchy.atoms()
all_i_seqs = pdb_atoms.extract_i_seq()
if all_i_seqs.all_eq(0):
pdb_atoms.reset_i_seq()
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
prev_rezes, next_rezes = None, None
prev_resid = None
cur_resseq = None
next_resseq = None
for model in pdb_hierarchy.models():
for chain in model.chains():
prev_rezes, next_rezes = None, None
prev_resid = None
cur_resseq = None
next_resseq = None
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
residues = list(chain.residue_groups())
for i, residue_group in enumerate(residues):
# The reason I pass lists of atom_groups to get_phi and get_psi is to
# deal with the particular issue where some residues have an A alt
# conf that needs some atoms from a "" alt conf to get calculated
# correctly. See 1jxt.pdb for examples. This way I can search both
# the alt conf atoms and the "" atoms if necessary.
prev_atom_list, next_atom_list, atom_list = None, None, None
if cur_resseq is not None:
prev_rezes = rezes
prev_resseq = cur_resseq
rezes = construct_residues(residues[i])
cur_resseq = residue_group.resseq_as_int()
cur_icode = residue_group.icode.strip()
if (i > 0):
#check for insertion codes
if (cur_resseq == residues[i-1].resseq_as_int()) :
if (cur_icode == '') and (residues[i-1].icode.strip() == '') :
continue
elif (cur_resseq != (residues[i-1].resseq_as_int())+1):
continue
for atom_group in residue_group.atom_groups():
alt_conf = atom_group.altloc
if rezes is not None:
atom_list = rezes.get(alt_conf)
if prev_rezes is not None:
prev_atom_list = prev_rezes.get(alt_conf)
if (prev_atom_list is None):
prev_keys = sorted(prev_rezes.keys())
prev_atom_list = prev_rezes.get(prev_keys[0])
omega=get_omega(prev_atom_list, atom_list)
highest_mc_b = get_highest_mc_b(prev_atom_list, atom_list)
if omega is not None:
resname = atom_group.resname[0:3]
coords = get_center(atom_group)
if resname == "PRO":
res_type = OMEGA_PRO
else:
res_type = OMEGA_GENERAL
self.residue_count[res_type] += 1
omega_type = find_omega_type(omega)
is_nontrans = False
if omega_type == OMEGALYZE_CIS or omega_type == OMEGALYZE_TWISTED:
self.n_outliers += 1
is_nontrans = True
self.omega_count[res_type][omega_type] += 1
markup_atoms = [None, None, None, None] #for kinemage markup
if is_nontrans:
for a in prev_atom_list:
if a is None: continue
a_ = atom(pdb_atom=a)
if a.name.strip() == "CA":
markup_atoms[0] = kin_atom(
id_str=a_.atom_group_id_str(),xyz=a_.xyz)
elif a.name.strip() == "C":
markup_atoms[1] = kin_atom(
id_str=a_.atom_group_id_str(),xyz=a_.xyz)
for a in atom_list:
if a is None: continue
a_ = atom(pdb_atom=a)
if a.name.strip() == "N":
markup_atoms[2] = kin_atom(
id_str=a_.atom_group_id_str(),xyz=a_.xyz)
elif a.name.strip() == "CA":
markup_atoms[3] = kin_atom(
id_str=a_.atom_group_id_str(),xyz=a_.xyz)
#------------
#prevres=residues[i-1]
#find prev res identities for printing
prev_alts = []
prev_resnames = {}
for ag in residues[i-1].atom_groups():
prev_alts.append(ag.altloc)
prev_resnames[ag.altloc] = ag.resname
if alt_conf in prev_alts:
prev_altloc = alt_conf
else:
if len(prev_alts) > 1:
prev_altloc = prev_alts[1]
else:
prev_altloc = prev_alts[0]
prev_resname = prev_resnames[prev_altloc]
#done finding prev res identities
result = omega_result(
chain_id=chain_id,
resseq=residue_group.resseq,
icode=residue_group.icode,
resname=atom_group.resname,
altloc=atom_group.altloc,
prev_resseq=residues[i-1].resseq,
prev_icode=residues[i-1].icode,
prev_resname=prev_resname,
prev_altloc=prev_altloc,
segid=None,
omega=omega,
omega_type=omega_type,
res_type=res_type,
is_nontrans=is_nontrans,
outlier=is_nontrans,
highest_mc_b=highest_mc_b,
xyz=coords,
markup_atoms=markup_atoms)
if is_nontrans or not nontrans_only: #(not nontrans_only or is_nontrans)
self.results.append(result)
if is_nontrans:
i_seqs = atom_group.atoms().extract_i_seq()
assert (not i_seqs.all_eq(0)) #This assert copied from ramalyze
self._outlier_i_seqs.extend(i_seqs)
def __init__(self,
pdb_hierarchy,
nontrans_only=False,
out=sys.stdout,
quiet=True):
validation.__init__(self)
self.residue_count = [0, 0]
#[OMEGA_GENERAL, OMEGA_PRO]
self.omega_count = [[0,0,0], [0,0,0]]
#[OMEGA_GENERAL, OMEGA_PRO], then
#[OMEGALYZE_TRANS, OMEGALYZE_CIS, OMEGALYZE_TWISTED]
from mmtbx.validation import utils
from scitbx.array_family import flex
self._outlier_i_seqs = flex.size_t()
pdb_atoms = pdb_hierarchy.atoms()
all_i_seqs = pdb_atoms.extract_i_seq()
if all_i_seqs.all_eq(0):
pdb_atoms.reset_i_seq()
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
prev_rezes, next_rezes = None, None
prev_resid = None
cur_resseq = None
next_resseq = None
for model in pdb_hierarchy.models():
for chain in model.chains():
prev_rezes, next_rezes = None, None
prev_resid = None
cur_resseq = None
next_resseq = None
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
residues = list(chain.residue_groups())
for i, residue_group in enumerate(residues):
# The reason I pass lists of atom_groups to get_phi and get_psi is to
# deal with the particular issue where some residues have an A alt
# conf that needs some atoms from a "" alt conf to get calculated
# correctly. See 1jxt.pdb for examples. This way I can search both
# the alt conf atoms and the "" atoms if necessary.
prev_atom_list, next_atom_list, atom_list = None, None, None
if cur_resseq is not None:
prev_rezes = rezes
prev_resseq = cur_resseq
rezes = construct_residues(residues[i])
cur_resseq = residue_group.resseq_as_int()
cur_icode = residue_group.icode.strip()
if (i > 0):
#check for insertion codes
if (cur_resseq == residues[i-1].resseq_as_int()) :
if (cur_icode == '') and (residues[i-1].icode.strip() == '') :
continue
elif (cur_resseq != (residues[i-1].resseq_as_int())+1):
continue
for atom_group in residue_group.atom_groups():
alt_conf = atom_group.altloc
if rezes is not None:
atom_list = rezes.get(alt_conf)
if prev_rezes is not None:
prev_atom_list = prev_rezes.get(alt_conf)
if (prev_atom_list is None):
prev_keys = sorted(prev_rezes.keys())
prev_atom_list = prev_rezes.get(prev_keys[0])
omega=get_omega(prev_atom_list, atom_list)
highest_mc_b = get_highest_mc_b(prev_atom_list, atom_list)
if omega is not None:
resname = atom_group.resname[0:3]
coords = get_center(atom_group)
if resname == "PRO":
res_type = OMEGA_PRO
else:
res_type = OMEGA_GENERAL
self.residue_count[res_type] += 1
omega_type = find_omega_type(omega)
is_nontrans = False
if omega_type == OMEGALYZE_CIS or omega_type == OMEGALYZE_TWISTED:
self.n_outliers += 1
is_nontrans = True
self.omega_count[res_type][omega_type] += 1
markup_atoms = [None, None, None, None] #for kinemage markup
if is_nontrans:
for a in prev_atom_list:
if a is None: continue
a_ = atom(pdb_atom=a)
if a.name.strip() == "CA":
markup_atoms[0] = kin_atom(
id_str=a_.atom_group_id_str(),xyz=a_.xyz)
elif a.name.strip() == "C":
markup_atoms[1] = kin_atom(
id_str=a_.atom_group_id_str(),xyz=a_.xyz)
for a in atom_list:
if a is None: continue
a_ = atom(pdb_atom=a)
if a.name.strip() == "N":
markup_atoms[2] = kin_atom(
id_str=a_.atom_group_id_str(),xyz=a_.xyz)
elif a.name.strip() == "CA":
markup_atoms[3] = kin_atom(
id_str=a_.atom_group_id_str(),xyz=a_.xyz)
#------------
#prevres=residues[i-1]
#find prev res identities for printing
prev_alts = []
prev_resnames = {}
for ag in residues[i-1].atom_groups():
prev_alts.append(ag.altloc)
prev_resnames[ag.altloc] = ag.resname
if alt_conf in prev_alts:
prev_altloc = alt_conf
else:
if len(prev_alts) > 1:
prev_altloc = prev_alts[1]
else:
prev_altloc = prev_alts[0]
prev_resname = prev_resnames[prev_altloc]
#done finding prev res identities
result = omega_result(
chain_id=chain_id,
resseq=residue_group.resseq,
icode=residue_group.icode,
resname=atom_group.resname,
altloc=atom_group.altloc,
prev_resseq=residues[i-1].resseq,
prev_icode=residues[i-1].icode,
prev_resname=prev_resname,
prev_altloc=prev_altloc,
segid=None,
