def __init__(self,
pdb_hierarchy,
geometry_restraints_manager,
outliers_only=True):
rna_geometry.__init__(self)
self.n_triaged = self.n_incomplete = self.n_suites = 0
self.average_suiteness = None
total_suiteness = 0
suitename = "phenix.suitename -report -pointIDfields 7 -altIDfield 6 -"
backbone_dihedrals = utils.get_rna_backbone_dihedrals(
processed_pdb_file=None,
pdb_hierarchy=pdb_hierarchy,
geometry=geometry_restraints_manager)
suitename_out = easy_run.fully_buffered(
suitename, stdin_lines=backbone_dihedrals).stdout_lines
for line in suitename_out:
if line.startswith(' :'):
temp = line.split(":")
altloc = temp[5]
chain_id = temp[2]
resname = temp[6][0:3]
resseq = temp[3]
icode = temp[4]
key = temp[5] + temp[6][0:3] + temp[2] + temp[3] + temp[
4] # ewwwww....
suite = temp[6][9:11]
suiteness = temp[6][12:17]
temp2 = temp[6].split(" ")
triaged_angle = None
is_outlier = False
self.n_total += 1
if ('!!' in line):
if (temp2[3] == 'trig'):
triaged_angle = temp2[6]
self.n_triaged += 1
is_outlier = True
self.n_outliers += 1
if (is_outlier or not outliers_only):
self.results.append(
rna_suite(altloc=temp[5],
chain_id=temp[2],
resname=temp[6][0:3],
resseq=temp[3],
icode=temp[4],
suite=temp[6][9:11],
suite_id=key,
suiteness=suiteness,
triaged_angle=triaged_angle,
outlier=is_outlier))
if (triaged_angle is None):
try:
total_suiteness += float(suiteness)
self.n_suites += 1
except ValueError:
self.n_incomplete += 1
if (self.n_suites > 0):
self.average_suiteness = total_suiteness / self.n_suites
def __init__ (self, pdb_hierarchy, geometry_restraints_manager,
outliers_only=True) :
rna_geometry.__init__(self)
self.n_triaged = self.n_incomplete = self.n_suites = 0
self.average_suiteness = None
total_suiteness = 0
suitename = "phenix.suitename -report -pointIDfields 7 -altIDfield 6 -"
backbone_dihedrals = utils.get_rna_backbone_dihedrals(
processed_pdb_file=None,
pdb_hierarchy=pdb_hierarchy,
geometry=geometry_restraints_manager)
suitename_out = easy_run.fully_buffered(suitename,
stdin_lines=backbone_dihedrals).stdout_lines
for line in suitename_out:
if line.startswith(' :'):
temp = line.split(":")
altloc = temp[5]
chain_id = temp[2]
resname = temp[6][0:3]
resseq = temp[3]
icode = temp[4]
key = temp[5]+temp[6][0:3]+temp[2]+temp[3]+temp[4] # ewwwww....
suite = temp[6][9:11]
suiteness = temp[6][12:17]
temp2 = temp[6].split(" ")
triaged_angle = None
is_outlier = False
self.n_total += 1
if ('!!' in line) :
if (temp2[3] == 'trig'):
triaged_angle = temp2[6]
self.n_triaged += 1
is_outlier = True
self.n_outliers += 1
if (is_outlier or not outliers_only) :
self.results.append(rna_suite(
altloc = temp[5],
chain_id = temp[2],
resname = temp[6][0:3],
resseq = temp[3],
icode = temp[4],
suite = temp[6][9:11],
suite_id = key,
suiteness = suiteness,
triaged_angle=triaged_angle,
outlier=is_outlier))
if (triaged_angle is None) :
try :
total_suiteness += float(suiteness)
self.n_suites += 1
except ValueError :
self.n_incomplete += 1
if (self.n_suites > 0) :
self.average_suiteness = total_suiteness / self.n_suites
def run(args):
"""
I suggest adding here:
cctbx_project/mmtbx/validation/regression/tst_mp_geo.py
test cases with just .pdb, without arguments, etc.
