def find_missing_atoms (self, out=None) :
'''
Function for finding missing protein atoms
Derived from run_find_missing function in phenix/validation/__init__.py
'''
if out is None :
out = sys.stdout
self.missing_atoms = []
# make_header("Finding missing atoms", out=out)
try :
missing_list = rotamer_eval.eval_sidechain_completeness(
pdb_hierarchy=self.pdb_hierarchy,
ignore_hydrogens=True,
report_whole_res=True,
return_ca_pos=True)
except Exception as e :
print(to_str(e), file=out)
else :
for (res_info, missing_atoms, xyz) in missing_list :
if len(missing_atoms) == 0 :
continue
chain_id = res_info[0:2].strip()
try :
resseq = int(res_info[2:6])
except ValueError : # FIXME use hybrid36?
print(" warning: indecipherable residue number '%s'" % \
res_info[2:6], file=out)
print(res_info)
continue
alt = res_info[-4]
resname = res_info[-3:]
# self.get_residue_info((chain_id, resseq, resname, alt), "missing")
self.missing_atoms.append((chain_id, "%s %s" % (resname, str(resseq)),
alt, ", ".join(missing_atoms),
"chain '%s' and resseq %s" % (chain_id, str(resseq)), xyz))
def find_missing_atoms(self, out=None):
'''
Function for finding missing protein atoms
Derived from run_find_missing function in phenix/validation/__init__.py
'''
if out is None:
out = sys.stdout
self.missing_atoms = []
# make_header("Finding missing atoms", out=out)
try:
missing_list = rotamer_eval.eval_sidechain_completeness(
pdb_hierarchy=self.pdb_hierarchy,
ignore_hydrogens=True,
report_whole_res=True,
return_ca_pos=True)
except Exception, e:
print >> out, to_str(e)