omega=omega,
omega_type=omega_type,
res_type=res_type,
is_nontrans=is_nontrans,
outlier=is_nontrans,
highest_mc_b=highest_mc_b,
xyz=coords,
markup_atoms=markup_atoms)
if is_nontrans or not nontrans_only: #(not nontrans_only or is_nontrans)
self.results.append(result)
if is_nontrans:
i_seqs = atom_group.atoms().extract_i_seq()
assert (not i_seqs.all_eq(0)) #This assert copied from ramalyze
self._outlier_i_seqs.extend(i_seqs)
def __init__(self, pdb_hierarchy,
data_version="8000",
outliers_only=False,
show_errors=False,
out=sys.stdout,
quiet=False):
validation.__init__(self)
self.n_allowed = 0
self.n_favored = 0
from mmtbx.rotamer.sidechain_angles import SidechainAngles
from mmtbx.rotamer import rotamer_eval
from mmtbx.rotamer.rotamer_eval import RotamerID
from mmtbx.validation import utils
self.data_version = data_version
# if self.data_version == "500": self.outlier_threshold = 0.01
if self.data_version == "8000": self.outlier_threshold = OUTLIER_THRESHOLD
else: raise ValueError(
"data_version given to RotamerEval not recognized (%s)." % data_version)
sidechain_angles = SidechainAngles(show_errors)
rotamer_evaluator = rotamer_eval.RotamerEval(
data_version=data_version)
rotamer_id = rotamer_eval.RotamerID() # loads in the rotamer names
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
current_rotamers = {}
for model in pdb_hierarchy.models():
for chain in model.chains():
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
for rg in chain.residue_groups():
all_dict = construct_complete_sidechain(rg)
for atom_group in rg.atom_groups():
coords = get_center(atom_group)
resname = atom_group.resname
occupancy = get_occupancy(atom_group)
kwargs = {
"chain_id" : chain_id,
"resseq" : rg.resseq,
"icode" : rg.icode,
"altloc" : atom_group.altloc,
"resname" : resname,
"xyz" : coords,
"occupancy" : occupancy,
}
atom_dict = all_dict.get(atom_group.altloc)
res_key = get_residue_key(atom_group=atom_group)
try:
chis = sidechain_angles.measureChiAngles(
atom_group,
atom_dict)#.get(conformer.altloc))
except AttributeError:
if show_errors:
kwargs['incomplete'] = True
result = rotamer(**kwargs)
print >> out, '%s is missing some sidechain atoms' % \
result.id_str()
self.results.append(result)
continue
if (chis is not None):
if None in chis:
continue
cur_res = resname.lower().strip()
if cur_res == 'mse':
cur_res = 'met'
value = rotamer_evaluator.evaluate(cur_res, chis)
if value is not None:
self.n_total += 1
kwargs['score'] = value * 100
wrap_chis = rotamer_id.wrap_chis(resname.strip(), chis,
symmetry=False)
sym_chis = wrap_chis[:]
sym_chis = rotamer_id.wrap_sym(resname.strip(), sym_chis)
evaluation = self.evaluateScore(value)
kwargs['evaluation'] = evaluation
if evaluation == "OUTLIER":
kwargs['outlier'] = True
kwargs['rotamer_name'] = evaluation
else:
kwargs['outlier'] = False
kwargs['rotamer_name'] = rotamer_id.identify(resname,
wrap_chis)
#deal with unclassified rotamers
if kwargs['rotamer_name'] == '':
kwargs['rotamer_name'] = "UNCLASSIFIED"
while (len(wrap_chis) < 4):
wrap_chis.append(None)
kwargs['chi_angles'] = wrap_chis
result = rotamer(**kwargs)
if (result.is_outlier()) or (not outliers_only):
self.results.append(result)
out_count, out_percent = self.get_outliers_count_and_fraction()
self.out_percent = out_percent * 100.0
def __init__(self,
pdb_hierarchy,
outliers_only=False,
out=sys.stdout,
collect_ideal=False,
quiet=False):
validation.__init__(self)
self._outlier_i_seqs = flex.size_t()
self.beta_ideal = {}
relevant_atom_names = {
" CA ": None,
" N ": None,
" C ": None,
" CB ": None
} # FUTURE: set
output_list = []
self.stats = group_args(n_results=0,
n_weighted_results=0,
n_weighted_outliers=0)
from mmtbx.validation import utils
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
for model in pdb_hierarchy.models():
for chain in model.chains():
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
for rg in chain.residue_groups():
for i_cf, cf in enumerate(rg.conformers()):
for i_residue, residue in enumerate(cf.residues()):
if (residue.resname == "GLY"):
continue
is_first = (i_cf == 0)
is_alt_conf = False
relevant_atoms = {}
for atom in residue.atoms():
if (atom.name in relevant_atom_names):
relevant_atoms[atom.name] = atom
if (len(atom.parent().altloc) != 0):
is_alt_conf = True
if ((is_first or is_alt_conf)
and len(relevant_atoms) == 4):
result = calculate_ideal_and_deviation(
relevant_atoms=relevant_atoms,
resname=residue.resname)
dev = result.deviation
dihedralNABB = result.dihedral
betaxyz = result.ideal
if (dev is None): continue
resCB = relevant_atoms[" CB "]
self.stats.n_results += 1
self.stats.n_weighted_results += resCB.occ
if (dev >= 0.25 or outliers_only == False):
if (dev >= 0.25):
self.n_outliers += 1
self.stats.n_weighted_outliers += resCB.occ
self._outlier_i_seqs.append(atom.i_seq)
if (is_alt_conf):
altchar = cf.altloc
else:
altchar = " "
res = residue.resname.lower()
sub = chain.id
if (len(sub) == 1):
sub = " " + sub
result = cbeta(chain_id=chain_id,
resname=residue.resname,
resseq=residue.resseq,
icode=residue.icode,
altloc=altchar,
xyz=resCB.xyz,
occupancy=resCB.occ,
deviation=dev,
dihedral_NABB=dihedralNABB,
ideal_xyz=betaxyz,
outlier=(dev >= 0.25))
self.results.append(result)
key = result.id_str()
if (collect_ideal):
self.beta_ideal[key] = betaxyz
def __init__ (self, pdb_hierarchy, xray_structure, fmodel,
distance_cutoff=4.0, collect_all=True) :
validation.__init__(self)
from mmtbx.real_space_correlation import extract_map_stats_for_single_atoms
from cctbx import adptbx
from scitbx.matrix import col
self.n_bad = 0
self.n_heavy = 0
pdb_atoms = pdb_hierarchy.atoms()
if(len(pdb_atoms)>1):
assert (not pdb_atoms.extract_i_seq().all_eq(0))
unit_cell = xray_structure.unit_cell()
pair_asu_table = xray_structure.pair_asu_table(
distance_cutoff = distance_cutoff)
asu_mappings = pair_asu_table.asu_mappings()
asu_table = pair_asu_table.table()
u_isos = xray_structure.extract_u_iso_or_u_equiv()
occupancies = xray_structure.scatterers().extract_occupancies()
sites_cart = xray_structure.sites_cart()
sites_frac = xray_structure.sites_frac()
sel_cache = pdb_hierarchy.atom_selection_cache()
water_sel = sel_cache.selection("resname HOH and name O")
map_stats = extract_map_stats_for_single_atoms(
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
fmodel=fmodel,
selection=water_sel)
waters = []
for i_seq, atom in enumerate(pdb_atoms) :
if (water_sel[i_seq]) :
rt_mx_i_inv = asu_mappings.get_rt_mx(i_seq, 0).inverse()
self.n_total += 1
asu_dict = asu_table[i_seq]
nearest_atom = nearest_contact = None
for j_seq, j_sym_groups in asu_dict.items() :
atom_j = pdb_atoms[j_seq]
site_j = sites_frac[j_seq]
# Filter out hydrogens
if atom_j.element.upper().strip() in ["H", "D"]:
continue
for j_sym_group in j_sym_groups:
rt_mx = rt_mx_i_inv.multiply(asu_mappings.get_rt_mx(j_seq,
j_sym_group[0]))
site_ji = rt_mx * site_j
site_ji_cart = xray_structure.unit_cell().orthogonalize(site_ji)
vec_i = col(atom.xyz)
vec_ji = col(site_ji_cart)
dxyz = abs(vec_i - vec_ji)
if (nearest_contact is None) or (dxyz < nearest_contact) :
nearest_contact = dxyz
nearest_atom = atom_info(pdb_atom=atom_j, symop=rt_mx)
w = water(
pdb_atom=atom,
b_iso=adptbx.u_as_b(u_isos[i_seq]),
occupancy=occupancies[i_seq],
nearest_contact=nearest_contact,
nearest_atom=nearest_atom,
score=map_stats.two_fofc_ccs[i_seq],
fmodel=map_stats.fmodel_values[i_seq],
two_fofc=map_stats.two_fofc_values[i_seq],
fofc=map_stats.fofc_values[i_seq],
anom=map_stats.anom_values[i_seq],
n_hbonds=None) # TODO
if (w.is_bad_water()) :
w.outlier = True
self.n_bad += 1
elif (w.is_heavy_atom()) :
w.outlier = True
self.n_heavy += 1
if (w.outlier) or (collect_all) :
self.results.append(w)
self.n_outliers = len(self.results)
def __init__ (self,
pdb_hierarchy,
outliers_only=False,
show_errors=False,
out=sys.stdout,
quiet=False) :