"""
master_phil = get_master_phil()
import iotbx.phil
input_objects = iotbx.phil.process_command_line_with_files(
args=args, master_phil=master_phil, pdb_file_def="mp_geo.pdb")
work_params = input_objects.work.extract()
assert len(work_params.mp_geo.pdb) == 1, "Need a model file to run"
file_name = work_params.mp_geo.pdb[0]
out_file = None
if work_params.mp_geo.out_file != None:
out_file = work_params.mp_geo.out_file
do_bonds_and_angles = work_params.mp_geo.bonds_and_angles
do_kinemage = work_params.mp_geo.kinemage
do_rna_backbone = work_params.mp_geo.rna_backbone
outliers_only = work_params.mp_geo.outliers_only
use_cdl = work_params.mp_geo.cdl
log = StringIO()
basename = os.path.basename(file_name)
if out_file == None:
import sys
out = sys.stdout
else:
if do_bonds_and_angles:
out = file(out_file, 'w')
elif do_kinemage:
out = file(out_file, 'a')
elif do_rna_backbone:
out = file(out_file, 'w')
restraints_loading_flags = {}
restraints_loading_flags["use_neutron_distances"] = False
from mmtbx.validation import utils
params = pdb_interpretation.master_params.extract()
params.restraints_library.cdl = use_cdl
params.clash_guard.nonbonded_distance_threshold = None
processed_pdb_file = pdb_interpretation.process(
params=params,
mon_lib_srv=server.server(),
ener_lib=server.ener_lib(),
file_name=file_name,
strict_conflict_handling=True,
restraints_loading_flags=restraints_loading_flags,
force_symmetry=True,
substitute_non_crystallographic_unit_cell_if_necessary=True,
log=log)
grm = processed_pdb_file.geometry_restraints_manager()
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy)
if do_bonds_and_angles or do_kinemage:
rc = get_bond_and_angle_outliers(
pdb_hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy,
xray_structure=processed_pdb_file.xray_structure(),
geometry_restraints_manager=grm,
use_segids=use_segids,
outliers_only=outliers_only)
#get chain types
chain_types = {}
for chain in processed_pdb_file.all_chain_proxies.\
pdb_hierarchy.models()[0].chains():
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
main_conf = chain.conformers()[0]
if chain_types.get(chain_id) not in ["NA", "PROTEIN"]:
if (main_conf.is_na()):
chain_types[chain_id] = "NA"
elif (main_conf.is_protein()):
chain_types[chain_id] = "PROTEIN"
else:
chain_types[chain_id] = "UNK"
outliers = []
#bonds
#for result in rc.bonds.results:
for result in sorted(
rc.bonds.results,
key=lambda x:
(x.atoms_info[0].resseq, get_altloc(atoms_info=x.atoms_info),
get_atoms_str(atoms_info=x.atoms_info))):
atom_info = result.atoms_info[0]
# label:chain:number:ins:alt:type:measure:value:sigmas:class
atoms_str = get_atoms_str(atoms_info=result.atoms_info)
altloc = get_altloc(atoms_info=result.atoms_info)
chain_id = atom_info.chain_id
outliers.append([
chain_id, atom_info.resseq, atom_info.icode, altloc,
atom_info.resname, atoms_str, result.model, result.score,
chain_types[atom_info.chain_id]
])
#angles
#for result in rc.angles.results:
for result in sorted(
rc.angles.results,
key=lambda x:
(x.atoms_info[0].resseq, get_altloc(atoms_info=x.atoms_info),
get_atoms_str(atoms_info=x.atoms_info))):
atom_info = result.atoms_info[0]
# label:chain:number:ins:alt:type:measure:value:sigmas:class
atoms_str = get_atoms_str(atoms_info=result.atoms_info)
altloc = get_altloc(atoms_info=result.atoms_info)
chain_id = atom_info.chain_id
outliers.append([
chain_id, atom_info.resseq, atom_info.icode, altloc,
atom_info.resname, atoms_str, result.model, result.score,
chain_types[atom_info.chain_id]
])
if do_bonds_and_angles:
for outlier in outliers:
print >> out, "%s:%2s:%s:%s:%s:%s:%s:%.3f:%.3f:%s" % (
basename, outlier[0], outlier[1], outlier[2], outlier[3],
outlier[4], outlier[5], outlier[6], outlier[7], outlier[8])
elif do_kinemage:
print >> out, rc.bonds.kinemage_header
for result in rc.bonds.results:
print >> out, result.as_kinemage()
print >> out, rc.angles.kinemage_header
for result in rc.angles.results:
print >> out, result.as_kinemage()
out.close()
elif do_rna_backbone:
from mmtbx.validation import utils
rna_bb = utils.get_rna_backbone_dihedrals(processed_pdb_file)
print >> out, rna_bb
if out_file is not None:
out.close()