# Optimization hint: make it possible to pass
# ramachandran_eval.RamachandranEval() from outside.
# Better - convert this to using mmtbx.model.manager where
# RamachandranEval is already available.
validation.__init__(self)
self.n_allowed = 0
self.n_favored = 0
self.n_type = [ 0 ] * 6
self._outlier_i_seqs = flex.size_t()
pdb_atoms = pdb_hierarchy.atoms()
all_i_seqs = pdb_atoms.extract_i_seq()
if (all_i_seqs.all_eq(0)) :
pdb_atoms.reset_i_seq()
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
analysis = ""
output_list = []
count_keys = []
uniqueness_keys = []
r = ramachandran_eval.RamachandranEval()
##if use_segids:
## chain_id = utils.get_segid_as_chainid(chain=chain)
## else:
## chain_id = chain.id
for three in generate_protein_threes(hierarchy=pdb_hierarchy, geometry=None):
main_residue = three[1]
phi_psi_atoms = three.get_phi_psi_atoms()
if phi_psi_atoms is None:
continue
phi_atoms, psi_atoms = phi_psi_atoms
phi = get_dihedral(phi_atoms)
psi = get_dihedral(psi_atoms)
coords = get_center(main_residue) #should find the CA of the center residue
if (phi is not None and psi is not None):
res_type = RAMA_GENERAL
#self.n_total += 1
if (main_residue.resname[0:3] == "GLY"):
res_type = RAMA_GLYCINE
elif (main_residue.resname[0:3] == "PRO"):
is_cis = is_cis_peptide(three)
if is_cis:
res_type = RAMA_CISPRO
else:
res_type = RAMA_TRANSPRO
elif (three[2].resname == "PRO"):
res_type = RAMA_PREPRO
elif (main_residue.resname[0:3] == "ILE" or \
main_residue.resname[0:3] == "VAL"):
res_type = RAMA_ILE_VAL
#self.n_type[res_type] += 1
value = r.evaluate(res_types[res_type], [phi, psi])
ramaType = self.evaluateScore(res_type, value)
is_outlier = ramaType == RAMALYZE_OUTLIER
c_alphas = None
# XXX only save kinemage data for outliers
if is_outlier :
c_alphas = get_cas_from_three(three)
assert (len(c_alphas) == 3)
markup = self.as_markup_for_kinemage(c_alphas)
else:
markup = None
result = ramachandran(
model_id=main_residue.parent().parent().parent().id,
chain_id=main_residue.parent().parent().id,
resseq=main_residue.resseq,
icode=main_residue.icode,
resname=main_residue.resname,
#altloc=main_residue.parent().altloc,
altloc=get_altloc_from_three(three),
segid=None, # XXX ???
phi=phi,
psi=psi,
rama_type=ramaType,
res_type=res_type,
score=value*100,
outlier=is_outlier,
xyz=coords,
markup=markup)
#if result.chain_id+result.resseq+result.icode not in count_keys:
result_key = result.model_id+result.chain_id+result.resseq+result.icode
if result.altloc in ['','A'] and result_key not in count_keys:
self.n_total += 1
self.n_type[res_type] += 1
self.add_to_validation_counts(ramaType)
count_keys.append(result_key)
if (not outliers_only or is_outlier) :
if (result.altloc != '' or
result_key not in uniqueness_keys):
#the threes/conformers method results in some redundant result
# calculations in structures with alternates. Using the
# uniqueness_keys list prevents redundant results being added to
# the final list
self.results.append(result)
uniqueness_keys.append(result_key)
if is_outlier :
i_seqs = main_residue.atoms().extract_i_seq()
assert (not i_seqs.all_eq(0))
self._outlier_i_seqs.extend(i_seqs)
self.results.sort(key=lambda r: r.model_id+r.id_str())
out_count, out_percent = self.get_outliers_count_and_fraction()
fav_count, fav_percent = self.get_favored_count_and_fraction()
self.out_percent = out_percent * 100.0
self.fav_percent = fav_percent * 100.0
def __init__(
self, pdb_hierarchy, data_version="8000", outliers_only=False, show_errors=False, out=sys.stdout, quiet=False
):
validation.__init__(self)
self.n_allowed = 0
self.n_favored = 0
from mmtbx.rotamer.sidechain_angles import SidechainAngles
from mmtbx.rotamer import rotamer_eval
from mmtbx.rotamer.rotamer_eval import RotamerID
from mmtbx.validation import utils
self.data_version = data_version
# if self.data_version == "500": self.outlier_threshold = 0.01
if self.data_version == "8000":
self.outlier_threshold = 0.003
else:
raise ValueError("data_version given to RotamerEval not recognized (%s)." % data_version)
sidechain_angles = SidechainAngles(show_errors)
rotamer_evaluator = rotamer_eval.RotamerEval(data_version=data_version)
rotamer_id = rotamer_eval.RotamerID() # loads in the rotamer names
use_segids = utils.use_segids_in_place_of_chainids(hierarchy=pdb_hierarchy)
current_rotamers = {}
for model in pdb_hierarchy.models():
for chain in model.chains():
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
for rg in chain.residue_groups():
all_dict = construct_complete_sidechain(rg)
for atom_group in rg.atom_groups():
coords = get_center(atom_group)
resname = atom_group.resname
occupancy = get_occupancy(atom_group)
kwargs = {
"chain_id": chain_id,
"resseq": rg.resseq,
"icode": rg.icode,
"altloc": atom_group.altloc,
"resname": resname,
"xyz": coords,
"occupancy": occupancy,
}
atom_dict = all_dict.get(atom_group.altloc)
res_key = get_residue_key(atom_group=atom_group)
try:
chis = sidechain_angles.measureChiAngles(atom_group, atom_dict) # .get(conformer.altloc))
except AttributeError:
if show_errors:
kwargs["incomplete"] = True
result = rotamer(**kwargs)
print >> out, "%s is missing some sidechain atoms" % result.id_str()
self.results.append(result)
continue
if chis is not None:
if None in chis:
continue
cur_res = resname.lower().strip()
if cur_res == "mse":
cur_res = "met"
value = rotamer_evaluator.evaluate(cur_res, chis)
if value is not None:
self.n_total += 1
kwargs["score"] = value * 100
wrap_chis = rotamer_id.wrap_chis(resname.strip(), chis, symmetry=False)
sym_chis = wrap_chis[:]
sym_chis = rotamer_id.wrap_sym(resname.strip(), sym_chis)
evaluation = self.evaluateScore(value)
kwargs["evaluation"] = evaluation
if evaluation == "OUTLIER":
kwargs["outlier"] = True
kwargs["rotamer_name"] = evaluation
else:
kwargs["outlier"] = False
kwargs["rotamer_name"] = rotamer_id.identify(resname, wrap_chis)
# deal with unclassified rotamers
if kwargs["rotamer_name"] == "":
kwargs["rotamer_name"] = "UNCLASSIFIED"
while len(wrap_chis) < 4:
wrap_chis.append(None)
kwargs["chi_angles"] = wrap_chis
result = rotamer(**kwargs)
if (result.is_outlier()) or (not outliers_only):
self.results.append(result)
out_count, out_percent = self.get_outliers_count_and_fraction()
self.out_percent = out_percent * 100.0
def __init__ (self, pdb_hierarchy,
outliers_only=False,
out=sys.stdout,
collect_ideal=False,
quiet=False) :
validation.__init__(self)
self._outlier_i_seqs = flex.size_t()
self.beta_ideal = {}
relevant_atom_names = {
" CA ": None, " N ": None, " C ": None, " CB ": None} # FUTURE: set
output_list = []
from mmtbx.validation import utils
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
for model in pdb_hierarchy.models():
for chain in model.chains():
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
for rg in chain.residue_groups():
for i_cf,cf in enumerate(rg.conformers()):
for i_residue,residue in enumerate(cf.residues()):
if (residue.resname == "GLY") :
continue
is_first = (i_cf == 0)
is_alt_conf = False
relevant_atoms = {}
for atom in residue.atoms():
if (atom.name in relevant_atom_names):
relevant_atoms[atom.name] = atom
if (len(atom.parent().altloc) != 0):
is_alt_conf = True
if ((is_first or is_alt_conf) and len(relevant_atoms) == 4):
result = calculate_ideal_and_deviation(
relevant_atoms=relevant_atoms,
resname=residue.resname)
dev = result.deviation
dihedralNABB = result.dihedral
betaxyz = result.ideal
if (dev is None) : continue
if(dev >=0.25 or outliers_only==False):
if(dev >=0.25):
self.n_outliers+=1
self._outlier_i_seqs.append(atom.i_seq)
if (is_alt_conf):
altchar = cf.altloc
else:
altchar = " "
res=residue.resname.lower()
sub=chain.id
if(len(sub)==1):
sub=" "+sub
resCB = relevant_atoms[" CB "]
result = cbeta(
chain_id=chain_id,
resname=residue.resname,
resseq=residue.resseq,
icode=residue.icode,
altloc=altchar,
xyz=resCB.xyz,
occupancy=resCB.occ,
deviation=dev,
dihedral_NABB=dihedralNABB,
ideal_xyz=betaxyz,
outlier=(dev >= 0.25))
self.results.append(result)
key = result.id_str()
if (collect_ideal) :
self.beta_ideal[key] = betaxyz
def __init__ (self,
pdb_hierarchy,
keep_hydrogens=True,
nuclear=False,
force_unique_chain_ids=False,
time_limit=120,
b_factor_cutoff=None,
save_probe_unformatted_file=None,
save_modified_hierarchy=False,
verbose=False,
out=sys.stdout) :
validation.__init__(self)
self.b_factor_cutoff = b_factor_cutoff
self.clashscore = None
self.clashscore_b_cutoff = None
self.clash_dict = {}
self.clash_dict_b_cutoff = {}
self.list_dict = {}
self.probe_file = None
if (not libtbx.env.has_module(name="probe")):
raise RuntimeError(
"Probe could not be detected on your system. Please make sure "+
"Probe is in your path.\nProbe is available at "+
"http://kinemage.biochem.duke.edu/")
if verbose:
if not nuclear:
print "\nUsing electron cloud x-H distances and vdW radii"
else:
print "\nUsing nuclear cloud x-H distances and vdW radii"
import iotbx.pdb.hierarchy
from scitbx.array_family import flex
from mmtbx.validation import utils
n_models = len(pdb_hierarchy.models())
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
for i_mod, model in enumerate(pdb_hierarchy.models()):
input_str,_ = check_and_add_hydrogen(
pdb_hierarchy=pdb_hierarchy,
model_number=i_mod,
nuclear=nuclear,
verbose=verbose,
time_limit=time_limit,
keep_hydrogens=keep_hydrogens,
log=out)
r = iotbx.pdb.hierarchy.root()
mdc = model.detached_copy()
r.append_model(mdc)
occ_max = flex.max(r.atoms().extract_occ())
pcm = probe_clashscore_manager(
h_pdb_string=input_str,
nuclear=nuclear,
largest_occupancy=occ_max,
b_factor_cutoff=b_factor_cutoff,
use_segids=use_segids,
verbose=verbose)
if (save_modified_hierarchy) :
self.pdb_hierarchy = iotbx.pdb.hierarchy.input(
pdb_string=pcm.h_pdb_string).hierarchy
self.clash_dict[model.id] = pcm.clashscore
self.clash_dict_b_cutoff[model.id] = pcm.clashscore_b_cutoff
self.list_dict[model.id] = pcm.bad_clashes
if (n_models == 1) or (self.clashscore is None) :
self.results = pcm.bad_clashes
self.n_outliers = len(self.results)
self.clashscore = pcm.clashscore
self.clashscore_b_cutoff = pcm.clashscore_b_cutoff
if (save_probe_unformatted_file is not None) and (n_models == 1) :
open(save_probe_unformatted_file, "w").write(pcm.probe_unformatted)
self.probe_file = save_probe_unformatted_file
def __init__(self, model, fmodel, cc_min=0.8, molprobity_map_params=None):
from iotbx.pdb.amino_acid_codes import one_letter_given_three_letter
from mmtbx import real_space_correlation
validation.__init__(self)
pdb_hierarchy = model.get_hierarchy()
crystal_symmetry = model.crystal_symmetry()
# arrays for different components
self.everything = list()
self.protein = list()
self.other = list()
self.water = list()
aa_codes = one_letter_given_three_letter.keys()
# redo real_space_corelation.simple to use map objects instead of filenames
self.overall_rsc = None
rsc = None
try:
rsc_params = real_space_correlation.master_params().extract()
rsc_params.detail = "residue"
rsc_params.map_1.fill_missing_reflections = False
rsc_params.map_2.fill_missing_reflections = False
use_maps = False
if (molprobity_map_params is not None):
rsc_params.map_coefficients_file_name = \
molprobity_map_params.map_coefficients_file_name
rsc_params.map_coefficients_label = \
molprobity_map_params.map_coefficients_label
if (molprobity_map_params.map_file_name is not None):
use_maps = True
# use mmtbx/command_line/map_model_cc.py for maps
self.fsc = None
if (use_maps):
from iotbx import map_and_model
from mmtbx.maps import map_model_cc
from mmtbx.command_line.map_model_cc import get_fsc
from iotbx.file_reader import any_file
params = map_model_cc.master_params().extract()
params.map_model_cc.resolution = molprobity_map_params.d_min
map_object = any_file(
molprobity_map_params.map_file_name).file_object
# check that model crystal symmetry matches map crystal symmetry
mmi = map_and_model.input(map_data=map_object.map_data(),
model=model)
rsc_object = map_model_cc.map_model_cc(
mmi.map_data(),
mmi.model().get_hierarchy(), mmi.crystal_symmetry(),
params.map_model_cc)
rsc_object.validate()
rsc_object.run()
rsc = rsc_object.get_results()
self.overall_rsc = (rsc.cc_mask, rsc.cc_volume, rsc.cc_peaks)
self.fsc = get_fsc(mmi.map_data(), mmi.model(),
params.map_model_cc)
self.fsc.atom_radius = rsc.atom_radius
rsc = rsc.cc_per_residue
# mmtbx/real_space_correlation.py for X-ray/neutron data and map
# coefficients
else:
self.overall_rsc, rsc = real_space_correlation.simple(
fmodel=fmodel,
pdb_hierarchy=pdb_hierarchy,
params=rsc_params,
log=null_out())
except Exception, e:
raise
def __init__(self, model, fmodel, cc_min=0.8, molprobity_map_params=None):
from iotbx.pdb.amino_acid_codes import one_letter_given_three_letter
from mmtbx import real_space_correlation
validation.__init__(self)
pdb_hierarchy = model.get_hierarchy()
crystal_symmetry = model.crystal_symmetry()
# arrays for different components
self.everything = list()
self.protein = list()
self.other = list()
self.water = list()
aa_codes = one_letter_given_three_letter
# redo real_space_corelation.simple to use map objects instead of filenames
self.overall_rsc = None
rsc = None
try:
rsc_params = real_space_correlation.master_params().extract()
rsc_params.detail = "residue"
rsc_params.map_1.fill_missing_reflections = False
rsc_params.map_2.fill_missing_reflections = False
use_maps = False
if (molprobity_map_params is not None):
rsc_params.map_coefficients_file_name = \
molprobity_map_params.map_coefficients_file_name
rsc_params.map_coefficients_label = \
molprobity_map_params.map_coefficients_label
if (molprobity_map_params.map_file_name is not None):
use_maps = True
# use mmtbx/command_line/map_model_cc.py for maps
self.fsc = None
if (use_maps):
from iotbx import map_and_model
from mmtbx.maps import map_model_cc
from mmtbx.command_line.map_model_cc import get_fsc
from iotbx.file_reader import any_file
params = map_model_cc.master_params().extract()
params.map_model_cc.resolution = molprobity_map_params.d_min
map_object = any_file(
molprobity_map_params.map_file_name).file_object
# check that model crystal symmetry matches map crystal symmetry
mmi = map_and_model.input(map_data=map_object.map_data(),
model=model)
rsc_object = map_model_cc.map_model_cc(
mmi.map_data(),
mmi.model().get_hierarchy(), mmi.crystal_symmetry(),
params.map_model_cc)
rsc_object.validate()
rsc_object.run()
rsc = rsc_object.get_results()
self.overall_rsc = (rsc.cc_mask, rsc.cc_volume, rsc.cc_peaks)
self.fsc = get_fsc(mmi.map_data(), mmi.model(),
params.map_model_cc)
self.fsc.atom_radius = rsc.atom_radius
rsc = rsc.cc_per_residue
# mmtbx/real_space_correlation.py for X-ray/neutron data and map
# coefficients
else:
self.overall_rsc, rsc = real_space_correlation.simple(
fmodel=fmodel,
pdb_hierarchy=pdb_hierarchy,
params=rsc_params,
log=null_out())
except Exception as e:
raise
else:
assert ((self.overall_rsc is not None) and (rsc is not None))
for i, result_ in enumerate(rsc):
if (use_maps
): # new rsc calculation (mmtbx/maps/model_map_cc.py)
result = residue_real_space(chain_id=result_.chain_id,
resname=result_.resname,
resseq=result_.resseq,
icode=result_.icode,
altloc="",
score=result_.cc,
b_iso=result_.b_iso_mean,
occupancy=result_.occ_mean,
outlier=result_.cc < cc_min,
xyz=result_.xyz_mean)
else: # old rsc calculation (mmtbx/maps/real_space_correlation.py)
result = residue_real_space(
chain_id=result_.chain_id,
resname=result_.residue.resname,
resseq=result_.residue.resseq,
icode=result_.residue.icode,
altloc="",
score=result_.cc,
b_iso=result_.b,
occupancy=result_.occupancy,
fmodel=result_.map_value_1,
two_fofc=result_.map_value_2,
outlier=result_.cc < cc_min,
xyz=result_.residue.atoms().extract_xyz().mean())
if result.is_outlier():
self.n_outliers += 1
# XXX unlike other validation metrics, we always save the results for
# the real-space correlation, since these are used as the basis for
# the multi-criterion plot in Phenix. The show() method will only
# print outliers, however.
if (result_.residue.resname !=
'HOH'): # water is handled by waters.py
self.everything.append(result)
if result_.residue.resname in one_letter_given_three_letter:
self.protein.append(result)
else:
self.other.append(result)
self.everything += self.water
self.results = self.protein
def __init__ (self, fmodel, pdb_hierarchy, crystal_symmetry=None, cc_min=0.8,
molprobity_map_params=None) :
from iotbx.pdb.amino_acid_codes import one_letter_given_three_letter
from mmtbx import real_space_correlation
validation.__init__(self)
# arrays for different components
self.everything = list()
self.protein = list()
self.other = list()
self.water = list()
aa_codes = one_letter_given_three_letter.keys()
# redo real_space_corelation.simple to use map objects instead of filenames
self.overall_rsc = None
rsc = None
try :
rsc_params = real_space_correlation.master_params().extract()
rsc_params.detail="residue"
rsc_params.map_1.fill_missing_reflections = False
rsc_params.map_2.fill_missing_reflections = False
use_maps = False
if (molprobity_map_params is not None):
rsc_params.map_coefficients_file_name = \
molprobity_map_params.map_coefficients_file_name
rsc_params.map_coefficients_label = \
molprobity_map_params.map_coefficients_label
if (molprobity_map_params.map_file_name is not None):
use_maps = True
# use mmtbx/command_line/map_model_cc.py for maps
self.fsc = None
if (use_maps):
from scitbx.array_family import flex
import iotbx.pdb
from mmtbx.maps import map_model_cc
from mmtbx.command_line.map_model_cc import get_fsc
from iotbx.file_reader import any_file
from cctbx import crystal, sgtbx
params = map_model_cc.master_params().extract()
params.map_model_cc.resolution = molprobity_map_params.d_min
map_object = any_file(molprobity_map_params.map_file_name).file_object
# ---------------------------------------------------------------------
# check that model crystal symmetry matches map crystal symmetry
# if inconsistent, map parameters take precedence
# TODO: centralize data consistency checks prior to running validation
map_crystal_symmetry = crystal.symmetry(
unit_cell=map_object.unit_cell(),
space_group=sgtbx.space_group_info(
map_object.space_group_number).group())
if (not map_crystal_symmetry.is_similar_symmetry(crystal_symmetry)):
crystal_symmetry = map_crystal_symmetry
# ---------------------------------------------------------------------
map_data = map_object.map_data()
rsc_object = map_model_cc.map_model_cc(
map_data, pdb_hierarchy, crystal_symmetry, params.map_model_cc)
rsc_object.validate()
rsc_object.run()
rsc = rsc_object.get_results()
self.overall_rsc = (rsc.cc_mask, rsc.cc_volume, rsc.cc_peaks)
# pdb_hierarchy.as_pdb_input is being phased out since that function
# just re-processes the file from text and can be lossy
# this is a placeholder until tools get updated to use the model class
pdb_input = iotbx.pdb.input(
source_info='pdb_hierarchy',
lines=flex.split_lines(pdb_hierarchy.as_pdb_string()))
model = mmtbx.model.manager(model_input = pdb_input)
self.fsc = get_fsc(map_data, model, params.map_model_cc)
#
self.fsc.atom_radius = rsc.atom_radius
rsc = rsc.cc_per_residue
# mmtbx/real_space_correlation.py for X-ray/neutron data and map
# coefficients
else:
self.overall_rsc, rsc = real_space_correlation.simple(
fmodel=fmodel,
pdb_hierarchy=pdb_hierarchy,
params=rsc_params,
log=null_out())
except Exception, e :
raise
def __init__ (self, pdb_hierarchy, xray_structure, ignore_hd=True,
collect_outliers=True) :
for name in self.__slots__ :
setattr(self, name, None)
validation.__init__(self)
assert len(xray_structure.scatterers()) != 0
from cctbx import adptbx
from scitbx.array_family import flex
xrs = xray_structure
self.n_total = xrs.scatterers().size() # always include H/D
self.results = None
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
hd_selection = xrs.hd_selection()
subtract_hd = True
self.n_all = hd_selection.size()
self.n_hd = hd_selection.count(True)
if (ignore_hd) and (0 < self.n_hd < self.n_all) :
xrs = xrs.select(~hd_selection)
subtract_hd = False
u_isos = xrs.extract_u_iso_or_u_equiv()
occ = xrs.scatterers().extract_occupancies()
self.n_atoms = xrs.scatterers().size()
self.n_non_hd = self.n_all - self.n_hd
self.n_aniso = xrs.use_u_aniso().count(True)
self.n_aniso_h = (xray_structure.use_u_aniso() & hd_selection).count(True)
self.n_npd = xrs.is_positive_definite_u().count(False)
self.n_zero_b = (u_isos == 0).count(True)
self.n_zero_occ = (occ == 0).count(True)
u_cutoff_high = sys.maxint
u_cutoff_low = 0
u_non_zero = u_isos.select(u_isos > 0)
if (len(u_non_zero) > 1) :
mv = flex.mean_and_variance(u_non_zero)
sigma = mv.unweighted_sample_standard_deviation()
u_cutoff_high = mv.mean() + (4.0 * sigma)
u_cutoff_low = mv.mean() - (4.0 * sigma)
self.b_mean = adptbx.u_as_b(flex.mean(u_isos))
self.b_min = adptbx.u_as_b(flex.min(u_isos))
self.b_max = adptbx.u_as_b(flex.max(u_isos))
self.o_mean = flex.mean(occ)
self.o_min = flex.min(occ)
self.o_max = flex.max(occ)
self.n_outliers = self.n_aniso_h + self.n_npd
self.zero_occ = []
self.partial_occ = []
self.different_occ = []
self.bad_adps = []
self.b_histogram = None # TODO
def is_u_iso_outlier (u) :
return (u < u_cutoff_low) or (u > u_cutoff_high) or (u <= 0)
# these statistics cover all atoms!
occupancies = xray_structure.scatterers().extract_occupancies()
u_isos = xray_structure.extract_u_iso_or_u_equiv()
collected = flex.bool(occupancies.size(), False)
if (collect_outliers) :
for i_seq, occ in enumerate(occupancies) :
if (hd_selection[i_seq] and ignore_hd) or collected[i_seq] :
continue
pdb_atom = pdb_atoms[i_seq]
parent = pdb_atom.parent()
if (occ <= 0) :
group_atoms = parent.atoms()
labels = pdb_atom.fetch_labels()
if (len(group_atoms) > 1) and (group_atoms.extract_occ().all_eq(0)) :
i_seqs = group_atoms.extract_i_seq()
b_mean = adptbx.u_as_b(flex.mean(u_isos.select(i_seqs)))
outlier = residue_occupancy(
chain_id=labels.chain_id,
resseq=labels.resseq,
icode=labels.icode,
altloc=labels.altloc,
resname=labels.resname,
occupancy=occ,
outlier=True,
xyz=group_atoms.extract_xyz().mean(),
b_iso=b_mean)
self.zero_occ.append(outlier)
self.n_outliers += 1
collected.set_selected(i_seqs, True)
else :
assert (pdb_atom.occ == occ), "%s: %s <--> %s" % (pdb_atom.id_str(),
pdb_atom.occ, occ)
outlier = atom_occupancy(
pdb_atom=pdb_atom,
occupancy=occ,
b_iso=adptbx.u_as_b(u_isos[i_seq]),
xyz=pdb_atom.xyz,
outlier=True)
self.zero_occ.append(outlier)
self.n_outliers += 1
elif is_u_iso_outlier(u_isos[i_seq]) :
# zero displacements will always be recorded on a per-atom basis
if (u_isos[i_seq] <= 0) :
outlier = atom_bfactor(
pdb_atom=pdb_atom,
occupancy=occ,
b_iso=adptbx.u_as_b(u_isos[i_seq]),
xyz=pdb_atom.xyz,
outlier=True)
self.bad_adps.append(outlier)
self.n_outliers += 1
else :
# if the average displacement for the entire residue falls outside
# the cutoffs, save as a single residue outlier
group_atoms = parent.atoms()
i_seqs = group_atoms.extract_i_seq()
u_mean = flex.mean(u_isos.select(i_seqs))
if is_u_iso_outlier(u_mean) :
labels = pdb_atom.fetch_labels()
outlier = residue_bfactor(
chain_id=labels.chain_id,
resseq=labels.resseq,
icode=labels.icode,
altloc=labels.altloc,
resname=labels.resname,
occupancy=occ,
outlier=True,
xyz=group_atoms.extract_xyz().mean(),
b_iso=adptbx.u_as_b(u_mean))
self.bad_adps.append(outlier)
self.n_outliers += 1
collected.set_selected(i_seqs, True)
# otherwise, just save this atom
else :
outlier = atom_bfactor(
pdb_atom=pdb_atom,
occupancy=occ,
b_iso=adptbx.u_as_b(u_isos[i_seq]),
xyz=pdb_atom.xyz,
outlier=True)
self.bad_adps.append(outlier)
self.n_outliers += 1
# analyze occupancies for first model
model = pdb_hierarchy.models()[0]
for chain in model.chains() :
residue_groups = chain.residue_groups()
for residue_group in chain.residue_groups() :
# get unique set of atom names
atom_names = set()
for atom in residue_group.atoms():
atom_names.add(atom.name.strip())
# check total occupancy for each atom
for name in atom_names:
occupancy = 0.0
atoms = list()
for atom_group in residue_group.atom_groups():
atom = atom_group.get_atom(name)
if (atom is not None):
occupancy += atom.occ
atoms.append(atom)
if ( not approx_equal(occupancy, 1.0, out=None, eps=1.0e-3) ):
for atom in atoms:
outlier = atom_occupancy(
pdb_atom=atom,
occupancy=atom.occ,
b_iso=adptbx.u_as_b(atom.b),
xyz=atom.xyz,
outlier=True)
self.partial_occ.append(outlier)
self.n_outliers += 1
# check that atoms in an atom group have the same occupancy
for atom_group in residue_group.atom_groups():
residue_is_okay = True
base_occupancy = atom_group.atoms()[0].occ
for atom in atom_group.atoms():
if (not approx_equal(base_occupancy, atom.occ,
out=None, eps=1.0e-3)):
labels = atom.fetch_labels()
i_seqs = atom_group.atoms().extract_i_seq()
b_mean = adptbx.u_as_b(flex.mean(u_isos.select(i_seqs)))
outlier = residue_occupancy(
chain_id=labels.chain_id,
resseq=labels.resseq,
icode=labels.icode,
altloc=labels.altloc,
resname=labels.resname,
occupancy=occ,
outlier=True,
xyz=atom_group.atoms().extract_xyz().mean(),
b_iso=b_mean)
self.different_occ.append(outlier)
self.n_outliers += 1
residue_is_okay = False
break
if (not residue_is_okay):
break
def __init__(self,
pdb_hierarchy,
outliers_only=False,
out=sys.stdout,
collect_ideal=False,
apply_phi_psi_correction=False,
display_phi_psi_correction=False,
quiet=False):
validation.__init__(self)
self._outlier_i_seqs = flex.size_t()
self.beta_ideal = {}
output_list = []
self.stats = group_args(n_results=0,
n_weighted_results=0,
n_weighted_outliers=0)
if apply_phi_psi_correction:
phi_psi_angles = get_phi_psi_dict(pdb_hierarchy)
new_outliers = 0
outliers_removed = 0
total_residues = 0
from mmtbx.validation import utils
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
for model in pdb_hierarchy.models():
for chain in model.chains():
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
for rg in chain.residue_groups():
for i_cf, cf in enumerate(rg.conformers()):
for i_residue, residue in enumerate(cf.residues()):
if (residue.resname == "GLY"):
continue
is_first = (i_cf == 0)
is_alt_conf = False
relevant_atoms = {}
for atom in residue.atoms():
if (atom.name in relevant_atom_names):
relevant_atoms[atom.name] = atom
if (len(atom.parent().altloc) != 0):
is_alt_conf = True
if ((is_first or is_alt_conf)
and len(relevant_atoms) == 4):
result = calculate_ideal_and_deviation(
relevant_atoms=relevant_atoms,
resname=residue.resname)
dev = result.deviation
dihedralNABB = result.dihedral
betaxyz = result.ideal
if (dev is None): continue
resCB = relevant_atoms[" CB "]
self.stats.n_results += 1
self.stats.n_weighted_results += resCB.occ
if (is_alt_conf):
altchar = cf.altloc
else:
altchar = " "
if apply_phi_psi_correction:
total_residues += 1
id_str = '|%s:%s|' % (residue.id_str(),
altchar)
phi_psi = phi_psi_angles.get(id_str, None)
if phi_psi:
rc = cbd_utils.get_phi_psi_correction(
result,
residue,
phi_psi,
display_phi_psi_correction=
display_phi_psi_correction,
)
if rc:
dev, dihedralNABB, start, finish = rc
if start and not finish:
outliers_removed += 1
elif not start and finish:
new_outliers += 1
if (dev >= 0.25 or outliers_only == False):
if (dev >= 0.25):
self.n_outliers += 1
self.stats.n_weighted_outliers += resCB.occ
self._outlier_i_seqs.append(atom.i_seq)
res = residue.resname.lower()
sub = chain.id
if (len(sub) == 1):
sub = " " + sub
result = cbeta(chain_id=chain_id,
resname=residue.resname,
resseq=residue.resseq,
icode=residue.icode,
altloc=altchar,
xyz=resCB.xyz,
occupancy=resCB.occ,
deviation=dev,
dihedral_NABB=dihedralNABB,
ideal_xyz=betaxyz,
outlier=(dev >= 0.25))
self.results.append(result)
key = result.id_str()
if (collect_ideal):
self.beta_ideal[key] = betaxyz
if apply_phi_psi_correction:
print('''
Outliers removed : %5d
New outliers : %5d
Num. of outliers : %5d
Num. of residues : %5d
''' % (
outliers_removed,
new_outliers,
self.n_outliers,
total_residues,
))
def __init__(self,
pdb_hierarchy,
keep_hydrogens=True,
nuclear=False,
force_unique_chain_ids=False,
time_limit=120,
b_factor_cutoff=None,
save_modified_hierarchy=False,
verbose=False,
do_flips=False,
out=sys.stdout):
validation.__init__(self)
self.b_factor_cutoff = b_factor_cutoff
self.clashscore = None
self.clashscore_b_cutoff = None
self.clash_dict = {}
self.clash_dict_b_cutoff = {}
self.list_dict = {}
self.probe_file = None
if (not libtbx.env.has_module(name="probe")):
raise RuntimeError(
"Probe could not be detected on your system. Please make sure "
+ "Probe is in your path.\nProbe is available at " +
"http://kinemage.biochem.duke.edu/")
if verbose:
if not nuclear:
print "\nUsing electron cloud x-H distances and vdW radii"
else:
print "\nUsing nuclear cloud x-H distances and vdW radii"
import iotbx.pdb.hierarchy
from scitbx.array_family import flex
from mmtbx.validation import utils
n_models = len(pdb_hierarchy.models())
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
for i_mod, model in enumerate(pdb_hierarchy.models()):
input_str, _ = check_and_add_hydrogen(
pdb_hierarchy=pdb_hierarchy,
model_number=i_mod,
nuclear=nuclear,
verbose=verbose,
time_limit=time_limit,
keep_hydrogens=keep_hydrogens,
do_flips=do_flips,
log=out)
r = iotbx.pdb.hierarchy.root()
mdc = model.detached_copy()
r.append_model(mdc)
occ_max = flex.max(r.atoms().extract_occ())
self.probe_clashscore_manager = probe_clashscore_manager(
h_pdb_string=input_str,
nuclear=nuclear,
largest_occupancy=occ_max,
b_factor_cutoff=b_factor_cutoff,
use_segids=use_segids,
verbose=verbose)
if (save_modified_hierarchy):
self.pdb_hierarchy = iotbx.pdb.hierarchy.input(
pdb_string=self.probe_clashscore_manager.h_pdb_string
).hierarchy
self.clash_dict[
model.id] = self.probe_clashscore_manager.clashscore
self.clash_dict_b_cutoff[model.id] = self.probe_clashscore_manager.\
clashscore_b_cutoff
self.list_dict[
model.id] = self.probe_clashscore_manager.bad_clashes
if (n_models == 1) or (self.clashscore is None):
self.results = self.probe_clashscore_manager.bad_clashes
self.n_outliers = len(self.results)
self.clashscore = self.probe_clashscore_manager.clashscore
self.clashscore_b_cutoff = self.probe_clashscore_manager.\
clashscore_b_cutoff
def __init__ (self,
pdb_hierarchy,
outliers_only=False,
show_errors=False,
out=sys.stdout,
quiet=False) :
validation.__init__(self)
self.n_allowed = 0
self.n_favored = 0
self.n_type = [ 0 ] * 6
self._outlier_i_seqs = flex.size_t()
pdb_atoms = pdb_hierarchy.atoms()
all_i_seqs = pdb_atoms.extract_i_seq()
if (all_i_seqs.all_eq(0)) :
pdb_atoms.reset_i_seq()
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
analysis = ""
output_list = []
count_keys = []
uniqueness_keys = []
r = ramachandran_eval.RamachandranEval()
##if use_segids:
## chain_id = utils.get_segid_as_chainid(chain=chain)
## else:
## chain_id = chain.id
for three in generate_protein_threes(hierarchy=pdb_hierarchy, geometry=None):
main_residue = three[1]
phi_psi_atoms = three.get_phi_psi_atoms()
if phi_psi_atoms is None:
continue
phi_atoms, psi_atoms = phi_psi_atoms
phi = get_dihedral(phi_atoms)
psi = get_dihedral(psi_atoms)
coords = get_center(main_residue) #should find the CA of the center residue
if (phi is not None and psi is not None):
res_type = RAMA_GENERAL
#self.n_total += 1
if (main_residue.resname[0:3] == "GLY"):
res_type = RAMA_GLYCINE
elif (main_residue.resname[0:3] == "PRO"):
is_cis = is_cis_peptide(three)
if is_cis:
res_type = RAMA_CISPRO
else:
res_type = RAMA_TRANSPRO
elif (three[2].resname == "PRO"):
res_type = RAMA_PREPRO
elif (main_residue.resname[0:3] == "ILE" or \
main_residue.resname[0:3] == "VAL"):
res_type = RAMA_ILE_VAL
#self.n_type[res_type] += 1
value = r.evaluate(res_types[res_type], [phi, psi])
ramaType = self.evaluateScore(res_type, value)
is_outlier = ramaType == RAMALYZE_OUTLIER
c_alphas = None
# XXX only save kinemage data for outliers
if is_outlier :
c_alphas = get_cas_from_three(three)
assert (len(c_alphas) == 3)
markup = self.as_markup_for_kinemage(c_alphas)
else:
markup = None
result = ramachandran(
chain_id=main_residue.parent().parent().id,
resseq=main_residue.resseq,
icode=main_residue.icode,
resname=main_residue.resname,
#altloc=main_residue.parent().altloc,
altloc=get_altloc_from_three(three),
segid=None, # XXX ???
phi=phi,
psi=psi,
rama_type=ramaType,
res_type=res_type,
score=value*100,
outlier=is_outlier,
xyz=coords,
markup=markup)
#if result.chain_id+result.resseq+result.icode not in count_keys:
if result.altloc in ['','A'] and result.chain_id+result.resseq+result.icode not in count_keys:
self.n_total += 1
self.n_type[res_type] += 1
self.add_to_validation_counts(ramaType)
count_keys.append(result.chain_id+result.resseq+result.icode)
if (not outliers_only or is_outlier) :
if (result.altloc != '' or
result.chain_id+result.resseq+result.icode not in uniqueness_keys):
#the threes/conformers method results in some redundant result
# calculations in structures with alternates. Using the
# uniqueness_keys list prevents redundant results being added to
# the final list
self.results.append(result)
uniqueness_keys.append(result.chain_id+result.resseq+result.icode)
if is_outlier :
i_seqs = main_residue.atoms().extract_i_seq()
assert (not i_seqs.all_eq(0))
self._outlier_i_seqs.extend(i_seqs)
self.results.sort(key=lambda r: r.id_str())
out_count, out_percent = self.get_outliers_count_and_fraction()
fav_count, fav_percent = self.get_favored_count_and_fraction()
self.out_percent = out_percent * 100.0
self.fav_percent = fav_percent * 100.0
def __init__(self,
pdb_hierarchy,
xray_structure,
fmodel,
distance_cutoff=4.0,
collect_all=True,
molprobity_map_params=None):
validation.__init__(self)
from mmtbx.real_space_correlation import extract_map_stats_for_single_atoms
from cctbx import adptbx
from scitbx.matrix import col
self.n_bad = 0
self.n_heavy = 0
pdb_atoms = pdb_hierarchy.atoms()
if (len(pdb_atoms) > 1):
assert (not pdb_atoms.extract_i_seq().all_eq(0))
unit_cell = xray_structure.unit_cell()
pair_asu_table = xray_structure.pair_asu_table(
distance_cutoff=distance_cutoff)
asu_mappings = pair_asu_table.asu_mappings()
asu_table = pair_asu_table.table()
u_isos = xray_structure.extract_u_iso_or_u_equiv()
occupancies = xray_structure.scatterers().extract_occupancies()
sites_frac = xray_structure.sites_frac()
sel_cache = pdb_hierarchy.atom_selection_cache()
water_sel = sel_cache.selection("water")
if (molprobity_map_params is not None):
# assume parameters have been validated (symmetry of pdb and map matches)
two_fofc_map = None
fc_map = None
d_min = None
crystal_gridding = None
# read two_fofc_map
if (molprobity_map_params.map_file_name is not None):
f = any_file(molprobity_map_params.map_file_name)
two_fofc_map = f.file_object.map_data()
d_min = molprobity_map_params.d_min
crystal_gridding = maptbx.crystal_gridding(
f.file_object.unit_cell(),
space_group_info=space_group_info(
f.file_object.space_group_number),
pre_determined_n_real=f.file_object.unit_cell_grid)
pdb_atoms = pdb_hierarchy.atoms()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=f.crystal_symmetry())
unit_cell = xray_structure.unit_cell()
# check for origin shift
# ---------------------------------------------------------------------
soin = maptbx.shift_origin_if_needed(
map_data=two_fofc_map,
sites_cart=xray_structure.sites_cart(),
crystal_symmetry=xray_structure.crystal_symmetry())
two_fofc_map = soin.map_data
xray_structure.set_sites_cart(soin.sites_cart)
# ---------------------------------------------------------------------
pair_asu_table = xray_structure.pair_asu_table(
distance_cutoff=distance_cutoff)
asu_mappings = pair_asu_table.asu_mappings()
asu_table = pair_asu_table.table()
u_isos = xray_structure.extract_u_iso_or_u_equiv()
occupancies = xray_structure.scatterers().extract_occupancies()
sites_frac = xray_structure.sites_frac()
sel_cache = pdb_hierarchy.atom_selection_cache()
water_sel = sel_cache.selection("water")
elif (molprobity_map_params.map_coefficients_file_name
is not None):
f = any_file(molprobity_map_params.map_coefficients_file_name)
fourier_coefficients = f.file_server.get_miller_array(
molprobity_map_params.map_coefficients_label)
crystal_symmetry = fourier_coefficients.crystal_symmetry()
d_min = fourier_coefficients.d_min()
crystal_gridding = maptbx.crystal_gridding(
crystal_symmetry.unit_cell(),
d_min,
resolution_factor=0.25,
space_group_info=crystal_symmetry.space_group_info())
two_fofc_map = miller.fft_map(
crystal_gridding=crystal_gridding,
fourier_coefficients=fourier_coefficients).apply_sigma_scaling().\
real_map_unpadded()
# calculate fc_map
assert ((d_min is not None) and (crystal_gridding is not None))
f_calc = xray_structure.structure_factors(d_min=d_min).f_calc()
fc_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_calc)
fc_map = fc_map.apply_sigma_scaling().real_map_unpadded()
map_stats = extract_map_stats_for_single_atoms(
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
fmodel=None,
selection=water_sel,
fc_map=fc_map,
two_fofc_map=two_fofc_map)
else:
map_stats = extract_map_stats_for_single_atoms(
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
fmodel=fmodel,
selection=water_sel)
waters = []
for i_seq, atom in enumerate(pdb_atoms):
if (water_sel[i_seq]):
rt_mx_i_inv = asu_mappings.get_rt_mx(i_seq, 0).inverse()
self.n_total += 1
asu_dict = asu_table[i_seq]
nearest_atom = nearest_contact = None
for j_seq, j_sym_groups in asu_dict.items():
atom_j = pdb_atoms[j_seq]
site_j = sites_frac[j_seq]
# Filter out hydrogens
if atom_j.element.upper().strip() in ["H", "D"]:
continue
for j_sym_group in j_sym_groups:
rt_mx = rt_mx_i_inv.multiply(
asu_mappings.get_rt_mx(j_seq, j_sym_group[0]))
site_ji = rt_mx * site_j
site_ji_cart = xray_structure.unit_cell(
).orthogonalize(site_ji)
vec_i = col(atom.xyz)
vec_ji = col(site_ji_cart)
dxyz = abs(vec_i - vec_ji)
if (nearest_contact is None) or (dxyz <
nearest_contact):
nearest_contact = dxyz
nearest_atom = atom_info(pdb_atom=atom_j,
symop=rt_mx)
w = water(pdb_atom=atom,
b_iso=adptbx.u_as_b(u_isos[i_seq]),
occupancy=occupancies[i_seq],
nearest_contact=nearest_contact,
nearest_atom=nearest_atom,
score=map_stats.two_fofc_ccs[i_seq],
fmodel=map_stats.fmodel_values[i_seq],
two_fofc=map_stats.two_fofc_values[i_seq],
fofc=map_stats.fofc_values[i_seq],
anom=map_stats.anom_values[i_seq],
n_hbonds=None) # TODO
if (w.is_bad_water()):
w.outlier = True
self.n_bad += 1
elif (w.is_heavy_atom()):
w.outlier = True
self.n_heavy += 1
if (w.outlier) or (collect_all):
self.results.append(w)
self.n_outliers = len(self.results)
def __init__(self,
pdb_hierarchy,
nontrans_only=False,
out=sys.stdout,
quiet=True):
validation.__init__(self)
self.residue_count = [0, 0]
#[OMEGA_GENERAL, OMEGA_PRO]
self.omega_count = [[0, 0, 0], [0, 0, 0]]
#[OMEGA_GENERAL, OMEGA_PRO], then
#[OMEGALYZE_TRANS, OMEGALYZE_CIS, OMEGALYZE_TWISTED]
from mmtbx.validation import utils
from scitbx.array_family import flex
self._outlier_i_seqs = flex.size_t()
pdb_atoms = pdb_hierarchy.atoms()
all_i_seqs = pdb_atoms.extract_i_seq()
if all_i_seqs.all_eq(0):
pdb_atoms.reset_i_seq()
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
first_conf_altloc = None
prev_chain_id = None
for twores in generate_protein_fragments(
pdb_hierarchy,
length=2,
geometry=None,
include_non_standard_peptides=True):
main_residue = twores[
1] #this is the relevant residue for id-ing cis-Pro
conf_altloc = get_conformer_altloc(twores)
prevres_altloc, mainres_altloc = get_local_omega_altlocs(twores)
twores_altloc = prevres_altloc or mainres_altloc #default '' evals False
chain = main_residue.parent().parent()
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
if chain_id != prev_chain_id: #if we've moved to a new chain...
first_conf_altloc = conf_altloc #...reset reference altloc
prev_chain_id = chain_id
if (conf_altloc != first_conf_altloc) and twores_altloc == '':
#skip non-alternate residues unless this is the first time thru a chain
continue
omega_atoms = get_omega_atoms(twores)
#omega_atoms is the list [CA1 C1 N2 CA2], with None for missing atoms
if None in omega_atoms:
continue
omega = get_omega(omega_atoms)
if omega is None: continue
omega_type = find_omega_type(omega)
if omega_type == OMEGALYZE_TRANS:
is_nontrans = False
else:
is_nontrans = True
self.n_outliers += 1
if main_residue.resname == "PRO": res_type = OMEGA_PRO
else: res_type = OMEGA_GENERAL
self.residue_count[res_type] += 1
self.omega_count[res_type][omega_type] += 1
highest_mc_b = get_highest_mc_b(twores[0].atoms(),
twores[1].atoms())
coords = get_center(main_residue)
markup_atoms = []
for omega_atom in omega_atoms:
markup_atoms.append(
kin_atom(omega_atom.parent().id_str(), omega_atom.xyz))
result = omega_result(
model_id=twores[0].parent().parent().parent().id,
chain_id=chain_id,
resseq=main_residue.resseq,
icode=main_residue.icode,
resname=main_residue.resname,
altloc=mainres_altloc,
prev_resseq=twores[0].resseq,
prev_icode=twores[0].icode,
prev_resname=twores[0].resname,
prev_altloc=prevres_altloc,
segid=None,
omega=omega,
omega_type=omega_type,
res_type=res_type,
is_nontrans=is_nontrans,
outlier=is_nontrans,
highest_mc_b=highest_mc_b,
xyz=coords,
markup_atoms=markup_atoms)
if is_nontrans or not nontrans_only: #(not nontrans_only or is_nontrans)
self.results.append(result)
if is_nontrans:
i_seqs = main_residue.atoms().extract_i_seq()
assert (not i_seqs.all_eq(0)
) #This assert copied from ramalyze
self._outlier_i_seqs.extend(i_seqs)
self.results.sort(key=lambda x: x.model_id + ':' + x.id_str())
def __init__ (self, pdb_hierarchy, xray_structure, fmodel,
distance_cutoff=4.0, collect_all=True,
molprobity_map_params=None) :
validation.__init__(self)
from mmtbx.real_space_correlation import extract_map_stats_for_single_atoms
from cctbx import adptbx
from scitbx.matrix import col
self.n_bad = 0
self.n_heavy = 0
pdb_atoms = pdb_hierarchy.atoms()
if(len(pdb_atoms)>1):
assert (not pdb_atoms.extract_i_seq().all_eq(0))
unit_cell = xray_structure.unit_cell()
pair_asu_table = xray_structure.pair_asu_table(
distance_cutoff = distance_cutoff)
asu_mappings = pair_asu_table.asu_mappings()
asu_table = pair_asu_table.table()
u_isos = xray_structure.extract_u_iso_or_u_equiv()
occupancies = xray_structure.scatterers().extract_occupancies()
sites_cart = xray_structure.sites_cart()
sites_frac = xray_structure.sites_frac()
sel_cache = pdb_hierarchy.atom_selection_cache()
water_sel = sel_cache.selection("resname HOH and name O")
if (molprobity_map_params is not None):
# assume parameters have been validated (symmetry of pdb and map matches)
two_fofc_map = None
fc_map = None
d_min = None
crystal_gridding = None
# read two_fofc_map
if (molprobity_map_params.map_file_name is not None):
f = any_file(molprobity_map_params.map_file_name)
two_fofc_map = f.file_object.map_data()
d_min = molprobity_map_params.d_min
crystal_gridding = maptbx.crystal_gridding(
f.file_object.unit_cell(),
space_group_info=space_group_info(f.file_object.space_group_number),
pre_determined_n_real=f.file_object.unit_cell_grid)
elif (molprobity_map_params.map_coefficients_file_name is not None):
f = any_file(molprobity_map_params.map_coefficients_file_name)
fourier_coefficients = f.file_server.get_miller_array(
molprobity_map_params.map_coefficients_label)
crystal_symmetry = fourier_coefficients.crystal_symmetry()
d_min = fourier_coefficients.d_min()
crystal_gridding = maptbx.crystal_gridding(
crystal_symmetry.unit_cell(), d_min, resolution_factor=0.25,
space_group_info=crystal_symmetry.space_group_info())
two_fofc_map = miller.fft_map(
crystal_gridding=crystal_gridding,
fourier_coefficients=fourier_coefficients).apply_sigma_scaling().\
real_map_unpadded()
# calculate fc_map
assert( (d_min is not None) and (crystal_gridding is not None) )
f_calc = xray_structure.structure_factors(d_min=d_min).f_calc()
fc_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_calc)
fc_map = fc_map.apply_sigma_scaling().real_map_unpadded()
map_stats = extract_map_stats_for_single_atoms(
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
fmodel=None,
selection=water_sel,
fc_map=fc_map,
two_fofc_map=two_fofc_map)
else:
map_stats = extract_map_stats_for_single_atoms(
pdb_atoms=pdb_atoms,
xray_structure=xray_structure,
fmodel=fmodel,
selection=water_sel)
waters = []
for i_seq, atom in enumerate(pdb_atoms) :
if (water_sel[i_seq]) :
rt_mx_i_inv = asu_mappings.get_rt_mx(i_seq, 0).inverse()
self.n_total += 1
asu_dict = asu_table[i_seq]
nearest_atom = nearest_contact = None
for j_seq, j_sym_groups in asu_dict.items() :
atom_j = pdb_atoms[j_seq]
site_j = sites_frac[j_seq]
# Filter out hydrogens
if atom_j.element.upper().strip() in ["H", "D"]:
continue
for j_sym_group in j_sym_groups:
rt_mx = rt_mx_i_inv.multiply(asu_mappings.get_rt_mx(j_seq,
j_sym_group[0]))
site_ji = rt_mx * site_j
site_ji_cart = xray_structure.unit_cell().orthogonalize(site_ji)
vec_i = col(atom.xyz)
vec_ji = col(site_ji_cart)
dxyz = abs(vec_i - vec_ji)
if (nearest_contact is None) or (dxyz < nearest_contact) :
nearest_contact = dxyz
nearest_atom = atom_info(pdb_atom=atom_j, symop=rt_mx)
w = water(
pdb_atom=atom,
b_iso=adptbx.u_as_b(u_isos[i_seq]),
occupancy=occupancies[i_seq],
nearest_contact=nearest_contact,
nearest_atom=nearest_atom,
score=map_stats.two_fofc_ccs[i_seq],
fmodel=map_stats.fmodel_values[i_seq],
two_fofc=map_stats.two_fofc_values[i_seq],
fofc=map_stats.fofc_values[i_seq],
anom=map_stats.anom_values[i_seq],
n_hbonds=None) # TODO
if (w.is_bad_water()) :
w.outlier = True
self.n_bad += 1
elif (w.is_heavy_atom()) :
w.outlier = True
self.n_heavy += 1
if (w.outlier) or (collect_all) :
self.results.append(w)
self.n_outliers = len(self.results)
def __init__ (self,
pdb_hierarchy,
outliers_only=False,
show_errors=False,
out=sys.stdout,
quiet=False) :
validation.__init__(self)
self.n_allowed = 0
self.n_favored = 0
self.n_type = [ 0 ] * 6
from mmtbx.validation import utils
import mmtbx.rotamer
from mmtbx.rotamer import ramachandran_eval
from scitbx.array_family import flex
self._outlier_i_seqs = flex.size_t()
pdb_atoms = pdb_hierarchy.atoms()
all_i_seqs = pdb_atoms.extract_i_seq()
if (all_i_seqs.all_eq(0)) :
pdb_atoms.reset_i_seq()
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=pdb_hierarchy)
analysis = ""
output_list = []
r = ramachandran_eval.RamachandranEval()
prev_rezes, next_rezes = None, None
prev_resid = None
cur_resseq = None
next_resseq = None
for model in pdb_hierarchy.models():
for chain in model.chains():
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
residues = list(chain.residue_groups())
for i, residue_group in enumerate(residues):
# The reason I pass lists of atom_groups to get_phi and get_psi is to
# deal with the particular issue where some residues have an A alt
# conf that needs some atoms from a "" alt conf to get calculated
# correctly. See 1jxt.pdb for examples. This way I can search both
# the alt conf atoms and the "" atoms if necessary.
prev_atom_list, next_atom_list, atom_list = None, None, None
if cur_resseq is not None:
prev_rezes = rezes
prev_resseq = cur_resseq
rezes = construct_complete_residues(residues[i])
cur_resseq = residue_group.resseq_as_int()
cur_icode = residue_group.icode.strip()
if (i > 0):
#check for insertion codes
if (cur_resseq == residues[i-1].resseq_as_int()) :
if (cur_icode == '') and (residues[i-1].icode.strip() == '') :
continue
elif (cur_resseq != (residues[i-1].resseq_as_int())+1):
continue
if (i < len(residues)-1):
#find next residue
if residue_group.resseq_as_int() == \
residues[i+1].resseq_as_int():
if (cur_icode == '') and (residues[i+1].icode.strip() == '') :
continue
elif residue_group.resseq_as_int() != \
(residues[i+1].resseq_as_int())-1:
continue
next_rezes = construct_complete_residues(residues[i+1])
next_resid = residues[i+1].resseq_as_int()
else:
next_rezes = None
next_resid = None
for atom_group in residue_group.atom_groups():
alt_conf = atom_group.altloc
if rezes is not None:
atom_list = rezes.get(alt_conf)
if prev_rezes is not None:
prev_atom_list = prev_rezes.get(alt_conf)
if (prev_atom_list is None):
prev_keys = sorted(prev_rezes.keys())
prev_atom_list = prev_rezes.get(prev_keys[0])
if next_rezes is not None:
next_atom_list = next_rezes.get(alt_conf)
if (next_atom_list is None):
next_keys = sorted(next_rezes.keys())
next_atom_list = next_rezes.get(next_keys[0])
phi = get_phi(prev_atom_list, atom_list)
psi = get_psi(atom_list, next_atom_list)
coords = get_center(atom_group)
if (phi is not None and psi is not None):
res_type = RAMA_GENERAL
self.n_total += 1
if (atom_group.resname[0:3] == "GLY"):
res_type = RAMA_GLYCINE
elif (atom_group.resname[0:3] == "PRO"):
is_cis = is_cis_peptide(prev_atom_list, atom_list)
if is_cis:
res_type = RAMA_CISPRO
else:
res_type = RAMA_TRANSPRO
elif (isPrePro(residues, i)):
res_type = RAMA_PREPRO
elif (atom_group.resname[0:3] == "ILE" or \
atom_group.resname[0:3] == "VAL"):
res_type = RAMA_ILE_VAL
self.n_type[res_type] += 1
value = r.evaluate(res_types[res_type], [phi, psi])
ramaType = self.evaluateScore(res_type, value)
is_outlier = ramaType == RAMALYZE_OUTLIER
c_alphas = None
# XXX only save kinemage data for outliers
if is_outlier :
c_alphas = []
for atoms in [prev_atom_list, atom_list, next_atom_list] :
for a in atoms :
if (a.name.strip() == "CA") :
a_ = atom(pdb_atom=a)
c_alphas.append(c_alpha(
id_str=a_.atom_group_id_str(),
xyz=a_.xyz))
assert (len(c_alphas) == 3)
result = ramachandran(
chain_id=chain_id,
resseq=residue_group.resseq,
icode=residue_group.icode,
resname=atom_group.resname,
altloc=atom_group.altloc,
segid=None, # XXX ???
phi=phi,
psi=psi,
rama_type=ramaType,
res_type=res_type,
score=value*100,
outlier=is_outlier,
xyz=coords,
c_alphas=c_alphas)
if (not outliers_only or is_outlier) :
self.results.append(result)
if is_outlier :
i_seqs = atom_group.atoms().extract_i_seq()
assert (not i_seqs.all_eq(0))
self._outlier_i_seqs.extend(i_seqs)
out_count, out_percent = self.get_outliers_count_and_fraction()
fav_count, fav_percent = self.get_favored_count_and_fraction()
self.out_percent = out_percent * 100.0
self.fav_percent = fav_percent * 100.0